1 2<a name="output.1"></a> 3<h3>Output files for usage example </h3> 4<p><h3>File: amir.pep</h3> 5<table width="90%"><tr><td bgcolor="#CCFFCC"> 6<pre> 7>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 8GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR*SACCSP 9KPASPPISSARTRMAHCSRSSN*TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGG 10YGSSWAATCRTRARR*CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT* 11FATTASGWCSSARTTSIRGKATM*CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTR 12RAPTWSSPPWWAPAPPSCIAPSPVATATAGGRRSPA*PPARRRWRRWRVTWQRGRWWSRL 13TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC 14TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG 15PPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRPGLAADPHRLFGAPVLAAAGSLRR 16AGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGVRKPRGALADHRAGVPRRDHPAAR 17CPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGPDQPGQGVADAAPWLGRARGAPAP 18VAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ*QEGYRHHAGTGSAVRWRGAVSQCRL 19VAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSRAGLAEGRSADPAIRFYLSVGGRQPV 20PRX 21</pre> 22</td></tr></table><p> 23 24<a name="output.2"></a> 25<h3>Output files for usage example 2</h3> 26<p><h3>File: amir.pep</h3> 27<table width="90%"><tr><td bgcolor="#CCFFCC"> 28<pre> 29>X13776_2 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 30VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLR 31NRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNAVPGPRRRPGPLSAVRRGLHSQPGG 32TVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAEPEQCAAGGVPD 33SPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGARGNLHSAVSLRRRLAARRRAHLPG 34ARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQPDHQRGGGGEDGE*RGRGAGGGRAL 35LLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQLAGGRRAAAPV 36RHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRPLCRRA*PRRLV 37RQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDV 38PVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLD 39AHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHL 40SREAMKRREPILKIAQELLGNEPSA*AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVW 41LLGKISGREVAVINFLVGVLSACVAFYLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQF 42LE 43</pre> 44</td></tr></table><p> 45 46<a name="output.3"></a> 47<h3>Output files for usage example 3</h3> 48<p><h3>File: amir.pep</h3> 49<table width="90%"><tr><td bgcolor="#CCFFCC"> 50<pre> 51>X13776_4 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 52SRNWLAATHR*VKANSRVSAPAFSEPCPAAAEKIR*NATQALSTPTRKLITATSRPLILP 53SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS*AIFRIGSRRFIAS 54RDRCWCASRSSQPWRCISNTLAWLIRAWPAMRSWSCSVFCFSFAISSLMRRADTSTGSTR 55WASSGWVITPWHSSSMICESTAGLSYSTSATRVVRGVPAASSAAISSWWPFWKMLVKTTS 56TGTSKASGGGQHWRTEQPMRISCKTRASLTSPGGLRTSTCNSRRLPSSELALMGAVPRPC 57WRTSRRGYARRHKGRGESVRATASGPGTRRAHRFPRCAKTGGCGCSGAPPGPAPVARRCR 58CRTGAAARLPPASCLRPARRGRATRSASRPPRPRR*WSRSPGRNHGRPGRRPGWRAYRCW 59RSKARPPPAPLPRHSPSSPPPPRWWSGWRSAAACRRRSDGRWRDTARRCRCPPRWRRPRR 60RAPGRCARRRAASRRRRDTAECRFPRAPCRRAGDTGGASHGCFPADRCSPSR*TPPARRS 61GESGTPPAAHCSGSAPDRRRRCSANTRSPRRGSGSRAARRRARPPASPPCACATCSSPRG 62TVPPGCE*SPRRTADSGPGRRRGPGTAFRSGDRRRRPRGSVARPRAMRHTRASARYRR*R 63RFRRTAGRSAAAPGAIPSVSSPVTVAQRRTKRTRSCSRLAR*IVQFPSPGWW*SSRCSAS 64GT 65</pre> 66</td></tr></table><p> 67 68<a name="output.4"></a> 69<h3>Output files for usage example 4</h3> 70<p><h3>File: amir.pep</h3> 71<table width="90%"><tr><td bgcolor="#CCFFCC"> 72<pre> 73>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 74GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR*SACCSP 75KPASPPISSARTRMAHCSRSSN*TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGG 76YGSSWAATCRTRARR*CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT* 77FATTASGWCSSARTTSIRGKATM*CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTR 78RAPTWSSPPWWAPAPPSCIAPSPVATATAGGRRSPA*PPARRRWRRWRVTWQRGRWWSRL 79TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC 80TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG 81PPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRPGLAADPHRLFGAPVLAAAGSLRR 82AGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGVRKPRGALADHRAGVPRRDHPAAR 83CPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGPDQPGQGVADAAPWLGRARGAPAP 84VAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ*QEGYRHHAGTGSAVRWRGAVSQCRL 85VAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSRAGLAEGRSADPAIRFYLSVGGRQPV 86PRX 87>X13776_2 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 88VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLR 89NRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNAVPGPRRRPGPLSAVRRGLHSQPGG 90TVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAEPEQCAAGGVPD 91SPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGARGNLHSAVSLRRRLAARRRAHLPG 92ARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQPDHQRGGGGEDGE*RGRGAGGGRAL 93LLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQLAGGRRAAAPV 94RHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRPLCRRA*PRRLV 95RQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDV 96PVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLD 97AHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHL 98SREAMKRREPILKIAQELLGNEPSA*AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVW 99LLGKISGREVAVINFLVGVLSACVAFYLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQF 100LE 101>X13776_3 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 102YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE 103TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV 104RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI 105RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA 106RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY 107FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY 108DIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWS 109ASMGGGPLP*APTRCSAACASCRCWSSTRRGRSATPWSCS*SASVVRCASAGRRRKPSTC 110RWTWSSPAFSRMATTTRSLRCSPPGLRALPWWRWWSTKAPRCSRRSSSWSATA*SPSRSM 111PTGCCLCWYRRGASARKWRS*SRRPSSSRTASPARPGSTRPRCC*CSAMAGTSARRTSTC 112RGKR*SGASRS*RSLRSCWETSRPPERSGPTRTITRGVSSSCWDWFCCTLARCCFSMPSG 113CWARSAVGRWR*STSWSAC*APASRST*SFPQQPGRAR*RPER*PCYSLLPICGWPPTSS 114SX 115</pre> 116</td></tr></table><p> 117 118<a name="output.5"></a> 119<h3>Output files for usage example 5</h3> 120<p><h3>File: amir.pep</h3> 121<table width="90%"><tr><td bgcolor="#CCFFCC"> 122<pre> 123>X13776_4 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 124SRNWLAATHR*VKANSRVSAPAFSEPCPAAAEKIR*NATQALSTPTRKLITATSRPLILP 125SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS*AIFRIGSRRFIAS 126RDRCWCASRSSQPWRCISNTLAWLIRAWPAMRSWSCSVFCFSFAISSLMRRADTSTGSTR 127WASSGWVITPWHSSSMICESTAGLSYSTSATRVVRGVPAASSAAISSWWPFWKMLVKTTS 128TGTSKASGGGQHWRTEQPMRISCKTRASLTSPGGLRTSTCNSRRLPSSELALMGAVPRPC 129WRTSRRGYARRHKGRGESVRATASGPGTRRAHRFPRCAKTGGCGCSGAPPGPAPVARRCR 130CRTGAAARLPPASCLRPARRGRATRSASRPPRPRR*WSRSPGRNHGRPGRRPGWRAYRCW 131RSKARPPPAPLPRHSPSSPPPPRWWSGWRSAAACRRRSDGRWRDTARRCRCPPRWRRPRR 132RAPGRCARRRAASRRRRDTAECRFPRAPCRRAGDTGGASHGCFPADRCSPSR*TPPARRS 133GESGTPPAAHCSGSAPDRRRRCSANTRSPRRGSGSRAARRRARPPASPPCACATCSSPRG 134TVPPGCE*SPRRTADSGPGRRRGPGTAFRSGDRRRRPRGSVARPRAMRHTRASARYRR*R 135RFRRTAGRSAAAPGAIPSVSSPVTVAQRRTKRTRSCSRLAR*IVQFPSPGWW*SSRCSAS 136GT 137>X13776_5 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 138LEELVGGHPQIGKSE*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA 139QQPDGIEKQHRANVQQNQSQHDDDTPLVIVLVGPDRSGGRLVSQQLLSDLQDRLAPLHRF 140PRQVLVRLALVPAMALHQQHLGLVDPGLAGDAVLELLGLLLQLRHFLADAPRRYQHRQHP 141VGIERLGDHAVALQLDDLREHRGAFVLHQRHQGSARSPGGEQRSDLVVVAILENAGEDHV 142HRHVEGFRRRPALAHRTTDADQLQDQGVADLPRRVEDQHLQLAQAAEQRVGAHGSGPPPM 143LADQSSRLCTTT*GSGRIGSGDCQRTWNTPRASISAMREDRRLWLFWRSTRTGPCGASMS 144MSYRCRCTSSTRQLPAACAARPSNKVCQ*AASAQAVMVAFSGKKPWQAWTKARLAGVSML 145EK*GATTTCPSATSLSIFATSASLVVRLAIGGRLPSP*RRAMARYSSAVPVPTTVEKTTS 146ARAW*MRSTARCKSSSEGYSGM*ISSSTVPPCWRYRWRITWLLSRG*M*SEPMNTTRSP* 147WRIRYAASGALFWFGAGPP*TMFGEYSKPS*GVG*QSSASARSTTGITALRVCDM*QPTR 148NRTPRLRMKSSAHSR*RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVT 149PVSENSRPISGRSWCDPIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQ 150RYX 151>X13776_6 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 152RGTGWRPPTDR*KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS*SPPPPDR*SCP 153ATRRH*ETAPRQRTAEPVPA**RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLP 154ATGAGAPRARPSHGAASATPWPG*SGPGRRCGPGAARSSASASPFPR*CAAPIPAQAAPG 155GHRAAG*SRRGTPAR*SARAPRGFRTPPAPPG*CAESRRRAAQRSRRGGHSGKCW*RPRP 156PARRRLPAAASTGAPNNRCGSAARPGRR*PPPAG*GPAPATRAGCRAASWRSWERSPAHA 157GGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFRDARRQAAVVVLALHPDRPLWRVDVD 158VVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGGDGRVLREETMAGLDEGPAGGRIDAG 159EVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAVAVATGDGAIQLGGAGAHHGGEDHVG 160ARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQVAHHMVAFPRIDVVRADEHHPLAVV 161ANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVAEQRVGALDHRHHRLARVRHVAAHEE 162PYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADAALAVQLLDREQCAIRVRALDIGGDA 163GFGEQQADQRPLLVRSHPFPLL*LSLSAVRSEPARAPGSPGRSCSSRRPAGGDRADARPA 164VP 165</pre> 166</td></tr></table><p> 167 168<a name="output.6"></a> 169<h3>Output files for usage example 6</h3> 170<p><h3>File: amir.pep</h3> 171<table width="90%"><tr><td bgcolor="#CCFFCC"> 172<pre> 173>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 174GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR*SACCSP 175KPASPPISSARTRMAHCSRSSN*TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGG 176YGSSWAATCRTRARR*CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT* 177FATTASGWCSSARTTSIRGKATM*CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTR 178RAPTWSSPPWWAPAPPSCIAPSPVATATAGGRRSPA*PPARRRWRRWRVTWQRGRWWSRL 179TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC 180TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG 181PPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRPGLAADPHRLFGAPVLAAAGSLRR 182AGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGVRKPRGALADHRAGVPRRDHPAAR 183CPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGPDQPGQGVADAAPWLGRARGAPAP 184VAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ*QEGYRHHAGTGSAVRWRGAVSQCRL 185VAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSRAGLAEGRSADPAIRFYLSVGGRQPV 186PRX 187>X13776_2 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 188VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLR 189NRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNAVPGPRRRPGPLSAVRRGLHSQPGG 190TVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAEPEQCAAGGVPD 191SPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGARGNLHSAVSLRRRLAARRRAHLPG 192ARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQPDHQRGGGGEDGE*RGRGAGGGRAL 193LLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQLAGGRRAAAPV 194RHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRPLCRRA*PRRLV 195RQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDV 196PVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLD 197AHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHL 198SREAMKRREPILKIAQELLGNEPSA*AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVW 199LLGKISGREVAVINFLVGVLSACVAFYLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQF 200LE 201>X13776_3 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 202YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE 203TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV 204RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI 205RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA 206RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY 207FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY 208DIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWS 209ASMGGGPLP*APTRCSAACASCRCWSSTRRGRSATPWSCS*SASVVRCASAGRRRKPSTC 210RWTWSSPAFSRMATTTRSLRCSPPGLRALPWWRWWSTKAPRCSRRSSSWSATA*SPSRSM 211PTGCCLCWYRRGASARKWRS*SRRPSSSRTASPARPGSTRPRCC*CSAMAGTSARRTSTC 212RGKR*SGASRS*RSLRSCWETSRPPERSGPTRTITRGVSSSCWDWFCCTLARCCFSMPSG 213CWARSAVGRWR*STSWSAC*APASRST*SFPQQPGRAR*RPER*PCYSLLPICGWPPTSS 214SX 215>X13776_4 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 216SRNWLAATHR*VKANSRVSAPAFSEPCPAAAEKIR*NATQALSTPTRKLITATSRPLILP 217SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS*AIFRIGSRRFIAS 218RDRCWCASRSSQPWRCISNTLAWLIRAWPAMRSWSCSVFCFSFAISSLMRRADTSTGSTR 219WASSGWVITPWHSSSMICESTAGLSYSTSATRVVRGVPAASSAAISSWWPFWKMLVKTTS 220TGTSKASGGGQHWRTEQPMRISCKTRASLTSPGGLRTSTCNSRRLPSSELALMGAVPRPC 221WRTSRRGYARRHKGRGESVRATASGPGTRRAHRFPRCAKTGGCGCSGAPPGPAPVARRCR 222CRTGAAARLPPASCLRPARRGRATRSASRPPRPRR*WSRSPGRNHGRPGRRPGWRAYRCW 223RSKARPPPAPLPRHSPSSPPPPRWWSGWRSAAACRRRSDGRWRDTARRCRCPPRWRRPRR 224RAPGRCARRRAASRRRRDTAECRFPRAPCRRAGDTGGASHGCFPADRCSPSR*TPPARRS 225GESGTPPAAHCSGSAPDRRRRCSANTRSPRRGSGSRAARRRARPPASPPCACATCSSPRG 226TVPPGCE*SPRRTADSGPGRRRGPGTAFRSGDRRRRPRGSVARPRAMRHTRASARYRR*R 227RFRRTAGRSAAAPGAIPSVSSPVTVAQRRTKRTRSCSRLAR*IVQFPSPGWW*SSRCSAS 228GT 229>X13776_5 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 230LEELVGGHPQIGKSE*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA 231QQPDGIEKQHRANVQQNQSQHDDDTPLVIVLVGPDRSGGRLVSQQLLSDLQDRLAPLHRF 232PRQVLVRLALVPAMALHQQHLGLVDPGLAGDAVLELLGLLLQLRHFLADAPRRYQHRQHP 233VGIERLGDHAVALQLDDLREHRGAFVLHQRHQGSARSPGGEQRSDLVVVAILENAGEDHV 234HRHVEGFRRRPALAHRTTDADQLQDQGVADLPRRVEDQHLQLAQAAEQRVGAHGSGPPPM 235LADQSSRLCTTT*GSGRIGSGDCQRTWNTPRASISAMREDRRLWLFWRSTRTGPCGASMS 236MSYRCRCTSSTRQLPAACAARPSNKVCQ*AASAQAVMVAFSGKKPWQAWTKARLAGVSML 237EK*GATTTCPSATSLSIFATSASLVVRLAIGGRLPSP*RRAMARYSSAVPVPTTVEKTTS 238ARAW*MRSTARCKSSSEGYSGM*ISSSTVPPCWRYRWRITWLLSRG*M*SEPMNTTRSP* 239WRIRYAASGALFWFGAGPP*TMFGEYSKPS*GVG*QSSASARSTTGITALRVCDM*QPTR 240NRTPRLRMKSSAHSR*RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVT 241PVSENSRPISGRSWCDPIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQ 242RYX 243>X13776_6 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 244RGTGWRPPTDR*KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS*SPPPPDR*SCP 245ATRRH*ETAPRQRTAEPVPA**RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLP 246ATGAGAPRARPSHGAASATPWPG*SGPGRRCGPGAARSSASASPFPR*CAAPIPAQAAPG 247GHRAAG*SRRGTPAR*SARAPRGFRTPPAPPG*CAESRRRAAQRSRRGGHSGKCW*RPRP 248PARRRLPAAASTGAPNNRCGSAARPGRR*PPPAG*GPAPATRAGCRAASWRSWERSPAHA 249GGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFRDARRQAAVVVLALHPDRPLWRVDVD 250VVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGGDGRVLREETMAGLDEGPAGGRIDAG 251EVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAVAVATGDGAIQLGGAGAHHGGEDHVG 252ARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQVAHHMVAFPRIDVVRADEHHPLAVV 253ANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVAEQRVGALDHRHHRLARVRHVAAHEE 254PYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADAALAVQLLDREQCAIRVRALDIGGDA 255GFGEQQADQRPLLVRSHPFPLL*LSLSAVRSEPARAPGSPGRSCSSRRPAGGDRADARPA 256VP 257</pre> 258</td></tr></table><p> 259 260<a name="output.7"></a> 261<h3>Output files for usage example 7</h3> 262<p><h3>File: amir.pep</h3> 263<table width="90%"><tr><td bgcolor="#CCFFCC"> 264<pre> 265>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 266VPLAEHLLDHHQPGEASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLRNRRHRRY 267VRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAE 268X 269</pre> 270</td></tr></table><p> 271 272<a name="output.8"></a> 273<h3>Output files for usage example 8</h3> 274<p><h3>File: mito.pep</h3> 275<table width="90%"><tr><td bgcolor="#CCFFCC"> 276<pre> 277>NC_001321.1_1 Balaenoptera physalus mitochondrion, complete genome 278VNY*SAHDHNMTEVSYIWYFFIFFGGLARTPLWP**VSSQSDKL*LGLDVFVIWLAQPTC 279AVKLMVTGHSTPLFPPGSKNCMS**TKPPSFHTMLTLCLDIHHPP*QARP*I*KPFYL*I 280NTKSDTSPMMKMHERHPYPMRWCSLNTYKA*HWKCLDGSSQPHWH**FGPSLSISS*QTY 281TCKYPHPSENAL*IMKIK*SGYQAR*H*QLTTPRLATPPRDTAVMKIKL*TKVRLSHVNL 282*VGKLRASHRGHTIDPN**KHGVKSVKEPHEMKSNLN*AVKSPN*N*AKLRKWL*YNLIT 283RQL*SKLGLDTPLCLVVNPNSHKT*LFA*VLLATA*NSKDLAVPHTHLEEPVL*PMNPDQ 284PHQPLLLQSMYRHLQQTLKGEK*A*PSYMKTLGQGVTHGLGSNGLHFLS*EHPLYSHESF 285YET*KLKEDLVVNQEQSAWLNKAM*ARTHRPSPSSSTPAMNPSSLTQAKQLYE**QVVT* 286*AYRKVCLDKT*YSLNKACSLHLEDSTARVYLELALAHTLPTSTTTNQSNKTFTIPSKY* 287**KFKYQWRY*DSTV*KDE*KT*K**KAKLTTCTFCMMT*LVMN*Q*DLKLNYPKPDELL 288MSST*NELIYVAK*WEDL*VEVKSLTSLVMAGCPWKESQFNIK*Y*KPMPSLNVYLTVNL 289K*YSFLEMGTTLT*E*NQT*T*LA*KQPSIKKAFKLDNKMMF*FQH*VNQLLAWLLD*SM 290QM*KQYC*YE*QEIFLLAQAYTSNW*YTDN*QQMNKTQH*IIY*NTVNPTQACIKE*LKK 291VKGTRQTQTPPVYQKHHL*HNQY*STACPVTNR*TAAVSWPCKGSMITCSLI*DLYEWPH 292EGFTVSYF*SVKLTSPW*GGDNKM*REDPMELQLINPKTMTLNHQGMTKPYMGWQFRLGW 293PRSTKNPPSD*NLGPLAKVQYHLLIQSFDQRNKLP*G*QRNPILESMSTMGFTTSMLDQD 294ILMVQLLL*VRLFND*SPTWSEF*PE*S*SVSIYYAFLPVRKDK*NKANFKQAPSNN*WP 295SLNLMIKRKQTCP*PGPCWGG*VR*LHKT*TFTP*GSNPLPNKMFMINILTLILPILLAV 296AFLTLVERKILGYMQFRKGPNIVGPHGLLQPFADAIKLFTKEPLRPATSSTTMFIIAPVL 297ALTLALTMWSPLPMPYPLINMNLGVLFMLAMSSLAVYSILWSGWASNSKYALIGALRAVA 298QTISYEVTLAIILLSVLLMNGSYTLSTLATTQEQLWLLFPSWPLAMMWFISTLAETNRAP 299FDLTEGESELVSGFNVEYAAGPFALFFLAEYANIIMMNMLTAILFLGTFHNPHNPELYTA 300NLIIKTLLLTMSFLWIRASYPRFRYDQLMHLLWKNFLPLTLALCMWHISLPIMTASIPPQ 301T*EMCLMKELLW*SK***PKSSYF*NN*NRTYP*EFKVLRATMLHYNLQ*GQLNKLSGPY 302PENVGSYPSHTNKPINPYYPPDNPYP*YNNGSHQLSLTISLNWLRNEHNSLHPYHNKKSY 303SPGH*SFYQVPPNTSHCFRTPHNSSHH*LNAL*PMNYYKTI*PNSIHTHNSSPSHQTGIS 304PLPLLSS*SNT*YPPNH*PNPINMTKTSSLINPMPNFTIN*PTPNINHILTFHLN**L*W 305TKPNTTSKNHSLLINCPH*MNNGHSTM*SNPNITKSTNLHHNNLHHIYIIYPKLNYHYIV 306TVSNLK*NTRHHNPYHTHFTLD**TPTTIGVYTQMNNYS*TNKKWYTHCTNIHSHYSITQ 307PMLLYTSYLLHSTNTISLHK*YKNKMTIQLHKTNSSPTNSNRNFHYATTPHTNTLNPTMG 308V*VKP*P*AFKALSKYNLLNSCPM*TA*LYLTSIECKSNALIKLNPH*IGGMHLPRIFS* 309QLNTLINWLQSTSPAA*KK*REKSRQDLKLLPWICNSKWSFTTGLGKK*TQPLSLDLQSN 310TYSAILPMFMNRWLFSTNHKDIGTLYLLFGAWAGMVGTGLSLLIRAELGQPGTLIGDDQV 311YNVLVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLM 312ASSMIEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKP 313PAMTQYQTPLFVWSVLVTAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQH 314LFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMVSIGFLGFIVWAHHMF 315TVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPALMWALGFIFLFTVGGL 316TGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNTTWAKIH 317FMIMFVGVNLTFFPQHFLGLSGMPRRYSDYPDAYTTWNTISSMGSFISLTAVMLMIFIIW 318EAFTSKREVLAVDLTSTNLEWLNGCPPPYHTFEEPAFVNPKWS*KEGIEPSPIGFKPTS* 319LLCLSL*T*Y**NLM*LCQS*VTSENPVYLHGMSIPT*FP*CSITHH**APTLSRSYTNN 320RFSN*LFSSLHYYPNAYNQINTY*YN*RP*S*NCLNYPPSHYLNFNCLAFITDPLHN*RS 321Q*PLPHCKNN*SPMMLKLWVYRLR*PKLRLLYNPNI*PKA**TTII*S**PSCLTY*NNN 322PNISLI**RTPLMGRTLLGPKN*CNP*TPKPNNLNINTT*PILWTML*DLRLKPQFHTNC 323P*TSTP*SLWKMICINTMTSL*S*ISINLLS**L*VYNSP*WYATI*YINMTPYYSINTL 324NPLCIIPIKNLKALLFP*PQTSTYQNTKTTSSLKHHMNENLFAPFMIPVMLGIPITTLII 325ILPSMLFPAPNRLINNRTIAIQQWLTKLTSKQLMNVHSPKGQTWSLMLISLFLFIASTNL 326LGMLPHSFTPTTQLSMNVGMAIPLWAGTVTTGFRNKTKMSLAHLLPQGTPTFLIPMLVII 327ETISLFIQPVAWAVRLTANITAGHLLMHLIGETTLALMNINLFSAFITFTILALLTILEF 328AVALIQAYVFTLLVSLYLHDNT*WPTKPTHTT**TPALDPSPELYQPF**HQA*LYDFTS 329TQYSY*L*ACQQMF*QYTNDGEMSSEKAPSKAIMHQPSK*AYDTE*FYLSSQKSYFSQAS 330SEPSTTQALPLLQN*ADVDHQQASAL*IP*KFPFSTPPYY*PLAYLLPEPTMAW*KETAN 331TYFKHSSSQLH*ASTSPYYKHQSTTKPLSQSQTESTAPPSL*PQAFMGYM*SLDLLSLSS 332VSYVK*NSTSHQTTTLALNVPLDTDIS*TSYDYFFMYLSIDEVPSPFSINKYNWLPIS*F 333RCTPKKNNKPSTNTTNKYNTSPTTRIHRLLTSTTKRMR*KNKPMWMRIWPH*ISPPTLLH 334KILLGGHYFPSLWL*NRSLTPPSLSNSVKQPKHNTHNSLILNLPTSSQPSLWMNS**P*M 335SWMWYLV*DKTSDFDPLDCDQIHNYQMTLIHMNILMAFSMSLMGLLMYRSHLMSALLCLE 336GMMLSLFVLAALTILSSHFTLANMMPIILLVFAACEAAIGLALLVMVSNTYGTDYVQNLN 337LLQC*NLLFLQSY*YP*PDYQKMT*SELTPQPTVY*LASQAFSSSINSTTTALTTH*YSS 338PTPFLPHSWS*QYDSFP*Y**QVNPISSKNHQSEKNSTLRY*SHYKPS*L*HLLPLN*SY 339FMSYLKPH*SLPLSLSLAGATKQNDSMPDYTSYSMH*LDLSHY**H*YIYKMQQDP*TFY 340SYNTELNHYLRPDPTSSYD*PA**PS**KYLSMDYTFDCPKHT*KPPLQAP*SLQPYY*N 341LEAMAYYELHPYSIP*QNT*HTHFLYSLFEE*S*PALSVYVKQT*NH*LHIPQLVT*HSS 342SQLSSSKPPEAM*GPLP**LPTASHPPYYSVWQTRTTNAFMAEP*FCPEAYKSFYH**PV 343DDY*QA*QILHYPQPST*SENYS*SCRSSHDQIPLFS**EQML*LLLSTLYMY*S*HNVA 344NTHTTSMMSPLPSHESMP**PYTLFPSCSYH*TLKSS*ALSTVSMV*K*R*FVKLTMEDQ 345NFLLTEKVLQELLIHAPTPNSCGFFKLLQDSSYPLVLGAKKLVQLQMKVMNLFTSFTLLT 346LLILTTPIMMSHTGSHVNNKYQSYVKNIVFCAFITSLVPAMVYLHTNQETLISNWHWITI 347QTLKLTLSFKMDYFSLMFMPVALFITWSIMEFSMWYMHSDPYINQFFKYLLLFLITMLIL 348VTANNLFQLFIGWEGVGIMSFLLIGWWFGRTDANTAALQAILYNRIGDIGLLASMAWFLS 349NMNTWDLEQIFMLNQNPLNFPLMGLVLAAAGKSAQFGLHPWLPSAMEGPTPVSALLHSST 350MVVAGIFLLVRFYPLMENNKLIQTVTLCLGAITTLFTAICALTQNDIKKIIAFSTSSQLG 351LMMVTIGLNQPYLAFLHICTHAFFKAMLFLCSGSIIHNLNNEQDIRKMGGLFKALPFTTT 352ALIIGCLALTGMPFLTGFYSKDPIIEAATSSYTNAWALLLTLIATSLTAVYSTRIIFFAL 353LGQPRFPPSTTINENNPLLINPIKRLLVGSIFAGFILSNSIPPMTTPLMTMPLHLKLTAL 354AMTTLGFIIAFEINLDTQNLKHKHPSNSFKFSTLLGYFPTIMHRLPPHLDLLMSQKLATS 355LLDLTWLETILPKTTALIQLKASTLTSNQQGLIKLYFLSFLITITLSMILFNYPE*SP** 356LQH**MKTNP*QSPTKHHNYMMPQSL*PPH*KPQNPQYHKQPSPLVHQTQT*SSPPHSSK 357HKSQLKTPPPTLKQMLLVQLY*KPKPQDTVQ*P*LLYNQMLPAFPPNKSKTPLTPKTNHQ 358NSK*LHIQHHHPQSTLNPHK*VKALKKPPQN*LQK*YLKWKQYTLSLFSHGLQPWPMTWK 359IIVVIQLQEHQWPTSEKHTH**KSSTTHSSISPPHQMSLHDGTSAPYSASA*LYKS*QAY 360S*QYTTHQTQQPPSHQSHTSAETWITAELSDTYMQMGLLYSSSASTLT*DEAYTTAPTPS 361EKHEMLELFYYSQL*PPHS*ATSCPEDKYHSEAQL*SLTSYQQSHTLVPP*SNESEAVSL 362*MKQH*HAFLPFTLSSPSSS*H*QLSTLFSFTKQDPTTPQASHPT*MKSHSTPTTQLKTF 363*VPYY*S*SY*Y*PYSHPTYLETQTTMPQQTHSVPQHTLNQNGIFYSHTQSYDQSPTN*A 364ES*PYYSQS*S*PSSQYSTHPINEA*YFDPLASSCSES*SQIY*P*HGSAANQ*NTPT*L 365*ANSHPSSISS*F*Y*YQ*LVLS*TNL*NEESL*YN*MPRFCKPEKET*HTSL*LKEEVL 366HSTISTQSWSST*TIPWKSMLYNNH*TTVLCPYWK*LALLDIIM*LVHACTST*LMASFH 367GYEQMYMLCMIVHSIIFTTSSWSSY*ILLILHIT*YVLMVQ*RMFLCIP*SI*IKWFLWP 368LH*ITSLVSMPRETSNPLG*DPSSRTGPITRGGSYLMIFM*HLVLTSGPY*LKIAHSFPL 369NKTSRW 370</pre> 371</td></tr></table><p> 372