Align Phenylacetyl-CoA:acceptor oxidoreductase large subunit PadB; EC 1.8.5.3 (characterized, see rationale)
to candidate WP_011384418.1 AMB_RS10170 phenylacetyl CoA
Query= uniprot:A0A2R4BLL6 (914 letters) >NCBI__GCF_000009985.1:WP_011384418.1 Length = 911 Score = 1147 bits (2967), Expect = 0.0 Identities = 546/901 (60%), Positives = 666/901 (73%), Gaps = 3/901 (0%) Query: 13 VATYCYQCVAGPDLLKVKVEDGVATAIEPNFDAEGVHPAAGRVCVKAFGLVQKTYNPNRV 72 V TYCY CVAGPDL+ V V+DGVA A+ PN G+HPA GR CVKA+GLVQKTYNP+RV Sbjct: 8 VPTYCYNCVAGPDLMCVTVKDGVAVAVTPNHAGMGIHPADGRPCVKAYGLVQKTYNPHRV 67 Query: 73 LTPMKRTNPKKGRDEDPGFVPISWDEALDLIADKLNTVRANGLLDASGYPRVAASFGGGG 132 LTPMKRTNP+KGRDEDPGFVPISWDEALDL+A KL +VR GLL+ G PR+AA+FG GG Sbjct: 68 LTPMKRTNPRKGRDEDPGFVPISWDEALDLVAGKLRSVREMGLLNEQGMPRLAATFGHGG 127 Query: 133 TPTAYMGTFPAFLSAWGPVDLSFGSGQGVKCTHSEHLYGELWHRAFTVCPDTPRTKYIVS 192 TP YMGTFPAFL+AWGP+D SFGSGQGVKC HSEHLYGE WHRAFTV DTP +IVS Sbjct: 128 TPANYMGTFPAFLAAWGPIDFSFGSGQGVKCVHSEHLYGEYWHRAFTVAADTPNANFIVS 187 Query: 193 FGSNIEASGGVCGVWRHAEARVEQGVKRVQVEPHLSVTGGCSAEWVPIKPKTDPAFMHAM 252 FG+N+E SGG CGV RHA+AR+ +G+KRVQVEPHLS TG CSA+WVPI+PKTDPAFM AM Sbjct: 188 FGTNVEVSGGPCGVRRHADARI-RGIKRVQVEPHLSPTGACSAQWVPIRPKTDPAFMFAM 246 Query: 253 IHVMLFENARTRLDIDFLKHMTASPYLVAPNGLYLRDPDTRKPLVWDLKRAAAVPFDTAD 312 +HVML E R+ LD+DFL+ TASPYLV G YLRD T KPL+WD VP D Sbjct: 247 LHVMLHEAPRSALDLDFLRDRTASPYLVDDEGWYLRDEATGKPLMWDGITGQPVPHDHPG 306 Query: 313 IDPALDGEFTA-SGLEVLPDNETVDHVQVRVLTAFGKLAEHERTFTPEWAAKVCDVPADT 371 PAL+G FT + + LPD E V TAF L + R +TP+WA +CDVPA Sbjct: 307 AVPALEGSFTVPAAVAKLPDGEMVRRENATARTAFTLLVDGMRGYTPDWAETICDVPAKV 366 Query: 372 IRRVANEYLDHAQIGATIEIEGRTLPFRPVAITLGKTVNNGWGGYDCCWARTLMACLVGA 431 +R+VA EYLD+A +G T E++G+ LP RPVA+TLGKTVNNGWG Y+CCWART++A LVGA Sbjct: 367 VRQVALEYLDNACVGQTTEVDGKVLPHRPVAVTLGKTVNNGWGAYECCWARTVLATLVGA 426 Query: 432 LDVPGGTIGTTVRLNRPASDRQSSAKPGPDGFMDYPFNPTDKENWVSRPQIRNANRTLVP 491 L+VPGGT+GTTVRLNRP +R S KPG DGFM+ N T K W +P+ RNA+ TL+P Sbjct: 427 LEVPGGTLGTTVRLNRPYENRLKSVKPGEDGFMNAQMNSTKKGGWAEKPKGRNAHTTLIP 486 Query: 492 LVANSAWSAALGPTHLAWMQQRHGFENFPEPTQPDVWFFYRTNPVISFWDTPQVAEAVSK 551 +V +S+W+ ALGPTHLAWM + + P PDVW YRTNP ISFWDT Q++ ++K Sbjct: 487 IVGDSSWAQALGPTHLAWMFLKDSPAEWAPPEPPDVWIAYRTNPAISFWDTAQLSGNMAK 546 Query: 552 FPFVVAFTYTRDETNHFADVLLPDCTDLEGLQLIRIGGTKYVEQFWDKQGFALRQPAVVP 611 PFVV F YT DETNH AD+LLP+ TDLE QLIR GG+K+VEQ W QGF LRQPAV P Sbjct: 547 MPFVVCFAYTMDETNHMADILLPEATDLESTQLIRAGGSKFVEQHWQHQGFVLRQPAVAP 606 Query: 612 QGETRDFTWIASELARRAGIQEPYNKAINRGAAGVPLKGASYDFSLDLEQTHGVEEIWNA 671 QGE+RDFTWI +EL+RR G+ E YN+ +N+G A VPLKG +DF+L +Q H V+ IW+A Sbjct: 607 QGESRDFTWITTELSRRVGLLESYNRGLNKGFALVPLKGEGFDFTLPEDQVHDVDTIWDA 666 Query: 672 SCRAASAELTGGAEDHGLDWWREHGFRTIDYPRLQWYLYPHMKDNGLRFEMPYQERIFRI 731 C+AA+A T G E GLDW +E+GF + R WYL+ M + GLR+E+PYQER+ R+ Sbjct: 667 VCKAATAGATKGQEVRGLDWMKENGFFMQPFAREDWYLHATMVEQGLRYELPYQERLMRV 726 Query: 732 GTELGRRLHESGIDWWDRQLTEYQPLPDFHDFSHLIKSAVISNLGGREEDFPFWLLTSRS 791 G EL RRLHE+GI WWD QL EYQ +P +HD AV G + EDFPFW +T+++ Sbjct: 727 GEELRRRLHEAGIQWWDEQLEEYQGIPHWHDVPGRWVKAV-ERAGAKAEDFPFWGITTKT 785 Query: 792 MQYAWGGNVSLQMVREVAANVAGHRGVIMNPASAAKLGIEDGDLVEVRSPLRETRGRVVL 851 M Y G N + ++ EVA N+ GH VI+N +SAAKL I+DGD VEV S + TRGR L Sbjct: 786 MPYTTGNNAGIPLMNEVAGNLRGHGSVIINASSAAKLDIKDGDWVEVSSVVGHTRGRAAL 845 Query: 852 RQGIRPDTLLMVGQFDHWITPYAKDFDVPSMNSLVPMLMDLTDATGSAADIVPVSIKRVG 911 QG RPDT+++ GQF HW TPYAKD + PS+N++ M ++LTDATGS AD+V V+++RV Sbjct: 846 VQGCRPDTVVIPGQFQHWKTPYAKDLNFPSLNTITQMSLELTDATGSGADVVRVALRRVD 905 Query: 912 G 912 G Sbjct: 906 G 906 Lambda K H 0.320 0.137 0.438 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 2759 Number of extensions: 127 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 914 Length of database: 911 Length adjustment: 43 Effective length of query: 871 Effective length of database: 868 Effective search space: 756028 Effective search space used: 756028 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 56 (26.2 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory