Align Phenylacetyl-CoA:acceptor oxidoreductase large subunit PadB; EC 1.8.5.3 (characterized, see rationale)
to candidate WP_011383653.1 AMB_RS06300 phenylacetyl CoA
Query= uniprot:A0A2R4BLL6 (914 letters) >NCBI__GCF_000009985.1:WP_011383653.1 Length = 922 Score = 1214 bits (3142), Expect = 0.0 Identities = 567/902 (62%), Positives = 703/902 (77%), Gaps = 4/902 (0%) Query: 10 VTKVATYCYQCVAGPDLLKVKVEDGVATAIEPNFDAEGVHPAAGRVCVKAFGLVQKTYNP 69 V KV TYCYQCVAGPDL+ VKV DGVAT IEPNF A HPA G+VCVKAFGL+QK+Y P Sbjct: 13 VEKVQTYCYQCVAGPDLMTVKVVDGVATEIEPNFKAADTHPAEGKVCVKAFGLIQKSYTP 72 Query: 70 NRVLTPMKRTNPKKGRDEDPGFVPISWDEALDLIADKLNTVRANGLLDASGYPRVAASFG 129 +R+LTPMKRTNPKKG+D+DPGFVPISWDEA+ IA++LN +RA GLLDA GYP+ AASFG Sbjct: 73 HRILTPMKRTNPKKGKDQDPGFVPISWDEAMGTIAERLNAIRAEGLLDAQGYPKFAASFG 132 Query: 130 GGGTPTAYMGTFPAFLSAWGPVDLSFGSGQGVKCTHSEHLYGELWHRAFTVCPDTPRTKY 189 G GTPT YMG+ AFLSAWGP+D FGSGQGVKC HSEHLYGE WHR + + PDTPR Y Sbjct: 133 GAGTPTQYMGSLTAFLSAWGPIDFGFGSGQGVKCYHSEHLYGEFWHRGYVITPDTPRANY 192 Query: 190 IVSFGSNIEASGGVCGVWRHAEARVEQGVKRVQVEPHLSVTGGCSAEWVPIKPKTDPAFM 249 I+S G+N EAS GVCGV+RHAEAR +G RVQVEPHLSVTG CSAEW+PIKPKTD AF+ Sbjct: 193 IISCGTNTEASSGVCGVYRHAEARA-RGAIRVQVEPHLSVTGACSAEWLPIKPKTDAAFL 251 Query: 250 HAMIHVMLFENARTRLDIDFLKHMTASPYLVAPNGLYLRDPDTRKPLVWDLKRAAAVPFD 309 +++V++FE R RLD+DFL++ T+SPYLV P+G YLRDP+T KPL+WD K AVP D Sbjct: 252 MTLLNVLVFEAPRERLDLDFLRNTTSSPYLVGPDGWYLRDPETHKPLLWDEKTGRAVPHD 311 Query: 310 TADIDPALDGEFTASGLEVL-PDNETVDHVQVRVLTAFGKLAEHERTFTPEWAAKVCDVP 368 T PAL+G FT L D + +H V +TAF K EH + +TP W AKVCDVP Sbjct: 312 TPGAVPALEGRFTVPKAVTLGADEDRWEHTDVEGVTAFTKFIEHVKGYTPAWGAKVCDVP 371 Query: 369 ADTIRRVANEYLDHAQIGATIEIEGRTLPFRPVAITLGKTVNNGWGGYDCCWARTLMACL 428 IR++AN++LDHA +G TIEI+G+ +P+RPVA+ LGKTVNNGWGG +CCWART++A L Sbjct: 372 EARIRKIANDFLDHACVGQTIEIDGQVMPYRPVAVVLGKTVNNGWGGAECCWARTMLAVL 431 Query: 429 VGALDVPGGTIGTTVRLNRPASDRQSSAKPGPDGFMDYPFNPTDKENWVSRPQIRNANRT 488 VGAL+VPGGT+GTT+R+NRPA++R S + DGFM+YPFNPTDK+ W + P IRNA + Sbjct: 432 VGALEVPGGTVGTTIRINRPAANRLESFEGCLDGFMEYPFNPTDKDTWKANPIIRNAYKM 491 Query: 489 LVPLVANSAWSAALGPTHLAWMQQRHGFENFPEPTQPDVWFFYRTNPVISFWDTPQVAEA 548 LVPLV NS+WS ALGPT ++M + P T P+ YRTNPVISFWDT +VA Sbjct: 492 LVPLVGNSSWSPALGPTQFSYMFLDEPQDQIPRATFPEFLLVYRTNPVISFWDTDRVASV 551 Query: 549 VSKFPFVVAFTYTRDETNHFADVLLPDCTDLEGLQLIRIGGTKYVEQFWDKQGFALRQPA 608 VS+ PFVV F +TRDETNHFAD+LLPD TDLEG+QLIRIGGTK+ EQFW +QGFALRQP+ Sbjct: 552 VSRMPFVVCFAHTRDETNHFADILLPDATDLEGMQLIRIGGTKFQEQFWKQQGFALRQPS 611 Query: 609 VVPQGETRDFTWIASELARRAGIQEPYNKAINRGAAGVPLKGASYDFSLDLEQTHGVEEI 668 V PQGE RDFT IA++LA R G+QE Y AINRG+ GVPLKG ++DFSL +++ +EE+ Sbjct: 612 VKPQGEARDFTDIATDLAVRTGLQEKYVAAINRGSHGVPLKGPNWDFSLPVDKAPSLEEV 671 Query: 669 WNASCRAASAELTGGAEDHGLDWWREHGFRTIDYPRLQWYLYPHMKDNGLRFEMPYQERI 728 W+ASCR+ASAEL+ GAE GLDWW+E+GFRTI + W+L P +K GLR+E+PYQER+ Sbjct: 672 WDASCRSASAELSDGAESQGLDWWKENGFRTIPFSETNWFLTPALKAKGLRYELPYQERL 731 Query: 729 FRIGTELGRRLHESGIDWWDRQLTEYQPLPDFHDFSHLIKSAVISNLGGREEDFPFWLLT 788 RIG +L RL E+GI WWD QLTEY+PL ++HDF + +V+ + GG+ DFPFW++T Sbjct: 732 TRIGRQLANRLKEAGITWWDHQLTEYRPLMEWHDFPGYWEQSVVEH-GGKVADFPFWVVT 790 Query: 789 SRSMQYAWGGNVSLQMVREVAANVAGHRGVIMNPASAAKLGIEDGDLVEVRSPL-RETRG 847 +RSMQYAWG N+ + ++REV+ ++ GH GV+MNP +A K+G+++G+ + V +P + G Sbjct: 791 ARSMQYAWGSNMHIPLMREVSGHIKGHDGVVMNPEAARKVGVKEGERIVVTAPTGKSVAG 850 Query: 848 RVVLRQGIRPDTLLMVGQFDHWITPYAKDFDVPSMNSLVPMLMDLTDATGSAADIVPVSI 907 RVVL QGIRPDT+LM+ QFDHW TP AKDFDVPSMN L M M LTDATGSAAD+ V+I Sbjct: 851 RVVLSQGIRPDTILMMSQFDHWATPIAKDFDVPSMNRLTAMTMQLTDATGSAADLSRVAI 910 Query: 908 KR 909 ++ Sbjct: 911 RK 912 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: 2798 Number of extensions: 121 Number of successful extensions: 5 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: 922 Length adjustment: 43 Effective length of query: 871 Effective length of database: 879 Effective search space: 765609 Effective search space used: 765609 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: 57 (26.6 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