Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate WP_011383893.1 AMB_RS07490 aldehyde oxidase
Query= SwissProt::O33819 (769 letters) >NCBI__GCF_000009985.1:WP_011383893.1 Length = 913 Score = 353 bits (906), Expect = e-101 Identities = 254/778 (32%), Positives = 386/778 (49%), Gaps = 42/778 (5%) Query: 3 PKLPQHGT-VGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSA 61 P +P+ G+ VG R +DG ++V G Y D+ PD L+ R++RSPH HAR D +A Sbjct: 156 PVVPEAGSSVGTRLRRLDGRQRVDGSEIYGDDVCPPDCLLVRVIRSPHPHARFTIGDLTA 215 Query: 62 AE-ALEGVIAVCTGAETPVP--FGVLPIAENEYPLARDKVRYRGDPVAAVAAIDEVTAEK 118 A G++ V T A+ P F V+P E++ A VRYRG+ VAAV + Sbjct: 216 LRVAYPGIVQVLTAADVPGINLFSVIPGMEDQPAFAEGLVRYRGEAVAAVVMEADTNDIF 275 Query: 119 ALALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILREVHAEFGDVAAAFAEADLIRE 178 A V +EVL ++ + A A A+ LH +P NIL + GD+ +A+A + E Sbjct: 276 QDADFPVLWEVLEPALSMEQATAADAVLLHAKRPGNILVRGFVQKGDLDLHWAKAAQVVE 335 Query: 179 KTYTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIK 238 ++T V H ++E A A V D + + TQ PY VAA + + ++R+I Sbjct: 336 DSFTTGFVEHAYIEPEAGYARR--VGDTIEIYACTQAPYMDRDSVAAIMALPPEQVRIIP 393 Query: 239 PFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVKMKIGLKK 298 +GGGFG + + + + L A VR L TR E+ + R + ++G Sbjct: 394 TAVGGGFGGKLD-VSLQPYVALAAWSLGRPVRCLYTRTESMASSTKRHPAAITARVGAGA 452 Query: 299 DGKIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMR 358 DGK+ A+ + GAYA +G G Y IPA++ ++TN PP GA R Sbjct: 453 DGKLTAMEFDGDFNTGAYASWGPTVANRVPVHCSGPYFIPALRARTRAIHTNNPPSGAFR 512 Query: 359 GHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLP--------QIPYVTMYAQRVMSYG 410 G G A E+L ++ ++LG+D L+ R+IN + QI ++ Q Sbjct: 513 GFGIPQASIAQESLFDQLADKLGLDRLEFRRINAITAGQPTATGQILTASVGQQACFDAL 572 Query: 411 VPECLEKVKAASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDG 470 VP E + AA + G + RG+G+A + G ++ + +T+ + L DG Sbjct: 573 VPRWQEALAAAEAFNRTAGD--RRRGVGVAGMWYGCGNTSMSN-----PSTIRVALRADG 625 Query: 471 GITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTFMVG 530 + L GA DIGQGSNT+ +Q+ A+ LG+ + + ++ D+ALT + +SR TF+ G Sbjct: 626 AVVLFQGAVDIGQGSNTVITQICADALGIEIGKFTLVMGDTALTADAGKTSASRQTFVSG 685 Query: 531 NASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVS-GSQDPGLSFQEVVKAAMVDS 589 AS A +L+ +++ D+R + + + VS G+ + Q + + D Sbjct: 686 RASQLAGLDLRDKILRMVNAGADSR---LSLDGSILCVSDGADTHQIDLQSLARDQ--DG 740 Query: 590 GTITVKGTYTCPTEFQGDKKIRGSAIG---ATMGFCYAAQVVEASVDEITGKVTAHKVWV 646 + +GT+ PTE K+ + G AT GF AQ+ E VD G V K+ Sbjct: 741 LVMDGEGTFDPPTE-----KLDANGQGIPYATYGF--GAQMAEVEVDTALGTVKVLKIIA 793 Query: 647 AVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVYDNGRMVHGNILDYRVPTIVESPDIE 706 A DVG+A+NP+ +EGQ +GG+ G+G AL EE Y GR N+ DY +PT + P IE Sbjct: 794 AHDVGRAINPMLLEGQIEGGIAQGLGLALMEE--YIQGRT--ENLHDYLIPTAGDIPPIE 849 Query: 707 VIIVESMDPNGPFGAKEASEGMLAGFLPAIHEAVYEAVGVRATDFPLSPDRITELLDA 764 II+E +P GPFGAK E L PAI A+ A GV P +PDR+ + A Sbjct: 850 TIIIEDAEPLGPFGAKGIGEQALIPTAPAILGAIRHATGVTIRQVPATPDRVRAAIRA 907 Lambda K H 0.317 0.134 0.386 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: 1372 Number of extensions: 56 Number of successful extensions: 9 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: 769 Length of database: 913 Length adjustment: 42 Effective length of query: 727 Effective length of database: 871 Effective search space: 633217 Effective search space used: 633217 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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