Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate WP_011384423.1 AMB_RS10200 4-hydroxybenzoyl-CoA reductase subunit alpha
Query= SwissProt::O33819 (769 letters) >NCBI__GCF_000009985.1:WP_011384423.1 Length = 769 Score = 1421 bits (3679), Expect = 0.0 Identities = 709/768 (92%), Positives = 747/768 (97%) Query: 1 MSPKLPQHGTVGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTS 60 MSPK P++GTVG RTPLVDGVEKVTGKAKYTADIAAP ALVGRILRSP AHARI++IDTS Sbjct: 1 MSPKFPKNGTVGARTPLVDGVEKVTGKAKYTADIAAPGALVGRILRSPVAHARIISIDTS 60 Query: 61 AAEALEGVIAVCTGAETPVPFGVLPIAENEYPLARDKVRYRGDPVAAVAAIDEVTAEKAL 120 AAEAL+GV AVCTGAETPVP+GVLPIAENEYPLARDKVRYRGDPVAAVAA+DE+TAE+AL Sbjct: 61 AAEALDGVYAVCTGAETPVPYGVLPIAENEYPLARDKVRYRGDPVAAVAAVDELTAEQAL 120 Query: 121 ALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILREVHAEFGDVAAAFAEADLIREKT 180 LIKV+YEVLPAYMTPKAAMK GAIALHDDKPNN+LREVHAEFGDV AAF EA+LIREK Sbjct: 121 NLIKVEYEVLPAYMTPKAAMKEGAIALHDDKPNNVLREVHAEFGDVEAAFGEAELIREKV 180 Query: 181 YTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIKPF 240 YTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIKPF Sbjct: 181 YTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIKPF 240 Query: 241 LGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVKMKIGLKKDG 300 LGGGFGARTE LHFEIIAGLLARKAKGTV+L+QTREETFIAHRGRPWTEVKMKIGL +DG Sbjct: 241 LGGGFGARTECLHFEIIAGLLARKAKGTVKLVQTREETFIAHRGRPWTEVKMKIGLMRDG 300 Query: 301 KIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMRGH 360 KIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMRGH Sbjct: 301 KIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMRGH 360 Query: 361 GTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRVMSYGVPECLEKVKA 420 GTVDTRAAFEALLTEMGEELGIDSL IRQ NMLPQIPY TMYAQ+VMSYGVPECLEKVKA Sbjct: 361 GTVDTRAAFEALLTEMGEELGIDSLDIRQRNMLPQIPYTTMYAQKVMSYGVPECLEKVKA 420 Query: 421 ASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDGGITLLTGAAD 480 ASGW ERKGK+PKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDGGITLLTGAAD Sbjct: 421 ASGWAERKGKMPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDGGITLLTGAAD 480 Query: 481 IGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTFMVGNASISAAEEL 540 IGQGSNTMA+QVAAEVLGVR+SRIRVISADSALTPKDNGSYSSRVTFMVGNASISAAEEL Sbjct: 481 IGQGSNTMATQVAAEVLGVRMSRIRVISADSALTPKDNGSYSSRVTFMVGNASISAAEEL 540 Query: 541 KGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQDPGLSFQEVVKAAMVDSGTITVKGTYTC 600 K +LVKAAAKKLDAREEDIEVIDE+FMV+GSQDPGL+FQEVVKAA++D+GTITVKGT+TC Sbjct: 541 KAILVKAAAKKLDAREEDIEVIDEVFMVAGSQDPGLTFQEVVKAALIDTGTITVKGTFTC 600 Query: 601 PTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGKVTAHKVWVAVDVGKALNPLAVE 660 PTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITG+VTAHKVWVAVDVGKALNPLAVE Sbjct: 601 PTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGRVTAHKVWVAVDVGKALNPLAVE 660 Query: 661 GQTQGGVWMGMGQALSEETVYDNGRMVHGNILDYRVPTIVESPDIEVIIVESMDPNGPFG 720 GQTQGGVWMGMGQALSEET +D+G+M+HGNILDYRVPT+ ESPDIEV+IVES+DPNGPFG Sbjct: 661 GQTQGGVWMGMGQALSEETRWDDGKMMHGNILDYRVPTMAESPDIEVMIVESLDPNGPFG 720 Query: 721 AKEASEGMLAGFLPAIHEAVYEAVGVRATDFPLSPDRITELLDAKEAA 768 AKEASEGMLAGFLPA+HEAVYEAVGVR+T FPLSP+ ITELLDAKEAA Sbjct: 721 AKEASEGMLAGFLPAVHEAVYEAVGVRSTKFPLSPETITELLDAKEAA 768 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: 1806 Number of extensions: 57 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 769 Length of database: 769 Length adjustment: 41 Effective length of query: 728 Effective length of database: 728 Effective search space: 529984 Effective search space used: 529984 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: 55 (25.8 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