Align 4-hydroxybenzoyl-CoA reductase, α subunit (EC 1.3.7.9) (characterized)
to candidate AZOBR_RS29690 AZOBR_RS29690 carbon monoxide dehydrogenase
Query= metacyc::MONOMER-14376 (794 letters) >FitnessBrowser__azobra:AZOBR_RS29690 Length = 789 Score = 268 bits (685), Expect = 9e-76 Identities = 240/802 (29%), Positives = 343/802 (42%), Gaps = 64/802 (7%) Query: 13 AANAAPRGVGARLPLIDGVEKVTGTARYTADLPAQGALVGKLLRSPYAHAELLEVDISEA 72 A + A GVGAR+ + + G R+ D+ G +RSP AHA + ++I E Sbjct: 7 AGSGAGSGVGARVRRKEDDRLLRGRGRFVGDIALVGMKELAFVRSPVAHATITGIEIPEE 66 Query: 73 LKLPGVRGIVTGNDCDTPYGVIPIAQ---------NEFP-LARGRIRYVGEPVAAVAAVD 122 + + T D GV PI +E P LA G++R+VGEPVA A Sbjct: 67 HR----GAVFTWADLAAG-GVKPIRAVSGLPGFKVSEQPALADGKVRFVGEPVAVCVAAT 121 Query: 123 EATTDAALALIRLKVRELPAYFDAADARKADVVLLHDNKKGNIEREVHNEFGDAAAGFAA 182 A + A + + ELP D +A +HD+ N+ E N G+ A A Sbjct: 122 RAEAEDIAASVFVDYAELPVNSDMLEAVAPGAPKVHDHWPDNVFLET-NVGGNIAEIAAT 180 Query: 183 ADLICEETFECAEVHHAMMEPNASLAAWDNERGHLTLWSVTQVPYYVHESLARCMKLDAA 242 A + T A +E +A WD L L + TQ+P+ V L+ C+ LD Sbjct: 181 APVKVSRTIRTARQCMVPLEGKGVVAHWDRHVEQLVLTTSTQMPHIVRAGLSECLDLDQG 240 Query: 243 YIRVIKPFVGGGFGHRVETLNFEIIAGLLARAARGTVRLLQTREEAFLTHRGRPQTYVRM 302 IRV+ P VGGGFG + EI+A +A VR + R E + + + + Sbjct: 241 LIRVVAPDVGGGFGWKGLLQPEEIVAAWIAMRLDRPVRWTEDRREHLVAAANAREHHYEI 300 Query: 303 KLGLTRDGRMTACEAEVVQRGGAYGGYGLVTILYA---GALLNGLYDLPAVKYDGYRVYT 359 GR+ EA+ GAY Y L A G++L G YD + + V T Sbjct: 301 TAYADARGRLLGIEADAWVDAGAYSVYPFSACLEAAQVGSILPGPYDFAHYRCRTFSVCT 360 Query: 360 NTPPCGAMRGHGTVNIRFAFESLLDMMAAELGLDAFAVRRRNLL---KAPTETINGLKVM 416 N PP RG + FA E ++D +A +G + + VR NL+ K P + + Sbjct: 361 NKPPIVPYRGVARTGVCFAMEQMIDAVADAVGREPWQVRLENLVPPEKMPFDNVTKKHFD 420 Query: 417 SYGLPECLDWVEQA---SGWRERAARLEANSDGPIRRGIGIA--CSHFVSGSAKPVHFTG 471 S PE + A GWR R EA DG + G+G A C G+A H G Sbjct: 421 SGDYPESVRRAVAAIELEGWRARQKAGEA--DGRL-IGVGFATYCEQSAHGTA-VYHGWG 476 Query: 472 QP----HATIALRVDFDAGITILTGASDIGQGSSTIITQVVAEILGVEYRRLRLIATDSA 527 P H R+ D G+ + G GQ T QV E+LG+ +++L+ D+ Sbjct: 477 IPMVPGHEQAQARITPDGGLELRVGVQSHGQSMETTFAQVAHEVLGIPLEKIKLVHGDTG 536 Query: 528 LTPKDNGSYSSRVTFMVGNAAADAARNLKAVLVAAAAKRLQVAEADVDWLGEAAAVVGDA 587 LTP G++ SR M G A A A R L L A +Q A D L + A G A Sbjct: 537 LTPYSTGTWGSRSMVMAGGAVATACRTLAERLRKIGAHLMQ-AGPDGVVLKDGAVTAGPA 595 Query: 588 SRQIPFHDIVE---------EALVDVGMLTVKGTFTCPPEFQGGKQRGGAVGSTMGFSYA 638 + + +I A VD G L E G + G G+ FSYA Sbjct: 596 A--VTIREIAHTWYRAPQLLPADVDRGGL----------EVTAGYKPGSDHGT---FSYA 640 Query: 639 AQAVEVSVDTELGKVTVEKVWSAIDCGFAINPMSVEGQVQGAIWMGMGQAISEETVYE-N 697 AV V+VD E+G+V + D G +NPM V+GQ+ G + G+G A+ E Y+ Sbjct: 641 THAVAVAVDPEIGQVEILDYVVVEDAGTMVNPMVVDGQIYGGVAQGVGTALYERMPYDAE 700 Query: 698 GRHKAVSLLDYRVPTIIESPDIAVHIVESLDPNGPFGAKEASEGPLAGVMSAIAAAIEDA 757 G+ A + DY +P E P + + + + P FG K EG +AI AI DA Sbjct: 701 GQPLASTFADYLIPGFTEVPHVRIIHMLTPSPYTEFGVKGIGEGGAIAPPAAICNAINDA 760 Query: 758 ---TGTRIRATPFTPDRVFDAL 776 G + P TP+ + A+ Sbjct: 761 LKPLGVIVTNAPMTPEVILTAI 782 Lambda K H 0.319 0.135 0.397 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: 1469 Number of extensions: 84 Number of successful extensions: 8 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: 794 Length of database: 789 Length adjustment: 41 Effective length of query: 753 Effective length of database: 748 Effective search space: 563244 Effective search space used: 563244 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: 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