Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate BPHYT_RS01765 BPHYT_RS01765 carbon-monoxide dehydrogenase
Query= SwissProt::O33819 (769 letters) >FitnessBrowser__BFirm:BPHYT_RS01765 Length = 793 Score = 300 bits (769), Expect = 2e-85 Identities = 243/801 (30%), Positives = 370/801 (46%), Gaps = 58/801 (7%) Query: 6 PQHGTVGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEAL 65 P +G + +TG +YT DI P LRSPHAHA+I +IDT+AA+ Sbjct: 4 PDTHLIGASVERKEDYRFLTGNGQYTDDIVLPQQTYAIFLRSPHAHAKINSIDTAAAKQS 63 Query: 66 EGVIAVCTGAETP------VPFGVL-------PIAENEYPL-ARDKVRYRGDPVAAVAAI 111 GV+A+ TGA+ +P G L P+ E +P+ A KVR+ GD VA V A Sbjct: 64 PGVVAIFTGADMAADNVGGLPCGWLIHSTDGKPMNEPPHPIIAHTKVRHVGDQVALVIAD 123 Query: 112 DEVTAEKALALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILREV-HAEFGDVAAAF 170 A+ A LI+VDY+VLPA + A AG A+HD+ P+NI H + AAF Sbjct: 124 SIKAAKDAAELIEVDYDVLPAVVDTAHAADAGQPAVHDEVPDNICYNWGHGDKAATDAAF 183 Query: 171 AEADLIREKTYTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAA-CLQM 229 A+A + + +E A A Y D TL Q P+ L +AA L + Sbjct: 184 AKAAHVTTLDIVNNRLVPNAIEPRAVNASYSVQDDSYTLYVANQNPHVERLLMAAFVLSL 243 Query: 230 DSARIRVIKPFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTE 289 +++RVI P +GGGFG++ ++ ++K + V+ R E F++ Sbjct: 244 PESKLRVIAPDVGGGFGSKIFLYAEDVALTWASKKIRRPVKWTAERSEAFVSDAHGRDHV 303 Query: 290 VKMKIGLKKDGKIAALALEATQAGGAYAGY---GIITILYTGALMHGLYHIPAIKHDAWR 346 K ++ + DGK + + T GAY + TILY L+ G Y PAI + Sbjct: 304 TKAELAMDADGKFLGMRIHTTANMGAYLSTFASSVPTILYA-TLLAGQYATPAIYAEVKA 362 Query: 347 VYTNTPPCGAMRGHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRV 406 V+TNT P A RG G + E L+ ++ +D +IR+ N + + PY T Sbjct: 363 VFTNTVPVDAYRGAGRPEATYVVERLVETAARDMKLDPAEIRRRNFIREFPYATPVG--- 419 Query: 407 MSYGVPEC---------LEKVKAASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWTGE 457 ++Y + L VK + ++ K K RGLG + G + P + G Sbjct: 420 LTYDTGDYETILARSLELADVKGFAARKQESEKNGKLRGLGYSCYIEACGLA-PSNIAGA 478 Query: 458 PHATVNL------KLDFDGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADS 511 A L ++ G +T+ TG+ GQG T +QV A+ LG+ L + ++ D+ Sbjct: 479 LGARAGLFEVGQIRVHPTGSVTVFTGSHSHGQGHETTFAQVVADRLGIALESVEIVHGDT 538 Query: 512 ALTPKDNGSYSSRVTFMVGNASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGS 571 P G+Y SR + G+A + A ++++ K AA L+A EDIE D +F V+G+ Sbjct: 539 GRIPFGMGTYGSRSIAVGGSAIMKALDKIETKAKKIAAHLLEAAAEDIEFKDGVFRVAGT 598 Query: 572 QDPGLSFQEVVKAAMVDSGTITVKGTYTCPTEFQGDKKIRGSAIGATMGFCY--AAQVVE 629 D +F ++ AA V + P + + + SA F Y A + E Sbjct: 599 -DRTKAFADISLAAYV---------PHNYPLDVL-EPGLEESAFYDPTNFTYPSGAYICE 647 Query: 630 ASVDEITGKVTAHKVWVAVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVYDN--GRMV 687 VD TG + D G +NP+ VEGQ GG+ G+GQA+ E VYDN G+++ Sbjct: 648 IEVDPETGVCRIQQFTAVDDFGNVINPMIVEGQVHGGLAQGIGQAMLERCVYDNESGQLL 707 Query: 688 HGNILDYRVPTIVESPDIEVIIVESMD-PNGPFGAKEASEGMLAGFLPAIHEAVYEA--- 743 G+ +DY +P + P+ V V+ + P G K E G PA+ A+ +A Sbjct: 708 SGSYMDYAMPHASDLPNFTVETVKGTPCTHNPLGVKGCGEAGAIGSPPAVINAILDALAP 767 Query: 744 VGVRATDFPLSPDRITELLDA 764 +GV P +P R+ + A Sbjct: 768 LGVTDLQMPATPHRVWSAIHA 788 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: 1434 Number of extensions: 58 Number of successful extensions: 7 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: 793 Length adjustment: 41 Effective length of query: 728 Effective length of database: 752 Effective search space: 547456 Effective search space used: 547456 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