Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate RR42_RS02365 RR42_RS02365 carbon monoxide dehydrogenase
Query= SwissProt::O33819 (769 letters) >FitnessBrowser__Cup4G11:RR42_RS02365 Length = 793 Score = 281 bits (719), Expect = 1e-79 Identities = 236/777 (30%), Positives = 352/777 (45%), Gaps = 59/777 (7%) Query: 24 VTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVIAVCTGAETP----- 78 +TG +YT DI P G LRSPHAHARI++ID + A A GV+A+ TG + Sbjct: 23 LTGNGQYTDDIVLPQQSYGYFLRSPHAHARIVSIDKTEALASPGVVAIFTGDDVAADKVG 82 Query: 79 -VPFGVL-------PIAENEYP-LARDKVRYRGDPVAAVAAIDEVTAEKALALIKVDYEV 129 +P G L P+ E +P LA+ K R+ GD VA V A A+ A I V Y+ Sbjct: 83 GLPCGWLIHSIDGSPMKEPAHPVLAQGKARHVGDQVALVIAETLQQAKDAAEKIDVQYDE 142 Query: 130 LPAYMTPKAAMKAGAIALHDDKPNNILREV-HAEFGDVAAAFAEADLIREKTYTFAEVNH 188 LPA + A A ++ +HDD P N H + AAFA+A + + Sbjct: 143 LPAVVNTAHAASATSL-VHDDVPENTSYVWGHGDRAATDAAFAKAAHVTTLEIINNRLIP 201 Query: 189 VHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAA-CLQMDSARIRVIKPFLGGGFGA 247 +E A A Y D T+ + Q P+ L + A L + +R+R+I P +GGGFG+ Sbjct: 202 NAIEPRAVNASYTRQDDSYTVYVSNQNPHVERLLMGAFVLGLPESRLRIIAPDVGGGFGS 261 Query: 248 RTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVKMKIGLKKDGKIAALAL 307 + ++ ++K K ++ R E+F+ K ++ + DGK A+ + Sbjct: 262 KIFLYAEDVALTWASKKIKRPIKWTAERSESFLTDAHGRDHVTKAELAMDADGKFLAMRV 321 Query: 308 EATQAGGAYAGY---GIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMRGHGTVD 364 T GAY + TILY L+ G Y PAI + V+TNT P A RG G + Sbjct: 322 HTTANMGAYLSTFASSVPTILYA-TLLAGQYATPAIYAEVRAVFTNTAPVDAYRGAGRPE 380 Query: 365 TRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRVMSYGVPECLEK------V 418 E L+ E+ +D +IR+ N + PY T + CL + V Sbjct: 381 ATYVVERLVEAAAREMKMDPAQIRRKNFIHDFPYATPVGLTYDTGDYEPCLARAQELADV 440 Query: 419 KAASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNL------KLDFDGGI 472 K E + K RGLG + G + P + G A L ++ G + Sbjct: 441 KGFPARREEAKQRGKLRGLGYSCYIEACGLA-PSNIAGALGARAGLFEVGEIRVHPTGTV 499 Query: 473 TLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTFMVGNA 532 T+ TG+ GQG T +Q+ A+ LG+ L + V+ D+ P G+Y SR + G+A Sbjct: 500 TVFTGSHSHGQGHETTFAQIVADRLGIALDAVEVVHGDTGRVPFGMGTYGSRSLSVGGSA 559 Query: 533 SISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQDPGLSFQEVVKAAMVDSGTI 592 + A ++++ K AA L+A + DIE + F V+G+ D +F EV A V Sbjct: 560 IMKALDKIEAKAKKIAAHLLEASDADIEFKNGTFSVAGT-DRSKTFGEVALTAYV----- 613 Query: 593 TVKGTYTCPTEFQGDKKIRG---SAIGATMGFCY--AAQVVEASVDEITGKVTAHKVWVA 647 P + DK G +A F Y A + E VD TG+ K Sbjct: 614 --------PHNYPLDKLEPGLNENAFYDPTNFTYPSGAYICEVEVDPDTGESKVIKFTAV 665 Query: 648 VDVGKALNPLAVEGQTQGGVWMGMGQALSEETVY--DNGRMVHGNILDYRVPTIVESPDI 705 D G +NP+ VEGQ GG+ G+GQA+ E+ VY D+G+++ G+ +DY +P + PD Sbjct: 666 DDFGNIINPMIVEGQVHGGIGQGLGQAMLEQCVYDDDSGQLLTGSYMDYAMPRAGDLPDF 725 Query: 706 EVIIVESMD-PNGPFGAKEASEGMLAGFLPAIHEAVYEA---VGVRATDFPLSPDRI 758 V + + P G K E G PA A+ +A +GV P +P R+ Sbjct: 726 TVETAKGTPCTHNPLGVKGCGEAGAIGSPPAFINALVDALSPLGVHDIQMPATPHRV 782 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: 1464 Number of extensions: 75 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: 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