Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate AZOBR_RS08560 AZOBR_RS08560 carbon-monoxide dehydrogenase
Query= SwissProt::O33819 (769 letters) >FitnessBrowser__azobra:AZOBR_RS08560 Length = 796 Score = 298 bits (764), Expect = 6e-85 Identities = 247/788 (31%), Positives = 361/788 (45%), Gaps = 70/788 (8%) Query: 24 VTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVIAVCTGAETPVP-FG 82 +TG+ YT DI P +RSP+AHARI ID + A GVIAV TGA+ G Sbjct: 20 LTGRGTYTDDINRPGQTHAVFVRSPYAHARITGIDAAEAMRAPGVIAVLTGADMEADKVG 79 Query: 83 VLPIAEN-------------EYPLARDKVRYRGDPVAAVAAIDEVTAEKALALIKVDYEV 129 LP +P+ARD+ RY GD VA V A A+ A L+ VDYE Sbjct: 80 SLPCGWQIHSKDGSPMKEPPHFPIARDRARYVGDAVAVVIAETREQAKDAAELVMVDYEE 139 Query: 130 LPAYMTPKAAMKAGAIALHDDKPNNILREVHAEFGDVAA---AFAEADLIREKTYTFAEV 186 LPA +T A++ GA +HDD N+ + H GD AA AF++A + + + Sbjct: 140 LPAAVTSLKALEGGAPLVHDDVGGNLCFDWH--LGDAAAVDAAFSQAAHVAKLDLVNQRL 197 Query: 187 NHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAA-CLQMDSARIRVIKPFLGGGF 245 ME A L EYD TL TT+Q P+ + L + A L + ++RV+ P +GGGF Sbjct: 198 VPNAMEPRAALGEYDRATGEHTLTTTSQNPHVIRLLMGAFVLGIPEHKLRVVAPDVGGGF 257 Query: 246 GARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAH-RGRPWTEVKMKIGLKKDGKIAA 304 G++ E + A+K V+ R E+F+ GR ++ + KDG A Sbjct: 258 GSKIFHYGEEAVVTWAAKKVGRPVKWTAERSESFLTDAHGRDHVS-HAELAMDKDGNFLA 316 Query: 305 LALEATQAGGAYAGY---GIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMRGHG 361 L + GAY I T LY L+ G Y PAI + V+TNT P A RG G Sbjct: 317 LRVATIANMGAYLSTFAPSIPTYLYA-TLLAGQYKTPAIYAEVKAVFTNTVPVDAYRGAG 375 Query: 362 TVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQ--IPYVTMYAQRVMSYGVPECLEKVK 419 + E L+ E GID ++R+ N +P +PY T A + Y + + + Sbjct: 376 RPEACYLIERLVEVAAAETGIDKAELRRRNFVPASAMPYQTPVA---LQYDTGDFAKNLD 432 Query: 420 AA------SGWEERKGKLPK-GRGLGIALSHFVSGTS-TPKHWTGEPHATVNL------K 465 A G+ RK + + G+ GI + ++ P + G A L + Sbjct: 433 IALPLVDYDGFAARKAESARRGKLRGIGFATYIEACGIAPSNVAGALGARAGLYESAEVR 492 Query: 466 LDFDGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRV 525 G +T+ TG+ GQG T +Q+ +E GV + + ++ D++ P G+Y SR Sbjct: 493 FHPTGSVTVFTGSHSHGQGHETTFAQLVSERFGVPIENVEIVHGDTSKIPFGMGTYGSRS 552 Query: 526 TFMVGNASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQDPGLSFQEVVKAA 585 + G+A + A ++++ K AA L+A E DIEV D F+V+G+ D L+ ++ A Sbjct: 553 LAVGGSAIVKAMDKVERKAKKIAAHMLEAAEADIEVKDGRFVVAGT-DKALTIGDIALQA 611 Query: 586 MVDSGTITVKGTYTCPTEFQGDKKIRG---SAIGATMGFCY--AAQVVEASVDEITGKVT 640 V P F D+ G A F Y V E +D TG V Sbjct: 612 YV-------------PHNFPLDELEPGLDEQAFYDPKNFTYPNGCHVCEVEIDPDTGVVQ 658 Query: 641 AHKVWVAVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVY--DNGRMVHGNILDYRVPT 698 D G+ +NPL VEGQ GG+ G+GQAL E VY D+G+++ G+ +DY +P Sbjct: 659 VVNFAAVDDFGRVINPLIVEGQVHGGLVQGIGQALYENCVYDEDSGQLITGSYMDYCMPR 718 Query: 699 IVESPDIEVIIVESMD-PNGPFGAKEASEGMLAGFLPAIHEAVYEAV---GVRATDFPLS 754 + P V E + P G K E G A+ AV A+ GV D P + Sbjct: 719 ADDVPSFTVRYHEDQPCTHNPLGVKGCGEAGTIGASAAVMNAVVHALSEYGVTHLDMPAT 778 Query: 755 PDRITELL 762 P+R+ + + Sbjct: 779 PERVWQAI 786 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: 1400 Number of extensions: 64 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: 796 Length adjustment: 41 Effective length of query: 728 Effective length of database: 755 Effective search space: 549640 Effective search space used: 549640 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