Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 6935814 Sama_0032 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= BRENDA::Q64428 (763 letters) >FitnessBrowser__SB2B:6935814 Length = 716 Score = 352 bits (903), Expect = e-101 Identities = 239/721 (33%), Positives = 368/721 (51%), Gaps = 32/721 (4%) Query: 49 VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108 +A + N+P S VN ++E + ++ + +D ++AVL S K F+ GADI Sbjct: 17 IARLCFNAPGS-VNKFDRETLASLNAALDVLKDSDA-KAAVLTSGKD-TFIVGADITEFL 73 Query: 109 SCTTPQEAARISQEGQK--MFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRK 166 + ++A + Q +F KLE P P V+AI G LGGG E +A +R+A D Sbjct: 74 ALFAEEDAKLMEWIAQANVVFNKLEDLPFPTVSAIKGFALGGGCEAILATDFRVA--DTS 131 Query: 167 TVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLG 226 +G+PE LG++PG GGT RLP+++G A + + TG++ R + A K+G +D +V P Sbjct: 132 AKIGLPETKLGLIPGFGGTVRLPRLIGADNALEWITTGKDQRPEDALKVGAIDAVVAP-- 189 Query: 227 PGIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTV 286 ++ E I+ L + A R + KQ+ + KL + M+ + VY Sbjct: 190 ---ENLEAAAIQMLNDALAGKLDWQARR--ARKQAPLTLPKLEAM-MSFTTAKGMVYAVA 243 Query: 287 EEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQ 346 + YPAP+ + V+ + E F +LA T + AL+G++ Sbjct: 244 GKH--------YPAPMAAVSVVEQAAGMSRAEALVVEHNAFIKLAKTDVATALIGIFLND 295 Query: 347 VLCK--KNKFGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKTLLKDTTVTGLGRGQQQV 404 L K K K ++ A+LGAG+MG GIA S KG ++KD L G + Sbjct: 296 QLVKGKAKKASKLAKDIKHAAVLGAGIMGGGIAYQSASKGTPIVMKDINQAALDLGVNEA 355 Query: 405 FKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVES 464 K L+ +V + T + + +N+ LDY + ++V+EAV E+ VK VL +VE+ Sbjct: 356 AKLLSAQVARGRSTPDKMAKVLNNITPALDYAPLKDVNVVVEAVVENPKVKAMVLADVEN 415 Query: 465 VTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTAS 524 V + I ASNTS + I+ +A + P + GMH+F+PV KM L+E+I TS++T AS Sbjct: 416 VVADDAIIASNTSTISIDLLAKSLKNPARFCGMHFFNPVHKMPLVEVIRGKDTSEETVAS 475 Query: 525 AVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLD-ALTTGFGFPVG 583 VA K GK IVV D PGF+ R L P + +L +G D +D + FG+P+G Sbjct: 476 VVAYASKMGKTPIVVNDCPGFFVNRVLFPYFAGFNGLLADGGDFAAIDKVMEKQFGWPMG 535 Query: 584 AATLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIY---Q 640 A L D VG+D H + F +R G + + +M G LG+K+GKGFY Y + Sbjct: 536 PAYLLDVVGLDTGHHAQAVMADGFPDRMGKSDKDAIDVMYEAGRLGQKNGKGFYQYSIDK 595 Query: 641 SGSKNKNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEAVLCLQEGILATPEEG 700 G K+++ +L A+ +DE I R + + E V CL+EGI+A+P E Sbjct: 596 RGKPKKDVDPASYTMLAE-AFGAQKAFEADEIIA-RTMIPMIIETVRCLEEGIVASPAEA 653 Query: 701 DIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANNSSKK 760 D+G V+GLGFPP GG FR++D G V KY + G + +R+LA+N+ Sbjct: 654 DMGLVYGLGFPPFRGGVFRYLDTMGVANFVALADKY-AHLGGLYQVTDAMRELASNNGSY 712 Query: 761 F 761 + Sbjct: 713 Y 713 Lambda K H 0.317 0.135 0.380 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: 1128 Number of extensions: 71 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: 763 Length of database: 716 Length adjustment: 40 Effective length of query: 723 Effective length of database: 676 Effective search space: 488748 Effective search space used: 488748 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