Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_085772004.1 B1812_RS13170 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
Query= BRENDA::Q64428 (763 letters) >NCBI__GCF_002117405.1:WP_085772004.1 Length = 728 Score = 335 bits (860), Expect = 4e-96 Identities = 235/757 (31%), Positives = 370/757 (48%), Gaps = 62/757 (8%) Query: 36 LSRTHINYGVKGDVAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKP 95 L + G G VA++ + P +N + +EV SE +V+ ++ A+ I+ V+ S K Sbjct: 3 LQNFRFDVGADG-VALLTWDMPGRSMNVITEEVMSELAQVVEKVAADAAIKGCVIASGK- 60 Query: 96 GCFVAGADINMLASCTTP----------QEAARISQEGQK----MFEKLEKSPKPVVAAI 141 F GAD++ML +EA R+ E + ++ +LE KP AI Sbjct: 61 NAFSGGADLSMLQKSRAAHGKALGEKGAEEANRLFFESARKLSQLYRRLETCGKPFAIAI 120 Query: 142 SGSCLGGGLELAIACQYRIATKDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMM 201 G CLGG ELA+AC +R+ D KT +G+PEV +G+ PGAGGTQR+ +++ A + Sbjct: 121 HGVCLGGAFELALACHHRVLADDDKTKVGLPEVKVGLFPGAGGTQRVARIMPTGDALQFL 180 Query: 202 LTGRNIRADRAKKMGLVDQLVDPLGPGIKSPEERTIEYLEEVAVNFAKGLA--DRKVSAK 259 G + AK GL +L +P+ + ++ + K +A D+K K Sbjct: 181 FKGEQLSGKAAKAAGLAQEL---------APQSEIVSRAKDWILGGGKAIAPWDQK-DFK 230 Query: 260 QSKGLMEKLTSYAMTIPFVRQQVYKTVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAG 319 G + + M I +Y+ ++T YPA I+ V GL+ D G Sbjct: 231 PPSGRI--FSPGGMMIWMPANAIYR-------RETYDNYPAVKAILHCVYEGLQLPIDQG 281 Query: 320 YLAESEKFGELALTKESKALMGLYNGQVLCKKNKF--GA------PQKTVQQLAILGAGL 371 E+ F + +KE+ A++ + KN+ GA P ++++ +LGAG Sbjct: 282 LTVEARWFAHILRSKEAAAMIR----SLFLSKNELDKGARRPKDEPPTQLKKIGVLGAGF 337 Query: 372 MGAGIAQVSVDKGLKTLLKDTTVTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLIG 431 MGAG+ VS GL+ +L D +G+ + K ++ +V + T+ ++++ + + Sbjct: 338 MGAGVGYVSALNGLEVVLIDRDQESADKGKATIDKLISGQVSRGKATASAKEALLARVEA 397 Query: 432 QLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESVTPEHCIFASNTSALPINQIAAVSQRP 491 DY+ + D+++EAVFED AVK + K ++ +FASNTS LPI +A S +P Sbjct: 398 TPDYERLKGCDLILEAVFEDRAVKAEATKRAQAAVGPDVVFASNTSTLPITSLAETSLKP 457 Query: 492 EKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASAVAVGLKQGKVIIVVKDGPGFYTTRCL 551 E IG+H+FSPV+KM L+EII +KTS A+A+ K IVV D GF+ RC+ Sbjct: 458 ENFIGVHFFSPVEKMLLVEIILGEKTSDKALATALDFVRMIKKTPIVVNDSRGFFANRCV 517 Query: 552 APMMSEVIRILQEGVDPKKLDALTTGFGFPVGAATLADEVGID----VAQHVAEDLGKAF 607 + E +L EGV P ++ G PVG +L DEVG+D + Q +DLG A Sbjct: 518 LAYVREGQTMLVEGVPPAMIENAARMAGMPVGPLSLNDEVGLDLGWKILQATKKDLGAA- 576 Query: 608 GERFGGGSVELLKLMVSK-GFLGRKSGKGFYIYQSGSKNKNLNSEIDNILVNLRLPAKPE 666 +L +V K G GRK+GKGFY Y + K K L + + P+ Sbjct: 577 --AVDPAQERVLGFLVEKNGRFGRKNGKGFYDYPASGK-KTLWPGLAGL---AEKTLDPD 630 Query: 667 VSSDEDIQYRVITRFVNEAVLCLQEGILATPEEGDIGAVFGLGFPPCLGGPFRFVDLYGA 726 ++++ R + EA E ++ P E D+G++ G GF P GG ++D G Sbjct: 631 AIDVKELERRFLVAQAVEAARTFAEHVVTDPREADVGSILGFGFAPFTGGALSYIDGMGL 690 Query: 727 QKVVDRLRKYESAYGTQFTPCQLLRDLANNSSKKFYQ 763 + V + YG +F P QLLRD+A + FY+ Sbjct: 691 KAFVALCDTLAAKYGPRFAPPQLLRDMA-REGETFYR 726 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: 1144 Number of extensions: 54 Number of successful extensions: 6 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: 728 Length adjustment: 40 Effective length of query: 723 Effective length of database: 688 Effective search space: 497424 Effective search space used: 497424 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 Apr 09 2024. 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