Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate YP_004145058.1 Mesci_6001 3-hydroxyacyl-CoA dehydrogenase NAD-binding protein
Query= BRENDA::Q64428 (763 letters) >NCBI__GCF_000185905.1:YP_004145058.1 Length = 739 Score = 364 bits (934), Expect = e-104 Identities = 242/750 (32%), Positives = 374/750 (49%), Gaps = 51/750 (6%) Query: 39 THINYGVKGD---VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKP 95 ++ N+ + D +A++ + P +N +E E +++++ + I+ AV+ S K Sbjct: 2 SYTNFALDTDADGIALVTWDMPGRSMNVFTEEAMRELNAIVDKVAGDAAIKGAVITSGKD 61 Query: 96 GCFVAGADINMLASCTTPQEAARISQEGQK--------------MFEKLEKSPKPVVAAI 141 F GADI++L T AA ++ +K +F KLE KP V+AI Sbjct: 62 -TFSGGADISLLQKMLTTF-AAEKGKDAEKATKALFDNAGMMTGLFRKLETCGKPWVSAI 119 Query: 142 SGSCLGGGLELAIACQYRIATKDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMM 201 +G+C+GG EL++AC R+A K + +PEV +GI PGAGGTQR+P++ A M+ Sbjct: 120 NGTCMGGAFELSLACHGRVAADSDKVKMALPEVKIGIFPGAGGTQRVPRLTDQQQALQML 179 Query: 202 LTGRNIRADRAKKMGLVDQLVDPLGPGIKSPEERTIEYLEEVAVNFAKGLA--DRKVSAK 259 +G+ + +AK MGL+ ++ +P R +E + + N K +A D K K Sbjct: 180 TSGQTLSPQKAKSMGLIHEIAEP---------TRLVETAKAMIRNGLKPVAPWDEK-GFK 229 Query: 260 QSKGLMEKLTSYAMTIPFVRQQVYKTVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAG 319 G + + + P + ++++T G YPA I+ V GL D Sbjct: 230 LPGGQIYSPAGFNLWPPAI---------AILRRETYGNYPAAAAILKCVYEGLLVPFDTA 280 Query: 320 YLAESEKFGELALTKESKALMG--LYNGQVLCK--KNKFGAPQKTVQQLAILGAGLMGAG 375 E F E+ T+E+ A++ + Q L K + G P+ +++ ILGAG MGAG Sbjct: 281 LRIEQRYFTEIMQTREAAAMIRSLFVSLQELNKGARRPAGVPETKFKKIGILGAGFMGAG 340 Query: 376 IAQVSVDKGLKTLLKDTTVTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDY 435 IA V+ G+ +L D + +G+ ++D+VKK ++D + S + DY Sbjct: 341 IAYVTAKAGIPVVLLDRDLESAAKGKAHSDSLVSDQVKKGRAKPEDKDKLLSLITPTADY 400 Query: 436 KGFEKADMVIEAVFEDLAVKHKVLKEVESVTPEHCIFASNTSALPINQIAAVSQRPEKVI 495 D+V+EAVFED VK ++ E+V IFASNTS +PI+ +A S RP+ I Sbjct: 401 ADLAGCDLVVEAVFEDSGVKKSATEQAEAVLKPSAIFASNTSTIPISSLAKNSARPKNFI 460 Query: 496 GMHYFSPVDKMQLLEIITTDKTSKDTTASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMM 555 G+H+FSPVDKM L+EII KT A+A+ K IVV D GFY RC+ M Sbjct: 461 GIHFFSPVDKMMLVEIILGKKTGDKALATAIDFVRAIKKTPIVVNDTRGFYVNRCVLRYM 520 Query: 556 SEVIRILQEGVDPKKLDALTTGFGFPVGAATLADEVGIDVAQHVAEDLGKAFGER-FGGG 614 SE ++L EGV ++ G PVG L DE ID+AQ + + + G++ Sbjct: 521 SEAYKMLIEGVPAPMIENAAKAAGMPVGPLALTDETAIDLAQKIMKQTIRDLGDKAVDPK 580 Query: 615 SVELLKLMV-SKGFLGRKSGKGFYIYQSGSKNKNLNSEIDNILVNLRLPAKPEVSSDEDI 673 + L+ MV G GRK+GKGFY Y + K L + + L PE E++ Sbjct: 581 QMALINTMVDDHGRFGRKNGKGFYDYPAKPAKKKLWPGLKELYPQL----APEKVDYEEL 636 Query: 674 QYRVITRFVNEAVLCLQEGILATPEEGDIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRL 733 Q R++ EA ++EGI+ P E D+G++ GF P GG ++D GA+ V Sbjct: 637 QQRLLVTIALEAARVMEEGIVTDPREADVGSILAFGFAPYTGGALSYIDGIGAKAFVKIA 696 Query: 734 RKYESAYGTQFTPCQLLRDLANNSSKKFYQ 763 R + YG +F +LL D+A + FYQ Sbjct: 697 RNLQKKYGAEFKAPKLLLDMA-EKGESFYQ 725 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: 1173 Number of extensions: 51 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 763 Length of database: 739 Length adjustment: 40 Effective length of query: 723 Effective length of database: 699 Effective search space: 505377 Effective search space used: 505377 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 24 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