Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 16447 b2341 fused enoyl-CoA hydratase and epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase (NCBI)
Query= BRENDA::Q64428 (763 letters) >FitnessBrowser__Keio:16447 Length = 714 Score = 535 bits (1379), Expect = e-156 Identities = 296/708 (41%), Positives = 436/708 (61%), Gaps = 26/708 (3%) Query: 48 DVAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINML 107 ++AVI I+ P K+NTL E S+ ++ ++ N ++R V +S+KP F+AGADINM+ Sbjct: 15 NIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGADINMI 74 Query: 108 ASCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKT 167 +C T QEA ++++GQ++ ++ P V+AAI G+CLGGGLELA+AC R+ T D KT Sbjct: 75 GNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRVCTDDPKT 134 Query: 168 VLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGP 227 VLG+PEV LG+LPG+GGTQRLP+++GV A +M+LTG+ +RA +A K+GLVD +V Sbjct: 135 VLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVPH--- 191 Query: 228 GIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTVE 287 L E AV AK ++ + + + E++ + P R ++K V Sbjct: 192 ----------SILLEAAVELAK----KERPSSRPLPVRERI----LAGPLGRALLFKMVG 233 Query: 288 EKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQV 347 +K + +T+G YPA +I++ V+TGL QG +GY AE+ FGELA+T +S+AL ++ Sbjct: 234 KKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFAST 293 Query: 348 LCKKNKFG-APQKTVQQLAILGAGLMGAGIAQVSVDK-GLKTLLKDTTVTGLGRGQQQVF 405 KK+ AP + + ILG GLMG GIA V+ K G+ +KD G+ + + Sbjct: 294 DVKKDPGSDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSW 353 Query: 406 KGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESV 465 L KV+++ L + ERD + + G DY+GF D++IEAVFE+L +K +++ EVE Sbjct: 354 DQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQN 413 Query: 466 TPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASA 525 H IFASNTS+LPI IAA + RPE+VIG+H+FSPV+KM L+EII TS T A+ Sbjct: 414 CAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATT 473 Query: 526 VAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPVGAA 585 V + KQGK IVV+D GFY R LAP ++E IR+L +G + +DA FGFPVG Sbjct: 474 VKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPI 533 Query: 586 TLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKN 645 L DEVGID + L A+GERF ++ +++ GRK+G+GFY+Y G K Sbjct: 534 QLLDEVGIDTGTKIIPVLEAAYGERF-SAPANVVSSILNDDRKGRKNGRGFYLY--GQKG 590 Query: 646 KNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEAVLCLQEGILATPEEGDIGAV 705 + ++D + L S + R + +NEAV C+ E ++ + +GDIGAV Sbjct: 591 RKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAV 650 Query: 706 FGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDL 753 FG+GFPP LGGPFR++D GA +VV +++ + YG++FTPC+ L ++ Sbjct: 651 FGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEM 698 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: 1095 Number of extensions: 43 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: 714 Length adjustment: 40 Effective length of query: 723 Effective length of database: 674 Effective search space: 487302 Effective search space used: 487302 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