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_057507300.1 ABB28_RS03505 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::Q64428 (763 letters) >NCBI__GCF_001431535.1:WP_057507300.1 Length = 687 Score = 326 bits (836), Expect = 2e-93 Identities = 223/702 (31%), Positives = 350/702 (49%), Gaps = 54/702 (7%) Query: 49 VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108 V V+ ++ ++ VN ++++V E +++ I A D + V+ S+K F+AGAD+ Sbjct: 22 VVVLNLDRQDANVNAMSQDVLLELGDLIERI-AIDPPKGVVIQSAKKAGFIAGADLKEFQ 80 Query: 109 SCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKTV 168 + GQ ++KL + P P VAAI G CLGGG ELA+AC+YR+A+ D T Sbjct: 81 EFDRRGTVNDAIRRGQVTYQKLAELPCPTVAAIHGHCLGGGTELALACRYRVASNDSSTR 140 Query: 169 LGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGPG 228 +G+PE LGI PG GG+ RLP++VG PAA DMMLTGR + A A+ +GLVD++V P Sbjct: 141 IGLPETQLGIFPGWGGSARLPQLVGAPAAMDMMLTGRTLSASAARNIGLVDKVVAP---- 196 Query: 229 IKSPEERTIEYLEEVAVNFA-KGLADRKVSAKQSKGLMEKLTSYAM-TIPFVRQQVYKTV 286 L + AV A KG + ++ T++A T P + + Sbjct: 197 ---------ALLLDTAVALALKGTV---------RPFKQRATAWATNTWPARKLLAPQMA 238 Query: 287 EEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQ 346 ++ +K K YPAP +I+ + + A AE +LA T ++ L+ ++ Sbjct: 239 KQVARKARKEHYPAPYALINTWERSGGKPVQARLDAERRAVVKLASTPTARNLIRIF--- 295 Query: 347 VLCKKNK-FGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKTLLKDTTVTGLGRGQQQVF 405 L ++ K G+ + + ++GAG+MG IA S KG L+D + Q+ Sbjct: 296 FLTERLKALGSGDHGIHHVHVVGAGVMGGDIAAWSAYKGFNVTLQDREQRFIDPAMQRAQ 355 Query: 406 KGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESV 465 KV+ ++ +R ++ + L L G +AD+VIEA+ E+ K + + +E Sbjct: 356 TLFEKKVRDES----KRPAVAARLQADLAGAGAAQADLVIEAIIENPQAKRDLYQTLEPK 411 Query: 466 TPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASA 525 + +NTS++P+ ++ QRP + G+HYF+PV +M L+EII D + +T Sbjct: 412 MKADALLTTNTSSIPLIELRDHIQRPAQFAGLHYFNPVAQMPLVEIIHHDGMAPETERRL 471 Query: 526 VAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPVGAA 585 A GK + V PGF R L P M E EG+ +D FG P+G Sbjct: 472 AAFCKALGKFPVPVAGTPGFLVNRVLFPYMLEAATAYAEGIPGPVIDKAAVKFGMPMGPI 531 Query: 586 TLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKN 645 L D VG+DVA V E+L F G + V G G+K G+G Y +++G Sbjct: 532 ELLDTVGLDVAAGVGEELAP-----FLGLQIPAALQTVEPGKRGKKDGQGIYAWENGRAK 586 Query: 646 KNLNSEIDNILVNLRLPAKPE-VSSDEDIQYRVITRFVNEAVLCLQEGILATPEEGDIGA 704 K P P+ + D++ R+I +NEAV CL EG++A + D G Sbjct: 587 K---------------PEVPKGYQAPGDLEDRLILPLLNEAVACLHEGVVADADLLDAGV 631 Query: 705 VFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTP 746 +FG GF P GGP +++ GA +V+RL+ + +G +F+P Sbjct: 632 IFGTGFAPFRGGPVQYIRATGADALVERLKVLQQRHGDRFSP 673 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: 1064 Number of extensions: 53 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: 687 Length adjustment: 40 Effective length of query: 723 Effective length of database: 647 Effective search space: 467781 Effective search space used: 467781 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