Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 3607421 Dshi_0835 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)
Query= BRENDA::Q64428 (763 letters) >FitnessBrowser__Dino:3607421 Length = 737 Score = 351 bits (901), Expect = e-101 Identities = 237/739 (32%), Positives = 370/739 (50%), Gaps = 53/739 (7%) Query: 49 VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108 VA+I + +N +N++ + ++++ A+D ++ ++ S K F G D+N++A Sbjct: 16 VAIITWDVQGKSMNVMNQQGFEDLDALVDKALADDTVKGIIITSGKDS-FAGGMDLNVIA 74 Query: 109 SCTTP--QEAARISQEGQK-------------MFEKLEKSPKPVVAAISGSCLGGGLELA 153 + AR EG M K K KPV AA+ G+ LG GLE+ Sbjct: 75 KMRDDAGDDPARGLFEGVMAMHGILRKIERAGMDPKTNKGGKPVAAALPGTALGIGLEIP 134 Query: 154 IACQYRIATKDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAK 213 +AC A + K +G+PE+++GI PGAGGT R+ + +G A ++L G+ +AK Sbjct: 135 LACHRIFAADNPKAKIGLPEIMVGIFPGAGGTMRVSRKLGAMQAAPILLEGKLFEPKKAK 194 Query: 214 KMGLVDQLV------DPLGPGIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEK 267 G+VD++V D + S ++ I ++ KG + G M Sbjct: 195 MAGIVDEVVPAEELLDAAKAWVLSAKDTDIVKPWDL-----KGYKFPGGAPYHPAGFMTF 249 Query: 268 LTSYAMTIPFVRQQVYKTVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKF 327 + + AM + +T G+YPA ++ AV G D E+ F Sbjct: 250 VGASAM----------------IHSKTMGVYPAAKALLSAVYEGAMVPFDTALKIEARWF 293 Query: 328 GELALTKESKALM-GLYNGQVLCKKNKF--GAPQKTVQQLAILGAGLMGAGIAQVSVDKG 384 + + S A++ L+ + +K P + V+++ ILGAG+MGAGIA VS + G Sbjct: 294 TNVLMNPSSSAMIRSLFINKEALEKGAVRPDVPDQKVKKVGILGAGMMGAGIAYVSANAG 353 Query: 385 LKTLLKDTTVTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMV 444 ++ +L D RG+ L+ + +K +T ++D + + + DY E D+V Sbjct: 354 IEVVLIDAAQESADRGKAHAAGILDKGIARKKVTPEKKDEVLARITATTDYAALEGCDLV 413 Query: 445 IEAVFEDLAVKHKVLKEVESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVD 504 +EAVFED VK +V + E+V P IFA+NTS LPI+++A S RPE+ IG+H+FSPVD Sbjct: 414 VEAVFEDPGVKAEVTAKAEAVIPGDAIFATNTSTLPISELAKASARPEQFIGIHFFSPVD 473 Query: 505 KMQLLEIITTDKTSKDTTASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQE 564 KM L+EII +T A A+ + K IVV D FY RC+ P ++E IR++ E Sbjct: 474 KMLLVEIIKGRQTGDVAVAKALDFVRQIRKTPIVVNDARFFYANRCIIPYINEGIRMVAE 533 Query: 565 GVDPKKLDALTTGFGFPVGAATLADEVGIDVAQHVAEDLGKAFGERFGGGSV-ELLKLMV 623 GV P ++ G P+G L DE ID+ +A+ A G+ + G+V E+L M Sbjct: 534 GVTPALVENAAKLVGMPLGPLQLVDETSIDLGVKIAKATKAAMGDAYPDGAVDEVLFWMA 593 Query: 624 SKGFLGRKSGKGFYIYQSGSKNKNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVN 683 +G LGRKS GFY Y K L + + R PA E +Q+R++ V Sbjct: 594 DEGRLGRKSNAGFYTYDEAGKRGLLWEGLAD-----RYPAAKEQPELTAVQHRLLMAQVL 648 Query: 684 EAVLCLQEGILATPEEGDIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQ 743 EAV L++G+L EGD+GA+ G GF P GGP ++D+ GA + V+ +G + Sbjct: 649 EAVRALEDGVLMDIREGDVGAILGWGFAPWSGGPLSWLDMIGAARAVEICDALTDTHGAR 708 Query: 744 FTPCQLLRDLANNSSKKFY 762 FT LLR++A + FY Sbjct: 709 FTTPALLREMA-EKGETFY 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: 1175 Number of extensions: 66 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: 2 Length of query: 763 Length of database: 737 Length adjustment: 40 Effective length of query: 723 Effective length of database: 697 Effective search space: 503931 Effective search space used: 503931 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