Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 6938034 Sama_2167 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= BRENDA::Q64428 (763 letters) >FitnessBrowser__SB2B:6938034 Length = 706 Score = 548 bits (1411), Expect = e-160 Identities = 312/718 (43%), Positives = 437/718 (60%), Gaps = 29/718 (4%) Query: 49 VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108 +A++ ++ P +NTL + E ++ EI A+ I+ VLIS K FVAGADI+ML Sbjct: 14 IALLTMDVPGETMNTLKAQFAPEITAILQEIKADSSIKGLVLISGKADSFVAGADISMLD 73 Query: 109 SCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKTV 168 +C T ++A +S++G +F +LE PVVAAI G+CLGGGLELA+AC R+ + KT+ Sbjct: 74 ACETAEDARLLSRQGHHVFAELEGLNIPVVAAIHGACLGGGLELALACHQRVCSDSSKTM 133 Query: 169 LGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGPG 228 LGVPEV LG+LPG GGTQRLP+++G+ A D+MLTG+ +R +A KMGLVD +V Sbjct: 134 LGVPEVQLGLLPGGGGTQRLPRLIGIAKALDLMLTGKQVRPKQAVKMGLVDDVV------ 187 Query: 229 IKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTVEE 288 PE ++ E+A LA +K + L+ KL P R ++ + Sbjct: 188 ---PESILLDTAIEMA------LAGKKTRKPLKQPLVTKLLEGT---PVGRNIMFDQATK 235 Query: 289 KVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQVL 348 +V K+T+G YP+PLKIID V+ G+ +G + G E+ FG L T ES AL ++ Sbjct: 236 QVLKKTQGNYPSPLKIIDCVREGMAKGMEKGLEVEAAHFGALVATPESAALRSIFFATTE 295 Query: 349 CKKNKFG--APQKTVQQLAILGAGLMGAGIAQVSVDKG-LKTLLKDTTVTGLGRGQQQVF 405 KK A + V + +LG GLMG GIA V+ K + +KD + GL + Sbjct: 296 MKKETGAGDAKPRKVAKAVVLGGGLMGGGIASVTTTKAKVPVRVKDISDKGLSNALGYAY 355 Query: 406 KGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESV 465 K L+ VK++ +TS ERD + + + +Y+G + AD+V+EAVFEDL +KH++++++E Sbjct: 356 KLLDKGVKRRHMTSAERDKLMALMTTTTEYRGVKDADIVVEAVFEDLNLKHQMVRDIERE 415 Query: 466 TPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASA 525 EH IFASNTS+LPI QIAA + RPE VIG+HYFSPV+KM L+E+I +KTS +T A+ Sbjct: 416 CGEHTIFASNTSSLPITQIAAAASRPENVIGLHYFSPVEKMPLVEVIAHEKTSPETIATT 475 Query: 526 VAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPVGAA 585 VA KQGK IVVKD GFY R LA M+E ++L EG LD FGFPVG Sbjct: 476 VAFARKQGKTPIVVKDCAGFYVNRILALYMNEAAQLLLEGQAVDHLDKALVKFGFPVGPM 535 Query: 586 TLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKN 645 TL DEVGIDV ++ L K GERF + +++ GRK+GKGFY+Y +K Sbjct: 536 TLLDEVGIDVGAKISPILEKELGERFKAPAA--FDKLMADDRKGRKNGKGFYLYGKAAKK 593 Query: 646 KNLNSEIDNILVNLRLPAKPEVSSDE-DIQYRVITRFVNEAVLCLQEGILATPEEGDIGA 704 ++D + +L L P + +I R + + +NEAV CL+EGI+A+P +GDIGA Sbjct: 594 ---GKKVDESVYSL-LGLTPATGKEAGEIAERCVVQMLNEAVRCLEEGIIASPRDGDIGA 649 Query: 705 VFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANNSSKKFY 762 +FG+GFPP LGGPFR++D GA K+V L Y+S YG +F P LL+ +A K FY Sbjct: 650 IFGIGFPPFLGGPFRYMDTLGAAKMVRLLEGYQSKYGDRFAPAALLKAMA-AEGKTFY 706 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: 1172 Number of extensions: 52 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: 706 Length adjustment: 40 Effective length of query: 723 Effective length of database: 666 Effective search space: 481518 Effective search space used: 481518 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