Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 202205 SO3088 fatty oxidation complex, alpha subunit (NCBI ptt file)
Query= BRENDA::Q64428 (763 letters) >FitnessBrowser__MR1:202205 Length = 707 Score = 563 bits (1451), Expect = e-164 Identities = 318/717 (44%), Positives = 441/717 (61%), Gaps = 29/717 (4%) Query: 49 VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108 +A++ ++ P +NTL E E E+++EI + IR VLIS K FVAGADI+ML Sbjct: 16 IAILTMDVPGETMNTLKAEFGPEISEILSEIKRDSSIRGLVLISGKKDSFVAGADISMLD 75 Query: 109 SCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKTV 168 +C T +A +SQ+G +F +LE PVVAAI G+CLGGGLELA+AC R+ + D KT+ Sbjct: 76 ACQTAGDAKALSQQGHVVFNELEALNIPVVAAIHGACLGGGLELALACHQRVCSDDGKTM 135 Query: 169 LGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGPG 228 LGVPEV LG+LPG GGTQRLP++VG+ A DMMLTG+ IR +A KMGLV+ +V Sbjct: 136 LGVPEVQLGLLPGGGGTQRLPRLVGITTALDMMLTGKQIRPKQALKMGLVNDVVP----- 190 Query: 229 IKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTVEE 288 +TI L + AV A LA ++++ K L+ +L F R ++ + Sbjct: 191 ------QTI--LLQTAVEMA--LAGKQIAKPVKKSLVNQLLEGT---GFGRNIIFDQAAK 237 Query: 289 KVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQVL 348 +V K+T+G YPAP KIID V+ G+ +G G E+ F EL ++KES+AL ++ Sbjct: 238 QVAKKTQGNYPAPAKIIDCVRQGIAKGMQKGLEVEASHFAELVVSKESEALRSIFFATTE 297 Query: 349 CKKNKF--GAPQKTVQQLAILGAGLMGAGIAQVSVDKG-LKTLLKDTTVTGLGRGQQQVF 405 KK GA + V++ ILG GLMG GIA V+ K + +KD GL + Sbjct: 298 MKKETGAEGATPRKVKKAVILGGGLMGGGIASVTTTKAKIPARVKDINEKGLSNALSYAY 357 Query: 406 KGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESV 465 K L+ VK++ +T RD++ + + +YKG + AD+V+EAVFEDLA+KH+++K++E Sbjct: 358 KLLDKGVKRRHMTPAARDNLMALMTTTTEYKGVKDADIVVEAVFEDLALKHQMVKDIERE 417 Query: 466 TPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASA 525 EH IFASNTS+LPI QIA + RPE VIG+HYFSPV+KM L+E+I KTS +T A+ Sbjct: 418 CGEHTIFASNTSSLPIGQIAQAASRPENVIGLHYFSPVEKMPLVEVIAHAKTSPETIATT 477 Query: 526 VAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPVGAA 585 VA KQGK IVV+DG GFY R LA M+E ++L EG + LD FGFPVG Sbjct: 478 VAFARKQGKTPIVVQDGAGFYVNRILALYMNEAAQLLLEGQSVEHLDKALVKFGFPVGPI 537 Query: 586 TLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKN 645 TL DEVGIDV ++ L K GERF + ++S GRK+GKGFY Y + SK Sbjct: 538 TLLDEVGIDVGAKISPILEKELGERFKAPAA--FDKLLSDDRKGRKNGKGFYQYGAASKK 595 Query: 646 KNLNSEIDNILVNLRLPAKPEVSSD-EDIQYRVITRFVNEAVLCLQEGILATPEEGDIGA 704 K ++ + + L KP V + + R + + +NEAV CL GI+A+P +GDIGA Sbjct: 596 KAVDETVYGV-----LGIKPGVDKEMSAVAERCVVQMLNEAVRCLDAGIIASPRDGDIGA 650 Query: 705 VFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANNSSKKF 761 +FG+GFPP LGGPF ++D GA +V L +Y++ YG +F PCQ L+ +A ++ F Sbjct: 651 IFGIGFPPFLGGPFHYIDTLGADNLVKILERYQTQYGDRFEPCQRLKAMAAEKARFF 707 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: 1167 Number of extensions: 53 Number of successful extensions: 5 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: 707 Length adjustment: 40 Effective length of query: 723 Effective length of database: 667 Effective search space: 482241 Effective search space used: 482241 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