Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 5209977 Shew_2425 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= BRENDA::Q64428 (763 letters) >FitnessBrowser__PV4:5209977 Length = 706 Score = 563 bits (1450), Expect = e-164 Identities = 318/718 (44%), Positives = 445/718 (61%), Gaps = 28/718 (3%) Query: 49 VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108 +AV+ ++ P +NTL E E E++ EI A+ IR V+IS K FVAGADI+ML Sbjct: 14 IAVLTMDVPGETMNTLRAEFGPEICEMLAEIKADAGIRGVVIISGKKDSFVAGADISMLD 73 Query: 109 SCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKTV 168 +C T ++A +S++G ++F LE PVVAAI+G+CLGGGLELA+AC R+ T KT+ Sbjct: 74 ACATAEDARELSKQGHEVFFALESLSIPVVAAINGACLGGGLELALACHQRVCTDSNKTM 133 Query: 169 LGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGPG 228 LG+PEV LG+LPG GGTQRLP++VG+ + DMMLTG+ +RA +A KMGLVD +V Sbjct: 134 LGLPEVQLGLLPGGGGTQRLPRLVGIAKSLDMMLTGKQLRAKQALKMGLVDDVV------ 187 Query: 229 IKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTVEE 288 PE ++ E+A LA + + K +EKL P R +++ + Sbjct: 188 ---PESILLQTAIEMA------LAGARPAKKPKLSTVEKLLEGT---PVGRNIIFEQALK 235 Query: 289 KVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQVL 348 +V K+T+G YPAP KIID V+ G+ +G G E++ FG+L ++ ES+AL ++ Sbjct: 236 QVNKKTQGNYPAPEKIIDCVRQGVTKGIVKGLEVEAQHFGDLVVSNESEALRSIFFATTE 295 Query: 349 CKKNKFGAP--QKTVQQLAILGAGLMGAGIAQVSVDKG-LKTLLKDTTVTGLGRGQQQVF 405 KK K V ++ +LG GLMG GIA V+ K + +KD + GL + Sbjct: 296 MKKESGAGDVSPKAVNKVMVLGGGLMGGGIASVTTTKAKIPVRVKDISEIGLSNALAYAY 355 Query: 406 KGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESV 465 K L VK++ +T RD++ + + +YKG + ADMV+EAVFEDL +KH+++K+VE Sbjct: 356 KLLAKGVKRRHMTPAVRDNLMALMTTTTEYKGIKDADMVVEAVFEDLNLKHQMVKDVERE 415 Query: 466 TPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASA 525 EH IFASNTS+LPI QIA ++RPE VIG+HYFSPV+KM L+E+I DKTS T A+ Sbjct: 416 CGEHTIFASNTSSLPIKQIAEAAERPENVIGLHYFSPVEKMPLVEVIAHDKTSPQTIATT 475 Query: 526 VAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPVGAA 585 VA KQGK IVVKDG GFY R LA M+E +L EG LD FGFPVG Sbjct: 476 VAFARKQGKTPIVVKDGAGFYVNRILALYMNEAANLLLEGQSVDHLDKALVKFGFPVGPM 535 Query: 586 TLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKN 645 TL DEVGIDV ++ L K GERF + +++ GRK+GKGFY Y + SK Sbjct: 536 TLLDEVGIDVGAKISPILEKELGERFKAPAA--FDKLLADDRKGRKNGKGFYQYGAKSKK 593 Query: 646 KNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEAVLCLQEGILATPEEGDIGAV 705 K ++ + +L L A E + + R + + +NEAV CL+EGI+A+P +GDIGA+ Sbjct: 594 KLVDESVYGVL-GLTPGADGEPIA---LAERCVVQMLNEAVRCLEEGIIASPRDGDIGAI 649 Query: 706 FGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANNSSKKFYQ 763 FG+GFPP LGGPFR++D GA+ +V+ L++Y+ +G +F PC L ++A + S KFY+ Sbjct: 650 FGIGFPPFLGGPFRYMDSLGAKHLVETLKRYQDQFGDRFAPCDRLVEMAESGS-KFYE 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: 1212 Number of extensions: 60 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: 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