Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate 202759 SO3664 long-chain-fatty-acid--CoA ligase (NCBI ptt file)
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__MR1:202759 Length = 532 Score = 136 bits (342), Expect = 2e-36 Identities = 143/507 (28%), Positives = 224/507 (44%), Gaps = 56/507 (11%) Query: 68 SIGPGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQ 127 ++ PG +AI PNI A +G G +L N + + S + ++V Sbjct: 62 NLKPGDRIAIQLPNITQFVIAAYGALRAGLILVNTNPLYTERELIHQFNDSGAKALVV-- 119 Query: 128 EFFTLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCA---PESLNRALSKGAIEYEDFLATG 184 D L + + ++ P+ +VI H P+ + K +E+ L G Sbjct: 120 -----LSDLLPTLAKVVATT---PIELVISTHPLDLIDPQVQPKTGLKN-VEFCHVLQQG 170 Query: 185 D--PNYPWQPPADEWQSIALGYTSGTTASPKGVVLHH-----RGAYIMALSNPLIWGMQD 237 P + P + AL YT GTT KG +L H A + + +I +D Sbjct: 171 ALLPFTRFVPTLSDLA--ALQYTGGTTGLSKGAMLTHGNMLANAAQVKSRIGSVISEGED 228 Query: 238 GAVYLWTLPMFHCNGWCFPWSLAVL---SGTSICL---RQVTAKEVYSMIAKYKVTHFCA 291 +++ LP++H + F +L + G S+ + R + + +AKY T F Sbjct: 229 --IFVAPLPIYHI--YAFMVNLVLYFECGGCSVLIPNPRDING--LIKTLAKYPFTGFAG 282 Query: 292 APVVLNAIVNAPKEDTILPLPHTVHVMTAGAAPPPSVLFSMNQK-GFRVAHTYGLSETYG 350 + A+ + P E L H ++ G A + Q G ++ YGLSET Sbjct: 283 LNTLFVALCHQP-EFKALNFSHLKITISGGTALTAAAANLWQQTTGNTISEGYGLSET-- 339 Query: 351 PSTVCAWKPEWDSLPPETQAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFR 410 P P Q + V T ++ LD ++G V TAGE+ R Sbjct: 340 -------SPVISLNAPGYQKIGTIGKPVLGTEVKLLD----ESGNEVTQG--TAGELAAR 386 Query: 411 GNMVMKGYLKNPEANKETFA-GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVE 469 G VM GY NP+ G+F +GDIA+ + + + +I DR KD+II G N+ E Sbjct: 387 GPQVMLGYWNNPQETANVMTPDGFFKTGDIAILNEEGFHQIVDRKKDMIIVSGFNVYPNE 446 Query: 470 VENVVYHHPAVLEASVVARPDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPA 529 VENV+ HP ++E +VV D+ E+ AF+ LK D + H++ K A I+ FCRE+L A Sbjct: 447 VENVLASHPNIIECAVVGVKDDHSGEAVKAFIVLKDDSQDHEKIKTA--ILNFCREQLTA 504 Query: 530 YWVPKSVVF-GPLPKTATGKIQKHILR 555 Y +PK + F LPK+ GKI + L+ Sbjct: 505 YKLPKQIEFMSQLPKSTVGKILRRELK 531 Lambda K H 0.319 0.134 0.422 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: 662 Number of extensions: 40 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: 1 Length of query: 569 Length of database: 532 Length adjustment: 36 Effective length of query: 533 Effective length of database: 496 Effective search space: 264368 Effective search space used: 264368 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 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