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 GFF1184 PGA1_c11990 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__Phaeo:GFF1184 Length = 542 Score = 513 bits (1321), Expect = e-150 Identities = 275/556 (49%), Positives = 345/556 (62%), Gaps = 21/556 (3%) Query: 8 DIDDLPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADR 67 D L K ANY LTPL L RAA V +V++G+ T+ YDRC RLASALA Sbjct: 6 DESGLEKTAANYVPLTPLSHLRRAAHVFADVPAVVYGNHRKTYAAYYDRCTRLASALAGM 65 Query: 68 SIGPGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQ 127 + PG VA + PN+PA EAHFGVP CGAVLN +N RL+ TVA++ H ++ V++VD Sbjct: 66 GVRPGEVVATLIPNLPAQAEAHFGVPACGAVLNTINTRLDVSTVAYIFDHGEAKVVLVDS 125 Query: 128 EFFTLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCA-PESLNRALSKGAIEYEDFLATGDP 186 +F TLAE E KA PL+I + D + P S + YED LA Sbjct: 126 QFLTLAE------EAKAACDGLGPLIIEVPDDQASYPASGRHPI------YEDILAAAAH 173 Query: 187 NYPWQPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLP 246 ++ W P DEW+S+AL YTSGTT PKGVV HHRGAY+M + + W M YL +P Sbjct: 174 DFDWIMPQDEWESLALNYTSGTTGRPKGVVYHHRGAYLMTMGTVISWRMVMQPKYLAIVP 233 Query: 247 MFHCNGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKED 306 +FHCNGW W + VL GT IC R +TA +Y IA THF AP+VLN +VNA +ED Sbjct: 234 LFHCNGWNHTWMMPVLGGTLICCRDITAPAIYGAIADEGATHFGGAPIVLNMLVNAAEED 293 Query: 307 TILPLPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPE-WDSLP 365 HTV V TAGA P P+ L + GF V YGL+ETYG T C WK + WD+L Sbjct: 294 R-RQFDHTVEVFTAGAPPAPATLEKIEALGFHVTQVYGLTETYGHVTECLWKGDSWDTLD 352 Query: 366 PETQAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEAN 425 + +A + ARQGV + M+ + V+ + + +G+ GEIV RGN VMKGYLKNP+A Sbjct: 353 QQGRAAIKARQGVAFPMMDHITVMRDDM-QQIAMNGQDQGEIVMRGNSVMKGYLKNPDAT 411 Query: 426 KETFAGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASV 485 E F GG+FHSGDIAV+HPD YI+I DR+KD+IISGGENISSVEVE V+ HP V A+V Sbjct: 412 AEAFQGGYFHSGDIAVQHPDGYIQIADRAKDIIISGGENISSVEVEGVLMGHPDVNLAAV 471 Query: 486 VARPDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTA 545 VA+PD++W E PCAFV LK D+++F RE L + PK VVF LPKT+ Sbjct: 472 VAKPDDKWGEVPCAFVELKPGATVD-----PADLIRFARETLAGFKAPKQVVFQELPKTS 526 Query: 546 TGKIQKHILRTKAKEM 561 TGKIQK LR +AK + Sbjct: 527 TGKIQKFELRQQAKAL 542 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: 885 Number of extensions: 38 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: 569 Length of database: 542 Length adjustment: 36 Effective length of query: 533 Effective length of database: 506 Effective search space: 269698 Effective search space used: 269698 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