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 RR42_RS25360 RR42_RS25360 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__Cup4G11:RR42_RS25360 Length = 554 Score = 543 bits (1400), Expect = e-159 Identities = 278/548 (50%), Positives = 363/548 (66%), Gaps = 19/548 (3%) Query: 12 LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71 L + AN+ LTPL FLDR A +P R ++IHG +W+ T +RCR+LASAL R +G Sbjct: 10 LDRRAANHMPLTPLHFLDRCAEQYPDRTAIIHGPVRQSWKVTRERCRQLASALVKRGVGR 69 Query: 72 GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131 G TV+I+APN PAM EAH G+P+ GAVLN +N RL+A V F+++H + V+ VD+EF Sbjct: 70 GDTVSILAPNTPAMVEAHHGIPLSGAVLNAINCRLDADGVRFIVAHGECKVLFVDREFSA 129 Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTC-APESLNRALSKGAIEYEDFLATGDPNYPW 190 LA ++L+ + PL+I I D A E + GA+EYE FL GD ++P Sbjct: 130 LAAEALQGLPNA-------PLVIDIADALAPAGEPI------GAMEYEQFLREGDIDFPG 176 Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250 P DEW +IAL YTSGTT+ PKGVV HRGAY+M++ WGM YLWTLPMFH Sbjct: 177 VWPDDEWNAIALNYTSGTTSDPKGVVPSHRGAYLMSMLQLTDWGMPRAPKYLWTLPMFHA 236 Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310 NGWCF W++ +GT +CLR+VTA ++S I Y HFCAAP+VL+++ A +E+ P Sbjct: 237 NGWCFSWAVTAAAGTHVCLRKVTAANIFSAIEAYGADHFCAAPIVLSSLATATQEER-RP 295 Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370 H V + TAG+ PP SVL ++ ++GF V H YG++E G P W+ + +A Sbjct: 296 FSHVVRIRTAGSPPPASVLKAVIEQGFDVEHVYGITEASGTPVSSYANPAWNEKSGDEKA 355 Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430 +L ARQG R G+E L V D T + VP DG T GE++ RGN+VMKGYLKNPEA + FA Sbjct: 356 RLMARQGNRAAGLEGLRVADPDTMESVPWDGTTQGELLLRGNIVMKGYLKNPEATEAAFA 415 Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490 GGWFH+GD+AV HPD Y++I DRSKDVIISGGENISSVEVE+V++ HPAVL A+VVA+P Sbjct: 416 GGWFHTGDLAVVHPDGYVQITDRSKDVIISGGENISSVEVEDVLHQHPAVLIAAVVAQPH 475 Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550 +W ESPCAF+ LK+ + +I+ FCR +L Y P VV+G LPKT TGKIQ Sbjct: 476 PKWGESPCAFIELKNGVAAPTE----AEIIAFCRSRLAHYKCPTRVVYGALPKTGTGKIQ 531 Query: 551 KHILRTKA 558 K+ LR A Sbjct: 532 KYRLRALA 539 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: 906 Number of extensions: 39 Number of successful extensions: 4 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: 554 Length adjustment: 36 Effective length of query: 533 Effective length of database: 518 Effective search space: 276094 Effective search space used: 276094 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