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 WP_030535166.1 C1M55_RS25270 AMP-binding protein
Query= SwissProt::Q8VZF1 (569 letters) >NCBI__GCF_002893965.1:WP_030535166.1 Length = 534 Score = 439 bits (1130), Expect = e-127 Identities = 241/546 (44%), Positives = 317/546 (58%), Gaps = 26/546 (4%) Query: 15 IPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGPGST 74 + AN T L+PL FL+R+A V P R +V+HG R Y++R+ D LA L +R I PG Sbjct: 7 VAANNTPLSPLRFLERSAAVFPERTAVVHGDRTYSYREFGDEVAALARVLRER-IQPGDR 65 Query: 75 VAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFTLAE 134 VA +APN+P M AHF VP+ G VL +N RL P + ++L HS ++++ VD EF Sbjct: 66 VAYLAPNVPEMLFAHFAVPLAGGVLIALNSRLAGPELEYILDHSGTTILFVDSEFVGSVT 125 Query: 135 DSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATG----DPNYPW 190 S KA R + + I D T + + G +Y D +A G D W Sbjct: 126 SS------KANVGSLREI-VEIPDSTVPYPDVPTGIVTG--QYADLIAEGEALSDQPLHW 176 Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250 DE Q IA+ YTSGTT PKGV+ HRGAY+ +L G YLWTLPMFHC Sbjct: 177 GVD-DEQQCIAINYTSGTTGKPKGVMYSHRGAYLNSLGETFHNGFDGATKYLWTLPMFHC 235 Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310 NGWC PW++ +GT ICLR V A ++ I VTH C AP V + I +A + + Sbjct: 236 NGWCTPWAVTQAAGTHICLRAVRADAIWDAIDNLGVTHLCGAPTVCSTIADADQAHKV-- 293 Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370 + + TAGA P P+++ + G V H YGL+E YGP T+C ++ WD P +A Sbjct: 294 --DALRITTAGAPPSPTIIGKLEDIGVTVVHVYGLTEVYGPYTICEYQEAWDDKPQSERA 351 Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430 L +RQGV E V+D + VPADG+T GEIV RGN VM GY ++ A E FA Sbjct: 352 ALLSRQGVGMVQAENARVVDAEMND-VPADGQTMGEIVLRGNNVMLGYYRDEAATAEAFA 410 Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490 GGWFHSGD+ V HPD YI++KDR+KD+IISGGENIS+VEVE + HPAV++ +VV PD Sbjct: 411 GGWFHSGDLGVMHPDGYIQLKDRAKDIIISGGENISTVEVEQAIMSHPAVIDVAVVGVPD 470 Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFG-PLPKTATGKI 549 E+W E P AFV L + A+DI++ R L Y VP+ +VF LP+T TGK+ Sbjct: 471 EKWGERPKAFVVLGKGLQAS-----AEDIVEHTRTLLAGYKVPRDIVFPLDLPRTPTGKV 525 Query: 550 QKHILR 555 K LR Sbjct: 526 LKFQLR 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: 822 Number of extensions: 37 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: 569 Length of database: 534 Length adjustment: 36 Effective length of query: 533 Effective length of database: 498 Effective search space: 265434 Effective search space used: 265434 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 24 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