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_022603146.1 NSB1T_RS28555 AMP-binding protein
Query= SwissProt::Q8VZF1 (569 letters) >NCBI__GCF_000473955.1:WP_022603146.1 Length = 550 Score = 144 bits (362), Expect = 1e-38 Identities = 136/558 (24%), Positives = 233/558 (41%), Gaps = 50/558 (8%) Query: 27 FLDRAAVVHPTRKSVIHGSRE--YTWRQTYDRCRRLASALADRSIGPGSTVAIIAPNIPA 84 FL+ A P ++ +++ R+ +T+ + R LA + + S V I A N+P Sbjct: 11 FLEYWAEKTPDKEFIVYSDRDLRFTYSEFNKRVNNLAKGMMAIGVEKDSKVGIWATNVPD 70 Query: 85 MYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMV-----DQEFFTLAEDSLRL 139 F GA+L VN + +L+ ++ + + D ++ + L Sbjct: 71 WLTFLFASAKIGAILVTVNTNYKQHELEYLVENADIHTLCISNGTFDSDYVDMTYTMLPE 130 Query: 140 MEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQPPADE--- 196 ++ K + + + +R + A + L G+ + + Sbjct: 131 LKTSQRGHLKSNKFPYMRNVVYIGQEKHRGMYNTA----ELLLLGNTITDEKLETQKQKF 186 Query: 197 --WQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCNGWC 254 + + + YTSGTT PKGV+L H + +P+FHC G Sbjct: 187 NCYDVVNMQYTSGTTGFPKGVMLTHHNITNNGYCIGQCMKFSENDRVCLPVPLFHCFGIV 246 Query: 255 FP-WSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPLPH 313 ++ G ++ L + V + + K + T P + A +N P ++ L Sbjct: 247 LGIMAIITNGGCAVMLERFDPLVVLASVHKERCTALYGVPTMFIAELNHPMF-SMFDLSS 305 Query: 314 TVHVMTAGAAPPPSVLFSMNQKGF--RVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371 + AG+ P ++ + K + + YGL+ET P TQ+K Sbjct: 306 LRTGIMAGSLCPEWLMREVMDKMYMKEITSVYGLTETS---------------PGMTQSK 350 Query: 372 LNARQGVRYTGME------QLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEAN 425 ++ VR + + ++ VID +T + P GE+ RG +MKGY K PEA Sbjct: 351 VDDPVEVRASTVGSDLPGVEVRVIDPETLEECPVG--VQGEMCCRGYNIMKGYYKMPEAT 408 Query: 426 KETF-AGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEAS 484 G+ HSGD+ +K P+ +I R KD+II GGENI E+E +Y P + + Sbjct: 409 AAIIDKNGFLHSGDLGIKTPEGNYKITGRIKDMIIRGGENIYPREIEEFLYQIPQIKDVQ 468 Query: 485 VVARPDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVF-GPLPK 543 V A P +++ E AF+ LK HD D+ FC+ K+ + +PK + F P Sbjct: 469 VAAVPSKKYGEEVGAFIILKEGESLHD-----CDVKDFCKGKISRHKIPKYIFFIDQFPL 523 Query: 544 TATGKIQKHILRTKAKEM 561 T +GKIQK+ L+ E+ Sbjct: 524 TGSGKIQKYKLKDLGLEL 541 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: 647 Number of extensions: 28 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 569 Length of database: 550 Length adjustment: 36 Effective length of query: 533 Effective length of database: 514 Effective search space: 273962 Effective search space used: 273962 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