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_082679212.1 V473_RS18440 AMP-binding protein
Query= SwissProt::Q8VZF1 (569 letters) >NCBI__GCF_001046645.1:WP_082679212.1 Length = 622 Score = 165 bits (417), Expect = 6e-45 Identities = 157/515 (30%), Positives = 228/515 (44%), Gaps = 47/515 (9%) Query: 52 QTYDRCRRLASALADRSIGPGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTV 111 Q +++ R L IGPG VA+ P A G+ GAVL V A + Sbjct: 140 QLHEQGLRFGEHLRAHGIGPGDIVAVQLPAWIEWMIAAVGIAHAGAVLLPVVSIYGAKEL 199 Query: 112 AFLLSHSQSSVIMVDQEFFTLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALS 171 F+L+ S + +I V + + A+ + L E G ++IGD AP Sbjct: 200 RFILAQSGAKLI-VTPDRWRKADYAQTLAE--VGRLPALATHVMIGD--AAP-------- 246 Query: 172 KGAIEYEDFLA--TGDPNYPWQPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSN 229 G + +E LA P P P A L YTSGTTA PKGV H I++ + Sbjct: 247 -GTVPWEAMLAPIAVGPAAPRSPDA----LALLVYTSGTTADPKGV--KHSARTILSEID 299 Query: 230 PLIWGMQD--GAVYLWTLPMFHCNGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVT 287 + W +D V P H G V + + Q E ++ KY++ Sbjct: 300 AVAWSRRDLGAEVAFCPWPPGHVAGALQLMRFLVTGTPVVLMDQWEPGEAAMLVEKYRIV 359 Query: 288 HFCAAPVVLNAIVNAPKEDTILPLPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSE 347 P L+ +++A + D L M A PP+++ + +G + YG SE Sbjct: 360 SSSFTPFHLSGLLDAAERDG-RDLSSLRSCMVGAAPVPPTLITRCSAQGLKTYRCYGSSE 418 Query: 348 TYGPSTVCAWKPEWDSLPPETQAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEI 407 +T P + K +G+ G E LD +D G+ VP + GE+ Sbjct: 419 HPTVTT---------GHPDDIMEKRLTTEGLPMRGTE-LDFVDDD-GQRVPEGME--GEL 465 Query: 408 VFRGNMVMKGYLKNPEANKETFAGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISS 467 V RG + GYL + + GGWF +GDI D ++ I DR KDVII GGENISS Sbjct: 466 VVRGPELFLGYLDDSLNSAAFLPGGWFRTGDIGRLDQDGFLMITDRKKDVIIRGGENISS 525 Query: 468 VEVENVVYHHPAVLEASVVARPDERWQESPCAFVTLKSDYE---KHDQNKLAQDIMKFCR 524 EVE++++ HPA+ EA+VVA PDER E CA+V + + + AQ R Sbjct: 526 REVEDLLFAHPAIAEAAVVAAPDERMGEIVCAYVVPRPGASVDLESVRTHFAQ--AGIAR 583 Query: 525 EKLPAYWVPKSVVFGPLPKTATGKIQKHILRTKAK 559 +K P + +V P+ +TGKI KH LR +A+ Sbjct: 584 QKTP----ERLIVVDDFPRNSTGKILKHELRAQAR 614 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: 902 Number of extensions: 49 Number of successful extensions: 5 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: 622 Length adjustment: 37 Effective length of query: 532 Effective length of database: 585 Effective search space: 311220 Effective search space used: 311220 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