Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_011765880.1 AZO_RS10865 acetoacetate--CoA ligase
Query= BRENDA::A0B8F1 (659 letters) >NCBI__GCF_000061505.1:WP_011765880.1 Length = 661 Score = 216 bits (549), Expect = 3e-60 Identities = 178/584 (30%), Positives = 269/584 (46%), Gaps = 26/584 (4%) Query: 79 PYAKWFLGGKCNVAHNAVDRHAKSWRRNKVAYYFVGEPVGDTKTITYYQLYQAVNKMANG 138 P A+WF + N A N + R R A F GE + +T+ +LY+ V + + Sbjct: 83 PGAQWFPDARLNFAQNLLRR-----RDGDDAVVFWGEDKVRDR-LTHGELYRRVAQFSAA 136 Query: 139 LKSLGVKKGDRVSIYLPMIPELPITMLACAKIGAIHSVVFSGFSAGGLQSRVTDAEAKVV 198 L+ GV KGDRV+ Y+P +PE I MLA A IGAI + F G+ R E KV+ Sbjct: 137 LREQGVGKGDRVAAYMPNMPETLIAMLAAASIGAIFTSASPDFGVQGVLDRFGQTEPKVL 196 Query: 199 VTSDGFYRRGKPLPLKPNVDEAVQNAPSVEKVVVVKRVGLD-----VPMKEGRDIWYHDL 253 + DG+Y GK + + E V PSVE+VV+V V D +P Y D Sbjct: 197 LACDGYYYNGKMVDCLAKLGEIVPQLPSVERVVIVPYVHRDHALGGIPHAR----MYADF 252 Query: 254 VKDQPA--ECYTEELDPEDRLFILYTSGTTGKPKGIEHAHGGFCVGPAYTTAWALDVHEE 311 V A E E L L+++Y+SGTTG PK I H+ GG + DV Sbjct: 253 VAPHHAATEIGFEALPFSHPLYVMYSSGTTGVPKCIVHSAGGALLQHLKEHRLHCDVKPG 312 Query: 312 DVYWCTADCGWITGHSYVVYGPLCLGATSILYEGAPDYPDIGRWWSIIEEYGVSVFYTAP 371 D + CGW+ +++V G L GAT +LY+G+P D + + ++ F T+ Sbjct: 313 DRVFYFTTCGWMM-WNWLVSG-LAAGATILLYDGSPFAADNRILFDYADAERMTHFGTSA 370 Query: 372 TAIRMFMKAGDQWPKKYNLKSIRILASVGEPLNPEAYVWFRNNIGGGQAPIIDTWWQTET 431 I K G + + ++L ++R + S G PL PE + + +I + Sbjct: 371 KFIDAAAKFGLKPRETHSLATVRAMMSTGSPLVPEGFDYVYRDIKADLQLSSISGGTDIL 430 Query: 432 GCHVIAPLPMTPEKPGSVAFPLPGFNTDIYDEDGNSVPLGYGGNIVQKTPWPSMLRAFFR 491 C V+ P+ P G + G D++D++G V G G +V P+P+M F+R Sbjct: 431 SCFVLGN-PVLPVWRGEIQCRGLGLAVDVWDDEGRPV-RGEKGELVCARPFPAMPVGFWR 488 Query: 492 DPERYMKEYWQMYWDIKPGTYLAGDKATRDKDGYWWIQGRIDDVLKVAGHRISNAEVESA 551 D + +Y Y++ + GD G I GR D L G RI AE+ Sbjct: 489 DEDG--SKYRAAYFERFDNVWCHGDFCEITAHGGLIIYGRSDATLNPGGVRIGTAEIYRQ 546 Query: 552 AVSHPAVAEAAVIGK---PDEVKGEVIVAFIILKEGVQESEDLKKDIAKHVRSVLGPVAY 608 V E+ VIG+ P +V F+ L++G+ + L I + +R P Sbjct: 547 VEKLHEVVESIVIGQDWPPQNPNDVRVVLFVKLRDGMTLDDTLADRIKRTIRDNTTPRHV 606 Query: 609 PEIVYFVKDVPKTRSGKIMRRVIKAKALGKPVGDISALANPESV 652 P V V D+P+T+SGKI+ ++ G+ V + ALANPE++ Sbjct: 607 PAKVLQVADIPRTKSGKIVELAVRNVVHGRAVKNQEALANPEAL 650 Lambda K H 0.318 0.137 0.438 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: 1154 Number of extensions: 63 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: 659 Length of database: 661 Length adjustment: 38 Effective length of query: 621 Effective length of database: 623 Effective search space: 386883 Effective search space used: 386883 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 (21.7 bits) S2: 54 (25.4 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