Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_084275418.1 B8779_RS04840 acetate--CoA ligase
Query= SwissProt::P31638 (660 letters) >NCBI__GCF_900176045.1:WP_084275418.1 Length = 650 Score = 733 bits (1892), Expect = 0.0 Identities = 367/654 (56%), Positives = 477/654 (72%), Gaps = 11/654 (1%) Query: 8 MQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQ 67 M++ VF+P +A I SM+ Y + EAE DYEGFW + A+E ++W +P+TKVLD+ Sbjct: 1 MEKVPVFDPTPRIKERARINSMDQYWQMVKEAESDYEGFWDKLAKEKINWREPYTKVLDE 60 Query: 68 SNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFA 127 S APFYKWF G+LN + C+DR+L+ +K AI++E + G +TY EL+ +V RFA Sbjct: 61 SEAPFYKWFVGGKLNVTEQCIDRHLET-KKNKAAIIWEGEPGDKRVITYLELYYEVNRFA 119 Query: 128 NGLKA-LGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGA 186 N LK+ GI+KGDRVVIYMPM E AM ACAR+GA HSVVFGGFSA++L++R+ D A Sbjct: 120 NLLKSKFGIKKGDRVVIYMPMIPEAAFAMLACARIGAIHSVVFGGFSAEALRDRIQDAQA 179 Query: 187 VALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDV 246 +ITAD R GK LK + D ALA CE+V V+V RR ++ W + RD ++ Sbjct: 180 KLVITADGAYRRGKPYMLKPVVDVALAKD-CESVEAVLVVRRNNEEIKWHDHRDYDYNEL 238 Query: 247 SAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDL 306 P CE E + +E PLF+LYTSGSTGKPKGVQHS GY+LWA +TM+W FDIK D Sbjct: 239 IKDMPARCEPEIMDSEDPLFLLYTSGSTGKPKGVQHSQAGYILWAQLTMEWVFDIKDTDT 298 Query: 307 FWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTA 366 +WCTAD+GW+TGHTYI YGPLAAGAT +++EGVP YP+AGR+W MI ++V+ FYTAPTA Sbjct: 299 YWCTADVGWITGHTYIVYGPLAAGATTMMYEGVPVYPDAGRWWRMIEEYRVNQFYTAPTA 358 Query: 367 IRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQT 426 IR L K ADE P +YDLSSL +LGTVGEPINP+AWMWY++ +G +CPIVDT+WQT Sbjct: 359 IRLLHKLG-ADE---PDKYDLSSLYILGTVGEPINPDAWMWYFEKVGRGQCPIVDTWWQT 414 Query: 427 ETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRT 486 ETGGHMI+PLPGATP+ PGS T PLPGI A I+D G+ G L + +PWP+MIRT Sbjct: 415 ETGGHMISPLPGATPIKPGSATFPLPGIFAEIIDTDGNKKEPNEKGYLCITKPWPSMIRT 474 Query: 487 IWGDPERFRKSYFP--EELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTME 544 IWGDP+RF KSYF ++ G +Y +GDG+I D++ GY I GR+DDV+NVSGHR+GT E Sbjct: 475 IWGDPDRFVKSYFGTCKKDGKPVYFSGDGAIYDEE-GYIWITGRMDDVINVSGHRLGTAE 533 Query: 545 IESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIG 604 IE+A+ +P VAE AVVG+P ++ GE++ AFVVLK +E +++ E+ + K+IG Sbjct: 534 IEAAIGHHPRVAECAVVGKPHEVKGESVFAFVVLKDDEGVADE-MELIKEINEVITKDIG 592 Query: 605 PIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658 P+AK +I F LPKTRSGKIMRR+LRS+AKGEEI QDTSTLE+P+++E++ Q Sbjct: 593 PLAKCDEIAFVPGLPKTRSGKIMRRILRSIAKGEEIKQDTSTLEDPSVVEKIIQ 646 Lambda K H 0.319 0.136 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: 1347 Number of extensions: 81 Number of successful extensions: 8 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: 660 Length of database: 650 Length adjustment: 38 Effective length of query: 622 Effective length of database: 612 Effective search space: 380664 Effective search space used: 380664 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 Jul 25 2024. The underlying query database was built on Jul 25 2024.
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