Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate HSERO_RS07770 HSERO_RS07770 acetyl-CoA synthetase
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__HerbieS:HSERO_RS07770 Length = 660 Score = 1112 bits (2877), Expect = 0.0 Identities = 518/657 (78%), Positives = 592/657 (90%) Query: 4 IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63 IE+ QE+RVF PP AAI M+AY AL E +DYEG WAR A++ L W KPFT+ Sbjct: 4 IETFKQENRVFAPPAELVKHAAISGMDAYHALNAEFAKDYEGTWARLAKDNLKWHKPFTQ 63 Query: 64 VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123 LD+SNAPFYKWF DG++N SYNCLD NL+NGNADK A++FE+DDG VTRV+YRELH KV Sbjct: 64 TLDESNAPFYKWFADGQVNVSYNCLDVNLENGNADKTAVIFESDDGKVTRVSYRELHQKV 123 Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183 C+FANGLK+LGI+KGDRVVIYMPMSVEGV AMQACAR+GATHSVVFGGFSAKSL ER++D Sbjct: 124 CQFANGLKSLGIKKGDRVVIYMPMSVEGVAAMQACARIGATHSVVFGGFSAKSLHERVID 183 Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243 GAVA++TAD Q+RGGK LPLK+I D+AL +GGC+ +++V+VY+R G ++ W EGRD W+ Sbjct: 184 AGAVAVLTADYQVRGGKQLPLKSIVDEALDMGGCDTLKHVVVYKRAGAEINWVEGRDLWL 243 Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303 DV A Q DTCE E V AEHPLF+LYTSGSTGKPKGVQH++ GYLLWA++TMKWTFDIKP Sbjct: 244 SDVVANQSDTCEPEWVDAEHPLFILYTSGSTGKPKGVQHASAGYLLWAVLTMKWTFDIKP 303 Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363 DD++WCTADIGW+TGHTYIAYGPLA GATQ+VFEGVPTYPNAGRFWDM+ARHK +IFYTA Sbjct: 304 DDVYWCTADIGWITGHTYIAYGPLAVGATQIVFEGVPTYPNAGRFWDMVARHKATIFYTA 363 Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423 PTAIRSLIKAA+ADEK+HPKQYDLSSLR+LG+VGEPINPEAWMWYYKN+G+E CPIVDTF Sbjct: 364 PTAIRSLIKAADADEKVHPKQYDLSSLRILGSVGEPINPEAWMWYYKNVGHENCPIVDTF 423 Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483 WQTETGGHMI+PLPGATP VPGSCTLPLPGI AAIVDETG+D+PNGNGGILVVKRPWP+M Sbjct: 424 WQTETGGHMISPLPGATPQVPGSCTLPLPGITAAIVDETGNDIPNGNGGILVVKRPWPSM 483 Query: 484 IRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTM 543 IRTIW DPERF+KSYFPEELGGK+YLAGDG++R+K+TGYFTI GRIDDVLNVSGHRMGTM Sbjct: 484 IRTIWNDPERFKKSYFPEELGGKIYLAGDGAVRNKETGYFTITGRIDDVLNVSGHRMGTM 543 Query: 544 EIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEI 603 EIESALV+N +VAEAAVVG+PD+ TGE+ICAFVVLKR RPTG+EA +IA ELR+WV KEI Sbjct: 544 EIESALVANSIVAEAAVVGKPDETTGESICAFVVLKRPRPTGDEAKQIAKELRDWVAKEI 603 Query: 604 GPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQAQ 660 GPIAKPK+IRFGDNLPKTRSGKIMRRLLR LAKGE ITQD STLENPAIL+QLK+AQ Sbjct: 604 GPIAKPKEIRFGDNLPKTRSGKIMRRLLRVLAKGEAITQDVSTLENPAILDQLKEAQ 660 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: 1529 Number of extensions: 64 Number of successful extensions: 1 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: 660 Length adjustment: 38 Effective length of query: 622 Effective length of database: 622 Effective search space: 386884 Effective search space used: 386884 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 17 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