Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate BPHYT_RS27780 BPHYT_RS27780 acetyl-CoA synthetase
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__BFirm:BPHYT_RS27780 Length = 658 Score = 1028 bits (2657), Expect = 0.0 Identities = 477/631 (75%), Positives = 555/631 (87%) Query: 25 AIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQSNAPFYKWFEDGELNAS 84 AI M+AY+AL EAE D++ FWAR ARE L W +PFTK+LD SNAPFYKWFEDGELNAS Sbjct: 23 AISGMDAYRALVAEAETDHQAFWARLAREHLQWRRPFTKILDDSNAPFYKWFEDGELNAS 82 Query: 85 YNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFANGLKALGIRKGDRVVIY 144 YNCLDRNL G ADK AIVFEADDG+VTR+TY+ L+ +VCR AN L+A G+ +GDRVVIY Sbjct: 83 YNCLDRNLAKGLADKTAIVFEADDGTVTRITYQALYHRVCRLANALRARGVTRGDRVVIY 142 Query: 145 MPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVALITADEQMRGGKALPL 204 MPMS+EG+ AM ACAR+GA HSVVFGGFSAKSL ERLV+VGAVA++TADEQ+RGGK LPL Sbjct: 143 MPMSIEGIAAMLACARIGAPHSVVFGGFSAKSLHERLVNVGAVAVMTADEQVRGGKTLPL 202 Query: 205 KAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSAGQPDTCEAEPVSAEHP 264 KAI D+ALA+GG AV+ V+VYRRTGG++ W RD W+ ++ Q DTCE E V AEHP Sbjct: 203 KAIVDEALAMGGTVAVKTVVVYRRTGGRIPWITQRDAWLHELEHAQSDTCEPEWVGAEHP 262 Query: 265 LFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFWCTADIGWVTGHTYIAY 324 LFVLYTSGSTG PKGVQHSTGGYLLWA +TMKWTFDIKPDD+FWCTADIGW+TGHTYI Y Sbjct: 263 LFVLYTSGSTGAPKGVQHSTGGYLLWAAVTMKWTFDIKPDDVFWCTADIGWITGHTYICY 322 Query: 325 GPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIKAAEADEKIHPKQ 384 GP A GATQV+FEGVPTYP+AGRFW MI RHKVSIFYTAPTAIRSLIKAA+A+E +HP+ Sbjct: 323 GPTAVGATQVIFEGVPTYPDAGRFWQMIERHKVSIFYTAPTAIRSLIKAADANEAVHPRS 382 Query: 385 YDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTETGGHMITPLPGATPLVP 444 +DLSSLR+LGTVGEPINP AW WY +++G RCP++DTFWQTETGGHMI+PLPG TPLVP Sbjct: 383 FDLSSLRILGTVGEPINPSAWTWYAQHVGGGRCPVLDTFWQTETGGHMISPLPGVTPLVP 442 Query: 445 GSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIWGDPERFRKSYFPEELG 504 GSCTLP+PGI AAIVDETGH+VPNG+GG+LV+++PWP+MIRTIWG+PERFR Y+P++LG Sbjct: 443 GSCTLPMPGIDAAIVDETGHEVPNGHGGVLVIRKPWPSMIRTIWGNPERFRHGYYPDDLG 502 Query: 505 GKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALVSNPLVAEAAVVGRP 564 GKLYLAGDG+IRD+DTGYFTI GRIDDVLNVSGHR+GTMEIESAL ++P VAEAAVVGRP Sbjct: 503 GKLYLAGDGAIRDRDTGYFTITGRIDDVLNVSGHRLGTMEIESALSAHPSVAEAAVVGRP 562 Query: 565 DDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKPKDIRFGDNLPKTRSG 624 D+ GEAI AFVVLK +RP+G +A ++A ELR WVGKEIGPIAKPKDIRFGD +PKTRSG Sbjct: 563 DETCGEAIVAFVVLKTARPSGPDAKRVADELRAWVGKEIGPIAKPKDIRFGDAMPKTRSG 622 Query: 625 KIMRRLLRSLAKGEEITQDTSTLENPAILEQ 655 K++RRLLRS+AKGE ITQDTS++ENP ++ Q Sbjct: 623 KVVRRLLRSVAKGEAITQDTSSVENPTVISQ 653 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: 1574 Number of extensions: 77 Number of successful extensions: 2 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: 658 Length adjustment: 38 Effective length of query: 622 Effective length of database: 620 Effective search space: 385640 Effective search space used: 385640 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 Apr 09 2024. The underlying query database was built on Apr 09 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