Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_100848375.1 C0J26_RS15220 AMP-binding protein
Query= curated2:C1AA44 (654 letters) >NCBI__GCF_003031005.1:WP_100848375.1 Length = 554 Score = 275 bits (704), Expect = 3e-78 Identities = 192/556 (34%), Positives = 278/556 (50%), Gaps = 52/556 (9%) Query: 75 LNASVNCIDRHVHGPRRNKAALIWEGEPGDRRTFTYWDLYREVNLAANMLKKLGVGRGDR 134 LNA V C DRH R AL WEG G ++T+ +L + AN L GV +GD+ Sbjct: 28 LNACVECCDRHALPGR---IALFWEGRDGASASYTFNELQDKTARFANFLLAQGVQKGDK 84 Query: 135 VAIYLPMIPEAVIAMLACARIGAIHTVVFGGFAPESLRDRINDCGCKLLITADGGSRRGQ 194 VA LP E +I + A RIGA++ +F F P++L R+N G K+++T Sbjct: 85 VAGLLPRNIELLITVFATWRIGAVYQPLFTAFGPKALEHRLNSSGAKVVVT--------D 136 Query: 195 MVPLKRNADVALKECPSIENVLVVMRRRSGVGDETFAEMQEGRDHWWHRLKRQVPRYCEP 254 V + A+VA CP+ LV + G G + G +W L CEP Sbjct: 137 AVNRPKLAEVA--NCPT----LVTVGGAKGQG------IVRGDFSFWAELANY-SNACEP 183 Query: 255 EAMDAEDVLFVLYTSGTTGKPKGIVHTTGGFLTGVATTTKYTFDLKEEDVYWCTADIGWI 314 + ED +++TSGTTG K + + + T+ DL+ +D +W AD GW Sbjct: 184 VLLTGEDPFLLMFTSGTTGPSKALSVPLKA-IVAFQSYTRDAVDLRPQDAFWNVADPGWA 242 Query: 315 TGHSYLVYGPLANGATCVMYEGAPDWPDKDRFWQICERYGVTILYTAPTAIRAFMKWGTE 374 G + V GPL+ G Y+G R + +YG+T L +PTA R + G E Sbjct: 243 YGIYFGVTGPLSMGHPITFYDGPFTLESTCR---VINKYGITNLTGSPTAYRLLIAGGDE 299 Query: 375 YVKKHDLSQLRVLGSVGEPINPEAWMWYHEHIGDFQCPIVDTWWQTETGAIMITPLPGVT 434 + K +LR++ S GEP+NPE W+ +++ I D + QTE G ++ Sbjct: 300 FAKSIK-GKLRIVSSAGEPLNPEVIRWFADNL---DVVIHDHYGQTELGMVLCNHHGIDH 355 Query: 435 TTKPGSATVPFPGIRTALLDANANELTVGG-GLLAITHPWPSMLRTIWGDDQRYVDTYFS 493 G+A PG R +LD NEL VG G+LAI P M +F Sbjct: 356 PVHIGAAGFASPGHRIVVLDDQYNELGVGQPGILAIDRPKSPMC-------------WFG 402 Query: 494 KWPGRP------DLYFPGDGAKLDEDGYLWILGRVDDVLNVSGHRIGTMEVESALVDHPS 547 + G P D Y GD + + DG + +GR DDV+ SG+R+G +VESAL++HP+ Sbjct: 403 GYEGAPTKAFVGDYYLSGDTVEWNPDGSISFVGRSDDVITTSGYRVGPFDVESALIEHPA 462 Query: 548 VAEAAVVGKHHDLKGQAIAAFVTLRAGFTASGSLRDELRDHVAQKIGALARPDDILFSAD 607 V EAAVVGK + + + AFV L A + AS L +ELR HV +++ A + P +I F ++ Sbjct: 463 VVEAAVVGKPDPERTELVKAFVVLSAQYRASPELAEELRQHVRKRLAAHSYPREIEFVSE 522 Query: 608 LPKTRSGKIMRRLLRD 623 LPKT SGK+ R +LR+ Sbjct: 523 LPKTPSGKLQRFILRN 538 Lambda K H 0.320 0.137 0.441 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: 927 Number of extensions: 53 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: 654 Length of database: 554 Length adjustment: 37 Effective length of query: 617 Effective length of database: 517 Effective search space: 318989 Effective search space used: 318989 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