Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_084199337.1 C0029_RS09615 AMP-binding protein
Query= curated2:O93730 (670 letters) >NCBI__GCF_002869505.1:WP_084199337.1 Length = 1803 Score = 252 bits (643), Expect = 1e-70 Identities = 168/512 (32%), Positives = 254/512 (49%), Gaps = 71/512 (13%) Query: 224 TGVESVIVLPRLGLKDVPMTEGRDYWWNKLM----QGIPPNA------------------ 261 +GV+ VIV+ L ++ EGRD W ++ I NA Sbjct: 328 SGVQKVIVVRHADLPEISWHEGRDLWAEDILIQAEATILSNAGLQKRSELMALGDTELTQ 387 Query: 262 ----YIEPEPVESEHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIR-DDDIF 316 ++P PV ++ P FI+YTSG+TGKPKG+VH GG+ V + K FD R +DI Sbjct: 388 ALWRSVKPVPVSADFPLFIIYTSGSTGKPKGVVHVHGGYTAGVSYSTKISFDARAGEDII 447 Query: 317 WCTADIGWVTGHSYVVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAI 376 W AD GW+TG SY++ L T V+ EG P +P R+ SIIERYGVTIF T + Sbjct: 448 WVIADPGWITGQSYLISAALTNRLTSVVTEGPPTFPNAGRFASIIERYGVTIFKAGVTFL 507 Query: 377 RMFMRYGEEW--PRKHDLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETG 434 + + + ++ S++R+ EP +P R+A ++ + + +++W TE G Sbjct: 508 KGIISNPQNRLDVERYSRSSVRVATFCAEPTSPSVQRFAMDLVTPQYI---NSYWATEHG 564 Query: 435 GIVISHAPGLYLVPMKPGTNGPPLPGFEVDVVDENGNP----------APPGVKGYLVIK 484 GIV +H G +P++ PLP D+ N P A P KG +VI Sbjct: 565 GIVWTHPYGNAEMPLRADAQTYPLPWIFGDIWIGNSEPDETGRVTYSQARPDEKGEIVIT 624 Query: 485 KPWPGMLHGIWGDP------------ERYIKTYWSRFPG-------MFYAGDYAIKDKDG 525 +P+P + IWGDP ER+ TY+ R+ + GD+A + +G Sbjct: 625 RPYPYLARTIWGDPDNVNSDEWMGDIERFKATYFGRYRSDSGEPEYTYVQGDFARRYTNG 684 Query: 526 YIWVLGRADEVIKVAGHRLGTYELESALIS------HPAVAESAVVGVPDAIKGEVPIAF 579 + GR+D+VI V+GHR+GT E+E A++ V V+G P KG P+AF Sbjct: 685 SYSLHGRSDDVINVSGHRMGTEEIEGAILKDRQLNPESKVGNCIVIGAPHQDKGLTPLAF 744 Query: 580 V--VLKQGVAPSDELRKELREHVRRTIGPIAEPAQIFFVTKLPKTRSGKIMRRLLKAVAT 637 + V +Q ++ DE + L E V+ G +A P+ V P+TRSGK +RR LKA+ Sbjct: 745 ILPVARQSLSSDDE--RHLAELVQTEKGSLAVPSAFLCVDAFPETRSGKYLRRFLKAIVL 802 Query: 638 GAPLGDVTTLEDETSVEEAKRAYEEIKAEMAR 669 LGD +TL + + + +R E+ + + R Sbjct: 803 DQELGDTSTLRNPECLPKIRRVVEQWRRQEDR 834 Score = 100 bits (248), Expect = 8e-25 Identities = 64/185 (34%), Positives = 97/185 (52%), Gaps = 8/185 (4%) Query: 52 AKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRHVKTWRKNKLAIEWEGEPVDE 111 A L W +PW + LD S+ PFY+WF G N ++ +DRHV +++A +EG+ D Sbjct: 77 ADALAW-QPWQQALDESSAPFYRWFSGAMTNAAFNELDRHVLAGHGDEIAFYYEGDRWDP 135 Query: 112 -----NGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLYLPMVPELPITMLAA 166 G P ++ +L A L + G+ KGD+I + +P + E + AA Sbjct: 136 ALNAGKGGPVQHNAISRRELLLRSVIAAQALLE-LGLVKGDRIAINMPNILEQIVWTEAA 194 Query: 167 WRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVRLKEV-VDAALEKATG 225 RIG I + VF GFS LA+RI ++ + +VITADG R +V KE D AL+ Sbjct: 195 KRIGVIYTPVFGGFSDKTLADRIENAGASVVITADGASRNAELVPFKEAYCDPALDLYIS 254 Query: 226 VESVI 230 ++S + Sbjct: 255 LKSAL 259 Lambda K H 0.319 0.138 0.440 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: 3036 Number of extensions: 151 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 670 Length of database: 1803 Length adjustment: 46 Effective length of query: 624 Effective length of database: 1757 Effective search space: 1096368 Effective search space used: 1096368 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: 58 (26.9 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