Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_033100144.1 JG50_RS0105805 AMP-binding protein
Query= curated2:O93730 (670 letters) >NCBI__GCF_000763315.1:WP_033100144.1 Length = 646 Score = 470 bits (1209), Expect = e-136 Identities = 255/631 (40%), Positives = 382/631 (60%), Gaps = 23/631 (3%) Query: 33 YFKFHRQTVENLESFWESVAKEL--EWFKPWDKVLDASNP-PFYKWFVGGRLNLSYLAVD 89 Y +F+ Q+++N+ FW+ V +L W P+ +VLD S+ + +WFV G++N+S +D Sbjct: 30 YDRFYEQSIKNIAWFWDEVVNDLGLRWMMPYRQVLDMSDGIAWTRWFVDGKINISDNCLD 89 Query: 90 RHVKT-WRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDK 148 R V+ +++LA+ WEG+ +K TY DL+ EVNR+A LK+ GV GD Sbjct: 90 RFVEEPAARHRLALIWEGDD-------GTTKKYTYRDLWLEVNRLACGLKK-LGVAAGDC 141 Query: 149 ITLYLPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGR 208 + +Y+PM+ E I MLA RIGAI + FSG+ A+A+A RI Q++ +ITADG+ RRG+ Sbjct: 142 VAIYMPMIAENVIAMLAVARIGAIFTPCFSGYGAEAVATRIQGCQAKWLITADGYLRRGK 201 Query: 209 VVRLKEVVDAALEKATGVESVIVLPRLGLKDVPMTEGRDYWWNKLMQGIPPNAYIEPEPV 268 VV +KE D A + + VE V+V+ RLG +D P RD W++L + + P Sbjct: 202 VVAMKEEADRAADLSPSVEKVVVVSRLG-RDCPWNPDRDVKWDQLTAEMKT---LSPAVT 257 Query: 269 ESEHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGH 328 ++ P I+YTSGTTGKPKG VH G+ + + FD+ DI + D+GW+ G Sbjct: 258 DANDPFMIIYTSGTTGKPKGTVHVHSGFPLKAAFDAGYAFDVGPGDILFWVTDMGWMMG- 316 Query: 329 SYVVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPR 388 ++V G LL+G+T +++EG PDYP P R W + E++GVT SPT IR M++G W Sbjct: 317 PWMVFGTLLLGSTMLVFEGTPDYPIPGRLWELTEKHGVTHLGISPTLIRALMKHGTSWFS 376 Query: 389 KHDLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTE-TGGIVISHAPGLYLV 447 + DLS+LR+ S GEP NPE W W + +G ++V + TE +GGI+ +H + Sbjct: 377 QRDLSSLRVFGSTGEPWNPEPWHWLFEQVGGKRVPIFNYSGGTEISGGILGNH----FFK 432 Query: 448 PMKPGTNGPPLPGFEVDVVDENGNPAPPGVKGYLVIKKPWPGMLHGIWGDPERYIKTYWS 507 P+ P PLPG + +V D+ G G G LV+++PW GM G W D RY TYWS Sbjct: 433 PIVPCGFAGPLPGMDAEVFDDQGKTVR-GEVGELVLRQPWVGMTSGFWQDARRYEDTYWS 491 Query: 508 RFPGMFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGV 567 R+P + GD+ I D+ G ++ GR+D+ +K+AG RLG E+ES L+ HP+V E+A +GV Sbjct: 492 RWPKTWLHGDWVIVDEGGQWFITGRSDDTLKIAGKRLGPAEMESVLVDHPSVIEAATIGV 551 Query: 568 PDAIKGEVPIAFVVLKQGVAPSDELRKELREHVRRTIGPIAEPAQIFFVTKLPKTRSGKI 627 PDA KGE + FVV++ L +EL V +G +P ++ V +LPKTR+GKI Sbjct: 552 PDADKGESAVCFVVVRGDGEEVQSLTEELVRFVGERMGKALKPKRVHIVDELPKTRNGKI 611 Query: 628 MRRLLKAVATGAPLGDVTTLEDETSVEEAKR 658 +RR+++A G GD+++LE+ +VE+ +R Sbjct: 612 LRRVIRAAYLGENAGDLSSLENAHAVEKIRR 642 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: 1391 Number of extensions: 93 Number of successful extensions: 6 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: 670 Length of database: 646 Length adjustment: 38 Effective length of query: 632 Effective length of database: 608 Effective search space: 384256 Effective search space used: 384256 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 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