Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_047007498.1 AAW01_RS06755 AMP-binding protein
Query= curated2:O93730 (670 letters) >NCBI__GCF_001010925.1:WP_047007498.1 Length = 542 Score = 116 bits (291), Expect = 2e-30 Identities = 145/524 (27%), Positives = 211/524 (40%), Gaps = 54/524 (10%) Query: 116 TDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLYLPMVPELPITMLAAWRIGAITSV 175 T R+ TY +L + R+A F + G+++ ++ P +PE + AA G Sbjct: 49 TTGRRWTYAELLHDAERMAKGFAARF--QPGERVAVWGPNIPEWVLVEYAAALAGLTLVT 106 Query: 176 VFSGFSADALAERINDSQSRIVITADGFWRRGRVVRLKEVVDAALEKATGVESVIVLPRL 235 V + L + S S + F RG +K + E + ++ Sbjct: 107 VNPAYQKRELDFVLRQSNSAALFLISEF--RGNP--MKSIAQGVAEDLPTLREIV----- 157 Query: 236 GLKDVPMTEGRDYWWNKLMQGIPPNAYIEPE----PVESEHPSFILYTSGTTGKPKGIVH 291 ++D + Y +P V++ P+ I YTSGTTG PKG+V Sbjct: 158 DMQD------------------EASLYTDPSGSLPDVDTNDPAQIQYTSGTTGFPKGVVL 199 Query: 292 DTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSYVVLGPLLMGATEVIYEGAPDY 351 + +K V D+ + + G S VLG L G Sbjct: 200 SHRNLTNNARLFVK-VGDLPKNLSTIGLTPLFHTMGCSMGVLGSLQSGGAYCPLLAF--- 255 Query: 352 PQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKHDLSTLRIIHSVGEPINPEAWR 411 P IIER V+ PT + + PR DLS+L II G + PE R Sbjct: 256 -DPGAALDIIEREKVSWTICVPTMAVAMVAAQKAQPR--DLSSLEIIGMGGAMVAPELAR 312 Query: 412 WAYRVLGNEK-VAFGSTWWMTETGGIVISHAPGLYLVPMKPGTNGPPLPGFEVDVVDE-N 469 LG + VA+G T E+ ++ S P + T G P G EV +VD Sbjct: 313 AVEATLGAKALVAYGQT----ESSPLITSGRPTDDFEDIVT-TIGQPALGCEVAIVDAAT 367 Query: 470 GNPAPPGVKGYLVIKKPWPGMLHGIWGDPERYIKTYWSRFPGMFYAGDYAIKDKDGYIWV 529 G P G + + + ML G +PE +T G GD D GY+ + Sbjct: 368 GEVLPCDTVGE-IRSRSYATML-GYNDNPEATAETVTG--DGWLCTGDLGTMDDRGYVKI 423 Query: 530 LGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGVPDAIKGEVPIAFVVLKQGVAPS 589 GR E+I G L E+E+ L+ HPA+AE AVVGVPD + GE AF+ ++ G Sbjct: 424 TGRVKEMIIRGGENLFPAEIENVLLEHPAIAECAVVGVPDDVLGEAVAAFIRVQDGAEFD 483 Query: 590 DELRKELREHVRRTIGPIAEPAQIFFVTKLPKTRSGKIMRRLLK 633 + + HVR I P PA VT+ P T SGKI + L+ Sbjct: 484 PD---AFKAHVRSQIAPQKCPAYWTQVTEWPLTGSGKIRKFQLR 524 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: 948 Number of extensions: 63 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 670 Length of database: 542 Length adjustment: 37 Effective length of query: 633 Effective length of database: 505 Effective search space: 319665 Effective search space used: 319665 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: 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