Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate HSERO_RS00095 HSERO_RS00095 AMP-dependent synthetase
Query= curated2:O93730 (670 letters) >FitnessBrowser__HerbieS:HSERO_RS00095 Length = 539 Score = 226 bits (576), Expect = 2e-63 Identities = 185/575 (32%), Positives = 270/575 (46%), Gaps = 55/575 (9%) Query: 67 ASNPPFYKWFVGGRLNLSYLAVDRHVKTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDL 126 A NP Y+W + N++ A DR + AI E Y D+ K+ D Sbjct: 8 AGNPSPYEWQIPTHFNIAQAACDRWADG--SGRTAIICEDADGSVTSYSYDQLKILS-DR 64 Query: 127 YREVNRVAYMLKQNFGVKKGDKITLYLPMVPELPITMLAAWRIGAITSVVFSGFSADALA 186 + R A GV +GD+I +YL E IT LAA+++GAIT +F F DA+A Sbjct: 65 FANALRAA-------GVGRGDRIGIYLSQRIETVITHLAAYKLGAITVPLFYLFGPDAIA 117 Query: 187 ERINDSQSRIVITADGFWRRGRVVRLKEVVDAA-LEKATGVESVIVLPRLGL------KD 239 R+++S + ++T DA+ +EKAT LP L L D Sbjct: 118 YRLDNSGAVALVT-----------------DASGMEKATLAGE---LPALRLVFCVESSD 157 Query: 240 VPMTEGRDYWWNKLMQGIPPNAYIEPEPVESEHPSFILYTSGTTGKPKGIVHDTGGWAVH 299 + + + D+W + P A ++P ++ P+ I+YTSGTTGK KG +H H Sbjct: 158 LVLPQTTDFW--DRLHAAP--AELDPVLTLADDPAMIIYTSGTTGKAKGALHAHRVLLGH 213 Query: 300 VYAT-MKWVFDIRDDDIFWCTADIGWVTGHSYVVLGPLLMGATEVIYEGAPDYPQPDRWW 358 + + ++ D FW AD W+ G V+L P L V+ + + + Sbjct: 214 LPGVEVSHDSFPQEGDRFWTPADWAWIGGLLDVLL-PSLYHGVAVVARRLEKFDAAEVF- 271 Query: 359 SIIERYGVTIFYTSPTAIRMFMRYGEEWPRKHDLSTLRIIHSVGEPINPEAWRWAYRVLG 418 ++ R+ + + PTA++M G R +LR + S GE + + W LG Sbjct: 272 GLLARHQIRNVFFPPTALKMLR--GAATVRAQADFSLRSVASGGETLGDDLIAWGREALG 329 Query: 419 NEKVAFGSTWWMTETGGIVISHAPGLYLVPMKPGTNGPPLPGFEVDVVDENGNPAPPGVK 478 V + TE +V S + + P G+ G +PG V +VDE G P G Sbjct: 330 ---VTINEFYGQTECNLVVSSSS---HCYPSVSGSMGRAVPGHVVQIVDEQGQVLPHGTV 383 Query: 479 GYLVIKKPWPGMLHGIWGDPERYIKTYWSRFPGMFYAGDYAIKDKDGYIWVLGRADEVIK 538 G + I+ P P M W + E + + F GD D+ GYI LGR D+VI Sbjct: 384 GNIAIRAPDPVMFLRYWRNEEATREKFAGDF---LLTGDLGSMDEQGYIRYLGRNDDVIT 440 Query: 539 VAGHRLGTYELESALISHPAVAESAVVGVPDAIKGEVPIAFVVLKQGVAPSDELRKELRE 598 AG+R+G +E L+ HPAV +AVVGV DA++ EV AFVVLK GV P + L+ EL++ Sbjct: 441 SAGYRIGPAAIEECLMRHPAVRIAAVVGVKDALRTEVVKAFVVLKDGVTPDEALKAELQQ 500 Query: 599 HVRRTIGPIAEPAQIFFVTKLPKTRSGKIMRRLLK 633 HVR + P I FV LP T +GKIMR+ LK Sbjct: 501 HVRAQLAAHEYPRLISFVAALPTTATGKIMRKTLK 535 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: 905 Number of extensions: 43 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: 539 Length adjustment: 37 Effective length of query: 633 Effective length of database: 502 Effective search space: 317766 Effective search space used: 317766 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 17 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