Alignments for a candidate for acs in Halobacillus alkaliphilus FP5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Halobacillus alkaliphilus FP5

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_089749917.1 BMZ06_RS02730 AMP-binding protein

Query= curated2:O93730
         (670 letters)



>NCBI__GCF_900113125.1:WP_089749917.1
          Length = 653

 Score =  490 bits (1262), Expect = e-143
 Identities = 258/642 (40%), Positives = 399/642 (62%), Gaps = 24/642 (3%)

Query: 22  KWRSKYTPIDAYFKFHRQTVENLESFWESVAKEL--EWFKPWDKVLDASNPPFY-KWFVG 78
           KW  K    D Y  FH++++E++E FW+   KEL  EW + ++K +D S+   Y KWF G
Sbjct: 22  KWMQKLG-YDNYDVFHQKSIEDIEWFWDEALKELGIEWDQSYEKTVDLSSGIAYPKWFTG 80

Query: 79  GRLNLSYLAVDRH-VKTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYML 137
           G++N+ + A+D+  +   +K+ +A+ WEG+  D   Y       TY +LY+EVNRVA  L
Sbjct: 81  GKMNVVHNALDKWALDDTKKHAVALYWEGDDGDTIQY-------TYEELYKEVNRVANGL 133

Query: 138 KQNFGVKKGDKITLYLPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIV 197
            +  G+ +GD ITLY+PM+PE  I+MLA  +IGA+ S  FSG+ ADA+A RI  ++S+ +
Sbjct: 134 NK-LGIVEGDIITLYMPMIPETLISMLAVSKIGAVFSPAFSGYKADAVATRIQAARSKAL 192

Query: 198 ITADGFWRRGRVVRLKEVVDAALEKATGVESVIVLPRLGLKDVPMTEGRDYWWNKLMQGI 257
           ITADGF+RRG+ + +K   D A ++   +E VIV+ R    ++   E RD  W++L++  
Sbjct: 193 ITADGFYRRGKTIPMKMEADLACDQCPSLEHVIVVERASC-EIEWNEYRDTQWSRLLEN- 250

Query: 258 PPNAYIEPEPVESEHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDI-RDDDIF 316
                   + +E++ P  I+YTSGTTG+PKG VH   G+            D+ +DD +F
Sbjct: 251 --ETVYNTKSMEADDPFMIIYTSGTTGRPKGAVHTHSGFPTKAAFDAGVCMDVTKDDTLF 308

Query: 317 WCTADIGWVTGHSYVVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAI 376
           W T D+GW+ G  ++V G L+ G++ V++EG PD+P PDR WS++E+Y VT    SPT +
Sbjct: 309 WYT-DMGWMMG-PFLVYGGLVNGSSIVMFEGTPDFPNPDRLWSLVEKYKVTHLGISPTLV 366

Query: 377 RMFMRYGEEWPRKHDLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGI 436
           R  M++GEEW +KH+LS+L++I S GEP NPE W W ++  GN  V   +    TE  G 
Sbjct: 367 RSMMKHGEEWIKKHNLSSLKLIGSTGEPWNPEPWYWLFKHAGNSDVPIFNYSGGTEISGG 426

Query: 437 VISHAPGLYLVPMKPGTNGPPLPGFEVDVVDENGNPAPPGVKGYLVIKKPWPGMLHGIWG 496
           ++ +   + + P++P T    LPG + DV DE+G+     V G LV++KPW GM  G + 
Sbjct: 427 ILGN---VLVKPIQPVTFNAALPGMDADVYDESGDSLKNQV-GELVLRKPWVGMTSGFYN 482

Query: 497 DPERYIKTYWSRFPGMFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISH 556
           + +RY +TYW+RF   +  GD+ I D +G+  + GR+D+V+ VAG RLG  E+ES L+ H
Sbjct: 483 ENKRYEETYWTRFKDTWVHGDWVILDDEGFYTITGRSDDVLNVAGKRLGPAEVESVLVEH 542

Query: 557 PAVAESAVVGVPDAIKGEVPIAFVVLKQGVAPSDELRKELREHVRRTIGPIAEPAQIFFV 616
           P++ E+ V+G+P  IKGE  +AF VL   +  S++L  EL+ H+   +G    P +++ V
Sbjct: 543 PSITEAGVIGIPHEIKGEEAVAFAVLNPNIEGSEQLVNELKSHLVEKLGKALAPKKVYIV 602

Query: 617 TKLPKTRSGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKR 658
             LPKTR+ K+MRR +K+     P GD++ LE+  ++E+ +R
Sbjct: 603 DDLPKTRNAKVMRRAIKSAYLNNPAGDLSALENPNTIEQIQR 644


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: 1352
Number of extensions: 71
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: 670
Length of database: 653
Length adjustment: 38
Effective length of query: 632
Effective length of database: 615
Effective search space:   388680
Effective search space used:   388680
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.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources