Alignments for a candidate for acs in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Burkholderia phytofirmans PsJN

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate BPHYT_RS13830 BPHYT_RS13830 acetyl-CoA synthetase

Query= curated2:O93730
         (670 letters)



>FitnessBrowser__BFirm:BPHYT_RS13830
          Length = 634

 Score =  479 bits (1233), Expect = e-139
 Identities = 256/640 (40%), Positives = 386/640 (60%), Gaps = 21/640 (3%)

Query: 32  AYFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRH 91
           +Y  FHR+++E+ E+FW   A+ + W  P+D VLD SNPPF +WFVGGR NL + AVDRH
Sbjct: 3   SYRDFHRRSIEDPEAFWRDEARRIHWHTPFDTVLDRSNPPFARWFVGGRTNLCHNAVDRH 62

Query: 92  VKTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITL 151
           +    +    +    E   E       R+ TY +LY EVNR+A +++ +  VK+GD + L
Sbjct: 63  LAERAQQNALVYVSTETGIE-------RRYTYAELYGEVNRMAAVMR-SLDVKRGDVVLL 114

Query: 152 YLPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVR 211
           YLPM+PE    MLA  R+GAI SVVF GF+A  LA RI+D++  +++TAD   R G+V+ 
Sbjct: 115 YLPMIPEALFAMLACARLGAIHSVVFGGFAAPNLAARIDDAKPVLIVTADAGARGGKVID 174

Query: 212 LKEVVDAALEKATGVESVIVLPRLGLKDVPMTEGRDYWWNKLMQGIPPNAYIEPEPVESE 271
              ++D AL +A      ++L    L    +       +  L +    +A++  E +ES 
Sbjct: 175 YTPLMDEALARAQHKTPRVLLIDRQLAPERLNASYLVAYEPLREQFF-DAHVPCEWLESN 233

Query: 272 HPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSYV 331
            PS++LYTSGTTGKPKG+  D GG+AV + A+M+ +F  +  D+ +  +D+GWV GHSY+
Sbjct: 234 EPSYVLYTSGTTGKPKGVQRDVGGYAVALAASMEHIFQGKAGDVMFTASDVGWVVGHSYI 293

Query: 332 VLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKHD 391
           V  PL+ G T V+YEG P  P    WW ++  + + + +T+PTA+R+  +      ++ D
Sbjct: 294 VYAPLIAGLTTVMYEGTPIRPDGGIWWRLVAHHRINLMFTAPTALRVLKKQDPALLKQAD 353

Query: 392 LSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMKP 451
           L++LR +   GEP++     W    L    +     +W TETG  +++   G+  +P + 
Sbjct: 354 LTSLRALFLAGEPLDEPTAAWIAGALDKPVI---DNYWQTETGWPMLAIPRGVEALPTRL 410

Query: 452 GTNGPPLPGFEVDVVDE-NGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSRF 509
           G+ G P  GF + + +E  G P PPG KG L +  P  PG +  +WGD +R++ TYWS  
Sbjct: 411 GSPGVPSAGFNLTLRNELTGEPCPPGEKGVLTLDYPLPPGCMSTVWGDDKRFVSTYWSSI 470

Query: 510 PG--MFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGV 567
           P   ++   D+ ++D+DGY+ +LGR D+VI VAGHRLGT E+E AL SH AVAE AVVGV
Sbjct: 471 PNQQVYSTFDWGVQDEDGYVTILGRTDDVINVAGHRLGTREIEEALSSHAAVAEVAVVGV 530

Query: 568 PDAIKGEVPIAFVVLKQGVAPSD-----ELRKELREHVRRTIGPIAEPAQIFFVTKLPKT 622
            D +KG+  +AFVVL+   A +D     +L  EL   V R +G IA P+++  V  LPKT
Sbjct: 531 TDPLKGQAAMAFVVLRDAQAYADTKKRSKLDAELTATVDRQLGAIARPSRVVVVPMLPKT 590

Query: 623 RSGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKRAYEE 662
           RSGK++RR + A+A G   GD+ T+ED  ++++ + A ++
Sbjct: 591 RSGKLLRRAIAALAEGREPGDLPTIEDPAALQQVREALDD 630


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: 1262
Number of extensions: 79
Number of successful extensions: 9
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: 634
Length adjustment: 38
Effective length of query: 632
Effective length of database: 596
Effective search space:   376672
Effective search space used:   376672
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 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 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