Aligments for a candidate for acs in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Paraburkholderia bryophila 376MFSha3.1

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate H281DRAFT_04471 H281DRAFT_04471 propionyl-CoA synthetase

Query= curated2:O93730
         (670 letters)



>FitnessBrowser__Burk376:H281DRAFT_04471
          Length = 635

 Score =  495 bits (1275), Expect = e-144
 Identities = 266/641 (41%), Positives = 395/641 (61%), Gaps = 25/641 (3%)

Query: 33  YFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRHV 92
           Y  FHR+++EN E+FW   A+ + W  P+D VLD SNPPF +WFVGGR NL + AVDRH+
Sbjct: 4   YRDFHRRSIENPEAFWRDEARRIHWETPFDTVLDRSNPPFARWFVGGRTNLCHNAVDRHL 63

Query: 93  KTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLY 152
               +    +    E   E       R+ TY +LY E+NR+A +++ + GVK+GD + LY
Sbjct: 64  VDRAQQNALVYVSTETGIE-------RRYTYAELYAEINRMAAVMR-SLGVKRGDVVLLY 115

Query: 153 LPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVRL 212
           LPM+PE    MLA  R+GAI SVVF GF+A  LA RI+D++  +++TAD   R G+V+  
Sbjct: 116 LPMIPEALFAMLACARLGAIHSVVFGGFAAPNLAARIDDAKPVLIVTADAGARGGKVIDY 175

Query: 213 KEVVDAALEKATGVESVIVL--PRLGLKDVPMTEGRDYWWNKLMQGIPPNAYIEPEPVES 270
             +VD A+ +AT   + ++L   +L  + +  T   DY   + ++    +A++  E +ES
Sbjct: 176 TPLVDEAIARATHKTARVLLIDRQLAPERLNATYLVDY---EPLREQFFDAHVSCEWLES 232

Query: 271 EHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSY 330
             PS++LYTSGTTGKPKG+  D GG+AV + A+M+++F+ +  D  +  +D+GWV GHSY
Sbjct: 233 SEPSYVLYTSGTTGKPKGVQRDVGGYAVALAASMEYIFEGKAGDTMFTASDVGWVVGHSY 292

Query: 331 VVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKH 390
           +V  PL+ G T V+YEG P  P    WW ++E++ + + +T+PTA+R+  +         
Sbjct: 293 IVYAPLIAGLTTVMYEGTPIRPDGGIWWRLVEQHKINLMFTAPTALRVLKKQDPALLESA 352

Query: 391 DLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMK 450
           DLS+LR +   GEP++     W    LG   +     +W TETG  +++   G+  +P K
Sbjct: 353 DLSSLRTLFLAGEPLDEPTASWITGALGKPVI---DNYWQTETGWPMLAIPRGVEALPTK 409

Query: 451 PGTNGPPLPGFEVDVVDE-NGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSR 508
            G+ G P  GF + + +E  G P PPG KG L +  P  PG +  +WGD +R+I TYWS 
Sbjct: 410 LGSPGVPSAGFNLTLRNELTGEPCPPGEKGVLTLNYPLPPGCMSTVWGDDKRFISTYWSS 469

Query: 509 FPG--MFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVG 566
           FP   ++   D+ I+D+DGY+ +LGR D+VI VAGHRLGT E+E AL SH AVAE AVVG
Sbjct: 470 FPDQQVYSTFDWGIQDEDGYVTILGRTDDVINVAGHRLGTREIEEALSSHAAVAEVAVVG 529

Query: 567 VPDAIKGEVPIAFVVLKQGVAPSD-----ELRKELREHVRRTIGPIAEPAQIFFVTKLPK 621
           V D +KG+  +AFVVL+   A +D     +L  EL   V R +G IA P+++  V+ LPK
Sbjct: 530 VADPLKGQAAMAFVVLRDAQAYADVDARTKLEAELTATVDRQLGAIARPSRVVIVSMLPK 589

Query: 622 TRSGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKRAYEE 662
           TRSGK++RR + A+A G   G++ T+ED  ++++ +    E
Sbjct: 590 TRSGKLLRRAIAALAEGREPGELPTIEDPAALQQVREGLSE 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: 1274
Number of extensions: 77
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: 635
Length adjustment: 38
Effective length of query: 632
Effective length of database: 597
Effective search space:   377304
Effective search space used:   377304
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.

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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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