GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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