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_RS31920 BPHYT_RS31920 acetate--CoA ligase

Query= curated2:Q8KBY0
         (659 letters)



>FitnessBrowser__BFirm:BPHYT_RS31920
          Length = 650

 Score =  324 bits (830), Expect = 9e-93
 Identities = 212/633 (33%), Positives = 319/633 (50%), Gaps = 38/633 (6%)

Query: 39  MEQYEKLYADAAADPDKYWGDLAEQFHWFKKWDSVLEWNAPYA------------KWFNG 86
           +  Y++LYA + A+P +YW       H    W  +  W APY+            +WF G
Sbjct: 30  LRDYDELYAYSIANPGEYW-------HRLMVWLGI-RWQAPYSAYVDLSDGKPFPQWFPG 81

Query: 87  GTTNIAYNCLDVHVGSWRKNKAAIIWEGEEGNERILTYGELHRQVSKFANVLKIAGIKPG 146
           G  N   +  +      R  + A+I E E G     TY EL   V  FA  L  + + PG
Sbjct: 82  GKLNWVDSIFECEADKERLQRIALIAEDESGRVTQRTYAELREDVQSFAAGLMTSKLGPG 141

Query: 147 DKVAIYMGMVPELVIAVLACARVGAVHNVIFAGFAAHAITERVNDSRAKIVICADGTRRR 206
           D V + M    E V+  LA + +GA+   +F+GF A AI  R+    AK ++   G  RR
Sbjct: 142 DCVGLLMESSVESVVTYLALSYIGAIAVPLFSGFGADAIVARLQGCDAKGLVATAGFMRR 201

Query: 207 GSTINLKNIVDEAIINTPSVKNVIVLKVTGEEIHMHDG-MDHWWHDLMGLA----VDECE 261
           G  +  ++ ++ +I   PS++ ++V  + G +  +H G +D  W+D++       +D   
Sbjct: 202 GKPVLTRDAIESSIPALPSLEVLVVKPMRGSQGSVHAGALD--WYDVLAAGRAEPLDHAV 259

Query: 262 PAQVDSEHPLFLLYTSGSTGKPKGILHTTAGYMVHAASSFKYVFDIKDEDIYFCTADIGW 321
           PA+ ++  P  ++YTSG+TGKPKG +HT  G+ +  A      F++   D +   AD+GW
Sbjct: 260 PAEANT--PCMIVYTSGTTGKPKGTVHTHGGFPLKIAHDAAVYFNLGAGDRWLWPADMGW 317

Query: 322 ITGHTYIIYGPLLNGATVFMYEGAPNYPQWDRFWDIINRHKITILYTAPTAIRAFIRAGN 381
           + G    I G  L GAT+  Y+GAPN P W R   +I R+ +T    +PT IR  + A  
Sbjct: 318 VAG-PITIAGAFLRGATLVCYDGAPNCPDWSRLPQLIRRYAVTHFGASPTLIRT-LSAHE 375

Query: 382 EWVTKHDLSSLRLLGTVGEPINPEAWMWYHKYVGQEKCPIVDTWWQTETGGIMISPMPGA 441
             +   DLSS+RL  T GE I+ E++ WY +   +  CP+++    +E  G ++  +   
Sbjct: 376 SSIAPDDLSSVRLAITAGEVIDSESFRWYGE---RFACPVINFTGGSEVSGGLLGNVV-V 431

Query: 442 TPTKPGTATRPLPGIMVDVVRKDGTPCNANEGGYLVVKRPWPSMLRTIYGDNERYEKTYW 501
            P  PG      PGI VDV   DG      E G L V  P+  M R+ + + ERY  TYW
Sbjct: 432 KPIVPGGFNAIAPGIRVDVRGADGKQVR-GEVGELAVLEPFVGMTRSFWKNPERYLDTYW 490

Query: 502 SEFPGMYFTGDGARKDDDGYIWIMGRVDDVVNVSGHRLGTSEVESALVSHEAVAEAAVVS 561
              P ++  GD A + DD    + GR DD + ++G R+G SE+E  +V    VAEAA V 
Sbjct: 491 RNVPDVWIHGDLAIQFDDHAFVLCGRSDDTLKIAGKRVGPSEIEDVIVEIAEVAEAAAVG 550

Query: 562 RPDEIKGNALVAFVTLKDGYEGDAKLRDSLGKHVAKEIGAIAKPDEIRWAKGLPKTRSGK 621
             D +KG  LV FV + D        R+ +   V++ +G    P ++     LPKTRSGK
Sbjct: 551 ISDPVKGQRLVVFV-VADKERCTVAFREQIVDMVSRRLGKPFAPSQVYVVGELPKTRSGK 609

Query: 622 IMRRLLRELATSNEIKGDVTTLEDLGVIENLRE 654
           IMRRL++  A   +  GD  +LE+   IE +RE
Sbjct: 610 IMRRLIKR-AYEGQPLGDTASLENPWAIEMIRE 641


Lambda     K      H
   0.318    0.135    0.424 

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: 1083
Number of extensions: 63
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: 659
Length of database: 650
Length adjustment: 38
Effective length of query: 621
Effective length of database: 612
Effective search space:   380052
Effective search space used:   380052
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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