GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS31920 BPHYT_RS31920 acetate--CoA
           ligase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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