GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sinorhizobium meliloti 1021

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate SMc00261 SMc00261 acyl-CoA synthetase

Query= metacyc::MONOMER-20125
         (556 letters)



>FitnessBrowser__Smeli:SMc00261
          Length = 549

 Score =  159 bits (402), Expect = 3e-43
 Identities = 158/565 (27%), Positives = 248/565 (43%), Gaps = 48/565 (8%)

Query: 8   PASSSPLTPLGFLERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIA-SLGIENGHV 66
           P S+  +    FL +AA    D  ++V+    + WS+   R   +A ++    G+  G  
Sbjct: 12  PVSTRVMNLANFLSQAARRNPDEIALVHGDRRWRWSEMEARVDAMAYALVHEFGVRKGDR 71

Query: 67  VSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLIL 126
           + V + N  QM+E  FA   AGA+    N R     ++ L   S ++L+           
Sbjct: 72  ILVHSANCNQMFESMFAAFRAGAVWVPTNFRQLPEEVAYLAESSGARLVIFQ-------- 123

Query: 127 EAIALFPKQAPVPRLVFMADESESGN-----SSELGKEFFCSYKDLIDRGDPDFKWVMPK 181
              A F   A   R    A   + G+     SS +G++    Y  ++ R        +  
Sbjct: 124 ---AAFEAHAEACR----AAGEQIGSCIPIGSSRVGED----YDAIVARNLGRSVSPVAV 172

Query: 182 SEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDW--GVPKQPVYLWTLPMFHANG 239
              DP    YTSGTT  PK  V  H  +  +  + + D       +   +   P+ H  G
Sbjct: 173 DRDDPCWYFYTSGTTGRPKAAVLTHGQMAFVINNHIGDLFPATTHRDRSIVVAPLSHGAG 232

Query: 240 WSYPWGMAAVGGTNICL--RKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSEPL-- 295
             +     A G T I L   K D    + ++++  V ++   P ++ +L   P  +    
Sbjct: 233 -IHQLCQVARGATTILLPSEKLDIPQFWALVEKWRVNNLFAVPTIVKLLIEDPSVDRYDH 291

Query: 296 KTTVQIMTAGAPPPSAVLFRT-ESLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERA 354
            +   ++ AGAP   A   +  E LG  +   +GL E  G +        ++       A
Sbjct: 292 SSLRYVIYAGAPMYRADQKKALEKLGAVLVQYFGLGEVTGAIT--VLPPAFHSSEDGPDA 349

Query: 355 RLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMT 414
           R+ +     T MQ +I   D     A    G+T GE+ + G +V  GY ++PE  AK+  
Sbjct: 350 RIGTCGFERTGMQLQIQDEDGNEVPA----GAT-GEICVIGPAVFAGYYRNPEANAKAFR 404

Query: 415 ADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARP 474
            +GWF TGD+G +   G+L I  R+ D+ ISGG N+   E+E  L  HPDI EAA+V  P
Sbjct: 405 -NGWFRTGDLGHVDAQGFLYITGRASDMYISGGSNVYPREIEEKLLMHPDISEAAIVGVP 463

Query: 475 DEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQK 534
           D  WGE   A    + G T       + E+   K+ RY +PK +VF  E+PK++ GK+ K
Sbjct: 464 DPVWGEVGIAVCVARGGATVGAA--ALREWLDGKIARYKLPKKIVFWSEMPKSAYGKITK 521

Query: 535 FILRD--MARG---MGSATAGASRS 554
            ++R+    RG   +GSA  G  RS
Sbjct: 522 KLIREELERRGELDIGSAGIGERRS 546


Lambda     K      H
   0.319    0.135    0.412 

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: 772
Number of extensions: 30
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 556
Length of database: 549
Length adjustment: 36
Effective length of query: 520
Effective length of database: 513
Effective search space:   266760
Effective search space used:   266760
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: 53 (25.0 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