GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Shewanella amazonensis SB2B

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate 6937207 Sama_1377 butyryl-CoA dehydrogenase (RefSeq)

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__SB2B:6937207
          Length = 385

 Score =  259 bits (663), Expect = 7e-74
 Identities = 143/373 (38%), Positives = 210/373 (56%), Gaps = 2/373 (0%)

Query: 39  EEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDI 98
           E+Q+   ++ R  A  E+ P A + DE H FP        +LG  S   P   GG G+  
Sbjct: 7   EDQRQFADLARQFAADELTPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGMGLSR 66

Query: 99  TTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFAAT 158
              +++ EE+ K C +T  ML         +   G+ A + ++       + L  ++  T
Sbjct: 67  LDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTEAFRAEWSEALTTGAKL-ASYCLT 125

Query: 159 EPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTFVV 218
           EPGAGSD  ++ T+AV++GD+YVING K FI+     ++L V   T  + G KG+S   +
Sbjct: 126 EPGAGSDAASLTTKAVREGDEYVINGSKMFISGAGATELLVVMCRTGEA-GPKGISAIAI 184

Query: 219 ERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRVFC 278
                G+IYG  E KMG    P   + FE++ VP +NL+GEEG+GF + M  L   R+  
Sbjct: 185 PADAEGVIYGKAEDKMGWNAQPTRLITFENVRVPVQNLLGEEGQGFTFAMKGLDGGRINI 244

Query: 279 ASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATTLL 338
           A+ +VG AQ ALER++ +  ER+QFGKP+A    +QF +ADMATE+ AAR +VR A   L
Sbjct: 245 ATCSVGTAQAALERSIAYMNERKQFGKPLAAFQALQFKLADMATELVAARQMVRLAAFKL 304

Query: 339 DAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIYTGT 398
           D++D        MAK FA+D    V   A+Q+ GG GY++EY +ER  R+ ++ QI  GT
Sbjct: 305 DSQDPEATAYCAMAKRFATDIGFAVCDAALQIHGGYGYIREYPLERHFRDVRVHQILEGT 364

Query: 399 NQITRMVTGRSLL 411
           N+I R++  R LL
Sbjct: 365 NEIMRLIISRRLL 377


Lambda     K      H
   0.318    0.133    0.375 

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: 369
Number of extensions: 13
Number of successful extensions: 3
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: 414
Length of database: 385
Length adjustment: 31
Effective length of query: 383
Effective length of database: 354
Effective search space:   135582
Effective search space used:   135582
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: 50 (23.9 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