GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Sinorhizobium meliloti 1021

Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate SMc01030 SMc01030 pyruvate dehydrogenase alpha2 subunit protein

Query= metacyc::MONOMER-11683
         (330 letters)



>FitnessBrowser__Smeli:SMc01030
          Length = 348

 Score =  158 bits (400), Expect = 2e-43
 Identities = 105/307 (34%), Positives = 161/307 (52%), Gaps = 9/307 (2%)

Query: 14  QEAVDMYRTMLLARKIDERMWLLNRSGKIP-FVISCQGQEAAQVGAAFALDREMDYVLPY 72
           ++ +  YR MLL R+ +E+   L   G I  F     GQEA  VG   AL +E D V+  
Sbjct: 34  EDDLKAYREMLLIRRFEEKAGQLYGMGFIGGFCHLYIGQEAVVVGMQLAL-KEGDQVITG 92

Query: 73  YRDMGVVLAFGMTAKDLM--MSGFAKAADPNSGGRQMPGHFGQKKNRIVTGSSPVTTQVP 130
           YRD G +LA GM+A+ +M  ++G         GG     H   K+     G   V  QV 
Sbjct: 93  YRDHGHMLACGMSARGVMAELTGRRGGLSKGKGGSM---HMFSKEKHFYGGHGIVGAQVS 149

Query: 131 HAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYAISVP 190
              G+A A R    D  +   FG+G++NQG  +E  N AA+ KLPVI++ ENN+YA+   
Sbjct: 150 LGTGLAFANRYRGNDNVSLAYFGDGAANQGQVYESFNMAALWKLPVIYIVENNRYAMGTS 209

Query: 191 YDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETISYRLT 250
             +  A  + S R   +G+PG  V+G D   V  A  EA E  R G+GP ++E ++YR  
Sbjct: 210 VSRASAQTDFSQRGASFGIPGYQVDGMDVRAVKAAADEAVEHCRSGKGPIILEMLTYRYR 269

Query: 251 PHSSDDDDSSYRGREEVEEAK-KSDPLLTYQAYLKETGLLSDEIEQTMLDEIMAIVNEAT 309
            HS   D + YR ++EV++ + + DP+   +A L + G  +++  + +  E+  IV ++ 
Sbjct: 270 GHSM-SDPAKYRSKDEVQKMRSEHDPIEQVKARLTDKGWATEDELKQIDKEVRDIVADSA 328

Query: 310 DEAENAP 316
           D A++ P
Sbjct: 329 DFAQSDP 335


Lambda     K      H
   0.316    0.132    0.377 

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: 277
Number of extensions: 15
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: 330
Length of database: 348
Length adjustment: 28
Effective length of query: 302
Effective length of database: 320
Effective search space:    96640
Effective search space used:    96640
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 (21.6 bits)
S2: 49 (23.5 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