GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdB in Sinorhizobium meliloti 1021

Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate SMc01031 SMc01031 pyruvate dehydrogenase subunit beta

Query= metacyc::MONOMER-11684
         (327 letters)



>lcl|FitnessBrowser__Smeli:SMc01031 SMc01031 pyruvate dehydrogenase
           subunit beta
          Length = 460

 Score =  271 bits (692), Expect = 3e-77
 Identities = 144/323 (44%), Positives = 204/323 (63%), Gaps = 3/323 (0%)

Query: 1   MSVMSYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAE 60
           M+ M+  +A+  AM EEM  +  VFV+GE+V    G +K T GL ++FG  RV+DTP+ E
Sbjct: 135 MATMTVREALRDAMAEEMRANEDVFVMGEEVAEYQGAYKVTQGLLQEFGARRVVDTPITE 194

Query: 61  SAIAGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYG 120
              AGVG+GAAM G+RPI E    +F M A++QII+ AAK  Y S      PIV R P G
Sbjct: 195 HGFAGVGVGAAMTGLRPIVEFMTFNFAMQAIDQIINSAAKTLYMSGGQMGAPIVFRGPSG 254

Query: 121 GGVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLI 180
                A  HSQ   A +++ PGLK+VMP T  DAKGLLKAA+RD +PV+F E++  Y   
Sbjct: 255 AAARVAAQHSQCYAAWYSHIPGLKVVMPYTAADAKGLLKAAIRDPNPVIFLENEILYGQ- 313

Query: 181 KGEVP-ADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTV 239
             EVP  DD+VLPIGKA + R G D T++++G+ + +A++AA  LE  GI   ++DLRT+
Sbjct: 314 SFEVPKLDDFVLPIGKARIHRTGKDATLVSFGIGMTYAIKAAAELEAQGIDVEIIDLRTI 373

Query: 240 YPLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPA 299
            P+D   +IE+  KTG+++ V E   + S+ +E+A  + +     LDAPI  +AG D+P 
Sbjct: 374 RPMDLPTVIESVKKTGRLVTVEEGYPQSSVGTEIATRVMQQAFDYLDAPILTIAGKDVP- 432

Query: 300 MPYAPTMEKYFMVNPDKVEAAMR 322
           MPYA  +EK  + N  +V  A++
Sbjct: 433 MPYAANLEKLALPNVAEVVDAVK 455


Lambda     K      H
   0.319    0.136    0.392 

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: 409
Number of extensions: 19
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: 327
Length of database: 460
Length adjustment: 30
Effective length of query: 297
Effective length of database: 430
Effective search space:   127710
Effective search space used:   127710
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 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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