GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMc01031
          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.

Links

Downloads

Related tools

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