GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdB in Sinorhizobium meliloti 1021

Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate SM_b20020 SM_b20020 pyruvate dehydrogenase E1 component, subunits alpha and beta

Query= reanno::Smeli:SMc03202
         (337 letters)



>lcl|FitnessBrowser__Smeli:SM_b20020 SM_b20020 pyruvate
           dehydrogenase E1 component, subunits alpha and beta
          Length = 692

 Score =  246 bits (627), Expect = 2e-69
 Identities = 140/337 (41%), Positives = 195/337 (57%), Gaps = 21/337 (6%)

Query: 3   RMTMIEAVRSAMDVSMARDDNVVVFGEDVGYFGGVFRCTQGLQAKYGKTRCFDTPISESG 62
           R+ M+ A+R  +D  M  +  VV+FGED+G  GGV   T GLQ K+G  R FDT +SE G
Sbjct: 373 RINMVTAIRRTLDHEMTVNQRVVLFGEDIGPKGGVHAVTLGLQEKFGTARVFDTSLSEEG 432

Query: 63  IVGTAIGMAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTGGG 122
           I+G A+GMA  GL P  EIQF  Y  PA +QL  +   IR+R++  F  PIVVRM  G  
Sbjct: 433 IIGRAVGMALAGLVPVPEIQFRKYAEPAIEQL-NDCGTIRWRTSNRFAAPIVVRMAGGFL 491

Query: 123 IFGGQTHSQSPEALFTHVCGLKVVVPSNPYDAKGLLISAIEDPDPVMFLEPKRLYNGPFD 182
             G   HSQ+ E  F H  G K+ VPSN  DA GLL +A+   DPV+F E + + + P  
Sbjct: 492 KCGDPWHSQTNEVAFVHQPGWKIAVPSNAEDAVGLLRTALRGNDPVIFFEHRAMLDHP-- 549

Query: 183 GHHERPVTAWSKHELGDVPDGHYTIPIGKAEIRRKGSGVTVIAYGTMVHVALAAAEETGI 242
                    W++      P   + +P GKA+  R+G  +T++ +G MV     AAE  GI
Sbjct: 550 ---------WARR---PYPGDAFALPFGKAKFTREGRDITIVTWGAMVPRCEEAAE--GI 595

Query: 243 DAEVIDLRSLLPLDLETIVQSAKKTGRCVVVHEATLTSGFGAELAALVQEHCFYHLESPV 302
            A+VIDLR+L+P D + ++ S ++T RC++VHE   T+GFGAE+AA V +  F  L++P+
Sbjct: 596 SADVIDLRTLMPWDRKAVIASVRRTRRCLIVHEDLATAGFGAEIAAAVADEAFIDLDAPI 655

Query: 303 VRLTGWDTPYPH---AQEWDYFPGPARVGRALAEAME 336
            RLT  D P PH     +W   P   R+ R + + +E
Sbjct: 656 SRLTMPDIPSPHNPALLDW-AVPSTERIRRKIIDLLE 691


Lambda     K      H
   0.321    0.138    0.424 

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: 611
Number of extensions: 32
Number of successful extensions: 4
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: 337
Length of database: 692
Length adjustment: 34
Effective length of query: 303
Effective length of database: 658
Effective search space:   199374
Effective search space used:   199374
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: 51 (24.3 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