GapMind for catabolism of small carbon sources

 

Aligments for a candidate for icd in Burkholderia phytofirmans PsJN

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate BPHYT_RS25050 BPHYT_RS25050 3-isopropylmalate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS25050 BPHYT_RS25050
           3-isopropylmalate dehydrogenase
          Length = 376

 Score =  205 bits (522), Expect = 1e-57
 Identities = 138/352 (39%), Positives = 192/352 (54%), Gaps = 25/352 (7%)

Query: 3   YRICLIEGDGIGHEVIPAARRVLEATG-----LPLEFVEAEAGWETFERRGTSVPEETVE 57
           YRI  I GDGIG EV+PA RRVLEA          EF   + G + +   G  +P + ++
Sbjct: 4   YRIATIPGDGIGKEVVPAGRRVLEAIAGSGDAFGFEFENFDWGGDYYREHGVMMPADGLD 63

Query: 58  KILSCHATLFGAATSPTRKVPG---FFGAIRYLRRRLDLYANVRPAKSRP---VPGSRPG 111
            I    A LFG+A  P   +P     +G    + +  D YANVRP +  P    P  R G
Sbjct: 64  AIRHKDAILFGSAGDPD--IPDHVTLWGLRLKICQGFDQYANVRPTRILPGIDAPLKRCG 121

Query: 112 ---VDLVIVRENTEGLYV-----EQERRYLDVAIADAVISKKASERIGRAALRIAEGRPR 163
              +D VIVREN+EG Y        +   ++VA   +++++   ERI R A ++A+ RPR
Sbjct: 122 PEDLDWVIVRENSEGEYAGVGGRAHQGHPIEVATDVSMMTRAGVERILRFAFQLAQSRPR 181

Query: 164 KTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTT 223
           K L +  K+N       ++ +   +V+K+FP V     +VD    ++V RP   D IV T
Sbjct: 182 KLLTVITKSNAQRHAMVMWDEIAVQVSKEFPDVRWDKELVDAATARMVNRPATLDTIVAT 241

Query: 224 NLLGDILSDLAAGLVGGLGLAPSGNIGDT---TAVFEPVHGSAPDIAGKGIANPTAAILS 280
           NL  DILSDLAA L G LG+AP+ N+       ++FEP+HGSA DI GKG+ANP     S
Sbjct: 242 NLHADILSDLAAALAGSLGIAPTANLDPERRYPSMFEPIHGSAFDIMGKGLANPVGTFWS 301

Query: 281 AAMMLDYLGEKEAAKRVEKAVDLV-LERGPRTPDLGGDATTEAFTEAVVEAL 331
             MML++LGE  AA+++  A++ V  +    T DLGG ATT   T+AV   L
Sbjct: 302 VVMMLEHLGEHAAAQQLMAAIERVTADPSLHTGDLGGTATTARVTDAVCAIL 353


Lambda     K      H
   0.319    0.137    0.391 

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: 337
Number of extensions: 22
Number of successful extensions: 7
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: 334
Length of database: 376
Length adjustment: 29
Effective length of query: 305
Effective length of database: 347
Effective search space:   105835
Effective search space used:   105835
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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