GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Dechlorosoma suillum PS

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_0628 Dsui_0628 ABC-type branched-chain amino acid transport system, permease component

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__PS:Dsui_0628
          Length = 358

 Score =  257 bits (657), Expect = 4e-73
 Identities = 160/333 (48%), Positives = 204/333 (61%), Gaps = 21/333 (6%)

Query: 113 IALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAV 172
           I L + P +V A  G   +   + NF    ++Y+MLA GLNIVVG AGLLDLGY+AFYAV
Sbjct: 22  IVLAVLPFLVGA--GLGNAWLRILNFA---MLYIMLALGLNIVVGFAGLLDLGYIAFYAV 76

Query: 173 GAYSYALLSS-YFGLSF--WVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEII 229
           GAY YALL+S +FGL +  W +LPL  + A   G +LG P LRLRGDYLAIVTL FGEII
Sbjct: 77  GAYLYALLASPHFGLHWPVWAILPLGAVVAGGAGALLGAPTLRLRGDYLAIVTLGFGEII 136

Query: 230 RLVLINWT---DVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYL 286
           R+ + N     ++T G  GISSI    + G+              +P   AYY     YL
Sbjct: 137 RIFMNNLNAPVNITNGPQGISSIDPFHVGGVTLAKPLSVLGVT--VPSLHAYY-----YL 189

Query: 287 ILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAG 346
            L L ++  +VTIRL    IGRAW A+REDEIA ++ GIN    KL AF+ GA F G AG
Sbjct: 190 FLLLALVIIFVTIRLEDSRIGRAWVAIREDEIAAKACGINVRNIKLLAFSMGATFGGVAG 249

Query: 347 SFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLRE--MSFL 404
             FA+ QGFVSPESF  +ES ++L +VVLGGMG + G+ +  I++    E  R   +   
Sbjct: 250 GLFASFQGFVSPESFGLMESIMVLCMVVLGGMGHIPGVILGGILLTILPEAFRHAAVPLQ 309

Query: 405 KLIFGPDFT-PELYRMLIFGLAMVVVMLFKPRG 436
           K  FG     PE  RML+FGLA++ VML++P G
Sbjct: 310 KYAFGKVVVDPESLRMLLFGLALIAVMLYRPAG 342


Lambda     K      H
   0.330    0.145    0.432 

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: 571
Number of extensions: 31
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: 463
Length of database: 358
Length adjustment: 31
Effective length of query: 432
Effective length of database: 327
Effective search space:   141264
Effective search space used:   141264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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:

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