GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_1695 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter permease (characterized, see rationale)
to candidate 8502038 DvMF_2751 inner-membrane translocator (RefSeq)

Query= uniprot:A0A165KC95
         (309 letters)



>lcl|FitnessBrowser__Miya:8502038 DvMF_2751 inner-membrane
           translocator (RefSeq)
          Length = 301

 Score =  256 bits (654), Expect = 5e-73
 Identities = 141/312 (45%), Positives = 204/312 (65%), Gaps = 16/312 (5%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGA---LTSWSCIGMM 57
           M+   QQ+ NGL +G +YALIALGYTMVYG+++LINFAHG++  IGA    T ++  G+ 
Sbjct: 1   MEEFFQQLTNGLAVGGIYALIALGYTMVYGVLKLINFAHGDLFTIGAYLGFTLFTAFGL- 59

Query: 58  QGAMPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQT 117
            G + G PG V+L+L  ++  V  A + F++E+VAYRPLRSS RL+ +++A+G SI  Q 
Sbjct: 60  SGFVSG-PGGVLLVLVMVMGLV--ALIGFLLERVAYRPLRSSSRLSAVVSALGASIFFQN 116

Query: 118 LAMIIWKPNYKPYPTML-PSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRA 176
             M+I+   ++ YP  + PS    I G  +   +I+++  +   + +L +    T +G A
Sbjct: 117 AVMLIYGAKFQVYPNDIRPSYVLSIMGIDVPLVRIMMIAASLGLMLALYWFTQRTRIGAA 176

Query: 177 MRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAF 236
           +RATA +   A LMG+  + VIS  F+IG  L  +AG+M    YG    TMG++ GLKAF
Sbjct: 177 IRATAIDQGAAKLMGIDVNRVISLVFMIGPALGGVAGVMVGLYYGQVDFTMGWVYGLKAF 236

Query: 237 TAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLR 296
           TAA+ GGIGN+ GA+VGG+LLG+IEA+G+ YI           + D  AF+VLI+IL +R
Sbjct: 237 TAAILGGIGNIPGAMVGGLLLGVIEALGAAYISIA--------WKDAIAFLVLILILIIR 288

Query: 297 PSGLLGERVADR 308
           P+GLLGERVAD+
Sbjct: 289 PTGLLGERVADK 300


Lambda     K      H
   0.327    0.142    0.419 

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: 265
Number of extensions: 15
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: 309
Length of database: 301
Length adjustment: 27
Effective length of query: 282
Effective length of database: 274
Effective search space:    77268
Effective search space used:    77268
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 (21.7 bits)
S2: 48 (23.1 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