GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Miya:8502038
          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:

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