GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00885 in Marinobacter adhaerens HP15

Align ABC transporter permease (characterized, see rationale)
to candidate GFF4156 HP15_4096 inner-membrane translocator

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__Marino:GFF4156
          Length = 292

 Score =  141 bits (356), Expect = 2e-38
 Identities = 94/300 (31%), Positives = 151/300 (50%), Gaps = 23/300 (7%)

Query: 11  GLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAPGWVIL 70
           GL +G +YALIALG+ ++Y   ++INFA GE++M  A    +  G M+        W+ L
Sbjct: 13  GLAMGGLYALIALGFVIIYKATRVINFAIGEIMMFAAYLFLAFAGGME-----MSPWIAL 67

Query: 71  LLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWKPNYKPY 130
            LA I   +    L  VIEK   RP+     ++ ++  IG++ +L  L   IW  + +  
Sbjct: 68  PLAVIGGSI----LGGVIEKTMIRPMLGESPISVVMVTIGIASILVGLVEFIWTADPQLL 123

Query: 131 PTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLV--NHTNLGRAMRATAENPRVAS 188
           P  LP  P  IG  ++ P   +  G    +   +VYL+    +  G A+RATA +   A 
Sbjct: 124 PNFLPREPVFIGELYLAPK--IAYGFLIGSALLIVYLLYFRFSRGGVALRATASDQAAAY 181

Query: 189 LMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGIGNLA 248
            MG+    V +  ++ G++ A++AG++ A+  G +    G + GL      + GG+ ++ 
Sbjct: 182 SMGINVRRVFNMAWVFGSLAASLAGVLVAATGGLSPQ-FGII-GLSVLVVVIVGGLDSIL 239

Query: 249 GAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLGERVADR 308
           GA+V G+ +G +E        T+ G  LG  Y     F+VL IIL +RP GL G    +R
Sbjct: 240 GALVAGVFIGWLE--------TVAGAYLGGEYRMPATFLVLAIILVIRPYGLFGTHEIER 291


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: 239
Number of extensions: 13
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: 292
Length adjustment: 27
Effective length of query: 282
Effective length of database: 265
Effective search space:    74730
Effective search space used:    74730
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