GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msdC1 in Phaeobacter inhibens BS107

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate GFF260 PGA1_c02720 sn-glycerol-3-phosphate transport system permease protein UgpA

Query= uniprot:A3DHA3
         (284 letters)



>FitnessBrowser__Phaeo:GFF260
          Length = 293

 Score =  105 bits (263), Expect = 9e-28
 Identities = 86/278 (30%), Positives = 134/278 (48%), Gaps = 12/278 (4%)

Query: 11  LFSSPYLAGFLIFFAIPSAMSVYYCFTR----GVGSFEFAGLDNFKSVIASNSYRLAVKN 66
           L   P L    IFF  P+  ++   F      G GS  F GLDN+  ++ ++ YR     
Sbjct: 14  LLLMPQLVIIAIFFYWPAWHAIQSSFYLQDPFGFGS-TFVGLDNYTDLLGNSEYRRVAIF 72

Query: 67  TLIFNSVSVPVIMIVSLLLAMLLNKALRGARYFR--MFFVLPLVIPVASIILVWQITFNE 124
           TL+F  +     + ++LLLA+  +  LRGAR +R  + +V  +  PVA  I +  I F++
Sbjct: 73  TLVFTVLVTFFSLAIALLLAVKADNVLRGARTYRTLLMWVYAVAPPVAGFIGL--IMFDQ 130

Query: 125 -FGVLNNLLNHFGIAGVEWLNSKWSIAVLVLLYVWKNCGYNIILFTAGLNSIPKDYYDAA 183
            +G L  L   FG   V  +N   + A +VL+ VWK    N I F +GL SIP+   +AA
Sbjct: 131 SWGPLTRLAGFFGWDFVLGVNFNDTAAAMVLVSVWKQIPVNFIFFLSGLQSIPRSVREAA 190

Query: 184 SIDGAGGFKCFTSITLPLLVPTIFFVFIISIINS-FKVFREAYLLCGNYPPLN-MYMLQH 241
            ID       F  +T PLL PT FF+ II+I  + F  F     L    P  N M ++  
Sbjct: 191 LIDNRSATGRFWDVTFPLLAPTGFFLLIINITYALFDTFGIVDTLVKGEPGNNPMTLVYK 250

Query: 242 FMNNNFNNLNYQRLSTASLLMELFIVAIVFLMYKIEGR 279
              + F   +    S  S+++ + ++A+    +++  R
Sbjct: 251 VYVDGFRGNDLGGSSAQSVILMVLVLALTIFQFRLIDR 288


Lambda     K      H
   0.331    0.144    0.444 

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: 207
Number of extensions: 6
Number of successful extensions: 2
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: 284
Length of database: 293
Length adjustment: 26
Effective length of query: 258
Effective length of database: 267
Effective search space:    68886
Effective search space used:    68886
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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