GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Sphingomonas koreensis DSMZ 15582

Align Inositol transport system ATP-binding protein (characterized)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component

Query= reanno::Phaeo:GFF717
         (261 letters)



>FitnessBrowser__Korea:Ga0059261_3874
          Length = 243

 Score = 79.0 bits (193), Expect = 9e-20
 Identities = 68/211 (32%), Positives = 99/211 (46%), Gaps = 17/211 (8%)

Query: 23  LAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPL--HFADPRDAI 80
           L GVSV V PGE   ++G +G GKST +  +SG+  P +G++   G P+    A  RDA 
Sbjct: 28  LFGVSVSVMPGELTLVVGPSGCGKSTLLAILSGLTLPDQGEVDALGNPICRMKAGARDAF 87

Query: 81  A-AGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINL 139
             A    V Q   +        N     E +  +          A +     +  +G+  
Sbjct: 88  RLANTGFVFQGFNLF-------NALTAEEQVAYVLQCMKVKPAEARQRARAALEAVGL-- 138

Query: 140 RGPDQAVGT--LSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATI-DKVRK 196
            GP   +    LSGGE+Q VAIARA+    ++L  DEPTSAL       V+A + D    
Sbjct: 139 -GPRMRLRPFELSGGEKQRVAIARALAKQPRILFADEPTSALDSHNGHAVIALLRDIAHN 197

Query: 197 QGVAVVFITHNVRHALAVGDRFTVLNRGKTL 227
           QG AV+ +TH+ R  L+  DR   +  G+ +
Sbjct: 198 QGAAVLCVTHDPR-LLSFADRIIHMEDGRII 227


Lambda     K      H
   0.321    0.137    0.395 

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: 154
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 261
Length of database: 243
Length adjustment: 24
Effective length of query: 237
Effective length of database: 219
Effective search space:    51903
Effective search space used:    51903
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 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