GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Sphingomonas koreensis DSMZ 15582

Align ATPase (characterized, see rationale)
to candidate Ga0059261_0341 Ga0059261_0341 ABC-type antimicrobial peptide transport system, ATPase component

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__Korea:Ga0059261_0341
          Length = 224

 Score =  129 bits (323), Expect = 7e-35
 Identities = 85/223 (38%), Positives = 125/223 (56%), Gaps = 12/223 (5%)

Query: 19  ETMIYAEGVEKWY---GNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQ 75
           E ++   G+++ +   G     L G+ LTV +GE+V ++GPSGSGKST L+ +  LE   
Sbjct: 3   EPVLQTSGLKRTFSQGGADIHVLRGIDLTVGQGEIVALLGPSGSGKSTLLQAVGLLEGGF 62

Query: 76  RGEIWIEGHRL----SHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPV 131
            G I I G  +    SH R    T R ++G V+Q  +L P    L+N+ L P  ++   +
Sbjct: 63  EGSIRISGVEVGKLESHART--VTRRDKLGFVYQFHHLLPDFNALENVEL-PQLIQNATL 119

Query: 132 AQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPE 191
           A A A +  LL  + +  +    P QLSGG+QQRVA+ARALA +P ++L DEPT  LD  
Sbjct: 120 ADARARSEGLLTALGLGARLTHRPSQLSGGEQQRVAVARALANRPALVLADEPTGNLDEH 179

Query: 192 MVREVL-DVMRDLASEGMTMLVATHEVGFAREVADRVVLMADG 233
               VL + +R +  EG   L+ATH    A ++ DRVV + +G
Sbjct: 180 TADIVLAEFLRLVRGEGAAALIATHNERLAAKM-DRVVRLHEG 221


Lambda     K      H
   0.321    0.134    0.387 

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: 145
Number of extensions: 8
Number of successful extensions: 3
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: 261
Length of database: 224
Length adjustment: 23
Effective length of query: 238
Effective length of database: 201
Effective search space:    47838
Effective search space used:    47838
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