GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17605 in Echinicola vietnamensis KMM 6221, DSM 17526

Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate Echvi_2909 Echvi_2909 ABC-type antimicrobial peptide transport system, ATPase component

Query= uniprot:A0A1N7U8S3
         (276 letters)



>FitnessBrowser__Cola:Echvi_2909
          Length = 218

 Score =  122 bits (305), Expect = 9e-33
 Identities = 76/224 (33%), Positives = 128/224 (57%), Gaps = 14/224 (6%)

Query: 27  LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86
           L+ +GIHK YG+  VLKGV +    G+++S++GASG+GKST+L  +  L+  D G++++D
Sbjct: 2   LRAKGIHKYYGDLHVLKGVDVEIAAGEIVSIVGASGAGKSTLLHILGTLDDADKGLVSID 61

Query: 87  GISIEMRQGRAGTRAPHQDQLQNLRTR-LAMVFQHFNLWSHMTVLENITMAPRRVLDVSA 145
             S+   +G         D+L   R + +  +FQ  NL    T  ENI + P  +     
Sbjct: 62  DKSLTALKG---------DKLAAYRNQEVGFIFQFHNLLPEFTAEENI-IIPGLIAKKDE 111

Query: 146 AEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDP 205
               ++A+     +G+  R+  + P+ LSGG+QQRVA+ARAL  +P+II  DEP+  LD 
Sbjct: 112 KYLTEKAKELARLLGIMDRLGHK-PSELSGGEQQRVAVARALINDPKIIFADEPSGNLDT 170

Query: 206 ELVGEVLKVIQTLAEE-GRTMLMVTHEMGFARQVSSQVLFLHQG 248
           +    + ++  TL +  G++ ++VTH    A Q++ ++L +  G
Sbjct: 171 QSAESLHELFFTLRDRFGQSFVIVTHNQQLA-QMADRMLTMQDG 213


Lambda     K      H
   0.319    0.133    0.372 

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: 137
Number of extensions: 9
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: 276
Length of database: 218
Length adjustment: 24
Effective length of query: 252
Effective length of database: 194
Effective search space:    48888
Effective search space used:    48888
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 (21.8 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