GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Thiothrix lacustris DSM 21227

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  106 bits (264), Expect = 7e-28
 Identities = 73/219 (33%), Positives = 118/219 (53%), Gaps = 14/219 (6%)

Query: 5   LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64
           LE+++V K +G + A+  VS+EI  GE +  +G +G GKSTL+++I+G    + G L+ +
Sbjct: 4   LELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILD 63

Query: 65  GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLA---REVTNKIFLNKKKMMEES 121
           G+  I   P   R L +  ++Q  AL P + +  N+  A    +V   I   K KM  + 
Sbjct: 64  GRD-ITEVPPSQRDLAM--VFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120

Query: 122 KKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAAL-SVVEARKV 180
             L   LQ R P      + LSGGQRQ VA+ R++  S K+ L DEP + L + +     
Sbjct: 121 LNLTAYLQ-RTP------KALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTR 173

Query: 181 LELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKI 219
           +E+A   ++ G   + +TH+ ++   +ADR+ VL  G I
Sbjct: 174 VEIASLHRELGATTVYVTHDQVEAMTLADRVVVLRDGII 212


Lambda     K      H
   0.318    0.137    0.371 

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: 151
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: 251
Length of database: 348
Length adjustment: 26
Effective length of query: 225
Effective length of database: 322
Effective search space:    72450
Effective search space used:    72450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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