GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Desulfotomaculum hydrothermale Lam5

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_008411393.1 DESHY_RS06575 ABC transporter ATP-binding protein

Query= SwissProt::Q9YGA6
         (372 letters)



>NCBI__GCF_000315365.1:WP_008411393.1
          Length = 227

 Score =  192 bits (489), Expect = 6e-54
 Identities = 96/212 (45%), Positives = 150/212 (70%), Gaps = 4/212 (1%)

Query: 15  EVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGI 74
           +++ + +++L +  GE + +LG SG GK+T LR++AGLE+P  G I I +K++ D     
Sbjct: 16  QLSTINKVNLSISRGEIIAILGQSGSGKSTILRLLAGLEKPCSGTIVIDNKVMFD--NNT 73

Query: 75  FVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLGLTELLN 134
           +V P++R + MVFQ YAL+PHMTV  NI + L   K+ R+E  +R++EV  L+ L E  +
Sbjct: 74  YVNPENRGVGMVFQDYALFPHMTVEKNIIYGLA--KLDRKERTKRLKEVLTLVNLEEFRD 131

Query: 135 RKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTI 194
           R P ELSGGQ+QRVAL RA+  KP V L+DEP SNLDA LR ++R ELK++ + +G+T+I
Sbjct: 132 RYPYELSGGQQQRVALARALAPKPAVLLLDEPFSNLDADLRCKIRDELKRIIKDVGITSI 191

Query: 195 YVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDE 226
           +VTHDQ +A+++ DR+  +++G + +V + +E
Sbjct: 192 FVTHDQEDAISLADRVVYLHKGTVLKVKTKEE 223


Lambda     K      H
   0.323    0.142    0.406 

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: 197
Number of extensions: 5
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: 372
Length of database: 227
Length adjustment: 26
Effective length of query: 346
Effective length of database: 201
Effective search space:    69546
Effective search space used:    69546
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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