GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= SwissProt::Q9YGA6
         (372 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  234 bits (596), Expect = 4e-66
 Identities = 120/243 (49%), Positives = 168/243 (69%), Gaps = 6/243 (2%)

Query: 1   MAGVRLVDVWKVFGEVT--AVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRG 58
           M+ ++  +V K +      AV +++LE+ +GE + LLGPSGCGKTTTLRM+AG E+P+ G
Sbjct: 1   MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60

Query: 59  QIYIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQ 118
           +I IGD++V D  + +  PP+ R I MVFQ YAL+PH+T+  N+ F L   K   ++  +
Sbjct: 61  KIRIGDEVVYDDRRAL--PPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRWK--NRDKKK 116

Query: 119 RVREVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRM 178
           R +EV EL+GL E  +R P ELSGGQ+QRVAL RA+  +P+V LMDEP SNLDA LR +M
Sbjct: 117 RAQEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKM 176

Query: 179 RAELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAG 238
           R ++  + R+   T I VTHDQ +A  + DR+ VMN G++QQ+ +P E+Y  PAN FVA 
Sbjct: 177 RYDVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQ 236

Query: 239 FIG 241
           F+G
Sbjct: 237 FVG 239


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: 355
Number of extensions: 11
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: 351
Length adjustment: 29
Effective length of query: 343
Effective length of database: 322
Effective search space:   110446
Effective search space used:   110446
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: 49 (23.5 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