GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Phaeacidiphilus oryzae TH49

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

Query= TCDB::Q9R9Q4
         (342 letters)



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  211 bits (536), Expect = 3e-59
 Identities = 109/258 (42%), Positives = 162/258 (62%), Gaps = 6/258 (2%)

Query: 3   ELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAF 62
           +L+L  + K FG+F  + GV + I  G F   +G SGCGK+T LR+I+GLE  T+G +  
Sbjct: 18  DLRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHL 77

Query: 63  DGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQ 122
             Q V    P RR +  VFQ+YAL+PH+ ++EN+AFG++  G   +  +K VE   ++++
Sbjct: 78  GDQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRG--IRSVKKPVEDMLDLVE 135

Query: 123 LTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRS 182
           L     R P QLSGGQ+QR+A+ RA++  P+V L DEPL  LD  LR   ++E+ ++   
Sbjct: 136 LGHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLE 195

Query: 183 MHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKMNF 242
           +   T ++VTHDQ EAMT+AD I V+  G +EQ+G+P ELYE PN+ FVA F+G  + N 
Sbjct: 196 V-GLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLG--QSNL 252

Query: 243 LSGAFAEPYKADTIGIRA 260
           ++G   E    D + + A
Sbjct: 253 IAGT-VESVSGDVVQVAA 269


Lambda     K      H
   0.321    0.138    0.396 

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: 334
Number of extensions: 20
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: 342
Length of database: 386
Length adjustment: 29
Effective length of query: 313
Effective length of database: 357
Effective search space:   111741
Effective search space used:   111741
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: 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