GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1A in Lactobacillus silagei IWT126

Align major cell-binding factor (characterized)
to candidate WP_054653754.1 CES79_RS00810 transporter substrate-binding domain-containing protein

Query= CharProtDB::CH_021449
         (259 letters)



>NCBI__GCF_002217945.1:WP_054653754.1
          Length = 277

 Score =  114 bits (285), Expect = 2e-30
 Identities = 74/229 (32%), Positives = 112/229 (48%), Gaps = 10/229 (4%)

Query: 35  KSKGQLIVGVKNDVPHYALLDQATGEIKGFEVDVAKLLAKSILGDDKKIKLVAVNAKTRG 94
           K    +  GVK D   + L+D    +IKGFEVD+AK L K ILG   K   V V + TR 
Sbjct: 39  KQSNTITWGVKADTKLFGLMDVKNSQIKGFEVDMAKALTKQILGPKGKADFVQVTSSTRM 98

Query: 95  PLLDNGSVDAVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEKKYKSLADM--KGANIG 152
           PLL NG++DA++AT TITPER +  +FS  Y+     LLV      K++ D+   GA + 
Sbjct: 99  PLLKNGNIDAIMATMTITPERLKQVDFSRSYFDAGQSLLVKNGSPIKNVKDLNKNGATVL 158

Query: 153 VAQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVDKSILLGYVDDKS 212
               + + + + + A K     K  +  DY     AL + + +A + D  IL G   +  
Sbjct: 159 GVVGSNSVQNVAKFAPK----AKVLQLSDYAQAMTALKSGQGEALTTDNGILAGMSVENP 214

Query: 213 --EILPDSFEPQSYGIVTKKDDPAFAKYVDDFVK--EHKNEIDALAKKW 257
              +   +F  + YGI   K+ P F   ++  +   E   + + + KKW
Sbjct: 215 GYHLAGGAFTKEPYGIAINKNQPEFKHDLNHALTKVEQSGQYNRILKKW 263


Lambda     K      H
   0.316    0.135    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: 161
Number of extensions: 12
Number of successful extensions: 1
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: 259
Length of database: 277
Length adjustment: 25
Effective length of query: 234
Effective length of database: 252
Effective search space:    58968
Effective search space used:    58968
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 (21.6 bits)
S2: 47 (22.7 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