GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluC in Rhizorhabdus wittichii RW1

Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit

Query= TCDB::P48244
         (228 letters)



>NCBI__GCF_000016765.1:WP_012048835.1
          Length = 374

 Score = 76.3 bits (186), Expect = 8e-19
 Identities = 64/222 (28%), Positives = 104/222 (46%), Gaps = 14/222 (6%)

Query: 13  LPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPL-TLVVLFC 71
           LP  ++T +    + +G  I GT L  +      +  TL TA+   +    L TL  +  
Sbjct: 152 LPGLFLTNRGITVTTVG--ITGTALPMIVTVLGGLTLTLITAWRGHLHKASLCTLGTIVA 209

Query: 72  SFGLYQNLGLTLAGRESSTF---------LVDNNFRLAVLGFILYTSTFVAESLRSGINT 122
              L+  L L LA R+   F          +   F   + G ++Y S F AE +R G++ 
Sbjct: 210 GSALWIVLDLGLA-RDVPHFDRFNFTGGLTLTPEFVAVLWGSVIYASAFAAEIVRGGLDG 268

Query: 123 VHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASL 182
           V  GQ EA+R+LGL    + R +I PQA+R  + P+ +  I + KN+T+A V+G  + + 
Sbjct: 269 VPRGQWEASRALGLSKRQSLRLVIVPQALRMIVPPMNSQFITILKNSTLALVVGYPDLNF 328

Query: 183 LMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERL 224
           +    I NH        AI  + F  L   + L + +L+ R+
Sbjct: 329 VANTAI-NHTGQGLEGVAILMLVFFTLASAISLAMNRLNARV 369



 Score = 30.8 bits (68), Expect = 4e-05
 Identities = 16/52 (30%), Positives = 29/52 (55%)

Query: 19  TIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVLF 70
           +I LT+   + + + G  +   R S   + RTL+  +++ VRN PL + +LF
Sbjct: 82  SIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLVVQLLF 133


Lambda     K      H
   0.327    0.139    0.397 

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: 210
Number of extensions: 7
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 228
Length of database: 374
Length adjustment: 26
Effective length of query: 202
Effective length of database: 348
Effective search space:    70296
Effective search space used:    70296
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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