GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluC in Luteipulveratus mongoliensis MN07-A0370

Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate WP_052592082.1 VV02_RS13170 amino acid ABC transporter permease

Query= TCDB::P48244
         (228 letters)



>NCBI__GCF_001190945.1:WP_052592082.1
          Length = 226

 Score =  225 bits (573), Expect = 6e-64
 Identities = 112/228 (49%), Positives = 163/228 (71%), Gaps = 2/228 (0%)

Query: 1   MSTLWADLGPSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVR 60
           MS L+++    +  AFW+TIKLT+ +AIG+++ GT++  +R+SPV +LR L T+Y+N  R
Sbjct: 1   MSQLFSEF--EVWSAFWMTIKLTVLAAIGSLVIGTLVAVLRLSPVPMLRFLGTSYVNVFR 58

Query: 61  NTPLTLVVLFCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGI 120
           NTPLTL++L C+  L+  LG+TLA  +   F   NNFRLA++G  +Y +++V E+LRSG+
Sbjct: 59  NTPLTLIILSCNLVLWAKLGVTLADDKDPKFFDINNFRLALVGLTIYHASYVCEALRSGV 118

Query: 121 NTVHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEA 180
           NT+  GQAEAARS+GL F  + R ++ PQA R ++VPLGNTLIALTKNTT+A  IGV E 
Sbjct: 119 NTIPLGQAEAARSIGLTFRQSLREVVLPQAFRGSVVPLGNTLIALTKNTTVAVTIGVAEM 178

Query: 181 SLLMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERLAVKK 228
           + ++    E+    L   F + A  F++LTLP+GL +G+L +RLAVK+
Sbjct: 179 AAVLAKVTEDDPGKLNQAFFVSAALFVLLTLPVGLLIGRLGKRLAVKR 226


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: 196
Number of extensions: 2
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: 228
Length of database: 226
Length adjustment: 22
Effective length of query: 206
Effective length of database: 204
Effective search space:    42024
Effective search space used:    42024
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: 46 (22.3 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