GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluC in Mesorhizobium ciceri WSM1271

Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate YP_004139338.1 Mesci_0115 polar amino acid ABC transporter inner membrane subunit

Query= TCDB::P48244
         (228 letters)



>NCBI__GCF_000185905.1:YP_004139338.1
          Length = 224

 Score = 85.1 bits (209), Expect = 1e-21
 Identities = 69/221 (31%), Positives = 113/221 (51%), Gaps = 18/221 (8%)

Query: 10  PSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVL 69
           P+LL  F  T+ L I S    +  G  ++ +R+   K LR L+  Y +  R  P+ +V++
Sbjct: 18  PALLRGFLNTLLLGILSIGIGIPIGLGISLVRLYAPKPLRWLAVGYTDIFRALPVLVVLI 77

Query: 70  FCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVHFGQAE 129
              + L   LG+ L+   S           AV  F    S + AE  RSGI ++  GQ E
Sbjct: 78  LIYYAL-PFLGIRLSSWAS-----------AVTAFAFIMSAYSAEVFRSGIESIPRGQFE 125

Query: 130 AARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASLLMKATIE 189
           A+++LGL F  T R ++ PQA+R  I P+ +  +++ K+T++AS + + E  LL +AT  
Sbjct: 126 ASQALGLPFLLTLRKVVLPQAIRVVIPPMTSNCVSMFKDTSLASTVALPE--LLKEATNA 183

Query: 190 N--HANMLFVVFAIFAVGFMILTLPMGLGLGKLSERLAVKK 228
              +AN   ++ A  A+ ++I   PM   +  L ER   +K
Sbjct: 184 QSLYANPSPLIGA--ALVYLIFLWPMVRLVSLLEERFKTEK 222


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: 141
Number of extensions: 8
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: 224
Length adjustment: 22
Effective length of query: 206
Effective length of database: 202
Effective search space:    41612
Effective search space used:    41612
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