GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluC in Desulfoscipio geothermicus DSM 3669

Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease

Query= TCDB::P48244
         (228 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  107 bits (267), Expect = 2e-28
 Identities = 71/208 (34%), Positives = 108/208 (51%), Gaps = 23/208 (11%)

Query: 18  VTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVLFCSFGLYQ 77
           +T+++TI S     + G I    R+S  K+LR L+TAY++  R TPL + +    FG+ +
Sbjct: 18  ITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFIVYFGIPK 77

Query: 78  NLGLTLAGRESSTFLVDN-------------NFRLAVLGFILYTSTFVAESLRSGINTVH 124
            L       +  +F+VD+              F  AV+   L +  +VAE  R+G+ ++ 
Sbjct: 78  LL------MDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSIE 131

Query: 125 FGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGE----A 180
            GQ EAARSLG+  G   R +I PQA +  I PLGN  IA+ K+T++ SVIG  E     
Sbjct: 132 RGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTRNG 191

Query: 181 SLLMKATIENHANMLFVVFAIFAVGFMI 208
            L++  T E+ A  L V F    + F +
Sbjct: 192 QLIIARTYESFAIWLTVGFIYLIMTFTL 219


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: 143
Number of extensions: 10
Number of successful extensions: 2
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: 234
Length adjustment: 23
Effective length of query: 205
Effective length of database: 211
Effective search space:    43255
Effective search space used:    43255
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 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