GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluC in Kocuria turfanensis HO-9042

Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate WP_047803717.1 AYX06_RS05075 amino acid ABC transporter permease

Query= TCDB::P48244
         (228 letters)



>NCBI__GCF_001580365.1:WP_047803717.1
          Length = 228

 Score =  206 bits (523), Expect = 4e-58
 Identities = 103/217 (47%), Positives = 148/217 (68%), Gaps = 5/217 (2%)

Query: 12  LLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVLFC 71
           +L AFWV ++LT ++AIG+ + G ++  MR+SP+  LR L T Y+N  RNTPLT++++F 
Sbjct: 17  VLAAFWVNLRLTFWAAIGSAVLGGLIALMRISPIASLRLLGTGYVNLFRNTPLTIILVFL 76

Query: 72  SFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVHFGQAEAA 131
             G++  LG+ L+G  +  F     F  AV+G  LY + FV E++RSG+NTV  GQAEAA
Sbjct: 77  VLGVWSQLGINLSGDFNQNF-----FNWAVIGLSLYHAAFVCEAIRSGVNTVPVGQAEAA 131

Query: 132 RSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASLLMKATIENH 191
           R++GL F    R IIFPQA+R A+ PLGNTLIALTKNTT+A+   V E S LMK  IE  
Sbjct: 132 RAIGLSFLPAARLIIFPQALRGAVTPLGNTLIALTKNTTVAAAASVTEISSLMKTMIEFR 191

Query: 192 ANMLFVVFAIFAVGFMILTLPMGLGLGKLSERLAVKK 228
            +++  +F + A+GF+++ +P+GL     S +LAVK+
Sbjct: 192 PDVIIAIFLVVALGFVLIVVPVGLLTTWASRKLAVKR 228


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: 200
Number of extensions: 14
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: 228
Length adjustment: 23
Effective length of query: 205
Effective length of database: 205
Effective search space:    42025
Effective search space used:    42025
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