GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Cupriavidus basilensis 4G11

Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate RR42_RS16450 RR42_RS16450 hypothetical protein

Query= SwissProt::P0AER5
         (224 letters)



>FitnessBrowser__Cup4G11:RR42_RS16450
          Length = 211

 Score =  113 bits (283), Expect = 2e-30
 Identities = 72/211 (34%), Positives = 120/211 (56%), Gaps = 8/211 (3%)

Query: 5   DWSSIVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFR 64
           D+  ++P LP LL   ++T+ + V   V G ++G +LA+ R S  A +   A  Y+ +FR
Sbjct: 4   DFVQVLPYLPILLKAALLTILLAVVTQVCGTVFGLLLALGRDSRHAVLRGAAFIYIWIFR 63

Query: 65  SIPLVMVLLWFYLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSIS 124
             P+++ L + Y   P F     GL  +    L +A++A SM  AAY +EIIRAGI+++ 
Sbjct: 64  GTPVLLHLFFVYYAAPMF-----GLRLE---ALPAAIIALSMSSAAYNAEIIRAGIRAVH 115

Query: 125 RGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTA 184
           RGQ  AA A+GMT+ + ++ +ILPQA R ++P  +   I   + TSL  V+++ +   +A
Sbjct: 116 RGQREAAQAVGMTNPRILRHVILPQATRIVLPPYMGNFISHTKSTSLASVITVPELMLSA 175

Query: 185 STIGERDGTQVEMILFAGFVYFVISLSASLL 215
            TI       VE++  AG +Y  ++   +L+
Sbjct: 176 QTIYSSTYRAVEVLTIAGAIYLALTTVLTLV 206


Lambda     K      H
   0.330    0.140    0.412 

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: 103
Number of extensions: 5
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: 224
Length of database: 211
Length adjustment: 22
Effective length of query: 202
Effective length of database: 189
Effective search space:    38178
Effective search space used:    38178
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 (21.9 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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