GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluC in Pseudomonas fluorescens FW300-N2E3

Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate AO353_08870 AO353_08870 amino acid ABC transporter permease

Query= TCDB::P48244
         (228 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_08870
          Length = 216

 Score = 98.2 bits (243), Expect = 1e-25
 Identities = 71/226 (31%), Positives = 112/226 (49%), Gaps = 22/226 (9%)

Query: 3   TLWADLGPSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNT 62
           T W D+  +LL     T+ L++ + IG  + G ++ T+R+S   + R  +  YI   + T
Sbjct: 5   TFW-DIVRNLLTGLQWTLALSLVAFIGGGLIGLLIMTLRISKNALPRGFARTYIELFQGT 63

Query: 63  PLTLVVLFCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINT 122
           PL L+ LF  F      G+ L G E S +L       A +   L+TS ++AE  R  +++
Sbjct: 64  PL-LMQLFLVF-----FGVALLGIEISPWLA------AAIALTLFTSAYLAEIWRGCVDS 111

Query: 123 VHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGE--- 179
           +  GQ EA+ SL L      R +I PQA+R A+ P     + + K T + S+IG  E   
Sbjct: 112 IANGQWEASASLALNPFEQLRHVILPQALRIAVAPTVGFSVQVVKGTAVTSIIGFTELTK 171

Query: 180 -ASLLMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERL 224
              +L  AT E      F+V+ + A+G+ +L  P+ L    L  RL
Sbjct: 172 TGGMLANATFEP-----FMVYGLVALGYFLLCYPLSLSARYLERRL 212


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: 133
Number of extensions: 10
Number of successful extensions: 3
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: 216
Length adjustment: 22
Effective length of query: 206
Effective length of database: 194
Effective search space:    39964
Effective search space used:    39964
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: 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