GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Pseudomonas fluorescens FW300-N1B4

Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate Pf1N1B4_4805 ABC transporter permease protein

Query= SwissProt::P0AER5
         (224 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4805
          Length = 292

 Score =  108 bits (270), Expect = 1e-28
 Identities = 71/229 (31%), Positives = 127/229 (55%), Gaps = 7/229 (3%)

Query: 3   EFDWSSIVPSLPY--LLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYV 60
           + +WS I   L    ++ GL+ T+ + V A+ +GI++G + A+MR+S+   + + A  Y 
Sbjct: 57  KIEWSYIGQFLTSQAIMWGLLNTIVMAVLAMALGIVFGVITAIMRMSANPILRYVALTYT 116

Query: 61  NVFRSIPLVM-VLLWFYLIVPGFLQNVLGLSPKNDIRLIS----AMVAFSMFEAAYYSEI 115
            +FR  PL++ +LLWF L +      + GL   + + L++    A++  S+ + AY +E+
Sbjct: 117 WLFRGTPLILQLLLWFNLALIFPTIGIPGLFEMDTVSLMTPFAAALLGLSINQGAYTAEV 176

Query: 116 IRAGIQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVL 175
           +RAG+ S+  GQ  AA ++GM   Q+++ IILPQA R ++P +  + I + + TSL  V+
Sbjct: 177 VRAGLLSVDTGQYEAAKSIGMPRLQALRRIILPQAMRIIIPPVGNEFIGMVKMTSLASVI 236

Query: 176 SLADFFRTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRRTA 224
             ++    A  I   +   +E+++ AG  Y       S   S L+RR A
Sbjct: 237 QYSELLYNAQNIYYANARVMELLIVAGIWYLATVTVLSFGQSRLERRFA 285


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: 169
Number of extensions: 12
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: 224
Length of database: 292
Length adjustment: 24
Effective length of query: 200
Effective length of database: 268
Effective search space:    53600
Effective search space used:    53600
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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