GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltP in Pseudomonas fluorescens FW300-N2E2

Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate Pf6N2E2_5707 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate

Query= CharProtDB::CH_088342
         (421 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5707
          Length = 450

 Score =  345 bits (886), Expect = 1e-99
 Identities = 165/413 (39%), Positives = 272/413 (65%), Gaps = 9/413 (2%)

Query: 6   LAWQIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65
           L +Q+ + + +GI++G  +   P+    L+P GD F++LIKM++ PI+  ++V G+  + 
Sbjct: 11  LYFQVIVAIAIGILLGHFY---PQTGVALKPFGDGFIKLIKMVIAPIIFCTVVSGIGGMQ 67

Query: 66  DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAG--VNMKSLEKTDIQSYVDTTN 123
           ++K +GK GG  ++YFEI++TIA+++GL+  NI QPG G  +++ +L+ + I  +++ + 
Sbjct: 68  NMKSVGKTGGYALLYFEIVSTIALLIGLVVVNIVQPGVGMHIDVSTLDTSKIAGFINASK 127

Query: 124 EVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183
           +    S++   +N++P  I  + + GD+L ++ FSV+FG  +  +G  GKPVL F    A
Sbjct: 128 D---QSIIAFILNVIPNTIVGAFANGDILQVLMFSVLFGFALHRLGAYGKPVLDFIDRFA 184

Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVA 243
             MF + N IMK AP G F  +  T+  +GV SL+ L +L+I  Y T + F+  VLG + 
Sbjct: 185 HVMFIIINMIMKLAPIGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCVVFVLVVLGAIC 244

Query: 244 KLFGINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNL 303
           +  G ++  +I+ +++EL++   T+SSE+ LPR++ KME+ G  K++   VIPTGYSFNL
Sbjct: 245 RAHGFSVVKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNL 304

Query: 304 DGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG 363
           DG+++Y  +AA+FIAQ     M ++ QI+LLLVL+++SKG AGV G  F+VL ATL  VG
Sbjct: 305 DGTSIYLTMAAVFIAQATDTPMDLTHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVG 364

Query: 364 -IPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGKQYLA 415
            +PV GLA I GIDR +  AR   N++GN++A I+++KW  + +E++ +  LA
Sbjct: 365 TLPVAGLALILGIDRFMSEARALTNLVGNAVATIVVAKWVKELDEDQLQTELA 417


Lambda     K      H
   0.326    0.143    0.402 

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: 378
Number of extensions: 14
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: 421
Length of database: 450
Length adjustment: 32
Effective length of query: 389
Effective length of database: 418
Effective search space:   162602
Effective search space used:   162602
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 (21.6 bits)
S2: 51 (24.3 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