GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltP in Pseudomonas fluorescens FW300-N2E3

Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate AO353_02800 AO353_02800 C4-dicarboxylate transporter

Query= CharProtDB::CH_088342
         (421 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_02800 AO353_02800
           C4-dicarboxylate transporter
          Length = 444

 Score =  344 bits (883), Expect = 3e-99
 Identities = 170/413 (41%), Positives = 272/413 (65%), Gaps = 9/413 (2%)

Query: 6   LAWQIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65
           L +Q+ I + +GI +G  +   P+ A  L+P+GD F++LIKM++ PI+  ++V G+A + 
Sbjct: 11  LYFQVIIAIAIGIALGHYY---PQTAVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQ 67

Query: 66  DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAG--VNMKSLEKTDIQSYVDTTN 123
           ++K +GK GG  ++YFEI++TIA++VGL+  NI QPG G  +++ +L+ + + +YV    
Sbjct: 68  NMKSVGKTGGYALLYFEIVSTIALLVGLVVVNIVQPGNGMHIDVSTLDASKVAAYVAAGA 127

Query: 124 EVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183
           +    S+V   +NI+P  I  + + GD+L ++ FSV+FG  +  +G  GKP+L F    A
Sbjct: 128 D---QSVVGFLLNIIPATIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPILDFIDRFA 184

Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVA 243
             MF + N IMK AP G    +  T+  +GV SL+ L +L+   Y T + FI  VLGG+A
Sbjct: 185 HVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMACFYITCVVFILVVLGGIA 244

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

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

Query: 364 -IPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGKQYLA 415
            +PV GLA I GIDR +  AR   N++GN++A ++++KW  + + ++  + LA
Sbjct: 365 HLPVAGLALILGIDRFMSEARALTNLVGNAVATLVVAKWVKELDVDQMHEELA 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: 373
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: 444
Length adjustment: 32
Effective length of query: 389
Effective length of database: 412
Effective search space:   160268
Effective search space used:   160268
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.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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