GapMind for catabolism of small carbon sources

 

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

Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate Pf1N1B4_4413 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate

Query= SwissProt::P24943
         (421 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4413
          Length = 451

 Score =  320 bits (820), Expect = 6e-92
 Identities = 153/402 (38%), Positives = 250/402 (62%), Gaps = 5/402 (1%)

Query: 9   QIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68
           Q+ I +ILG IVG      P+  T L+P+GD F++LIKM++ P++  ++V G+A + ++K
Sbjct: 11  QVLIAVILGAIVGVFV---PETGTALKPLGDAFIKLIKMLLAPVIFLTVVTGIARMENMK 67

Query: 69  KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMKSLEKTDIQSYVDTTNEVQHH 128
           +LG++G + +IYFE+++T+A+VVGL+  ++F+PG G+N+  +   D  S    T  V+H 
Sbjct: 68  ELGRVGFRALIYFEVVSTLALVVGLVVVDVFKPGAGMNI-DVASLDTSSLATYTTAVKHA 126

Query: 129 SMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFY 188
           S ++  +NI+P  I ++  KG++L I+ FS++ G+ +A +G + K  +       + MF 
Sbjct: 127 SFMDFVMNIIPDTIVDAFAKGNVLQILLFSILLGVALAHVGPRAKVFVDTLDSLMQGMFR 186

Query: 189 VTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVAKLFGI 248
           + N +M+ AP G F  I  T+ K+G  SL  L KL+  VY T   F+  VLG + +  G 
Sbjct: 187 IVNMVMRLAPIGAFGAIAFTIGKYGFGSLFSLGKLMACVYLTCAVFVIFVLGPICRYSGF 246

Query: 249 NIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNLDGSTL 308
           +++  +K +K+EL     T+SSE+VLP+++ KME  G  K +   +IP+G +FN DG  +
Sbjct: 247 SLWKFLKFIKEELFTVLGTSSSESVLPQMISKMEKAGVSKPVAGMIIPSGLTFNPDGQAI 306

Query: 309 YQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG-IPIE 367
           Y  +AAIFIAQ     + ++ Q+ +L VLM TSKG AGV G  F++L ATL ++G IP+ 
Sbjct: 307 YYTIAAIFIAQATNTPLTLTDQLIVLAVLMFTSKGSAGVTGSGFIILAATLSSLGTIPVA 366

Query: 368 GLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409
           G+  + G+DR +  AR   N IGN +  + ++KW G  +  K
Sbjct: 367 GMVLLLGVDRFMSEARAITNTIGNGVGTMAIAKWVGALDTVK 408


Lambda     K      H
   0.326    0.143    0.404 

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: 410
Number of extensions: 23
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: 451
Length adjustment: 32
Effective length of query: 389
Effective length of database: 419
Effective search space:   162991
Effective search space used:   162991
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