GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltP in Dechlorosoma suillum PS

Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate Dsui_3158 Dsui_3158 Na+/H+ dicarboxylate symporter

Query= SwissProt::P24943
         (421 letters)



>FitnessBrowser__PS:Dsui_3158
          Length = 448

 Score =  353 bits (907), Expect = e-102
 Identities = 163/403 (40%), Positives = 268/403 (66%), Gaps = 6/403 (1%)

Query: 9   QIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68
           Q+   + LG+ +GA F   P+    ++P+GD F++LIKM++ PI+ +++VVG+A +GD+K
Sbjct: 13  QVLFAIALGVALGAFF---PETGATMKPLGDAFIKLIKMMIAPIIFATVVVGIAKMGDMK 69

Query: 69  KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMKSLEKTDIQSYVDTTNEVQHH 128
           ++G++G K +IYFE+++T+A+ +GL+  NI QPG G+N+      D ++  +      + 
Sbjct: 70  EVGRVGLKALIYFEVVSTVALAIGLIVVNILQPGAGMNVDP-STLDTKAIANYAAAAHNQ 128

Query: 129 SMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFY 188
           S  +  +NI+P ++ ++  KG++L ++ FSV+FGL ++ +G+K KP+++     +  +F 
Sbjct: 129 STTDFLMNIIPNSVVDAFAKGEILQVLLFSVLFGLALSRLGDKAKPLVKILDEFSHGLFG 188

Query: 189 VTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVAKLFGI 248
           V   IM FAP G F  +  T+ K+G+ SL  L  L+  VY T   F+FVVLG +AK  G 
Sbjct: 189 VIGMIMHFAPIGAFGAMAFTIGKYGIGSLKQLGFLMANVYITCALFVFVVLGLIAKFTGF 248

Query: 249 NIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNLDGSTL 308
           ++   +  +K+EL++   T+SSE+ LP++M K+EN GC K +   VIPTGYSFNLDG+++
Sbjct: 249 SLLKFLAYIKEELLIVLGTSSSESALPRMMTKLENLGCHKPVVGMVIPTGYSFNLDGTSI 308

Query: 309 YQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG--IPI 366
           Y  +AAIFIAQ   + + +++Q+++L VL++TSKG A V G  F+ L ATL T+G  +P+
Sbjct: 309 YLTMAAIFIAQALNVPLTLTEQLTILGVLLLTSKGAAAVTGGGFITLAATLATLGGKLPV 368

Query: 367 EGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409
           EGLA + G+DR +  AR   N+IGN +A I++SKWE   N ++
Sbjct: 369 EGLALLLGVDRFMSEARAITNLIGNGVATIVVSKWENALNTDR 411


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: 456
Number of extensions: 25
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: 448
Length adjustment: 32
Effective length of query: 389
Effective length of database: 416
Effective search space:   161824
Effective search space used:   161824
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:

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