GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltP in Pedobacter sp. GW460-11-11-14-LB5

Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate CA265_RS10595 CA265_RS10595 dicarboxylate/amino acid:cation symporter

Query= CharProtDB::CH_088342
         (421 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS10595 CA265_RS10595
           dicarboxylate/amino acid:cation symporter
          Length = 458

 Score =  309 bits (791), Expect = 1e-88
 Identities = 163/386 (42%), Positives = 245/386 (63%), Gaps = 19/386 (4%)

Query: 29  KVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLKKLGKLGGKTIIYFEIITTIA 88
           K   Y   + DIFLRLIKMIV P+V ++LVVGVA VGD+K +G++GGKT+ +F  ++ ++
Sbjct: 84  KKLEYFTLLSDIFLRLIKMIVAPLVFTTLVVGVAKVGDIKAVGRIGGKTLGWFLAMSLMS 143

Query: 89  IVVGLLAANIFQPGAGVNMKSLEKTDIQSYVDTTNEVQHHSMVETFVNIVPKNIFESLST 148
           +V+G++  N+F+PG  + +   ++      V+T  +    S+ +   ++ PK+I ES+ST
Sbjct: 144 LVLGMVLVNLFEPGRHMKLSLPDQL-----VNTGIQKAAMSVKDFIAHVFPKSIAESMST 198

Query: 149 GDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAMFYVTNQIMKFAPFGVFALIGVT 208
            ++L I+ FS+ FG+  AAIG+ G+ V++ F   A  +  +T  +M FAP  VF  +   
Sbjct: 199 NEILQIVVFSLFFGVATAAIGDLGQIVIKAFDAIAHVILKMTGYVMNFAPLAVFGAMTAI 258

Query: 209 VSKFGVESLIPLSKLV-------IVVYATMLFFIFAVLGGVAKLFGINIFHIIKILKDEL 261
           V+K G+  L   +  +        +++A ++F  F VL          IF ++  +K+  
Sbjct: 259 VAKQGLNVLNTYAIFIGEFYLGLAILWAVLIFLGFLVLKK-------RIFRLVNDMKEPA 311

Query: 262 ILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDGSTLYQALAAIFIAQLY 321
           +LA+STASSE   P+ M  +E+FGC   I SFV+P GYSFNLDGS +Y   A++FIAQ Y
Sbjct: 312 LLAFSTASSEAAYPKTMMLLERFGCKDKIVSFVLPLGYSFNLDGSMMYMTFASLFIAQAY 371

Query: 322 GIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVGIPVEGLAFIAGIDRILDM 381
           GI +   QQIS+LL+LM+TSKGIAGVP  S VV+  T+ +  IP  GLA + GID +LDM
Sbjct: 372 GIHLGFEQQISMLLILMLTSKGIAGVPRASLVVIAGTIASFNIPEAGLALLIGIDPLLDM 431

Query: 382 ARTAVNVIGNSLAAIIMSKWEGQYNE 407
            R+A NV+GNS+A  ++SKWEG+  E
Sbjct: 432 GRSATNVVGNSIATAVVSKWEGELKE 457


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: 427
Number of extensions: 22
Number of successful extensions: 4
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: 458
Length adjustment: 32
Effective length of query: 389
Effective length of database: 426
Effective search space:   165714
Effective search space used:   165714
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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