GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS10595
          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:

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