GapMind for catabolism of small carbon sources

 

Aligments for a candidate for citA in Dyella japonica UNC79MFTsu3.2

Align citrate transporter (characterized)
to candidate N515DRAFT_3073 N515DRAFT_3073 Arabinose efflux permease

Query= CharProtDB::CH_014606
         (431 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3073 N515DRAFT_3073
           Arabinose efflux permease
          Length = 551

 Score =  186 bits (472), Expect = 2e-51
 Identities = 106/318 (33%), Positives = 168/318 (52%), Gaps = 11/318 (3%)

Query: 14  ILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLMRPIGAVVL 73
           IL  + G   E +DF+L+G  A  I K FF   +E +A +     F +GF +RP GA+V 
Sbjct: 19  ILASSLGTVFEWYDFYLYGSLAVLIGKHFFSGLNETSAFIFALLAFAAGFAVRPFGAIVF 78

Query: 74  GAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQGFSAGVELG 133
           G   D +GR+   +IT+ IMG  T L+ ++P Y T+G++APVL++V RLLQG + G E G
Sbjct: 79  GRLGDLVGRKYTFLITIIIMGLSTFLVGVLPSYSTVGMIAPVLLIVLRLLQGLALGGEYG 138

Query: 134 GVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDEISEWGWRIPFFI 193
           G + Y++E A  G +G YTS+   +    + ++ L+  G  + LG     +WGWRIPF I
Sbjct: 139 GAATYVAEHAPDGKRGLYTSFIQITATFGLFLSLLVILGTRMALGDKVFEDWGWRIPFLI 198

Query: 194 GCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIA----KNWRII----TAGTLLVA 245
             +++ +   +R  LQE+  F Q K      +   T A    KN +++       T   A
Sbjct: 199 SSVLVAVSVYIRLQLQESPVFQQMKAEGKHSKAPLTEAFGHWKNLKVVILALLGATAGQA 258

Query: 246 MTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRRPVLM 305
           +   T  F  +Y  T    +   +A   +   +++G   F++    G +SDRIGR+ +++
Sbjct: 259 VVWYTGQFYALYFLTQSLKIDGTTANLLIAAALIIGTPFFVFF---GWLSDRIGRKSIVL 315

Query: 306 GITLLALVTTLPVMNWLT 323
              LLA +T  P+   LT
Sbjct: 316 AGCLLAALTYFPIFKGLT 333



 Score = 37.4 bits (85), Expect = 1e-06
 Identities = 21/77 (27%), Positives = 33/77 (42%)

Query: 331 MTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTVGFSLAFSLATAIFGGLTPAISTALVQ 390
           + ++L     +  M  G + A L E+ P  +R    SL + +    FGG  P I   LV 
Sbjct: 455 LVILLAILVLYVTMVYGPIAAWLVEMFPTRIRYTSMSLPYHIGNGWFGGFVPTIGFMLVA 514

Query: 391 LTGDKSSPGWWLMCAAL 407
             GD     W+ +  A+
Sbjct: 515 WKGDIYYGLWYPIIVAV 531


Lambda     K      H
   0.328    0.141    0.432 

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: 629
Number of extensions: 34
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 431
Length of database: 551
Length adjustment: 34
Effective length of query: 397
Effective length of database: 517
Effective search space:   205249
Effective search space used:   205249
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 (21.8 bits)
S2: 52 (24.6 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 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