GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Pseudomonas fluorescens FW300-N2C3

Align Aromatic amino acid permease, AroP (characterized)
to candidate AO356_11625 AO356_11625 GABA permease

Query= TCDB::Q46065
         (463 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11625 AO356_11625 GABA
           permease
          Length = 464

 Score =  361 bits (927), Expect = e-104
 Identities = 188/448 (41%), Positives = 276/448 (61%), Gaps = 5/448 (1%)

Query: 3   KSNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQM 62
           ++++ L  GL+ RH+TM+ +   IGAGLF+G+G  I AAGPAVLLAY  AGA+VVLVM+M
Sbjct: 5   QTSDNLAQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVLVMRM 64

Query: 63  LGEMAAARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWF-GV 121
           LGEMA A P +GSFS Y + A GHWAGF++GWLYW+  ++V+  E   AA I+ AWF  V
Sbjct: 65  LGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPNV 124

Query: 122 EPWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFV 181
             W+ +LV  +   V NL +V+ +GEFE+WFA +KV  II F+ +G+  IFG LP S   
Sbjct: 125 AIWVFTLVITLLLTVTNLFSVKNYGEFEFWFALVKVVAIIGFIGLGLMAIFGVLPTSQVS 184

Query: 182 GTSNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWR 241
           G S+     GF+PNG+  V   +L   F+F G EIVTIAAAES  P + IS A  +VIWR
Sbjct: 185 GVSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWR 244

Query: 242 ISVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAF 301
           I +FYL S+ ++  L+P+   N    A+   +  +L    IP     ++ ++++A+ S  
Sbjct: 245 IGLFYLVSIFIVVALVPW---NDPLLASVGSYQTVLERMGIPNAKLIVDIVVLVAVTSCL 301

Query: 302 NAQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLD 361
           N+ +Y  SR++FS+  R DAP V  + + S  P  AV+LS   AF++V   Y  PA + +
Sbjct: 302 NSALYTASRMMFSLGKRGDAPAVSQRTNKSGTPHWAVMLSTGAAFLAVFANYVAPAAVFE 361

Query: 362 FLLNAVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALM 421
           FLL + G   ++V+ +I +SQL++RK+  A  E     MW  P L    +V + G + +M
Sbjct: 362 FLLASSGAIALLVYLVIAVSQLRMRKQRMARGEKIAFSMWLFPGLTYAVIVFIVGALTIM 421

Query: 422 LGDAASRSQVYSVAIVYGFLVLLSFVTV 449
           L   A R ++ +  ++   LV++S V +
Sbjct: 422 LFQEAHRVEILATGLL-SVLVVISGVLI 448


Lambda     K      H
   0.327    0.140    0.428 

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: 585
Number of extensions: 32
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: 463
Length of database: 464
Length adjustment: 33
Effective length of query: 430
Effective length of database: 431
Effective search space:   185330
Effective search space used:   185330
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 (21.7 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 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