GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Pseudomonas fluorescens FW300-N2E2

Align Aromatic amino acid permease, AroP (characterized)
to candidate Pf6N2E2_1423 Gamma-aminobutyrate permease

Query= TCDB::Q46065
         (463 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1423 Gamma-aminobutyrate
           permease
          Length = 466

 Score =  358 bits (918), Expect = e-103
 Identities = 182/446 (40%), Positives = 274/446 (61%), Gaps = 8/446 (1%)

Query: 4   SNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQML 63
           SN  L  G + RH+TM+ +   IGAGLF+G+G  I AAGPAV+LAY+ +G +VVLVM+ML
Sbjct: 9   SNGHLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVMLAYLFSGLLVVLVMRML 68

Query: 64  GEMAAARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWF-GVE 122
           GEMA A P +GSFS Y + A G WAGF++GWLYW+  ++V+  E   A  ++  WF  ++
Sbjct: 69  GEMAVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPAID 128

Query: 123 PWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVG 182
            W+ + V +V  AV NL +V  +GEFE+WFA  KV  II F+ +G A++ GW+P     G
Sbjct: 129 AWLFASVSIVLLAVTNLFSVSKYGEFEFWFAMAKVVAIIGFISLGFAVLMGWIPEREASG 188

Query: 183 TSNFIGDH-GFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWR 241
            S  + +H GF PNG+S V    + + F+F G E VTIAAAESD P + I+ A R+VIWR
Sbjct: 189 LSRLMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPAQNIAKATRSVIWR 248

Query: 242 ISVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAF 301
           I VFYL S+ V+  ++P+   N    A+   + + L + NIP     ++ ++++A+ S  
Sbjct: 249 IGVFYLLSIFVVISVVPW---NDPLLASVGSYQRALELMNIPHAKFLVDMVVLIAVASCM 305

Query: 302 NAQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLD 361
           N+ IY  SR+++S+  R DAP+     S++ VP +AV+ S           Y+ PAGL  
Sbjct: 306 NSSIYIASRMLYSLGRRGDAPKALKVTSSAGVPRSAVIASTVLGAGVTLFSYFMPAGLFQ 365

Query: 362 FLLNAVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALM 421
           FLL + G   ++V+ +I +SQL++R+ LQ  +     RMW  PWL  L +V ++  +A+M
Sbjct: 366 FLLASSGAIALLVYLVIAISQLRMRRMLQRQNIELPFRMWLFPWLTWLVIVFISAALAVM 425

Query: 422 LGDAASRSQVYSVAIVYGFLVLLSFV 447
           +     RS+   V+   G  +++SF+
Sbjct: 426 MVTPEHRSE---VSTTLGLALVISFI 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: 581
Number of extensions: 33
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: 463
Length of database: 466
Length adjustment: 33
Effective length of query: 430
Effective length of database: 433
Effective search space:   186190
Effective search space used:   186190
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 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