GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Pseudomonas fluorescens FW300-N1B4

Align Aromatic amino acid permease, AroP (characterized)
to candidate Pf1N1B4_5139 Gamma-aminobutyrate permease

Query= TCDB::Q46065
         (463 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5139
          Length = 501

 Score =  350 bits (897), Expect = e-101
 Identities = 182/459 (39%), Positives = 273/459 (59%), Gaps = 8/459 (1%)

Query: 4   SNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQML 63
           SN  L  G + RH+TM+ +   IGAGLF+G+G  I AAGPAVLLAY+ +G +VVLVM+ML
Sbjct: 42  SNGQLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVLLAYLFSGLLVVLVMRML 101

Query: 64  GEMAAARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWF-GVE 122
           GEMA A P +GSFS Y + A G WAGF++GWLYW+  ++V+  E   A  ++  WF  ++
Sbjct: 102 GEMAVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPQID 161

Query: 123 PWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVG 182
            W+ +L  ++   V NL +V  +GEFE+WFA  KV  II F+ +G A++ GW+P     G
Sbjct: 162 TWLFALTSIILLVVTNLFSVSKYGEFEFWFAMAKVVAIIGFIGLGFAVLMGWIPEREASG 221

Query: 183 TSNFIGDH-GFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWR 241
            S  + +H GF PNG+S V    + + F+F G E VTIAAAES  P + I+ A R+VIWR
Sbjct: 222 LSRLMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESSNPAQNIAKATRSVIWR 281

Query: 242 ISVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAF 301
           I VFYL S+ V+  ++P+   N    A+   + + L + NIP     ++ ++++A+ S  
Sbjct: 282 IGVFYLLSIFVVISVVPW---NDPLLASVGSYQRALELMNIPHAKLMVDVVVLIAVASCM 338

Query: 302 NAQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLD 361
           N+ IY  SR++FS+  R DAP+     S+  VP  AV+ S           Y+ PAGL  
Sbjct: 339 NSSIYIASRMLFSLGKRGDAPKPLKVTSSDGVPRAAVIASTVLGAGVTLFSYFMPAGLFQ 398

Query: 362 FLLNAVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALM 421
           FLL + G   ++V+ +I +SQL++RK L   +   T +MW  PWL  L +  +   +A+M
Sbjct: 399 FLLASSGAIALLVYLVIAVSQLRMRKILLRQNVTLTFKMWLFPWLTWLVIAFICAALAVM 458

Query: 422 LGDAASRSQVYSVAIVYGFLVLLSFVTVNSPLRGGRTPS 460
           +     R +V S     G  +++SF+ + +  + G+  S
Sbjct: 459 MVTPEHRMEVSS---TIGLALVISFIGLVTARQHGQPRS 494


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: 613
Number of extensions: 37
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: 501
Length adjustment: 34
Effective length of query: 429
Effective length of database: 467
Effective search space:   200343
Effective search space used:   200343
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: 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:

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