GapMind for catabolism of small carbon sources

 

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

Align Aromatic amino acid permease, AroP (characterized)
to candidate Pf6N2E2_4195 transport permease protein of gamma-aminobutyrate

Query= TCDB::Q46065
         (463 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4195
          Length = 464

 Score =  360 bits (923), Expect = e-104
 Identities = 190/448 (42%), Positives = 274/448 (61%), Gaps = 5/448 (1%)

Query: 3   KSNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQM 62
           +++  L  GL+ RH+TM+ +   IGAGLF+G+G  I AAGPAVLLAY  AGA+VVLVM+M
Sbjct: 5   QTSNHLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVLVMRM 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 AIWAFTLVITLLLTVTNLFSVKNYGEFEFWFALVKVVAIIGFIGLGVMAIFGVLPTSQVS 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 + D
Sbjct: 302 NSALYTASRMMFSLGKRGDAPAVSQRTNKSGTPYWAVMLSTGAAFLAVFANYVAPAAVFD 361

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

Query: 422 LGDAASRSQVYSVAIVYGFLVLLSFVTV 449
           L   A R ++ +  ++   LV++S V V
Sbjct: 422 LFQEAHRVEILATGLL-SVLVVISGVLV 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: 583
Number of extensions: 31
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.

Links

Downloads

Related tools

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