GapMind for catabolism of small carbon sources

 

Alignments for a candidate for permease in Pseudomonas fluorescens FW300-N2E3

Align Aromatic amino acid permease, AroP (characterized)
to candidate AO353_12005 AO353_12005 GABA permease

Query= TCDB::Q46065
         (463 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_12005
          Length = 463

 Score =  363 bits (933), Expect = e-105
 Identities = 185/436 (42%), Positives = 269/436 (61%), Gaps = 4/436 (0%)

Query: 3   KSNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQM 62
           +S+ GL  GL+ RH+TM+ +   IGAGLF+G+G  I AAGPAVLLAY  AG +VVLVM+M
Sbjct: 5   QSSNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGMLVVLVMRM 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  +L+  +   V NL +V+ +GEFE+WFA IKV  II F+++G+  IFG+LPGS   
Sbjct: 125 AIWAFTLIITLLLTVTNLFSVKNYGEFEFWFALIKVLAIIGFIVLGVMAIFGFLPGSQVS 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---NDPVLASVGSYQTVLERMGIPNAKLIVDLVVLVAVTSCL 301

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

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

Query: 422 LGDAASRSQVYSVAIV 437
           L   A R ++ +  ++
Sbjct: 422 LFQDAHRVEILATGLL 437


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: 27
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: 463
Length adjustment: 33
Effective length of query: 430
Effective length of database: 430
Effective search space:   184900
Effective search space used:   184900
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:

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