GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ansP in Pseudomonas putida KT2440

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate PP_1059 PP_1059 Uncharacterized amino acid permease YtnA

Query= TCDB::P40812
         (497 letters)



>FitnessBrowser__Putida:PP_1059
          Length = 472

 Score =  357 bits (917), Expect = e-103
 Identities = 172/415 (41%), Positives = 269/415 (64%), Gaps = 2/415 (0%)

Query: 28  KAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLH 87
           + +G R ++++A+G  IG GLFLG+   ++MAGPA+ L Y+I G+    I+RALGE+ +H
Sbjct: 20  RELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMAVH 79

Query: 88  RPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVF 147
            P +GSF  YA+++LG  A ++ GW Y+  W +T + +ITAVA+YM  W  F DVP+W++
Sbjct: 80  NPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAIYMGIW--FPDVPRWIW 137

Query: 148 ALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLEGNATGFHL 207
           AL AL  +G +N++ VK F E EFWFALIK++ I+  ++ G   +  G   +G A G   
Sbjct: 138 ALAALGSMGAVNLVAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGNDGVAVGISN 197

Query: 208 ITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIGLF 267
           +  NGGF P+G+   L+ +Q V+FA+  +E++G  AGE ++PQK +P+AI SV WRI LF
Sbjct: 198 LWSNGGFMPNGVTGVLMSLQMVMFAYLGVEMIGLTAGEARNPQKTIPQAIGSVFWRILLF 257

Query: 268 YVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYCTG 327
           YVG++ +++ + PWN   +  SPFV  F +LG+     I+N VV+TAALSS N G++ TG
Sbjct: 258 YVGALFVILSIYPWNEIGSQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317

Query: 328 RILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFASL 387
           R+L S++  G AP   A+ S+  VP   +L ++   ++GV  NYLVP +VF  V + A+ 
Sbjct: 318 RMLYSLAQNGQAPAAFARTSKNGVPRNALLLSIGALLLGVLANYLVPEKVFVWVTSIATF 377

Query: 388 GIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAF 442
           G I +W  I++ Q++ R  +   +   + +++   P +S+L L FL+ V+ LMA+
Sbjct: 378 GAIWTWVMILLAQLKFRAGLTTAERKALKYRMWLWPLSSYLALAFLVLVVGLMAY 432


Lambda     K      H
   0.328    0.140    0.434 

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: 696
Number of extensions: 43
Number of successful extensions: 2
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: 497
Length of database: 472
Length adjustment: 34
Effective length of query: 463
Effective length of database: 438
Effective search space:   202794
Effective search space used:   202794
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