GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ansP in Pseudomonas fluorescens FW300-N1B4

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate Pf1N1B4_1580 Histidine transport protein (permease)

Query= TCDB::P40812
         (497 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580 Histidine transport
           protein (permease)
          Length = 469

 Score =  325 bits (834), Expect = 2e-93
 Identities = 160/442 (36%), Positives = 265/442 (59%), Gaps = 4/442 (0%)

Query: 24  EGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGE 83
           +G  + +  R ++ +A+G AIGTGLF G+ + +QMAGPA+ L YLI G   F ++RALGE
Sbjct: 6   KGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGE 65

Query: 84  LVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVP 143
           + +H P +GSF  YA  +LG  A ++ GW Y     + G+ D+TA  +YM +W  F +V 
Sbjct: 66  MAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFW--FPEVD 123

Query: 144 QWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLV--VGTIFLGTGQPLEGN 201
           +W++ LG +++VG +N+  VK F EMEFW +L+KV AIV  ++   G +  G        
Sbjct: 124 RWIWVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGAQ 183

Query: 202 ATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVI 261
           AT    +  +GGF P+G+   +     V+FAF  IE++G  AGE KDPQ+++P+AIN+V 
Sbjct: 184 ATDISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINAVP 243

Query: 262 WRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNS 321
            RI LFYV ++++L+ + PW    +  SPFV  F  LG+    +I+NIVV++AA+S++NS
Sbjct: 244 LRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSAINS 303

Query: 322 GLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIV 381
            ++  GR++  ++  G APK  A++SR  VP+  ++      ++GV LNYL+P  VF ++
Sbjct: 304 DIFGAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPENVFLLI 363

Query: 382 LNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMA 441
            + A+   +  W  I+  Q+ +R+++   + A + F +P  P+     + F+L +  ++ 
Sbjct: 364 ASVATFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFIFGVLG 423

Query: 442 FDYPNGTYTIASLPLIAILLVA 463
           +        I  +  I +L++A
Sbjct: 424 YFPDTQAALIVGVVWIVLLVLA 445


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: 632
Number of extensions: 37
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: 497
Length of database: 469
Length adjustment: 34
Effective length of query: 463
Effective length of database: 435
Effective search space:   201405
Effective search space used:   201405
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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