GapMind for catabolism of small carbon sources

 

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

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate AO353_12275 AO353_12275 proline-specific permease

Query= TCDB::P40812
         (497 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_12275
          Length = 468

 Score =  328 bits (841), Expect = 2e-94
 Identities = 166/440 (37%), Positives = 263/440 (59%), Gaps = 3/440 (0%)

Query: 25  GYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGEL 84
           G  + +  R ++ +A+G AIGTGLF G+ + +QMAGPA+ L YLI G   F ++RALGE+
Sbjct: 7   GLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEM 66

Query: 85  VLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQ 144
            +H P +GSF  YA  +LG  A ++ GW Y     + G+ D+TA  +YM +W  F +V +
Sbjct: 67  AVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFW--FPEVSR 124

Query: 145 WVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGT-IFLGTGQPLEGNAT 203
           W++ LG ++IVG +N+  VK F EMEFW +L+KV AIV  ++ G  I L       G  T
Sbjct: 125 WIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVT 184

Query: 204 GFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWR 263
               +   GGF P+G+   +     V+FAF  IE++G  AGE KDPQ ++P+AIN+V  R
Sbjct: 185 DISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLR 244

Query: 264 IGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGL 323
           I LFYV ++++L+ + PW    +  SPFV  F KLG+    +I+NIVV+TAA+S++NS +
Sbjct: 245 ILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDI 304

Query: 324 YCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLN 383
           +  GR++  ++  G APK  A +SR  VP+  ++   V  ++GV LNYL+P  VF ++ +
Sbjct: 305 FGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIAS 364

Query: 384 FASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFD 443
            A+   +  W  I+  Q+ +R+++   + A + F +P  P+     + F+L V  ++ + 
Sbjct: 365 IATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYF 424

Query: 444 YPNGTYTIASLPLIAILLVA 463
                  I  +  I +L++A
Sbjct: 425 PDTQAALIVGVVWIVLLVLA 444


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: 646
Number of extensions: 36
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: 468
Length adjustment: 34
Effective length of query: 463
Effective length of database: 434
Effective search space:   200942
Effective search space used:   200942
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