GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Pseudomonas fluorescens GW456-L13

Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate PfGW456L13_318 Histidine transport protein (permease)

Query= TCDB::P24207
         (458 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_318
          Length = 468

 Score =  402 bits (1033), Expect = e-116
 Identities = 202/443 (45%), Positives = 285/443 (64%), Gaps = 4/443 (0%)

Query: 16  EPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQLG 75
           E  L RGL  RHI+ +ALG AIGTGLF G   AIQMAGPAVLL Y + G   F++MR LG
Sbjct: 5   EKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALG 64

Query: 76  EMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVPT 135
           EM V  PV+GSF  +A  Y GP AGF+ GW Y    V+VGMA++TA GIYM +WFP+V  
Sbjct: 65  EMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSR 124

Query: 136 WIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMI--GFGL-WLLFSGHGGEKA 192
           WIW      I+  +NL NV+++GE EFW +L+KV AI+ MI  GFG+ W   S   G+  
Sbjct: 125 WIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMWFGISSAPGQAT 184

Query: 193 SIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYR 252
            I NLW +GGF   G  GLI S AV+MF+FGG+E+IG+TA EA+DP+  +P+A+N V  R
Sbjct: 185 DISNLWSHGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLR 244

Query: 253 ILLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGV 312
           ILLFY+ +++VL++++PW ++ S  SPFV IF  L  +  A+ LN V++ A++S  NS +
Sbjct: 245 ILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDI 304

Query: 313 YSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMA 372
           +   RM+FGL+ QG+APK   R+SR GVP  ++++  A   L VL+NYL+P+  F L+ +
Sbjct: 305 FGAGRMMFGLAQQGHAPKGFARLSRNGVPWMTVVVMSAALLLGVLLNYLIPENVFLLIAS 364

Query: 373 LVVATLLLNWIMICLAHLRFRAAM-RRQGRETQFKALLYPFGNYLCIAFLGMILLLMCTM 431
           +     +  W+MI +  +  R +M   Q  + +F   L+P+     IAF+  I  ++   
Sbjct: 365 VATFATVWVWLMILVTQVAMRRSMSAEQVAQLKFPVPLWPYAPAAAIAFMLFIFGVLGYF 424

Query: 432 DDMRLSAILLPVWIVFLFMAFKT 454
            D + + I+  VWIV L +A+ T
Sbjct: 425 PDTQAALIVGVVWIVLLVLAYLT 447


Lambda     K      H
   0.329    0.143    0.447 

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: 647
Number of extensions: 26
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: 458
Length of database: 468
Length adjustment: 33
Effective length of query: 425
Effective length of database: 435
Effective search space:   184875
Effective search space used:   184875
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 (21.8 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