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

GapMind for catabolism of small carbon sources

Aligments 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources