GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Kocuria flava HO-9041

Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate WP_058857461.1 AS188_RS02160 amino acid permease

Query= TCDB::P24207
         (458 letters)



>NCBI__GCF_001482365.1:WP_058857461.1
          Length = 498

 Score =  315 bits (807), Expect = 2e-90
 Identities = 171/437 (39%), Positives = 252/437 (57%), Gaps = 19/437 (4%)

Query: 9   EDTASNQEPT-------LHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPA-VLLGY 60
           + TA  + PT       L R L  RH+ +IA+GGAIGTGLF+  G  I  AGP   L  Y
Sbjct: 8   QTTAPTRPPTPAEAHARLRRSLKPRHLTMIAMGGAIGTGLFVASGNTIATAGPGGALAAY 67

Query: 61  GVAGIIAFLIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELT 120
              G++ FL+M+ LGEM    PVSG+F  ++ ++  P  GF  GWNYW  + +   AEL 
Sbjct: 68  VAIGLMVFLLMQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNWAITVAAELV 127

Query: 121 AAGIYMQYWFPDVPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGL 180
           AA + M+YW PDVP+WIW+A F  I+  +N ++ R YGE+EFWF+LIKV  ++  +  G+
Sbjct: 128 AAALIMRYWLPDVPSWIWSALFLAILFGLNALSTRAYGESEFWFSLIKVATVVIFLVLGV 187

Query: 181 WLLFSGHGGEKASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEK 240
            ++    GGE    DN       F  G  G++    V  FSF G EL+G+ A EA DPEK
Sbjct: 188 LMIVGILGGESPGFDNWTTGEAPFVGGGAGILAIFMVAGFSFQGTELVGVAAGEAEDPEK 247

Query: 241 SIPKAVNQVVYRILLFYIGSLVVLLALYPWVE-------VKSNS-SPFVMIFHNLDSNVV 292
           ++P+A+  V  RILLFY+G++ ++  L P+         V+  S SPF ++F N      
Sbjct: 248 NVPRAIRTVFVRILLFYVGAITIVGFLIPYTSPHLLGSGVEDISISPFTLVFENAGVLAA 307

Query: 293 ASALNFVILVASLSVYNSGVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAIT 352
           AS +N VIL A LS  NSG+Y+++RML+ L+  G APKFL +V+RRGVP+N+L+ +  + 
Sbjct: 308 ASVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPKFLAKVNRRGVPMNALLATTTVG 367

Query: 353 SLVVLINYLLPQKAFGLLMALVVATLLLNWIMICLAHLRFRAAMRRQGR---ETQFKALL 409
           +   L   +    A+  L++       + W+ I  +H RFR A   QG+   +  +KA  
Sbjct: 368 AACFLTTLIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRKAYTAQGKDLGDLPYKARF 427

Query: 410 YPFGNYLCIAFLGMILL 426
           +P G  + +A   +++L
Sbjct: 428 FPLGPMIALALCAVVIL 444


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: 582
Number of extensions: 38
Number of successful extensions: 4
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: 498
Length adjustment: 34
Effective length of query: 424
Effective length of database: 464
Effective search space:   196736
Effective search space used:   196736
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 24 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