GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Pseudomonas fluorescens FW300-N1B4

Align Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)
to candidate Pf1N1B4_1580 Histidine transport protein (permease)

Query= TCDB::P15993
         (457 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580
          Length = 469

 Score =  392 bits (1007), Expect = e-113
 Identities = 205/452 (45%), Positives = 287/452 (63%), Gaps = 5/452 (1%)

Query: 5   QQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMR 64
           QQ  + LKRGL  RHI+ +ALG AIGTGLF GSAS IQ AGP ++L Y I G   F++MR
Sbjct: 2   QQPAKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMR 61

Query: 65  QLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPE 124
            LGEM V  PVAGSF  +A  Y G  AGF  GW Y    V+V MA++TA G Y+ FW+PE
Sbjct: 62  ALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPE 121

Query: 125 IPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFG-GWLLF--SGNGG 181
           +  W+       V+  +NL NVKVFGEMEFW +++KV A+VAMI+ G G +LF  S   G
Sbjct: 122 VDRWIWVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPG 181

Query: 182 PQAT-VSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQ 240
            QAT +SNLW  GGF+P+G  GL+   A++MF+FGG+E++G+TA EA +P++ +P+A N 
Sbjct: 182 AQATDISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINA 241

Query: 241 VIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVY 300
           V  RIL+FY+ ++ VL+S+ PW ++ +  SPFV IF  LG +  A  LNIVV++AA+S  
Sbjct: 242 VPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSAI 301

Query: 301 NSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFG 360
           NS ++   RM++GLAQQG+APK  A + + GVP  T++V +    L VL+NYL PE+ F 
Sbjct: 302 NSDIFGAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPENVFL 361

Query: 361 LLMALVVSALVINWAMISLAHMKFRRA-KQEQGVVTRFPALLYPLGNWICLLFMAAVLVI 419
           L+ ++   A V  W MI    +  RR+   EQ    +FP   +P      + FM  +  +
Sbjct: 362 LIASVATFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFIFGV 421

Query: 420 MLMTPGMAISVYLIPVWLIVLGIGYLFKEKTA 451
           +   P    ++ +  VW+++L + YL   K A
Sbjct: 422 LGYFPDTQAALIVGVVWIVLLVLAYLTWVKPA 453


Lambda     K      H
   0.328    0.141    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: 680
Number of extensions: 43
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: 457
Length of database: 469
Length adjustment: 33
Effective length of query: 424
Effective length of database: 436
Effective search space:   184864
Effective search space used:   184864
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: 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