GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Cupriavidus basilensis 4G11

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 RR42_RS14635 RR42_RS14635 proline-specific permease

Query= TCDB::P15993
         (457 letters)



>FitnessBrowser__Cup4G11:RR42_RS14635
          Length = 466

 Score =  373 bits (957), Expect = e-108
 Identities = 190/445 (42%), Positives = 278/445 (62%), Gaps = 5/445 (1%)

Query: 5   QQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMR 64
           Q+  + L+RGL  RHI+ +ALG AIGTGLF GSAS IQ+AGP ++L Y I G   +++MR
Sbjct: 2   QEQSQGLQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVMR 61

Query: 65  QLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPE 124
            LGEM V  PVAGSF  +A    G  AGF  GW Y    ++V +A++TA G Y+ FW+P+
Sbjct: 62  ALGEMAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFWFPD 121

Query: 125 IPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSG----NG 180
           +P W+       +I  +NL +VKVFGE+EFW +++KV A+VAMI  G  ++  G    +G
Sbjct: 122 VPRWIWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGMADG 181

Query: 181 GPQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQ 240
           G    + NLW  GGF+P+G  G++   A++MF+FGG+E++GITA EA +P++ IP+A N 
Sbjct: 182 GVATGIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRAINA 241

Query: 241 VIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVY 300
           V  RIL+FY+ +LAVL+SL PW R+ ++ SPFV IF  LG    A  LNIVV++AA+S  
Sbjct: 242 VPLRILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAVSAI 301

Query: 301 NSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFG 360
           NS ++   RML+G+A Q  AP+  ASV ++GVP  T++V A      V++NY+ PE  F 
Sbjct: 302 NSDIFGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPEDVFT 361

Query: 361 LLMALVVSALVINWAMISLAHMKFRRAKQEQGVVT-RFPALLYPLGNWICLLFMAAVLVI 419
           L+ ++   A V  W MI L+ +  RR      V   +FP   +P+       FM  +  +
Sbjct: 362 LIASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFIFGV 421

Query: 420 MLMTPGMAISVYLIPVWLIVLGIGY 444
           +   P    ++ +  VWL++L + +
Sbjct: 422 LGWFPQTRAALLVGAVWLLLLVVAW 446



 Score = 25.8 bits (55), Expect = 0.003
 Identities = 23/102 (22%), Positives = 44/102 (43%), Gaps = 9/102 (8%)

Query: 361 LLMALVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPAL-LYPLGNWICLLFMAAVLVI 419
           +L+A V+    +   M +L  M  R      G   ++ +  L PL  ++     A  +++
Sbjct: 45  VLLAYVIGGAAVYMVMRALGEMAVRNPVA--GSFGQYASTGLGPLAGFLLGWTYAFEMIV 102

Query: 420 MLMTPGMAISVYL------IPVWLIVLGIGYLFKEKTAKAVK 455
           + +    A  +Y+      +P W+ VLGI +L       +VK
Sbjct: 103 VCLADVTAFGIYMGFWFPDVPRWIWVLGIVFLIGGLNLLSVK 144


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: 653
Number of extensions: 44
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 457
Length of database: 466
Length adjustment: 33
Effective length of query: 424
Effective length of database: 433
Effective search space:   183592
Effective search space used:   183592
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