GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Escherichia coli BW25113

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 14540 b0402 predicted cryptic proline transporter (NCBI)

Query= TCDB::P15993
         (457 letters)



>lcl|FitnessBrowser__Keio:14540 b0402 predicted cryptic proline
           transporter (NCBI)
          Length = 457

 Score =  386 bits (991), Expect = e-112
 Identities = 195/447 (43%), Positives = 285/447 (63%), Gaps = 11/447 (2%)

Query: 10  QLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGEM 69
           +LKRGL  RHI+ +ALG AIGTGLF GSA  I+ AGP ++L Y I G  A++IMR LGEM
Sbjct: 6   KLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGIAAYIIMRALGEM 65

Query: 70  VVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTWV 129
            V  P A SFS +A +  G  AG+ +GW Y    ++VA+A++TA G Y+  W+P +P W+
Sbjct: 66  SVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPTVPHWI 125

Query: 130 SAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLF--SGNGGPQATVS 187
                 ++I A+NL +VKVFGE+EFWF+  KV  ++ MI+ G  ++    GNGG    + 
Sbjct: 126 WVLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMIVAGFGIIIWGIGNGGQPTGIH 185

Query: 188 NLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRILI 247
           NLW  GGF  +G+ G+VM + ++MF++GG+E++GITA EA +PE+SIP+A N V  RIL+
Sbjct: 186 NLWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILV 245

Query: 248 FYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVYCN 307
           FY+G+L V++S+ PW +V    SPFVL F  +G TF A+ LN VVLTA+LS  NS V+  
Sbjct: 246 FYVGTLFVIMSIYPWNQVGTAGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGV 305

Query: 308 SRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMALVV 367
            RML G+A+QG+APK  +   +RG+P  T+LV        V +NY+ PE+ F ++ +L  
Sbjct: 306 GRMLHGMAEQGSAPKIFSKTSRRGIPWVTVLVMTTALLFAVYLNYIMPENVFLVIASLAT 365

Query: 368 SALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWIC-----LLFMAAVLVIMLM 422
            A V  W MI L+ + FRR    + V     AL + +   +      L+F+  ++ ++  
Sbjct: 366 FATVWVWIMILLSQIAFRRRLPPEEV----KALKFKVPGGVATTIGGLIFLLFIIGLIGY 421

Query: 423 TPGMAISVYLIPVWLIVLGIGYLFKEK 449
            P   IS+Y+   W++VL IG++FK +
Sbjct: 422 HPDTRISLYVGFAWIVVLLIGWMFKRR 448


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: 648
Number of extensions: 42
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: 457
Length adjustment: 33
Effective length of query: 424
Effective length of database: 424
Effective search space:   179776
Effective search space used:   179776
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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