GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ansP in Escherichia coli BW25113

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate 14258 b0112 aromatic amino acid transporter (NCBI)

Query= TCDB::P40812
         (497 letters)



>lcl|FitnessBrowser__Keio:14258 b0112 aromatic amino acid
           transporter (NCBI)
          Length = 457

 Score =  331 bits (849), Expect = 3e-95
 Identities = 170/446 (38%), Positives = 271/446 (60%), Gaps = 10/446 (2%)

Query: 22  HEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRAL 81
           H E   + + NR +Q+IA+GGAIGTGLFLG+ + +Q AGP + L Y I G  +F I+R L
Sbjct: 7   HGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQL 66

Query: 82  GELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGD 141
           GE+V+  P +GSF  +A ++ G  A + +GW Y++ + +  + ++TAV  Y+ +W  + +
Sbjct: 67  GEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFW--YPE 124

Query: 142 VPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVG--TIFLGTGQPLE 199
           +P WV A     ++  +N+  VK F EMEFWFA+IKV+A+V  ++ G   +F G G P  
Sbjct: 125 IPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGGP-- 182

Query: 200 GNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINS 259
             AT  +L  D GGF PHG    ++++  ++F+F  +ELVG  A E  +P++ +PKA N 
Sbjct: 183 -QATVSNL-WDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQ 240

Query: 260 VIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSL 319
           VI+RI +FY+GS+ +L+ L+PW    A  SPFV  F +LG  ++ + +NIVVLTAALS  
Sbjct: 241 VIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVY 300

Query: 320 NSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFE 379
           NS +YC  R+L  ++  G+APK +A + ++ VP   IL + +V  + V +NYL P   F 
Sbjct: 301 NSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFG 360

Query: 380 IVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVL 439
           +++      ++ +WA I +  M+ R+A K+ +     F     P  +W+ LLF+ +VLV+
Sbjct: 361 LLMALVVSALVINWAMISLAHMKFRRA-KQEQGVVTRFPALLYPLGNWICLLFMAAVLVI 419

Query: 440 MAFDYPNGTYTIASLPLIAILLVAGW 465
           M    P    ++  +P+  I+L  G+
Sbjct: 420 MLMT-PGMAISVYLIPVWLIVLGIGY 444


Lambda     K      H
   0.328    0.140    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: 592
Number of extensions: 31
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: 497
Length of database: 457
Length adjustment: 33
Effective length of query: 464
Effective length of database: 424
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 (21.7 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 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