GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Bap2 in Pseudomonas fluorescens FW300-N2E3

Align Leu/Val/Ile amino-acid permease; Branched-chain amino-acid permease 2 (characterized)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter

Query= SwissProt::P38084
         (609 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_05965 AO353_05965 aromatic
           amino acid transporter
          Length = 466

 Score =  209 bits (532), Expect = 2e-58
 Identities = 127/402 (31%), Positives = 216/402 (53%), Gaps = 16/402 (3%)

Query: 91  LKKSMKSRHVVMMSLGTGIGTGLLVANAKGLHYGGPAALIIGYILVSFVTYFMIQAAGEM 150
           LK+ +K+RH+ +++LG  IGTGL + +A  L   GP+ +I+GY +  F+ + +++  GEM
Sbjct: 11  LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAIAGFIAFLIMRQLGEM 69

Query: 151 AVTYPTLPANFNAYSSIFISKSFGFATVWLYCFQWLTVLPLELITASMTIQFWNDKINPD 210
            V  P +  +F+ ++  +     GF + W Y   ++ V   EL      +QFW  ++   
Sbjct: 70  IVEEP-VAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTW 128

Query: 211 IYILIFYVFLVFIHFFGVKAYGETEFIFNCCKILMIAGFIILSIVINCGGAGNDGYIGAT 270
           +   +F+V +  I+   VK +GE EF F   K++ I G I L   +   G G      + 
Sbjct: 129 VSAAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSGTGGPQASVSN 188

Query: 271 YWHNPGAFAGDTSIGRFKNVCYILVTAYFSFGGMELFALSVQEQSNPRKSTPVAAKRSIY 330
            W + G F   T+ G    + +I+    FSFGG+EL  ++  E S PRK  P A  + +Y
Sbjct: 189 LWSHGGFFPNGTN-GLLMAMAFIM----FSFGGLELVGITAAEASEPRKVIPKAINQVVY 243

Query: 331 RIVVIYLLTMILIGFNVPYNDD-QLMGAGGSATHASPYVLAASIHGVKIVPHIINAVILI 389
           R+++ Y+  + ++    P++   Q +GA G A   SP+V   ++ G      I+N V+L 
Sbjct: 244 RVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQILNFVVLT 303

Query: 390 SVVSVANSSLYAGPRLICSLAQQGYAPKFLDYVDREGRPLRAL----IVCCVFGVIAFVA 445
           + +SV NS +Y   R++  LA+QG APK L  ++++G PLRAL    ++  +  V+ +VA
Sbjct: 304 AALSVYNSGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLCVVVNYVA 363

Query: 446 ASSKEEIVFTWLAAIAGLSELFTWTSIMLSHLRFRQAMKVQG 487
            +   E++F  + A    S +  W  I L+HL+FR+AM  +G
Sbjct: 364 PNEALELLFALVVA----SLMINWAMISLTHLKFRKAMGQRG 401


Lambda     K      H
   0.325    0.139    0.423 

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: 714
Number of extensions: 37
Number of successful extensions: 5
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: 609
Length of database: 466
Length adjustment: 35
Effective length of query: 574
Effective length of database: 431
Effective search space:   247394
Effective search space used:   247394
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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