GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocE in Burkholderia phytofirmans PsJN

Align Amino-acid permease RocE (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter

Query= SwissProt::P39137
         (467 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS15500 BPHYT_RS15500 aromatic
           amino acid transporter
          Length = 461

 Score =  296 bits (759), Expect = 7e-85
 Identities = 157/461 (34%), Positives = 262/461 (56%), Gaps = 10/461 (2%)

Query: 1   MNTNQDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIM 60
           MN+ Q     L+R +K+RH+ +I+LGG IGTG FLG+   +  AGP   +L Y +GG I 
Sbjct: 1   MNSAQQQDG-LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGP-SMILGYAIGGIIA 58

Query: 61  FLTMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQ 120
           F+ M  LGE+    PV+GSF  +A K+     GF  GW YW+ + +    E  + G  + 
Sbjct: 59  FMIMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIH 118

Query: 121 RWFPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLI 180
            W+P +  W+  LV  AL+  +N    KA+ E+EFWF+ IK++ ++  I+ GG   + LI
Sbjct: 119 YWWPGVPTWVSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGG---YLLI 175

Query: 181 DLKGGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPR 240
              GG QA     +   G FP+G   + + +  + F+F G ELIG+ A E++ P+K+IP+
Sbjct: 176 SGHGGPQASITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPK 235

Query: 241 SIKQTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIAL 300
           ++ Q ++R L+F++ S+ V+  + PW +     SPFV +F QIG    A+++N V+L A 
Sbjct: 236 AVNQVIYRILIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAA 295

Query: 301 LSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAE 360
           LSV NSG+YA++R+LY +A +G A +AL K ++RGVP  ++ ++       ++  +    
Sbjct: 296 LSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPA 355

Query: 361 TVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLN 420
               +L++L   +  + W  ISL+ +  R+  +  G   E L FK+  +PV   I L   
Sbjct: 356 EALGLLMALVVAALVLNWALISLTHLKSRKAMVAAG---ETLVFKSFWFPVSNWICLAFM 412

Query: 421 TVVLISLAFDPEQRIALYCGVPFMIICYIIYHVVIKKRQQA 461
            ++L+ LA  P   ++++    ++++ +  Y  V K+R+ A
Sbjct: 413 ALILVILAMTPGLSVSVWLVPAWLVVMWAGY--VFKRRRAA 451


Lambda     K      H
   0.329    0.142    0.438 

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: 548
Number of extensions: 27
Number of successful extensions: 4
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: 467
Length of database: 461
Length adjustment: 33
Effective length of query: 434
Effective length of database: 428
Effective search space:   185752
Effective search space used:   185752
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 (21.8 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