GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bztB in Sinorhizobium meliloti 1021

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate SMc02119 SMc02119 general L-amino acid transport permease ABC transporter protein

Query= CharProtDB::CH_011913
         (426 letters)



>lcl|FitnessBrowser__Smeli:SMc02119 SMc02119 general L-amino acid
           transport permease ABC transporter protein
          Length = 397

 Score =  279 bits (713), Expect = 1e-79
 Identities = 167/424 (39%), Positives = 246/424 (58%), Gaps = 34/424 (8%)

Query: 5   SDPPKAGFRLSMLIYDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLW 64
           ++ P+       +I D + R I  Q + +++  A + W+++N   NL        + F+ 
Sbjct: 6   TNAPERSRSSGSIINDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASGYDFVR 65

Query: 65  TRAGYDLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLV 124
           +RAG+D+ Q+LI +++D T+ RAL+ G +NTLLV++ G I ATI+G I+G+ RLS NW++
Sbjct: 66  SRAGFDVGQSLISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWII 125

Query: 125 ARIMTVYVETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSV 184
           A++   YVE FRNIP LL I    + +    P  +D               A    FD +
Sbjct: 126 AKLSLAYVEVFRNIPPLLVIFFWYSGVLSILPQARD---------------ALALPFD-I 169

Query: 185 AVTNRGTNLPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEA 244
            ++NRG   P P  +                  LA +  ++AS +    F   A+  Q A
Sbjct: 170 FLSNRGVAFPRPIAEEG-----------AEYTLLAFVIAVAASVF----FARYARKRQLA 214

Query: 245 TGTR-PTTWWPSLLILFAP-ISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALT 302
           TG R P  W    LI+  P ++ L+ G     D P   KF+ TGG  +   F +L +AL+
Sbjct: 215 TGERLPVLWTVLGLIIGLPLVTFLVTGAPITFDIPVAGKFNLTGGSVVGPEFMSLFLALS 274

Query: 303 LYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNL 362
            YTAAFIAEIVRAGI+ +S+GQTEAA+ALG+RP  T  LV++PQA+R+I+PPL SQ+LNL
Sbjct: 275 FYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNL 334

Query: 363 TKNSSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIK 422
           TKNSSLA+A+ Y DL   +GG  LNQTG+ +E + + +++YL++SL  S  MN YN  + 
Sbjct: 335 TKNSSLAVAIGYADL-VAVGGTILNQTGQSIEIVSIWLIVYLSLSLATSLFMNWYNARMA 393

Query: 423 LKER 426
           L ER
Sbjct: 394 LVER 397


Lambda     K      H
   0.326    0.139    0.419 

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: 402
Number of extensions: 20
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: 426
Length of database: 397
Length adjustment: 31
Effective length of query: 395
Effective length of database: 366
Effective search space:   144570
Effective search space used:   144570
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: 50 (23.9 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