GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gyaR in Burkholderia phytofirmans PsJN

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate BPHYT_RS31960 BPHYT_RS31960 hypothetical protein

Query= curated2:A1RYE4
         (339 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS31960 BPHYT_RS31960 hypothetical
           protein
          Length = 316

 Score =  198 bits (504), Expect = 1e-55
 Identities = 127/324 (39%), Positives = 179/324 (55%), Gaps = 15/324 (4%)

Query: 5   KVYVTRIIPEPGLSMLKECCDVVVHESKDWPPSREELLRN-IRDKDALLCLLTDKIDAEV 63
           +V  T  I    L +L+  C++VV      P   EE LR  + D DAL+  +  ++  ++
Sbjct: 6   RVLATSPIHLSALPILEPSCELVVA-----PDDSEETLRKFVADADALIVRV--RLPDDI 58

Query: 64  MDAAPNLKVISTYSVGFDHIDIPEATKRGIYVTHTPGVLTDAVAEFTVGLILAVTRRIVE 123
            D AP LK    + VG D I +  AT+  I V + P   T AVAE  VG ILA+ R    
Sbjct: 59  FDHAPRLKACVRHGVGLDFIPVERATRADIAVANLPDSNTQAVAEHVVGAILAMARGF-- 116

Query: 124 ADKIIRTGQWDKPWNPYFLTGPELKGKTIGLVGLGRIGVATAKRLS-SFDVKILYYDIER 182
            D++ R  + D         G EL+ +T+G+VGLGRIG+  A  L   F +++L  D   
Sbjct: 117 -DRLPRAWRNDGWLVRQTFQGIELRDRTVGIVGLGRIGLQVAAALHHGFGMRVLGCDNGA 175

Query: 183 RWDVETVIPNMEFTDLDTLLEKSDIVSIHVPLTKETYHLINEERLRKMKKTAYLINTARG 242
           R  + + +     T ++ +   SD +++H PL K T HL+N E L   K  A L+N ARG
Sbjct: 176 REGLPSYVDQ---TSIENVFSGSDFITLHAPLVKSTRHLVNAELLSLAKPGALLVNAARG 232

Query: 243 PVVDTEALVKALKEGWIAGAALDVFEQEPLPPNHPLTKFDNVVLAPHIASATIEARQRMA 302
            ++D +ALV AL+ G I  AALDVFE EPLPP+HP    DNV+L PH+A+ T E   RM+
Sbjct: 233 GLIDDDALVAALRSGQIGCAALDVFEPEPLPPDHPYWSIDNVLLTPHVAAFTSEGLVRMS 292

Query: 303 ELAARNLIAVLKGEMPPALVNKEV 326
             AAR ++ +L G  P  LVN+EV
Sbjct: 293 TGAARAVVEILHGRRPEHLVNEEV 316


Lambda     K      H
   0.319    0.137    0.404 

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: 244
Number of extensions: 11
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: 339
Length of database: 316
Length adjustment: 28
Effective length of query: 311
Effective length of database: 288
Effective search space:    89568
Effective search space used:    89568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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