GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS31960
          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.

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:

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