GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsB in Burkholderia phytofirmans PsJN

Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate BPHYT_RS20560 BPHYT_RS20560 sugar ABC transporter substrate-binding protein

Query= uniprot:D8IUD0
         (314 letters)



>FitnessBrowser__BFirm:BPHYT_RS20560
          Length = 316

 Score =  317 bits (813), Expect = 2e-91
 Identities = 169/311 (54%), Positives = 226/311 (72%), Gaps = 3/311 (0%)

Query: 6   RRHFAIA-ALACAVLPGAA-MAQTPA-KPKVALVMKSLANEFFLNMENGAREYQKANASK 62
           RR   IA ALA A + GAA  A TP  K K+ALV+KSL + F + M + A+ YQ+  AS+
Sbjct: 2   RRRVVIAGALAAAGIGGAADAAATPGGKLKIALVLKSLGDPFTIAMASAAQNYQQHYASQ 61

Query: 63  FDLIANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVNID 122
           FDL   G   E DT  QI++VE+MI +K+NA+VIAP DSKAL  VV +AI AG+IVV+ID
Sbjct: 62  FDLTVRGTATESDTTGQIRMVEEMIKAKMNAIVIAPTDSKALTAVVARAIKAGVIVVSID 121

Query: 123 NKLDDAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRTL 182
           N LD+A     GI+VPFVGP+NRKGA+   +YL ++L+ GD+V +IEG S   NAQQRT 
Sbjct: 122 NPLDEAFQDAAGISVPFVGPNNRKGAQQVSNYLAERLKTGDQVGVIEGSSADRNAQQRTD 181

Query: 183 GFQDAMKDVGANVVTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAIRA 242
           G +DAM   G N+V VQ+G WE  +G   A+ +L+ HP I+ ++ GNDNMA+GAV A+R 
Sbjct: 182 GCRDAMNAAGINIVAVQTGDWEYGKGRDAASKMLSEHPQIRGLMCGNDNMAMGAVDAVRD 241

Query: 243 AGKTGKVQLVGYDNINAIKPMLKDGRVLATVDQFAQQQAVFGIETALKALSEKKPQSALG 302
           AG+TG V + GY++I+AIKP++ DGRVLATV+QFA +QAVFG++ ALKA++E++ QS L 
Sbjct: 242 AGRTGGVYVTGYNDIDAIKPLIADGRVLATVNQFAARQAVFGVDVALKAVTEQRKQSELS 301

Query: 303 GVVETKVSLVT 313
            V+ET + LVT
Sbjct: 302 SVIETPLQLVT 312


Lambda     K      H
   0.315    0.131    0.355 

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: 255
Number of extensions: 8
Number of successful extensions: 1
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: 314
Length of database: 316
Length adjustment: 27
Effective length of query: 287
Effective length of database: 289
Effective search space:    82943
Effective search space used:    82943
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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:

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