GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araUsh in Burkholderia phytofirmans PsJN

Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate BPHYT_RS01825 BPHYT_RS01825 sugar ABC transporter substrate-binding protein

Query= uniprot:A0KWY4
         (313 letters)



>FitnessBrowser__BFirm:BPHYT_RS01825
          Length = 339

 Score =  204 bits (519), Expect = 2e-57
 Identities = 112/267 (41%), Positives = 163/267 (61%), Gaps = 11/267 (4%)

Query: 25  VGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADAQQKQENQIKAVRSFIAQGVDAIII 84
           VGF+Q  S + WR + +++ K  A + G  L   DA      Q+  +++ IAQ VD ++ 
Sbjct: 53  VGFAQTESNNPWRLAETKSFKDIAAKCGWQLVMTDANSSNSKQVSDIQNMIAQHVDLLVF 112

Query: 85  APVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSL------FLTRIASDFSEEGRKIGQ 138
            P  E    PV+ +AK+A IPV++VDR++   D S+      ++T I SDF ++G +   
Sbjct: 113 PPREEKPLAPVVLQAKKAGIPVILVDRDV---DQSVAKAGRDYITFIGSDFIDQGHRAAD 169

Query: 139 WLMDKTQGNCDIAELQGTVGATAAIDRAAGFNQVIANYPNAKIVRSQTGEFTRAKGKEVM 198
           WL+  T G   I EL+GT GA+AA DR  GF+++IA  P   I+ SQ+G+F R KG++VM
Sbjct: 170 WLVKATGGKAKIIELEGTTGASAANDRKKGFDEIIAKNPGMTIIASQSGDFARDKGRQVM 229

Query: 199 EGFLKAQNGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKDILIVSVDGVPDYFKAMADGD 258
           E  L+A     + AV++HNDEMALGA+ AIK AG +PGKDI IV++DG      A+A G+
Sbjct: 230 ETLLQAH--PDVTAVYAHNDEMALGAIAAIKAAGKQPGKDIQIVTIDGTKGGMDAIAAGE 287

Query: 259 VNATVELSPYLGGPAFDAIDAYLKGNK 285
           + A+V+ SP+ G  A D    Y KG K
Sbjct: 288 LGASVQSSPFFGPLACDVAQRYAKGEK 314


Lambda     K      H
   0.316    0.131    0.376 

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: 270
Number of extensions: 12
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 313
Length of database: 339
Length adjustment: 28
Effective length of query: 285
Effective length of database: 311
Effective search space:    88635
Effective search space used:    88635
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.

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