GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0028 in Burkholderia phytofirmans PsJN

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate BPHYT_RS31200 BPHYT_RS31200 peptide ABC transporter substrate-binding protein

Query= TCDB::Q9WXN5
         (330 letters)



>FitnessBrowser__BFirm:BPHYT_RS31200
          Length = 325

 Score =  195 bits (496), Expect = 1e-54
 Identities = 112/310 (36%), Positives = 181/310 (58%), Gaps = 11/310 (3%)

Query: 6   LKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTL 65
           L  +N+R ++       KAVD  SF++   E++G+VGESG GK+     +   +  P  +
Sbjct: 6   LSVQNLRTHFFTGAGVAKAVDDTSFDVAPGEIVGLVGESGSGKSITGFSVLGLIDAPGRI 65

Query: 66  VDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAES 125
           V G++  +  GE  +L+++T  E  R+  G  I +I Q  M  L P +R++  +    ++
Sbjct: 66  VAGRVLFK--GE--DLTTLT-PEALRRLRGNRIAMIFQDPMMTLNPVLRIDTQMIEAVQA 120

Query: 126 HG-IDEEELLDKARRRFEEVGLDPL--WIKRYPFELSGGMRQRAVIAIATILNPSLLIAD 182
           H  + +     +AR     VG+      ++ YP +LSGGMRQR  IAIA + +P L+IAD
Sbjct: 121 HTRVSKHAARQRARDALASVGIPSPDERLRAYPHQLSGGMRQRVAIAIALLHDPELIIAD 180

Query: 183 EPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAP 242
           EPT+ALDV  Q  +L  + ++  +    ++++++HD+A V  +ADR+ +MYAG++VE   
Sbjct: 181 EPTTALDVTIQAQILAEMQKLCARSHT-AMVWVSHDLAVVAGLADRICVMYAGRVVETGS 239

Query: 243 VESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMD 302
           V+ +LE+P HPYT GL +S+  PE   +   +T IPG  P+ +  P GC F PRC +A  
Sbjct: 240 VDEILERPRHPYTIGLIDSL--PEKARRGESLTQIPGMAPSALKLPVGCAFAPRCVYATS 297

Query: 303 VCKEKEPPLT 312
           +C+  EPP+T
Sbjct: 298 LCRSAEPPVT 307


Lambda     K      H
   0.321    0.138    0.405 

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: 290
Number of extensions: 12
Number of successful extensions: 4
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: 330
Length of database: 325
Length adjustment: 28
Effective length of query: 302
Effective length of database: 297
Effective search space:    89694
Effective search space used:    89694
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:

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