GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpQ in Paraburkholderia bryophila 376MFSha3.1

Align GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate H281DRAFT_05890 H281DRAFT_05890 carbohydrate ABC transporter membrane protein 2, CUT1 family

Query= TCDB::G3LHZ1
         (273 letters)



>FitnessBrowser__Burk376:H281DRAFT_05890
          Length = 317

 Score =  152 bits (385), Expect = 7e-42
 Identities = 83/288 (28%), Positives = 139/288 (48%), Gaps = 33/288 (11%)

Query: 19  YIIFLILPIYWLINMSFKENSEITGAFSLWPTNPTLRNYTVIFTDPS------------- 65
           Y +  ILPI W+   SFK   +      +    P++  Y  +FT  S             
Sbjct: 28  YALIAILPILWICLTSFKTQEDAIAYPPVVLFQPSMEGYVNLFTIRSRQTPEFIASLPPA 87

Query: 66  --WYNG------------------YINSIIYVVMNTVISVAAALPAAYAFSRYRFLGDKH 105
             WY                    ++NS++    +T ++V     AAYAFSR++      
Sbjct: 88  QTWYERDVRKRNMVIAGPSKVLPRFVNSLVIGFGSTFLAVFLGTLAAYAFSRFKVPLADD 147

Query: 106 LFFWLLTNRMAPPAVFALPFFQLYSAFGLIDTHIAVALAHCLFNVPLAVWILEGFMSGVP 165
           L F++L+ RM PP   A+P + +Y A GL D+++ + + +   NV LAVW+L+GFM  +P
Sbjct: 148 LLFFILSTRMMPPIAVAIPIYLMYRALGLSDSYVGMIVLYTAVNVSLAVWLLKGFMDEIP 207

Query: 166 KEIDETAYIDGYSFPRFFIKIFIPLIASGVGVAGFFCFMFSWVELLLARTLTTTAAKPIS 225
           +E +E A +DGY+  + F+K+ +P   +G+     FC +F+W E   A  LT+  A+ + 
Sbjct: 208 REYEEAALVDGYTRLQAFVKVVLPQAITGIAATAIFCLIFAWNEYAFASLLTSGDAQTMP 267

Query: 226 AIMTRTVSASGMDWGVLAAAGVLTIIPGALVIYFVRNYIAKGFALGRV 273
             +   +   G DW  +AAA  L ++P  +    +R ++ +G   G V
Sbjct: 268 PFIPFIIGEGGQDWPAVAAATTLFVVPILIFTVVLRKHLLRGITFGAV 315


Lambda     K      H
   0.330    0.142    0.456 

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: 14
Number of successful extensions: 3
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: 273
Length of database: 317
Length adjustment: 26
Effective length of query: 247
Effective length of database: 291
Effective search space:    71877
Effective search space used:    71877
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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