GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpQ in Phaeobacter inhibens BS107

Align ABC transporter for Glycerol, permease component 2 (characterized)
to candidate GFF1646 PGA1_c16690 binding protein-dependent transport system, inner membrane component

Query= reanno::acidovorax_3H11:Ac3H11_794
         (270 letters)



>FitnessBrowser__Phaeo:GFF1646
          Length = 283

 Score =  146 bits (369), Expect = 4e-40
 Identities = 78/257 (30%), Positives = 136/257 (52%), Gaps = 2/257 (0%)

Query: 16  YLLFALLPIYWMVNMSFKTNAEILSTFS-FFPQHFTWDNYKTIFTDESWYSGYINSLIYV 74
           YL FAL P+YW++ ++   +A I S  +   P   T++N+ T+  +  + + + NSL   
Sbjct: 25  YLGFALFPLYWLMKIAITPDALIFSEGTRMLPSAVTFENFATVLFETEFLAYFRNSLTVS 84

Query: 75  SINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVFLLPFFQLYTTVGLMDT 134
                 T  +A  A YAFSR+ F G + +   +L  +M P  + + P +++   +GL+++
Sbjct: 85  LGTAFFTTLIAAGAGYAFSRFVFAGKRIIIAVMLITQMFPLLMIIAPIYKIVADLGLLNS 144

Query: 135 HIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPRFFMTIFLPLIKAGVGV 194
             ++ + +  F++P A ++++ F  GIP++++E A +DG S  +   T+  PL   G+G 
Sbjct: 145 LTSLIVVYTAFNIPFATFLMQSFFDGIPKDLEEAAMMDGCSRFQALRTVVFPLTLPGLGA 204

Query: 195 AAFFCFMFSWVELLLARTLTSVN-AKPIVATMTRTVSASGMDWATLAAAGVLTIVPGAIV 253
              F F  +W ELL A  L S N A      +   VS   +DW  + AAGVL +VP  + 
Sbjct: 205 TLGFVFTAAWSELLFALMLISKNDAMTFPVGLLTFVSKFSVDWGQMMAAGVLALVPSCLF 264

Query: 254 IWFVRHYIAKGFAMGRV 270
             F++ Y+ +G   G V
Sbjct: 265 FIFIQRYLVQGLTSGAV 281


Lambda     K      H
   0.332    0.141    0.451 

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: 216
Number of extensions: 13
Number of successful extensions: 2
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: 270
Length of database: 283
Length adjustment: 25
Effective length of query: 245
Effective length of database: 258
Effective search space:    63210
Effective search space used:    63210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 47 (22.7 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