GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpP in Azospirillum brasilense Sp245

Align ABC transporter for Glycerol, permease component 1 (characterized)
to candidate AZOBR_RS25585 AZOBR_RS25585 ABC transporter permease

Query= reanno::acidovorax_3H11:Ac3H11_793
         (298 letters)



>FitnessBrowser__azobra:AZOBR_RS25585
          Length = 301

 Score =  116 bits (290), Expect = 7e-31
 Identities = 83/269 (30%), Positives = 137/269 (50%), Gaps = 11/269 (4%)

Query: 12  AWFLILPVIICVAFSAILPLMTVVNYSVQDIISPERRVF--VGTEWFAAVMRDEELHAAL 69
           AW  +LP++I +A  A  PL   V +S  D        F  VG + +  +MRD     A+
Sbjct: 18  AWLFLLPMLIVLAGVAGWPLFRTVFFSFTDATLATLEGFQGVGLDNYLWLMRDPVWWRAV 77

Query: 70  WRQLTFSLAVLAVEIPLGILLAL----SMPAQGWKSSAVLVVVALSLLIPWNVVGTIWQ- 124
           W  L F++  + +E  LG+ +AL     +P +G   +AVL+  A+  ++   + G ++  
Sbjct: 78  WNTLVFTVVSVGIETALGLGIALILNAHLPGRGLLRAAVLIPWAIPTVVSAQMWGWMFHD 137

Query: 125 IYGRADIGLMGRMLQEMGIEYSYTGNATQAWLTVLLMDVWHWTPLVALLAFAGLRSIPDA 184
           +YG  +  LMG  L  +    ++T +   A   V+ +DVW  TP +ALL  A L+ +P  
Sbjct: 138 LYGVVNAILMGLGL--IAEPRAWTADPDLALPVVIAVDVWKSTPFMALLILAALQMLPRD 195

Query: 185 YYQAARIDGASKFAVFRYIQLPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNATTF 244
            Y+AAR+DG     VF  I LP +R  LM+AVL R +D+  ++   +VLTG     +T  
Sbjct: 196 LYEAARVDGVHPVKVFVRITLPLIRPALMVAVLFRTLDALRVFDLMYVLTGN--SRSTMS 253

Query: 245 LSQYLTTKAVGQFDLGPAAAFSLIYFFII 273
           +S Y     +   D+G  +A + +   ++
Sbjct: 254 MSVYARQYLIDFQDVGYGSAAATLLVLVL 282


Lambda     K      H
   0.328    0.140    0.439 

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: 254
Number of extensions: 14
Number of successful extensions: 3
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: 298
Length of database: 301
Length adjustment: 27
Effective length of query: 271
Effective length of database: 274
Effective search space:    74254
Effective search space used:    74254
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.

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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