GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Azospirillum brasilense Sp245

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate AZOBR_RS15690 AZOBR_RS15690 glutamine ABC transporter ATP-binding protein

Query= TCDB::Q52666
         (263 letters)



>FitnessBrowser__azobra:AZOBR_RS15690
          Length = 239

 Score =  345 bits (886), Expect = e-100
 Identities = 167/236 (70%), Positives = 199/236 (84%)

Query: 28  MNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVDGIELT 87
           + KWY  FHVL+DI L VH+GERIVI GPSGSGKST+IRCIN+LE+HQ G I V+G+ + 
Sbjct: 4   VQKWYDSFHVLKDIELEVHKGERIVICGPSGSGKSTLIRCINQLEKHQKGTITVNGVTID 63

Query: 88  SDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYYLEKVKI 147
           +  +++D+VR +VGMVFQ FNLFPHLT++EN  LAP+ VR   K+EA + AM YL +V+I
Sbjct: 64  AHHRHLDQVRRDVGMVFQQFNLFPHLTVVENCMLAPMRVRGTSKQEARDIAMKYLARVRI 123

Query: 148 PEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMIQLAEEG 207
           PEQA KYPGQLSGGQQQRVAIARSLCM PK+MLFDEPTSALDPEM+KEVLDTMI LAE+G
Sbjct: 124 PEQADKYPGQLSGGQQQRVAIARSLCMNPKVMLFDEPTSALDPEMVKEVLDTMIGLAEDG 183

Query: 208 MTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLSQILGH 263
           MTMLCVTHEMGFA++VA+RVIFM  G+IVEQ  P +FF NP+SERT+ FL QIL H
Sbjct: 184 MTMLCVTHEMGFAKSVADRVIFMDRGEIVEQATPAEFFTNPKSERTRNFLGQILTH 239


Lambda     K      H
   0.320    0.134    0.391 

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: 241
Number of extensions: 3
Number of successful extensions: 1
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: 263
Length of database: 239
Length adjustment: 24
Effective length of query: 239
Effective length of database: 215
Effective search space:    51385
Effective search space used:    51385
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: 46 (22.3 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