GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bgtA in Azospirillum brasilense Sp245

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate AZOBR_RS00690 AZOBR_RS00690 ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS00690 AZOBR_RS00690 ATP-binding
           protein
          Length = 268

 Score =  263 bits (671), Expect = 4e-75
 Identities = 141/256 (55%), Positives = 184/256 (71%), Gaps = 9/256 (3%)

Query: 2   TSPTAP-LISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPI 60
           T+P AP  +  + + K FG L+VL+GV+      DVI++IG SG GKST LRC+N LE  
Sbjct: 7   TNPNAPEAVLVENVHKRFGPLEVLKGVSLTAREGDVITLIGSSGSGKSTLLRCINMLEVP 66

Query: 61  SGGRLEVAG--VDLSGAK------IDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAP 112
             GR+ + G  + L  A+       D + + ++R R+GMVFQ FNL+ H+T+L+N++ AP
Sbjct: 67  DEGRIVIGGEAIGLKKARGGQTVPADSRQVDRIRTRLGMVFQSFNLWTHMTILENVIEAP 126

Query: 113 RKVLRIPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDE 172
             VL +P AEA DRA   LDKVG+  KA++YP QLSGGQ+QR AIAR L M+P+++LFDE
Sbjct: 127 VHVLGVPKAEAVDRARKLLDKVGILAKAESYPVQLSGGQQQRAAIARALAMQPKVMLFDE 186

Query: 173 PTSALDPELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNE 232
           PTSALDPELVGEVL V++QLAEEG TM +VTHEM FAREV++ V F +QG IEE G P+ 
Sbjct: 187 PTSALDPELVGEVLLVIRQLAEEGNTMILVTHEMGFAREVASEVVFLHQGRIEERGPPDR 246

Query: 233 VFRNPKSDRLRAFLSR 248
           V  NP+SDR+R FLSR
Sbjct: 247 VLVNPESDRVRQFLSR 262


Lambda     K      H
   0.321    0.139    0.397 

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: 234
Number of extensions: 10
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: 252
Length of database: 268
Length adjustment: 24
Effective length of query: 228
Effective length of database: 244
Effective search space:    55632
Effective search space used:    55632
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 (21.9 bits)
S2: 47 (22.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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