GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Rhizobium johnstonii 3841

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_011654832.1 RL_RS30155 amino acid ABC transporter ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_000009265.1:WP_011654832.1
          Length = 254

 Score =  246 bits (629), Expect = 2e-70
 Identities = 131/254 (51%), Positives = 171/254 (67%), Gaps = 8/254 (3%)

Query: 1   MTSPTAP-----LISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLN 55
           MTSP+       +I+ ++++K +GA Q LR +   +   + I + GPSG GKST +RC+N
Sbjct: 1   MTSPSPAQGAETMITMERVEKWYGAFQALRDINISVRSGERIVLCGPSGSGKSTLIRCIN 60

Query: 56  RLEPISGGRLEVAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKV 115
            LE    G + V G+ L       K +  +R  VGMVFQ FNLFPHLTVLQN +LAP K 
Sbjct: 61  HLETYERGEIRVGGILLGN---QAKTIDAIRREVGMVFQQFNLFPHLTVLQNCMLAPMKA 117

Query: 116 LRIPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTS 175
           + +  AEA++RA   L++V +  +AD YP QLSGGQ+QRVAIAR LCM+P+++LFDEPTS
Sbjct: 118 VGVSRAEAEERARGLLERVKILEQADKYPVQLSGGQQQRVAIARALCMRPKVMLFDEPTS 177

Query: 176 ALDPELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFR 235
           ALDPE+V EVL+ M  LA+EGMTM  VTHEM FAR+V++RV F   G I EE  P E F 
Sbjct: 178 ALDPEMVKEVLDTMIALADEGMTMICVTHEMGFARQVADRVIFMASGAIVEEAPPAEFFT 237

Query: 236 NPKSDRLRAFLSRI 249
           NP+ +R R FL  I
Sbjct: 238 NPQHERTRKFLGEI 251


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: 197
Number of extensions: 6
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: 254
Length adjustment: 24
Effective length of query: 228
Effective length of database: 230
Effective search space:    52440
Effective search space used:    52440
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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