GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Pseudomonas stutzeri RCH2

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate GFF139 Psest_0139 ABC-type histidine transport system, ATPase component

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__psRCH2:GFF139
          Length = 257

 Score =  244 bits (622), Expect = 2e-69
 Identities = 128/249 (51%), Positives = 171/249 (68%), Gaps = 8/249 (3%)

Query: 7   PLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLE 66
           P +    L K +G L+VL+G++      DVISI+G SG GKSTFLRC+N LE    G + 
Sbjct: 6   PALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHEGEIL 65

Query: 67  VAGVDLSGAK--------IDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRI 118
           VAG  L   +         D K L ++R  +G VFQ+FNL+PH+T+L N++ APR+VL  
Sbjct: 66  VAGEQLKLKRDKQGDLVAADGKQLNRIRSELGFVFQNFNLWPHMTILDNIIEAPRRVLGQ 125

Query: 119 PMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALD 178
             AEA + A   L KVG+  K   YP+QLSGGQ+QR AIAR L M+P+++LFDEPTSALD
Sbjct: 126 SKAEATEVAEALLAKVGIADKRHVYPNQLSGGQQQRAAIARTLAMQPKVILFDEPTSALD 185

Query: 179 PELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPK 238
           PE+V EVL V++ LAEEG TM +VTHEM FA++VS+ V F +QG++EE+G P +VF NP+
Sbjct: 186 PEMVQEVLAVIRSLAEEGRTMLLVTHEMNFAKQVSSEVVFLHQGLVEEQGTPEQVFDNPQ 245

Query: 239 SDRLRAFLS 247
           S R + F+S
Sbjct: 246 SARCKQFMS 254


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: 207
Number of extensions: 5
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: 257
Length adjustment: 24
Effective length of query: 228
Effective length of database: 233
Effective search space:    53124
Effective search space used:    53124
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:

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