GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF139 Psest_0139 ABC-type histidine
           transport system, ATPase component
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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