GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Thiothrix lacustris DSM 21227

Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  150 bits (379), Expect = 4e-41
 Identities = 86/250 (34%), Positives = 147/250 (58%), Gaps = 17/250 (6%)

Query: 5   TPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQI 64
           +P L + N+ KR+   EVL   +LT +DG+  +ILG SG GK+T LR I   E P++GQI
Sbjct: 4   SPILTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQI 63

Query: 65  LVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLG 124
           L++G+++          + A+ +  N        VFQ++ L+PH+++ DNV    +    
Sbjct: 64  LLNGDDIA--------RIPAEKRPFNT-------VFQSYALFPHLTVFDNVAFGLKMAGV 108

Query: 125 KSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSAL 184
             +  A+ +A+  LA V +++     P QLSGGQ+QR AIAR +  +PK++L DE  SAL
Sbjct: 109 DVQDIAVRVADA-LAIVRLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSAL 167

Query: 185 DPEMVQEVLNVIRALAEE-GRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFEN 243
           D ++ Q++   ++ L  + G T + VTH+   A  +S  ++ +H G  ++ GTP++++E+
Sbjct: 168 DYKLRQQMQLELKQLQRQLGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYES 227

Query: 244 PQSARCKQFM 253
           P++    QF+
Sbjct: 228 PRNLFVAQFI 237


Lambda     K      H
   0.317    0.133    0.367 

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: 196
Number of extensions: 7
Number of successful extensions: 4
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: 257
Length of database: 369
Length adjustment: 27
Effective length of query: 230
Effective length of database: 342
Effective search space:    78660
Effective search space used:    78660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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