GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Thiothrix lacustris DSM 21227

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= TCDB::Q52666
         (263 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  147 bits (370), Expect = 4e-40
 Identities = 86/243 (35%), Positives = 144/243 (59%), Gaps = 14/243 (5%)

Query: 23  IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82
           + +S ++K +    VL D NLT+  GE   I GPSG GK+T++R I   E+   G+I+++
Sbjct: 7   LTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLN 66

Query: 83  GIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILEN----LTLAPIWVRKVPKREAEETA 138
           G     D+  I   +     VFQ + LFPHLT+ +N    L +A + V+ +  R A+  A
Sbjct: 67  G----DDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALA 122

Query: 139 MYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLD 198
           +     V++ E A + P QLSGGQ+QRVAIAR++  +PKI+L DE  SALD ++ +++  
Sbjct: 123 I-----VRLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQL 177

Query: 199 TMIQLAEE-GMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFL 257
            + QL  + G+T + VTH+   A ++++R++ M +GQ  +   P + + +P++    QF+
Sbjct: 178 ELKQLQRQLGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFI 237

Query: 258 SQI 260
            +I
Sbjct: 238 GEI 240


Lambda     K      H
   0.320    0.134    0.391 

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: 233
Number of extensions: 9
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: 263
Length of database: 369
Length adjustment: 27
Effective length of query: 236
Effective length of database: 342
Effective search space:    80712
Effective search space used:    80712
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 (21.8 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