GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Thiothrix lacustris DSM 21227

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  219 bits (557), Expect = 1e-61
 Identities = 126/300 (42%), Positives = 183/300 (61%), Gaps = 15/300 (5%)

Query: 4   LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63
           L L NI KR+  A    + +FNL I D EF   +GPSGCGK+T LR+IAG E   EG + 
Sbjct: 7   LTLSNISKRF--ASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQIL 64

Query: 64  IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123
           ++   +     + R    VFQ+YAL+PH++V++N+AFGLK+      DI  RV +A  I+
Sbjct: 65  LNGDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIV 124

Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183
            L+EF  RKP  LSGGQ+QRVA+ RA+V   K+ L+DE LS LD KLR  M+ E+ ++ R
Sbjct: 125 RLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQR 184

Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243
           ++G T +YVTHDQ EA++++DRI++M            G+ +Q+GTP+E+Y  P N FVA
Sbjct: 185 QLGITFVYVTHDQEEALSMSDRILVMHN----------GQAQQVGTPREIYESPRNLFVA 234

Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDISSD 303
            FIG   +N F+  + +     Q   S+     +E   + +  +G KV + +RPED+  D
Sbjct: 235 QFIGE--INVFDGEIVQALGEYQYEASIN-GVVREIRCDHRFAVGDKVHVMLRPEDLRID 291


Lambda     K      H
   0.318    0.135    0.379 

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: 319
Number of extensions: 15
Number of successful extensions: 3
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: 377
Length of database: 369
Length adjustment: 30
Effective length of query: 347
Effective length of database: 339
Effective search space:   117633
Effective search space used:   117633
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: 50 (23.9 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