GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Thiothrix lacustris DSM 21227

Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= SwissProt::P19566
         (369 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  218 bits (554), Expect = 3e-61
 Identities = 109/230 (47%), Positives = 153/230 (66%)

Query: 6   LRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIGET 65
           L N++K +    V  D NL I DGEF   +GPSGCGK+T+LR+IAG E    G + +   
Sbjct: 9   LSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLNGD 68

Query: 66  RMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAEVLQLAH 125
            +  IP  +R    VFQSYAL+PHL+V +N++FGLK+AG   + +  RV     +++L+ 
Sbjct: 69  DIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRLSE 128

Query: 126 LLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLHKRLGR 185
              RKP  LSGGQ+QRVAI R +V  P++ LLDE LS LD  LR QM++E+ +L ++LG 
Sbjct: 129 FATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQLGI 188

Query: 186 TMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIG 235
           T +YVTHDQ EA++++D+I+V+  G+  QVG P E+Y  P + FVA FIG
Sbjct: 189 TFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIG 238


Lambda     K      H
   0.321    0.138    0.396 

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: 303
Number of extensions: 7
Number of successful extensions: 1
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: 369
Length of database: 369
Length adjustment: 30
Effective length of query: 339
Effective length of database: 339
Effective search space:   114921
Effective search space used:   114921
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: 49 (23.5 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