GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Chryseobacterium angstadtii KM

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_048508900.1 ACM46_RS22400 ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_001045465.1:WP_048508900.1
          Length = 311

 Score =  122 bits (306), Expect = 1e-32
 Identities = 79/248 (31%), Positives = 127/248 (51%), Gaps = 17/248 (6%)

Query: 4   LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63
           L+++N+Y  +   K    +N NL   + + I   G SGCGKST L +I GL D  +G + 
Sbjct: 3   LEINNLYFSHTQDKPL-FQNLNLAFEEGKIIALAGESGCGKSTLLNLIYGLLDWEKGEII 61

Query: 64  IDDKLM----NDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEA 119
            +   +     +  P + ++ +V QN+ L P+ +V EN+  G  +         + V E 
Sbjct: 62  FNGTHLLGPKGNLVPGEAEMKLVAQNFDLMPYATVAENV--GKFISNINLAQKKETVTEL 119

Query: 120 AEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIA 179
            E++GL EF    P  LSGGQ+QRVA+ RA+    K+ ++DEP SNLD   ++ +R  + 
Sbjct: 120 LEVVGLQEFAHILPKYLSGGQQQRVAIARALSVLPKLLILDEPFSNLDFPRKIELRERLF 179

Query: 180 KIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPAN 239
           +  ++   + I  TH+  E M   D+IV++            GR+ Q  +P+E Y  P N
Sbjct: 180 RYVKQHQISLIISTHELQEIMPWLDQIVVLKD----------GRLIQNDSPEETYRNPYN 229

Query: 240 KFVAGFIG 247
            +VA   G
Sbjct: 230 SYVAKLFG 237


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: 250
Number of extensions: 10
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: 377
Length of database: 311
Length adjustment: 29
Effective length of query: 348
Effective length of database: 282
Effective search space:    98136
Effective search space used:    98136
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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 (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