GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Alkalihalobacterium alkalinitrilicum DSM 22532

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_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  224 bits (572), Expect = 2e-63
 Identities = 128/302 (42%), Positives = 183/302 (60%), Gaps = 24/302 (7%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M+ ++ DN+ K Y  A   +V+  NL+I + E I  +GPSGCGK+TTLRM+AG E  T G
Sbjct: 1   MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60

Query: 61  NLYIDDKLMND----ASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRV 116
            + I D+++ D      P+ R I MVFQ+YAL+PH+++ +N+ FGL   ++K  D  KR 
Sbjct: 61  KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLN--RWKNRDKKKRA 118

Query: 117 HEAAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRA 176
            E  E++GL EF  R P++LSGGQ+QRVA+ RA+    KV LMDEP SNLDA LR  MR 
Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178

Query: 177 EIAKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNE 236
           ++  I R+  AT I VTHDQ +A  ++DR+V+M+           G I+QI  P+E+Y  
Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNE----------GIIQQIAAPKEMYRC 228

Query: 237 PANKFVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIR 296
           PAN FVA F+G   +    +  + + +    G  + LPQ  +K++E        V + IR
Sbjct: 229 PANCFVAQFVGKTNLISGTLCPDLKHVETHIG-RVCLPQETDKVIE-------NVMVSIR 280

Query: 297 PE 298
           PE
Sbjct: 281 PE 282


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: 299
Number of extensions: 12
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: 351
Length adjustment: 29
Effective length of query: 348
Effective length of database: 322
Effective search space:   112056
Effective search space used:   112056
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 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