GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Paucidesulfovibrio gracilis DSM 16080

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_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  221 bits (562), Expect = 4e-62
 Identities = 127/341 (37%), Positives = 207/341 (60%), Gaps = 23/341 (6%)

Query: 4   LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63
           ++L  + KR+   K  +V+  +L I   E +  +GPSGCGK+T LRMIAGLE  T+G++Y
Sbjct: 45  VRLQGLMKRF--GKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIY 102

Query: 64  IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123
           I  + +ND     R++ M+FQNYAL+PH +++EN+AFGLK R   ++++ ++V +A E++
Sbjct: 103 IKGRRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMV 162

Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183
            L    +R  + LSGGQ+QR+A+ RAIV +  V LMDEPLS LD KLR  MR EI  I +
Sbjct: 163 RLPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQ 222

Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243
           ++  TT++VTHDQ EA++++++IV+M            GR +Q GTP+++Y+ P N FVA
Sbjct: 223 QLNLTTLFVTHDQREALSMSNKIVVMKD----------GRKQQEGTPEDVYDYPDNYFVA 272

Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKG--YLGKKVTLGIRPE--D 299
            F+G    NFF+  V +  +++ D + + + +G E   +  G    G+ V L +R +  +
Sbjct: 273 DFLGH--ANFFDARVLE--VLDNDQVRVRIAEGLEFTADHVGRWRQGQDVHLVMRAQKIN 328

Query: 300 ISSDQIVHETFPNASVT---ADILVSELLGSESMLYVKFGS 337
           ++S  +  E   +  +      I     +G E+  +V+  +
Sbjct: 329 VTSPDLADEELESTDLNYYPGKIYDRSYMGGETSYFVELAN 369


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: 407
Number of extensions: 13
Number of successful extensions: 2
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: 406
Length adjustment: 31
Effective length of query: 346
Effective length of database: 375
Effective search space:   129750
Effective search space used:   129750
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