GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Shewanella amazonensis SB2B

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 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__SB2B:6938538
          Length = 378

 Score =  218 bits (554), Expect = 3e-61
 Identities = 123/301 (40%), Positives = 185/301 (61%), Gaps = 25/301 (8%)

Query: 4   LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63
           LK++ + K + + +  +V++ +L I+  E    +G SG GKST LRM+AG E  TEG +Y
Sbjct: 21  LKIERVSKLFDDVR--AVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIY 78

Query: 64  IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123
           +D + + D  P +R I M+FQ+YAL+PHM+V +N+AFGLK  K  K DI++RV E  +++
Sbjct: 79  LDGQDITDLPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLV 138

Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183
            + ++ +RKP  LSGGQRQRVA+ R++ +  K+ L+DEP+  LD KLR  M+ E+ +I  
Sbjct: 139 HMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILE 198

Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243
           R+G T + VTHDQ EAMT+A RI IMS           G I Q+G+P ++Y  P ++ +A
Sbjct: 199 RVGVTCVMVTHDQEEAMTMAGRIAIMSD----------GWIAQVGSPMDIYESPNSRMIA 248

Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQ------GQEKILEEKGYLGKKVTLGIRP 297
            FIG+  +N F+  + ++   +    S  LPQ      G    LE+     K V L +RP
Sbjct: 249 EFIGT--VNLFDCEIIEDEADHAILKSPTLPQPFLIGHGVTTSLED-----KHVWLAVRP 301

Query: 298 E 298
           E
Sbjct: 302 E 302


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: 341
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: 378
Length adjustment: 30
Effective length of query: 347
Effective length of database: 348
Effective search space:   120756
Effective search space used:   120756
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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