GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Pseudomonas litoralis 2SM5

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_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_900105005.1:WP_090274680.1
          Length = 378

 Score =  207 bits (528), Expect = 3e-58
 Identities = 128/343 (37%), Positives = 193/343 (56%), Gaps = 32/343 (9%)

Query: 4   LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63
           +K++ + K++ +A   +V++  L I+  E    +G SG GKST LR++AG E  +EG + 
Sbjct: 21  VKIERVSKQFDDA--LAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVL 78

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

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

Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243
           R+G T I VTHDQ EAMT+A RI IM            G I Q+GTP ++Y  P N+ VA
Sbjct: 199 RVGVTCIMVTHDQEEAMTMAQRIAIMDQ----------GWIVQVGTPMDIYESPVNRHVA 248

Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVT---------LG 294
            F+GS  +N FE  +  +     D + +  PQ     L+ + YLG  VT           
Sbjct: 249 EFVGS--VNIFEGEIVADM---DDHVIIECPQ-----LDRQIYLGHGVTTRAEDKSAIYA 298

Query: 295 IRPEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGS 337
           +RPE +       E  P      ++     LG  S+ Y+K  S
Sbjct: 299 LRPEKVFVTTEQPEQ-PYNWAHGEVHDIAYLGGHSVYYIKLDS 340


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: 349
Number of extensions: 16
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 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