GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Azospirillum brasilense Sp245

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 AZOBR_RS27980 AZOBR_RS27980 sugar ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__azobra:AZOBR_RS27980
          Length = 360

 Score =  310 bits (795), Expect = 3e-89
 Identities = 175/354 (49%), Positives = 218/354 (61%), Gaps = 24/354 (6%)

Query: 25  NLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMNDASPKDRDIAMVFQ 84
           ++DI D EF+  VGPSGCGKST LRMIAGLE+  EG + I  +L+ND  PKDRDIAMVFQ
Sbjct: 23  SVDIADGEFVALVGPSGCGKSTLLRMIAGLEEAGEGEIRIGGRLVNDVPPKDRDIAMVFQ 82

Query: 85  NYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLERKPADLSGGQRQRV 144
           NYALYPHM+V +N+ F L L+   + +I  RV  AAE+LGL+  L+R+P  LSGGQRQRV
Sbjct: 83  NYALYPHMTVAQNLGFALTLKDVDRGEIAARVARAAEVLGLSALLDRRPGQLSGGQRQRV 142

Query: 145 AMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVTHDQTEAMTLAD 204
           AMGRAIVRD ++FL DEPLSNLDAKLRV MRAEI  +H+R+  + IYVTHDQ EAMT+AD
Sbjct: 143 AMGRAIVRDPRLFLFDEPLSNLDAKLRVQMRAEIKALHQRLRTSAIYVTHDQIEAMTMAD 202

Query: 205 RIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIGSPAMNFF--EVTVEKER 262
           RIV+M            GR+EQ G P +LY+ PAN+FVAGFIGSPAMNF    + V    
Sbjct: 203 RIVVMRD----------GRVEQAGAPLDLYDRPANRFVAGFIGSPAMNFLTGRIAVNGRA 252

Query: 263 LVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDISSDQIVHETFPNASVTADILVS 322
               DG    LP     +  +    G+   LG+RPE    D       P   V   + V 
Sbjct: 253 SFRLDG-GPDLPLSAVPLEAD----GRPAVLGLRPEHALID-------PEEGVPLHVAVV 300

Query: 323 ELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQLTFNIAKGHFFDLETEKRI 376
           E  GSE+ +  +     F      R +  PG+ + L    A  H FD    +R+
Sbjct: 301 EPTGSETQVVGQLAGQPFVGVFRERVAARPGDILPLRLPAASAHLFDAGEGRRL 354


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: 350
Number of extensions: 17
Number of successful extensions: 3
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: 360
Length adjustment: 30
Effective length of query: 347
Effective length of database: 330
Effective search space:   114510
Effective search space used:   114510
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 17 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