GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Paraburkholderia bryophila 376MFSha3.1

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate H281DRAFT_02375 H281DRAFT_02375 amino acid/amide ABC transporter ATP-binding protein 1, HAAT family

Query= uniprot:D8J1T6
         (255 letters)



>FitnessBrowser__Burk376:H281DRAFT_02375
          Length = 259

 Score =  181 bits (458), Expect = 2e-50
 Identities = 97/253 (38%), Positives = 150/253 (59%), Gaps = 6/253 (2%)

Query: 1   MSQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTG 60
           +  T+L+ R +++ F G  A+NGV + + RG I+ LIGPNGAGKTT FN++T   +P  G
Sbjct: 3   LGDTILETRGLTREFKGFIAVNGVNLRVRRGSIHALIGPNGAGKTTCFNLLTKFLEPTAG 62

Query: 61  TFELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRH 120
               +G+  +   P ++A+ GI R+FQ   +F  +T L+NV +G      Q   G  F  
Sbjct: 63  QIVFNGEDITNERPAQIARRGIIRSFQISAVFPHLTALQNVRIGL-----QRSLGTAFHF 117

Query: 121 KAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEP 180
             +      + +++  LL  VG+  FA      LSYG +R LEIA  LA +P+L+ LDEP
Sbjct: 118 WKSERTLRQLDDRAMDLLTQVGLTDFADVLTVELSYGRKRALEIATTLAMEPELMLLDEP 177

Query: 181 AAGMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADV 240
             GM   E +     L+K  + G+TIL++EH++ ++ G+ + ITVL  G+ +AEG  A+V
Sbjct: 178 TQGM-GHEDVDRVTALIKKVSSGRTILMVEHNMNVIAGISDTITVLQRGEVLAEGSYAEV 236

Query: 241 QKNPAVIEAYLGA 253
            KNP V++AY+G+
Sbjct: 237 SKNPLVMQAYMGS 249


Lambda     K      H
   0.320    0.138    0.394 

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: 170
Number of extensions: 8
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: 255
Length of database: 259
Length adjustment: 24
Effective length of query: 231
Effective length of database: 235
Effective search space:    54285
Effective search space used:    54285
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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