GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Paraburkholderia bryophila 376MFSha3.1

Align Inositol transport system ATP-binding protein (characterized)
to candidate H281DRAFT_04460 H281DRAFT_04460 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= reanno::Phaeo:GFF717
         (261 letters)



>FitnessBrowser__Burk376:H281DRAFT_04460
          Length = 279

 Score =  292 bits (747), Expect = 6e-84
 Identities = 141/254 (55%), Positives = 195/254 (76%), Gaps = 1/254 (0%)

Query: 7   LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66
           ++ ++ + K+FG VIAL+GV++ +  GE HCLLGDNGAGKST IKT++GVH+P+ G  L 
Sbjct: 23  ILALENVNKYFGKVIALSGVTLRLKRGEVHCLLGDNGAGKSTLIKTLAGVHQPSSGQYLV 82

Query: 67  EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKI-GPLKLFDHDYAN 125
           +G+P+ F  P+DA+  GIATV+Q LA++PL+SV+RNFFMG EP RK+ G L + D + + 
Sbjct: 83  DGKPVLFESPKDALDLGIATVYQDLALVPLLSVARNFFMGREPQRKLFGFLNVMDLETSA 142

Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185
               +++ +MGIN+R P Q +GT+SGGE+Q +AIARA+HFGA+VLILDEPT+ALGV+Q+ 
Sbjct: 143 TTARDKLAEMGINVRDPHQPIGTMSGGEKQCLAIARAIHFGARVLILDEPTAALGVKQSF 202

Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMA 245
           NVL  I K R +G++V+FITHNV HA  +GD FT+LNRGK+LGT  +  IS +E+ DMMA
Sbjct: 203 NVLKLIHKARAKGISVIFITHNVHHAYPIGDSFTLLNRGKSLGTFTKETISKDEVLDMMA 262

Query: 246 GGQELATLEGSLGG 259
           GG E+  + G L G
Sbjct: 263 GGAEMQKMIGELEG 276


Lambda     K      H
   0.321    0.137    0.395 

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: 269
Number of extensions: 12
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: 261
Length of database: 279
Length adjustment: 25
Effective length of query: 236
Effective length of database: 254
Effective search space:    59944
Effective search space used:    59944
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 (21.9 bits)
S2: 47 (22.7 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