GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Burkholderia phytofirmans PsJN

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate BPHYT_RS35680 BPHYT_RS35680 sugar ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__BFirm:BPHYT_RS35680
          Length = 360

 Score =  342 bits (878), Expect = 7e-99
 Identities = 185/368 (50%), Positives = 242/368 (65%), Gaps = 12/368 (3%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA V+L  ++KR+G    V   +L+ +DGEFVV VGPSGCGK+T +RM+AGLEEIS G++
Sbjct: 1   MAAVQLSGIFKRYGDTQVVHGIDLDIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
            IG    N + P+ R+I+MVFQ+YALYPH++VYEN+AFG R+R+        R++ AA++
Sbjct: 61  MIGGTRANSLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESSASFKPRIEAAAKM 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           L +   L+R PR LSGGQRQRVAMGRA+VREP +FL DEPLSNLDAKLRV+MR EI  L 
Sbjct: 121 LNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALH 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
           +RL  T IYVTHDQ+EAMT+  RIVVM  G I+Q+  PL LYD PAN FVA F+GSPSMN
Sbjct: 181 QRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMN 240

Query: 241 FVRAGV--EVQGEKVYLVAPGFRIRANAVL-GSALKPYAGKEVWLGVRPEHLGLKGYTTI 297
           F    +    QG+ + L   G       VL G+      G +V LGVRPEH+     T  
Sbjct: 241 FAEGVIASRAQGQGLALNLTG---GGEIVLEGAPASAVVGAKVTLGVRPEHI----ETMT 293

Query: 298 PEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLHAF 357
           P  +  +  EVEVVEP GAET ++  + G+         + ++PG +V L    + +H F
Sbjct: 294 PTPDATM--EVEVVEPTGAETHLYGKIGGSTWCVTTRQRSKIEPGQRVTLRLPAEHIHLF 351

Query: 358 DLETDRTI 365
           D E+ R +
Sbjct: 352 DTESGRRL 359


Lambda     K      H
   0.320    0.139    0.400 

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: 388
Number of extensions: 13
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: 376
Length of database: 360
Length adjustment: 30
Effective length of query: 346
Effective length of database: 330
Effective search space:   114180
Effective search space used:   114180
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: 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