GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Phaeobacter inhibens BS107

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 GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Phaeo:GFF1645
          Length = 355

 Score =  337 bits (865), Expect = 2e-97
 Identities = 182/359 (50%), Positives = 240/359 (66%), Gaps = 15/359 (4%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA++ L  V KR+G V  ++D NL+ +DGEF+V VGPSGCGK+T LRMIAGLE I+ G+ 
Sbjct: 1   MARIELRDVAKRYGAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDF 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
            I  + +NDV P+DRDIAMVFQ+YALYPHM+V  NM F + +R+ P +E   RV  AA  
Sbjct: 61  EIDGQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAET 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           L +  L++R P+ LSGGQRQRVAMGRAI+R+P+ FL DEPLSNLDA LRVEMR EIA+L 
Sbjct: 121 LGLSSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLH 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
           ++LG T IYVTHDQVEA+TL  RIVV+  G+IQQV +PL LY+ PAN+FVA FIGSP+MN
Sbjct: 181 KQLGATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTMN 240

Query: 241 FVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEE 300
            +       G    +   G  +  + +  +A        V LG+RPEHL +     +   
Sbjct: 241 ILPVSGAASG---VMATNGMMLTLDHMHDTA------AAVELGIRPEHLDV-----VEPG 286

Query: 301 ENVLRGEVEVVEPLGAETEIHVAVNGT-LLVAKVDGHAPVKPGDKVELLADTQRLHAFD 358
           E  L    +VVE LG++T I+  V+G   L+ +  G+ PV+ G+++ L    Q  H FD
Sbjct: 287 EGHLIAVADVVERLGSDTNIYAKVDGLGPLMVRKHGNVPVRSGERLGLRVQAQNAHIFD 345


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: 408
Number of extensions: 12
Number of successful extensions: 4
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: 355
Length adjustment: 30
Effective length of query: 346
Effective length of database: 325
Effective search space:   112450
Effective search space used:   112450
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.

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