GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Dinoroseobacter shibae DFL-12

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 3609758 Dshi_3141 ABC transporter related (RefSeq)

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Dino:3609758
          Length = 352

 Score =  322 bits (824), Expect = 1e-92
 Identities = 180/369 (48%), Positives = 241/369 (65%), Gaps = 23/369 (6%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA+V L+ + KR+G  V V + +L   D EF+V +GPSGCGKTTT+RMIAGLE+ ++G I
Sbjct: 1   MAEVILKDLTKRWGDFVGVDNQSLHVRDEEFLVLLGPSGCGKTTTMRMIAGLEDPTDGEI 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
           +IGDR+VND  PKDRD+AMVFQNY LYPHM ++EN+A+ LR+R   K EI  RV+ AA  
Sbjct: 61  WIGDRMVNDDLPKDRDVAMVFQNYGLYPHMTIFENIAYPLRVRGVDKAEIPPRVQRAAEQ 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           +++   L+RKP+ LSGGQRQRVA+ RAIVR+PKVFLMDEPLSNLDAKLRV MRAE+  L 
Sbjct: 121 VELTKFLHRKPKALSGGQRQRVALARAIVRKPKVFLMDEPLSNLDAKLRVTMRAELKHLS 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
           R L +TT+YVTHDQ+EAMTL  R+ VMK G IQQ+ TP  +Y+ PAN FVAGFIGSP+MN
Sbjct: 181 RELQITTVYVTHDQIEAMTLADRVAVMKHGVIQQLGTPDEIYNDPANLFVAGFIGSPAMN 240

Query: 241 FVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEE 300
            +   VE   + +++   G R      L     P   + + LGVR + +         + 
Sbjct: 241 LINGSVE---DGMFVTTGGTR------LVKVPSPDRARAI-LGVRADDM---------QV 281

Query: 301 ENVLRGEVEVV----EPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLHA 356
               +G+++V     E  G  T + V      ++A+ D H   +  D V +  +T  L+ 
Sbjct: 282 HEAGQGDIDVTIYAFENTGESTLLTVQWGKQRVIARGDRHLRKEQDDVVGISLNTDHLYL 341

Query: 357 FDLETDRTI 365
           FD +T+  I
Sbjct: 342 FDPDTEERI 350


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: 15
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: 376
Length of database: 352
Length adjustment: 29
Effective length of query: 347
Effective length of database: 323
Effective search space:   112081
Effective search space used:   112081
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