GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Dechlorosoma suillum PS

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 Dsui_3464 Dsui_3464 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__PS:Dsui_3464
          Length = 263

 Score =  157 bits (398), Expect = 2e-43
 Identities = 88/212 (41%), Positives = 129/212 (60%), Gaps = 9/212 (4%)

Query: 1   MAKVRLEHVWKRF----GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEIS 56
           M+ + ++ V K F    G V A+KD NL  + GEFV  +GPSGCGK+T L  +AG +  S
Sbjct: 1   MSDILIKDVQKVFKTPGGDVTALKDINLTVKQGEFVCLLGPSGCGKSTLLNAVAGFQPPS 60

Query: 57  EGNIYI-GDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVK 115
            G I I G +++   P    D  MVFQ YAL+P M V +N+AFGL++++  K EID  V 
Sbjct: 61  AGEIVIEGKKILTPGP----DRGMVFQEYALFPWMTVAQNIAFGLQIQKKEKAEIDLTVN 116

Query: 116 EAARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAE 175
           +   +L ++   +R P++LSGG RQRVA+ R +  +  + LMDEP   LDA  R  ++ E
Sbjct: 117 QLLDLLHLKDFRDRFPKDLSGGMRQRVAIARVLALDSPIMLMDEPFGALDALTRRNLQDE 176

Query: 176 IAKLQRRLGVTTIYVTHDQVEAMTLGHRIVVM 207
           + ++  +L  T ++VTH   E++ L  RIVVM
Sbjct: 177 LLRIWEKLNKTILFVTHSIEESIYLADRIVVM 208


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: 247
Number of extensions: 11
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: 263
Length adjustment: 27
Effective length of query: 349
Effective length of database: 236
Effective search space:    82364
Effective search space used:    82364
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: 48 (23.1 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