GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Sinorhizobium meliloti 1021

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 SM_b20235 SM_b20235 sugar ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Smeli:SM_b20235
          Length = 363

 Score =  347 bits (889), Expect = e-100
 Identities = 194/366 (53%), Positives = 244/366 (66%), Gaps = 18/366 (4%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA V + +V KRFG +  V   + E  DGEFV  VGPSGCGK+T LRMIAGLEEIS+G +
Sbjct: 1   MASVEIRNVVKRFGALEVVHGVSAEIADGEFVALVGPSGCGKSTLLRMIAGLEEISDGAV 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
            IG  +VN+V PKDR+I+MVFQNYALYPHM V ENMAF LRL R PKDE  R+V EAA +
Sbjct: 61  VIGGDIVNEVAPKDRNISMVFQNYALYPHMTVAENMAFALRLARLPKDEQKRKVGEAATM 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           L +  LL+R P +LSGGQRQRVAMGRAIVR P+VFL DEPLSNLDAKLRV+MRAEI  L 
Sbjct: 121 LGLGGLLDRYPGQLSGGQRQRVAMGRAIVRRPEVFLFDEPLSNLDAKLRVQMRAEIKGLH 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
           +RL  T+IYVTHDQ+EAMT+  RIVVM+DG ++Q+ TPL ++D+P N FVA FIGSPSMN
Sbjct: 181 QRLRTTSIYVTHDQIEAMTMADRIVVMRDGNVEQIGTPLEIFDYPRNLFVASFIGSPSMN 240

Query: 241 FVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEE 300
           F      ++GE   +V   FR     ++ +    + G  V  G+RP  L +    T P  
Sbjct: 241 F------IEGE---VVGGTFRAPGGIIIPAPDLAHKGPTV-AGIRPNKLQIG--ATGPS- 287

Query: 301 ENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLHAFDLE 360
                 +V +VEP G ET + V + G  L   +     + PGD++ L   +  +H FD +
Sbjct: 288 -----AKVLIVEPTGDETHLLVELGGAQLAMLLRERTSLAPGDEIGLAFASADVHFFDGQ 342

Query: 361 TDRTIG 366
           T   +G
Sbjct: 343 TTLRLG 348


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: 417
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: 376
Length of database: 363
Length adjustment: 30
Effective length of query: 346
Effective length of database: 333
Effective search space:   115218
Effective search space used:   115218
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