GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Halococcus hamelinensis 100A6

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 WP_007693636.1 C447_RS10370 ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>NCBI__GCF_000336675.1:WP_007693636.1
          Length = 395

 Score =  342 bits (878), Expect = 8e-99
 Identities = 186/384 (48%), Positives = 245/384 (63%), Gaps = 26/384 (6%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA+V L +V KR+  +VAV D NLE  DGEFV  VGPSGCGK+TT+  +AGL   +EG I
Sbjct: 1   MAQVTLNNVTKRYDDIVAVDDMNLEIPDGEFVTLVGPSGCGKSTTMETVAGLTIPTEGEI 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
           YIGDR V ++PPKDR IAMVFQN AL+PHM+VY+N++FGLRLR + KDE DRRV  AA  
Sbjct: 61  YIGDREVTNLPPKDRGIAMVFQNIALFPHMDVYDNISFGLRLRNFDKDETDRRVDRAAET 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           +++E +L+R P E+SGGQRQRVA+ RA+VREP VFLMDEPL+NLDAKLRV MR E+ ++ 
Sbjct: 121 VQMEGMLDRMPSEMSGGQRQRVAIARALVREPDVFLMDEPLANLDAKLRVHMRTELQRIH 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
           R LG T IYVTHDQ EAMT+  RI V+ DG++QQ+  PL  Y+ PAN+FVAGFIGSPSMN
Sbjct: 181 RELGTTIIYVTHDQAEAMTMSDRIAVINDGKLQQIAPPLTCYNEPANQFVAGFIGSPSMN 240

Query: 241 FVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHL---GLKGYTTI 297
           F+R  V   G +   V   F          A+     + V +G+RPE +      G    
Sbjct: 241 FLRGTVGGNGFESEFVDVQFD-------PGAMNVSQDEPVTMGIRPEDVYPTDTAGSVAN 293

Query: 298 PEEENVLRGEVEVVEPLGAETEIHV--------------AVNGTLLVAKVDGHAPVKPGD 343
           P  E  +    +V+EP+G E  +++                 G  L+  VD  + +    
Sbjct: 294 PTTE--VEVTTDVLEPMGDEIFVYLLLADEAADTDLEDPGAGGNQLLMSVDPASDISEDQ 351

Query: 344 KVELLADTQRLHAFDLETDRTIGH 367
            + ++ D +++H FD ET   + H
Sbjct: 352 TMRVVLDREKVHLFDAETGDALEH 375


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: 464
Number of extensions: 23
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: 395
Length adjustment: 30
Effective length of query: 346
Effective length of database: 365
Effective search space:   126290
Effective search space used:   126290
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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