GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Thiothrix lacustris DSM 21227

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_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  320 bits (819), Expect = 5e-92
 Identities = 186/378 (49%), Positives = 235/378 (62%), Gaps = 35/378 (9%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA + L++V K +GK+ A+K  +LE + GEF+VFVGPSGCGK+T LRMIAGLE I+ G +
Sbjct: 1   MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
            +  R + +VPP  RD+AMVFQ+YALYPHM V ENM+F LRL +     I  +VK AA  
Sbjct: 61  ILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           L +   L R P+ LSGGQRQRVA+GR+IVR PKVFL DEPLSNLDA LR   R EIA L 
Sbjct: 121 LNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLH 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
           R LG TT+YVTHDQVEAMTL  R+VV++DG I+QV TPL LYD P NRFVA FIG P MN
Sbjct: 181 RELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMN 240

Query: 241 FVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEE 300
                          VAP           S    +  +   +G+RPEHL +     +  E
Sbjct: 241 ---------------VAP----------ASLFGQFPAQVAEVGIRPEHLQM-----VSPE 270

Query: 301 ENVLRGEVEVVEPLGAETEIHVAVNGTL----LVAKVDGHAPVKPGDKVEL-LADTQRLH 355
           + +L G+V +VE LG ET +HV  +       L+ ++ G   V  GD+V L   D++ +H
Sbjct: 271 DGLLAGKVVLVEALGNETLVHVRPDKVQLEEPLIVRLYGRTTVHVGDRVGLKWDDSKHIH 330

Query: 356 AFDLETDRTIGHAQERAA 373
            FD +  R     Q  AA
Sbjct: 331 YFDTKGMRLTHMTQGAAA 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: 396
Number of extensions: 18
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: 348
Length adjustment: 29
Effective length of query: 347
Effective length of database: 319
Effective search space:   110693
Effective search space used:   110693
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 Apr 09 2024. 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