GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Phaeacidiphilus oryzae TH49

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_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  241 bits (614), Expect = 3e-68
 Identities = 149/376 (39%), Positives = 219/376 (58%), Gaps = 14/376 (3%)

Query: 4   VRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIG 63
           +RL  + K+FG   AV   +L    G F   +G SGCGKTTTLRMI+GLE  + G I++G
Sbjct: 19  LRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLG 78

Query: 64  DRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKI 123
           D+ V D  P  R +  VFQNYAL+PH++++EN+AFGLR R      + + V++   ++++
Sbjct: 79  DQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGIRS--VKKPVEDMLDLVEL 136

Query: 124 EHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRL 183
            HL  RKP +LSGGQ+QR+A+ RA++ +P+V L+DEPL  LD KLR +M+ E+ ++Q  +
Sbjct: 137 GHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEV 196

Query: 184 GVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVR 243
           G+T ++VTHDQ EAMT+   I VM  G I+Q+ +P  LY+ P   FVA F+G    N + 
Sbjct: 197 GLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLG--QSNLIA 254

Query: 244 AGVE-VQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGL-KGYTTIPEEE 301
             VE V G+ V + A G   R+ A+  +  +  +G  V LGVRPE + + K    +P   
Sbjct: 255 GTVESVSGDVVQVAAHG---RSLALPAARCRTTSG-PVILGVRPEKVRIAKTEAEVPSGA 310

Query: 302 NVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVD---GHAPVKPGDKVELLADTQRLHAFD 358
           N L G+V     +G  T+  V +     +A  +   G    +PG +V +  D  +    D
Sbjct: 311 NHLTGKVTDASFIGVSTQYLVELPSGEELAVFEQNTGQEIQRPGAEVVVHWDPSQGFGLD 370

Query: 359 LETDRTIG-HAQERAA 373
            E D   G  A E AA
Sbjct: 371 GEQDIQAGADADEEAA 386


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: 337
Number of extensions: 14
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: 386
Length adjustment: 30
Effective length of query: 346
Effective length of database: 356
Effective search space:   123176
Effective search space used:   123176
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 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