GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Hydrogenovibrio kuenenii DSM 12350

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_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>NCBI__GCF_000526715.1:WP_024851725.1
          Length = 282

 Score =  138 bits (348), Expect = 2e-37
 Identities = 83/201 (41%), Positives = 120/201 (59%), Gaps = 10/201 (4%)

Query: 14  GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIGDRLVNDVPPK 73
           G V  ++  +L  ++ EFV  VG SGCGK+T LR+I GLE++++G + + + +VN  P K
Sbjct: 19  GAVEVLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKGQVLVDEEIVNK-PGK 77

Query: 74  DRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKD----EIDRRVKEAARILKI---EHL 126
           DR  AMVFQ+Y+LYP + V EN+ F   L+   +     +I   V  +  +L +   E +
Sbjct: 78  DR--AMVFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMVDRSYALLDLMGLEKV 135

Query: 127 LNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRLGVT 186
            +  P +LSGG RQRVA+ RA++ +P V LMDEP   LDA+ R  M   I  L      T
Sbjct: 136 QDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREVMHDLILHLFEIEKST 195

Query: 187 TIYVTHDQVEAMTLGHRIVVM 207
            ++VTHD  EA+ L  R+VVM
Sbjct: 196 IVFVTHDVEEAIYLADRVVVM 216


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: 238
Number of extensions: 14
Number of successful extensions: 3
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: 282
Length adjustment: 28
Effective length of query: 348
Effective length of database: 254
Effective search space:    88392
Effective search space used:    88392
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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