GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Brucella inopinata BO1

Align Maltose transport system permease protein malG aka TT_C1629, 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_004687920.1 BIBO1_RS12770 carbohydrate ABC transporter permease

Query= TCDB::Q72H66
         (280 letters)



>NCBI__GCF_000182725.1:WP_004687920.1
          Length = 291

 Score =  189 bits (479), Expect = 8e-53
 Identities = 99/283 (34%), Positives = 158/283 (55%), Gaps = 7/283 (2%)

Query: 3   RASRLLGRLFFYLLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYENV 62
           R  R + R+F+ + +   ++    P +W V+SS +P   + +  P ++P   +L+ Y  +
Sbjct: 11  RMRRRIARVFYLVGLFLAMLVICLPGFWIVLSSLRPPVEIMAKPPVWIPQDISLDAYRTM 70

Query: 63  FLQANFGR-----NLLNSLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTM 117
           F  A  G         NS+IV+  +T++SL++G+   YA  R  F  K+A     +    
Sbjct: 71  FSGAGAGGVPVWDYFRNSIIVSVTSTVVSLIIGMSGGYAFARFRFRGKSATFLGFMLTRS 130

Query: 118 FPQIAVLGGLFLLLRQTGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVD 177
            P IA+   LF++  + G+ +TH GLILTY+   +PFT+W++ G+FR +P++L EAA +D
Sbjct: 131 VPGIALSLPLFMVYSRIGIIDTHFGLILTYVALNIPFTIWLIDGFFRQVPKDLAEAAQID 190

Query: 178 GATPLQTLLKVMLPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGA 237
           G T  Q   +V  PL GPG+ + G+ AF+  WNEY  A   T   + KT+P  +  +   
Sbjct: 191 GCTRWQAFWQVEFPLAGPGIASAGIFAFLTCWNEYALASQLTRSVNSKTLPVGLLDY--T 248

Query: 238 TPFEIPWGSIMAASVVVTVPLVVLVLVFQQRIVAGLTAGAVKG 280
             F I W  + A +VV+ VP + L  V Q+ +V+GLT GAVKG
Sbjct: 249 AEFTIDWRGMCALAVVMIVPALALTFVIQKHLVSGLTFGAVKG 291


Lambda     K      H
   0.329    0.145    0.439 

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: 149
Number of extensions: 5
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: 280
Length of database: 291
Length adjustment: 26
Effective length of query: 254
Effective length of database: 265
Effective search space:    67310
Effective search space used:    67310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. 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