GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Pseudomonas putida KT2440

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 PP_5170 PP_5170 sulfate ABC transporter, inner membrane subunit CysT

Query= TCDB::Q72H66
         (280 letters)



>FitnessBrowser__Putida:PP_5170
          Length = 272

 Score = 59.7 bits (143), Expect = 7e-14
 Identities = 67/220 (30%), Positives = 95/220 (43%), Gaps = 23/220 (10%)

Query: 64  LQANFGRNLLNSLIVAGGATLLSLVL------GVLAAYALGRLPFPPKNAVMYIVLSMTM 117
           L+ +FG  L  ++I     TLL+ VL      G     A+  LPF    AV  I L+   
Sbjct: 59  LKLSFGTALFAAIINGVIGTLLAWVLVRYTFPGRKIIDAMIDLPFALPTAVAGIALTALY 118

Query: 118 FPQIAVLGGLFLLLRQTGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVD 177
            PQ  V  G F       +  T LG+ L     TLPF V  +      +PRE+EEAA   
Sbjct: 119 APQGWV--GQFATDLGFKIAYTPLGITLALTFVTLPFVVRTVQPVLADIPREVEEAAACL 176

Query: 178 GATPLQTLLKVMLPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKT-VPPAIA---- 232
           GA PLQ    ++ P   P  +T   LAF     EY   +       +KT + P +     
Sbjct: 177 GAKPLQVFRHILAPALLPAWLTGFALAFARGVGEYGSVIFIAGNMPMKTEILPLLIMVKL 236

Query: 233 ---SFGGATPFEIPWGSIMAASVVVTVPLVVLVLVFQQRI 269
               + GAT       +I    +VV+  L++L+ + Q+RI
Sbjct: 237 DQYDYTGAT-------AIGVLMLVVSFILLLLINLLQRRI 269


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: 137
Number of extensions: 3
Number of successful extensions: 1
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: 272
Length adjustment: 25
Effective length of query: 255
Effective length of database: 247
Effective search space:    62985
Effective search space used:    62985
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 17 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