GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Pseudomonas stutzeri RCH2

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 GFF3988 Psest_4061 sulfate ABC transporter, permease protein CysT

Query= TCDB::Q72H66
         (280 letters)



>FitnessBrowser__psRCH2:GFF3988
          Length = 271

 Score = 60.5 bits (145), Expect = 4e-14
 Identities = 62/210 (29%), Positives = 90/210 (42%), Gaps = 31/210 (14%)

Query: 82  ATLLSLVLGVLAAYALGR--------------LPFPPKNAVMYIVLSMTMFPQIAVLGGL 127
           A +L+ ++G L A+ L R              LPF    AV  I L+    P   +  G 
Sbjct: 68  AAVLNGIIGTLLAWVLVRYRFAGRKIIEAMIDLPFALPTAVAGIALTALYAPNGPI--GQ 125

Query: 128 FLLLRQTGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTLLK 187
           F       +  T LG+ L     TLPF V  +      +PRE+EEAA   GA PLQ +  
Sbjct: 126 FATDLGFKIAYTPLGITLALTFVTLPFVVRTIQPVLADIPREVEEAAACLGARPLQVVRH 185

Query: 188 VMLPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKT-VPPAIA-------SFGGATP 239
           V+LP   P  +T   LAF     EY   +       +KT + P +         + GAT 
Sbjct: 186 VLLPALLPAWLTGFALAFARGVGEYGSVIFIAGNMPMKTEILPLLIMVKLDQYDYAGAT- 244

Query: 240 FEIPWGSIMAASVVVTVPLVVLVLVFQQRI 269
                 +I    +VV+  L++L+ + Q+RI
Sbjct: 245 ------AIGVLMLVVSFVLLLLINLLQRRI 268


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: 130
Number of extensions: 2
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: 271
Length adjustment: 25
Effective length of query: 255
Effective length of database: 246
Effective search space:    62730
Effective search space used:    62730
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