GapMind for catabolism of small carbon sources

 

Aligments 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 GFF851 Psest_0865 ABC-type maltose transport systems, permease component

Query= TCDB::Q72H66
         (280 letters)



>lcl|FitnessBrowser__psRCH2:GFF851 Psest_0865 ABC-type maltose
           transport systems, permease component
          Length = 296

 Score =  112 bits (280), Expect = 1e-29
 Identities = 86/282 (30%), Positives = 136/282 (48%), Gaps = 22/282 (7%)

Query: 16  LVVFVVVYSVFPFYWAVISSFKPSD----ALFSPDPSF------LPVPFTLEHYENVFLQ 65
           L+ FV    +FP    +  SF+  +    +LF  +P+       L +P+T  H +    Q
Sbjct: 20  LLAFVAAI-LFPLLMVISISFREGNFATGSLFPENPTLEHWSLALGIPYT--HADGSVTQ 76

Query: 66  ANFGRNLL--NSLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAV 123
             F   L   NS+ +A  +++L L+L   +AYA  R+ F  K  ++  +L   MFP +  
Sbjct: 77  PPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQMFPPVLS 136

Query: 124 LGGLFLLLRQTGLFNTHLGL-----ILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDG 178
           L  ++ L  Q G   + LG+     ++   L  +   +W + GYF  +   LEEAA VDG
Sbjct: 137 LVAIYALFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDASLEEAAIVDG 196

Query: 179 ATPLQTLLKVMLPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGAT 238
           AT  Q    ++LP++ P L    +LAFI +  EY  A    +   V  +  ++ +     
Sbjct: 197 ATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLM--DVDKLTLSVGAQQYLY 254

Query: 239 PFEIPWGSIMAASVVVTVPLVVLVLVFQQRIVAGLTAGAVKG 280
           P    WG   AA+V+  +P+  + L  Q+ IV GLTAG VKG
Sbjct: 255 PQNYLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVKG 296


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: 169
Number of extensions: 6
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: 296
Length adjustment: 26
Effective length of query: 254
Effective length of database: 270
Effective search space:    68580
Effective search space used:    68580
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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