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 GFF851 Psest_0865 ABC-type maltose transport systems, permease component

Query= TCDB::Q72H66
         (280 letters)



>FitnessBrowser__psRCH2:GFF851
          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:

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