GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Herbaspirillum seropedicae SmR1

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 HSERO_RS16730 HSERO_RS16730 sugar ABC transporter permease

Query= TCDB::Q72H66
         (280 letters)



>FitnessBrowser__HerbieS:HSERO_RS16730
          Length = 293

 Score =  184 bits (466), Expect = 3e-51
 Identities = 104/265 (39%), Positives = 158/265 (59%), Gaps = 4/265 (1%)

Query: 16  LVVFVVVYSVFPFYWAVISSFKPSDALFSPDPS-FLPVPFTLEHYENVFLQANFGRNLLN 74
           L++F+ V  +FPFYW VI++FKP + L S   + F  +  TL H++ +     +   LLN
Sbjct: 31  LLIFLFVL-LFPFYWMVITAFKPDNELLSQSGNPFWVIAPTLAHFKKLLFDTQYPAWLLN 89

Query: 75  SLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLGGLFLLLRQT 134
           ++IV+  +T  SL   V AAYA+ RL F     V   +    + P   +   L  ++ + 
Sbjct: 90  TVIVSVVSTFASLAASVFAAYAIERLRFQGSKQVGLGIFLAYLIPPSILFIPLAAIVFKL 149

Query: 135 GLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTLLKVMLPLTG 194
           GLF+T   LILTY  F +PF  W+L+GYFR +P ELEE A +DGAT  + L+K++LPL  
Sbjct: 150 GLFDTRWALILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDGATRWEILVKIILPLAV 209

Query: 195 PGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATPFEIPWGSIMAASVVV 254
           PGL++ G+ AF  +WNE+++ALTF     VKTVP  I +          WG++MA +++ 
Sbjct: 210 PGLISAGIFAFTLSWNEFIYALTFISSSEVKTVPVGIVT-ELVEGDVYHWGALMAGALLG 268

Query: 255 TVPLVVLVLVFQQRIVAGLTAGAVK 279
           ++P+ V+   F +  V+G+T GAVK
Sbjct: 269 SLPVAVVYSFFVEYYVSGMT-GAVK 292


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: 178
Number of extensions: 7
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 280
Length of database: 293
Length adjustment: 26
Effective length of query: 254
Effective length of database: 267
Effective search space:    67818
Effective search space used:    67818
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