GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Phyllobacterium brassicacearum STM 196

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 WP_106712770.1 CU102_RS19475 carbohydrate ABC transporter permease

Query= TCDB::Q72H66
         (280 letters)



>NCBI__GCF_003010955.1:WP_106712770.1
          Length = 289

 Score =  206 bits (525), Expect = 4e-58
 Identities = 111/281 (39%), Positives = 159/281 (56%), Gaps = 4/281 (1%)

Query: 2   RRASRLLGRLFFYLLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYEN 61
           +R+  L  RL  YL ++  +V ++FP YW   +SFK    +F+  P +LP   TL+HY+ 
Sbjct: 11  KRSRELFVRLSAYLTILVALVVTLFPVYWIAANSFKFDIDIFAVPPEWLPRHPTLKHYDE 70

Query: 62  VFLQANFGRNLLNSLIVAGGATLLSLVLGVLAAYALGRLPFPP--KNAVMYIVLSMTMFP 119
            F+Q  F R  LNS +VA G T++S+  G +A YAL R  +P   +  + + +LS  M P
Sbjct: 71  AFIQRPFLRYALNSFLVAMGTTVVSVGFGTMAGYALARFSYPWQWRKQISFWILSTRMMP 130

Query: 120 QIAVLGGLFLLLRQTGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGA 179
            I  +  L+L      + NT   LI+ Y  F LPF  W++  YF+ LP ELEEAA VDG 
Sbjct: 131 PIVSIIPLYLFFNYFDMLNTKSALIIAYTAFNLPFATWMMKSYFQDLPVELEEAAIVDGD 190

Query: 180 TPLQTLLKVMLPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATP 239
           T     L V LPL  PGL  T +   I +WNE+L +L  T+ +  +T+P  IA  G  T 
Sbjct: 191 TRWGAFLHVALPLARPGLAATAIFCLIISWNEFLLSLIITLTEQSQTLPIGIA--GRVTQ 248

Query: 240 FEIPWGSIMAASVVVTVPLVVLVLVFQQRIVAGLTAGAVKG 280
           ++  WG I AA  +  VP+V+   + Q+ +V GL+ GAVKG
Sbjct: 249 YKTYWGEISAAGFMACVPIVIFAFIVQKHLVRGLSLGAVKG 289


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: 146
Number of extensions: 5
Number of successful extensions: 3
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: 289
Length adjustment: 26
Effective length of query: 254
Effective length of database: 263
Effective search space:    66802
Effective search space used:    66802
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 24 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