GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Desulfotomaculum hydrothermale Lam5

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_008412465.1 DESHY_RS10040 carbohydrate ABC transporter permease

Query= TCDB::Q72H66
         (280 letters)



>NCBI__GCF_000315365.1:WP_008412465.1
          Length = 279

 Score =  180 bits (457), Expect = 3e-50
 Identities = 97/274 (35%), Positives = 149/274 (54%), Gaps = 4/274 (1%)

Query: 6   RLLGRLFFYLLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYENVFLQ 65
           +L+  +  Y  +   +V+++ P  W V+SS K    +FS  P F   P T   Y  +F +
Sbjct: 10  KLIATVLIYTALAIAMVWALLPIIWMVLSSLKTEANMFSMPPKFTFKP-TFSTYAFMFTE 68

Query: 66  ANFGRNLLNSLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLG 125
            NFG  L NS+I A  +T ++L+LG L  YAL R  +     + + ++S  M P  A + 
Sbjct: 69  GNFGSFLKNSMIAAFSSTAIALILGTLGGYALARGNYRRGKDIAFWIISTRMTPVAAAIV 128

Query: 126 GLFLLLRQTGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTL 185
            L+++  +  L  T  GL+  Y  F LPF +W+++ +F  LP ++E AA VDGAT  Q  
Sbjct: 129 PLYIIFAKFNLIGTTFGLVFAYTTFNLPFALWMMMTFFAELPPDMEHAAMVDGATKFQAF 188

Query: 186 LKVMLPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATPFEIPWG 245
            ++ LP   PGLV TG+L  + AWN++ FA  FT   S +T+P A +     T   I WG
Sbjct: 189 YRIALPQVTPGLVATGILCLMFAWNDFAFASVFT-SHSNQTIPVAASLLVSQT--GIAWG 245

Query: 246 SIMAASVVVTVPLVVLVLVFQQRIVAGLTAGAVK 279
             MA   V+  P+++  L  ++ +V GL+ GAVK
Sbjct: 246 QAMATGTVIITPMLIAGLAVRKYLVRGLSMGAVK 279


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: 155
Number of extensions: 11
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: 279
Length adjustment: 26
Effective length of query: 254
Effective length of database: 253
Effective search space:    64262
Effective search space used:    64262
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