GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Synechococcus elongatus PCC 7942

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 Synpcc7942_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like

Query= TCDB::Q72H66
         (280 letters)



>FitnessBrowser__SynE:Synpcc7942_0471
          Length = 276

 Score =  147 bits (372), Expect = 2e-40
 Identities = 90/271 (33%), Positives = 145/271 (53%), Gaps = 5/271 (1%)

Query: 11  LFFYLLVVFVVVYSVFPFYWAVISSFKPS-DALFSPDPSFLPVPFTLEHYENVFLQANFG 69
           L  YLL+  + V  + P  W V ++FK + + +F   P FLP   TL+++  V+ +   G
Sbjct: 10  LLLYLLLGTIAVAMLIPLLWLVSTAFKSAGEDIFQFPPQFLPTQPTLDNFRRVWTENPLG 69

Query: 70  RNLLNSLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLGGLFL 129
           +  LNS  VA     L+L+   LAAY L RL F  +  +  ++++  + P   V+  L++
Sbjct: 70  QYFLNSTWVALLTVGLNLLFCSLAAYPLARLEFKGRQTLFLLIVATILIPFQVVMIPLYV 129

Query: 130 LLRQTGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTLLKVM 189
           L+   GL NT+LGL+  YL     F +++L   F+G+P++LEEAA +DG   L     VM
Sbjct: 130 LIINLGLRNTYLGLVFPYL--ASAFGIFLLRQAFQGIPKDLEEAARIDGCNDLGVWWNVM 187

Query: 190 LPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATPFEIPWGSIMA 249
           +P   P L+T  +  FI +W+++L+ L         T+P  IA+   A+ F + W  + A
Sbjct: 188 IPSARPALITLAIFVFIGSWSDFLWPLIILDEPDRYTLPLGIATL--ASGFSLDWRLVAA 245

Query: 250 ASVVVTVPLVVLVLVFQQRIVAGLTAGAVKG 280
            SV+  +P+  + L  Q+ IV    A  VKG
Sbjct: 246 GSVLSILPVFGVFLALQRYIVPSAAASGVKG 276


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: 149
Number of extensions: 11
Number of successful extensions: 4
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: 276
Length adjustment: 25
Effective length of query: 255
Effective length of database: 251
Effective search space:    64005
Effective search space used:    64005
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