GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Synechococcus elongatus PCC 7942

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, 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_0960 Synpcc7942_0960 ATPase

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__SynE:Synpcc7942_0960
          Length = 417

 Score =  324 bits (830), Expect = 3e-93
 Identities = 192/400 (48%), Positives = 252/400 (63%), Gaps = 43/400 (10%)

Query: 1   MAKVRLEHVWKRF---------GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAG 51
           +A V  E + KRF         G+VV +   NLE  DGEF+V VGPSGCGK+T LR++AG
Sbjct: 23  VAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAG 82

Query: 52  LEEISEGNIYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLR---------- 101
           LE  S G I +GDR V+ +P K RDIAMVFQ+YALYPH++VY+N+AFGLR          
Sbjct: 83  LETPSRGLIKVGDRRVDRLPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQ 142

Query: 102 ------------LRRYPKDE--IDRRVKEAARILKIEHLLNRKPRELSGGQRQRVAMGRA 147
                       L+  P+ E  I RRV+E A +L+++ LL+R+P++LSGGQ+QRVA+GRA
Sbjct: 143 QLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRA 202

Query: 148 IVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRLGVTTIYVTHDQVEAMTLGHRIVVM 207
           I R P+VFLMDEPLSNLDAKLR E RA+I  LQR+LGVTT+YVTHDQ EAMT+G RI V+
Sbjct: 203 IARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVL 262

Query: 208 KDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVRAGVEVQGEKVYLVAPGFRIRANAV 267
             G +QQV +PL +YD PANRFVA FIGSP MN +   V      + L    FR      
Sbjct: 263 NRGHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIPVTVRA---PLQLTTENFRCTLPEA 319

Query: 268 LGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEEENVLRGEVEVVEPLGAETEI--HVAVN 325
               L+ Y G+ V LG+RPEHL +    +    +N+L   V  VE LG++T I   +  +
Sbjct: 320 WEPVLRLYDGQTVELGIRPEHLEVGAAAS----KNLLI-TVTGVEALGSDTFIAGELKES 374

Query: 326 GTLLVAKVDGHAPVKPGDKVELLADTQRLHAFDLETDRTI 365
           G  + A++      + GD++ L     ++H FDLET + I
Sbjct: 375 GIAVQARLAPQQCWQMGDRLWLTFKPDQIHLFDLETGKAI 414


Lambda     K      H
   0.320    0.139    0.400 

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: 479
Number of extensions: 17
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: 376
Length of database: 417
Length adjustment: 31
Effective length of query: 345
Effective length of database: 386
Effective search space:   133170
Effective search space used:   133170
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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