GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Herbaspirillum seropedicae SmR1

Align Glucose kinase (characterized, see rationale)
to candidate HSERO_RS17870 HSERO_RS17870 glucokinase

Query= uniprot:Q8P6M4
         (344 letters)



>FitnessBrowser__HerbieS:HSERO_RS17870
          Length = 333

 Score =  152 bits (385), Expect = 9e-42
 Identities = 102/302 (33%), Positives = 149/302 (49%), Gaps = 10/302 (3%)

Query: 23  LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASL-DAILADF-LRDSRAVDAVVI 80
           L AD+GGT+ R    +     P  + Q +  R AD+    DA+ A   L     V   V+
Sbjct: 18  LLADIGGTNARFALET----GPGRIEQVQILRGADYGEFTDAVQAYLKLAGHPPVRHAVV 73

Query: 81  ASAGVALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVVQLS 140
           A A     D   ++N+  W  +    R  LG   + +VNDF A++ A PQ+    + Q+ 
Sbjct: 74  AIANPVQGDQIKMTNH-DWAFSIEAARQLLGFELLLVVNDFTALSMAVPQLRADELQQVG 132

Query: 141 GPTPRHAQPGGPILVVGPGTGLGAAVWINGPRQPTVLATEAGQVALASNDPDTAQVLRIL 200
           G  P+   PG PI +VG GTGLG    ++       LA+E G  A A  DP  A VL   
Sbjct: 133 GGAPK---PGAPIGLVGAGTGLGVGGLLHADGHWLPLASEGGHAAFAPADPREAAVLAYA 189

Query: 201 ARDASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHSDDALARRCLQLF 260
            +   ++  E ++SGPGL  ++ AL  +          A I   A    DAL +  L LF
Sbjct: 190 WQFHEHVSAERLVSGPGLELIHRALLAIDGHPAAELSAAQIVEGARQHGDALCQETLALF 249

Query: 261 CALLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLERIPVK 320
           C++LG+   D+AL  GA GG+Y+  G++P +G + A S FR RF  KGRM  + + IP  
Sbjct: 250 CSMLGTVAADLALTLGALGGIYIGVGVVPHLGDYFARSPFRARFENKGRMSVLTKAIPTY 309

Query: 321 LV 322
           ++
Sbjct: 310 VI 311


Lambda     K      H
   0.321    0.136    0.410 

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: 357
Number of extensions: 23
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: 344
Length of database: 333
Length adjustment: 28
Effective length of query: 316
Effective length of database: 305
Effective search space:    96380
Effective search space used:    96380
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 (21.9 bits)
S2: 49 (23.5 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