GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Nocardiopsis gilva YIM 90087

Align Polyphosphate glucokinase; EC 2.7.1.63; ATP-dependent glucokinase; EC 2.7.1.2; Polyphosphate--glucose phosphotransferase (uncharacterized)
to candidate WP_017616663.1 CDO52_RS13700 ROK family protein

Query= curated2:Q49988
         (324 letters)



>NCBI__GCF_002263495.1:WP_017616663.1
          Length = 260

 Score =  265 bits (676), Expect = 1e-75
 Identities = 134/245 (54%), Positives = 177/245 (72%), Gaps = 6/245 (2%)

Query: 79  GFGIDIGGSSIKGGIVDLDIGQLIGDRIKLLTPQPATPLAVAKTIAEVVNAF----GWTA 134
           G GIDIGGS IKG  VDLD G  + DR+K+ TPQPAT  AVAK +AE+  +F        
Sbjct: 9   GLGIDIGGSGIKGAPVDLDSGTFVVDRVKVATPQPATREAVAKVLAEIAASFPEQVSADC 68

Query: 135 PLGVTYPGVVTQGVVRTAANVDDSWIGTNARDIISAELNSQEVTILNDADAAGLAEGRYG 194
           PLGVT+P VV  GV  +AANVDDSW+G N   + S E+  + V +LNDADAA +AE RYG
Sbjct: 69  PLGVTFPAVVQHGVAYSAANVDDSWVGANLEHVFS-EVTGRRVHVLNDADAAAVAEHRYG 127

Query: 195 AGKNNSGLIVLLTFGTGIGSAVIHNGKLIPNTEFGHLEVDGKEAEQRAASSVKDKYKWSY 254
           A ++  G+++L T GTGIG+A++ +G+L+PNTEFGHLE+DG +AE RAASS +++   SY
Sbjct: 128 AARDAEGVVLLTTLGTGIGTALLVDGRLVPNTEFGHLEIDGHDAESRAASSAREREDLSY 187

Query: 255 RTWAKQ-VTRVLVAIENAMCPDLFIAGGGISRKADRWIPLLENRTPMVAAALQNTAGIVG 313
             WA Q + R    +E+ + PDL + GGG+SRKADR++PLL  R P++AA L+NTAGIVG
Sbjct: 188 EEWATQRLQRYYSVVEDLLSPDLIVVGGGVSRKADRFLPLLHLRAPILAARLRNTAGIVG 247

Query: 314 AAMAS 318
           AA+A+
Sbjct: 248 AAVAA 252


Lambda     K      H
   0.316    0.131    0.382 

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: 250
Number of extensions: 10
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: 324
Length of database: 260
Length adjustment: 26
Effective length of query: 298
Effective length of database: 234
Effective search space:    69732
Effective search space used:    69732
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 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