GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Caulobacter crescentus NA1000

Align Glucose kinase (characterized, see rationale)
to candidate CCNA_02133 CCNA_02133 glucokinase

Query= uniprot:Q8P6M4
         (344 letters)



>FitnessBrowser__Caulo:CCNA_02133
          Length = 331

 Score =  169 bits (427), Expect = 1e-46
 Identities = 116/316 (36%), Positives = 162/316 (51%), Gaps = 12/316 (3%)

Query: 23  LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASLDAILADFLRDS--RAVDAVVI 80
           L  D+GGT+ R   V      P  L +   YR  D+ + +  + ++LR    +  D  V+
Sbjct: 11  LVGDIGGTNARFALVEFDGQDP-RLIEPTAYRGEDYGTAEDAIEEYLRKVGVKHPDQAVV 69

Query: 81  ASAGVALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVVQLS 140
           A AG  +D G+    NL W I+   LR   G R   L+NDF A A AAP++  + + Q+ 
Sbjct: 70  AVAG-PIDHGQVHMTNLDWRISEDGLRRAGGFRNAKLINDFTAQALAAPRVGPKDLRQI- 127

Query: 141 GPTPRHAQPGGPILVVGPGTGLGAAVWINGPRQPTVLATEAGQVALASNDPDTAQVLRIL 200
           G  P   +  G + ++GPGTG G A  +    Q   LATE G VA A  D    +VLR L
Sbjct: 128 GELPTSGE--GDLAILGPGTGFGVAGLVRRHGQEIPLATEGGHVAFAPVDDVEIEVLRAL 185

Query: 201 AR--DASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHS-DDALARRCL 257
            R  D   + +E +LSGPG+ +L++ L               IT  A+    D+LA   +
Sbjct: 186 TRRLDGGRVSVERILSGPGMEDLHVDLAAAEGRGVEALTAKQITERAVEGCADSLAT--V 243

Query: 258 QLFCALLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLERI 317
             FCA+LGS  GD+AL  GA GGV++AGGI P I   L  S FRERF +KGR+      I
Sbjct: 244 NRFCAILGSTAGDIALTLGARGGVFIAGGIAPRIIDILEKSPFRERFDSKGRLSGFTRSI 303

Query: 318 PVKLVEHGQLGVLGAA 333
           P  ++ H    ++GAA
Sbjct: 304 PTHVILHPHTALIGAA 319


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: 392
Number of extensions: 23
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: 344
Length of database: 331
Length adjustment: 28
Effective length of query: 316
Effective length of database: 303
Effective search space:    95748
Effective search space used:    95748
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