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.
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:
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