Align Glucose kinase (characterized, see rationale)
to candidate N515DRAFT_0393 N515DRAFT_0393 glucokinase
Query= uniprot:Q8P6S9 (338 letters) >FitnessBrowser__Dyella79:N515DRAFT_0393 Length = 333 Score = 280 bits (717), Expect = 3e-80 Identities = 151/318 (47%), Positives = 202/318 (63%), Gaps = 3/318 (0%) Query: 13 PRPETFVAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELSC 72 PRP+ +AADVGGTH R+ L ++ P VL Y +Y AD+PGLAEI+A F A Sbjct: 11 PRPKLVLAADVGGTHARIGLV-DAAAPAGASGVLAYERYAGADWPGLAEILADFLARHPG 69 Query: 73 APVRRGVIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYMT 132 V IA AGY + DG ++ NL W + ++R++L ++ L +VNDFEA+A+A Y+ Sbjct: 70 HAVDEAAIAVAGY-VRDGELVAENLRWPVRLAELRERLRLRRLQVVNDFEALAFATQYLG 128 Query: 133 GNQVMQLSGPAQGAPGPALVLGPGTGLGAALWIPNGGNSVVLPTEAGHAALAAASDLEVA 192 + + + A A GP V+GPGTGLG AL +P+G VLP+E GH ALA S+ E+A Sbjct: 129 ADDSLAVID-APAAAGPVAVVGPGTGLGCALLVPDGNGVTVLPSEGGHVALAPGSEREMA 187 Query: 193 LLQELRRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHE 252 LLQ L R R +V T H LSGPGL+ LY A+ L AVHA P ++AAAL G D LA + Sbjct: 188 LLQLLSRGRDYVHTGHVLSGPGLVNLYRAIGELDGLSAVHAQPEQISAAALDGGDALALD 247 Query: 253 ALQTFCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALE 312 L TFC +G VGD+ +L+ GV+LAGG LPQ+ +F+ S F R +KG +R L Sbjct: 248 TLHTFCAMLGGFVGDLAVLFKASGGVFLAGGILPQLREFLPYSAFRERFFNKGVMRDFLA 307 Query: 313 QVPVRIVEHGQLGVIGAA 330 VPVR++EHG+LGV+GAA Sbjct: 308 GVPVRLIEHGRLGVLGAA 325 Lambda K H 0.321 0.136 0.407 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: 287 Number of extensions: 11 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: 338 Length of database: 333 Length adjustment: 28 Effective length of query: 310 Effective length of database: 305 Effective search space: 94550 Effective search space used: 94550 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