Align Glucose kinase (characterized, see rationale)
to candidate RR42_RS37395 RR42_RS37395 glucokinase
Query= uniprot:Q8P6S9 (338 letters) >FitnessBrowser__Cup4G11:RR42_RS37395 Length = 345 Score = 144 bits (362), Expect = 4e-39 Identities = 106/314 (33%), Positives = 147/314 (46%), Gaps = 19/314 (6%) Query: 12 FPRPETFVAADVGGTHVRLALACESNDPRK--PVTVLDYRKYRCADYPGLAEIMAAFFAE 69 FPR + DVGGT+VR AL P++ PVT L + AD+P L + + Sbjct: 4 FPR----LLGDVGGTNVRFAL---ETAPQRIGPVTAL-----KVADFPSLEAAVQHYLGG 51 Query: 70 L--SCAPVRRGVIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYA 127 L A R I A D RV N W + Q+++ LG+ L +NDF A+A Sbjct: 52 LPPGSARPRHAAIGLANPVTGD-RVKLTNHAWAFSISQMQRSLGLDLLLAINDFTALALG 110 Query: 128 ANYMTGNQVMQLSGPAQGAPGPALVLGPGTGLGAALWIP-NGGNSVVLPTEAGHAALAAA 186 ++ + + L P ++GPGTGLG + +P G +V L E GH L Sbjct: 111 LPHLGAHDLTLLRQGVAVTGAPLALVGPGTGLGVSGLVPARSGPAVALAGEGGHIELMPQ 170 Query: 187 SDLEVALLQELRRTRTHVATEHFLSGPGLLTLYTALATLRDAP-AVHATPAAVTAAALAG 245 ++ E + ++ V+ E LSG GL + AL P A PA VT A+ Sbjct: 171 TEDEWTAWRAAQQAFGRVSAERLLSGMGLSLTHAALHAETGTPLARQLEPAEVTEGAIHR 230 Query: 246 DDVLAHEALQTFCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKG 305 D L AL FCG +GSV D+ L+ G R GVYL GG +P+ + S F AR KG Sbjct: 231 HDPLCERALAVFCGLLGSVAADIALVLGARGGVYLGGGIVPRFVPALRNSAFNARFTAKG 290 Query: 306 PLRPALEQVPVRIV 319 L LE +PV ++ Sbjct: 291 RLSAYLESLPVYVI 304 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: 250 Number of extensions: 15 Number of successful extensions: 3 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: 345 Length adjustment: 29 Effective length of query: 309 Effective length of database: 316 Effective search space: 97644 Effective search space used: 97644 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