Align Glucose kinase (characterized, see rationale)
to candidate GFF1854 Psest_1893 glucokinase, proteobacterial type
Query= uniprot:Q8P6S9 (338 letters) >FitnessBrowser__psRCH2:GFF1854 Length = 320 Score = 164 bits (416), Expect = 2e-45 Identities = 116/318 (36%), Positives = 163/318 (51%), Gaps = 16/318 (5%) Query: 17 TFVAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELS--CAP 74 T + D+GGT+ R AL + + R ADY + A+ E+ Sbjct: 3 TALVGDIGGTNARFALWRDQR-------IEQIRVLPTADYASPELAIRAYLREVDQPLDA 55 Query: 75 VRRGVIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYM-TG 133 + +A AG D T N W L+ E ++LG++ L L+NDF A+A + G Sbjct: 56 LEAVCLACAGPVGGDLFRFTNN-HWQLSREAFCRELGVKELLLINDFTAMALGMTRLHDG 114 Query: 134 NQVMQLSGPAQGAPG-PALVLGPGTGLGAALWIP-NGGNSVVLPTEAGHAALAAASDLEV 191 ++ G + PG P LV+GPGTGLG A +P +GG LP E GH L S+ E Sbjct: 115 ERITVCQGEPE--PGRPRLVIGPGTGLGVAGLLPLSGGGWRALPGEGGHICLPIGSEREA 172 Query: 192 ALLQELRRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAH 251 A+ L R++ HV E LSGPGLLTLY A L +PAA+T AALAG D A Sbjct: 173 AIWAHLHRSQGHVNAEAVLSGPGLLTLYRACCALDGQQVEFDSPAAITKAALAG-DAYAT 231 Query: 252 EALQTFCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPAL 311 L+ FC ++G +VGD +L G R GVY+ GG +P+ A+ RS F+ L +KG + Sbjct: 232 AVLEQFCRWLGRIVGDNVLTLGARGGVYIVGGVVPRFAEMFLRSGFSEALREKGQMSRYF 291 Query: 312 EQVPVRIVEHGQLGVIGA 329 +++PV +V G+ GA Sbjct: 292 DRLPVWLVTAPYPGLEGA 309 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: 227 Number of extensions: 8 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: 320 Length adjustment: 28 Effective length of query: 310 Effective length of database: 292 Effective search space: 90520 Effective search space used: 90520 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