Align Glucose kinase (characterized, see rationale)
to candidate GFF836 Psest_0850 glucokinase, proteobacterial type
Query= uniprot:Q8P6S9 (338 letters) >FitnessBrowser__psRCH2:GFF836 Length = 319 Score = 155 bits (393), Expect = 1e-42 Identities = 121/315 (38%), Positives = 153/315 (48%), Gaps = 14/315 (4%) Query: 19 VAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELSCAP--VR 76 + D+GGT+ R AL +S + R AD+ + + A L AP V Sbjct: 5 LVGDIGGTNARFALWRDSR-------LESVRVLAAADFATPEMAVEYYLASLGLAPGSVE 57 Query: 77 RGVIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYM-TGNQ 135 +A AG + T N W L L M L L+NDF A+A + + Sbjct: 58 AACLACAGPVKGEQFTFTNN-HWRLTRSDFCGALQMGELLLINDFAAMALGMTRVGEAGR 116 Query: 136 VMQLSGPAQGAPGPALVLGPGTGLGAALWIPNGGNSV-VLPTEAGHAALAAASDLEVALL 194 M +G A+ PALV+GPGTGLG A +P GG S LP E GH L A E AL Sbjct: 117 RMICAGEAE-PDAPALVIGPGTGLGVAGLLPLGGGSWRALPGEGGHVDLPVADAHEAALW 175 Query: 195 QELRRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHEAL 254 Q L HV E LSG GLL LY + T+ A+PA VTAAALAGD V A L Sbjct: 176 QMLFAQLGHVRAEDVLSGGGLLLLYRTVCTVAGLAPRLASPAEVTAAALAGDHV-AVATL 234 Query: 255 QTFCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALEQV 314 + FC ++G V G+ +L G R GVY+ GG +P+ ADF A S FA KG + L V Sbjct: 235 EQFCVWLGRVAGNNVLTLGARGGVYIVGGVVPRFADFFAASGFARGFTSKGCMSRYLGDV 294 Query: 315 PVRIVEHGQLGVIGA 329 PV +V G+ GA Sbjct: 295 PVWLVTAEFPGLEGA 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: 252 Number of extensions: 12 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: 319 Length adjustment: 28 Effective length of query: 310 Effective length of database: 291 Effective search space: 90210 Effective search space used: 90210 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