Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate BWI76_RS23730 BWI76_RS23730 glycerate kinase
Query= BRENDA::P23524 (381 letters) >FitnessBrowser__Koxy:BWI76_RS23730 Length = 391 Score = 285 bits (730), Expect = 1e-81 Identities = 160/383 (41%), Positives = 227/383 (59%), Gaps = 6/383 (1%) Query: 1 MKIVIAPDSYKESLSASEVAQAIEKGFREIFPDAQYVSVPVADGGEGTVEAMIAATQ--G 58 MKIVIA DS+K S SA A+ +G R + + V +PV+DGGEG + + + Q G Sbjct: 1 MKIVIALDSFKGSCSAQAACAAVARGLRRVDEALELVEMPVSDGGEGLLSTLAESPQLKG 60 Query: 59 AE-RHAWVTGPLGEKVNASWGISGDGKTAFIEMAAASGLELVPAEKRDPLVTTSRGTGEL 117 A + T P G V A++ I G+ A IEMA + GLEL P +RD + +S G GE Sbjct: 61 ARWQQQRCTSPYGLAVQAAFLIL-PGERAIIEMAQSCGLELTPKAQRDVRLASSFGLGEQ 119 Query: 118 ILQALESGATNIIIGIGGSATNDGGAGMVQALGAKLCDANGN--EIGFGGGSLNTLNDID 175 + AL++G +IIG+GGSATNDGG G QALGA+ +G + G L + ID Sbjct: 120 VKAALDAGCRRLIIGLGGSATNDGGIGFAQALGARFLRKDGTLLPVPAAGQDLAHIQRID 179 Query: 176 ISGLDPRLKDCVIRVACDVTNPLVGDNGASRIFGPQKGASEAMIVELDNNLSHYAEVIKK 235 +S LDPRL+ I+ +CDVTNPL+G +GA+ ++G QKGA EA + EL+ ++HY+ + + Sbjct: 180 LSELDPRLRQAEIQASCDVTNPLLGTDGATWVYGAQKGADEAALSELEAGMAHYSRQLTQ 239 Query: 236 ALHVDVKDVPGAGAAGGMGAALMAFLGAELKSGIEIVTTALNLEEHIHDCTLVITGEGRI 295 L DV + PGAGAAGGMGAAL+A+ G L+ GI++V LN + H+ D L I GEG + Sbjct: 240 TLGYDVSEAPGAGAAGGMGAALIAYAGGTLRPGIDLVLELLNADRHLSDAALTIVGEGWL 299 Query: 296 DSQSIHGKVPIGVANVAKKYHKPVIGIAGSLTDDVGVVHQHGIDAVFSVLTSIGTLDEAF 355 D QS GK P+GVA A ++ PV+ + G + ++QH IDA++S+ L E+ Sbjct: 300 DRQSAFGKAPVGVAGKAARHGVPVVALCGGRDESSRQLYQHHIDAMWSICQRPMPLAESM 359 Query: 356 RGAYDNICRASRNIAATLAIGMR 378 + A+ N+ T G R Sbjct: 360 NTCEQLLADAAENVLRTFLSGRR 382 Lambda K H 0.315 0.135 0.385 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: 403 Number of extensions: 19 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: 381 Length of database: 391 Length adjustment: 30 Effective length of query: 351 Effective length of database: 361 Effective search space: 126711 Effective search space used: 126711 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 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