Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate Echvi_4031 Echvi_4031 glycerate kinase
Query= metacyc::MONOMER-20837 (380 letters) >FitnessBrowser__Cola:Echvi_4031 Length = 370 Score = 170 bits (431), Expect = 5e-47 Identities = 115/327 (35%), Positives = 170/327 (51%), Gaps = 12/327 (3%) Query: 1 MKIIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGEL 60 M I+IAP++FK ++ A+ A I L + A+ +CP+ADGG+GT L + +L Sbjct: 1 MNILIAPNAFKGTIPADRAAALIEEVLRQYLSHAEYQRCPIADGGDGT--CFLLGNQLKL 58 Query: 61 RRQQVRGPLG-GTVEARWGWLADSHT-AIIEMAEASGLQLVPPGQRDACTSTTYGTGELI 118 + + G G E +L +S A I+++ SGL +PP +A ++T+GTG+LI Sbjct: 59 NKIEAVGLNAIGLTEQGLIFLNESRKEAWIDVSTLSGLAGLPPFGVNAQLTSTFGTGQLI 118 Query: 119 RAALDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLP---PGGLALSRLAHIS 175 A+ GAE IIL +GGSAT D G G ++ALG D + +P PG L R+AHI Sbjct: 119 MEAIRRGAEHIILGLGGSATVDMGTGILRALGYLFLDKNGREIPMFSPG--FLERIAHI- 175 Query: 176 LENLDPRLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCAR 235 + +VRF DV N G GA +FGPQKG S ++A + Sbjct: 176 --QRPVAMNKVRFTCLCDVKNTFFGSQGAIPVFGPQKGLSEADQHVFESAAKGVFELLKA 233 Query: 236 VLPKDVRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRF 295 + D+PG GAAGG+ AF + G E V +++ V AD VITGEG+F Sbjct: 234 KGDGQLTDQPGFGAAGGIALGLSAFFSVKIEEGAHYFFEQVNMQEKVSWADWVITGEGKF 293 Query: 296 DAQTLRGKTPFGVARIAGQHNVPVIVI 322 D+Q+ GK + + +A +H ++I Sbjct: 294 DSQSAAGKGSYKLLGLANKHQKKTLLI 320 Lambda K H 0.318 0.135 0.398 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: 291 Number of extensions: 17 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: 380 Length of database: 370 Length adjustment: 30 Effective length of query: 350 Effective length of database: 340 Effective search space: 119000 Effective search space used: 119000 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: 41 (21.7 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