Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate BWI76_RS22820 BWI76_RS22820 glycerate kinase
Query= BRENDA::P23524 (381 letters) >FitnessBrowser__Koxy:BWI76_RS22820 Length = 379 Score = 480 bits (1236), Expect = e-140 Identities = 251/376 (66%), Positives = 296/376 (78%) Query: 1 MKIVIAPDSYKESLSASEVAQAIEKGFREIFPDAQYVSVPVADGGEGTVEAMIAATQGAE 60 MKIVIAPDSYKESLSA +VA AIE+GFREI+ DA+YV +PVADGGEGTVEAM+AATQG Sbjct: 1 MKIVIAPDSYKESLSALDVATAIEQGFREIYADAEYVKLPVADGGEGTVEAMVAATQGCR 60 Query: 61 RHAWVTGPLGEKVNASWGISGDGKTAFIEMAAASGLELVPAEKRDPLVTTSRGTGELILQ 120 VTGPLGE V+A +G+SGD + AFIEMAAASGLE VP +R+PL+TTS GTGELI Sbjct: 61 IAVTVTGPLGEPVDAFYGLSGDKQCAFIEMAAASGLESVPPARRNPLLTTSWGTGELIRH 120 Query: 121 ALESGATNIIIGIGGSATNDGGAGMVQALGAKLCDANGNEIGFGGGSLNTLNDIDISGLD 180 AL++G T IIIGIGGSATNDGGAGMVQALGAKL + +I GG +L L ID+S LD Sbjct: 121 ALDAGVTQIIIGIGGSATNDGGAGMVQALGAKLLTKDNQQIAAGGRALENLARIDVSELD 180 Query: 181 PRLKDCVIRVACDVTNPLVGDNGASRIFGPQKGASEAMIVELDNNLSHYAEVIKKALHVD 240 RL C I VACDVTNPL G GA+ +FGPQKGA+ MI LD+ L+H+AE+I + L +D Sbjct: 181 KRLAGCRIDVACDVTNPLTGPEGATAVFGPQKGATAEMIPCLDSALAHFAEIIHRDLELD 240 Query: 241 VKDVPGAGAAGGMGAALMAFLGAELKSGIEIVTTALNLEEHIHDCTLVITGEGRIDSQSI 300 V + G GAAGGMGA L AF GA+L+ GIEIVT AL+L + + D LVITGEGRIDSQ++ Sbjct: 241 VLHLEGGGAAGGMGAGLYAFCGAKLRPGIEIVTDALHLADIVADADLVITGEGRIDSQTV 300 Query: 301 HGKVPIGVANVAKKYHKPVIGIAGSLTDDVGVVHQHGIDAVFSVLTSIGTLDEAFRGAYD 360 HGKVP+GVA VAK+Y+ PVIGIAGSLT DVGVVHQHG+DAVFSV+ SI TLDEA A + Sbjct: 301 HGKVPVGVARVAKRYNLPVIGIAGSLTSDVGVVHQHGLDAVFSVIYSICTLDEALENAAE 360 Query: 361 NICRASRNIAATLAIG 376 N+ +RN+AA L IG Sbjct: 361 NVRMTARNVAAVLKIG 376 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: 512 Number of extensions: 23 Number of successful extensions: 2 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: 379 Length adjustment: 30 Effective length of query: 351 Effective length of database: 349 Effective search space: 122499 Effective search space used: 122499 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