Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate BWI76_RS24820 BWI76_RS24820 glycerate 2-kinase
Query= BRENDA::P23524 (381 letters) >FitnessBrowser__Koxy:BWI76_RS24820 Length = 381 Score = 613 bits (1580), Expect = e-180 Identities = 315/381 (82%), Positives = 341/381 (89%) Query: 1 MKIVIAPDSYKESLSASEVAQAIEKGFREIFPDAQYVSVPVADGGEGTVEAMIAATQGAE 60 MKIVIAPDSYKESLSA+EVAQAIEKGFREIFPDA YV VP+ADGGEGTVEAMIAATQG E Sbjct: 1 MKIVIAPDSYKESLSATEVAQAIEKGFREIFPDALYVKVPLADGGEGTVEAMIAATQGTE 60 Query: 61 RHAWVTGPLGEKVNASWGISGDGKTAFIEMAAASGLELVPAEKRDPLVTTSRGTGELILQ 120 A VTGPLG V+A WG+SGDGKTAFIEMAAASGL LVP +R+PL+TTSRGTGELIL Sbjct: 61 MSACVTGPLGVPVDACWGLSGDGKTAFIEMAAASGLGLVPPAQRNPLLTTSRGTGELILH 120 Query: 121 ALESGATNIIIGIGGSATNDGGAGMVQALGAKLCDANGNEIGFGGGSLNTLNDIDISGLD 180 AL+ GA NIIIGIGGSATNDGGAGMVQALGA+LCDANG EIG GGGSL LN IDI+GLD Sbjct: 121 ALDHGAKNIIIGIGGSATNDGGAGMVQALGARLCDANGAEIGHGGGSLGGLNSIDITGLD 180 Query: 181 PRLKDCVIRVACDVTNPLVGDNGASRIFGPQKGASEAMIVELDNNLSHYAEVIKKALHVD 240 RL DC IRVACDVTNPL+GD GASRIFGPQKGA+EAMI ELD+NL+HYA+VIK LHVD Sbjct: 181 ARLHDCAIRVACDVTNPLIGDTGASRIFGPQKGATEAMIRELDSNLAHYADVIKADLHVD 240 Query: 241 VKDVPGAGAAGGMGAALMAFLGAELKSGIEIVTTALNLEEHIHDCTLVITGEGRIDSQSI 300 VK V GAGAAGGMGAALMAFL AEL+SGIEIVT ALNLEEHI DC+LV+TGEGR+DSQSI Sbjct: 241 VKQVAGAGAAGGMGAALMAFLNAELRSGIEIVTQALNLEEHILDCSLVVTGEGRLDSQSI 300 Query: 301 HGKVPIGVANVAKKYHKPVIGIAGSLTDDVGVVHQHGIDAVFSVLTSIGTLDEAFRGAYD 360 +GKVP+GVA+VAKKYHKPVIGIAGSLT DVGVVHQ+GIDAVFSVLTS+ TL+EAFRGA D Sbjct: 301 NGKVPVGVASVAKKYHKPVIGIAGSLTRDVGVVHQYGIDAVFSVLTSVTTLEEAFRGAAD 360 Query: 361 NICRASRNIAATLAIGMRNAG 381 NI RASRNIAATL +GM G Sbjct: 361 NIYRASRNIAATLQVGMATEG 381 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: 622 Number of extensions: 28 Number of successful extensions: 1 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: 381 Length adjustment: 30 Effective length of query: 351 Effective length of database: 351 Effective search space: 123201 Effective search space used: 123201 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