Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate WP_019386038.1 P735_RS0100530 glycerate kinase
Query= BRENDA::P23524 (381 letters) >NCBI__GCF_000283015.1:WP_019386038.1 Length = 374 Score = 298 bits (762), Expect = 2e-85 Identities = 157/359 (43%), Positives = 227/359 (63%) Query: 1 MKIVIAPDSYKESLSASEVAQAIEKGFREIFPDAQYVSVPVADGGEGTVEAMIAATQGAE 60 MKIV+APD +KESL+ + A E+G +E FP+AQ + +P+ADGG+GT++ + QG Sbjct: 1 MKIVLAPDKFKESLTGMQFCAAAEEGIKETFPNAQIIKLPLADGGDGTIDVLEYHLQGKR 60 Query: 61 RHAWVTGPLGEKVNASWGISGDGKTAFIEMAAASGLELVPAEKRDPLVTTSRGTGELILQ 120 V PL + +S+ +TAFIEMA ASG+ L+ E+++ TT+ GTGELI+ Sbjct: 61 IKIKVNDPLFRPIESSYLFMDTIETAFIEMAEASGMHLLKKEEQNCYFTTTLGTGELIVD 120 Query: 121 ALESGATNIIIGIGGSATNDGGAGMVQALGAKLCDANGNEIGFGGGSLNTLNDIDISGLD 180 A++ GA II+GIGGSATND G GM ALG K D NG ++ G +LN ++ I+ + Sbjct: 121 AIDKGAKTIILGIGGSATNDCGIGMATALGFKFEDENGKDLLPIGKNLNKIHAINTHKVL 180 Query: 181 PRLKDCVIRVACDVTNPLVGDNGASRIFGPQKGASEAMIVELDNNLSHYAEVIKKALHVD 240 LK +VACDVTNPL G GA+ I+GPQKGASE I LD+ L + A + KK ++D Sbjct: 181 SGLKHIKFKVACDVTNPLYGKEGAAYIYGPQKGASETEIKNLDDGLKNIAMLFKKQFNID 240 Query: 241 VKDVPGAGAAGGMGAALMAFLGAELKSGIEIVTTALNLEEHIHDCTLVITGEGRIDSQSI 300 V+ + G GAAGGMGA FL A+LKSGI+++ + ++ I + ++TGEG++DSQ++ Sbjct: 241 VQKIKGTGAAGGMGAGTFTFLNADLKSGIDLIKDLIGFDDKIKEADWIVTGEGKLDSQTL 300 Query: 301 HGKVPIGVANVAKKYHKPVIGIAGSLTDDVGVVHQHGIDAVFSVLTSIGTLDEAFRGAY 359 GK GV AKKY+ PV + GS+T + + GI V +V+ +L++A + Y Sbjct: 301 SGKTISGVLESAKKYNIPVAALCGSVTLSIKQANDLGICYVGAVIKKANSLEDAMQNGY 359 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: 418 Number of extensions: 20 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: 374 Length adjustment: 30 Effective length of query: 351 Effective length of database: 344 Effective search space: 120744 Effective search space used: 120744 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 24 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