Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate WP_092350489.1 BLU87_RS15075 glycerate kinase
Query= BRENDA::O58231 (440 letters) >NCBI__GCF_900107645.1:WP_092350489.1 Length = 441 Score = 328 bits (840), Expect = 3e-94 Identities = 187/437 (42%), Positives = 269/437 (61%), Gaps = 10/437 (2%) Query: 7 REIGLRLVGEAIKAADPYRAVLNAVKVSDDKIIVQGKEFEIKG--KVYVIALGKAACEMA 64 R+ +++ ++A P A+ N ++ D+ V +++ ++VI GKAA MA Sbjct: 6 RQDAIKIFHAGLQAVAPGIAIKNFCRLEDEIFTVADHRYDLSRFRNLFVIGAGKAAASMA 65 Query: 65 RAIEDILD--VEDGVAVTKYGYGKELKRIKVIEAGHPIPDEKSILGAKEALSILNRAREN 122 +A+E+IL + G+ KY + +ELKR+K+ +AGHPIPD+ + GA+ + A E Sbjct: 66 KAVEEILGERISAGLITVKYAHLEELKRVKISQAGHPIPDQNGLAGARAIYQLATSADEQ 125 Query: 123 DIVFILISGGGSALFELPEEGISLEDLKLTTDLLLKSGAKIHEINTVRKHISKVKGGKLA 182 +V LISGGGSAL LP +GISLED + TT LL GA IHEINTVRKH+S +KGG LA Sbjct: 126 TLVVCLISGGGSALLPLPVDGISLEDKQKTTQSLLSCGATIHEINTVRKHLSLLKGGGLA 185 Query: 183 KMI-KGTGIVLIISDVVGDNLEAIASGPTVKDPTTFEDAKRILELYDIWEKVPESVRLHI 241 + + T I LI+SDVVGD+L++IASGP V DP TF D K I E Y I +P +V HI Sbjct: 186 RAVYPATLISLILSDVVGDDLDSIASGPCVPDPRTFADCKSIFERYAIINVIPRNVLRHI 245 Query: 242 ERGLRGEVEETLK---EDLPNVHNFLIASNSISCEAIAREAQRLGFKAYIMTTTLEGEAK 298 + G+ G V ET K + N ++ASN + +A+ LG+ ++++ LEGEA+ Sbjct: 246 DAGIAGTVAETPKAGQKFFKRTQNVIVASNFDALLKAKEKAEDLGYHTVLLSSMLEGEAR 305 Query: 299 DAGLFIGSIVQEIAERGRPFEPPVVLVFGGETTVTIEGKGGKGGPNQEIALSATRKISDL 358 + +I +E+A G+P + P L+ GGETTV I G GKGG NQE AL+A K++ + Sbjct: 306 ELAATHVAIAREVATHGQPLQRPACLLSGGETTVKILGT-GKGGRNQEFALAAAIKMAGM 364 Query: 359 E-ALIVAFDTDGTDGPTDAAGGIVDGTTYKKLREKGIDVEKVLKEHNSYEALKKVGGLLF 417 E + I + TDG+DGPTDAAG IVDGTT+++ G+D L++++SY + L Sbjct: 365 ENSTIFSAGTDGSDGPTDAAGAIVDGTTWQRALVAGLDPHLYLEDNDSYHFFASLNDLYK 424 Query: 418 TGPTGTNVNSIVIAIVT 434 TGPT TNV + I ++T Sbjct: 425 TGPTNTNVMDLRIVLMT 441 Lambda K H 0.315 0.137 0.376 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: 444 Number of extensions: 19 Number of successful extensions: 5 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: 440 Length of database: 441 Length adjustment: 32 Effective length of query: 408 Effective length of database: 409 Effective search space: 166872 Effective search space used: 166872 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: 51 (24.3 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