Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate 8502088 DvMF_2801 Hydroxypyruvate reductase (RefSeq)
Query= BRENDA::O58231 (440 letters) >FitnessBrowser__Miya:8502088 Length = 452 Score = 298 bits (762), Expect = 3e-85 Identities = 184/442 (41%), Positives = 260/442 (58%), Gaps = 19/442 (4%) Query: 13 LVGEAIKAADPYRAVLNAVKVSDDKIIVQGKEFEIKG--KVYVIALGKAACEMARAIEDI 70 ++ A+ A P RAV V+ + + + + G+++++ +VYV+ GK A MA A+EDI Sbjct: 12 ILSRALDAVAPDRAVHRHVRRNGNILHIAGRDYDLSAHERVYVVGAGKGAAPMAAALEDI 71 Query: 71 LD--VEDGVAVTKYGYGKELKRIKVIEAGHPIPDEKSILGAKEALSILNRARENDIVFIL 128 L V DGV V KYG+ LKRI + EA HP+PD A E L ++ A D+V Sbjct: 72 LGDRVHDGVVVVKYGHTAPLKRIALREAAHPVPDAAGERAANEILDLVRTAGPRDLVLCA 131 Query: 129 ISGGGSALFELPEEGISLEDLKLTTDLLLKSGAKIHEINTVRKHISKVKGGKLAKMIKGT 188 ++GG SAL + GI+L+D++ T LLL+ GA IHEIN +RKH+S GG LA+ Sbjct: 132 LTGGASALTPALQPGITLDDMRAATTLLLECGATIHEINALRKHLSAFGGGNLARAAAPA 191 Query: 189 GIV-LIISDVVGDNLEAIASGPTVKDPTTFEDAKRILELYDIWEKVPESVRLHIERGLRG 247 +V LIISDVVGD+L+ IASGPT D +T+ D K I + I ++PE V + GLRG Sbjct: 192 RVVSLIISDVVGDDLDVIASGPTSPDVSTYADCKSIAYRFGILHRLPEPVVERLTAGLRG 251 Query: 248 EVEETLKEDLP---NVHNFLIASNSISCEAIAREAQRLGFKAYIMTTTLEGEAKDAGLFI 304 ET K P V N ++ASN ++ EA A A G++ I+T T+ GEA+ + Sbjct: 252 MAAETPKPGDPVFGAVQNCIVASNRLALEAAAEAAAAHGYRPRILTDTMTGEAR---VRA 308 Query: 305 GSIVQEIAE--RGRPF-EPPVVLVFGGETTVTIEGKGGKGGPNQEIALSATRKISDL--- 358 +V+E A G P E P L+ GGETTVTI G GG GG NQE+AL+A ++ +L Sbjct: 309 RELVEEAASAAEGLPHPEGPFCLLAGGETTVTITG-GGLGGRNQEMALAAAIRMDELADC 367 Query: 359 -EALIVAFDTDGTDGPTDAAGGIVDGTTYKKLREKGIDVEKVLKEHNSYEALKKVGGLLF 417 ++ TDGTDGPTDAAGG G+T R+ G+D L ++++Y L + G LL Sbjct: 368 QHIAMLCAGTDGTDGPTDAAGGYASGSTLCVARQCGVDAHGHLADNDAYHFLDRTGHLLR 427 Query: 418 TGPTGTNVNSIVIAIVTSKRGR 439 TGPT TNV + + +V + +G+ Sbjct: 428 TGPTLTNVMDLAVLLVDAPKGK 449 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: 449 Number of extensions: 22 Number of successful extensions: 7 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: 452 Length adjustment: 32 Effective length of query: 408 Effective length of database: 420 Effective search space: 171360 Effective search space used: 171360 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 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