Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate RR42_RS02605 RR42_RS02605 hydroxypyruvate reductase
Query= reanno::psRCH2:GFF1145 (423 letters) >FitnessBrowser__Cup4G11:RR42_RS02605 Length = 439 Score = 407 bits (1047), Expect = e-118 Identities = 231/434 (53%), Positives = 296/434 (68%), Gaps = 19/434 (4%) Query: 4 DPQALLRQLFDSAIEAAHPRHVLADHLPEDRSG-RAIVIGAGKAAAAMAEAIEKVWEGE- 61 D +ALL F +A+ AA P ++ADHLP ++G R +V+GAGKAAA+MA A+E+ + + Sbjct: 7 DARALLLDSFHAAVAAADPLRIVADHLPSPQAGGRTLVVGAGKAAASMALAVERAYASQN 66 Query: 62 ----LSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLL 117 L GLVVTRY H + + V+EA HPVPD+AGER A +L L DR+I L+ Sbjct: 67 SAVQLDGLVVTRYAHGLPTEHVRVIEAGHPVPDEAGERAAAEILARAGELGPDDRLIVLV 126 Query: 118 SGGGSSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPAS 177 SGGGSSLL+LPAEGI +AD +A + LLR GA I +MN VRKHLS I+GG LA+AC A Sbjct: 127 SGGGSSLLSLPAEGIGMADLKATTQELLRCGAPITDMNIVRKHLSRIQGGHLARAC-RAP 185 Query: 178 VYTYAISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLE----DPRS 233 V T +SDV GD+ + IASGPTV D +T AL +L RY VP V+A+LE + Sbjct: 186 VTTLIVSDVAGDDPSAIASGPTVPDASTYADALAVLRRYGAVVPPVVQAYLERGARGEVA 245 Query: 234 ETLKPGDPMLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGI 292 ET KPGDP+ +R R+IAT SL AAA+ RA GI P++LGD + GEA+EVA+V+A + Sbjct: 246 ETPKPGDPLFARVENRVIATAHGSLMAAADHFRARGIQPVVLGDTVTGEAQEVARVYAAL 305 Query: 293 ARQVVLHGQPIAAPCVILSGGETTVTV-RGNG------RGGRNAEFLLALTENLQGLPNV 345 R++ + P A P V++SGGE TVT+ +GNG RGGR +EFLL+L L G+ NV Sbjct: 306 VREIRAYNAPFAVPVVLISGGECTVTLPQGNGAAAGKPRGGRCSEFLLSLALELDGVDNV 365 Query: 346 YALAGDTDGIDGSEDNAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGP 405 YA+A DTDGIDGSEDNAGAL+ P + ARA+ G A L +D +G F A DL+VTGP Sbjct: 366 YAIAADTDGIDGSEDNAGALLDPSTLARAQAAGASARARLDAHDAWGLFDAAGDLVVTGP 425 Query: 406 TRTNVNDFRAILIL 419 TRTNVND+RAILIL Sbjct: 426 TRTNVNDYRAILIL 439 Lambda K H 0.316 0.134 0.384 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: 530 Number of extensions: 24 Number of successful extensions: 6 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: 423 Length of database: 439 Length adjustment: 32 Effective length of query: 391 Effective length of database: 407 Effective search space: 159137 Effective search space used: 159137 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: 41 (21.6 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