Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate 3609663 Dshi_3046 Hydroxypyruvate reductase (RefSeq)
Query= reanno::psRCH2:GFF1145 (423 letters) >FitnessBrowser__Dino:3609663 Length = 415 Score = 419 bits (1077), Expect = e-122 Identities = 230/420 (54%), Positives = 280/420 (66%), Gaps = 9/420 (2%) Query: 1 MTLDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEG 60 M DP+ LR LF +A+ AA P + + LP +GR +V+GAGKA+A MA+A+E W G Sbjct: 1 MIADPEPFLRGLFRAAVAAADPGLAVPNFLPAKPAGRVVVVGAGKASAKMAQAVEAAW-G 59 Query: 61 ELSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGG 120 G+V+ Y + IE+VEA HPVPD AGE A R+L LVS L E D + L+SGG Sbjct: 60 PCEGIVIVPYGGALPTEGIEIVEARHPVPDAAGEAAAGRILNLVSGLGEGDLALCLISGG 119 Query: 121 GSSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYT 180 GS+L+A P EG++LADKQA+NKALL GA I EMNC+RKHLS IKGGRL A WPA T Sbjct: 120 GSALMAAPGEGLTLADKQAVNKALLSCGAAIDEMNCLRKHLSRIKGGRLTVAAWPARTVT 179 Query: 181 YAISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGD 240 ISDVPGD+ +IASGPTVADPTT+ +A I RYH+ + V A+L+ P +ET P Sbjct: 180 LTISDVPGDDPAIIASGPTVADPTTATEARAIAARYHLALSDAVAAYLQTPAAETPDPSH 239 Query: 241 PMLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLH 299 P + + LIATPQ +L+AAA ARA G+TPLILGD LEGEA E+ V AGIAR V H Sbjct: 240 PAFAAAECHLIATPQMALEAAAATARAEGVTPLILGDALEGEAAELGIVLAGIARAAVTH 299 Query: 300 GQPIAAPCVILSGGETTVTVRGN-GRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGS 358 G P+ P V+LSGGETTVTVRG GRGGRN+E LL+ L V A+A DTDGIDGS Sbjct: 300 GHPVTGPAVLLSGGETTVTVRGGAGRGGRNSECLLSF--GLHAPEGVSAIACDTDGIDGS 357 Query: 359 EDNAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILI 418 EDNAGAL +P R A L +D Y +F L+V+GPT TNVNDFRA+ I Sbjct: 358 EDNAGALWVP----RVAAHKAEARKYLEAHDAYSFFEKAGGLVVSGPTHTNVNDFRAVYI 413 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: 523 Number of extensions: 23 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: 423 Length of database: 415 Length adjustment: 32 Effective length of query: 391 Effective length of database: 383 Effective search space: 149753 Effective search space used: 149753 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: 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