Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate 206191 DVU0765 hydroxypyruvate reductase, putative
Query= reanno::psRCH2:GFF1145 (423 letters) >MicrobesOnline__882:206191 Length = 454 Score = 279 bits (713), Expect = 1e-79 Identities = 182/443 (41%), Positives = 241/443 (54%), Gaps = 22/443 (4%) Query: 1 MTLDPQALLRQLFDSAIEAAHPRHVLADHL------------PEDRSG--RAIVIGAGKA 46 MT + +++L + +A+ A P + H+ P D +G R +V+GAGK Sbjct: 1 MTPEQRSVLNDIIGAALGAVAPDRAVHRHVRRNDETLYIGDVPYDLAGYERILVVGAGKG 60 Query: 47 AAAMAEAIEKVWEGELSG-LVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVS 105 AA MA A+E V L G LV+ +Y H +R+ + EAAHPVPD AGER A VL+LV+ Sbjct: 61 AAPMAHALEGVLGDRLDGGLVIVKYGHTMPLRRVRLREAAHPVPDAAGERAAHDVLDLVA 120 Query: 106 NLEESDRVIFLLSGGGSSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIK 165 E D V+ +L+GG S+L +GISL D + + LL GA I E+N +RKH+SA Sbjct: 121 QTTERDLVLCVLTGGASALTPALCDGISLDDMRTATRLLLECGATIHEVNALRKHVSAFG 180 Query: 166 GGRLAKACWPASVYTYAISDVPGDEATVIASGPTVADPTTSEQALEILERYHI--EVPAN 223 GG LA+ PA + ISDV GD+ VIASGPT D +T I+ RY I +PA+ Sbjct: 181 GGNLARRAAPARTASLIISDVVGDDLDVIASGPTAPDASTYADCHGIVTRYGIGTRLPAS 240 Query: 224 VRAWLEDPRS----ETLKPGDPMLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-L 278 +R LED + ET KPGDP+ RL+AT +Q+L+AAA ARA G P IL D + Sbjct: 241 IRRRLEDGLAGHAPETPKPGDPLFDHVQNRLVATNRQALEAAATAARARGYIPRILTDSM 300 Query: 279 EGEAREVAKVHAGIARQVVLHGQPIAAPCVILSGGETTVTVRGNGRGGRNAEFLLALTEN 338 GEAR A A + PC +L+GGETTVT+RG+G GGRN E LA Sbjct: 301 TGEARHKASELVDEAFRTADTFVCAEGPCCLLAGGETTVTLRGDGTGGRNQEMALAAAIA 360 Query: 339 LQGLPNVYALAGDTDGIDGSEDNAGALMMPDSYARAETLGLRAADALANNDGYGYFAALD 398 L G ++ L TDG DG D AG + A GL L +N+ Y + Sbjct: 361 LDGADHIAMLCLGTDGSDGPTDAAGGFASGLTLRTARERGLDPHRHLDDNNAYPFLEGTG 420 Query: 399 DLIVTGPTRTNVNDFRAILILPP 421 L+ TGPT TNV D A+L+ P Sbjct: 421 CLLRTGPTLTNVMDITAVLVDAP 443 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: 486 Number of extensions: 25 Number of successful extensions: 3 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: 454 Length adjustment: 32 Effective length of query: 391 Effective length of database: 422 Effective search space: 165002 Effective search space used: 165002 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