Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate WP_011842659.1 RSPH17029_RS19190 glycerate kinase
Query= reanno::psRCH2:GFF1145 (423 letters) >NCBI__GCF_000015985.1:WP_011842659.1 Length = 423 Score = 375 bits (963), Expect = e-108 Identities = 218/415 (52%), Positives = 273/415 (65%), Gaps = 10/415 (2%) Query: 9 LRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEG--ELSGLV 66 LR LF A+EA+ P +A LP GR +V+GAGKAAA MA A+E + LSGLV Sbjct: 13 LRHLFTEAVEASKPEARIAPLLPPPPEGRILVLGAGKAAAGMARAVEAHYADAPRLSGLV 72 Query: 67 VTRY-EHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGGGSSLL 125 +TR+ + A RI V EAAHPVPD+AG +L L L D VI L+SGG SSL+ Sbjct: 73 ITRHGQGEAAPGRIAVREAAHPVPDEAGIAATEELLALTQALGPEDLVIALISGGASSLM 132 Query: 126 ALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYTYAISD 185 P G++LADK +N+ALL SGA I EMNC+R+HLS +KGGRLA AC PA V +SD Sbjct: 133 VAPLAGLTLADKVELNRALLASGATISEMNCLRRHLSRVKGGRLAAACAPARVLALLVSD 192 Query: 186 VPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGDPMLSR 245 VPGD+ +VIASGP D TT A +L R +++P A L P +E++KPGDP L+R Sbjct: 193 VPGDDPSVIASGPCHGDATTVADAQAVLGRLGLDLPRIADA-LARPEAESVKPGDPRLAR 251 Query: 246 SHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLHGQPIA 304 ++ +PQ +L+AAAE ARAAG+ ILGD LEGEARE ++ AGIARQVVL QP A Sbjct: 252 VESHIVCSPQMALEAAAEAARAAGVAAHILGDALEGEAREAGRLMAGIARQVVLRDQPFA 311 Query: 305 APCVILSGGETTVTVRG-NGRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGSEDNAG 363 PC++LSGGETTV++RG G GGRN EFLLA + LP +ALA DTDG+DG + AG Sbjct: 312 RPCLLLSGGETTVSIRGPAGVGGRNVEFLLAYLLAARDLPG-WALAADTDGVDGGAEVAG 370 Query: 364 ALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILI 418 A+ A G A+ALA +D + +FAA +VTGPT TNVNDFRAIL+ Sbjct: 371 AV---GGAAVLHAAGRDPAEALAGHDAHSFFAAAGAQVVTGPTGTNVNDFRAILL 422 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: 502 Number of extensions: 31 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: 423 Length of database: 423 Length adjustment: 32 Effective length of query: 391 Effective length of database: 391 Effective search space: 152881 Effective search space used: 152881 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 Apr 10 2024. 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