Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate Ac3H11_1084 D-glycerate 2-kinase (EC 2.7.1.-)
Query= reanno::psRCH2:GFF1145 (423 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1084 Length = 465 Score = 459 bits (1180), Expect = e-133 Identities = 258/429 (60%), Positives = 293/429 (68%), Gaps = 18/429 (4%) Query: 9 LRQLFDSAIEAAHPRHVLADHLP----EDRSGRAIVIGAGKAAAAMAEAIEKVWEGE--L 62 L L+ A+ A P H A LP + GR +V+GAGKA AMA+A+E +W + L Sbjct: 37 LEYLYRVAVRRALPLHNTAAFLPAPPSRESGGRTLVLGAGKAGGAMAQAVEALWPADAPL 96 Query: 63 SGLVVTRYEHHADC-----KRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLL 117 SGLVVTRY H +RIEVVEAAHPVPD AG A R+L L L E+D V+ L+ Sbjct: 97 SGLVVTRYHHTPPRPDGLPQRIEVVEAAHPVPDAAGLAAAERILALTEGLTENDLVLCLI 156 Query: 118 SGGGSSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPAS 177 SGGGS+LL LPA+G++L DKQ INKALL SGA I EMNCVRKHLS IKGGRLA AC PA Sbjct: 157 SGGGSALLTLPADGLTLEDKQRINKALLESGAAIDEMNCVRKHLSRIKGGRLAAACAPAR 216 Query: 178 VYTYAISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLK 237 V T ISDVPGD+ +VIASGPTV D TT AL IL RY IEVP VRA LE ET K Sbjct: 217 VVTLTISDVPGDDPSVIASGPTVPDATTCADALAILARYGIEVPPAVRAALEAGTLETPK 276 Query: 238 PGDPMLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQV 296 PGD + + + ATPQQSL AAAE ARAA + IL D +EGE+REV KVHA +AR V Sbjct: 277 PGDAVFANHVVHMTATPQQSLQAAAEAARAADVAAYILSDEIEGESREVGKVHAALARAV 336 Query: 297 VLHGQPIAAPCVILSGGETTVTVR------GNGRGGRNAEFLLALTENLQGLPNVYALAG 350 HGQP A PCVILSGGETTVT+R GRGGR EF + L + LQG V+ALA Sbjct: 337 ARHGQPFARPCVILSGGETTVTIRPRAPGAAKGRGGRAGEFCMGLAQALQGQAGVWALAA 396 Query: 351 DTDGIDGSEDNAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNV 410 DTDGIDG EDNAGA + PD+ ARA GL AD L ND YGYF AL DL++TGPT TNV Sbjct: 397 DTDGIDGVEDNAGARVAPDTLARAAAQGLSIADHLDRNDAYGYFDALGDLVITGPTHTNV 456 Query: 411 NDFRAILIL 419 NDFRAILIL Sbjct: 457 NDFRAILIL 465 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: 588 Number of extensions: 29 Number of successful extensions: 4 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: 465 Length adjustment: 32 Effective length of query: 391 Effective length of database: 433 Effective search space: 169303 Effective search space used: 169303 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