Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate RR42_RS19865 RR42_RS19865 hydroxypyruvate reductase
Query= reanno::psRCH2:GFF1145 (423 letters) >FitnessBrowser__Cup4G11:RR42_RS19865 Length = 437 Score = 535 bits (1378), Expect = e-156 Identities = 279/417 (66%), Positives = 321/417 (76%), Gaps = 1/417 (0%) Query: 4 DPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEGELS 63 DP+ALLR LFD+A+ A H L HLP GR +VIGAGKAAAAMA+A E W+GE+S Sbjct: 21 DPRALLRDLFDTAVAAVSASHCLVPHLPTPPKGRTVVIGAGKAAAAMAQAAEAHWQGEIS 80 Query: 64 GLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGGGSS 123 GLVVTRY H A C+RIEVVEAAHPVPD+AG+R A+R++ LV +L D V+ L+SGGGS+ Sbjct: 81 GLVVTRYGHGAPCQRIEVVEAAHPVPDEAGQRAAQRMVALVKDLSADDLVLCLISGGGSA 140 Query: 124 LLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYTYAI 183 LLA PA+GI+LADKQA+NKALL+SGA+IGEMNCVRKHLSA+KGGRLA C PA V T I Sbjct: 141 LLAAPADGITLADKQAVNKALLKSGANIGEMNCVRKHLSALKGGRLALHCAPARVETLLI 200 Query: 184 SDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGDPML 243 SD+PGD+ T+IASGPT+ D TT AL ++ +Y IEVPANVRA LE ET KPGD Sbjct: 201 SDIPGDDPTLIASGPTLPDATTCADALAVIAKYGIEVPANVRAHLESGAGETPKPGDARF 260 Query: 244 SRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLHGQP 302 +AT QQSL AAA AR G+ IL D +EGE+R+VA VHA IARQV HGQP Sbjct: 261 DGHRSVTLATAQQSLQAAAARARELGVEAHILSDSIEGESRDVALVHAAIARQVAQHGQP 320 Query: 303 IAAPCVILSGGETTVTVRGNGRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGSEDNA 362 PCVILSGGETTVTVRG+GRGGRNAEFLLAL L GLP V+A+A DTDGIDGSEDNA Sbjct: 321 FRKPCVILSGGETTVTVRGSGRGGRNAEFLLALAVALDGLPGVHAIACDTDGIDGSEDNA 380 Query: 363 GALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILIL 419 GAL+ PD+ RAE GL A L NNDGYG+FA LDDLIVTGPTRTNVNDFRAILI+ Sbjct: 381 GALLAPDTLTRAEARGLSARAHLGNNDGYGFFAGLDDLIVTGPTRTNVNDFRAILIV 437 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: 541 Number of extensions: 18 Number of successful extensions: 2 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: 437 Length adjustment: 32 Effective length of query: 391 Effective length of database: 405 Effective search space: 158355 Effective search space used: 158355 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