Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate SMc04389 SMc04389 hydroxypyruvate reductase
Query= reanno::psRCH2:GFF1145 (423 letters) >FitnessBrowser__Smeli:SMc04389 Length = 455 Score = 381 bits (979), Expect = e-110 Identities = 207/420 (49%), Positives = 273/420 (65%), Gaps = 3/420 (0%) Query: 2 TLDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEGE 61 +++P+ L LF++A+ AA P + HLP GR IV+GAGKAA+ MA A E++W+G Sbjct: 35 SIEPRPFLISLFEAAVAAADPEAAIRAHLPARPKGRTIVVGAGKAASQMAAAFERLWDGP 94 Query: 62 LSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGGG 121 L+G VV R+ C RI V+++AHPVPD+AG + +LE V L D V+ L+SGGG Sbjct: 95 LAGAVVARHGPVEKCGRIRVLQSAHPVPDEAGLAASAALLETVGGLTADDLVVALISGGG 154 Query: 122 SSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYTY 181 S+LL P G++L D+ A+NKALL SGA I MN VRKH+S IKGGRLA A PA V + Sbjct: 155 SALLPAPPGGLTLEDEIAVNKALLASGAPISAMNVVRKHVSRIKGGRLALAAAPARVVSL 214 Query: 182 AISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGDP 241 +SDVPGD +ASGPTVAD ++ E+A EI+ RY I +P V A L + +P D Sbjct: 215 VVSDVPGDNPAFVASGPTVADRSSLEEAREIVARYAIALPERVTAHLASDAARAPRPDDA 274 Query: 242 MLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLHG 300 + + +IA+ SL+AAA AR +GI +IL D +EGEAR++ ++HA +AR+V Sbjct: 275 AFAGNEVHVIASASVSLEAAAARARESGIEAMILSDAIEGEARDIGRMHAALAREVASRN 334 Query: 301 QPIAAPCVILSGGETTVTVRGN--GRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGS 358 +P + P V+LSGGETTVT+ G G+GGRN+EFLL+L ++ G+ + ALA DTDGIDGS Sbjct: 335 RPFSKPVVLLSGGETTVTISGERYGKGGRNSEFLLSLALDIDGIGGIDALAADTDGIDGS 394 Query: 359 EDNAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILI 418 EDNAGA S R G LA +D + FAA DL V GPT TNVND RAILI Sbjct: 395 EDNAGAFADGASIGRMRAAGADPRSHLAGHDAWTAFAASGDLFVPGPTGTNVNDLRAILI 454 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: 510 Number of extensions: 23 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: 455 Length adjustment: 32 Effective length of query: 391 Effective length of database: 423 Effective search space: 165393 Effective search space used: 165393 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