Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate WP_086510173.1 BZY95_RS12040 glycerate kinase
Query= reanno::psRCH2:GFF1145 (423 letters) >NCBI__GCF_002151265.1:WP_086510173.1 Length = 434 Score = 454 bits (1169), Expect = e-132 Identities = 248/425 (58%), Positives = 301/425 (70%), Gaps = 10/425 (2%) Query: 2 TLDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWE-- 59 T D LR+L D A+ A HP ++AD LP+ GR +V+GAGKAAAAMA A+E+ W+ Sbjct: 11 TTDIATWLRRLADVAVTAVHPDSLVADLLPDPPPGRTVVVGAGKAAAAMAAALERAWQER 70 Query: 60 ---GELSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFL 116 L+GLVVTRY H +C+ IEV+EA+HP+PDD GE+ ARR+LE V+ L + DRVI L Sbjct: 71 CPDAPLTGLVVTRYGHAEECEVIEVLEASHPMPDDLGEKAARRMLEAVAGLGQDDRVIAL 130 Query: 117 LSGGGSSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPA 176 +SGGGS+L+ LPAEGISLADKQAIN+ LLR GA IG+MN VR+HLSAIKGGRLA A PA Sbjct: 131 ISGGGSALMTLPAEGISLADKQAINRELLRCGAPIGQMNTVRRHLSAIKGGRLAAAAHPA 190 Query: 177 SVYTYAISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETL 236 V T+ ISD+PGD AT IASGPT+ D +T AL +LERY IE+PA+VR LE + Sbjct: 191 QVVTWLISDIPGDVATQIASGPTLPDRSTPADALAVLERYAIEIPAHVRRHLEQAQGAP- 249 Query: 237 KPGDPMLSRSHFRLIATPQQSLDAAAEVARAAGITPLILG-DLEGEAREVAKVHAGIARQ 295 P D R +A Q +L+AA A AAG+T +LG DLEGEARE+ + A +A + Sbjct: 250 SPDDEAFERDDSVTLARAQDALEAARAAAEAAGVTVKVLGDDLEGEARELGRAQARLALE 309 Query: 296 VVLHGQPIAAPCVILSGGETTVTVRGNGRGGRNAEFLLALTENLQGLPNVYALAGDTDGI 355 I P +ILSGGET+VTVRG+GRGGRN E+LL L E L G ++ALA DTDGI Sbjct: 310 A---RDEIETPLLILSGGETSVTVRGDGRGGRNVEYLLGLFEALAGAEGIHALAIDTDGI 366 Query: 356 DGSEDNAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRA 415 DGSEDNAGAL PD +ARA L AD L+ ND Y +F ALD LIVTGPTRTNVNDFRA Sbjct: 367 DGSEDNAGALFSPDDWARAREQRLEPADYLSRNDAYTFFQALDRLIVTGPTRTNVNDFRA 426 Query: 416 ILILP 420 IL+LP Sbjct: 427 ILVLP 431 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: 540 Number of extensions: 24 Number of successful extensions: 5 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: 434 Length adjustment: 32 Effective length of query: 391 Effective length of database: 402 Effective search space: 157182 Effective search space used: 157182 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 24 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