Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate AZOBR_RS07950 AZOBR_RS07950 hydroxypyruvate reductase
Query= reanno::psRCH2:GFF1145 (423 letters) >FitnessBrowser__azobra:AZOBR_RS07950 Length = 420 Score = 518 bits (1333), Expect = e-151 Identities = 267/419 (63%), Positives = 329/419 (78%), Gaps = 2/419 (0%) Query: 2 TLDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEGE 61 T DP+ALL +F +A+ +A P + HLPE GR +V+GAGKAAA+MA+A+E W+G Sbjct: 3 TTDPRALLTDMFRAAVASAQPALCVPPHLPEPPKGRTVVVGAGKAAASMAKAVEDHWKGP 62 Query: 62 LSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGGG 121 LSGLVVTRY H+ C+RIEVVEA+HPVPD+AG++ A+R+L++ ++L D ++ L+SGGG Sbjct: 63 LSGLVVTRYGHNVPCERIEVVEASHPVPDEAGQQAAKRILDIAASLGPDDLMLCLISGGG 122 Query: 122 SSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYTY 181 S+LLALPA GIS+ADKQA++KALLRSGA+I EMNCVRKHLSAIKGGRLA A A V + Sbjct: 123 SALLALPAPGISMADKQAVSKALLRSGANITEMNCVRKHLSAIKGGRLA-AATKARVVSL 181 Query: 182 AISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGDP 241 ISDVPGD+ +VIASGPTV DPT+ AL +LE+Y I P V L R E+ KPGDP Sbjct: 182 VISDVPGDDLSVIASGPTVPDPTSYADALAVLEKYGISPPQPVMDHLLAGRDESPKPGDP 241 Query: 242 MLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLHG 300 L R L+ATPQ +L+ AAEVAR AG+TP+ILG+ LEGE+REVA VHAGIARQ+V H Sbjct: 242 RLERVSTILVATPQMALERAAEVARKAGVTPVILGNALEGESREVALVHAGIARQIVEHD 301 Query: 301 QPIAAPCVILSGGETTVTVRGNGRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGSED 360 QP A PCV+LSGGETTVTVRG GRGGRNAEFLLALT L G+ V+ALA DTDGIDG+ED Sbjct: 302 QPAAKPCVLLSGGETTVTVRGKGRGGRNAEFLLALTVALDGMKGVHALAADTDGIDGTED 361 Query: 361 NAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILIL 419 NAGAL+ PD+ ARA G+ A + LA+NDGY +F+AL DL+VTGPT TNVNDFRA+L++ Sbjct: 362 NAGALLSPDTLARAAEAGVNAKERLADNDGYSFFSALGDLLVTGPTLTNVNDFRAVLVV 420 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: 523 Number of extensions: 24 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: 420 Length adjustment: 32 Effective length of query: 391 Effective length of database: 388 Effective search space: 151708 Effective search space used: 151708 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 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