Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate PP_4300 PP_4300 putative hydroxypyruvate reductase
Query= reanno::psRCH2:GFF1145 (423 letters) >FitnessBrowser__Putida:PP_4300 Length = 424 Score = 654 bits (1687), Expect = 0.0 Identities = 334/419 (79%), Positives = 369/419 (88%) Query: 1 MTLDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEG 60 M++DPQ LLR+LFD+AI AAHPR VL +LP DRSGR IVIGAGKAAAAMAE +EK W+G Sbjct: 1 MSVDPQKLLRELFDTAIAAAHPRQVLEPYLPADRSGRVIVIGAGKAAAAMAEVVEKSWQG 60 Query: 61 ELSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGG 120 E+SGLVVTRY H A+C++IEVVEAAHPVPD AG VA+RVLELVSNL E DRVIFLLSGG Sbjct: 61 EVSGLVVTRYGHGANCQKIEVVEAAHPVPDAAGLAVAKRVLELVSNLNEEDRVIFLLSGG 120 Query: 121 GSSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYT 180 GS+LLALPAEG++LADKQ INKALL+SGA IGEMNCVRKHLSAIKGGRLAKACWPA+VYT Sbjct: 121 GSALLALPAEGLTLADKQQINKALLKSGATIGEMNCVRKHLSAIKGGRLAKACWPATVYT 180 Query: 181 YAISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGD 240 YAISDVPGD ATVIASGPTVADP+TS AL IL+RY+IE P V WL +P SET+K D Sbjct: 181 YAISDVPGDLATVIASGPTVADPSTSADALAILKRYNIEAPKAVIDWLNNPASETVKADD 240 Query: 241 PMLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGDLEGEAREVAKVHAGIARQVVLHG 300 P L+RSHF+LIA PQQSL+AAA AR AG +PLILGDLEGE+REVAKVHAGIARQ+V HG Sbjct: 241 PALARSHFQLIAKPQQSLEAAAVKARQAGFSPLILGDLEGESREVAKVHAGIARQIVQHG 300 Query: 301 QPIAAPCVILSGGETTVTVRGNGRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGSED 360 QP+ APCVILSGGETTVTVRGNGRGGRNAEFLL+LTE+L+GLP VYALAGDTDGIDGSE+ Sbjct: 301 QPLKAPCVILSGGETTVTVRGNGRGGRNAEFLLSLTESLKGLPGVYALAGDTDGIDGSEE 360 Query: 361 NAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILIL 419 NAGA M P SYA AE LGL A+D L NN+GYGYFAALD LIVT PTRTNVNDFRAILIL Sbjct: 361 NAGAFMTPASYASAEALGLSASDELDNNNGYGYFAALDALIVTEPTRTNVNDFRAILIL 419 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: 542 Number of extensions: 18 Number of successful extensions: 1 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: 424 Length adjustment: 32 Effective length of query: 391 Effective length of database: 392 Effective search space: 153272 Effective search space used: 153272 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