Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate RR42_RS33740 RR42_RS33740 hydroxypyruvate reductase
Query= reanno::psRCH2:GFF1145 (423 letters) >FitnessBrowser__Cup4G11:RR42_RS33740 Length = 431 Score = 460 bits (1184), Expect = e-134 Identities = 250/420 (59%), Positives = 300/420 (71%), Gaps = 1/420 (0%) Query: 4 DPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEGELS 63 +P+A L LF +A+ AA P+ LA LPE GR IV+GAGKAAA+MA A+E+ W G L+ Sbjct: 8 NPRAFLASLFRAAVSAADPQDCLACALPEPPVGRTIVVGAGKAAASMARALEQAWPGPLA 67 Query: 64 GLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGGGSS 123 GLVVTRY H A RIEVVEA HPVPD AG+R A R+L++VS L D VI L+SGGGSS Sbjct: 68 GLVVTRYGHAAPTSRIEVVEAGHPVPDAAGQRAAVRMLDMVSGLCPDDLVICLISGGGSS 127 Query: 124 LLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYTYAI 183 LL+L G+SL +K+A+N+ALL SGA I EMNCVR+HLS+IKGGRLA AC PA V T I Sbjct: 128 LLSLALAGMSLEEKRAVNQALLASGATISEMNCVRRHLSSIKGGRLAAACHPARVVTLLI 187 Query: 184 SDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGDPML 243 SDVPGD+ IASGPTV D TT + AL+I+ RY I +PA+ L E++KPGD L Sbjct: 188 SDVPGDDPVNIASGPTVCDATTCQDALDIVRRYGILLPASAERLLASGSGESVKPGDERL 247 Query: 244 SRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLHGQP 302 +RS R+IATP SL AAA+ A AAGI P +LGD +EGEA +V KV AGIA Q +P Sbjct: 248 ARSEVRMIATPAISLAAAAQAAAAAGIQPYVLGDRIEGEAADVGKVMAGIAFQAAQGTEP 307 Query: 303 IAAPCVILSGGETTVTVRGNGRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGSEDNA 362 PCV+LSGGETTVTV+G+GRGGRN EFLL+L L G PNV+ALA DTDG+DG E+ A Sbjct: 308 FQLPCVLLSGGETTVTVKGDGRGGRNVEFLLSLAIALDGHPNVFALAADTDGVDGIEEIA 367 Query: 363 GALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILILPPS 422 GA P + AR + LANNDG+ YF AL D IVTGPT TNVNDFRA+LI P+ Sbjct: 368 GAYADPTTLARGWQREMVPHAFLANNDGHTYFEALGDSIVTGPTLTNVNDFRALLITSPA 427 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: 479 Number of extensions: 19 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: 431 Length adjustment: 32 Effective length of query: 391 Effective length of database: 399 Effective search space: 156009 Effective search space used: 156009 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