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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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