Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate RR42_RS15115 RR42_RS15115 threonine aldolase
Query= reanno::pseudo3_N2E3:AO353_07670 (346 letters) >FitnessBrowser__Cup4G11:RR42_RS15115 Length = 343 Score = 478 bits (1229), Expect = e-139 Identities = 225/337 (66%), Positives = 269/337 (79%), Gaps = 1/337 (0%) Query: 6 QQFASDNYSGICPEAWAAMEQAN-QGHQRAYGDDEWTARASDDFRKLFETDCEVFFAFNG 64 Q FASDNY+G CPE+ +AN GH++AYGDD WT + D R LF+TDCEVFF FNG Sbjct: 2 QHFASDNYAGFCPESLKYFLEANGSGHEQAYGDDSWTQKVCDRIRDLFQTDCEVFFVFNG 61 Query: 65 TAANSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLIARTENGKLTPESIRE 124 TAANSLALS+LCQSYHSVIC E AH+ETDECG PEFFSNGSKLL A NGKLTP+++ Sbjct: 62 TAANSLALSALCQSYHSVICHELAHIETDECGGPEFFSNGSKLLTAPGANGKLTPDAVEA 121 Query: 125 IALKRQDIHYPKPRVVTLTQATEVGSIYTPEEIRAISATCKELGLNLHMDGARFSNACAF 184 + +R DIHYPKP+VV+LTQ+TEVG++YT EE+RAI+A K L +HMDGARF+NA A Sbjct: 122 LVTRRSDIHYPKPKVVSLTQSTEVGTVYTVEEVRAIAAIAKRRQLRVHMDGARFANAVAS 181 Query: 185 LNCSPADLTWKAGVDVLCFGGTKNGMAVGEAILFFNHKLAEDFDYRCKQAGQLASKMRFL 244 L P+++TW+AGVDVLCFGGTKNG+ VGEA++FF+ KLAEDF YR KQAGQLASKMRF+ Sbjct: 182 LGVHPSEITWRAGVDVLCFGGTKNGLPVGEAVVFFDRKLAEDFAYRVKQAGQLASKMRFI 241 Query: 245 SAPWVGLLENDAWLKHARHANYCAQLLAELVSDIPGVELMFPVQANGVFLQLSESAVAAL 304 SAPW+GLLEND WL +ARHAN AQLL E ++ IPGV +MFP ++N VF +L +A+ AL Sbjct: 242 SAPWLGLLENDVWLGNARHANAMAQLLHERIASIPGVRIMFPTESNAVFAELPLAAIEAL 301 Query: 305 TAKSWRFYTFIGKGGARFMCSWDTEVERVRELAADIR 341 AK WRFYTFIG GG RFMCSWD + E V LAAD+R Sbjct: 302 RAKGWRFYTFIGAGGCRFMCSWDLQPETVEALAADMR 338 Lambda K H 0.320 0.132 0.408 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: 429 Number of extensions: 10 Number of successful extensions: 2 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: 346 Length of database: 343 Length adjustment: 29 Effective length of query: 317 Effective length of database: 314 Effective search space: 99538 Effective search space used: 99538 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 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