Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_057508708.1 ABB28_RS11195 homoserine O-succinyltransferase
Query= SwissProt::Q8P6V8 (369 letters) >NCBI__GCF_001431535.1:WP_057508708.1 Length = 343 Score = 489 bits (1259), Expect = e-143 Identities = 253/332 (76%), Positives = 277/332 (83%), Gaps = 2/332 (0%) Query: 40 DTYTPAAD--SDAPPAVRGELVINLPMRHAGQRELRLRYELVGAEQAPVVFVAGGISAHR 97 D++ P + D A RGE L MRHAG R +RLRYE VG APVV +AGGISA+R Sbjct: 12 DSFVPVSVPVEDRVHAARGEFAAVLDMRHAGPRPIRLRYEWVGPADAPVVVLAGGISANR 71 Query: 98 HLAASAVFPEKGWVEGLVGAGRALDPASRRLLAFDFLGADGSLDAPIDTADQADAIAALL 157 H+AA+A F EKGW EGLVG GR LDP R+LAFDF+GADG+LD PIDTADQADA+A LL Sbjct: 72 HVAANAQFVEKGWAEGLVGPGRTLDPQLLRVLAFDFIGADGALDVPIDTADQADALAILL 131 Query: 158 DALGIARLHGFVGYSYGALVGLQFASRHAARLHTLVAVSGAHRAHPYAAAWRALQRRAVA 217 D LGIA+L FVGYSYGALV QF RH R+ LV VSGAHRAHPYAAAWRALQRRAVA Sbjct: 132 DHLGIAQLQAFVGYSYGALVAQQFGVRHRPRVQRLVVVSGAHRAHPYAAAWRALQRRAVA 191 Query: 218 LGQLQCAEHHGLALARQFAMLSYRTPEEFSERFDAPPELINGRVRVAAEDYLDAAGAQYV 277 LGQLQC++ +GLALARQFAMLSYRTPEEFSERFDA PE+INGRVRVAAEDYLDAA AQYV Sbjct: 192 LGQLQCSDENGLALARQFAMLSYRTPEEFSERFDAAPEVINGRVRVAAEDYLDAAAAQYV 251 Query: 278 ARTPVNAYLRLSESIDLHRIDPAAVAVPTVVVAVEGDRLVPLADLVSLVEGLGPRGSLRV 337 ARTPV A+LRLSESIDLHRI+PA + +PTVVVAVEGDRLVPLADLVSLVEGLGPRGSLRV Sbjct: 252 ARTPVTAWLRLSESIDLHRIEPAQLLLPTVVVAVEGDRLVPLADLVSLVEGLGPRGSLRV 311 Query: 338 LRSPFGHDAFLKEIDRIDAILTTALRTTGETA 369 LRSP+GHDAFLKE DRIDAIL A+R GETA Sbjct: 312 LRSPYGHDAFLKETDRIDAILANAIRIPGETA 343 Lambda K H 0.321 0.135 0.393 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: 434 Number of extensions: 8 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: 369 Length of database: 343 Length adjustment: 29 Effective length of query: 340 Effective length of database: 314 Effective search space: 106760 Effective search space used: 106760 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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