Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_041377281.1 PNAP_RS13775 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000015505.1:WP_041377281.1 Length = 433 Score = 239 bits (611), Expect = 9e-68 Identities = 146/418 (34%), Positives = 216/418 (51%), Gaps = 14/418 (3%) Query: 8 GFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVA 67 GF T LH+ G+ PIH + +F +E + A +F ++ G+ Y R NPT A Sbjct: 8 GFDTLALHAGAAPDPATGARAVPIHLTTSFVFESSDHAASLFNLERAGHVYSRISNPTNA 67 Query: 68 ALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMTVGAQ 126 LE +I+ +E G I A+G AA+ + L+ G H+V+S L+G + N L T+ Sbjct: 68 VLEQRISALEGGIGAIATASGQAALHLAIATLMGAGSHIVASTALYGGSQNLLHYTLRRF 127 Query: 127 GAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNT 186 G + V D+ AA+ TRL F ET+ NP +V D+ + + E + ++D+T Sbjct: 128 GIATTFVKPGDIDGWRAAVRPTTRLFFGETVGNPGLEVLDIPVVASMAHEAKVPLLIDST 187 Query: 187 MTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAE-------- 238 +TSP+L +P GA LV +S TK + GHG +GG + D G FDW + AE Sbjct: 188 LTSPWLIKPFDHGADLVYHSATKFLSGHGTVIGGLVVDGGSFDWDQSGKFAELSQPYDGF 247 Query: 239 ---NYKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALA 295 + + + + R + LRDFG + P A I G ET+ LR R N + Sbjct: 248 HHMVFSEESTVGAFLLRARREGLRDFGACMSPHTAWLILQGIETLPLRMARHIGNTEKVV 307 Query: 296 QMLQADERVAAVYYPGLESHPQHALSKALF-RSFGSLMSFELKDG-IDCFDYLNRLRLAI 353 L + V+ V +P LESHP HAL+K L R GS+ SF+LK ++ L++ Sbjct: 308 AFLASHPFVSRVGHPMLESHPSHALAKKLLPRGAGSVFSFDLKGSRAQGKAFVESLKVFS 367 Query: 354 PTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQAL 411 +N+GD R+LVI A T + M E GI + IR+S+GLED DDL+ D ++AL Sbjct: 368 HLANVGDCRSLVIHPASTTHFRMSDEALQGAGITQGTIRLSIGLEDPDDLIDDLKRAL 425 Lambda K H 0.319 0.134 0.391 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: 446 Number of extensions: 21 Number of successful extensions: 4 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: 413 Length of database: 433 Length adjustment: 32 Effective length of query: 381 Effective length of database: 401 Effective search space: 152781 Effective search space used: 152781 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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