Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_011444472.1 SARO_RS04055 aminotransferase class V-fold PLP-dependent enzyme
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000013325.1:WP_011444472.1 Length = 427 Score = 235 bits (599), Expect = 2e-66 Identities = 153/400 (38%), Positives = 211/400 (52%), Gaps = 17/400 (4%) Query: 30 PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89 PI+ + ++ ++ A A +F + G Y R NPT AALE KI +E G + + A+G Sbjct: 26 PIYQTASYVFDSAEHAANLFALAEFGNIYSRIMNPTNAALEAKIAALEGGVAALGVASGH 85 Query: 90 AAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMTVGAQGAKVSMVDATDVKNVEAAITAN 148 AA + L+ G +V++ L+G T N G K VDA D V AAIT Sbjct: 86 AAQFIVFHTLMEPGCEIVAAKKLYGGTLNQFAHGFAKFGWKAVFVDADDPAAVAAAITDK 145 Query: 149 TRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLT 208 TR VF+E++ANP V D+ I E+ G+ +VDNTM SP L RP GA +VV+S T Sbjct: 146 TRGVFIESLANPGGVVQDIAAIAEVAHAAGVPLIVDNTMASPALCRPIEHGADIVVHSCT 205 Query: 209 KSIGGHGNALGGALTDTGEFDWTRYPHIAENYKKNPA-----------PQWGMAQI---R 254 K + GHGN++GG + D G FDW + NP+ P +A I R Sbjct: 206 KFLNGHGNSIGGLIVDAGRFDWAASDKFPSLSQPNPSYHGAVLTEALKPVGPIAFIIGCR 265 Query: 255 AKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLES 314 LRD G ++ P A G ET+ALR ER C NAL LAQ LQ +VA V Y GL Sbjct: 266 VLGLRDLGPAMAPMNAFLTLTGMETLALRIERHCANALHLAQWLQNHPKVAWVSYAGLPE 325 Query: 315 HPQHALSKA-LFRSFGSLMSFELKDGIDC-FDYLNRLRLAIPTSNLGDTRTLVIPVAHTI 372 P H L+K L G++ +F +K G + + ++L +N+GDTR+L+I A T Sbjct: 326 DPYHQLAKQYLGGKGGAVFTFGVKGGYEAGVKLVQSVKLFSHLANIGDTRSLIIHPASTT 385 Query: 373 FYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALD 412 ++G E + G +RVSVG+E DD+VAD QAL+ Sbjct: 386 HSQLGEEELVAAGAGPDTVRVSVGIEHIDDIVADLAQALE 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: 459 Number of extensions: 20 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: 427 Length adjustment: 32 Effective length of query: 381 Effective length of database: 395 Effective search space: 150495 Effective search space used: 150495 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