Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_011764788.1 AZO_RS05350 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000061505.1:WP_011764788.1 Length = 389 Score = 289 bits (739), Expect = 1e-82 Identities = 164/383 (42%), Positives = 236/383 (61%), Gaps = 11/383 (2%) Query: 19 TLAIHGG----QSPDPSTGAVMPPIYATSTYAQSSP---GEHQGFEYSRTHNPTRFAYER 71 TLA+ G Q + S + + + AQ++ GE +G Y+R NPT A + Sbjct: 8 TLAVRAGIERSQFNEHSEALYLTSSFVFKSAAQAAARFSGEEEGNVYARFSNPTVTAMQT 67 Query: 72 CVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLD 130 +AALEG A ASGM+A S VM L AG H+VA + L+G T +L + + G++ Sbjct: 68 RLAALEGAEACVATASGMSAILSLVMATLQAGDHIVASNGLFGATQQLLGGIMSKF-GIE 126 Query: 131 FSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFAS 190 +FV TD AA++AA+R T++ +IETP+NP+ ++VDIAA+A +A + G L VDN F + Sbjct: 127 TTFVPATDIAAYRAAVRPRTRLFFIETPSNPLTEVVDIAAVAAVAHEAGALLAVDNCFCT 186 Query: 191 PMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFD 250 P LQRPL+LGAD+VVHSATKYL+G ++GG AV G A E FL+ + G PF+ Sbjct: 187 PALQRPLALGADVVVHSATKYLDGQGRVLGG-AVAGARAVTDEVFKFLRTA-GPTLSPFN 244 Query: 251 SFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFG 310 +++ L+GL+TL +RM A AL LA+WLE P + +V YPGL SHPQH LA RQ G Sbjct: 245 AWVILKGLETLRVRMEAQSATALELARWLEQQPGVARVYYPGLPSHPQHELAMRQQKTGG 304 Query: 311 GIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISD 370 I++ ++GG DAA R + T + ++ +LG ++ + HPA TH + R+ GI D Sbjct: 305 AILAFDVEGGRDAAWRVVDATRMISITANLGDTKTTITHPATTTHGRVSAEARKAAGIGD 364 Query: 371 ALVRLSVGIEDLGDLRGDLERAL 393 L+R++VG+E + DL+ DL R L Sbjct: 365 GLLRVAVGLESIEDLKADLARGL 387 Lambda K H 0.320 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: 442 Number of extensions: 18 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: 397 Length of database: 389 Length adjustment: 31 Effective length of query: 366 Effective length of database: 358 Effective search space: 131028 Effective search space used: 131028 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