Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_038213330.1 Q392_RS23495 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000745855.1:WP_038213330.1 Length = 437 Score = 253 bits (647), Expect = 6e-72 Identities = 163/420 (38%), Positives = 225/420 (53%), Gaps = 46/420 (10%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPG--------EHQGFEYSRTHNPTRFAYE 70 TLA+H G +PDP+TGA PI+ T+++ S E G YSR NPT E Sbjct: 11 TLAVHAGAAPDPATGARAVPIHLTTSFVFESSDHAAALFNLERSGHVYSRLSNPTNAVLE 70 Query: 71 RCVAALEGGTRAFAFASGMAATS-TVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129 + VAALEGG A A ASG AA V L+ AGSH+VA LYGG+ L RR G+ Sbjct: 71 QRVAALEGGIGAIATASGQAALHLAVATLMGAGSHIVASTALYGGSQNLLHYTMRRF-GI 129 Query: 130 DFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFA 189 + +FV D ++AAIR +TK+++ ET NP L ++DI +A IA + + +VD+T Sbjct: 130 ETTFVKPGDIDGWRAAIRPETKLLFGETVGNPGLDVLDIPTVAQIAHEAKVPLLVDSTLT 189 Query: 190 SPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDN----------AELA------E 233 SP L RP GADLV HSATK+L+GH ++GG+ V G + AEL+ Sbjct: 190 SPYLIRPFEHGADLVYHSATKFLSGHGTVIGGVLVDGGSFDWDASDGKFAELSAPYDGFH 249 Query: 234 QMAFLQNS----------------IGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQ 277 M F + S G P ++L L+G++TLPLRM H N + + Sbjct: 250 NMVFTEESTVGAFLLRARREGLRDFGAAMSPHTAWLILQGIETLPLRMERHIANTEKIVR 309 Query: 278 WLETHPAIEKVIYPGLASHPQHVLAKRQM----SGFGGIVSIVLKGGFDAAKRFCEKTEL 333 +L +HP + +V +P L +HP H LA R + G G + S +KG + K+F E +L Sbjct: 310 FLASHPFVSRVGHPLLEAHPSHALANRLLRHGARGAGSVFSFDIKGDREQGKKFIEALKL 369 Query: 334 FTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 F+ ++G SLV HPA TH + GI +RLS+G+ED DL DL+RAL Sbjct: 370 FSHLANVGDCRSLVIHPASTTHFRMTDEALAAGGIGQGTIRLSIGLEDPDDLIDDLKRAL 429 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: 517 Number of extensions: 27 Number of successful extensions: 7 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: 437 Length adjustment: 31 Effective length of query: 366 Effective length of database: 406 Effective search space: 148596 Effective search space used: 148596 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 Jul 25 2024. The underlying query database was built on Jul 25 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