Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Ac3H11_2928 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2928 Length = 436 Score = 252 bits (643), Expect = 2e-71 Identities = 161/419 (38%), Positives = 225/419 (53%), Gaps = 45/419 (10%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPG--------EHQGFEYSRTHNPTRFAYE 70 TLA+H G SPDP+TGA PI+ T+++ S E G YSR NPT E Sbjct: 11 TLALHAGASPDPATGARATPIHLTTSFVFESSDHAASLFNLERGGHVYSRISNPTNAVLE 70 Query: 71 RCVAALEGGTRAFAFASGMAATS-TVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129 + VAALEGG A A ASG AA + ++ AGSH+VA LYGG+ L R G+ Sbjct: 71 QRVAALEGGVGAIATASGQAALHLAIATIMGAGSHIVASTALYGGSQNLLHYTLSRF-GI 129 Query: 130 DFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFA 189 + +FV D A++AA+R +TK+ + ET NP L ++DI ++ IA + G+ +VD+T Sbjct: 130 ETTFVKPGDIDAWRAAVRPNTKLFFGETVGNPGLDVLDIPTVSSIAHEAGVPLLVDSTLT 189 Query: 190 SPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDN------------AELAE---- 233 SP L +P GADLV HSATK+L+GH +VGGI V G + AEL + Sbjct: 190 SPWLIKPFEHGADLVYHSATKFLSGHGTVVGGIVVDGGSFDWDGPKSAGKFAELTQPYDG 249 Query: 234 --QMAFLQNS----------------IGGVQGPFDSFLALRGLKTLPLRMRAHCENALAL 275 M F + S G P ++L L+G++TLPLRM H N + Sbjct: 250 FHNMVFTEESTVGAFLLRARREGLRDFGACMSPHTAWLILQGIETLPLRMAQHMRNTEKV 309 Query: 276 AQWLETHPAIEKVIYPGLASHPQHVLAKRQM-SGFGGIVSIVLKGGFDAAKRFCEKTELF 334 ++L P + +V +P L SHP H LA++ + G G + S LKG + K+F E ++F Sbjct: 310 VEFLAAQPFVSRVGHPMLESHPSHALAQKLLPRGAGSVFSFDLKGNREQGKKFIETLKVF 369 Query: 335 TLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 + ++G SLV HPA TH + GI+ +RLS+G+ED DL DL+RAL Sbjct: 370 SHLANVGDCRSLVIHPASTTHFRMSDEALAGAGITQGTIRLSIGLEDADDLIDDLKRAL 428 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: 507 Number of extensions: 26 Number of successful extensions: 6 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: 436 Length adjustment: 31 Effective length of query: 366 Effective length of database: 405 Effective search space: 148230 Effective search space used: 148230 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 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