Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate RR42_RS06465 RR42_RS06465 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Cup4G11:RR42_RS06465 Length = 436 Score = 263 bits (672), Expect = 7e-75 Identities = 163/416 (39%), Positives = 224/416 (53%), Gaps = 42/416 (10%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTY--------AQSSPGEHQGFEYSRTHNPTRFAYE 70 TLA+H G +PDP+TGA PI+ T+++ A E G YSR NPT E Sbjct: 8 TLALHAGAAPDPATGARATPIHLTTSFVFKDSEHAASLFNMERAGHVYSRISNPTVAVLE 67 Query: 71 RCVAALEGGTRAFAFASGMAATS-TVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129 +AALE G A ASG AA V L+ AGSH+VA LYGG+ L RR G+ Sbjct: 68 ERIAALENGAGAIGVASGQAALHLAVATLMGAGSHIVASSALYGGSHNLLHYTLRRF-GI 126 Query: 130 DFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFA 189 + +FV D A++AAIR +TK+++ ET NP L ++DI +A + + +G+ +VD+TF Sbjct: 127 ETTFVQARDIDAWRAAIRPETKLLFGETLGNPGLDVLDIPTLAQLGQDNGIPLLVDSTFT 186 Query: 190 SPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDN---------AELAEQMAFLQN 240 +P L +P LGA L+ HSATK+L GH +GG+ G EL+E A N Sbjct: 187 TPYLLKPFDLGAGLLYHSATKFLGGHGTTIGGVLAEGGTFDFEASGRFPELSEPYAGFHN 246 Query: 241 SI----------------------GGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQW 278 + G P ++ L+G++TLPLRM H +NA + Q+ Sbjct: 247 MVFTEESTVAPFLLRARREGLRDFGACLSPMAAWQLLQGIETLPLRMARHVDNARRVVQF 306 Query: 279 LETHPAIEKVIYPGLASHPQHVLAKRQM-SGFGGIVSIVLKGGFDAAKRFCEKTELFTLA 337 L +HP +E V YP L SHP + LA+R + G G + S LKG A +RF E LF+ Sbjct: 307 LVSHPMVESVAYPELESHPDYALARRLLPRGAGAVFSFNLKGNRAAGQRFIESLALFSHL 366 Query: 338 ESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 ++G SLV HPA TH + A + GIS+ +RLSVG+ED DL DL+R L Sbjct: 367 ANVGDARSLVIHPASTTHFRMDAAALQAAGISEGTIRLSVGLEDPDDLIDDLKRGL 422 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: 481 Number of extensions: 24 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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