Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate SMc01976 SMc01976 hypothetical protein
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Smeli:SMc01976 Length = 390 Score = 231 bits (589), Expect = 3e-65 Identities = 144/369 (39%), Positives = 213/369 (57%), Gaps = 18/369 (4%) Query: 34 AVMPPIYATSTYA--------QSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAF 85 AV+PPI TS + S GE Y+R NPT +E +A LEG A F Sbjct: 25 AVVPPIVQTSLFTFKDYDEMVASYRGERVRPIYTRGLNPTVRHFEEMLAKLEGAEDAIGF 84 Query: 86 ASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKA 144 ASGM+A +STV+ ++ G +VA+ +Y FRLF +R ++ ++VD D A Sbjct: 85 ASGMSAISSTVLSFVEPGDRIVAVKHVYPDAFRLFGTHLKRMR-VEVTYVDGRDEEAVAK 143 Query: 145 AIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLV 204 A+ K+ ++E+PT+ ++ D+AA+A +AR+ G++TV+DN++ASP+ Q+P+SLG DLV Sbjct: 144 ALPG-AKLFYMESPTSWVMDTHDVAALAALARRQGIVTVIDNSWASPVFQQPVSLGVDLV 202 Query: 205 VHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLR 264 +HSA+KYL GHSD+V G+ V G + + +GG PFD++L +RG++TLP+R Sbjct: 203 IHSASKYLGGHSDVVAGV-VAGSGELIGRIRSEAYPYLGGKLSPFDAWLLIRGMRTLPVR 261 Query: 265 MRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAA 324 M+AH +ALA+A+ L HP +E V +PGL +H +SG G+ S + + G D Sbjct: 262 MKAHERSALAVARRLAEHPLVETVCHPGLGNH-----LPPGLSGTSGLFSFIFREGVD-V 315 Query: 325 KRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGD 384 +RF + +LF L S GG ESL+ V+ GIS VRL VG+E Sbjct: 316 RRFADHLKLFKLGVSWGGHESLIVPGEVVLAQKAEPNSAAAFGISPRSVRLHVGLEGTEA 375 Query: 385 LRGDLERAL 393 L DLE A+ Sbjct: 376 LWSDLEAAM 384 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: 418 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: 390 Length adjustment: 31 Effective length of query: 366 Effective length of database: 359 Effective search space: 131394 Effective search space used: 131394 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