Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate SMc02217 SMc02217 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Smeli:SMc02217 Length = 394 Score = 240 bits (613), Expect = 5e-68 Identities = 146/389 (37%), Positives = 219/389 (56%), Gaps = 12/389 (3%) Query: 18 ATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSP--------GEHQGFEYSRTHNPTRFAY 69 AT +HGG G I+ T + S GE GF Y+R +PT + Sbjct: 8 ATQLVHGGTLRS-QYGETSEAIFLTQGFVYDSSEAAEARFKGETDGFIYARYGSPTNDMF 66 Query: 70 ERCVAALEGGTRAFAFASGMAATST-VMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAG 128 E+ + LEG A A ASGMAA S ++ + AG H+VA L+G + E + + G Sbjct: 67 EKRMCMLEGAEDARATASGMAAVSAAILCQVKAGDHIVAARALFGSCRWVVETLAPKY-G 125 Query: 129 LDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTF 188 ++ + VD D ++ A+R +TK+ ++E+PTNP L+++DIA +A +A + G VVDN F Sbjct: 126 VECTLVDGRDLKNWEDAVRPNTKVFFLESPTNPTLEVIDIAGVARLADQIGAKVVVDNVF 185 Query: 189 ASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGP 248 A+P+ Q+PL LGA +VV+SATK+++G +GG+ V+ D + E + G P Sbjct: 186 ATPLFQKPLELGAHVVVYSATKHIDGQGRCLGGV-VLSDKQWVDENLHDYFRHTGPAMSP 244 Query: 249 FDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSG 308 F+++ L+G++TLPLR++ E+A +A +L P + +VIYPG HPQ + +QMSG Sbjct: 245 FNAWTLLKGIETLPLRVKQQTESARRVADFLAEQPQVARVIYPGRKDHPQADVIAKQMSG 304 Query: 309 FGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGI 368 +V+ LKGG +AA E+ ++ +LG +SL+ HPA TH ++ R +LGI Sbjct: 305 GSTLVAFELKGGKEAAFALQNALEIIRISNNLGDSKSLITHPATTTHKNLTDEARAELGI 364 Query: 369 SDALVRLSVGIEDLGDLRGDLERALVNQN 397 S VR S GIED DL D RAL N Sbjct: 365 SAGTVRFSAGIEDSEDLIEDFARALKGVN 393 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: 397 Number of extensions: 13 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: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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