Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate CCNA_02321 CCNA_02321 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Caulo:CCNA_02321 Length = 394 Score = 247 bits (631), Expect = 4e-70 Identities = 141/347 (40%), Positives = 217/347 (62%), Gaps = 10/347 (2%) Query: 51 GEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMD 109 GE GF YSR +NPT +E +A LEG A A+GMA+ + +M L+ AG HVVA Sbjct: 51 GEDPGFVYSRFNNPTVKMFEDRLALLEGAEVCRAQATGMASIHAALMGLVRAGDHVVAGR 110 Query: 110 DLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIA 169 L+G + R G++ +FVD TDP A++AA+R +TK V +ETP+NP+L++ DI Sbjct: 111 ALFGSCRWIVSEWLPRF-GVETTFVDATDPKAWEAAMRPNTKAVLVETPSNPVLEITDIR 169 Query: 170 AIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNA 229 A++ +A G +VDN FA+P+ Q+PL LGAD+VV+SATK+++G ++GG + + Sbjct: 170 AVSELAHAVGAKVIVDNVFATPIFQKPLELGADVVVYSATKHIDGQGRVLGGAILTSE-- 227 Query: 230 ELAEQMAFLQNSI---GGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIE 286 A F ++S+ G PF++++ L+GL+TL LR+R ++A ALA + H ++ Sbjct: 228 --AINEEFYRDSLRHTGPSLSPFNAWVMLKGLETLDLRVRRQADSAFALANTIAEHKKVQ 285 Query: 287 KVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESL 346 V+YP HP H +AK QM+G G ++++ L G +AA +F E+ ++ +LG +S+ Sbjct: 286 TVLYPFRPDHPGHNVAKAQMTGGGTVIALDL-GSREAAFKFLNALEIVDISNNLGDAKSM 344 Query: 347 VNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 HP TH S+P A R LG+++ VRLSVG+E + DL+ D+ RAL Sbjct: 345 ATHPPTTTHRSVPEAERPSLGVTEGGVRLSVGLESVEDLKRDVIRAL 391 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: 455 Number of extensions: 19 Number of successful extensions: 5 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