Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate 351915 BT2387 O-acetylhomoserine (thiol)-lyase (NCBI ptt file)
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Btheta:351915 Length = 428 Score = 253 bits (647), Expect = 6e-72 Identities = 155/421 (36%), Positives = 222/421 (52%), Gaps = 43/421 (10%) Query: 15 LSLATLAIHGGQSP-DPSTGAVMPPIYATSTYAQSSPG--------EHQGFEYSRTHNPT 65 L TL +H GQ DP+T A PIY T++Y + + G Y R N T Sbjct: 6 LHFETLQVHVGQEQADPATDARAVPIYQTTSYVFHNSAHAAARFGLQDPGNIYGRLTNST 65 Query: 66 RFAYERCVAALEGGTRAFAFASGMAATSTVME-LLDAGSHVVAMDDLYGGTFRLFERVRR 124 + +E VA LEGG A ASG AA + E + AG H+VA +YGG++ L Sbjct: 66 QGVFEERVAVLEGGVAGLAVASGAAAITYAFENITRAGDHIVAAKTIYGGSYNLLAHTLP 125 Query: 125 RTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVV 184 G+ +FVD +D + F+ AI+ +TK V+IET NP ++DI A++ IA +H + ++ Sbjct: 126 NY-GVTTTFVDPSDLSNFEKAIQENTKAVFIETLGNPNSNIIDIEAVSEIAHRHKIPLII 184 Query: 185 DNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAV-------------------- 224 DNTF +P L RP+ GAD+VVHSATK++ GH +GG+ V Sbjct: 185 DNTFGTPYLIRPIEHGADIVVHSATKFIGGHGSSLGGVIVDSGKFDWVASGKFPQLTEPD 244 Query: 225 -----------VGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENAL 273 G A + A L G PF++F+ L+GL+TL LR+ H ENAL Sbjct: 245 PSYHGVRFVDAAGPAAYVTRIRATLLRDTGATISPFNAFILLQGLETLSLRVERHVENAL 304 Query: 274 ALAQWLETHPAIEKVIYPGLASHPQHVLAKRQM-SGFGGIVSIVLKGGFDAAKRFCEKTE 332 + +L HP ++KV +P L+ HP H L +R +G G I + +KGG + A RF + E Sbjct: 305 KVVNFLNNHPKVKKVNHPSLSDHPDHALYQRYFPNGAGSIFTFEVKGGQEEAHRFIDSLE 364 Query: 333 LFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERA 392 +F+L ++ V+SLV HPA TH+ + + I VRLS+G E + DL DLE+A Sbjct: 365 IFSLLANVADVKSLVIHPASTTHSQLNAQELAEQEIYPGTVRLSIGTEHINDLIADLEQA 424 Query: 393 L 393 L Sbjct: 425 L 425 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: 465 Number of extensions: 25 Number of successful extensions: 7 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: 428 Length adjustment: 31 Effective length of query: 366 Effective length of database: 397 Effective search space: 145302 Effective search space used: 145302 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