Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate PP_4594 PP_4594 putative Cystathionine gamma-synthase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Putida:PP_4594 Length = 393 Score = 379 bits (974), Expect = e-110 Identities = 194/382 (50%), Positives = 263/382 (68%), Gaps = 1/382 (0%) Query: 12 DRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYER 71 D+ + AT IH G+ + A+ P I S++ + S + + YSR NPTR AYE Sbjct: 7 DKPRNFATRTIHAGEQFSVADNAIFPAIVTASSFTKRSLDDKPEYSYSRVGNPTRHAYET 66 Query: 72 CVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDF 131 CVAALE G A A ASG+ AT+TV+ELL +HVV M+ +YGGTFR+ E R RT+GL Sbjct: 67 CVAALEEGVGAVACASGVNATATVLELLPKDAHVVVMNGVYGGTFRIMEDYRSRTSGLTT 126 Query: 132 SFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASP 191 ++VDL D A AAI+ +T+++WIE+PTNP+L LVDI A+ +A+ G+LT +DNTF SP Sbjct: 127 TYVDLNDIEAVAAAIKPETQLIWIESPTNPLLHLVDIKAVCDLAKAKGILTCIDNTFCSP 186 Query: 192 MLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDS 251 QRP++LG DLV+HSA+KY+ GHSD+ GG+ V ++A LA ++ + +IG VQGPFD Sbjct: 187 WNQRPITLGVDLVMHSASKYIGGHSDLTGGVVVAANDALLA-RLRRISMAIGAVQGPFDC 245 Query: 252 FLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGG 311 +LALRGLKTL +RM C NAL +A++LE H +E+V YPGL SHPQH L KRQM G Sbjct: 246 YLALRGLKTLDVRMERQCANALQVARFLEGHAQVEQVYYPGLESHPQHELCKRQMRSGGA 305 Query: 312 IVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDA 371 +V++ +KG A R E ++F LA+SLGGVES++NH M+H S+ ++ +GIS+ Sbjct: 306 VVAMKVKGDRAALNRLVEALQIFVLADSLGGVESMINHSWSMSHCSLSPEQKGVMGISEN 365 Query: 372 LVRLSVGIEDLGDLRGDLERAL 393 L+RLSVGIED DL DL+ AL Sbjct: 366 LLRLSVGIEDYRDLVEDLDGAL 387 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: 408 Number of extensions: 13 Number of successful extensions: 2 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: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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