Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate BPHYT_RS33835 BPHYT_RS33835 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__BFirm:BPHYT_RS33835 Length = 396 Score = 282 bits (722), Expect = 1e-80 Identities = 163/396 (41%), Positives = 233/396 (58%), Gaps = 17/396 (4%) Query: 12 DRALSLATLAIHGGQSPDPSTGAVMPPIYATSTY--------AQSSPGEHQGFEYSRTHN 63 D +L+ TLA+ G + I+ TS++ A+ + YSR N Sbjct: 2 DDSLNFDTLAVRSG-TVRSDFNEHSEAIFLTSSFVFESAADAAEKFKNSEDNYTYSRFTN 60 Query: 64 PTRFAYERCVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMDDLYGGTFRLFERV 122 PT ++ +AALEGG A ASGMAA S VM L AG H+V+ L+G T +F ++ Sbjct: 61 PTVSMFQDRLAALEGGEACMATASGMAAIMSVVMSTLQAGDHLVSSQALFGSTLGMFSQI 120 Query: 123 RRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLT 182 + G+ +FVD TD A+K A+R +TKM ++ETP+NP+ ++ DI AI+ IA L Sbjct: 121 FSKF-GITTTFVDPTDLDAWKNAVRPETKMFFLETPSNPLTEVADIEAISKIANASNALF 179 Query: 183 VVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSI 242 VVDN F SP LQ+PL LGAD+V+HSATK+L+G ++GG A+VG + E++ S Sbjct: 180 VVDNCFCSPALQQPLKLGADVVMHSATKFLDGQGRVLGG-ALVGSKQFIMEKVFPFVRSA 238 Query: 243 GGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLA 302 G F++++ L+G++TL LR+ NAL +A+WLE HPA+ +V YPGL SHPQH LA Sbjct: 239 GPTLSAFNAWVLLKGMETLSLRVEKQSANALEIARWLEAHPAVNRVFYPGLESHPQHALA 298 Query: 303 KRQMSGFGGIVSIVLKGGFDA-----AKRFCEKTELFTLAESLGGVESLVNHPAVMTHAS 357 RQ G I+S LKG A R + T++ ++ +LG + + HPA TH Sbjct: 299 MRQQKAGGAILSFELKGDTPEQMRANAWRVIDNTKICSITGNLGDTRTTITHPATTTHGR 358 Query: 358 IPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 + R GIS+ L+RL+VG+E+ GD+RGDLER L Sbjct: 359 VTPEARAAAGISEGLIRLAVGLENAGDIRGDLERGL 394 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: 411 Number of extensions: 15 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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