Align cystathionine γ-lyase (EC 2.5.1.48) (characterized)
to candidate H281DRAFT_06059 H281DRAFT_06059 O-succinylhomoserine sulfhydrylase
Query= metacyc::HP0106-MONOMER (380 letters) >FitnessBrowser__Burk376:H281DRAFT_06059 Length = 396 Score = 255 bits (651), Expect = 2e-72 Identities = 140/371 (37%), Positives = 217/371 (58%), Gaps = 15/371 (4%) Query: 22 SVPIYQTSTY----RQDAIGRHKG----YEYSRSGNPTRFALEELIADLEGGVKGFAFAS 73 S I+ TS++ DA R K Y YSR NPT ++ +A LEGG A AS Sbjct: 25 SEAIFLTSSFVFASAADAAERFKNSEDYYTYSRFTNPTVSMFQDRLAALEGGEACMATAS 84 Query: 74 GLAGIHAV-FSLLQSGDHVLLGDDVYGGTFRLFNQVLVKNGLSCTIIDTSDISQIKKAIK 132 G+A I +V S LQ+GDH++ ++G T +F+Q+ K G++ T +D +++ K A++ Sbjct: 85 GMAAIMSVVMSTLQAGDHLVSSQALFGSTLGMFSQIFSKFGITTTFVDPTNLDAWKNAVR 144 Query: 133 PNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPLLLGADIVAHS 192 P TK +LETPSNPL ++ D+ + +AK L +VDN F +P Q PL LGAD+V HS Sbjct: 145 PETKMFFLETPSNPLTEVADIEAISKIAKAANALFVVDNCFCSPALQQPLKLGADVVMHS 204 Query: 193 GTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQRGIKTLGLRMEAH 252 TK+L G V+ G + + + + +++ F + G L ++W+L +G++TL LR+E Sbjct: 205 ATKFLDGQGRVLGGALVGSKKFIMEKVFPFVRSAGPTLSAFNAWVLLKGMETLSLRVEKQ 264 Query: 253 QKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFTLKND------SE 306 NAL +A +L+ HP V+RV+YPGL +HP + LA +Q + ++SF LK D + Sbjct: 265 SANALEIARWLDDHPSVKRVFYPGLESHPQHALAMRQQKAGGAIVSFELKGDTPEQMRAN 324 Query: 307 AVAFVESLKLFILGESLGGVESLVGIPAFMTHACIPKTQREAAGIRDGLVRLSVGIEHEQ 366 A ++S K+ + +LG + + PA TH + R AAGI +GL+RL+VG+E+ Sbjct: 325 AWRVIDSTKICSITGNLGDTRTTITHPATTTHGRVTPEARAAAGITEGLIRLAVGLENAA 384 Query: 367 DLLEDLEQAFA 377 D+ DLE+ A Sbjct: 385 DIRADLERGLA 395 Lambda K H 0.319 0.137 0.394 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: 362 Number of extensions: 14 Number of successful extensions: 3 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: 380 Length of database: 396 Length adjustment: 30 Effective length of query: 350 Effective length of database: 366 Effective search space: 128100 Effective search space used: 128100 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 (21.7 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