Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate GFF750 PGA1_c07640 O-acetylhomoserine / O-acetylserine sulfhydrylase
Query= metacyc::HP_RS00540-MONOMER (380 letters) >FitnessBrowser__Phaeo:GFF750 Length = 430 Score = 219 bits (557), Expect = 1e-61 Identities = 152/417 (36%), Positives = 221/417 (52%), Gaps = 43/417 (10%) Query: 5 TKLIHGGISEDATTGAVSVPIYQTSTYR-QDAIG-------RHKGYEYSRSGNPTRFALE 56 T IH G D TGA PIYQT+ Y +DA + G+ YSR NPT L+ Sbjct: 11 TLQIHAGAKPDPATGARQTPIYQTTAYVFRDADHAAALFNLQEVGFIYSRLTNPTVAVLQ 70 Query: 57 ELIADLEGGVKGFAFASGLAG-IHAVFSLLQSGDHVLLGDDVYGGTFRLFNQVLVKNGLS 115 E IA LEGGV +SG A I A+F L+ G +V+ +YGGT F+Q + + G S Sbjct: 71 ERIATLEGGVGAVCCSSGHAAQIMALFPLMGPGCNVVASTRLYGGTVTQFSQTIKRFGWS 130 Query: 116 CTIIDTSDISQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFAT 175 +D + + AI +T+A++ E+ +NP +TD+ A VA G+ I+DNT AT Sbjct: 131 AKFVDFDNPEAVAAAIDDDTRAVFGESVANPGGYVTDIRSIADVADAAGVPLIIDNTSAT 190 Query: 176 PYYQNPLLLGADIVAHSGTKYLGGHSDVVAGLVTTNNE----------ALAQ-EIAF--- 221 PY +P+ GA +V HS TKYL G+ V G++ + + +L+Q E A+ Sbjct: 191 PYLCSPIAHGATLVVHSTTKYLTGNGTVTGGVIVDSGKFDWSANDKFPSLSQPEPAYHGL 250 Query: 222 -FQNAIGGV-----------------LGPQDSWLLQRGIKTLGLRMEAHQKNALCVAEFL 263 F GG+ + PQ + G++TL LRME H +NA VA +L Sbjct: 251 KFHETFGGLAFTFHGIAIGLRDLGMTMNPQAAHYTLMGVETLSLRMERHCENAKTVASWL 310 Query: 264 EKHPKVERVYYPGLPTHPNYELAKKQM-RGFSGMLSFTLKNDSEA-VAFVESLKLFILGE 321 E+ P+V+ V Y GLP+ P + AK+ +G G+ +F +K +A V V SL++F Sbjct: 311 EQDPRVDYVTYAGLPSSPYHARAKEHYPKGTGGLFTFAVKGGYDACVKLVNSLEIFSHVA 370 Query: 322 SLGGVESLVGIPAFMTHACIPKTQREAAGIRDGLVRLSVGIEHEQDLLEDLEQAFAK 378 +LG SL+ A TH + Q+EAAG +VR+S+GIE+ DL+ DL+QA +K Sbjct: 371 NLGDTRSLIIHSASTTHRQLTPEQQEAAGAGANVVRVSIGIENADDLIADLDQALSK 427 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: 441 Number of extensions: 22 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: 380 Length of database: 430 Length adjustment: 31 Effective length of query: 349 Effective length of database: 399 Effective search space: 139251 Effective search space used: 139251 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 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