Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_211260275.1 Q392_RS21735 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000745855.1:WP_211260275.1 Length = 403 Score = 270 bits (690), Expect = 5e-77 Identities = 154/371 (41%), Positives = 232/371 (62%), Gaps = 15/371 (4%) Query: 31 STGAVMPPIYATSTYAQS-SPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGM 89 +TG V P + T AQ S GE G+ YSRT NPT ++E+ +AA+EG A A ASGM Sbjct: 36 TTGFVQPD---SETSAQRFSSGE--GYTYSRTSNPTVTSFEQRLAAMEGTEAAIATASGM 90 Query: 90 AATST-VMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRA 148 A +M LL AG HVV ++G T LF + + G++ +F TD ++AA+R Sbjct: 91 GAILLMIMGLLRAGDHVVLSRSMFGSTLNLFAKEFGKF-GVETTFCSQTDVDEWRAAVRP 149 Query: 149 DTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSA 208 +TK+++ ETPTNP+ ++ DIAA+A IAR G L VDN FA+P+LQRP LGAD+V+HS Sbjct: 150 NTKLLFAETPTNPLTEVCDIAALADIARAAGALLAVDNAFATPILQRPTQLGADIVMHSG 209 Query: 209 TKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAH 268 TKYL+G ++ G A+ + + + A + + G V PF++++ L+GL+TL +R++A Sbjct: 210 TKYLDGQGRVMAG-ALCASHELITSKFAPIVRTAGMVLSPFNAWVVLKGLETLGIRVKAQ 268 Query: 269 CENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGF-GGIVSIVLKGGFDAAKR- 326 CE+ LA+A+WLE P + +V YPGL SHPQH LA RQ +G GG++S L G A R Sbjct: 269 CESTLAIARWLEAQPQVARVYYPGLPSHPQHELAMRQQNGLGGGVLSFQLAGDTPEAARA 328 Query: 327 ----FCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDL 382 + L ++A +LG +++++HPA +H + +R+ GI+ +R++VG+E + Sbjct: 329 KAFHVIDSCRLLSIATNLGDTKTIISHPASTSHGRLSEEQRQAAGITQGTIRVAVGLEHI 388 Query: 383 GDLRGDLERAL 393 D++ DL R L Sbjct: 389 EDIQDDLLRGL 399 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: 381 Number of extensions: 18 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: 403 Length adjustment: 31 Effective length of query: 366 Effective length of database: 372 Effective search space: 136152 Effective search space used: 136152 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 Jul 25 2024. The underlying query database was built on Jul 25 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