Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_012282805.1 HM1_RS07785 cystathionine gamma-synthase
Query= BRENDA::A2RM21 (380 letters) >NCBI__GCF_000019165.1:WP_012282805.1 Length = 377 Score = 385 bits (990), Expect = e-112 Identities = 193/374 (51%), Positives = 258/374 (68%) Query: 4 IKTKVIHGGISTDKTTGAVSVPIYQTSTYKQNGLGQPKEYEYSRSGNPTRHALEELIADL 63 I + + GG D TGAVS PIYQ++T++ LG+ ++YSRSGNPTR LEELIA L Sbjct: 3 IDSLLAQGGNGKDAGTGAVSFPIYQSATFRHPALGESTGFDYSRSGNPTRQVLEELIAKL 62 Query: 64 EGGVQGFAFSSGLAGIHAVLSLFSAGDHIILADDVYGGTFRLMDKVLTKTGIIYDLVDLS 123 EGG +G AFSSGLA I AV+SLF GDH+IL +D+YGGT+RL+++V G+ D V+ S Sbjct: 63 EGGRRGLAFSSGLAAITAVISLFGPGDHLILCEDLYGGTYRLLEQVFRPWGLTADYVNTS 122 Query: 124 NLDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTFATPYLQQPI 183 + + + AA TKAI+ ETP+NP +K+ D++EI I L +VDNTF +PYLQ+PI Sbjct: 123 DPEQVNAAVTSRTKAIFIETPTNPTMKITDLREIRRICDDGGLLLIVDNTFISPYLQRPI 182 Query: 184 ALGADIVLHSATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVLGPQDSWLVQRGI 243 GADIV+HS TKYLGGH+DVVAGL ++L ++ F QN+ GAVLGP DSWL+ RG+ Sbjct: 183 ECGADIVIHSGTKYLGGHNDVVAGLAVAAREDLGDKLAFYQNASGAVLGPFDSWLLVRGM 242 Query: 244 KTLALRMEAHSANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQMSAFGGMISFELT 303 KTL LR++ NA IA +L + AV +VYY GL++HPG E+ +Q S GGMISF L Sbjct: 243 KTLGLRLDRAQENASAIARWLASHPAVDQVYYIGLDNHPGREVHFQQASGPGGMISFTLH 302 Query: 304 DENAVKDFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLSVGV 363 D V + + + + AESLGGVESL+ PA TH IP+++R G+ D L+RLSVG+ Sbjct: 303 DAGKVPEVLSRIQLISFAESLGGVESLLTFPARQTHGDIPEDIRRRCGVTDCLLRLSVGI 362 Query: 364 EAIEDLLTDIKEAL 377 E + DL+ D+ +AL Sbjct: 363 ENVHDLIDDLAQAL 376 Lambda K H 0.315 0.133 0.366 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: 414 Number of extensions: 13 Number of successful extensions: 1 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: 377 Length adjustment: 30 Effective length of query: 350 Effective length of database: 347 Effective search space: 121450 Effective search space used: 121450 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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