Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate GFF659 HP15_641 homocysteine synthase
Query= BRENDA::A2RM21 (380 letters) >FitnessBrowser__Marino:GFF659 Length = 425 Score = 224 bits (570), Expect = 5e-63 Identities = 142/419 (33%), Positives = 220/419 (52%), Gaps = 44/419 (10%) Query: 5 KTKVIHGGISTDKTTGAVSVPIYQTSTYK----QNGLG----QPKEYEYSRSGNPTRHAL 56 +T +H G +D TT A + PIYQT++Y Q+G + + Y+R NPT L Sbjct: 4 ETLALHAGFKSDPTTRAATTPIYQTTSYTFDDTQHGADLFDLKVQGNIYTRIMNPTNAVL 63 Query: 57 EELIADLEGGVQGFAFSSGLAGI-HAVLSLFSAGDHIILADDVYGGTFRLMDKVLTKTGI 115 EE +A+LEGGV A +SG+A I +A+ ++ G++I+ +YGGT+ L L GI Sbjct: 64 EERMAELEGGVGALAVASGMAAITYALQTICKVGNNIVSTSQLYGGTYNLFAHSLPNQGI 123 Query: 116 IYDLVDLSNLDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTFA 175 +V + D ++ A E T+A++ E+ NP V+DI+ + IA H +VDNT A Sbjct: 124 ECKMVRHDDFDAVEKAIDENTRALFCESIGNPAGNVVDIQRWAEIAHKHGIPLMVDNTVA 183 Query: 176 TPYLQQPIALGADIVLHSATKYLGGHSDVVAGLVTTNSK--------------------- 214 TP+L +PI GADIV+HS TKY+GGH VAG+V + K Sbjct: 184 TPFLCRPIEHGADIVIHSLTKYIGGHGTTVAGVVVDSGKFDWKASADKFPMLNEPDPSYH 243 Query: 215 -----ELASEIGFL-------QNSIGAVLGPQDSWLVQRGIKTLALRMEAHSANAQKIAE 262 + F+ + GA L P +++L+ +G++TLALRME H NA+K+A Sbjct: 244 GVVYTDALGPAAFIGRCRVVPLRNTGAALAPFNAFLIMQGLETLALRMERHCENAEKVAN 303 Query: 263 FLETSKAVSKVYYPGLNSHPGHEIAKK-QMSAFGGMISFELT-DENAVKDFVENLSYFTL 320 FL+ +V V Y L + P +K G++SF + A F++ L Sbjct: 304 FLQEHPSVEWVNYATLANSPYKATCEKISGGKASGILSFGIKGGREAGAKFIDALELILR 363 Query: 321 AESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLSVGVEAIEDLLTDIKEALEK 379 ++G +SL PA TH + E + G+ + L+RLS+G+E ++D++ DI +AL+K Sbjct: 364 LVNIGDAKSLACHPATTTHRQLNPEELKSAGVSEDLVRLSIGIEHVDDIIADITQALDK 422 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: 413 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 380 Length of database: 425 Length adjustment: 31 Effective length of query: 349 Effective length of database: 394 Effective search space: 137506 Effective search space used: 137506 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 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