Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_028486937.1 B076_RS0108550 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::A2RM21 (380 letters) >NCBI__GCF_000483485.1:WP_028486937.1 Length = 425 Score = 220 bits (560), Expect = 7e-62 Identities = 138/421 (32%), Positives = 220/421 (52%), Gaps = 48/421 (11%) Query: 4 IKTKVIHGGISTDKTTGAVSVPIYQTSTYK----QNG-----LGQPKEYEYSRSGNPTRH 54 +++ +H G ++ TT + +VPIYQT++Y Q+G L P Y+R NPT Sbjct: 3 LESIALHHGYESEPTTKSAAVPIYQTTSYTFDDTQHGADLFDLKVPGNI-YTRIMNPTTA 61 Query: 55 ALEELIADLEGGVQGFAFSSGLAGI-HAVLSLFSAGDHIILADDVYGGTFRLMDKVLTKT 113 LE +A++EGGV A +SG++ I +A+ ++ AGD+I+ +YGGT+ L + Sbjct: 62 VLESRVAEMEGGVAALAVASGMSAITYAIQAIAQAGDNIVSTSQLYGGTYNLFAHTFPRQ 121 Query: 114 GIIYDLVDLSNLDDLKAAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNT 173 GI ++ + + + A E T+AI+ E+ NP V+DI +++ IA H +VDNT Sbjct: 122 GIEVRMIQADDFEGFEKAIDENTRAIFCESIGNPAGNVVDIAKLAEIANKHGVPLMVDNT 181 Query: 174 FATPYLQQPIALGADIVLHSATKYLGGHSDVVAGLVTTNSK------------------- 214 ATPYL +P GADIV+HS TK++GGH + G + + K Sbjct: 182 VATPYLCKPFEFGADIVIHSLTKFIGGHGTTLGGAIVDSGKFDWVANAKRFPMLNEPDPS 241 Query: 215 ----ELASEIGF-----------LQNSIGAVLGPQDSWLVQRGIKTLALRMEAHSANAQK 259 +IG L+N+ GA L P ++L+ +G++TL LRME H NA K Sbjct: 242 YHGVIYTRDIGAAAFIARCRVVPLRNT-GAALAPHSAFLIMQGLETLGLRMERHCENALK 300 Query: 260 IAEFLETSKAVSKVYYPGLNSHPGHEIAKK-QMSAFGGMISFELT-DENAVKDFVENLSY 317 AE+L+ VS V Y L + H I +K G++SF + A F++ L Sbjct: 301 AAEYLQNHPKVSWVNYAALPNDKYHAICQKITKGQASGILSFGIKGGREAGGQFIDALKM 360 Query: 318 FTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLSVGVEAIEDLLTDIKEAL 377 ++G +SL PA TH + ++ G+ + L+RLS+G+E I+D++ DI++AL Sbjct: 361 ILRLVNIGDAKSLACHPATTTHRQLSPAELQQAGVSEDLVRLSIGIEHIDDIIADIEQAL 420 Query: 378 E 378 + Sbjct: 421 D 421 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: 17 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 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