Align Cystathionine beta-lyase, chloroplastic; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_011307392.1 MBAR_RS12885 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::P53780 (464 letters) >NCBI__GCF_000195895.1:WP_011307392.1 Length = 457 Score = 219 bits (557), Expect = 2e-61 Identities = 148/417 (35%), Positives = 217/417 (52%), Gaps = 46/417 (11%) Query: 83 EEASVSTLLVNLDNKFDPFD-AMSTPLYQTATFKQPSAIENGPYD--------YTRSGNP 133 E VSTL V+ K DP A S P+YQTA + A E YTR NP Sbjct: 36 ESLGVSTLAVHAGAKPDPATGARSVPIYQTAAYVFKDAEEAADLFGLRKEGNIYTRLMNP 95 Query: 134 TRDALESLLAKLDKADRAFCFTSGMAALS-AVTHLIKNGEEIVAGDDVYGGSDRLLSQVV 192 T D E +A L+ A SGMAA++ A+ + G+EI++GD +YGG+ L + Sbjct: 96 TTDVFEKRIAALEGGIGALAVASGMAAITTALLTFTRPGDEIISGDKLYGGTYELFNYTF 155 Query: 193 PRSGVVVKRVNTTKLDEVAAAIGPQTKLVWLESPTNPRQQISDIRKISEMAHAQGALVLV 252 P+ G VK V+ K +E AI +TK +++ES NP I D K++E+AH G +V Sbjct: 156 PKLGRTVKFVDVGKPEEFKNAISEKTKAIYVESIGNPGLDIPDFEKLAEIAHGAGIPFVV 215 Query: 253 DNSIMSPVLSRPLELGADIVMHSATKFIAGHSDVMAGVLAVKG------EKLAK------ 300 DN++ SP++ RP++ G DIV++SATKFI GH + GV+ G EK + Sbjct: 216 DNTV-SPLILRPIDHGVDIVVYSATKFIGGHGTSIGGVIVDSGNFYWKPEKFPEICEPDP 274 Query: 301 --------------------EVYFLQNSEGSGLAPFDCWLCLRGIKTMALRIEKQQENAR 340 V F++++ G+ ++PF+ +L G++T+ LR++K +NA Sbjct: 275 GYHGLKYKEAFGKAAFIAKARVQFIRDT-GACISPFNSFLFTLGLETLPLRMKKHCDNAL 333 Query: 341 KIAMYLSSHPRVKKVYYAGLPDHPGHHLHFSQAK-GAGSVFSF-ITGSVALSKHLVETTK 398 +IA +L HP+V V Y GL H + L K G G++ F I G K +E + Sbjct: 334 EIAKFLEKHPKVSWVSYPGLESHCSYELAKKYLKSGYGALIGFGIKGGARECKKFIEGLE 393 Query: 399 YFSIAVSFGSVKSLISMPCFMSHASIPAEVREARGLTEDLVRISAGIEDVDDLISDL 455 FS + G KSL+ P +H + E + A G+TED +R+S GIED DLISD+ Sbjct: 394 IFSHLANIGDAKSLVIHPASTTHEQLSKEEQLACGVTEDFIRLSIGIEDAKDLISDI 450 Lambda K H 0.316 0.130 0.369 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: 421 Number of extensions: 23 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: 464 Length of database: 457 Length adjustment: 33 Effective length of query: 431 Effective length of database: 424 Effective search space: 182744 Effective search space used: 182744 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: 41 (21.6 bits) S2: 51 (24.3 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