Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_011384943.1 AMB_RS12895 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::Q83A83 (387 letters) >NCBI__GCF_000009985.1:WP_011384943.1 Length = 430 Score = 225 bits (573), Expect = 2e-63 Identities = 145/422 (34%), Positives = 214/422 (50%), Gaps = 49/422 (11%) Query: 12 DTRVIHAGQKPDPLTGAVMTPIYTASTYAQKSPGVHQ---------GYEYSRSQNPTRFA 62 +T V+HAG + DP TG+V P+Y ++Y Q H G Y+R NPT Sbjct: 9 ETIVLHAGYRADPATGSVAVPVYQTTSY-QFRDSEHAANLFALKELGNIYTRLMNPTTDV 67 Query: 63 YERCVADLESGQHGFAFASGMAA-TATILELLQPGDHVVVMDDVYGGSYRLFENVRKRSA 121 E+ +A LE G A ASG AA T IL L Q GD+ V D+YGG++ LF N K+ Sbjct: 68 LEQRLAALEGGVAALAVASGQAASTFAILNLAQAGDNFVTSTDLYGGTWNLFANTFKQ-L 126 Query: 122 GLSFSFVDFTDENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIAVADNT 181 G+ FVD D A KT+ + E+ NP+L++ +A++A++A + + + DNT Sbjct: 127 GIEARFVDPADPEAFVRATDDKTRAWYAETLPNPKLQVFPIAEVAKLANQVGVPLIVDNT 186 Query: 182 FATPIIQRPLELGFDIVTHSATKYLNGHSDIIGGVAVVGDNKTLAEQLK----------- 230 A+P+I +PL LG IV +S TKY+ GH IGG V G + K Sbjct: 187 -ASPVIAKPLSLGAHIVVYSCTKYIGGHGTSIGGAIVDGGTFDWEKHAKRFPLLNEPDPS 245 Query: 231 -----------------YLQNA-------IGAIAAPFDSFMVLRGLKTLAIRMERHCENA 266 Y+ A IGA +PF++F VL+G++TL +RM HC NA Sbjct: 246 YHGAVWTQAVKPLGPIAYIIRARVTLLRDIGAAISPFNAFQVLQGMETLPLRMREHCRNA 305 Query: 267 MQLAQWLEKHPKVKRVYYPGLPSHPQHSIAKKQMR-YFGGMISVELKCDLNETKKVLERC 325 +AQ+L H KV V +P L A ++ +GG++ ELK ++ ++ Sbjct: 306 SAVAQFLAGHHKVAHVIHPSLQDGEYRRRADAALKGGYGGLLGFELKGGAEAGRRFIDAL 365 Query: 326 QLFTLAESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLSVGIEAITDLRHDLEA 385 +L ++G SL HPA TH+ + ++ G+T G++RLS+GIE I D+ DL+ Sbjct: 366 KLLYHVANIGDARSLAIHPASTTHSQLSADDQLASGVTPGYVRLSIGIEHIDDILADLKQ 425 Query: 386 AL 387 AL Sbjct: 426 AL 427 Lambda K H 0.319 0.134 0.385 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: 404 Number of extensions: 21 Number of successful extensions: 7 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: 387 Length of database: 430 Length adjustment: 31 Effective length of query: 356 Effective length of database: 399 Effective search space: 142044 Effective search space used: 142044 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 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