Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; Osteotoxin; EC 4.4.1.13 (characterized)
to candidate Pf1N1B4_4430 Cystathionine beta-lyase (EC 4.4.1.8)
Query= SwissProt::Q07703 (396 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4430 Length = 919 Score = 304 bits (779), Expect = 6e-87 Identities = 168/394 (42%), Positives = 241/394 (61%), Gaps = 8/394 (2%) Query: 4 TSAKHIDTLLQHLGSAPFNPDTGAAPVNLPSVRASTVRFQSLAKLEDAQRRKAAGERAST 63 T I T L H SA +G VN+P R STV F +LA++ DA+ R+ + ER + Sbjct: 530 TRDARIRTRLVH--SARTEKGSGGRAVNVPVTRLSTVLFDNLAQMRDARARRDS-ERVLS 586 Query: 64 YGRMGMDTHAALEQVFAELEGGTHCYLASSGLAGISMVFLSLLSAGEHALVADCAYGPVH 123 YG G T ALE + ELEGG L +GLA ++ FL+ L G+H L+ D Y PV Sbjct: 587 YGARGNPTAFALEDLVTELEGGYRTRLYGTGLAAVAQTFLAYLRPGDHVLITDAVYAPVR 646 Query: 124 ELHEAVLSRLGIDVTFFDAKAD-LASLVRPTTRLIFAEAPGSLLFEMLDMPALARFAKQH 182 L +L GI V++F L + ++ T++++ E PGSLL+E+ D+PA+A K Sbjct: 647 RLARELLEPFGIQVSYFAPDGSGLQAQLQANTKMVYTEVPGSLLYELCDLPAIAALCKPR 706 Query: 183 DLILATDNTWGSGYIYRPLTLGAQVSVIAGTKYVGGHSDLMLGAVVTNDEAIAKRLNRTQ 242 ++LA DNTWGSGY+YRPLTLGA +S++A TKY+ GHSD+++G+V T E + + L+ Sbjct: 707 GILLAVDNTWGSGYLYRPLTLGADISIMALTKYLCGHSDVVMGSVCTRQE-VWQPLSSMS 765 Query: 243 YALGYSVSADDAWLALRGVRTMPVRMAQHARHALEVCEFLQNRPEVVRLYHPAWPADPGH 302 G +VS DDA+L LRG RT+ R+ H R ALE+ ++LQ +P+V R++HPA P P H Sbjct: 766 DTFGIAVSPDDAYLVLRGARTLAPRLDVHERQALEIAQWLQAQPQVKRVFHPALPDHPHH 825 Query: 303 ALWQRDCSGSNGMLAVQLGLSPQA-ARDFVNALTLFGIGFSWGGFESLVQLVTPGELARH 361 ALW+RD +GSNG+L+ +L + F++AL +FG+G SWGG+ESLV + + R+ Sbjct: 826 ALWRRDFNGSNGLLSFELREADATYVERFIDALQVFGLGASWGGYESLVTVADTKD--RN 883 Query: 362 QYWQGGSDALVRLHIGLESPADLIADLAQALDRA 395 + ++RLHIGLE LI DL + A Sbjct: 884 SAADRALNPVLRLHIGLEDVDALIEDLQRGFAAA 917 Lambda K H 0.321 0.134 0.403 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: 879 Number of extensions: 38 Number of successful extensions: 6 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: 396 Length of database: 919 Length adjustment: 37 Effective length of query: 359 Effective length of database: 882 Effective search space: 316638 Effective search space used: 316638 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 (21.9 bits) S2: 53 (25.0 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