Align cystathionine beta-lyase (EC 4.4.1.8) (characterized)
to candidate CCNA_01491 CCNA_01491 cystathionine beta-lyase
Query= BRENDA::P06721 (395 letters) >FitnessBrowser__Caulo:CCNA_01491 Length = 386 Score = 304 bits (779), Expect = 2e-87 Identities = 165/387 (42%), Positives = 237/387 (61%), Gaps = 14/387 (3%) Query: 7 DTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFS 66 +T+L++ G VN IQR S+++ A + +L YG G T + Sbjct: 4 ETRLIHTGSEPARLGRTVNPPIQRGSTVLLPD------AASLYDDDQLTYGITGLSTPVA 57 Query: 67 LQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLG 126 LQ A+ ELEG L+P G AA+ ++LA ++ GD VL+ ++AY+P++ FC ++L + G Sbjct: 58 LQNALAELEGATNVTLYPSGLAAITGAMLAVLKAGDEVLVVDSAYKPTRRFCDRVLGRFG 117 Query: 127 VTTSWFDPLIGADIVKHL-QPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMID 185 VTT ++DP + + + L +T+++ LE+PGS+T E+ D+PAI AA + + +ID Sbjct: 118 VTTRYYDPKLSPEALMGLVTSSTRLIVLEAPGSLTFEMQDIPAIAAAANA--RGVLTLID 175 Query: 186 NTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGT-AVCNARCWEQLRENAYLMGQMV 244 NTWAAG+LFK L G+ +S+QA TKY+ GHSD +G+ A C+ + L + + +G V Sbjct: 176 NTWAAGLLFKPLAHGVTMSVQALTKYVGGHSDCFMGSVATCDDAVAKLLGDAMWDIGWSV 235 Query: 245 DADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDF 304 +D AY RGLRTL RL +H E+ L +A WL E P+VARV HPALPG GH WKRDF Sbjct: 236 SSDDAYTMLRGLRTLATRLPRHAENGLAIARWLQERPEVARVLHPALPGDAGHAIWKRDF 295 Query: 305 TGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGEI 364 TG+ GLF VL K + + + +LD+ LF + +SWGGYESL L P+ A P + Sbjct: 296 TGACGLFGVVL-KPCSQKAVHAFLDSLKLFGLGFSWGGYESLALNCDPQLGARSIP---V 351 Query: 365 DFSGTLIRLHIGLEDVDDLIADLDAGF 391 D G L+R HIGLE ++DL ADL GF Sbjct: 352 DLEGPLLRFHIGLEGIEDLKADLRRGF 378 Lambda K H 0.321 0.135 0.402 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: 347 Number of extensions: 13 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: 395 Length of database: 386 Length adjustment: 31 Effective length of query: 364 Effective length of database: 355 Effective search space: 129220 Effective search space used: 129220 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: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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