Align Cystathionine gamma-lyase; CGL; CSE; Cysteine desulfhydrase; Cysteine-protein sulfhydrase; Gamma-cystathionase; Homocysteine desulfhydrase; EC 4.4.1.1; EC 4.4.1.2 (characterized)
to candidate CCNA_01491 CCNA_01491 cystathionine beta-lyase
Query= SwissProt::Q8VCN5 (398 letters) >FitnessBrowser__Caulo:CCNA_01491 Length = 386 Score = 196 bits (497), Expect = 1e-54 Identities = 135/386 (34%), Positives = 203/386 (52%), Gaps = 19/386 (4%) Query: 19 TQAIHVGQEPEQWNSRAVVLPISLATTFKQDFPGQSSGFE-----YSRSGNPTRNCLEKA 73 T+ IH G EP + R V PI +T P +S ++ Y +G T L+ A Sbjct: 5 TRLIHTGSEPARLG-RTVNPPIQRGSTVL--LPDAASLYDDDQLTYGITGLSTPVALQNA 61 Query: 74 VAALDGAKHSLAFASGLAA-TITITHLLKAGDEIICMDEVYGGTNRYFRRVASEFGLKIS 132 +A L+GA + + SGLAA T + +LKAGDE++ +D Y T R+ RV FG+ Sbjct: 62 LAELEGATNVTLYPSGLAAITGAMLAVLKAGDEVLVVDSAYKPTRRFCDRVLGRFGVTTR 121 Query: 133 FVDCSKT-KLLEAAITPQTKLVWIETPTNPTLKLADIGACAQIVHKRGDIILVVDNTFMS 191 + D + + L +T T+L+ +E P + T ++ DI A A + RG ++ ++DNT+ + Sbjct: 122 YYDPKLSPEALMGLVTSSTRLIVLEAPGSLTFEMQDIPAIAAAANARG-VLTLIDNTWAA 180 Query: 192 AYFQRPLALGADICMCSATKYMNGHSDVVMGLVSVNSDDLNSRLRFLQNSLGAVPSPFDC 251 +PLA G + + + TKY+ GHSD MG V+ D + L +G S D Sbjct: 181 GLLFKPLAHGVTMSVQALTKYVGGHSDCFMGSVATCDDAVAKLLGDAMWDIGWSVSSDDA 240 Query: 252 YLCCRGLKTLQVRMEKHFKNGMAVARFLETNPRVEKVVYPGLPSHPQHELAKRQCSGCPG 311 Y RGL+TL R+ +H +NG+A+AR+L+ P V +V++P LP H + KR +G G Sbjct: 241 YTMLRGLRTLATRLPRHAENGLAIARWLQERPEVARVLHPALPGDAGHAIWKRDFTGACG 300 Query: 312 MVSFYIKGALQHA-KAFLKNLKLFTLAESLGGYESLA-ELPAIMTHASVPEKDRATLGIN 369 + +K Q A AFL +LKLF L S GGYESLA + S+P + + Sbjct: 301 LFGVVLKPCSQKAVHAFLDSLKLFGLGFSWGGYESLALNCDPQLGARSIP------VDLE 354 Query: 370 DTLIRLSVGLEDEQDLLEDLDRALKA 395 L+R +GLE +DL DL R +A Sbjct: 355 GPLLRFHIGLEGIEDLKADLRRGFEA 380 Lambda K H 0.321 0.135 0.400 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: 333 Number of extensions: 25 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: 398 Length of database: 386 Length adjustment: 31 Effective length of query: 367 Effective length of database: 355 Effective search space: 130285 Effective search space used: 130285 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 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