Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate HSERO_RS14995 HSERO_RS14995 cystathionine beta-lyase
Query= BRENDA::O05394 (379 letters) >FitnessBrowser__HerbieS:HSERO_RS14995 Length = 392 Score = 178 bits (451), Expect = 3e-49 Identities = 123/388 (31%), Positives = 190/388 (48%), Gaps = 19/388 (4%) Query: 4 KTLMIHGGITGDEKTGAVSVPIYQVSTYKQPKAG--------QHTGYEYSRTANPTRTAL 55 +T ++H + A V I+ ST P + GY Y PT L Sbjct: 12 QTSLVHSSYRAPDGFEAFPVGIHHASTVLFPDVAAMRSRDWREKLGYTYGLHGTPTSFVL 71 Query: 56 EALVTELESGEAGYAFSSGMAAITAVMMLF-NSGDHVVLTDDVYGGTYRVMTKVLNRLGI 114 EA + E+E G+ SG+AAI V F SGD V+L D+VYG + + + I Sbjct: 72 EARLAEIEGGKYCRVTPSGLAAIAMVNFAFLKSGDDVLLPDNVYGPSKDLGQWLERDFQI 131 Query: 115 ESTFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDNTFN 174 + F D E + + IRP T+ ++ E P + +++ D+ + A GVL+ +DNT++ Sbjct: 132 TARFYDPMIGEGLAELIRPTTRLVWTEAPGSVSMEVPDIPALCRAAHAKGVLVAIDNTWS 191 Query: 175 TPYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVVTASKELGEELHFVQNSTGGVLGPQD 234 + G DIV+ + TKY G SDV+ G V+ + L E+L G +G D Sbjct: 192 AGIAFKAFEHGVDIVMQAVTKYQSGGSDVLMGAVIVRDQALNEKLELAHMRLGFGVGMDD 251 Query: 235 SWLLMRGIKTLGLRMEAIDQNARKIASFLENHPAVQTLYYPGSSNHPGHELAKTQGAGFG 294 ++++R + ++ LR EA D ARK+A++L+ P + + +P + PGH K +G G Sbjct: 252 VYMVLRSLSSMRLRFEAHDAAARKVAAWLKQRPEIVAVLHPAFEDCPGHAHWKRDFSGAG 311 Query: 295 GMIS--FDIG-SEERVDAFLGNLKLFTIAESLGAVESLISVPARMTHASIPRERRLELGI 351 G+ S FD E + D F+ +L+LF I S G SL VP RM + R Sbjct: 312 GLFSVIFDPRYVEAQTDRFVDSLRLFKIGYSWGGAHSL-CVPYRM------KGMRRAWMR 364 Query: 352 TDGLIRISVGIEDAEDLLEDIGQALENI 379 L+R ++G+E EDL+ DI QAL + Sbjct: 365 EGQLVRFNIGLESPEDLIADIEQALARL 392 Lambda K H 0.316 0.134 0.375 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: 324 Number of extensions: 13 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: 379 Length of database: 392 Length adjustment: 30 Effective length of query: 349 Effective length of database: 362 Effective search space: 126338 Effective search space used: 126338 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: 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