Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate 17085 b3008 cystathionine beta-lyase (NCBI)
Query= metacyc::HP_RS00540-MONOMER (380 letters) >FitnessBrowser__Keio:17085 Length = 395 Score = 188 bits (477), Expect = 3e-52 Identities = 124/397 (31%), Positives = 210/397 (52%), Gaps = 26/397 (6%) Query: 2 RMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGRHKGYE---------YSRSGNPTR 52 ++ T+L++ G S+ T GAV+ I + S+ D++ K Y R G T Sbjct: 5 KLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTH 64 Query: 53 FALEELIADLEGGVKGFAFASGLAGI-HAVFSLLQSGDHVLLGDDVYGGTFRLFNQVLVK 111 F+L++ + +LEGG F G A + +++ + ++ GDHVL+ + Y + +++L K Sbjct: 65 FSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSK 124 Query: 112 NGLSCTIIDTSDISQIKKAIKPNTKALYLETPSNPLLKITDL----AQCASVAKDHGLLT 167 G++ + D + I K ++PNTK ++LE+P + +++ D+ A SV D + Sbjct: 125 LGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPD--AII 182 Query: 168 IVDNTFATPYYQNPLLLGADIVAHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNA-- 225 ++DNT+A L G D+ + TKYL GHSD + G N Q +NA Sbjct: 183 MIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQ---LRENAYL 239 Query: 226 IGGVLGPQDSWLLQRGIKTLGLRMEAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYEL 285 +G ++ +++ RG++TLG+R+ H +++L VAE+L +HP+V RV +P LP +E Sbjct: 240 MGQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEF 299 Query: 286 AKKQMRGFSGMLSFTLK---NDSEAVAFVESLKLFILGESLGGVESLVGIPAFMTHACIP 342 K+ G SG+ SF LK N+ E ++++ LF + S GG ESL+ + H Sbjct: 300 WKRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLI-LANQPEHIAAI 358 Query: 343 KTQREAAGIRDGLVRLSVGIEHEQDLLEDLEQAFAKI 379 + Q E L+RL +G+E DL+ DL+ FA+I Sbjct: 359 RPQGE-IDFSGTLIRLHIGLEDVDDLIADLDAGFARI 394 Lambda K H 0.319 0.137 0.394 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: 305 Number of extensions: 20 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: 380 Length of database: 395 Length adjustment: 30 Effective length of query: 350 Effective length of database: 365 Effective search space: 127750 Effective search space used: 127750 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 (21.7 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