Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate BWI76_RS24285 BWI76_RS24285 cystathionine beta-lyase
Query= curated2:Q1M0P5 (380 letters) >FitnessBrowser__Koxy:BWI76_RS24285 Length = 395 Score = 191 bits (484), Expect = 4e-53 Identities = 121/397 (30%), Positives = 208/397 (52%), Gaps = 26/397 (6%) Query: 2 HMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYE---------YSRSGNPTR 52 H+ T L+H G S+ T G+V+ I + S+ D + K Y R G T Sbjct: 5 HLDTALVHAGRSKKYTQGSVNSVIQRASSLVFDTVEAKKHATRNRAKGELFYGRRGTLTH 64 Query: 53 FALEELIADLEGGVKGFAFASGLAGI-HAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVK 111 F+L+E + +LEGG F G A + + + + ++ GDH+L+ + Y T K+L K Sbjct: 65 FSLQEAMCELEGGAGCALFPCGAAAVANTILAFVEQGDHILVTNTAYEPTQDFCTKILAK 124 Query: 112 NGLSCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHG--LLTIV 169 G++ D I + ++PNT+ ++LE+P + +++ D+ + + + ++ Sbjct: 125 LGVTTGWFDPLIGGDIARLVQPNTRVVFLESPGSITMEVHDVPAIVAAVRRVAPEAIIMI 184 Query: 170 DNTFATPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNA--IG 227 DNT+A L G DI + +GTKYL GHSD + G +N AQ +NA +G Sbjct: 185 DNTWAAGVLFKALEFGIDISIQAGTKYLIGHSDAMVGTAVSNERCWAQ---LRENAYLMG 241 Query: 228 GVLGPQDSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAK 287 ++ +++ RG++TL +R++ H +++L +AE+L +HP+V RV +P LP +E + Sbjct: 242 QMVDADTAYMTSRGLRTLAVRLRQHHESSLQIAEWLAQHPQVARVNHPALPGSKGHEFWQ 301 Query: 288 KQMRGFSGMLSFTLK---NDSEATPFVESLKLFILGESLGGVESLV--GVPAFMTHACIP 342 + G SG+ SF L D+E + +++ LF + S GG ESL+ P + A P Sbjct: 302 RDFTGSSGLFSFVLNKRLTDAELSAYLDHFSLFSMAYSWGGFESLILANQPEHIA-AIRP 360 Query: 343 KTQREAAGIRDGLVRLSVGIEHEQDLLEDLEQAFAKI 379 + + +G L+RL +G+E+ DL +DL FA+I Sbjct: 361 DAEVDFSGT---LIRLHIGLENVTDLQDDLAAGFARI 394 Lambda K H 0.318 0.136 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: 321 Number of extensions: 20 Number of successful extensions: 7 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 ( 7.3 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