Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate 17085 b3008 cystathionine beta-lyase (NCBI)
Query= curated2:Q1M0P5 (380 letters) >FitnessBrowser__Keio:17085 Length = 395 Score = 191 bits (484), Expect = 4e-53 Identities = 126/398 (31%), Positives = 215/398 (54%), Gaps = 30/398 (7%) Query: 3 MQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYE---------YSRSGNPTRF 53 + T+L++ G S+ T GAV+ I + S+ D++ K Y R G T F Sbjct: 6 LDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHF 65 Query: 54 ALEELIADLEGGVKGFAFASGLAGI-HAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKN 112 +L++ + +LEGG F G A + +++ + ++ GDHVL+ + Y + +K+L K Sbjct: 66 SLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKL 125 Query: 113 GLSCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDL----AQCASVAKDHGLLTI 168 G++ + D + I K ++PNTK ++LE+P + +++ D+ A SV D + + Sbjct: 126 GVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPD--AIIM 183 Query: 169 VDNTFATPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNA--I 226 +DNT+A L G D+ + + TKYL GHSD + G N Q +NA + Sbjct: 184 IDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQ---LRENAYLM 240 Query: 227 GGVLGPQDSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELA 286 G ++ +++ RG++TLG+R++ H +++L VAE+L +HP+V RV +P LP +E Sbjct: 241 GQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFW 300 Query: 287 KKQMRGFSGMLSFTLK---NDSEATPFVESLKLFILGESLGGVESLV--GVPAFMTHACI 341 K+ G SG+ SF LK N+ E ++++ LF + S GG ESL+ P + A Sbjct: 301 KRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIA-AIR 359 Query: 342 PKTQREAAGIRDGLVRLSVGIEHEQDLLEDLEQAFAKI 379 P+ + + +G L+RL +G+E DL+ DL+ FA+I Sbjct: 360 PQGEIDFSGT---LIRLHIGLEDVDDLIADLDAGFARI 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: 308 Number of extensions: 19 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 ( 7.3 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