Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate AO356_19910 AO356_19910 cystathionine gamma-synthase
Query= curated2:Q1M0P5 (380 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_19910 Length = 381 Score = 224 bits (572), Expect = 2e-63 Identities = 130/380 (34%), Positives = 205/380 (53%), Gaps = 19/380 (5%) Query: 1 MHMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIA 60 M + T+++H + + +V+ PIYQ S + D+ + YSR NP LE+++A Sbjct: 1 MKVSTEILHIKVDDRDAHPSVT-PIYQCSAFNADS-----AFFYSRKANPNVTELEQVVA 54 Query: 61 DLEGGVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLSCTIID 120 LEG A+++G++ I+ V LL+ G +++ +YG +++LF + + G TI+D Sbjct: 55 SLEGSEHALAYSTGMSAIYMVLELLKPGASLVINKYIYGCSYKLFQRYAARIGAHLTILD 114 Query: 121 TSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHG--LLTIVDNTFATPYY 178 + +K A+ N + ETP+NP LK D+ + K H L +VDNT+ATP + Sbjct: 115 LTTAEGLK-ALPANVDMVIFETPTNPFLKDIDIHAVSRAVKQHNPQALVVVDNTWATPIF 173 Query: 179 QNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLL 238 Q PL GADI ++S TKY GHSDV+ GLV NNE + + + G +L P +WLL Sbjct: 174 QKPLNFGADISLYSATKYFSGHSDVMGGLVLVNNETIYNRLLEGRFYSGTILTPNSAWLL 233 Query: 239 QRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLS 298 +R ++T LRM+ H + + +L + P +E VYYP + +Q+ G+ G++ Sbjct: 234 RRSMQTFNLRMEKHSQTTASMLNYLRELPFIEHVYYP--------RIDGRQLSGYGGIVF 285 Query: 299 FTLKNDSEA--TPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLV 356 ++ D F +LK F G + V S+V P +HA + ++ GI GLV Sbjct: 286 VDIRPDLVPFYKTFTSALKWFGTGTGMACVTSMVAQPFSGSHASMTDQEKADMGIEKGLV 345 Query: 357 RLSVGIEHEQDLLEDLEQAF 376 RL G+E +DL EDL QAF Sbjct: 346 RLCFGLEDIEDLKEDLLQAF 365 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: 362 Number of extensions: 19 Number of successful extensions: 4 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: 381 Length adjustment: 30 Effective length of query: 350 Effective length of database: 351 Effective search space: 122850 Effective search space used: 122850 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