Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate WP_012043996.1 BBTA_RS18345 cystathionine beta-lyase
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_000015165.1:WP_012043996.1 Length = 397 Score = 212 bits (539), Expect = 2e-59 Identities = 139/382 (36%), Positives = 209/382 (54%), Gaps = 15/382 (3%) Query: 5 TKLIHGGISEDATTGAVSVPIYQTSTY----RQDAIGHHKGYEYSRSGNPTRFALEELIA 60 T+LI G A G V+ ++ ST D H ++Y R G PT AL++++ Sbjct: 17 TRLITAGRDTKAQHGFVNPAVFHGSTVLYPTADDLHAHRGEFQYGRHGTPTTKALQQVLM 76 Query: 61 DLEGG-VKGFAFA-SGLAGIHA-VFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLSCT 117 +LEG G A SGLA I + S+L++GDHVL+ D +Y T N +L + G+ T Sbjct: 77 ELEGPQCAGVGIAPSGLAAISTTLLSVLKAGDHVLVCDSIYRPTRNFCNGMLARYGVETT 136 Query: 118 IIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPY 177 D S I++ +KPNT+A+ +E P + ++ D+ A+VA HG L I DNT+ATP Sbjct: 137 YFDPLVGSGIEQLLKPNTRAVVVEAPGSQSFEMPDIPAIAAVAHAHGALVIDDNTWATPL 196 Query: 178 YQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWL 237 Y L G DI + + TKY+GGHSD++ G ++ N +A IA +G GP D +L Sbjct: 197 YHRSLEQGVDISMQAATKYIGGHSDIMFGTISANEKAWPL-IAEGIRLLGVCAGPDDVFL 255 Query: 238 LQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGML 297 RG++TLG+R+ H ++ L +A +L P+V V +P L +HP + + K+ G SG+ Sbjct: 256 ALRGVRTLGVRLAQHHRSGLEMARWLAARPEVIDVLHPALESHPGHAIWKRDFTGASGLF 315 Query: 298 SFTLKNDSEAT--PFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGL 355 S L+ +A +++L LF +G S GG ESL +P A R A G Sbjct: 316 SIVLQPRPQAAVDAMLDTLTLFGMGYSWGGFESL-AIP--FDCASYRTATRWAPG--GPT 370 Query: 356 VRLSVGIEHEQDLLEDLEQAFA 377 +RL +G+E+ +DL DLE+ FA Sbjct: 371 LRLHIGLENVEDLKADLERGFA 392 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: 403 Number of extensions: 26 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: 397 Length adjustment: 30 Effective length of query: 350 Effective length of database: 367 Effective search space: 128450 Effective search space used: 128450 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 10 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