Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate WP_078428932.1 BK574_RS13250 cystathionine gamma-synthase family protein
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_002019605.1:WP_078428932.1 Length = 401 Score = 279 bits (714), Expect = 9e-80 Identities = 149/384 (38%), Positives = 229/384 (59%), Gaps = 10/384 (2%) Query: 3 MQTKLIHGGISEDATTGAVSVPIYQTSTYRQD--------AIGHHKGYEYSRSGNPTRFA 54 M TK + G + GA VP+ + Y D A+G KG+ Y R+ NPT A Sbjct: 10 MGTKAVWAGEKDYLVHGATQVPVIPSVAYNYDDMDEWYEVAVGRKKGHIYGRNTNPTVQA 69 Query: 55 LEELIADLEGGVKGFAFASGLAGI-HAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNG 113 E+ + LE +F++G+A I + +++ L+ GD V+ D YGGT ++F + L + Sbjct: 70 FEDKLKLLENAAAATSFSTGMAAISNTLYTFLRPGDRVVTIKDTYGGTNKIFTEFLPQMD 129 Query: 114 LSCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTF 173 +S + +T + QI+ + K LYLETP+NP +KITD+ + A + G + IVDNTF Sbjct: 130 ISISFCETGNHEQIETEVAKGCKILYLETPTNPTVKITDIKRMAKAGHEAGAIVIVDNTF 189 Query: 174 ATPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQ 233 ATP Q PL LGADIV+HS TK+LGGH+D + G+ +NNE ++I ++ G + P Sbjct: 190 ATPLNQQPLELGADIVLHSATKFLGGHADALGGVACSNNEEYIEKIYHYREINGATMDPW 249 Query: 234 DSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGF 293 ++L+ RG+KTL LR++ ++NAL +A +L+ VE V+YPGL HPN+++AK+QM GF Sbjct: 250 AAYLILRGMKTLELRVRRQEENALKLANYLKSEEIVESVFYPGLEEHPNHDIAKQQMVGF 309 Query: 294 SGMLSFTLKNDSEAT-PFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIR 352 GMLSF +K + + +L +LG VE+ VG +H +R+A GI Sbjct: 310 GGMLSFAVKGGIDTVKKLLPNLTFANRAANLGAVETTVGPARTTSHVECTPEERKAMGIP 369 Query: 353 DGLVRLSVGIEHEQDLLEDLEQAF 376 +GL+R+S GIE+ +D++ D ++AF Sbjct: 370 EGLIRVSCGIENAEDIINDFKEAF 393 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: 395 Number of extensions: 23 Number of successful extensions: 3 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: 401 Length adjustment: 31 Effective length of query: 349 Effective length of database: 370 Effective search space: 129130 Effective search space used: 129130 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