Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate WP_013553393.1 NITSA_RS02180 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_000186245.1:WP_013553393.1 Length = 421 Score = 243 bits (619), Expect = 9e-69 Identities = 148/420 (35%), Positives = 221/420 (52%), Gaps = 47/420 (11%) Query: 1 MHMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGH--------HKGYEYSRSGNPTR 52 M T IH G + G ++VPIYQT+ Y H G Y+R NPT Sbjct: 1 MRENTLAIHAGYDGNEF-GTMAVPIYQTTAYEFRDAEHAANLFELKELGNIYTRLMNPTT 59 Query: 53 FALEELIADLEGGVKGFAFASGLAGI-HAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVK 111 E+ A LEGG A ASG++ I +A+ ++ ++GD++++ VYGGT L + + Sbjct: 60 DVFEKRFAALEGGAAAVATASGMSAIFYAIANVAEAGDNIIVAKQVYGGTTTLTGHTIRR 119 Query: 112 NGLSCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDN 171 G+ D + +++ I TK ++ E+ +NP + + D+A+ +A HG+LT DN Sbjct: 120 FGIEARYFDVYEPEELEAMIDERTKLIHFESITNPSVDVADIAEIVRIADRHGVLTCTDN 179 Query: 172 TFATPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNA------ 225 T ATP P+ G D+VVHS +KY G + G+V E L +++ Q Sbjct: 180 TVATPVICKPIEHGVDVVVHSASKYTTGQGLAIGGIVV-EREGLVEKLKGNQRYYHFNEP 238 Query: 226 ----------------------------IGGVLGPQDSWLLQRGIKTLGLRMQAHQKNAL 257 +G P +SWL +G++TL LRM+ H +AL Sbjct: 239 DPSYHGLVYTDLPLPPFTLRTRLALLRDLGAAPSPFNSWLYIQGLETLPLRMRQHSDSAL 298 Query: 258 CVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRG--FSGMLSFTLKNDSEATPFVESLK 315 +AEFLE HPKV++V YPGL + PNY L +K + SG+LSF +++ EA +S K Sbjct: 299 AIAEFLEAHPKVKKVNYPGLKSDPNYPLVQKYFKKGMASGLLSFEVESREEAQRIADSTK 358 Query: 316 LFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRLSVGIEHEQDLLEDLEQA 375 LF L ++G +SL+ PA TH + K + EAAG+ +GL+RLSVG+E +DL+EDL QA Sbjct: 359 LFKLVVNIGDSKSLITHPASTTHQQLSKEELEAAGVPEGLIRLSVGLEDTEDLIEDLRQA 418 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: 425 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 380 Length of database: 421 Length adjustment: 31 Effective length of query: 349 Effective length of database: 390 Effective search space: 136110 Effective search space used: 136110 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