Align Cystathionine gamma-lyase; CGL; CSE; Cysteine desulfhydrase; Cysteine-protein sulfhydrase; Gamma-cystathionase; Homocysteine desulfhydrase; EC 4.4.1.1; EC 4.4.1.2 (characterized)
to candidate WP_041245581.1 GURA_RS20075 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::Q8VCN5 (398 letters) >NCBI__GCF_000016745.1:WP_041245581.1 Length = 417 Score = 188 bits (478), Expect = 2e-52 Identities = 127/408 (31%), Positives = 205/408 (50%), Gaps = 34/408 (8%) Query: 17 FATQAIHVGQEPEQWNSRAVVLPISLATTFKQD--------FPGQSSGFEYSRSGNPTRN 68 F T IH G EP + A +PI +++F Q F G+ G Y+R GNPT Sbjct: 10 FDTLLIHGGLEPGP--AGATTVPIVQSSSFAQATAEELEDIFRGRKVGQVYTRVGNPTTE 67 Query: 69 CLEKAVAALDGAKHSLAFASGLAA-TITITHLLKAGDEIICMDEVYGGTNRYFRRVASEF 127 LEK +A L+G + ++A ASG+AA T + ++++GDEI+ ++GGT FR S + Sbjct: 68 SLEKRLALLEGGQAAIATASGMAAITTAVMTIVRSGDEILASSSLFGGTFSLFRDTLSGY 127 Query: 128 GLKISFVDCSKTKLLEAAITPQTKLVWIETPTNPTLKLADIGACAQIVHKRGDIILVVDN 187 G+ +FVD + + I +T+LV++ET NP + + DI A A I G I L+VD Sbjct: 128 GISTTFVDPTDLAAVRNGINDRTRLVFVETIGNPKMDVPDIPAIALIARAAG-IPLLVDA 186 Query: 188 TFMSAYFQRPLALGADICMCSATKYMNGHSDVVMG-LVSVNSDDLNS------------- 233 T + R LGADI + S +K++NG + G ++ + D S Sbjct: 187 TVTTPCLARGSDLGADIVIHSTSKFINGTGSAIGGVIIDLGRFDWQSDKFPHFEPFHKKY 246 Query: 234 --------RLRFLQNSLGAVPSPFDCYLCCRGLKTLQVRMEKHFKNGMAVARFLETNPRV 285 + + GA +P + +L G++TL +RME+H N +A+FL+ + RV Sbjct: 247 RAFAFTARARKLIHKDFGACAAPMNSFLLAEGVETLSLRMERHCANAQKLAQFLKAHDRV 306 Query: 286 EKVVYPGLPSHPQHELAKRQCSGCPGMVSFYIKGALQHAKAFLKNLKLFTLAESLGGYES 345 V YPGL P H++AK+ G V + A F+ ++L ++G ++ Sbjct: 307 RWVNYPGLEDSPHHQVAKKLYGDKFGGVLTFGLADKAAAFRFINGVRLAKNLANIGDAKT 366 Query: 346 LAELPAIMTHASVPEKDRATLGINDTLIRLSVGLEDEQDLLEDLDRAL 393 L PA +++ +G+ + ++R+SVG+E D++ED D AL Sbjct: 367 LVIHPASTICCDYGPEEKGLMGVGEEMVRVSVGIEAINDIIEDFDSAL 414 Lambda K H 0.321 0.135 0.400 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: 376 Number of extensions: 15 Number of successful extensions: 5 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: 398 Length of database: 417 Length adjustment: 31 Effective length of query: 367 Effective length of database: 386 Effective search space: 141662 Effective search space used: 141662 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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