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_004514406.1 GMET_RS04100 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::Q55DV9 (387 letters) >NCBI__GCF_000012925.1:WP_004514406.1 Length = 427 Score = 228 bits (580), Expect = 3e-64 Identities = 143/421 (33%), Positives = 216/421 (51%), Gaps = 42/421 (9%) Query: 5 NNYKIGTNVIHAGQSADKNTGAVIVPISLSTTFLQPSPGVLHSEYD-------YSRSGNP 57 +++KI T I G + K +V I STTF + + +D Y+R GNP Sbjct: 3 SSWKIETQAIQGGYTP-KAGDPRVVTICQSTTFKYDNADHVTKLFDLEEPGFFYTRLGNP 61 Query: 58 TRKAFEECIAACENAKYALSFASGLATLT-TITHLLKSGDEVISIDDVYGGTRRYFTRVA 116 T AFE+ +A E AL+ ++G A T +I ++ ++G ++ +YGGT F Sbjct: 62 TTDAFEQKLAMMEGGVGALATSAGQAATTLSIFNICQAGQHFVTASTLYGGTYNLFACTL 121 Query: 117 ANFDLKFSFVDLST-LDDLKNAFTDKTRLVWIETPTNPLLKVADIKAVADYVHSRGATLV 175 ++ SFVD D++ AF T+ ++ ET NP L V D + +G L+ Sbjct: 122 PKMGIEVSFVDPEAPADEILAAFRPNTKALFAETIGNPGLNVLDFAKFSAIAQEKGVPLI 181 Query: 176 VDNTFMSPYFQNPLDLGADIVMHSVTKYINGHSDCVMGVLA---------------TNND 220 +D+TF +PY P + GA++V+HS TKYI+G + V GV+ T D Sbjct: 182 IDSTFATPYLCRPFEHGANVVVHSATKYIDGLATSVGGVIVDGGNFDWGNGRFPELTEPD 241 Query: 221 ELYAKLKF----------------LQNSIGAVPSPFDCFLALRGLKTLHVRMEAHQKNAF 264 Y L++ L IG PSPF+ FL GL+TL +RM+ H NA Sbjct: 242 SSYHGLQYVKTFGNLAYIIKARVQLMRDIGTTPSPFNSFLFTNGLQTLPLRMQRHSDNAL 301 Query: 265 AICNFLEKHPKVERVIYPGLPSHPQHEICKRQM-KGYGGMVVFFVKGSIDQSRSFLENIK 323 A+ FLE HP V V YPGL SH H+ ++ + +G G++ F +KG + + F+E + Sbjct: 302 ALAQFLESHPSVSWVKYPGLSSHASHDRAQKYLPQGCSGVLTFGIKGGTEAGKKFMEACR 361 Query: 324 LFALAESLGGVESLIELPSVMTHASVPAEERAKLGISDTLIRLSVGIEDINDLLADISQA 383 L AL +G S + P+ TH + AE++ G++ LIRLSVGIE I+D++AD+ QA Sbjct: 362 LVALVVHVGDARSCVLHPASTTHRQLTAEQQTASGVTPDLIRLSVGIEHIDDIIADVDQA 421 Query: 384 L 384 L Sbjct: 422 L 422 Lambda K H 0.320 0.135 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: 441 Number of extensions: 25 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: 387 Length of database: 427 Length adjustment: 31 Effective length of query: 356 Effective length of database: 396 Effective search space: 140976 Effective search space used: 140976 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 (21.8 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