Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_058931648.1 AU252_RS16405 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_001484605.1:WP_058931648.1 Length = 387 Score = 263 bits (671), Expect = 8e-75 Identities = 154/385 (40%), Positives = 224/385 (58%), Gaps = 23/385 (5%) Query: 2 SQHVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGE-STGFDYVRTKNPTRQLVEDA 60 +Q T+ G + TG V P++ S+ Y GIG G++Y R NPTR +++ Sbjct: 6 NQGFNTRAVHAGQAFEPRTGAVVPPVHFSSTYAQDGIGGLRDGYEYGRGTNPTRDALQEQ 65 Query: 61 IANLENGARGLAFSSGMAAIQTIM-ALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFH 119 +A LE G+ +FSSG+AA +++ AL + GD +++ +D YGGTYRL + +G+ Sbjct: 66 LAALEGGSHAYSFSSGLAAEDSLIRALTRPGDHIVLGNDAYGGTYRLIDGVLGDWGIGNT 125 Query: 120 YDDFSDEDCLRSKITPN-TKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTP 178 D +D D +R + N T+ V+VETP+NPLM+ DIE +A I + G LL+VDNTF +P Sbjct: 126 PVDMADLDAVRKAVAANKTRFVWVETPSNPLMKITDIEALAAIAHDAGALLVVDNTFASP 185 Query: 179 VLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSW 238 LQ PL LGAD+V+HS TKY+GGH+D++ G +VV D L E++ Q A+GAV P D++ Sbjct: 186 YLQTPLALGADVVVHSTTKYIGGHSDVVGGAIVVNDAELAEKIGFVQFAVGAVSGPMDAF 245 Query: 239 LLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGM 282 L RG+KTL +RM +H N Q +A +L E+ E+ VLYPG GGM Sbjct: 246 LTTRGLKTLGVRMDRHSDNGQAVAEWLLERPEVEAVLYPGLPSHPGHELAKKQMKKFGGM 305 Query: 283 LSFRLQ-KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRL 341 +S + + E + AESLGG+ES + YP+ TH + + +A V L Sbjct: 306 VSVQFKGGEAAARTVAENTSVFTLAESLGGIESLMNYPSEMTHASV-KGTELAVPV--NL 362 Query: 342 LRFSVGIEHAEDLKEDLKQALCQVK 366 +R S GIE EDL DL++A +K Sbjct: 363 IRLSCGIEDVEDLIADLERAFTFLK 387 Lambda K H 0.319 0.135 0.392 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: 352 Number of extensions: 13 Number of successful extensions: 6 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: 373 Length of database: 387 Length adjustment: 30 Effective length of query: 343 Effective length of database: 357 Effective search space: 122451 Effective search space used: 122451 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 (21.7 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