Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_005456032.1 SACCYDRAFT_RS10560 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000244975.1:WP_005456032.1 Length = 401 Score = 192 bits (488), Expect = 1e-53 Identities = 133/388 (34%), Positives = 194/388 (50%), Gaps = 40/388 (10%) Query: 7 TKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGES------TGFD---YVRTKNPTRQLV 57 T GN D +G + PI ++ +Y + E +G D Y R + + Sbjct: 17 TNAVHAGNEIDAGSGAIRTPIVMANSY---ALPEDPAQLSWSGTDVPLYTRNSGANQLAL 73 Query: 58 EDAIANLENGARGLAFSSGMAAIQTIMAL-FKSGDELIVSSDLYGGTYRLF-ENEWKKYG 115 ++ + LE G + +SG+AA+ + ++GD ++V+ Y T+RLF E +YG Sbjct: 74 QNKLVALEGGEDAVVLASGVAALHAVFFTHLRTGDHVVVADVTYEATWRLFAELLPARYG 133 Query: 116 LTFHYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTF 175 + + D +D D +R+ I PNT+ V VET NP + DI +A I + G +L+VD+TF Sbjct: 134 IEATFVDMTDLDAVRAAIRPNTRMVHVETIANPTTKVTDIAAVASIAHDAGAILVVDSTF 193 Query: 176 YTPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPF 235 P L RPL GAD+V+HS TKY+ GH D + G V+ E + +G V+ PF Sbjct: 194 TPPPLYRPLSDGADLVVHSLTKYINGHGDAMGGAVIGSAELIAPIKNDAMVDVGGVISPF 253 Query: 236 DSWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYP------------------ 277 ++WL+ RG TL LR+RQ ++A +AA L E I+ V YP Sbjct: 254 NAWLITRGSVTLPLRLRQQNSSAARIAARLREDPRIAYVAYPGLPDHAQHDVATRQFGGR 313 Query: 278 GKGGMLSFRLQKE-EWVNPFLKALKTICFAESLGGVESFITYPATQ--THMDIPEEIRIA 334 G G M++F + + E N F+ L+ I A SLG ES I + T+ PEE R Sbjct: 314 GYGAMMAFAVAGDPETQNRFVANLRVITSAVSLGHDESLIVHVGTEGPRVAHYPEEFRKW 373 Query: 335 NGVCNRLLRFSVGIEHAEDLKEDLKQAL 362 LRFSVGIE +DL DL AL Sbjct: 374 GH-----LRFSVGIEDPDDLIADLTCAL 396 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: 387 Number of extensions: 23 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: 373 Length of database: 401 Length adjustment: 30 Effective length of query: 343 Effective length of database: 371 Effective search space: 127253 Effective search space used: 127253 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