Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_004514090.1 GMET_RS03510 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000012925.1:WP_004514090.1 Length = 378 Score = 324 bits (831), Expect = 2e-93 Identities = 161/372 (43%), Positives = 236/372 (63%), Gaps = 16/372 (4%) Query: 7 TKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLEN 66 T++ G+ D TG VS PIY ++ +R + +DY R+ NPTR+ +E+ IA LE Sbjct: 5 TRIIHTGHDIDPTTGAVSIPIYQTSTFRQESVDHFGKYDYARSDNPTREALEETIAQLEG 64 Query: 67 GARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSDE 126 G RG A++SGMAAI +++ LF GD L+V D+YGGT+R+ + + G+T + D +D Sbjct: 65 GTRGFAYASGMAAISSVLLLFSPGDHLVVCEDVYGGTFRVLTQLFSRLGITSTFVDATDL 124 Query: 127 DCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLEL 186 D + + P TK +F+E+P+NPL++ D+E ARI +E G + +VDNTF TP LQRPLE+ Sbjct: 125 DAIAAAFRPETKGLFLESPSNPLLKITDLEGAARIARERGAITLVDNTFMTPYLQRPLEV 184 Query: 187 GADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKT 246 G DIV+HS TK+L GH+D++ G VVKD LG+ + QNA GA+L P DSWL++RG+KT Sbjct: 185 GCDIVLHSGTKFLNGHSDVICGFAVVKDPELGKRIRFIQNAFGAILGPQDSWLVLRGLKT 244 Query: 247 LSLRMRQHQANAQELAAFLEEQEEISDVLYP----------------GKGGMLSFRLQKE 290 L +RM + Q +A +A++L ++ ++ VLYP G G +LSF L Sbjct: 245 LRVRMEESQRSATRIASWLAGEKRVTRVLYPGLPSHPGHAIHARQSSGPGAVLSFALDSL 304 Query: 291 EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGIEH 350 E L+ +K FA SLGGVES I+YPA +H +P E R A G+ + L+R SVG+E Sbjct: 305 EVTRRLLEGMKLAAFAVSLGGVESIISYPARMSHAAMPPEERAARGIGDTLVRLSVGLEE 364 Query: 351 AEDLKEDLKQAL 362 A+DL ++ + + Sbjct: 365 ADDLIAEMDRLI 376 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: 349 Number of extensions: 9 Number of successful extensions: 2 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: 378 Length adjustment: 30 Effective length of query: 343 Effective length of database: 348 Effective search space: 119364 Effective search space used: 119364 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 Jul 25 2024. The underlying query database was built on Jul 25 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