Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate YP_004140057.1 Mesci_0840 Cys/Met metabolism pyridoxal-phosphate-dependent protein
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000185905.1:YP_004140057.1 Length = 393 Score = 301 bits (772), Expect = 2e-86 Identities = 161/375 (42%), Positives = 233/375 (62%), Gaps = 19/375 (5%) Query: 7 TKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLEN 66 T+ G D +TG V PIY ++ Y + G GF+Y R++NPTR E A+A+LE+ Sbjct: 17 TRTIHGGQSHDPLTGAVMVPIYATSTYGQQSPGVHKGFEYARSQNPTRFAFERAVADLES 76 Query: 67 GARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYG-LTFHYDDFSD 125 G+ AF+SG+AAI T++ L SG ++ + D+YGG++RL E K+ L + DF+D Sbjct: 77 GSAAFAFASGLAAIATVLELLDSGAHIVATDDIYGGSFRLMERVRKRSADLRVSFVDFTD 136 Query: 126 EDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLE 185 + + I P TK ++VETPTNPL++ D+E +A + + G+L + DNTF +P +QRPLE Sbjct: 137 LAAVEAAIRPETKMLWVETPTNPLLRIVDLEGVAALARRKGILTVADNTFCSPYIQRPLE 196 Query: 186 LGADIVIHSATKYLGGHNDLLAGLVVVKDER-LGEEMFQHQNAIGAVLPPFDSWLLMRGM 244 LG DIV+HS TKYL GH+D++ G+ VV D + L ++ QNAIGA+ PFDS+L +RG+ Sbjct: 197 LGIDIVVHSTTKYLNGHSDMVGGVAVVGDNKDLAAQLKFLQNAIGAISGPFDSFLALRGL 256 Query: 245 KTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRLQ 288 KTL+LRM +H AN ++A +LE + ++ V+YPG GGM++ L Sbjct: 257 KTLALRMERHSANGLKIAQWLEARRDVRRVIYPGLASHPQHAVAVQQMHAFGGMITAVLD 316 Query: 289 KE-EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVG 347 ++ FL+ + AESLGGVES I +PA TH IP E R G+ + L+R S G Sbjct: 317 RDLAGTKKFLERTQLFTLAESLGGVESLIEHPALMTHGSIPAEKRAEIGISDSLVRLSAG 376 Query: 348 IEHAEDLKEDLKQAL 362 IE +DL DL+QAL Sbjct: 377 IEDGDDLIADLEQAL 391 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: 371 Number of extensions: 9 Number of successful extensions: 4 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: 393 Length adjustment: 30 Effective length of query: 343 Effective length of database: 363 Effective search space: 124509 Effective search space used: 124509 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