Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate WP_078428932.1 BK574_RS13250 cystathionine gamma-synthase family protein
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_002019605.1:WP_078428932.1 Length = 401 Score = 219 bits (559), Expect = 9e-62 Identities = 142/414 (34%), Positives = 211/414 (50%), Gaps = 45/414 (10%) Query: 22 HRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSNVLEERIAALEGGAAAL 81 H + VP+ + +Y +++ ++ G++Y R NPT E+++ LE AAA Sbjct: 25 HGATQVPVIPSVAYNYDDMDEWYEVAVGRKKGHIYGRNTNPTVQAFEDKLKLLENAAAAT 84 Query: 82 AVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRFGIEARFVEGDNPEEFE 141 + S+G AA + + GD +V+ YGGT F + I F E N E+ E Sbjct: 85 SFSTGMAAISNTLYTFLRPGDRVVTIKDTYGGTNKIFTEFLPQMDISISFCETGNHEQIE 144 Query: 142 KVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNTFGAGGYFCQPIKYGAD 201 + K +YLET NP + D +++ H+ G V+VDNTF A QP++ GAD Sbjct: 145 TEVAKGCKILYLETPTNPTVKITDIKRMAKAGHEAGAIVIVDNTF-ATPLNQQPLELGAD 203 Query: 202 IVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAEGYHGTIYNEAYGNLAY 261 IV HSATK++GGH +GG+ + ++Y EK YH N Sbjct: 204 IVLHSATKFLGGHADALGGVACSNN----EEYIEKI---------YHYREIN-------- 242 Query: 262 IVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALKLAKWLEQSPYVSWVSY 321 G M+P+A++L+L+G++TL LR R ENALKLA +L+ V V Y Sbjct: 243 ------------GATMDPWAAYLILRGMKTLELRVRRQEENALKLANYLKSEEIVESVFY 290 Query: 322 PGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLSGAQVVDNLKLASNLAN 381 PGL H +H+ AK+ + GFGG+LSF VK + K+ P NL A+ AN Sbjct: 291 PGLEEHPNHDIAKQQMV-GFGGMLSFAVKGGIDTVKKLLP----------NLTFANRAAN 339 Query: 382 VGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFIDDIIADFQQSF 435 +G +T V T+H + +E+ A G+ + LIRVS GIE +DII DF+++F Sbjct: 340 LGAVETTVGPARTTSHVECTPEERKAMGIPEGLIRVSCGIENAEDIINDFKEAF 393 Lambda K H 0.317 0.136 0.402 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: 435 Number of extensions: 19 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: 444 Length of database: 401 Length adjustment: 32 Effective length of query: 412 Effective length of database: 369 Effective search space: 152028 Effective search space used: 152028 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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