Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate AZOBR_RS08705 AZOBR_RS08705 cysteine synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__azobra:AZOBR_RS08705 Length = 334 Score = 192 bits (489), Expect = 7e-54 Identities = 119/318 (37%), Positives = 172/318 (54%), Gaps = 25/318 (7%) Query: 2 IYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLH 61 I + +IGNTPL+R+ + ++ K E NP GSVKDR AL ++ AE G L Sbjct: 3 IRTGFIGSIGNTPLIRLEGPSKATGCEILGKAEFLNPGGSVKDRAALAIVRDAERRGLLR 62 Query: 62 PGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILT------ 115 PG TI+E T+GNTGIGLA++G GY +IVM E S E++ M++ GA++ L Sbjct: 63 PGGTIVEGTAGNTGIGLALVGNALGYRTVIVMPETQSQEKKDMLRLIGADLRLVPAVPYS 122 Query: 116 --DKKLGTDGAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHF 173 D + G R EL K P NQF N N+ H TT EIW QT+G + F Sbjct: 123 NPDNYVRYSG--RLAEELAKTEPNGAVWANQFDNVANREGHRLTTGPEIWTQTEGRIDAF 180 Query: 174 VAAVGTSGTLMGVGKNLREKNPEIKIIEAQPTKG----HYIQGL-----KSMEEAI---- 220 AVG+ GTL GVG L+E+NP+++I+ A P HY G S+ E I Sbjct: 181 TCAVGSGGTLAGVGLALKERNPDVRIVLADPMGASLYHHYAHGTLKAEGSSITEGIGQGR 240 Query: 221 VPAIYQADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSG-VI 279 + A + +D+ + I EEA +++ +G+ +G SSG + AA ++A+++ G I Sbjct: 241 ITANLEGAPVDQALQITDEEALPVIFDLIKSQGLVLGGSSGINIAAAIRIAKEMGPGHTI 300 Query: 280 VVLFADRGEKYLSTKLFD 297 V + D G++Y S KLF+ Sbjct: 301 VTILCDGGQRYQS-KLFN 317 Lambda K H 0.315 0.133 0.367 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: 334 Number of extensions: 18 Number of successful extensions: 3 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: 299 Length of database: 334 Length adjustment: 27 Effective length of query: 272 Effective length of database: 307 Effective search space: 83504 Effective search space used: 83504 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: 42 (22.0 bits) S2: 48 (23.1 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