Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Echvi_4660 Echvi_4660 cystathionine beta-synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Cola:Echvi_4660 Length = 456 Score = 216 bits (550), Expect = 8e-61 Identities = 118/310 (38%), Positives = 180/310 (58%), Gaps = 19/310 (6%) Query: 1 MIYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKL 60 MIY++I++TIG+TPLV++N LN K +Y K+E FNP SVKDR+A+KMI+ AE G L Sbjct: 1 MIYNSIIDTIGDTPLVKLNRLNKGIKGTIYVKVEYFNPGNSVKDRMAIKMIDDAEKAGIL 60 Query: 61 HPGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLG 120 PG TIIE TSGNTG+GLA++G +GY I M++ S E+ ++KA GAE+++ + Sbjct: 61 KPGGTIIEGTSGNTGMGLALVGIARGYKCIFTMADKQSKEKIDVLKAMGAEVVVCPTNVS 120 Query: 121 TDG--AIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVG 178 D + VA+ + ++ F PNQ+ N N AHY+TT EIW T+G +THF A VG Sbjct: 121 PDDPRSYYSVAKKLNKDIPNSFYPNQYDNLSNWKAHYETTGPEIWKDTEGKITHFAAGVG 180 Query: 179 TSGTLMGVGKNLREKNPEI---------KIIEAQPTKGHYIQG------LKSMEEAIVPA 223 T GT+ G K L+E+NP I + + G + + + + E I+PA Sbjct: 181 TGGTMSGTAKYLKEQNPSIVSVGIDTYGSVFKKYKETGEFDENEIYPYLTEGIGEDILPA 240 Query: 224 IYQADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEK--IDSGVIVV 281 ID + + +++ R + +EG+F+G S G+A+ A + A + + +V+ Sbjct: 241 NVDFSMIDHFVKVTDKDSAVMTRRLSREEGLFVGWSCGSAVHGALEYARQHLTEQDTMVI 300 Query: 282 LFADRGEKYL 291 + D G +YL Sbjct: 301 ILPDHGTRYL 310 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: 400 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: 456 Length adjustment: 30 Effective length of query: 269 Effective length of database: 426 Effective search space: 114594 Effective search space used: 114594 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: 49 (23.5 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