Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Pf1N1B4_4889 Cystathionine beta-synthase (EC 4.2.1.22)
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4889 Length = 458 Score = 195 bits (496), Expect = 1e-54 Identities = 116/306 (37%), Positives = 176/306 (57%), Gaps = 23/306 (7%) Query: 6 ILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPGST 65 +LE IGNTPLVRI+ + P ++ KLE NP GS+KDRI L MI+ AE +G+L PG T Sbjct: 9 VLELIGNTPLVRISRFDTGP-CTLFLKLESQNPGGSIKDRIGLAMIDTAERDGRLRPGGT 67 Query: 66 IIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLG---TD 122 I+EAT+GNTG+GLA++GR KGY V++V+ + +S E+ +KA GAE+ +T +G D Sbjct: 68 IVEATAGNTGLGLALVGRAKGYRVVLVVPDKMSTEKVLHLKAMGAEVHITRSDVGKGHPD 127 Query: 123 GAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGT 182 A L ++ P +F +QF+N N +AH +TA EIWAQT+ V V VG++GT Sbjct: 128 YYQDVAARLARDIPDAFF-ADQFNNPANPLAHECSTAPEIWAQTQHDVDAIVVGVGSAGT 186 Query: 183 LMGVGKNLREKNPEIKIIEAQP---------------TKGHYIQGLKSMEEAIVPAIYQA 227 L G+ + + P ++++ A P T G + ++ + E +P+I Sbjct: 187 LTGLTRFFQRVQPNLEMVLADPVGSVMAEYSRSGTLGTPGSW--AVEGIGEDFIPSIADL 244 Query: 228 DKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLA-EKIDSGVIVVLFADR 286 + + I EE+F AR+++ EGI G S+G + AA + E+ + +V D Sbjct: 245 SSVRKAYSISDEESFDHARQLLRAEGILGGSSTGTLLAAALRYCREQTEPKRVVSFVCDT 304 Query: 287 GEKYLS 292 G +YLS Sbjct: 305 GTRYLS 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: 359 Number of extensions: 23 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: 299 Length of database: 458 Length adjustment: 30 Effective length of query: 269 Effective length of database: 428 Effective search space: 115132 Effective search space used: 115132 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