Align Phosphoserine phosphatase 1; PSP 1; PSPase 1; Metal-independent phosphoserine phosphatase 1; iPSP1; O-phosphoserine phosphohydrolase 1; EC 3.1.3.3 (characterized)
to candidate WP_011320358.1 AVA_RS18510 histidine phosphatase family protein
Query= SwissProt::D3DFG8 (211 letters) >NCBI__GCF_000204075.1:WP_011320358.1 Length = 449 Score = 116 bits (290), Expect = 8e-31 Identities = 71/209 (33%), Positives = 111/209 (53%), Gaps = 11/209 (5%) Query: 2 VKLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTYL 61 V+L+LVRH E+EWN R+QG +D L++ G++QA+ L +D SS + R Sbjct: 232 VRLLLVRHGETEWNRQTRFQGQIDVPLNDNGRQQAQKAGVFLQNVAIDFAVSSSMLRPKE 291 Query: 62 TA---LEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQG 118 TA L + NLE+ +D + EI HG+W G L E+ E++P + RW P +V+ Sbjct: 292 TAEIILRHHPSINLEL--QDGLREISHGLWEGKLEAEIEEEFPGELERWRTIPGQVQMPE 349 Query: 119 GESLASVYNRVKGFLEEVRKR---HWNQTVVVVSHTVPMRAMYCALLGVDLSKFWSFGCD 175 GE+L V+ R + + + + QT ++V+H + + C +LG+ FW+F Sbjct: 350 GENLQQVWERSTEAWQNIVQTALDNQRQTGLIVAHDATNKTLLCHILGLPTDNFWNFRQG 409 Query: 176 NASYSVIHMEERRN---VILKLNITCHLG 201 N + SVI N V+ +NIT HLG Sbjct: 410 NGAVSVIDYPSGLNGVPVLQAMNITTHLG 438 Score = 99.0 bits (245), Expect = 1e-25 Identities = 65/220 (29%), Positives = 110/220 (50%), Gaps = 18/220 (8%) Query: 1 MVKLILVRHAESEWNPVGRYQGLLDPD-LSERGKKQAKLLAQELSREHLDVIYSSPLKRT 59 M ++I+VRH +S +N R QG D L++RG+ A + + L+ + IYSSPL+R Sbjct: 1 MTRVIIVRHGQSTYNIERRIQGRADVSTLTDRGRSDASKVGKALTNISFNAIYSSPLQRA 60 Query: 60 YLTA------LEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHK 113 TA L ++ +V + + EID +W ML EV +K+PED+R W E P + Sbjct: 61 KQTAEIIHGELANEAVQSADVQISELLREIDLPLWEKMLTSEVKQKFPEDYRIWHENPQE 120 Query: 114 VEFQGGES--------LASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVD 165 ++ ++ + S+Y + + F + + H +T+++V H RA+ LG+ Sbjct: 121 LQMLVNDNGVTREHFPVLSLYEQARQFWQNILPHHRGETILIVGHNGINRALISTALGIH 180 Query: 166 LSKFWSFGCDNASYSVIHMEERRNVILKL---NITCHLGE 202 S++ S N SV++ ++L N T H GE Sbjct: 181 PSRYHSIQQSNCGISVLNFAGGLGDPVQLESMNQTQHTGE 220 Lambda K H 0.320 0.136 0.408 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: 245 Number of extensions: 10 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 211 Length of database: 449 Length adjustment: 27 Effective length of query: 184 Effective length of database: 422 Effective search space: 77648 Effective search space used: 77648 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 (21.8 bits) S2: 48 (23.1 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