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_011611782.1 TERY_RS10350 histidine phosphatase family protein
Query= SwissProt::D3DFG8 (211 letters) >NCBI__GCF_000014265.1:WP_011611782.1 Length = 452 Score = 108 bits (271), Expect = 1e-28 Identities = 67/202 (33%), Positives = 106/202 (52%), Gaps = 5/202 (2%) Query: 3 KLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTYLT 62 +L+LVRH E++WN G++QG +D L++ G+ QA + L HLD SS + R T Sbjct: 239 RLLLVRHGETDWNRDGKFQGQIDVPLNDNGRVQANQAREFLKDVHLDFAVSSSMLRPKET 298 Query: 63 A-LEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGGES 121 A + + ++E+ D + EI HG+W G E+ E +P ++W E P V+ GE+ Sbjct: 299 AEIILQHHPDVELKLLDGLWEISHGLWEGKFESEIEEGFPGLLKQWKEFPASVQMPEGEN 358 Query: 122 LASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWSFGCDNASYSV 181 L V+ R E+ R + +VV+H +A+ C L ++ FW+F N + SV Sbjct: 359 LQQVWKRALVSWNEI-IRSVSGVGIVVAHDAINKAILCQLFALEPEHFWNFKQGNGAVSV 417 Query: 182 IHMEERRN---VILKLNITCHL 200 I E + V+ +NIT HL Sbjct: 418 IDYPEGPDGLPVLEVMNITSHL 439 Score = 89.4 bits (220), Expect = 1e-22 Identities = 60/193 (31%), Positives = 100/193 (51%), Gaps = 13/193 (6%) Query: 3 KLILVRHAESEWNPVGRYQGLLDPD-LSERGKKQAKLLAQELSREHLDVIYSSPLKRTYL 61 ++ILVRH +S +N R QG LD L+E G+ A+ + + L D IYSSPL+R Sbjct: 4 RVILVRHGQSTYNIESRIQGRLDASVLTETGQNTARQVGEALQSLKFDAIYSSPLQRAKQ 63 Query: 62 TALEI---AEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQG 118 TA I ++ IKE+ + EID +W GM+ EEV+EKY ED+ W P ++ + Sbjct: 64 TAEIIHSYLDSPPPVQIKEN-LREIDLPLWEGMMREEVIEKYGEDYSLWKSSPQELCMEV 122 Query: 119 GE--------SLASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFW 170 + + S++ + K F E + ++T+++V+H R + LG+ S + Sbjct: 123 SKPEGQIKHFPILSLFEQAKKFWSETLNNNDHKTILLVAHNGINRCLISTALGIKPSYYH 182 Query: 171 SFGCDNASYSVIH 183 S N ++++ Sbjct: 183 SIQQSNCGINILN 195 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: 289 Number of extensions: 19 Number of successful extensions: 7 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: 452 Length adjustment: 27 Effective length of query: 184 Effective length of database: 425 Effective search space: 78200 Effective search space used: 78200 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