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 Synpcc7942_0485 Synpcc7942_0485 phosphoglycerate mutase
Query= SwissProt::D3DFG8 (211 letters) >FitnessBrowser__SynE:Synpcc7942_0485 Length = 445 Score = 119 bits (299), Expect = 7e-32 Identities = 70/204 (34%), Positives = 114/204 (55%), Gaps = 5/204 (2%) Query: 2 VKLILVRHAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTYL 61 V+L+LVRH E++WN R+QG +D L++ G+ QA+ A+ L+ +D SSP+ R Sbjct: 229 VRLLLVRHGETDWNRQKRFQGQIDIPLNDNGRAQARSAAEFLAPIQIDFAVSSPMARPKE 288 Query: 62 TALEIAEA-KNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGGE 120 TA I E N E+ +DR+ EI HG+W G L EE+ ++ E + W ++P +V+ GE Sbjct: 289 TAELILERHPNCELSVDDRLQEIGHGLWEGKLEEEIAAEFGELLQLWKDQPEQVQMPEGE 348 Query: 121 SLASVYNR-VKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWSFGCDNASY 179 +L V++R V + V T +VV+H + + C +LG+ + WS N + Sbjct: 349 NLQEVWDRSVAAWEAIVANAPEGSTGLVVAHDAVNKVILCHVLGLSPADIWSIKQGNGAV 408 Query: 180 SVIHMEER---RNVILKLNITCHL 200 +V+ +R R V+ +N+T HL Sbjct: 409 TVVDYPKRLDSRPVLQAMNLTLHL 432 Score = 101 bits (251), Expect = 2e-26 Identities = 67/215 (31%), Positives = 113/215 (52%), Gaps = 15/215 (6%) Query: 3 KLILVRHAESEWNPVGRYQGLLD-PDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTYL 61 +++LVRH +S +N GR QG D L++RG A +A L+ Y SPL+R Sbjct: 4 RVVLVRHGQSSYNAAGRIQGRCDNSQLTDRGAADAVKVAAALNGIPFAAAYCSPLQRAKR 63 Query: 62 TALEIAEAKNLE--VIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKV----- 114 TA I E + D ++E+D +W G+ EEV +Y E +R+W E PH++ Sbjct: 64 TAEIIIEQIETPPALAVSDGLLEVDLPLWEGLSREEVRSQYAELYRQWHEAPHELVLTVP 123 Query: 115 EFQGGE----SLASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFW 170 + QGG + +++ + + F +++ +RH +QTV++V+H +R++ LGVD S + Sbjct: 124 DGQGGSREHAPVLALFEQARQFWKDLLERHRDQTVLLVAHNGILRSLIATALGVDPSAYQ 183 Query: 171 SFGCDNASYSVIHMEERRNVILK---LNITCHLGE 202 N SV++ + N + LN+T LG+ Sbjct: 184 VIRQSNCGISVLNFADGTNQPAQLECLNLTAPLGD 218 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: 257 Number of extensions: 23 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: 445 Length adjustment: 27 Effective length of query: 184 Effective length of database: 418 Effective search space: 76912 Effective search space used: 76912 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 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