Align Phosphoserine phosphatase; PSP; PSPase; EC 3.1.3.3 (characterized)
to candidate GFF4123 PS417_21120 phosphoserine phosphatase
Query= SwissProt::Q883R9 (237 letters) >FitnessBrowser__WCS417:GFF4123 Length = 205 Score = 385 bits (990), Expect = e-112 Identities = 190/205 (92%), Positives = 201/205 (98%) Query: 33 VEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADI 92 +EIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADI Sbjct: 1 MEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADI 60 Query: 93 QAVISTLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITDETD 152 QAVI+TLKPL+GA+EFV+WLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITD+TD Sbjct: 61 QAVIATLKPLDGAIEFVNWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITDDTD 120 Query: 153 RVVSYQLRQKDPKRQSVLAFKSLYYRIIAAGDSYNDTTMLGEADAGILFHAPDNVIREFP 212 RVVSYQLRQKDPKRQSVLAFKSLYYR+IAAGDSYNDTTMLGEAD GILFHAP+NVIREFP Sbjct: 121 RVVSYQLRQKDPKRQSVLAFKSLYYRVIAAGDSYNDTTMLGEADCGILFHAPENVIREFP 180 Query: 213 QFPAVHTFDELKKEFIKASNRELVL 237 QFPAVHTF++LK+ FIKASNR L L Sbjct: 181 QFPAVHTFEDLKQAFIKASNRPLSL 205 Lambda K H 0.324 0.139 0.410 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: 266 Number of extensions: 3 Number of successful extensions: 1 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: 237 Length of database: 205 Length adjustment: 22 Effective length of query: 215 Effective length of database: 183 Effective search space: 39345 Effective search space used: 39345 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 45 (21.9 bits)
Align candidate GFF4123 PS417_21120 (phosphoserine phosphatase)
to HMM TIGR02137 (thrH: phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein (EC 3.1.3.3))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR02137.hmm # target sequence database: /tmp/gapView.28501.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02137 [M=203] Accession: TIGR02137 Description: HSK-PSP: phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-119 382.9 0.0 1.7e-119 382.7 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF4123 PS417_21120 phosphoserine phosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF4123 PS417_21120 phosphoserine phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 382.7 0.0 1.7e-119 1.7e-119 1 202 [. 1 202 [. 1 203 [. 0.99 Alignments for each domain: == domain 1 score: 382.7 bits; conditional E-value: 1.7e-119 TIGR02137 1 qevvtldlegvlvpeiwiavaektgiddlklttrdipdydvlmkqrlkileeenlklsdiqeviatlkllegave 75 +e+++ldlegvlvpeiwia+aektgi++l++ttrdipdydvlmkqrl+il+e++lkl+diq viatlk+l+ga e lcl|FitnessBrowser__WCS417:GFF4123 1 MEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADIQAVIATLKPLDGAIE 75 79************************************************************************* PP TIGR02137 76 fvdtlreeaqvvilsdtfqefaqplmkqlgfptllchklvvedsdrvkgyqlrqkdqkrkvvkalkelyykviaa 150 fv++lre++qvvilsdtf+ef+qplm+qlgfptllch+l +d+drv+ yqlrqkd+kr++v a+k+lyy+viaa lcl|FitnessBrowser__WCS417:GFF4123 76 FVNWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITDDTDRVVSYQLRQKDPKRQSVLAFKSLYYRVIAA 150 *************************************************************************** PP TIGR02137 151 gdsyndttmlkeadkgilfhapesvvaefpqleavktyeelkdkflkasdrs 202 gdsyndttml ead gilfhape+v++efpq++av+t+e+lk+ f kas+r lcl|FitnessBrowser__WCS417:GFF4123 151 GDSYNDTTMLGEADCGILFHAPENVIREFPQFPAVHTFEDLKQAFIKASNRP 202 *************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (203 nodes) Target sequences: 1 (205 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.74 // [ok]
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