Align Phosphoserine phosphatase; PSP; PSPase; EC 3.1.3.3 (characterized)
to candidate PfGW456L13_4124 Homoserine kinase (EC 2.7.1.39)
Query= SwissProt::Q883R9 (237 letters) >lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4124 Homoserine kinase (EC 2.7.1.39) Length = 205 Score = 380 bits (977), Expect = e-111 Identities = 188/205 (91%), Positives = 197/205 (96%) Query: 33 VEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADI 92 VEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKL+DI Sbjct: 1 VEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLSDI 60 Query: 93 QAVISTLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITDETD 152 Q VI+TLKPL+GA+EFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITD+T Sbjct: 61 QEVIATLKPLDGAIEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITDDTG 120 Query: 153 RVVSYQLRQKDPKRQSVLAFKSLYYRIIAAGDSYNDTTMLGEADAGILFHAPDNVIREFP 212 RV YQLRQKDPKRQSVLAFKSLYYR+IAAGDSYNDTTMLGEADAGILFHAPDNVI +FP Sbjct: 121 RVTDYQLRQKDPKRQSVLAFKSLYYRVIAAGDSYNDTTMLGEADAGILFHAPDNVIAQFP 180 Query: 213 QFPAVHTFDELKKEFIKASNRELVL 237 QFPAVHTF+ LK+EFIKASNR L L Sbjct: 181 QFPAVHTFEALKQEFIKASNRTLSL 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: 253 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 PfGW456L13_4124 (Homoserine kinase (EC 2.7.1.39))
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.7512.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-120 383.9 0.1 8.3e-120 383.7 0.1 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4124 Homoserine kinase (EC 2.7.1.39) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4124 Homoserine kinase (EC 2.7.1.39) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 383.7 0.1 8.3e-120 8.3e-120 2 203 .] 2 203 .. 1 203 [. 0.99 Alignments for each domain: == domain 1 score: 383.7 bits; conditional E-value: 8.3e-120 TIGR02137 2 evvtldlegvlvpeiwiavaektgiddlklttrdipdydvlmkqrlkileeenlk 56 e+++ldlegvlvpeiwia+aektgi++l++ttrdipdydvlmkqrl+il+e++lk lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4124 2 EIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLK 56 79***************************************************** PP TIGR02137 57 lsdiqeviatlkllegavefvdtlreeaqvvilsdtfqefaqplmkqlgfptllc 111 lsdiqeviatlk+l+ga efvd+lre++qvvilsdtf+ef+qplm+qlgfptllc lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4124 57 LSDIQEVIATLKPLDGAIEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLC 111 ******************************************************* PP TIGR02137 112 hklvvedsdrvkgyqlrqkdqkrkvvkalkelyykviaagdsyndttmlkeadkg 166 h+l +d+ rv yqlrqkd+kr++v a+k+lyy+viaagdsyndttml ead+g lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4124 112 HRLITDDTGRVTDYQLRQKDPKRQSVLAFKSLYYRVIAAGDSYNDTTMLGEADAG 166 ******************************************************* PP TIGR02137 167 ilfhapesvvaefpqleavktyeelkdkflkasdrsl 203 ilfhap++v+a+fpq++av+t+e lk++f kas+r+l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4124 167 ILFHAPDNVIAQFPQFPAVHTFEALKQEFIKASNRTL 203 **********************************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 5.37 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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