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) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4124 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.22903.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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.15 // [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