Align Phosphoserine phosphatase ThrH; PSP; PSPase; EC 3.1.3.3 (characterized)
to candidate WP_090438338.1 BLS63_RS00600 bifunctional phosphoserine phosphatase/homoserine phosphotransferase ThrH
Query= SwissProt::Q9I2Y2 (205 letters) >NCBI__GCF_900100495.1:WP_090438338.1 Length = 205 Score = 379 bits (973), Expect = e-110 Identities = 189/205 (92%), Positives = 196/205 (95%) Query: 1 MEIACLDLEGVLVPEIWIAFAEKTGIDALKATTRDIPDYDVLMKQRLRILDEHGLKLGDI 60 MEIACLDLEGVLVPEIWIAFAEKTGI+ALKATTRDIPDYDVLM+QRLRILDEHGLKL DI Sbjct: 1 MEIACLDLEGVLVPEIWIAFAEKTGIEALKATTRDIPDYDVLMQQRLRILDEHGLKLADI 60 Query: 61 QEVIATLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDDSD 120 QEVIATLKPL+GAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHKL D++D Sbjct: 61 QEVIATLKPLDGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLITDEND 120 Query: 121 RVVGYQLRQKDPKRQSVIAFKSLYYRVIAAGDSYNDTTMLSEAHAGILFHAPENVIREFP 180 RVV YQLRQKDPKRQSVIA KSLYYRVIAAGDSYNDTTMLSEAHAGILFHAP+NVIREFP Sbjct: 121 RVVSYQLRQKDPKRQSVIALKSLYYRVIAAGDSYNDTTMLSEAHAGILFHAPDNVIREFP 180 Query: 181 QFPAVHTYEDLKREFLKASSRSLSL 205 QFPAVH+Y DLK EFLKAS R LSL Sbjct: 181 QFPAVHSYADLKDEFLKASDRQLSL 205 Lambda K H 0.323 0.140 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: 246 Number of extensions: 4 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: 205 Length of database: 205 Length adjustment: 21 Effective length of query: 184 Effective length of database: 184 Effective search space: 33856 Effective search space used: 33856 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 45 (21.9 bits)
Align candidate WP_090438338.1 BLS63_RS00600 (bifunctional phosphoserine phosphatase/homoserine phosphotransferase ThrH)
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.8083.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-124 396.7 0.1 9.8e-124 396.5 0.1 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090438338.1 BLS63_RS00600 bifunctional phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090438338.1 BLS63_RS00600 bifunctional phosphoserine phosphatase/homoserine phosphotran # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 396.5 0.1 9.8e-124 9.8e-124 1 203 [] 1 203 [. 1 203 [. 0.99 Alignments for each domain: == domain 1 score: 396.5 bits; conditional E-value: 9.8e-124 TIGR02137 1 qevvtldlegvlvpeiwiavaektgiddlklttrdipdydvlmkqrlkileeenlklsdiqeviatlkl 69 +e+++ldlegvlvpeiwia+aektgi++lk+ttrdipdydvlm+qrl+il+e++lkl+diqeviatlk+ lcl|NCBI__GCF_900100495.1:WP_090438338.1 1 MEIACLDLEGVLVPEIWIAFAEKTGIEALKATTRDIPDYDVLMQQRLRILDEHGLKLADIQEVIATLKP 69 79******************************************************************* PP TIGR02137 70 legavefvdtlreeaqvvilsdtfqefaqplmkqlgfptllchklvvedsdrvkgyqlrqkdqkrkvvk 138 l+gavefvd+lre++qvvilsdtf+ef+qplm+qlgfptllchkl +++drv+ yqlrqkd+kr++v+ lcl|NCBI__GCF_900100495.1:WP_090438338.1 70 LDGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLITDENDRVVSYQLRQKDPKRQSVI 138 ********************************************************************* PP TIGR02137 139 alkelyykviaagdsyndttmlkeadkgilfhapesvvaefpqleavktyeelkdkflkasdrsl 203 alk+lyy+viaagdsyndttml+ea++gilfhap++v++efpq++av++y++lkd+flkasdr l lcl|NCBI__GCF_900100495.1:WP_090438338.1 139 ALKSLYYRVIAAGDSYNDTTMLSEAHAGILFHAPDNVIREFPQFPAVHSYADLKDEFLKASDRQL 203 **************************************************************976 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: 7.90 // [ok]
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