Align Phosphoserine phosphatase; PSP; PSPase; EC 3.1.3.3 (characterized)
to candidate WP_085987743.1 PST_RS10275 bifunctional phosphoserine phosphatase/homoserine phosphotransferase ThrH
Query= SwissProt::Q883R9 (237 letters) >NCBI__GCF_000013785.1:WP_085987743.1 Length = 223 Score = 383 bits (983), Expect = e-111 Identities = 192/221 (86%), Positives = 202/221 (91%) Query: 17 ARVPLPLILNAVGECAVEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMK 76 A V +P + + E VEIACLDLEGVLVPEIWIAFAE TGIESLRATTRDIPDYDVLMK Sbjct: 3 AAVRVPPSIFCIEEWPVEIACLDLEGVLVPEIWIAFAEATGIESLRATTRDIPDYDVLMK 62 Query: 77 QRLRILDEHGLKLADIQAVISTLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQL 136 QRLRILDEHGLKLADIQ VI+TLKPLEGA EF+DWLRERFQVVILSDTFYEFSQPLMRQL Sbjct: 63 QRLRILDEHGLKLADIQKVIATLKPLEGAPEFIDWLRERFQVVILSDTFYEFSQPLMRQL 122 Query: 137 GFPTLLCHRLITDETDRVVSYQLRQKDPKRQSVLAFKSLYYRIIAAGDSYNDTTMLGEAD 196 GFPTLLCHRLITDETDRVV YQLRQKDPKRQSV+A KSLYYR+IAAGDSYNDTTML EA Sbjct: 123 GFPTLLCHRLITDETDRVVDYQLRQKDPKRQSVIALKSLYYRVIAAGDSYNDTTMLSEAH 182 Query: 197 AGILFHAPDNVIREFPQFPAVHTFDELKKEFIKASNRELVL 237 AGILFHAPDNVI EFPQFPAVHTFD LK+EF+KASNR+L L Sbjct: 183 AGILFHAPDNVIAEFPQFPAVHTFDALKQEFLKASNRKLTL 223 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: 263 Number of extensions: 5 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: 223 Length adjustment: 23 Effective length of query: 214 Effective length of database: 200 Effective search space: 42800 Effective search space used: 42800 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: 46 (22.3 bits)
Align candidate WP_085987743.1 PST_RS10275 (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.25314.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-119 382.4 0.1 2.4e-119 382.2 0.1 1.0 1 lcl|NCBI__GCF_000013785.1:WP_085987743.1 PST_RS10275 bifunctional phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013785.1:WP_085987743.1 PST_RS10275 bifunctional phosphoserine phosphatase/homoserine phosphotransf # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 382.2 0.1 2.4e-119 2.4e-119 2 203 .] 20 221 .. 19 221 .. 0.99 Alignments for each domain: == domain 1 score: 382.2 bits; conditional E-value: 2.4e-119 TIGR02137 2 evvtldlegvlvpeiwiavaektgiddlklttrdipdydvlmkqrlkileeenlklsdiqeviatlkll 70 e+++ldlegvlvpeiwia+ae tgi++l++ttrdipdydvlmkqrl+il+e++lkl+diq+viatlk+l lcl|NCBI__GCF_000013785.1:WP_085987743.1 20 EIACLDLEGVLVPEIWIAFAEATGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADIQKVIATLKPL 88 79******************************************************************* PP TIGR02137 71 egavefvdtlreeaqvvilsdtfqefaqplmkqlgfptllchklvvedsdrvkgyqlrqkdqkrkvvka 139 ega ef+d+lre++qvvilsdtf+ef+qplm+qlgfptllch+l +++drv+ yqlrqkd+kr++v+a lcl|NCBI__GCF_000013785.1:WP_085987743.1 89 EGAPEFIDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITDETDRVVDYQLRQKDPKRQSVIA 157 ********************************************************************* PP TIGR02137 140 lkelyykviaagdsyndttmlkeadkgilfhapesvvaefpqleavktyeelkdkflkasdrsl 203 lk+lyy+viaagdsyndttml+ea++gilfhap++v+aefpq++av+t++ lk++flkas+r l lcl|NCBI__GCF_000013785.1:WP_085987743.1 158 LKSLYYRVIAAGDSYNDTTMLSEAHAGILFHAPDNVIAEFPQFPAVHTFDALKQEFLKASNRKL 221 ************************************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (203 nodes) Target sequences: 1 (223 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: 6.70 // [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