Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_027720565.1 H589_RS0102480 phosphoserine phosphatase SerB
Query= SwissProt::A0QJI1 (411 letters) >NCBI__GCF_000425265.1:WP_027720565.1 Length = 403 Score = 277 bits (709), Expect = 4e-79 Identities = 161/400 (40%), Positives = 252/400 (63%), Gaps = 15/400 (3%) Query: 9 VLITVTGVDQPGVTATLFEVLSGHGVELLNVEQVVIRHRLTLGVLVCCPADVADGPALRH 68 +LI ++G D+ G+T+ L EVL+G+G+++L++ Q VI ++L LG+L+ P + P L+ Sbjct: 5 ILIQISGEDKAGLTSALTEVLAGYGIDILDIGQSVIHNQLILGILIHIPQESESAPVLK- 63 Query: 69 DVEAAIRKVGLDVSIE--RSD---DVPIIREPSTHTIFVLGRPITAAAFGAVAREVAALG 123 D+ ++G++V + SD D + H I ++ R + A VA VA G Sbjct: 64 DIMFKGYELGVNVKFKPIESDKYMDWVNAQGKPRHIITLVARKASGTAISKVANIVAENG 123 Query: 124 VNIDLIRGVSD-YPVIG--------LELRVSVPPGADGALRTALNRVSSEEHVDVAVEDY 174 +NID+I +S P+ G +E V P +R++ +++EE VD+A+++ Sbjct: 124 LNIDMIHRLSGRIPMNGELIPRQACVEFSVRGTPQNLDLMRSSFLTMATEEQVDIALQED 183 Query: 175 TLERRAKRLIVFDVDSTLVQGEVIEMLAAKAGAEGQVAAITDAAMRGELDFAQSLQQRVA 234 + RR +RL+ FD+DSTL+Q EVI+ LA AG+ V++IT++AMRGE+DF +SL+QR+A Sbjct: 184 NVFRRNRRLVAFDMDSTLIQAEVIDELAKAAGSGDLVSSITESAMRGEIDFQESLRQRLA 243 Query: 235 TLAGLPATVIDEVAGQLELMPGARTTLRTLRRLGYACGVVSGGFRRIIEPLAEELMLDYV 294 TL GL +V+ E+A L + GA + L++ GY ++SGGF E L E L +DYV Sbjct: 244 TLKGLDESVMVEIAQNLPITEGAERLISNLKKFGYKTAIISGGFTYFGEKLQERLGVDYV 303 Query: 295 AANELEIVDGTLTGRVVGPIIDRAGKATALREFAQRAGVPMAQTVAVGDGANDIDMLAAA 354 AN LEI DG LTG V+G I+D KA LR+ A++ + + Q +AVGDGAND+ ML+ A Sbjct: 304 YANRLEIKDGKLTGGVIGDIVDGPKKAELLRKIAEKEQISLQQAIAVGDGANDLPMLSIA 363 Query: 355 GLGIAFNAKPALREVADASLSHPYLDTVLFLLGVTRGEIE 394 GLGIAF+AKP +++ A S+SH LD++L+L+G+ E++ Sbjct: 364 GLGIAFHAKPKVKKDARQSISHFGLDSILYLIGLRDREMD 403 Lambda K H 0.320 0.137 0.382 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: 394 Number of extensions: 15 Number of successful extensions: 3 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: 411 Length of database: 403 Length adjustment: 31 Effective length of query: 380 Effective length of database: 372 Effective search space: 141360 Effective search space used: 141360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
Align candidate WP_027720565.1 H589_RS0102480 (phosphoserine phosphatase SerB)
to HMM TIGR00338 (serB: phosphoserine phosphatase SerB (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/TIGR00338.hmm # target sequence database: /tmp/gapView.17931.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00338 [M=219] Accession: TIGR00338 Description: serB: phosphoserine phosphatase SerB 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-88 280.3 0.5 7e-88 279.9 0.5 1.1 1 lcl|NCBI__GCF_000425265.1:WP_027720565.1 H589_RS0102480 phosphoserine pho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000425265.1:WP_027720565.1 H589_RS0102480 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 279.9 0.5 7e-88 7e-88 1 219 [] 177 395 .. 177 395 .. 0.99 Alignments for each domain: == domain 1 score: 279.9 bits; conditional E-value: 7e-88 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 dia +e++ ++++++lv fD+Dstli++EvIde+ak+aG ++ Vs iTe+Amrge+dF+eslr+R+++l lcl|NCBI__GCF_000425265.1:WP_027720565.1 177 DIALQEDNVFRRNRRLVAFDMDSTLIQAEVIDELAKAAGSGDLVSSITESAMRGEIDFQESLRQRLATL 245 6889999************************************************************** PP TIGR00338 70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138 kgl+++++ +++++l++teG+e l+++Lk+ gyk+a+iSGgF+++ ekl+e+Lg+d+v aNrLe++dgk lcl|NCBI__GCF_000425265.1:WP_027720565.1 246 KGLDESVMVEIAQNLPITEGAERLISNLKKFGYKTAIISGGFTYFGEKLQERLGVDYVYANRLEIKDGK 314 ********************************************************************* PP TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207 ltG v g+ivd +ka+ l k++eke+isl++ +avGDGanDl+m++ Aglgiaf+akp++k+ a ++i lcl|NCBI__GCF_000425265.1:WP_027720565.1 315 LTGGVIGDIVDGPKKAELLRKIAEKEQISLQQAIAVGDGANDLPMLSIAGLGIAFHAKPKVKKDARQSI 383 ********************************************************************* PP TIGR00338 208 ekkdltdilell 219 ++ l +il+l+ lcl|NCBI__GCF_000425265.1:WP_027720565.1 384 SHFGLDSILYLI 395 ******999986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (403 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 9.92 // [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