Align phosphoserine phosphatase (EC 3.1.3.3) (characterized)
to candidate GFF484 Psest_0489 phosphoserine phosphatase SerB
Query= BRENDA::O53289 (409 letters) >FitnessBrowser__psRCH2:GFF484 Length = 404 Score = 251 bits (641), Expect = 3e-71 Identities = 158/392 (40%), Positives = 221/392 (56%), Gaps = 13/392 (3%) Query: 7 VLITVTGMDQPGVTSALFEVLAQHGVELLNVEQVVIRGRLTLGVLVSCPLDVADGTALRD 66 VLI +TG D+PG+T+A+ VLAQ GV +L++ Q VI L+ G+L+ P + + L+D Sbjct: 5 VLINITGEDRPGLTAAITGVLAQGGVNILDIGQAVIHDTLSFGILIEIPDNERASSVLKD 64 Query: 67 DVAAAI---HGVGLDVAIERSDDLPIIRQ-PSTHTIFVLGRPITAGAFSAVARGVAALGV 122 + V E + Q H + +L R +TA V+ A G+ Sbjct: 65 VLFMGYKHDQQVRFTPVAEADYQHWVAGQGKPRHIVTLLTRKVTAEQLQRVSSITAKYGL 124 Query: 123 NIDFIRGIS-----DYPVT----GLELRVSVPPGCVGPLQIALTKVAAEEHVDVAVEDYG 173 NID I +S D P +E V P L+ VA E +VD+A + Sbjct: 125 NIDHIDRLSGRMPLDMPEELGKGCIEFSVRGEPADTAALRAEFLSVAQELNVDIAFQRDS 184 Query: 174 LAWRTKRLIVFDVDSTLVQGEVIEMLAARAGAQGQVAAITEAAMRGELDFAESLQRRVAT 233 + R +RL VFD+DSTL++ EVI+ LA AG QV+ ITE AMRGELDF S + R+A Sbjct: 185 VYRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGEQVSEITERAMRGELDFRASFKERLAL 244 Query: 234 LAGLPATVIDDVAEQLELMPGARTTIRTLRRLGFRCGVVSGGFRRIIEPLARELMLDFVA 293 L GL V+ D+ L L GA L+RLG++ ++SGGF + L +L +D+V Sbjct: 245 LEGLSEDVLADIGASLRLTEGAEVLFAELKRLGYKTAILSGGFSYFAKQLQAKLGIDYVF 304 Query: 294 SNELEIVDGILTGRVVGPIVDRPGKAKALRDFASQYGVPMEQTVAVGDGANDIDMLGAAG 353 +NEL+I +G +TG V PIVD KA LR A Q G+ +EQT+AVGDGAND+ MLG AG Sbjct: 305 ANELQIENGKVTGVAVEPIVDAQRKADLLRQLAEQEGLCLEQTIAVGDGANDLPMLGLAG 364 Query: 354 LGIAFNAKPALREVADASLSHPYLDTVLFLLG 385 LG+AF AKP +++ A ++S LD +L+LLG Sbjct: 365 LGVAFRAKPLVKQSAKQAISTLGLDGILYLLG 396 Lambda K H 0.321 0.139 0.395 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: 444 Number of extensions: 28 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 409 Length of database: 404 Length adjustment: 31 Effective length of query: 378 Effective length of database: 373 Effective search space: 140994 Effective search space used: 140994 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate GFF484 Psest_0489 (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.31151.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-83 263.6 0.3 8.6e-83 263.3 0.3 1.1 1 lcl|FitnessBrowser__psRCH2:GFF484 Psest_0489 phosphoserine phospha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF484 Psest_0489 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.3 0.3 8.6e-83 8.6e-83 1 219 [] 177 395 .. 177 395 .. 0.99 Alignments for each domain: == domain 1 score: 263.3 bits; conditional E-value: 8.6e-83 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvel 76 dia + +s ++++++l+vfD+Dstlie+EvIde+ak+aGv+e+VseiTerAmrgeldF++s++eR++ll gl++++ lcl|FitnessBrowser__psRCH2:GFF484 177 DIAFQRDSVYRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGEQVSEITERAMRGELDFRASFKERLALLEGLSEDV 252 688899999******************************************************************* PP TIGR00338 77 lkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesa 152 l + +l+lteG+e l +Lk+ gyk+a++SGgF+++a++l++kLg+d+vfaN+L++e+gk tG +ivd++ lcl|FitnessBrowser__psRCH2:GFF484 253 LADIGASLRLTEGAEVLFAELKRLGYKTAILSGGFSYFAKQLQAKLGIDYVFANELQIENGKVTGVAVEPIVDAQR 328 **************************************************************************** PP TIGR00338 153 kaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilell 219 ka+ l +l+e+eg+ le+t+avGDGanDl+m+ Aglg+af akp +k+ a+++i++ l +il+ll lcl|FitnessBrowser__psRCH2:GFF484 329 KADLLRQLAEQEGLCLEQTIAVGDGANDLPMLGLAGLGVAFRAKPLVKQSAKQAISTLGLDGILYLL 395 **************************************************************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (404 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: 00:00:00.01 # Mc/sec: 6.53 // [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