Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_090440547.1 BLS63_RS04850 phosphoserine phosphatase SerB
Query= SwissProt::A0QJI1 (411 letters) >NCBI__GCF_900100495.1:WP_090440547.1 Length = 404 Score = 263 bits (672), Expect = 7e-75 Identities = 165/393 (41%), Positives = 230/393 (58%), Gaps = 15/393 (3%) Query: 9 VLITVTGVDQPGVTATLFEVLSGHGVELLNVEQVVIRHRLTLGVLVCCPADVADGPALRH 68 VLI +TG D+PG+TA + VL+ GV +L++ Q VI L+ G+LV P L+ Sbjct: 5 VLINITGEDRPGLTAAITGVLAQGGVNILDIGQAVIHDTLSFGILVEIPHTERASSVLK- 63 Query: 69 DVEAAIRKVGLDVS---IERSDDVPII--REPSTHTIFVLGRPITAAAFGAVAREVAALG 123 DV K+ V + +D + + H + +L R +TA V+ A G Sbjct: 64 DVLFTAYKLDQQVRFTPVSEADYQQWVGGQGKPRHIVTLLTRKVTAEQLHRVSTITARYG 123 Query: 124 VNIDLIRGVS-----DYPVIG----LELRVSVPPGADGALRTALNRVSSEEHVDVAVEDY 174 +NID I +S D P +E V P ALR V+ E +VD+A + Sbjct: 124 LNIDHIDRLSGRMPLDTPAEQGKGCVEFSVRGEPADPAALRAEFLSVAQELNVDIAFQRD 183 Query: 175 TLERRAKRLIVFDVDSTLVQGEVIEMLAAKAGAEGQVAAITDAAMRGELDFAQSLQQRVA 234 +L RR +RL VFD+DSTL++ EVI+ LA AG +V+AIT+ AMRGELDFA S ++R+A Sbjct: 184 SLFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGDKVSAITERAMRGELDFAASFRERLA 243 Query: 235 TLAGLPATVIDEVAGQLELMPGARTTLRTLRRLGYACGVVSGGFRRIIEPLAEELMLDYV 294 L GLP +V+ ++ L L GA T L RLGY ++SGGF + L +L +DYV Sbjct: 244 LLKGLPESVLADIGASLRLTEGAETLFSELHRLGYKTAILSGGFSYFAKQLQAKLGIDYV 303 Query: 295 AANELEIVDGTLTGRVVGPIIDRAGKATALREFAQRAGVPMAQTVAVGDGANDIDMLAAA 354 ANEL+IVDG +TG + PI+D KA LRE AQ+ G+ + QT+AVGDGAND+ MLA A Sbjct: 304 FANELQIVDGRVTGVALEPIVDAQRKADLLRELAQKEGLRLEQTIAVGDGANDLPMLAIA 363 Query: 355 GLGIAFNAKPALREVADASLSHPYLDTVLFLLG 387 GLG+AF AKP +++ A ++S LD +L+LLG Sbjct: 364 GLGVAFRAKPLVKQSAKQAISTLGLDGILYLLG 396 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: 425 Number of extensions: 16 Number of successful extensions: 2 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: 404 Length adjustment: 31 Effective length of query: 380 Effective length of database: 373 Effective search space: 141740 Effective search space used: 141740 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_090440547.1 BLS63_RS04850 (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.31959.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-84 266.9 0.1 8.3e-84 266.6 0.1 1.1 1 lcl|NCBI__GCF_900100495.1:WP_090440547.1 BLS63_RS04850 phosphoserine phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090440547.1 BLS63_RS04850 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 266.6 0.1 8.3e-84 8.3e-84 1 219 [] 177 395 .. 177 395 .. 0.99 Alignments for each domain: == domain 1 score: 266.6 bits; conditional E-value: 8.3e-84 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 dia + +s ++++++l+vfD+Dstlie+EvIde+ak+aGv+++Vs+iTerAmrgeldF +s+reR++ll lcl|NCBI__GCF_900100495.1:WP_090440547.1 177 DIAFQRDSLFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGDKVSAITERAMRGELDFAASFRERLALL 245 67888899999********************************************************** PP TIGR00338 70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138 kglp+++l + +l+lteG+e l ++L++ gyk+a++SGgF+++a++l++kLg+d+vfaN+L++ dg+ lcl|NCBI__GCF_900100495.1:WP_090440547.1 246 KGLPESVLADIGASLRLTEGAETLFSELHRLGYKTAILSGGFSYFAKQLQAKLGIDYVFANELQIVDGR 314 ********************************************************************* PP TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207 tG +ivd++ ka+ l +l++keg+ le+t+avGDGanDl+m++ Aglg+af akp +k+ a+++i lcl|NCBI__GCF_900100495.1:WP_090440547.1 315 VTGVALEPIVDAQRKADLLRELAQKEGLRLEQTIAVGDGANDLPMLAIAGLGVAFRAKPLVKQSAKQAI 383 ********************************************************************* PP TIGR00338 208 ekkdltdilell 219 ++ l +il+ll lcl|NCBI__GCF_900100495.1:WP_090440547.1 384 STLGLDGILYLL 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.51 // [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