Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_011801935.1 PNAP_RS12765 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >NCBI__GCF_000015505.1:WP_011801935.1 Length = 236 Score = 399 bits (1026), Expect = e-116 Identities = 197/236 (83%), Positives = 220/236 (93%) Query: 1 MQPTEISPGLVVNVATPDLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEA 60 M P E SPGLVVN+ATPDLKL DFKLIAFDMDSTLINIECVDEIADA GRKAEVAAITEA Sbjct: 1 MNPIEHSPGLVVNIATPDLKLRDFKLIAFDMDSTLINIECVDEIADAVGRKAEVAAITEA 60 Query: 61 AMRGEISDYKESLRQRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVS 120 AMRGEI+D+K+SLR+RVALLKGVS+ASMDEVYR RL+LNPGAA LV+ACKDAG+K+LLVS Sbjct: 61 AMRGEITDFKDSLRRRVALLKGVSMASMDEVYRERLKLNPGAAELVRACKDAGMKILLVS 120 Query: 121 GGFTFFTDRIRDELGIDYTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQL 180 GGFT+FTDR++ L ID+TRSNVLE DGLLTG+M+DQ WGDICDGEEKR+ML++TCGQL Sbjct: 121 GGFTYFTDRVKGLLDIDFTRSNVLEVRDGLLTGKMIDQSWGDICDGEEKRRMLIQTCGQL 180 Query: 181 GISPRQAIAMGDGANDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLELVK 236 GI+P QAIAMGDGANDLPMMG AGLSVAYHAKP+VREQAMVAIN GGLDRLLEL++ Sbjct: 181 GINPLQAIAMGDGANDLPMMGAAGLSVAYHAKPKVREQAMVAINAGGLDRLLELMR 236 Lambda K H 0.319 0.136 0.385 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: 284 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: 236 Length of database: 236 Length adjustment: 23 Effective length of query: 213 Effective length of database: 213 Effective search space: 45369 Effective search space used: 45369 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 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_011801935.1 PNAP_RS12765 (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.26933.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-70 222.5 0.3 2.9e-70 222.3 0.3 1.0 1 lcl|NCBI__GCF_000015505.1:WP_011801935.1 PNAP_RS12765 phosphoserine phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_011801935.1 PNAP_RS12765 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 222.3 0.3 2.9e-70 2.9e-70 11 218 .. 21 234 .. 12 235 .. 0.95 Alignments for each domain: == domain 1 score: 222.3 bits; conditional E-value: 2.9e-70 TIGR00338 11 lkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgel.dFkeslreRvkllkglpvellk 78 l+ kl+ fD+Dstli++E++deia ++G + eV++iTe Amrge+ dFk+slr Rv+llkg+++ ++ lcl|NCBI__GCF_000015505.1:WP_011801935.1 21 LRDFKLIAFDMDSTLINIECVDEIADAVGRKAEVAAITEAAMRGEItDFKDSLRRRVALLKGVSMASMD 89 56779****************************************769******************999 PP TIGR00338 79 kv.eeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkve.. 144 +v +e+l+l +G+ elv++ k++g+k+ ++SGgF+++++++k L++d+ +N Lev+dg ltGk+ lcl|NCBI__GCF_000015505.1:WP_011801935.1 90 EVyRERLKLNPGAAELVRACKDAGMKILLVSGGFTYFTDRVKGLLDIDFTRSNVLEVRDGLLTGKMIdq 158 983589**********************************************************97544 PP TIGR00338 145 ..geivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkd 211 g+i d ++k ++l + + + gi++ + +a+GDGanDl+m+ aAgl +a++akp+++e+a ++i+ lcl|NCBI__GCF_000015505.1:WP_011801935.1 159 swGDICDGEEKRRMLIQTCGQLGINPLQAIAMGDGANDLPMMGAAGLSVAYHAKPKVREQAMVAINAGG 227 4499***************************************************************99 PP TIGR00338 212 ltdilel 218 l +lel lcl|NCBI__GCF_000015505.1:WP_011801935.1 228 LDRLLEL 234 9999887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (236 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: 8.29 // [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