Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_013835004.1 THICY_RS02285 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >NCBI__GCF_000214825.1:WP_013835004.1 Length = 277 Score = 208 bits (529), Expect = 1e-58 Identities = 112/226 (49%), Positives = 152/226 (67%), Gaps = 5/226 (2%) Query: 10 LVVNVATPDLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDY 69 L +N+ D + ++ KL+ DMDSTLI+IEC+DEIAD K +VAAITE+AMRGE++ + Sbjct: 56 LDINILPNDFEPAEVKLVISDMDSTLISIECIDEIADMFHIKPQVAAITESAMRGELN-F 114 Query: 70 KESLRQRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDR 129 ++SL QRV LL+G+ ++D VY RL+LNPGA + K +K LVSGGF FFT R Sbjct: 115 EQSLTQRVTLLRGLDEKALDRVYNERLQLNPGAETWISGLKARDIKFALVSGGFDFFTSR 174 Query: 130 IRDELGIDYTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIA 189 + + L +D++R+N L G+LTG +V G I + K L E C L I+P+Q IA Sbjct: 175 LANRLNLDFSRANKLAIEQGVLTGSVV----GSIVGAQAKADFLHELCQHLAITPKQVIA 230 Query: 190 MGDGANDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLELV 235 +GDGANDL MM AGLS+AYHAKP V+ QA +N GLD +L+L+ Sbjct: 231 IGDGANDLLMMKAAGLSMAYHAKPTVQAQANCVLNYIGLDAMLDLL 276 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: 157 Number of extensions: 7 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: 236 Length of database: 277 Length adjustment: 24 Effective length of query: 212 Effective length of database: 253 Effective search space: 53636 Effective search space used: 53636 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: 47 (22.7 bits)
Align candidate WP_013835004.1 THICY_RS02285 (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.30515.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-73 231.5 0.1 5.6e-73 231.2 0.1 1.1 1 lcl|NCBI__GCF_000214825.1:WP_013835004.1 THICY_RS02285 phosphoserine phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214825.1:WP_013835004.1 THICY_RS02285 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 231.2 0.1 5.6e-73 5.6e-73 13 219 .] 69 276 .. 57 276 .. 0.96 Alignments for each domain: == domain 1 score: 231.2 bits; conditional E-value: 5.6e-73 TIGR00338 13 kkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkve 81 + klv+ D+Dstli++E+Ideia + ++ +V++iTe+Amrgel+F++sl++Rv+ll+gl+++ l++v+ lcl|NCBI__GCF_000214825.1:WP_013835004.1 69 EVKLVISDMDSTLISIECIDEIADMFHIKPQVAAITESAMRGELNFEQSLTQRVTLLRGLDEKALDRVY 137 679**************************************************************9996 PP TIGR00338 82 .eklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivd 149 e+l+l +G+e ++ Lk +++k a++SGgFd+++ +l+++L+ld+ aN+L +e+g ltG+v g+iv lcl|NCBI__GCF_000214825.1:WP_013835004.1 138 nERLQLNPGAETWISGLKARDIKFALVSGGFDFFTSRLANRLNLDFSRANKLAIEQGVLTGSVVGSIVG 206 378****************************************************************** PP TIGR00338 150 esakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218 ++aka+ l +l+++ i +++++a+GDGanDl m+kaAgl +a++akp ++ +a++v++ l ++l l lcl|NCBI__GCF_000214825.1:WP_013835004.1 207 AQAKADFLHELCQHLAITPKQVIAIGDGANDLLMMKAAGLSMAYHAKPTVQAQANCVLNYIGLDAMLDL 275 ***********************************************************9999888877 PP TIGR00338 219 l 219 l lcl|NCBI__GCF_000214825.1:WP_013835004.1 276 L 276 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (277 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: 8.14 // [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