Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_028486154.1 B076_RS0103895 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >NCBI__GCF_000483485.1:WP_028486154.1 Length = 276 Score = 213 bits (541), Expect = 4e-60 Identities = 121/236 (51%), Positives = 157/236 (66%), Gaps = 7/236 (2%) Query: 2 QPTEISPGLV--VNVATPDLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITE 59 Q TE+S L +N+ + + +L+ DMDSTLINIECVDEIAD K +VAAITE Sbjct: 45 QLTELSQTLQLDINLIPENFDAASVRLLISDMDSTLINIECVDEIADFINVKPQVAAITE 104 Query: 60 AAMRGEISDYKESLRQRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLV 119 AAMRGE++ ++ESL +RV+LLKG+ +++ VY RL LNPGA + K +K LV Sbjct: 105 AAMRGELN-FEESLIERVSLLKGLETSALQHVYDNRLGLNPGAETWIDGLKQNEVKFALV 163 Query: 120 SGGFTFFTDRIRDELGIDYTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQ 179 SGGFTFFT ++++ LGID+TR+NVL LTG + G I + K L+E C Q Sbjct: 164 SGGFTFFTQKLQERLGIDFTRANVLSIEHEQLTGSLE----GAIVGPQAKADFLIELCEQ 219 Query: 180 LGISPRQAIAMGDGANDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLELV 235 + I Q IA+GDGANDL MM EAGLSVAYHAKP V+EQA A+N GLD +L+ + Sbjct: 220 MEILMSQTIAVGDGANDLMMMQEAGLSVAYHAKPAVQEQADTALNYRGLDAILDFI 275 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: 179 Number of extensions: 5 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: 276 Length adjustment: 24 Effective length of query: 212 Effective length of database: 252 Effective search space: 53424 Effective search space used: 53424 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_028486154.1 B076_RS0103895 (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.29820.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-72 228.3 0.4 5.2e-72 228.0 0.4 1.1 1 lcl|NCBI__GCF_000483485.1:WP_028486154.1 B076_RS0103895 phosphoserine pho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_028486154.1 B076_RS0103895 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 228.0 0.4 5.2e-72 5.2e-72 12 218 .. 67 274 .. 56 275 .. 0.96 Alignments for each domain: == domain 1 score: 228.0 bits; conditional E-value: 5.2e-72 TIGR00338 12 kkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkv 80 + +l++ D+Dstli++E++deia + v+ +V++iTe Amrgel+F+esl eRv+llkgl+ + l++v lcl|NCBI__GCF_000483485.1:WP_028486154.1 67 ASVRLLISDMDSTLINIECVDEIADFINVKPQVAAITEAAMRGELNFEESLIERVSLLKGLETSALQHV 135 56789***************************************************************9 PP TIGR00338 81 ee.klelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeiv 148 ++ +l l +G+e + Lk++ +k a++SGgF+++++kl+e+Lg+d+ aN L++e ++ltG+ eg iv lcl|NCBI__GCF_000483485.1:WP_028486154.1 136 YDnRLGLNPGAETWIDGLKQNEVKFALVSGGFTFFTQKLQERLGIDFTRANVLSIEHEQLTGSLEGAIV 204 86269**************************************************************** PP TIGR00338 149 desakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdile 217 +aka+ l +l+e+ +i + +t+avGDGanDl m+++Agl +a++akp+++e+ad++++ + l +il lcl|NCBI__GCF_000483485.1:WP_028486154.1 205 GPQAKADFLIELCEQMEILMSQTIAVGDGANDLMMMQEAGLSVAYHAKPAVQEQADTALNYRGLDAILD 273 **************************************************************9999987 PP TIGR00338 218 l 218 + lcl|NCBI__GCF_000483485.1:WP_028486154.1 274 F 274 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (276 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: 11.56 // [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