Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_106710192.1 CU102_RS06440 phosphoserine phosphatase SerB
Query= SwissProt::Q12A06 (236 letters) >NCBI__GCF_003010955.1:WP_106710192.1 Length = 295 Score = 165 bits (418), Expect = 8e-46 Identities = 99/208 (47%), Positives = 129/208 (62%), Gaps = 5/208 (2%) Query: 25 KLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVALLKGVS 84 K++ DMDST+I EC+DE+A+ AG + +VAAIT AM GEI+ ++ +LR+RVALLKG+ Sbjct: 81 KILIADMDSTMIQQECIDELAEEAGLRDKVAAITARAMNGEIA-FEPALRERVALLKGLP 139 Query: 85 VASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYTRSNVL 144 + +D+V +R+ L PG LV+ K G LVSGGFT FT RI D +G +NVL Sbjct: 140 YSVIDKVIASRITLMPGGPELVRTMKKHGAYTALVSGGFTVFTQRIADMIGFHENSANVL 199 Query: 145 ETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPMMGEAG 204 LTG V +P I E K L C + +SP++AIA+GDGANDL M+ AG Sbjct: 200 IDNGIALTGE-VKKP---ILGREAKVAALTSICERFSLSPQEAIAVGDGANDLGMLQLAG 255 Query: 205 LSVAYHAKPRVREQAMVAINEGGLDRLL 232 VA HAKP V QA V I+ G L LL Sbjct: 256 TGVALHAKPSVAAQAKVRIDHGDLTALL 283 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: 192 Number of extensions: 10 Number of successful extensions: 4 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: 295 Length adjustment: 25 Effective length of query: 211 Effective length of database: 270 Effective search space: 56970 Effective search space used: 56970 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_106710192.1 CU102_RS06440 (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.3072990.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-66 209.6 0.3 2.8e-66 209.3 0.3 1.1 1 NCBI__GCF_003010955.1:WP_106710192.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106710192.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 209.3 0.3 2.8e-66 2.8e-66 7 218 .. 73 285 .. 68 286 .. 0.95 Alignments for each domain: == domain 1 score: 209.3 bits; conditional E-value: 2.8e-66 TIGR00338 7 lskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkk 79 +++ + kk+++ D+Dst+i++E+Ide+a +aG ++V++iT rAm+ge+ F+ +lreRv+llkglp ++++k NCBI__GCF_003010955.1:WP_106710192.1 73 QNQDSRRKKILIADMDSTMIQQECIDELAEEAGLRDKVAAITARAMNGEIAFEPALRERVALLKGLPYSVIDK 145 45667899*************************************************************7766 PP TIGR00338 80 .veeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdes 151 ++++++l++G elv+++k++g +a++SGgF+++++++++ +g aN L+ + +ltG+v+ +i+ + NCBI__GCF_003010955.1:WP_106710192.1 146 vIASRITLMPGGPELVRTMKKHGAYTALVSGGFTVFTQRIADMIGFHENSANVLIDNGIALTGEVKKPILGRE 218 15789*************************************************877779************* PP TIGR00338 152 akaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218 ak l++++e+ +s+++ +avGDGanDl m++ Ag g+a +akp + +a++ i++ dlt++l++ NCBI__GCF_003010955.1:WP_106710192.1 219 AKVAALTSICERFSLSPQEAIAVGDGANDLGMLQLAGTGVALHAKPSVAAQAKVRIDHGDLTALLYI 285 ***************************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (295 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: 15.54 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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