Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_041595115.1 HHAL_RS08035 phosphoserine phosphatase SerB
Query= SwissProt::Q9S281 (410 letters) >NCBI__GCF_000015585.1:WP_041595115.1 Length = 404 Score = 279 bits (713), Expect = 1e-79 Identities = 167/400 (41%), Positives = 232/400 (58%), Gaps = 16/400 (4%) Query: 12 LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEGDLRAT 71 +L+ + G+D+PG+T+ L LA Y VD++DI Q + + L L+ P + + Sbjct: 5 ILINVSGEDQPGLTSSLMGILAEYDVDILDIGQAMIHDTLSLGILIEVPEQKDVSPVLKD 64 Query: 72 VHSWAESLKLQAEIISGIGDN-----RPRGFGRSLVTVLGHPLTAEATAAIAARITESGS 126 V +Q + R G R ++T+LG ++AE A I++ +T G Sbjct: 65 VLFHLHDAGMQVRFTPVAQEQYEHWVRGAGKPRHIITLLGRSVSAEQIARISSVVTAQGL 124 Query: 127 NIDRIFRLA-KYPV--------TAVEFAVSG--VETEPLRTALATEAAALGVDIAVVAAG 175 NI+ I RL+ + P+ VE V G V+T+ ++ + LG+DI+ Sbjct: 125 NIEDIVRLSGRRPLHLEGRRSRACVELTVRGQPVDTDVMKRDFMEISQHLGIDISFQEDN 184 Query: 176 LHRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHARVAL 235 L+RR +R+V D+DSTLIQ EVI+ A AG DE A VT AMRGE+DF +SL RV L Sbjct: 185 LYRRNRRMVAFDMDSTLIQQEVIDEMAKAAGVGDECARVTEQAMRGEIDFRESLRQRVQL 244 Query: 236 LAGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLDFAQ 295 L GL +++V + LT GA L+RTLK GY ++SGGFT LQ+ LG+D+ Sbjct: 245 LEGLPEDTLERVAQSLTLTEGAERLMRTLKAFGYVTAIISGGFTYFGRHLQKHLGIDYVY 304 Query: 296 ANTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLNAAG 355 AN LEIVDGRLTGRV GEIVD KA LLR+ A G+ L Q +A+GDGANDL ML AG Sbjct: 305 ANDLEIVDGRLTGRVQGEIVDGPRKAELLRKIAEDEGLALEQVIAVGDGANDLPMLRLAG 364 Query: 356 LGVAFNAKPVVREAAHTAVNVPFLDTVLYLLGITREEVEA 395 LG+AF+AKPVV+E+A +++ LD LYL+GI + A Sbjct: 365 LGIAFHAKPVVQESARQSISTLGLDGTLYLMGIKDTDTPA 404 Lambda K H 0.319 0.135 0.374 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: 394 Number of extensions: 18 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: 410 Length of database: 404 Length adjustment: 31 Effective length of query: 379 Effective length of database: 373 Effective search space: 141367 Effective search space used: 141367 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_041595115.1 HHAL_RS08035 (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.2383.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-84 267.4 0.0 6.2e-84 267.0 0.0 1.2 1 lcl|NCBI__GCF_000015585.1:WP_041595115.1 HHAL_RS08035 phosphoserine phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_041595115.1 HHAL_RS08035 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 267.0 0.0 6.2e-84 6.2e-84 1 217 [. 177 393 .. 177 395 .. 0.98 Alignments for each domain: == domain 1 score: 267.0 bits; conditional E-value: 6.2e-84 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 di+ +e++ +++++++v fD+Dstli++EvIde+ak+aGv++e +++Te+Amrge+dF+eslr+Rv+ll lcl|NCBI__GCF_000015585.1:WP_041595115.1 177 DISFQEDNLYRRNRRMVAFDMDSTLIQQEVIDEMAKAAGVGDECARVTEQAMRGEIDFRESLRQRVQLL 245 68889999************************************************************* PP TIGR00338 70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138 glp+++l++v+++l+lteG+e l+++Lk gy +a+iSGgF+++ +l+++Lg+d+v aN Le+ dg+ lcl|NCBI__GCF_000015585.1:WP_041595115.1 246 EGLPEDTLERVAQSLTLTEGAERLMRTLKAFGYVTAIISGGFTYFGRHLQKHLGIDYVYANDLEIVDGR 314 ********************************************************************* PP TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207 ltG+v+geivd ka+ l k++e+eg+ le+++avGDGanDl+m++ Aglgiaf+akpv++e a ++i lcl|NCBI__GCF_000015585.1:WP_041595115.1 315 LTGRVQGEIVDGPRKAELLRKIAEDEGLALEQVIAVGDGANDLPMLRLAGLGIAFHAKPVVQESARQSI 383 ********************************************************************* PP TIGR00338 208 ekkdltdile 217 ++ l + l+ lcl|NCBI__GCF_000015585.1:WP_041595115.1 384 STLGLDGTLY 393 9988776665 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: 9.04 // [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