Align phosphoserine phosphatase (EC 3.1.3.3) (characterized)
to candidate WP_012504908.1 PAES_RS01570 phosphoserine phosphatase SerB
Query= BRENDA::O53289 (409 letters) >NCBI__GCF_000020625.1:WP_012504908.1 Length = 410 Score = 259 bits (663), Expect = 8e-74 Identities = 159/394 (40%), Positives = 238/394 (60%), Gaps = 16/394 (4%) Query: 7 VLITVTGMDQPGVTSALFEVLAQHGVELLNVEQVVIRGRLTLGVLVSCPLDVADGTALRD 66 +LIT++G DQPG+TS + E LA++ + +L++ Q VI +L++G+L+ P + + L+D Sbjct: 5 LLITLSGPDQPGLTSKISETLARYRINVLDIGQEVIHNQLSIGLLIEVPEEYSSSPVLKD 64 Query: 67 DVAAAIHGVGLDVAIERSDDLPIIRQPST-----HTIFVLGRPITAGAFSAVARGVAALG 121 + A H +GL ++ D + + I +LGR I A V+ + A Sbjct: 65 MLFTA-HTLGLQISFTPITDEEYTQWVGEQGKPRYLISLLGREIKAEQIMRVSSVITAHQ 123 Query: 122 VNIDFIRGISD-YPVTGLE---LRVSVPPGCVGPLQIA------LTKVAAEEHVDVAVED 171 +NID I +S P+ E + + G LQ L + + +D+A ++ Sbjct: 124 LNIDKINRLSGRIPLEQEEKKNTKACIELSIRGTLQNEDGFREQLLAITDDLGIDIAFQE 183 Query: 172 YGLAWRTKRLIVFDVDSTLVQGEVIEMLAARAGAQGQVAAITEAAMRGELDFAESLQRRV 231 + R +RL+VFD+DSTL+ EVI+ LA AGA +V+AITE AMRGE+DF SLQ+RV Sbjct: 184 DNVYRRNRRLMVFDMDSTLITSEVIDELAIEAGAGEEVSAITEQAMRGEIDFNVSLQKRV 243 Query: 232 ATLAGLPATVIDDVAEQLELMPGARTTIRTLRRLGFRCGVVSGGFRRIIEPLARELMLDF 291 ATL GL +V+ VAE+L+L GA T L LGF+ ++SGGF L ++L +D+ Sbjct: 244 ATLKGLEESVLQKVAERLKLTEGAETLFYNLHNLGFKTAIISGGFTYFGRYLQKKLNIDY 303 Query: 292 VASNELEIVDGILTGRVVGPIVDRPGKAKALRDFASQYGVPMEQTVAVGDGANDIDMLGA 351 V +NELEIV+G +TG+V+G IV+ KA+ L A+ + +EQT+AVGDGAND+ MLG Sbjct: 304 VFANELEIVNGRMTGQVLGEIVNGKRKAELLEQIATTEKISLEQTIAVGDGANDLPMLGK 363 Query: 352 AGLGIAFNAKPALREVADASLSHPYLDTVLFLLG 385 AGLGIAF AKP ++E A ++S LD +L+L+G Sbjct: 364 AGLGIAFRAKPIVKETAKQAISTLGLDAILYLMG 397 Lambda K H 0.321 0.139 0.395 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: 403 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: 409 Length of database: 410 Length adjustment: 31 Effective length of query: 378 Effective length of database: 379 Effective search space: 143262 Effective search space used: 143262 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate WP_012504908.1 PAES_RS01570 (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.14012.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-85 272.0 2.6 2.5e-85 271.6 2.6 1.2 1 lcl|NCBI__GCF_000020625.1:WP_012504908.1 PAES_RS01570 phosphoserine phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020625.1:WP_012504908.1 PAES_RS01570 phosphoserine phosphatase SerB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 271.6 2.6 2.5e-85 2.5e-85 1 218 [. 178 395 .. 178 396 .. 0.99 Alignments for each domain: == domain 1 score: 271.6 bits; conditional E-value: 2.5e-85 TIGR00338 1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 dia +e++ ++++++l+vfD+Dstli++EvIde+a +aG +eeVs+iTe+Amrge+dF+ sl++Rv++l lcl|NCBI__GCF_000020625.1:WP_012504908.1 178 DIAFQEDNVYRRNRRLMVFDMDSTLITSEVIDELAIEAGAGEEVSAITEQAMRGEIDFNVSLQKRVATL 246 6889999************************************************************** PP TIGR00338 70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138 kgl++++l+kv+e+l+lteG+e l +L++ g+k+a+iSGgF+++ +l++kL++d+vfaN+Le+ +g+ lcl|NCBI__GCF_000020625.1:WP_012504908.1 247 KGLEESVLQKVAERLKLTEGAETLFYNLHNLGFKTAIISGGFTYFGRYLQKKLNIDYVFANELEIVNGR 315 ********************************************************************* PP TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207 +tG+v geiv+ + ka+ l++++ +e+isle+t+avGDGanDl+m+ +Aglgiaf akp++ke+a+++i lcl|NCBI__GCF_000020625.1:WP_012504908.1 316 MTGQVLGEIVNGKRKAELLEQIATTEKISLEQTIAVGDGANDLPMLGKAGLGIAFRAKPIVKETAKQAI 384 ********************************************************************* PP TIGR00338 208 ekkdltdilel 218 ++ l +il+l lcl|NCBI__GCF_000020625.1:WP_012504908.1 385 STLGLDAILYL 395 *****999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (410 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: 9.02 // [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