Align phosphoserine phosphatase; EC 3.1.3.3 (characterized)
to candidate WP_085219702.1 B9N75_RS13275 phosphoserine phosphatase SerB
Query= CharProtDB::CH_024035 (322 letters) >NCBI__GCF_900177405.1:WP_085219702.1 Length = 291 Score = 178 bits (451), Expect = 2e-49 Identities = 107/240 (44%), Positives = 136/240 (56%), Gaps = 7/240 (2%) Query: 82 SLTARATRLAHE---AQLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGE 138 S + RA A E A +D+A G+ R LLV DMDST I +ECIDE+A AG Sbjct: 48 SASPRAAEAALEPLRAHVDIAVQGEAG--RRKRLLVADMDSTVITVECIDELADFAGVRA 105 Query: 139 MVAEVTERAMRGELDFTASLRSRVATLKGADANILQQV-RENLPLMPGLTQLVLKLETLG 197 VAEVTERAMRGE DF +L RVA LKG L + E + L PG L + G Sbjct: 106 RVAEVTERAMRGEFDFEGALEERVALLKGLPERTLARCYEERVKLTPGAKALAHTMRAHG 165 Query: 198 WKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLA 257 + + SGGFT+FA+ + + AN LE+ DG TG + ++ AQ K + L A Sbjct: 166 ARCLLVSGGFTYFADRVAQRAGFDRAAANRLEVADGALTGTALPPVLGAQAKKQALIDEA 225 Query: 258 QEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCILSG 317 I L++T+A+GDGAND+PMI+ AGLG+AYH K VN A+V I H DL G L G Sbjct: 226 IAMSIDLSETMAVGDGANDIPMIETAGLGVAYHGKAAVNAAAQVRIAHNDL-GALLYLQG 284 Lambda K H 0.320 0.136 0.399 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: 200 Number of extensions: 6 Number of successful extensions: 2 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: 322 Length of database: 291 Length adjustment: 27 Effective length of query: 295 Effective length of database: 264 Effective search space: 77880 Effective search space used: 77880 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: 48 (23.1 bits)
Align candidate WP_085219702.1 B9N75_RS13275 (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.3547366.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-69 219.4 0.1 3e-69 219.0 0.1 1.1 1 NCBI__GCF_900177405.1:WP_085219702.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085219702.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 219.0 0.1 3e-69 3e-69 10 218 .. 73 282 .. 65 283 .. 0.96 Alignments for each domain: == domain 1 score: 219.0 bits; conditional E-value: 3e-69 TIGR00338 10 llkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpve.llkkve 81 + k+l+v D+Dst+i+ E+Ide+a aGv V+e+TerAmrge dF+ +l+eRv+llkglp+ l++ e NCBI__GCF_900177405.1:WP_085219702.1 73 AGRRKRLLVADMDSTVITVECIDELADFAGVRARVAEVTERAMRGEFDFEGALEERVALLKGLPERtLARCYE 145 56789*************************************************************4455567 PP TIGR00338 82 eklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesaka 154 e+++lt+G++ l ++++ +g + ++SGgF+++a++++++ g d ++aNrLev dg+ltG+ +++ ++ak NCBI__GCF_900177405.1:WP_085219702.1 146 ERVKLTPGAKALAHTMRAHGARCLLVSGGFTYFADRVAQRAGFDRAAANRLEVADGALTGTALPPVLGAQAKK 218 89*********************************************************************** PP TIGR00338 155 ktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218 + l + i+l +t+avGDGanD++mi++Aglg+a+++k +++ +a++ i ++dl ++l+l NCBI__GCF_900177405.1:WP_085219702.1 219 QALIDEAIAMSIDLSETMAVGDGANDIPMIETAGLGVAYHGKAAVNAAAQVRIAHNDLGALLYL 282 **********************************************************999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (219 nodes) Target sequences: 1 (291 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: 18.43 // [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