Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate Ac3H11_2573 Phosphoserine aminotransferase (EC 2.6.1.52)
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2573 Length = 369 Score = 364 bits (935), Expect = e-105 Identities = 189/369 (51%), Positives = 244/369 (66%), Gaps = 9/369 (2%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 M + +NFS+GPA +PAEVL+QA E+ DW+G G VME+SHRGKEF+ + E+AE D R+L Sbjct: 1 MTRPYNFSAGPAAIPAEVLEQAAAEMLDWHGSGMGVMEMSHRGKEFLSIYEQAEADLREL 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 L VP+NYK+LF GGG + A VPLN L D+V G W+ + KEA+KY + Sbjct: 61 LAVPTNYKILFMQGGGLAENAIVPLN-LSRAGAVDFVVTGSWSQKSQKEARKYASEVNIV 119 Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDF---GADVVVAADFSS 177 A G + W +S A+Y+H C NETI+GI + PD G+D + DFSS Sbjct: 120 ASAEDTGFTTLPDPASWTVSRGASYLHICSNETINGIEFHQLPDLKALGSDAPLVIDFSS 179 Query: 178 TILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSM 237 + SRP+D SR G+ + GAQKN+GPAGLT+V+VREDLLG A ACPS DY + DN SM Sbjct: 180 HVASRPVDWSRVGLAFGGAQKNLGPAGLTLVVVREDLLGHALPACPSAFDYKTVADNQSM 239 Query: 238 FNTPPTFAWYLSGLVFKWLKAN-----GGVAEMDKINQQKAELLYGVIDNSDFYRNDVAK 292 +NTPPT+ Y++GL F+WLK GVA M++ N KA LLY ID+S Y N VA Sbjct: 240 YNTPPTWGVYIAGLTFQWLKRQTEGGLTGVAAMEQRNIAKAALLYNAIDSSQLYVNKVAA 299 Query: 293 ANRSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTD 352 RSRMN+PF L D + + FL + GL LKGH+ VGGMRAS+YNAMP+EGV+AL D Sbjct: 300 NCRSRMNIPFFLRDESRNDAFLAGAKERGLLQLKGHKSVGGMRASVYNAMPIEGVQALVD 359 Query: 353 FMVEFERRH 361 +M EFE++H Sbjct: 360 YMREFEQKH 368 Lambda K H 0.319 0.136 0.405 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: 399 Number of extensions: 17 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: 362 Length of database: 369 Length adjustment: 30 Effective length of query: 332 Effective length of database: 339 Effective search space: 112548 Effective search space used: 112548 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: 49 (23.5 bits)
Align candidate Ac3H11_2573 (Phosphoserine aminotransferase (EC 2.6.1.52))
to HMM TIGR01364 (serC: phosphoserine transaminase (EC 2.6.1.52))
# 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/TIGR01364.hmm # target sequence database: /tmp/gapView.3843.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01364 [M=358] Accession: TIGR01364 Description: serC_1: phosphoserine transaminase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-148 479.2 0.0 3.9e-148 479.1 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 Phosphoserine aminotransferase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 Phosphoserine aminotransferase (EC 2.6.1.52) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 479.1 0.0 3.9e-148 3.9e-148 2 358 .] 5 368 .. 4 368 .. 0.97 Alignments for each domain: == domain 1 score: 479.1 bits; conditional E-value: 3.9e-148 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdn 63 +nFsaGPaa+p evle+a++e+ld++g+g++vme+sHR kef ++ e+ae dlreLl +p n lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 5 YNFSAGPAAIPAEVLEQAAAEMLDWHGSGMGVMEMSHRGKEFLSIYEQAEADLRELLAVPTN 66 8************************************************************* PP TIGR01364 64 yevlflqGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekky 125 y++lf+qGG+ + a vplnl +++ +d++vtG+ws+k+ kea+k+ +ev++vas+e++ + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 67 YKILFMQGGGLAENAIVPLNLSRAG-AVDFVVTGSWSQKSQKEARKYASEVNIVASAEDTGF 127 **********************999.99********************************** PP TIGR01364 126 skipdeeelelkedaayvylcanetieGvefkelpevkk....aplvaDlssdilsrkidvs 183 +++pd +++++ a+y+++c+neti+G+ef++lp+ k aplv D+ss++ sr++d s lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 128 TTLPDPASWTVSRGASYLHICSNETINGIEFHQLPDLKAlgsdAPLVIDFSSHVASRPVDWS 189 ************************************99888889****************** PP TIGR01364 184 kygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvl 245 + gl ++GaqKn+GpaG+t+v+vr+dll++a +ps +dYk++a+n+s+yntppt+++y++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 190 RVGLAFGGAQKNLGPAGLTLVVVREDLLGHALPACPSAFDYKTVADNQSMYNTPPTWGVYIA 251 ************************************************************** PP TIGR01364 246 glvlkwlkek..G...GvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlk 302 gl+++wlk++ G Gv+++e++n +Ka+llY+aid+s ++y nkv++++Rs+mn++F l+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 252 GLTFQWLKRQteGgltGVAAMEQRNIAKAALLYNAIDSS-QLYVNKVAANCRSRMNIPFFLR 312 *******9864453446899*****************88.5********************* PP TIGR01364 303 keelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358 +e ++ Fl+ a+e+gl++lkGh+svGG+Ras+Yna+p+e+vqaLvd+m+eFe+kh lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 313 DESRNDAFLAGAKERGLLQLKGHKSVGGMRASVYNAMPIEGVQALVDYMREFEQKH 368 ******************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (369 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.02 // [ok]
This GapMind analysis is from Apr 09 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