Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate Dsui_1939 Dsui_1939 phosphoserine aminotransferase
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__PS:Dsui_1939 Length = 376 Score = 393 bits (1010), Expect = e-114 Identities = 207/372 (55%), Positives = 258/372 (69%), Gaps = 15/372 (4%) Query: 3 QIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLN 62 +++NFS+GPA LPAEVL+Q Q E+ DW G G VME+SHRGKEF +A+ AE D R+L+ Sbjct: 2 RLWNFSAGPAALPAEVLEQVQDEMLDWQGAGCGVMEMSHRGKEFTSIAQRAEADLRELMG 61 Query: 63 VPSNYKVLFCHGGGRGQFAAVPLNILG---DKTTADYVDAGYWAASAIKEAKKYC----- 114 +P+NYKVLF GG QFA VPLN+L DK ADY+ G W+ A KE + C Sbjct: 62 IPANYKVLFLQGGATQQFAQVPLNLLAGVKDKQPADYIVTGSWSKKAFKETLRVCGETAA 121 Query: 115 --TPNVFDAKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDF----GAD 168 + D DG + E Q++ +AAY+H C NETI G+ + + F A Sbjct: 122 RCIASTEDKAAVADGFTRLPAAAELQVNADAAYLHLCTNETIHGVELLDEAAFLAGVPAG 181 Query: 169 VVVAADFSSTILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDY 228 V V AD SS ILSRP+DVSRYG+IYAGAQKNIGP+GLT+VIVREDLLGKA + P++LDY Sbjct: 182 VPVVADMSSHILSRPMDVSRYGLIYAGAQKNIGPSGLTLVIVREDLLGKAPASLPTVLDY 241 Query: 229 SILNDNGSMFNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSD-FYR 287 +++ +N SM NTPPTFA Y++GLVF+WLK GG+ EM +IN +KA LLY ID SD FYR Sbjct: 242 AVMAENDSMLNTPPTFAIYVAGLVFQWLKRIGGINEMARINAEKARLLYAAIDGSDGFYR 301 Query: 288 NDVAKANRSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGV 347 N V A RS+MNVPF L D+ALD FL + AGL ALKGH+ VGGMRASIYNAMPL+GV Sbjct: 302 NPVDPACRSQMNVPFTLRDAALDAEFLAGAKEAGLLALKGHKSVGGMRASIYNAMPLDGV 361 Query: 348 KALTDFMVEFER 359 +AL +M F + Sbjct: 362 RALVAYMDAFAK 373 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: 410 Number of extensions: 17 Number of successful extensions: 5 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: 376 Length adjustment: 30 Effective length of query: 332 Effective length of database: 346 Effective search space: 114872 Effective search space used: 114872 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 Dsui_1939 Dsui_1939 (phosphoserine aminotransferase)
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.16270.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-157 510.3 0.0 1.3e-157 510.2 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_1939 Dsui_1939 phosphoserine aminotra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_1939 Dsui_1939 phosphoserine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 510.2 0.0 1.3e-157 1.3e-157 2 356 .. 4 373 .. 3 375 .. 0.94 Alignments for each domain: == domain 1 score: 510.2 bits; conditional E-value: 1.3e-157 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqfa 78 nFsaGPaalp evle++q+e+ld++g g++vme+sHR kef++++++ae dlreL+ ip ny+vlflqGGat+qfa lcl|FitnessBrowser__PS:Dsui_1939 4 WNFSAGPAALPAEVLEQVQDEMLDWQGAGCGVMEMSHRGKEFTSIAQRAEADLRELMGIPANYKVLFLQGGATQQFA 80 69*************************************************************************** PP TIGR01364 79 avplnllk...ekkvadyivtGawskkalkeakkltk..evkvvaseee.....kkyskipdeeelelkedaayvyl 145 +vplnll+ +k+ adyivtG+wskka+ke +++ ++ +as+e+ + ++++p el+++ daay++l lcl|FitnessBrowser__PS:Dsui_1939 81 QVPLNLLAgvkDKQPADYIVTGSWSKKAFKETLRVCGetAARCIASTEDkaavaDGFTRLPAAAELQVNADAAYLHL 157 ******997656779*******************999663444444433111115799******************* PP TIGR01364 146 canetieGvefkelpevkk.....aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakke 217 c+neti+Gve ++ + +p+vaD+ss+ilsr++dvs+ygliyaGaqKniGp+G+t+vivr+dll++a ++ lcl|FitnessBrowser__PS:Dsui_1939 158 CTNETIHGVELLDEAAFLAgvpagVPVVADMSSHILSRPMDVSRYGLIYAGAQKNIGPSGLTLVIVREDLLGKAPAS 234 ***********98887776678889**************************************************** PP TIGR01364 218 lpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRsl 294 lp+vldY+++aends++ntpptfaiyv+glv++wlk+ GG++++++ n eKa+llY aid s+gfy+n+v++++Rs+ lcl|FitnessBrowser__PS:Dsui_1939 235 LPTVLDYAVMAENDSMLNTPPTFAIYVAGLVFQWLKRIGGINEMARINAEKARLLYAAIDGSDGFYRNPVDPACRSQ 311 ***************************************************************************** PP TIGR01364 295 mnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFek 356 mnv+Ftl+++ l++eFl+ a+e+gl++lkGh+svGG+RasiYna+pl++v+aLv++m F+k lcl|FitnessBrowser__PS:Dsui_1939 312 MNVPFTLRDAALDAEFLAGAKEAGLLALKGHKSVGGMRASIYNAMPLDGVRALVAYMDAFAK 373 ************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (376 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.97 // [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