Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate H281DRAFT_03926 H281DRAFT_03926 phosphoserine aminotransferase apoenzyme
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__Burk376:H281DRAFT_03926 Length = 360 Score = 399 bits (1026), Expect = e-116 Identities = 195/358 (54%), Positives = 264/358 (73%), Gaps = 1/358 (0%) Query: 3 QIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLN 62 ++FNFS+GPA +P EVL+QA E+ DW G G SVME+SHRGKEF+ + EEA D R+LL Sbjct: 2 RVFNFSAGPAAMPEEVLRQAADEMLDWQGSGMSVMEMSHRGKEFMSIHEEALLDLRELLA 61 Query: 63 VPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAK 122 VP+++++LF GGG G+ A VP+N+LG K AD+V G W+ ++KEA+KY T +V + Sbjct: 62 VPASHRILFLQGGGLGENAIVPMNLLGWKPRADFVVTGSWSQKSLKEAQKYGTVHVAASG 121 Query: 123 VTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSR 182 T DG EWQ+SD+ AY+H C NETI G+ E PD G +V + AD SS ILSR Sbjct: 122 ETADGFTRAPAFSEWQMSDDPAYVHLCTNETIHGVETFEIPDLG-NVPLVADASSHILSR 180 Query: 183 PIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPP 242 P+D+++YGV++ GAQKNIG AG+T+VIVRED+L +A CPS ++ + +N SM+NTPP Sbjct: 181 PMDIAKYGVLFGGAQKNIGMAGVTVVIVREDMLDRAQAICPSAFEWKTVAENNSMYNTPP 240 Query: 243 TFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPF 302 T+A Y++GLVFKWLK GG+A ++ N +K++LLY ID+S FY N V +++RSRMNVPF Sbjct: 241 TYAIYIAGLVFKWLKKQGGLAAIEARNLEKSKLLYDTIDSSSFYLNKVERSSRSRMNVPF 300 Query: 303 QLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360 LAD + ++ FL + A G+ LKGH+ VGGMRASIYNA+PLEGVKAL ++M EFE+R Sbjct: 301 FLADESRNEEFLAGAKARGMVQLKGHKSVGGMRASIYNAVPLEGVKALVEYMKEFEQR 358 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: 385 Number of extensions: 8 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: 362 Length of database: 360 Length adjustment: 29 Effective length of query: 333 Effective length of database: 331 Effective search space: 110223 Effective search space used: 110223 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 H281DRAFT_03926 H281DRAFT_03926 (phosphoserine aminotransferase apoenzyme)
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.19982.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-159 515.7 0.0 3.1e-159 515.6 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_03926 H281DRAFT_03926 phosphoserine am Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_03926 H281DRAFT_03926 phosphoserine aminotransferase apoenzyme # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 515.6 0.0 3.1e-159 3.1e-159 1 357 [. 3 358 .. 3 359 .. 0.98 Alignments for each domain: == domain 1 score: 515.6 bits; conditional E-value: 3.1e-159 TIGR01364 1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyev 66 ++nFsaGPaa+peevl++a++e+ld++g+g+svme+sHR kef++++eea dlreLl +p ++++ lcl|FitnessBrowser__Burk376:H281DRAFT_03926 3 VFNFSAGPAAMPEEVLRQAADEMLDWQGSGMSVMEMSHRGKEFMSIHEEALLDLRELLAVPASHRI 68 58**************************************************************** PP TIGR01364 67 lflqGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvase.eekkyskipde 131 lflqGG+ ++ a vp+nll k ad++vtG+ws+k+lkea+k+++ v+v+as + +++ p lcl|FitnessBrowser__Burk376:H281DRAFT_03926 69 LFLQGGGLGENAIVPMNLLGWKPRADFVVTGSWSQKSLKEAQKYGT-VHVAASGeTADGFTRAPAF 133 ********************************************99.888888856789******* PP TIGR01364 132 eelelkedaayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniG 197 +e+++++d ayv+lc+neti+Gve e+p+ ++plvaD ss+ilsr++d++kyg++++GaqKniG lcl|FitnessBrowser__Burk376:H281DRAFT_03926 134 SEWQMSDDPAYVHLCTNETIHGVETFEIPDLGNVPLVADASSHILSRPMDIAKYGVLFGGAQKNIG 199 ****************************************************************** PP TIGR01364 198 paGvtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklek 263 +aGvtvvivr+d+l+ra++++ps +++k++aen+s+yntppt+aiy++glv+kwlk++GG++++e+ lcl|FitnessBrowser__Burk376:H281DRAFT_03926 200 MAGVTVVIVREDMLDRAQAICPSAFEWKTVAENNSMYNTPPTYAIYIAGLVFKWLKKQGGLAAIEA 265 ****************************************************************** PP TIGR01364 264 knqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvG 329 +n eK+kllY++id+s+ fy nkve+++Rs+mnv+F l++e ++eFl+ a+++g+v+lkGh+svG lcl|FitnessBrowser__Burk376:H281DRAFT_03926 266 RNLEKSKLLYDTIDSSS-FYLNKVERSSRSRMNVPFFLADESRNEEFLAGAKARGMVQLKGHKSVG 330 **************886.************************************************ PP TIGR01364 330 GiRasiYnalpleevqaLvdfmkeFekk 357 G+RasiYna+ple+v+aLv++mkeFe++ lcl|FitnessBrowser__Burk376:H281DRAFT_03926 331 GMRASIYNAVPLEGVKALVEYMKEFEQR 358 *************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (360 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: 00:00:00.01 # Mc/sec: 11.88 // [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