Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate AO356_03470 AO356_03470 3-phosphoserine/phosphohydroxythreonine aminotransferase
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_03470 Length = 361 Score = 406 bits (1043), Expect = e-118 Identities = 202/358 (56%), Positives = 252/358 (70%), Gaps = 2/358 (0%) Query: 5 FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64 +NF +GPA LP VLK+AQ EL DW+G G SVME+SHR EF+ +A +AE+D RDLLN+P Sbjct: 6 YNFCAGPAALPEAVLKRAQGELLDWHGKGLSVMEMSHRSDEFVSIATKAEQDLRDLLNIP 65 Query: 65 SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124 SNYKVLF GG QFA +PLN+L + ADY+D G W+ AI+EA +Y NV Sbjct: 66 SNYKVLFLQGGASQQFAQIPLNLLPENGKADYIDTGIWSQKAIEEASRYGHVNVAATAKP 125 Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184 D A+ EW LS +AAY+HY PNETI G+ + P+ G DV + AD SS ILSRP+ Sbjct: 126 YDYF-AIPGQNEWNLSKDAAYVHYAPNETIGGLEFNWIPETG-DVPLVADMSSDILSRPV 183 Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244 D+SR+G+IYAGAQKNIGP+G+ + I+REDLLG+A CP++L+Y + DNGSM+NTPPT Sbjct: 184 DISRFGMIYAGAQKNIGPSGILVSIIREDLLGRARSLCPTMLNYKVAADNGSMYNTPPTL 243 Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304 AWYLSGLVF+WLK GGV + K+N+ K LY ID S Y N + K +RS MNVPF+L Sbjct: 244 AWYLSGLVFEWLKEQGGVEAIGKLNEVKQRTLYDFIDASGLYSNPINKTDRSWMNVPFRL 303 Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362 AD LDK FL + GL LKGHR VGGMRASIYNA+ + V AL +M EFE+ HG Sbjct: 304 ADDRLDKPFLAGADERGLLNLKGHRSVGGMRASIYNAVDINAVNALIAYMAEFEKEHG 361 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: 419 Number of extensions: 12 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: 362 Length of database: 361 Length adjustment: 29 Effective length of query: 333 Effective length of database: 332 Effective search space: 110556 Effective search space used: 110556 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 AO356_03470 AO356_03470 (3-phosphoserine/phosphohydroxythreonine 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.11013.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-164 533.5 0.0 1.2e-164 533.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 AO356_03470 3-phosphoserine/phos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 AO356_03470 3-phosphoserine/phosphohydroxythreonine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 533.3 0.0 1.2e-164 1.2e-164 2 358 .] 6 360 .. 5 360 .. 0.99 Alignments for each domain: == domain 1 score: 533.3 bits; conditional E-value: 1.2e-164 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdny 64 +nF+aGPaalpe+vl++aq elld++g+glsvme+sHRs+ef +++++ae+dlr+Llnip+ny lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 6 YNFCAGPAALPEAVLKRAQGELLDWHGKGLSVMEMSHRSDEFVSIATKAEQDLRDLLNIPSNY 68 8************************************************************** PP TIGR01364 65 evlflqGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkysk 127 +vlflqGGa++qfa++plnll e+ +adyi tG ws+ka++ea+++++ v+v+a+++ +y + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 69 KVLFLQGGASQQFAQIPLNLLPENGKADYIDTGIWSQKAIEEASRYGH-VNVAATAKPYDYFA 130 **********************************************99.************** PP TIGR01364 128 ipdeeelelkedaayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliya 190 ip ++e++l++daayv+++ neti G+ef+++pe+ ++plvaD+ssdilsr++d+s++g+iya lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 131 IPGQNEWNLSKDAAYVHYAPNETIGGLEFNWIPETGDVPLVADMSSDILSRPVDISRFGMIYA 193 *************************************************************** PP TIGR01364 191 GaqKniGpaGvtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlk 253 GaqKniGp+G+ v i+r+dll+ra++ +p++l+Yk++a+n s+yntppt a+y++glv++wlk lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 194 GAQKNIGPSGILVSIIREDLLGRARSLCPTMLNYKVAADNGSMYNTPPTLAWYLSGLVFEWLK 256 *************************************************************** PP TIGR01364 254 ekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaee 316 e+GGv+++ k n+ K + lY+ id+s g+y n+++k++Rs+mnv+F+l++++l+k Fl+ a e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 257 EQGGVEAIGKLNEVKQRTLYDFIDAS-GLYSNPINKTDRSWMNVPFRLADDRLDKPFLAGADE 318 ************************99.6*********************************** PP TIGR01364 317 kglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358 +gl++lkGhrsvGG+RasiYna+ +++v+aL+++m eFek+h lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 319 RGLLNLKGHRSVGGMRASIYNAVDINAVNALIAYMAEFEKEH 360 ***************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (361 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: 10.89 // [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