Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_078429013.1 BK574_RS13850 3-phosphoserine/phosphohydroxythreonine transaminase
Query= SwissProt::Q9RME2 (361 letters) >NCBI__GCF_002019605.1:WP_078429013.1 Length = 360 Score = 514 bits (1325), Expect = e-150 Identities = 246/359 (68%), Positives = 302/359 (84%) Query: 2 VKQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLREL 61 +++ +NFNAGPSALP L+RAQ+EL+NF +T MSVMELSHRS+ YEEVHE+AQ++L+EL Sbjct: 1 MERAYNFNAGPSALPLEVLKRAQEELVNFKETGMSVMELSHRSKEYEEVHERAQSMLKEL 60 Query: 62 LQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAA 121 LQIPNDY+ILFLQGGASLQF +PMN L +G IGNYVLTGSWSEKALKEAKL+GET I A Sbjct: 61 LQIPNDYEILFLQGGASLQFAQIPMNFLKEGKIGNYVLTGSWSEKALKEAKLIGETFIGA 120 Query: 122 STKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSR 181 STK Y SIP+ + +N++DAYLHITSNNTIYGTQ+ +P + LIADMSSDIL R Sbjct: 121 STKEQGYCSIPNVEDIAINKDDAYLHITSNNTIYGTQWHKYPVFENTSLIADMSSDILCR 180 Query: 182 PLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTPP 241 P++VN F +IYAGAQKNLGPSGVT+VIVKK+LL + +PT+L+Y+TH ++SLYNTPP Sbjct: 181 PIQVNDFSLIYAGAQKNLGPSGVTIVIVKKELLENSKQDIPTILRYSTHSDANSLYNTPP 240 Query: 242 TFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVT 301 TF+IYML VL+W+ + GG A+ +N EKAK+IYD IDESNGFY GHAEK SRSLMN+T Sbjct: 241 TFAIYMLSKVLEWVIEQGGITAVETRNVEKAKLIYDAIDESNGFYRGHAEKDSRSLMNIT 300 Query: 302 FNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKEN 360 FNL+++ELN++FLA+AK GFVGLNGHRSVGGCRAS YN+VP++AC ALR+ MI FK+N Sbjct: 301 FNLQSDELNKKFLAEAKAAGFVGLNGHRSVGGCRASTYNSVPVEACEALRQFMITFKKN 359 Lambda K H 0.316 0.132 0.372 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: 477 Number of extensions: 14 Number of successful extensions: 1 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: 361 Length of database: 360 Length adjustment: 29 Effective length of query: 332 Effective length of database: 331 Effective search space: 109892 Effective search space used: 109892 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_078429013.1 BK574_RS13850 (3-phosphoserine/phosphohydroxythreonine transaminase)
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.25579.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-159 514.7 0.4 6.5e-159 514.5 0.4 1.0 1 lcl|NCBI__GCF_002019605.1:WP_078429013.1 BK574_RS13850 3-phosphoserine/ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078429013.1 BK574_RS13850 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 514.5 0.4 6.5e-159 6.5e-159 2 357 .. 5 359 .. 4 360 .] 0.99 Alignments for each domain: == domain 1 score: 514.5 bits; conditional E-value: 6.5e-159 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 +nF+aGP+alp evl++aq+el++f+++g+svme+sHRske+e+v+e+a+s l+eLl+ip++ye+lflq lcl|NCBI__GCF_002019605.1:WP_078429013.1 5 YNFNAGPSALPLEVLKRAQEELVNFKETGMSVMELSHRSKEYEEVHERAQSMLKELLQIPNDYEILFLQ 73 8******************************************************************** PP TIGR01364 71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139 GGa+ qfa++p+n+lke+k +y+ tG+ws+kalkeak +++ + + as++e+ y +ip+ e++ +++d lcl|NCBI__GCF_002019605.1:WP_078429013.1 74 GGASLQFAQIPMNFLKEGKIGNYVLTGSWSEKALKEAKLIGE-TFIGASTKEQGYCSIPNVEDIAINKD 141 ***************************************988.888888899***************** PP TIGR01364 140 aayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrk 208 ay+++++n+ti+G++++++p ++++ l+aD+ssdil r+i+v+++ liyaGaqKn+Gp+Gvt+viv+k lcl|NCBI__GCF_002019605.1:WP_078429013.1 142 DAYLHITSNNTIYGTQWHKYPVFENTSLIADMSSDILCRPIQVNDFSLIYAGAQKNLGPSGVTIVIVKK 210 ********************************************************************* PP TIGR01364 209 dllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaid 277 +lle++k+++p++l+Y+++++ +slyntpptfaiy+l++vl+w+ e+GG++++e +n eKakl+Y+aid lcl|NCBI__GCF_002019605.1:WP_078429013.1 211 ELLENSKQDIPTILRYSTHSDANSLYNTPPTFAIYMLSKVLEWVIEQGGITAVETRNVEKAKLIYDAID 279 ********************************************************************* PP TIGR01364 278 esegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqa 346 es+gfy++++ek++Rslmn++F+l+++el+k+Fl+ea+++g+v+l+GhrsvGG+Ras Yn++p+e+++a lcl|NCBI__GCF_002019605.1:WP_078429013.1 280 ESNGFYRGHAEKDSRSLMNITFNLQSDELNKKFLAEAKAAGFVGLNGHRSVGGCRASTYNSVPVEACEA 348 ********************************************************************* PP TIGR01364 347 LvdfmkeFekk 357 L +fm F+k+ lcl|NCBI__GCF_002019605.1:WP_078429013.1 349 LRQFMITFKKN 359 ********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: 11.93 // [ok]
This GapMind analysis is from Apr 10 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