Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_011189174.1 DP_RS09895 phosphoserine aminotransferase
Query= SwissProt::Q9RME2 (361 letters) >NCBI__GCF_000025945.1:WP_011189174.1 Length = 361 Score = 366 bits (940), Expect = e-106 Identities = 181/360 (50%), Positives = 254/360 (70%), Gaps = 2/360 (0%) Query: 1 MVKQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRE 60 M +V+NF+AGP+ LP LE+A K+++NF +T ++E+SHRS + EV E+ ++L+RE Sbjct: 1 MADRVYNFSAGPATLPFEVLEQAGKDIVNFKETGSGLIEISHRSPEFIEVIEKTESLVRE 60 Query: 61 LLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIA 120 LL++P++Y++LFLQGGAS QF M+PMNLL G Y+ TG+W++KA+KEA+L G+ +A Sbjct: 61 LLEVPDNYKVLFLQGGASSQFFMVPMNLLGAGKKATYLNTGTWAKKAIKEAQLFGDIDVA 120 Query: 121 ASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILS 180 S++ + + +P +Q+ E YL+ SNNTIYGTQ++ P+ + L+ADMSSDI S Sbjct: 121 YSSEESIFNHVPANDAYQVAEESEYLYFASNNTIYGTQFETMPQ-SKKMLVADMSSDIFS 179 Query: 181 RPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTP 240 R + V++FG+I+AGAQKNLGP+GVT+VI++ DLL PTML Y TH S++NTP Sbjct: 180 RKVDVSKFGLIFAGAQKNLGPAGVTLVIIRDDLLEKTPAHTPTMLSYKTHADKGSMFNTP 239 Query: 241 PTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNV 300 P F+IY++ VL W+K+LGG E I + N EKA ++Y ID S+ +Y HA+ GSRSLMNV Sbjct: 240 PCFAIYVMGEVLAWLKNLGGVEKIEEINREKAALLYSQIDASD-YYRVHAQDGSRSLMNV 298 Query: 301 TFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKEN 360 TFNL EL +F+A+A GL GHRS+GGCRASIYNA P + + L E M F N Sbjct: 299 TFNLPTAELEAKFIAEASALQMKGLKGHRSIGGCRASIYNAFPREGVVKLVEFMQVFAAN 358 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: 376 Number of extensions: 11 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: 361 Length of database: 361 Length adjustment: 29 Effective length of query: 332 Effective length of database: 332 Effective search space: 110224 Effective search space used: 110224 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_011189174.1 DP_RS09895 (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.15940.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-156 506.7 0.1 1.8e-156 506.5 0.1 1.0 1 lcl|NCBI__GCF_000025945.1:WP_011189174.1 DP_RS09895 phosphoserine aminotr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025945.1:WP_011189174.1 DP_RS09895 phosphoserine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 506.5 0.1 1.8e-156 1.8e-156 1 357 [. 5 358 .. 5 359 .. 0.99 Alignments for each domain: == domain 1 score: 506.5 bits; conditional E-value: 1.8e-156 TIGR01364 1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 ++nFsaGPa+lp evle+a k++++f+++g +++eisHRs ef +v+e++es +reLl++pdny+vlfl lcl|NCBI__GCF_000025945.1:WP_011189174.1 5 VYNFSAGPATLPFEVLEQAGKDIVNFKETGSGLIEISHRSPEFIEVIEKTESLVRELLEVPDNYKVLFL 73 59******************************************************************* PP TIGR01364 70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelke 138 qGGa++qf +vp+nll ++k+a+y++tG+w+kka+kea+ +++ ++v+ s+ee+ ++++p ++ ++++e lcl|NCBI__GCF_000025945.1:WP_011189174.1 74 QGGASSQFFMVPMNLLGAGKKATYLNTGTWAKKAIKEAQLFGD-IDVAYSSEESIFNHVPANDAYQVAE 141 *****************************************99.************************* PP TIGR01364 139 daayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivr 207 +++y+y+++n+ti+G++f+++p ++k++lvaD+ssdi+srk+dvsk+gli+aGaqKn+GpaGvt+vi+r lcl|NCBI__GCF_000025945.1:WP_011189174.1 142 ESEYLYFASNNTIYGTQFETMP-QSKKMLVADMSSDIFSRKVDVSKFGLIFAGAQKNLGPAGVTLVIIR 209 **********************.67789***************************************** PP TIGR01364 208 kdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeai 276 +dlle++ +++p++l+Yk++a++ s++ntpp+faiyv+g vl wlk+ GGv+k+e+ n+eKa+llY i lcl|NCBI__GCF_000025945.1:WP_011189174.1 210 DDLLEKTPAHTPTMLSYKTHADKGSMFNTPPCFAIYVMGEVLAWLKNLGGVEKIEEINREKAALLYSQI 278 ********************************************************************* PP TIGR01364 277 desegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevq 345 d+s+ +y+++++ +Rslmnv+F+l+ +ele++F++ea++ ++ +lkGhrs+GG+RasiYna+p e+v lcl|NCBI__GCF_000025945.1:WP_011189174.1 279 DASD-YYRVHAQDGSRSLMNVTFNLPTAELEAKFIAEASALQMKGLKGHRSIGGCRASIYNAFPREGVV 346 *996.**************************************************************** PP TIGR01364 346 aLvdfmkeFekk 357 +Lv+fm+ F+++ lcl|NCBI__GCF_000025945.1:WP_011189174.1 347 KLVEFMQVFAAN 358 *********876 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 6.96 // [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