Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate CA265_RS09005 CA265_RS09005 phosphoserine transaminase
Query= SwissProt::Q59196 (362 letters) >FitnessBrowser__Pedo557:CA265_RS09005 Length = 357 Score = 338 bits (868), Expect = 1e-97 Identities = 168/356 (47%), Positives = 253/356 (71%), Gaps = 5/356 (1%) Query: 6 YNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALLGNP 65 +NF AGP LP EV ++A +D+ + G+SI+E+SHR +EAV EA + LL P Sbjct: 3 HNFGAGPCILPQEVFKQAAQAVLDF-NDGLSILEISHRTTEFEAVVAEADKLVKELLNVP 61 Query: 66 TGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAASSEA 125 +GY VLF+QGGAS QFAM+PMN L +GQTA+Y+ +G WA+KALKEAK IG+ +V ASS+ Sbjct: 62 SGYSVLFLQGGASLQFAMVPMNLLGDGQTASYLDSGVWATKALKEAKFIGNVNVVASSKD 121 Query: 126 SNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRPFDL 185 +NY +PK + ++ ++AY H TSN TI G + P T +VP++ DMSSDI+SR D+ Sbjct: 122 ANYTFIPK--DFEIPADSAYFHYTSNNTIYGTELFEVPKT-NVPVVCDMSSDIMSRVIDV 178 Query: 186 NQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPSFGI 245 ++F L+YAGAQKN+GP+G+T+ IV+ +++ + + +P+ML Y +++ N+S+YNTPP F I Sbjct: 179 SKFDLIYAGAQKNVGPAGLTIAIVKNEVLGKIDRKIPSMLNYQSHIDNDSMYNTPPVFSI 238 Query: 246 YMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITFRLA 305 Y+ L+W++ +GG+ +++ N++KA +Y ID++ ++G V+ RS MN+ F + Sbjct: 239 YVALLNLRWLKSKGGVAEIEKENKQKAEALYREIDRN-PLFKGTCAVEDRSRMNVCFVME 297 Query: 306 SEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKRSR 361 + ELEK F+K +E++G VG+KGHRSVGG RAS+YNA+P S ALV M+ F+ + Sbjct: 298 NPELEKPFLKYAEEQGIVGIKGHRSVGGFRASMYNALPITSVHALVDAMQVFEEQQ 353 Lambda K H 0.316 0.132 0.378 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: 355 Number of extensions: 15 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: 357 Length adjustment: 29 Effective length of query: 333 Effective length of database: 328 Effective search space: 109224 Effective search space used: 109224 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 CA265_RS09005 CA265_RS09005 (phosphoserine 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.9161.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-149 483.6 0.1 1.8e-149 483.4 0.1 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS09005 CA265_RS09005 phosphoserine tran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS09005 CA265_RS09005 phosphoserine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 483.4 0.1 1.8e-149 1.8e-149 2 357 .. 3 352 .. 2 353 .. 0.99 Alignments for each domain: == domain 1 score: 483.4 bits; conditional E-value: 1.8e-149 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 +nF+aGP++lp+ev+++a++ +ldfn+ gls++eisHR+ efe+vv ea++ ++eLln+p+ y+vlfl lcl|FitnessBrowser__Pedo557:CA265_RS09005 3 HNFGAGPCILPQEVFKQAAQAVLDFND-GLSILEISHRTTEFEAVVAEADKLVKELLNVPSGYSVLFL 69 8************************86.9*************************************** PP TIGR01364 70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelk 137 qGGa+ qfa+vp+nll ++++a+y+ +G+w++kalkeak +++ v+vvas+++ +y+ ip +++e+ lcl|FitnessBrowser__Pedo557:CA265_RS09005 70 QGGASLQFAMVPMNLLGDGQTASYLDSGVWATKALKEAKFIGN-VNVVASSKDANYTFIP--KDFEIP 134 *****************************************99.****************..89**** PP TIGR01364 138 edaayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvi 205 d+ay+++++n+ti+G+e e+p ++++p+v+D+ssdi+sr idvsk++liyaGaqKn+GpaG+t+ i lcl|FitnessBrowser__Pedo557:CA265_RS09005 135 ADSAYFHYTSNNTIYGTELFEVP-KTNVPVVCDMSSDIMSRVIDVSKFDLIYAGAQKNVGPAGLTIAI 201 ***********************.789***************************************** PP TIGR01364 206 vrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllY 273 v++++l+++ +++ps+l+Y+++++nds+yntpp+f+iyv+ l l+wlk+kGGv+++ek+n++Ka+ lY lcl|FitnessBrowser__Pedo557:CA265_RS09005 202 VKNEVLGKIDRKIPSMLNYQSHIDNDSMYNTPPVFSIYVALLNLRWLKSKGGVAEIEKENKQKAEALY 269 ******************************************************************** PP TIGR01364 274 eaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpl 341 id++ ++k++ + ++Rs+mnv+F +++ elek Flk aee+g+v++kGhrsvGG+Ras+Ynalp+ lcl|FitnessBrowser__Pedo557:CA265_RS09005 270 REIDRNP-LFKGTCAVEDRSRMNVCFVMENPELEKPFLKYAEEQGIVGIKGHRSVGGFRASMYNALPI 336 ****886.************************************************************ PP TIGR01364 342 eevqaLvdfmkeFekk 357 +v+aLvd m+ Fe++ lcl|FitnessBrowser__Pedo557:CA265_RS09005 337 TSVHALVDAMQVFEEQ 352 *************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (357 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: 10.07 // [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