Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_015945317.1 DHAF_RS22860 3-phosphoserine/phosphohydroxythreonine transaminase
Query= SwissProt::Q59196 (362 letters) >NCBI__GCF_000021925.1:WP_015945317.1 Length = 362 Score = 367 bits (942), Expect = e-106 Identities = 180/357 (50%), Positives = 248/357 (69%), Gaps = 3/357 (0%) Query: 3 KRAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALL 62 KR YNF+AGPA LP EVL A E +DYQ TGMS+MEMSHR E + NEA L LL Sbjct: 2 KRVYNFSAGPAVLPEEVLREAAEEMLDYQGTGMSVMEMSHRSKTIEGMMNEAAQDLRDLL 61 Query: 63 GNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAAS 122 P YK+LF+QGGAS QFAM+PMN +K + A+++ TG WA KA+ E KL G +V AS Sbjct: 62 KVPDNYKILFLQGGASQQFAMVPMNLMKN-RVADHLNTGQWAKKAISEGKLYGKINVVAS 120 Query: 123 SEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRP 182 SE NY +P L++++ + A Y+++ N TI G +F P+ G PLI DMSSD LS P Sbjct: 121 SEDQNYSYIPDLKDLKFSEEADYVYICHNNTIFGTKFNELPEVGDKPLIADMSSDFLSEP 180 Query: 183 FDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESP-KHLPTMLRYDTYVKNNSLYNTPP 241 D++Q+G+++AGAQKN+GP+GV +VI+REDL+ E PTML+Y ++ NNS YNTPP Sbjct: 181 IDVSQYGIIFAGAQKNVGPAGVVIVIIREDLITEDVLPGTPTMLKYKVHLDNNSAYNTPP 240 Query: 242 SFGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNIT 301 +GIY+ +V KW+++ GGLE +Q+ N +KA+++YD +D S ++G V RS MN+ Sbjct: 241 VYGIYICGKVFKWLKKLGGLEAMQKINEEKAAILYDYLDAS-AMFKGTVAKKDRSLMNVP 299 Query: 302 FRLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFK 358 F SEEL+ +F+K ++ GF LKG+R+VGG+RASIYNA+P + + LV+FM F+ Sbjct: 300 FVTGSEELDAKFIKEAKTAGFENLKGYRTVGGMRASIYNAMPIQGVKDLVEFMRKFE 356 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: 387 Number of extensions: 17 Number of successful extensions: 4 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: 362 Length adjustment: 29 Effective length of query: 333 Effective length of database: 333 Effective search space: 110889 Effective search space used: 110889 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_015945317.1 DHAF_RS22860 (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.8178.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-162 524.6 0.2 6.4e-162 524.4 0.2 1.0 1 lcl|NCBI__GCF_000021925.1:WP_015945317.1 DHAF_RS22860 3-phosphoserine/pho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_015945317.1 DHAF_RS22860 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 524.4 0.2 6.4e-162 6.4e-162 1 357 [. 4 358 .. 4 359 .. 0.98 Alignments for each domain: == domain 1 score: 524.4 bits; conditional E-value: 6.4e-162 TIGR01364 1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 ++nFsaGPa+lpeevl++a++e+ld++g+g+svme+sHRsk++e +++ea +dlr+Ll++pdny++lfl lcl|NCBI__GCF_000021925.1:WP_015945317.1 4 VYNFSAGPAVLPEEVLREAAEEMLDYQGTGMSVMEMSHRSKTIEGMMNEAAQDLRDLLKVPDNYKILFL 72 59******************************************************************* PP TIGR01364 70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelke 138 qGGa++qfa+vp+nl+k++ vad+++tG+w+kka++e k ++k ++vvas+e+++ys ipd ++l+++e lcl|NCBI__GCF_000021925.1:WP_015945317.1 73 QGGASQQFAMVPMNLMKNR-VADHLNTGQWAKKAISEGKLYGK-INVVASSEDQNYSYIPDLKDLKFSE 139 ****************998.*********************98.************************* PP TIGR01364 139 daayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivr 207 +a+yvy+c+n+ti G++f+elpev ++pl+aD+ssd+ls++idvs+yg+i+aGaqKn+GpaGv++vi+r lcl|NCBI__GCF_000021925.1:WP_015945317.1 140 EADYVYICHNNTIFGTKFNELPEVGDKPLIADMSSDFLSEPIDVSQYGIIFAGAQKNVGPAGVVIVIIR 208 ********************************************************************* PP TIGR01364 208 kdllerakk.elpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYea 275 +dl+ + +p++l+Yk++ +n+s yntpp+++iy++g+v+kwlk+ GG+++++k n+eKa++lY++ lcl|NCBI__GCF_000021925.1:WP_015945317.1 209 EDLITEDVLpGTPTMLKYKVHLDNNSAYNTPPVYGIYICGKVFKWLKKLGGLEAMQKINEEKAAILYDY 277 ****9766559********************************************************** PP TIGR01364 276 idesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleev 344 +d+s ++k++v+kk+Rslmnv+F + +eel+++F+kea+++g+ +lkG+r+vGG+RasiYna+p+++v lcl|NCBI__GCF_000021925.1:WP_015945317.1 278 LDASA-MFKGTVAKKDRSLMNVPFVTGSEELDAKFIKEAKTAGFENLKGYRTVGGMRASIYNAMPIQGV 345 **996.9************************************************************** PP TIGR01364 345 qaLvdfmkeFekk 357 + Lv+fm++Fe++ lcl|NCBI__GCF_000021925.1:WP_015945317.1 346 KDLVEFMRKFEAE 358 **********986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (362 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: 7.58 // [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