Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_013075035.1 BTUS_RS05070 3-phosphoserine/phosphohydroxythreonine transaminase
Query= SwissProt::Q59196 (362 letters) >NCBI__GCF_000092905.1:WP_013075035.1 Length = 364 Score = 457 bits (1177), Expect = e-133 Identities = 223/357 (62%), Positives = 278/357 (77%) Query: 3 KRAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLALL 62 KRA NFNAGPAALPLEVLE+A+ EFVD+ TGMS+MEMSHR YEA+HNE A + LL Sbjct: 5 KRALNFNAGPAALPLEVLEQAREEFVDFGGTGMSVMEMSHRSKTYEAIHNETAALVRELL 64 Query: 63 GNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIGDTHVAAS 122 G P GY VLF+QGGAS QFAM+PMNFL +G+ A YV+TGSW+ KALKEA+ +G+T VAAS Sbjct: 65 GVPEGYDVLFLQGGASLQFAMVPMNFLPKGKAAGYVLTGSWSEKALKEAQRLGETFVAAS 124 Query: 123 SEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDILSRP 182 ++ +Y +P +EI ++AYLH+TSN TI G Q+ FPDTGSVPL+ DMSSDILSR Sbjct: 125 TKDGHYRRIPGAEEISFGRDSAYLHVTSNNTIFGTQWTRFPDTGSVPLVADMSSDILSRK 184 Query: 183 FDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNTPPS 242 D+ QF L+YAGAQKNLGPSGVT+V+VR+D+V +P+ LPTML+Y + KNNSLYNTPP+ Sbjct: 185 IDVRQFALIYAGAQKNLGPSGVTLVVVRQDMVERAPEDLPTMLQYRIHAKNNSLYNTPPT 244 Query: 243 FGIYMVNEVLKWIEERGGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDMNITF 302 FGIYM+ VLKW++ +GG+E V++ NR+KA LIY ID + FY G + SRS MN+TF Sbjct: 245 FGIYMMGLVLKWVKGQGGVEAVERRNREKAGLIYKVIDDNPDFYLGHAEPTSRSLMNVTF 304 Query: 303 RLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFKR 359 RL + ELEKEF+ ++ EGFVGL GHRSVGG RAS+YNAVP E C AL +M F++ Sbjct: 305 RLPTPELEKEFLDGAKAEGFVGLNGHRSVGGCRASLYNAVPVEHCAALRDYMVEFRK 361 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: 437 Number of extensions: 9 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: 362 Length of database: 364 Length adjustment: 29 Effective length of query: 333 Effective length of database: 335 Effective search space: 111555 Effective search space used: 111555 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_013075035.1 BTUS_RS05070 (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.3699011.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-158 513.3 0.0 1.7e-158 513.1 0.0 1.0 1 NCBI__GCF_000092905.1:WP_013075035.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000092905.1:WP_013075035.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 513.1 0.0 1.7e-158 1.7e-158 2 358 .] 8 363 .. 7 363 .. 0.99 Alignments for each domain: == domain 1 score: 513.1 bits; conditional E-value: 1.7e-158 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGat 74 nF+aGPaalp evle+a++e++df g+g+svme+sHRsk++e++++e+ +reLl +p+ y+vlflqGGa+ NCBI__GCF_000092905.1:WP_013075035.1 8 LNFNAGPAALPLEVLEQAREEFVDFGGTGMSVMEMSHRSKTYEAIHNETAALVRELLGVPEGYDVLFLQGGAS 80 69*********************************************************************** PP TIGR01364 75 tqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylca 147 qfa+vp+n+l ++k a y+ tG+ws+kalkea++l++ + v+as+++++y +ip ee+++ d+ay+++++ NCBI__GCF_000092905.1:WP_013075035.1 81 LQFAMVPMNFLPKGKAAGYVLTGSWSEKALKEAQRLGE-TFVAASTKDGHYRRIPGAEEISFGRDSAYLHVTS 152 ************************************98.8999999*************************** PP TIGR01364 148 netieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelps 220 n+ti G+++++ p++ ++plvaD+ssdilsrkidv +++liyaGaqKn+Gp+Gvt+v+vr+d++era ++lp+ NCBI__GCF_000092905.1:WP_013075035.1 153 NNTIFGTQWTRFPDTGSVPLVADMSSDILSRKIDVRQFALIYAGAQKNLGPSGVTLVVVRQDMVERAPEDLPT 225 ************************************************************************* PP TIGR01364 221 vldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRs 293 +l+Y+i+a+n+slyntpptf+iy++glvlkw+k +GGv+++e++n+eKa l+Y++id++ +fy +++e+++Rs NCBI__GCF_000092905.1:WP_013075035.1 226 MLQYRIHAKNNSLYNTPPTFGIYMMGLVLKWVKGQGGVEAVERRNREKAGLIYKVIDDNPDFYLGHAEPTSRS 298 ************************************************************************* PP TIGR01364 294 lmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358 lmnv+F+l+ elekeFl+ a+++g+v+l+GhrsvGG+Ras+Yna+p+e++ aL d+m eF+kkh NCBI__GCF_000092905.1:WP_013075035.1 299 LMNVTFRLPTPELEKEFLDGAKAEGFVGLNGHRSVGGCRASLYNAVPVEHCAALRDYMVEFRKKH 363 **************************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (364 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 15.37 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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