Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_011306304.1 MBAR_RS06945 phosphoserine aminotransferase
Query= SwissProt::P52878 (370 letters) >NCBI__GCF_000195895.1:WP_011306304.1 Length = 370 Score = 768 bits (1983), Expect = 0.0 Identities = 370/370 (100%), Positives = 370/370 (100%) Query: 1 MKPTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLP 60 MKPTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLP Sbjct: 1 MKPTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLP 60 Query: 61 DDYLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAE 120 DDYLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAE Sbjct: 61 DDYLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAE 120 Query: 121 YGKLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHK 180 YGKLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHK Sbjct: 121 YGKLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHK 180 Query: 181 LDVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGS 240 LDVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGS Sbjct: 181 LDVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGS 240 Query: 241 TINTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIR 300 TINTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIR Sbjct: 241 TINTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIR 300 Query: 301 SSTSVCFKVDLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLQCLCE 360 SSTSVCFKVDLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLQCLCE Sbjct: 301 SSTSVCFKVDLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLQCLCE 360 Query: 361 WIEWAYNLVK 370 WIEWAYNLVK Sbjct: 361 WIEWAYNLVK 370 Lambda K H 0.318 0.136 0.429 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: 656 Number of extensions: 15 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: 370 Length of database: 370 Length adjustment: 30 Effective length of query: 340 Effective length of database: 340 Effective search space: 115600 Effective search space used: 115600 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_011306304.1 MBAR_RS06945 (phosphoserine aminotransferase)
to HMM TIGR01365 (phosphoserine aminotransferase (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/TIGR01365.hmm # target sequence database: /tmp/gapView.19294.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01365 [M=374] Accession: TIGR01365 Description: serC_2: phosphoserine aminotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-229 747.9 0.3 1.3e-229 747.7 0.3 1.0 1 lcl|NCBI__GCF_000195895.1:WP_011306304.1 MBAR_RS06945 phosphoserine amino Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195895.1:WP_011306304.1 MBAR_RS06945 phosphoserine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 747.7 0.3 1.3e-229 1.3e-229 1 374 [] 6 369 .. 6 369 .. 0.99 Alignments for each domain: == domain 1 score: 747.7 bits; conditional E-value: 1.3e-229 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 +p+np+fssgpcak+pgys+eelk++++grshrs+lgkekl+eai+ktr++l++p+dyl+giv+asdtg lcl|NCBI__GCF_000195895.1:WP_011306304.1 6 VPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPDDYLVGIVPASDTG 74 69******************************************************************* PP TIGR01365 70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngt 138 a+em+lws+lg+rgvd+l++esf+kgw+td+tkqlklkdvrv+eaeygklpdlkkvdfk+dvvf+wngt lcl|NCBI__GCF_000195895.1:WP_011306304.1 75 AFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEYGKLPDLKKVDFKNDVVFVWNGT 143 ********************************************************************* PP TIGR01365 139 tsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarle 207 tsgv+vpngd+ip++reglt+cdatsa+fa+d++y+kldv+tfswqkvlggegahg+lilsprav+rle lcl|NCBI__GCF_000195895.1:WP_011306304.1 144 TSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKLDVITFSWQKVLGGEGAHGMLILSPRAVQRLE 212 ********************************************************************* PP TIGR01365 208 sytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavle 276 sytpawplpkifrltkggkl+k+ifeg+tintpsmla+ed+l++lkwaes+gglk+l++r++dnlav+e lcl|NCBI__GCF_000195895.1:WP_011306304.1 213 SYTPAWPLPKIFRLTKGGKLNKKIFEGSTINTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFE 281 ********************************************************************* PP TIGR01365 277 afvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapa 345 afvak++w++fla+tkeirs+tsvc+kv +++de+ +kel+++leke+vaydigsyrdap+ lcl|NCBI__GCF_000195895.1:WP_011306304.1 282 AFVAKNNWIHFLAETKEIRSSTSVCFKV-----DLSDEK-----LKELIKTLEKEKVAYDIGSYRDAPS 340 ***************************9.....899*99.....9************************ PP TIGR01365 346 glriwcgatveksdleallewldwafalv 374 glriwcgatvek+dl++l+ew++wa++lv lcl|NCBI__GCF_000195895.1:WP_011306304.1 341 GLRIWCGATVEKEDLQCLCEWIEWAYNLV 369 **************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (374 nodes) Target sequences: 1 (370 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: 8.96 // [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