Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate GFF3561 PGA1_c36150 phosphoserine aminotransferase SerC
Query= SwissProt::P52878 (370 letters) >FitnessBrowser__Phaeo:GFF3561 Length = 384 Score = 462 bits (1189), Expect = e-135 Identities = 227/372 (61%), Positives = 271/372 (72%), Gaps = 10/372 (2%) Query: 2 KPTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPD 61 +P P NP FSSGPCAK P + + +L P GRSHR+ +GK+KL AI+ TR++LG+P Sbjct: 5 QPATRPGNPRFSSGPCAKPPAFDLTKLAGAPLGRSHRAAIGKDKLLAAIEGTREILGVPA 64 Query: 62 DYLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEY 121 Y +GIVPASDTGA EM +W++LG RG ++L WESF GW TD+ KQLKL D V A+Y Sbjct: 65 GYRIGIVPASDTGAVEMAMWNLLGARGAEMLAWESFGAGWVTDVVKQLKL-DAVVKTADY 123 Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKL 181 G+L DL VDF NDVVF WNGTTSGV+VPNGDWIP +R GLT+CDATSA FA D+P+ KL Sbjct: 124 GELVDLASVDFNNDVVFTWNGTTSGVRVPNGDWIPADRAGLTICDATSAAFAQDLPWDKL 183 Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGST 241 DV TFSWQKVLGGE AHGM+ILSPRAV+RLESYTPAWPLPKIFRLTKGGKL IF+G+T Sbjct: 184 DVTTFSWQKVLGGEAAHGMIILSPRAVERLESYTPAWPLPKIFRLTKGGKLIDGIFKGAT 243 Query: 242 INTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIRS 301 INTPSMLA ED+L L WA SVGGL L R + N F A WI LA RS Sbjct: 244 INTPSMLAVEDYLLALDWARSVGGLDGLKGRADANAQAIFNFCANRPWIANLATDPATRS 303 Query: 302 STSVCFKVDLSDEKL-------KELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKED 354 +TSVC K +D ++ K + K LE E +A DIG+YRDAP+GLRIWCG TVE D Sbjct: 304 NTSVCLK--FTDPRIQDGATFAKAIAKRLEAENIALDIGAYRDAPAGLRIWCGGTVETSD 361 Query: 355 LQCLCEWIEWAY 366 ++ + W+EWA+ Sbjct: 362 IEAMLPWLEWAF 373 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: 490 Number of extensions: 19 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: 370 Length of database: 384 Length adjustment: 30 Effective length of query: 340 Effective length of database: 354 Effective search space: 120360 Effective search space used: 120360 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: 50 (23.9 bits)
Align candidate GFF3561 PGA1_c36150 (phosphoserine aminotransferase SerC)
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.29100.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-192 625.9 0.4 1.4e-192 625.7 0.4 1.0 1 lcl|FitnessBrowser__Phaeo:GFF3561 PGA1_c36150 phosphoserine aminot Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF3561 PGA1_c36150 phosphoserine aminotransferase SerC # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 625.7 0.4 1.4e-192 1.4e-192 1 373 [. 9 375 .. 9 376 .. 0.98 Alignments for each domain: == domain 1 score: 625.7 bits; conditional E-value: 1.4e-192 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavemalw 76 rp np fssgpcak p + + +l a+lgrshr+ +gk+kl +aie tre+l+vpa y+igiv+asdtgavema+w lcl|FitnessBrowser__Phaeo:GFF3561 9 RPGNPRFSSGPCAKPPAFDLTKLAGAPLGRSHRAAIGKDKLLAAIEGTREILGVPAGYRIGIVPASDTGAVEMAMW 84 799************************************************************************* PP TIGR01365 77 sllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpngdfipa 152 llgarg ++la+esfg gwvtdv+kqlkl+ v v a+yg+l dl+ vdf++dvvftwngttsgvrvpngd+ipa lcl|FitnessBrowser__Phaeo:GFF3561 85 NLLGARGAEMLAWESFGAGWVTDVVKQLKLDAV-VKTADYGELVDLASVDFNNDVVFTWNGTTSGVRVPNGDWIPA 159 ******************************887.558*************************************** PP TIGR01365 153 dreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkifrltkggkls 228 dr glticdatsaafaqdl+++kldv tfswqkvlgge ahg++ilsprav+rlesytpawplpkifrltkggkl+ lcl|FitnessBrowser__Phaeo:GFF3561 160 DRAGLTICDATSAAFAQDLPWDKLDVTTFSWQKVLGGEAAHGMIILSPRAVERLESYTPAWPLPKIFRLTKGGKLI 235 **************************************************************************** PP TIGR01365 229 kdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatkeirsntsvclkv 304 ++if+g+tintpsmlaved+l al wa+s+ggl+ l rad+n++ + +f a+ +w+ la+ +++rsntsvclk+ lcl|FitnessBrowser__Phaeo:GFF3561 236 DGIFKGATINTPSMLAVEDYLLALDWARSVGGLDGLKGRADANAQAIFNFCANRPWIANLATDPATRSNTSVCLKF 311 **************************************************************************** PP TIGR01365 305 vdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdleallewldwafal 373 +dp ++ d a+fak +++ le e++a+dig+yrdapaglriwcg tve+sd+ea+l+wl+waf++ lcl|FitnessBrowser__Phaeo:GFF3561 312 TDPRIQ----D-GATFAKAIAKRLEAENIALDIGAYRDAPAGLRIWCGGTVETSDIEAMLPWLEWAFET 375 ***985....3.589****************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (374 nodes) Target sequences: 1 (384 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: 00:00:00.07 # Mc/sec: 1.88 // [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