Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate 3609935 Dshi_3317 phosphoserine aminotransferase (RefSeq)
Query= SwissProt::P52878 (370 letters) >FitnessBrowser__Dino:3609935 Length = 384 Score = 462 bits (1188), Expect = e-135 Identities = 229/371 (61%), Positives = 270/371 (72%), Gaps = 10/371 (2%) Query: 3 PTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPDD 62 P P NP FSSGPCAK P ++++ L D GRSHR+ +GK+KL AI+ TR++LG+P D Sbjct: 6 PVTRPANPRFSSGPCAKPPTWTLDTLGDAALGRSHRATVGKDKLKAAIETTREVLGVPAD 65 Query: 63 YLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEYG 122 Y +GIVPASDTGA+EM +WS+LG R V++L WESF GW TD KQLKL D AEYG Sbjct: 66 YKIGIVPASDTGAYEMAMWSLLGERPVEMLAWESFGSGWVTDAIKQLKL-DATTRTAEYG 124 Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKLD 182 ++ DL VDF DV F WNGTTSGV+VP+GDWIP +R GLTLCDATSA FAMD+ + KLD Sbjct: 125 EIVDLAAVDFDKDVCFTWNGTTSGVRVPDGDWIPADRAGLTLCDATSAAFAMDLAWDKLD 184 Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGSTI 242 TFSWQKVLGGE AHG+LILSPRAV RLESYTP WPLPKIFRLTKGGKL IF G TI Sbjct: 185 ATTFSWQKVLGGEAAHGILILSPRAVARLESYTPPWPLPKIFRLTKGGKLIDGIFRGETI 244 Query: 243 NTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIRSS 302 NTPSML ED+L L WA+SVGGL LI R N A AFVA N+WI FLA RS+ Sbjct: 245 NTPSMLCVEDYLFALDWAKSVGGLPGLIARAEANTAAIAAFVAANDWIDFLAADPATRST 304 Query: 303 TSVCFKVDLSDEKL-------KELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDL 355 TSVC K +D+++ K + K LE E +A+DIG+YRDAP GLRIWCG TVE D+ Sbjct: 305 TSVCLK--FTDDRIADGAAFAKAVAKRLEAEGIAFDIGAYRDAPPGLRIWCGGTVETSDV 362 Query: 356 QCLCEWIEWAY 366 + L W+ WA+ Sbjct: 363 EALLPWLSWAF 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: 477 Number of extensions: 18 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 3609935 Dshi_3317 (phosphoserine aminotransferase (RefSeq))
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.28520.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-194 632.5 1.4 1.4e-194 632.3 1.4 1.0 1 lcl|FitnessBrowser__Dino:3609935 Dshi_3317 phosphoserine aminotra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3609935 Dshi_3317 phosphoserine aminotransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 632.3 1.4 1.4e-194 1.4e-194 1 373 [. 9 375 .. 9 376 .. 0.98 Alignments for each domain: == domain 1 score: 632.3 bits; conditional E-value: 1.4e-194 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavemalws 77 rpanp fssgpcak p ++++ l +aalgrshr+ +gk+klk+aie trevl+vpady+igiv+asdtga+ema+ws lcl|FitnessBrowser__Dino:3609935 9 RPANPRFSSGPCAKPPTWTLDTLGDAALGRSHRATVGKDKLKAAIETTREVLGVPADYKIGIVPASDTGAYEMAMWS 85 7**************************************************************************** PP TIGR01365 78 llgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpngdfipadr 154 llg+r+v++la+esfg+gwvtd +kqlkl d aeyg++ dl+ vdf+kdv ftwngttsgvrvp+gd+ipadr lcl|FitnessBrowser__Dino:3609935 86 LLGERPVEMLAWESFGSGWVTDAIKQLKL-DATTRTAEYGEIVDLAAVDFDKDVCFTWNGTTSGVRVPDGDWIPADR 161 ****************************9.566779***************************************** PP TIGR01365 155 eglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkifrltkggklskdi 231 glt+cdatsaafa+dl ++kld tfswqkvlgge ahg+lilspravarlesytp wplpkifrltkggkl+++i lcl|FitnessBrowser__Dino:3609935 162 AGLTLCDATSAAFAMDLAWDKLDATTFSWQKVLGGEAAHGILILSPRAVARLESYTPPWPLPKIFRLTKGGKLIDGI 238 ***************************************************************************** PP TIGR01365 232 fegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatkeirsntsvclkvvdpd 308 f+getintpsml+ved+l al wa+s+ggl l+ara++n a ++afva ++w+dflaa +++rs+tsvclk++d lcl|FitnessBrowser__Dino:3609935 239 FRGETINTPSMLCVEDYLFALDWAKSVGGLPGLIARAEANTAAIAAFVAANDWIDFLAADPATRSTTSVCLKFTDDR 315 *************************************************************************9998 PP TIGR01365 309 vaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdleallewldwafal 373 +a d a fak +++ le eg+a+dig+yrdap+glriwcg tve+sd+eall+wl waf++ lcl|FitnessBrowser__Dino:3609935 316 IA----D-GAAFAKAVAKRLEAEGIAFDIGAYRDAPPGLRIWCGGTVETSDVEALLPWLSWAFEA 375 85....3.478****************************************************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: 00:00:00.01 # Mc/sec: 8.00 // [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