Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_034995218.1 DL88_RS09605 phosphoserine transaminase
Query= SwissProt::P52878 (370 letters) >NCBI__GCF_000745425.1:WP_034995218.1 Length = 390 Score = 477 bits (1228), Expect = e-139 Identities = 234/378 (61%), Positives = 272/378 (71%), Gaps = 10/378 (2%) Query: 3 PTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPDD 62 P P N CFSSGPCAK PG+ LKD P GRSHR+ +GK KL AI TR++L +P D Sbjct: 6 PAARPANACFSSGPCAKRPGWDFSALKDAPLGRSHRAKIGKTKLKLAIDLTREILQVPAD 65 Query: 63 YLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEYG 122 Y +GIVP SDTGA EM LW++LG RGVDVL WESF +GW TDI KQLKL +VR +A YG Sbjct: 66 YRIGIVPGSDTGAVEMALWTLLGARGVDVLAWESFGQGWVTDIVKQLKLPNVRTLKAGYG 125 Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKLD 182 ++ DL VDF NDVVF WNGTTSGVKVPNGDWI +R+GLT+CDATSA FA + + KLD Sbjct: 126 EIVDLATVDFNNDVVFTWNGTTSGVKVPNGDWIAADRQGLTICDATSAAFAQKLDWAKLD 185 Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGSTI 242 V+TFSWQKVLGGEG HGMLILSPRAV+RL +YTPAWPLPKIFRLT GGKL + IF G TI Sbjct: 186 VVTFSWQKVLGGEGGHGMLILSPRAVERLTTYTPAWPLPKIFRLTSGGKLTEGIFVGETI 245 Query: 243 NTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIRSS 302 NTPSML ED++ L WA+S+GGL LI R + N +V K WI FLA IRS+ Sbjct: 246 NTPSMLCVEDYIDALNWAKSLGGLDSLIARADANTKAITDWVEKTAWIDFLAADPAIRSN 305 Query: 303 TSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEK 352 TSVC KV + + K+L LEKE VAYDIG+YRDAP GLRIWCGATVE Sbjct: 306 TSVCLKVSDPEITALPAEAQADFAKKLASLLEKENVAYDIGAYRDAPPGLRIWCGATVET 365 Query: 353 EDLQCLCEWIEWAYNLVK 370 D+ L W+++AY K Sbjct: 366 SDVTALTAWLDYAYAKTK 383 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: 513 Number of extensions: 19 Number of successful extensions: 2 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: 390 Length adjustment: 30 Effective length of query: 340 Effective length of database: 360 Effective search space: 122400 Effective search space used: 122400 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 WP_034995218.1 DL88_RS09605 (phosphoserine transaminase)
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.15840.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-216 702.8 2.8 6.4e-216 702.5 2.8 1.0 1 lcl|NCBI__GCF_000745425.1:WP_034995218.1 DL88_RS09605 phosphoserine trans Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_034995218.1 DL88_RS09605 phosphoserine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 702.5 2.8 6.4e-216 6.4e-216 1 373 [. 9 381 .. 9 382 .. 1.00 Alignments for each domain: == domain 1 score: 702.5 bits; conditional E-value: 6.4e-216 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 rpan +fssgpcakrpg+ +lk+a+lgrshr+k+gk+klk ai+ tre+l+vpady+igiv++sdtg lcl|NCBI__GCF_000745425.1:WP_034995218.1 9 RPANACFSSGPCAKRPGWDFSALKDAPLGRSHRAKIGKTKLKLAIDLTREILQVPADYRIGIVPGSDTG 77 7******************************************************************** PP TIGR01365 70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngt 138 avemalw+llgargvd+la+esfg+gwvtd++kqlkl++vr l+a+yg++ dl+ vdf++dvvftwngt lcl|NCBI__GCF_000745425.1:WP_034995218.1 78 AVEMALWTLLGARGVDVLAWESFGQGWVTDIVKQLKLPNVRTLKAGYGEIVDLATVDFNNDVVFTWNGT 146 ********************************************************************* PP TIGR01365 139 tsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarle 207 tsgv+vpngd+i+adr+glticdatsaafaq+ld+ kldvvtfswqkvlggeg hg+lilsprav+rl lcl|NCBI__GCF_000745425.1:WP_034995218.1 147 TSGVKVPNGDWIAADRQGLTICDATSAAFAQKLDWAKLDVVTFSWQKVLGGEGGHGMLILSPRAVERLT 215 ********************************************************************* PP TIGR01365 208 sytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavle 276 +ytpawplpkifrlt+ggkl+++if getintpsml+ved++dal+wa+s+ggl++l+arad+n + + lcl|NCBI__GCF_000745425.1:WP_034995218.1 216 TYTPAWPLPKIFRLTSGGKLTEGIFVGETINTPSMLCVEDYIDALNWAKSLGGLDSLIARADANTKAIT 284 ********************************************************************* PP TIGR01365 277 afvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapa 345 ++v+k++w+dflaa ++irsntsvclkv dp+++al+++aqadfak+l+s+leke+vaydig+yrdap+ lcl|NCBI__GCF_000745425.1:WP_034995218.1 285 DWVEKTAWIDFLAADPAIRSNTSVCLKVSDPEITALPAEAQADFAKKLASLLEKENVAYDIGAYRDAPP 353 ********************************************************************* PP TIGR01365 346 glriwcgatveksdleallewldwafal 373 glriwcgatve+sd+ al+ wld+a+a lcl|NCBI__GCF_000745425.1:WP_034995218.1 354 GLRIWCGATVETSDVTALTAWLDYAYAK 381 **************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (374 nodes) Target sequences: 1 (390 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: 8.38 // [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