Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_012042058.1 BBTA_RS08495 phosphoserine transaminase
Query= SwissProt::P52878 (370 letters) >NCBI__GCF_000015165.1:WP_012042058.1 Length = 390 Score = 474 bits (1221), Expect = e-138 Identities = 229/375 (61%), Positives = 273/375 (72%), Gaps = 10/375 (2%) Query: 2 KPTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPD 61 KP++ P P FSSGPCAK PG++ E LKD P GRSHR+ +GK KL +AI+ TRD+L +P Sbjct: 5 KPSQRPAVPHFSSGPCAKRPGWTAENLKDAPLGRSHRAKIGKAKLKQAIELTRDVLEVPA 64 Query: 62 DYLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEY 121 DY +GIVPASDTGA EM LWS+LG R V + WESF +GW +DI K+LKLKDV A Y Sbjct: 65 DYKIGIVPASDTGAVEMALWSLLGARPVTTIAWESFGEGWVSDIVKELKLKDVTKLHAGY 124 Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKL 181 G++PDL K D D+VF WNGTTSGV+VPN DWI +REGLT+CDATSA FA + + KL Sbjct: 125 GEIPDLSKADPATDIVFTWNGTTSGVRVPNADWISASREGLTICDATSAAFAQALDWPKL 184 Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGST 241 DV+TFSWQK LGGE AHGMLILSPRAV+RLE+Y PAWPLPKIFRLTKGGKLN IFEG T Sbjct: 185 DVVTFSWQKALGGEAAHGMLILSPRAVERLETYKPAWPLPKIFRLTKGGKLNAGIFEGET 244 Query: 242 INTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIRS 301 INTPSML ED+L L W +S+GGLK LI R + N V + A+ WI FLA+ IRS Sbjct: 245 INTPSMLCVEDYLDALNWGKSIGGLKALIARADANTKVLADWKARTPWIDFLAQDPAIRS 304 Query: 302 STSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVE 351 +TSVC KV D E K+L+ +EKE +D YRDAP+GLRIWCGATVE Sbjct: 305 NTSVCLKVVDPAITALSADAQAEFAKKLVSLVEKENAGFDFAHYRDAPAGLRIWCGATVE 364 Query: 352 KEDLQCLCEWIEWAY 366 D+ L +WI+WA+ Sbjct: 365 ASDVALLTQWIDWAF 379 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: 496 Number of extensions: 15 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_012042058.1 BBTA_RS08495 (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.5850.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-214 698.5 2.5 1.2e-214 698.3 2.5 1.0 1 lcl|NCBI__GCF_000015165.1:WP_012042058.1 BBTA_RS08495 phosphoserine trans Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015165.1:WP_012042058.1 BBTA_RS08495 phosphoserine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 698.3 2.5 1.2e-214 1.2e-214 1 372 [. 9 380 .. 9 382 .. 1.00 Alignments for each domain: == domain 1 score: 698.3 bits; conditional E-value: 1.2e-214 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 rpa p+fssgpcakrpg++ e+lk+a+lgrshr+k+gk+klk+aie tr+vlevpady+igiv+asdtg lcl|NCBI__GCF_000015165.1:WP_012042058.1 9 RPAVPHFSSGPCAKRPGWTAENLKDAPLGRSHRAKIGKAKLKQAIELTRDVLEVPADYKIGIVPASDTG 77 79******************************************************************* PP TIGR01365 70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngt 138 avemalwsllgar+v +a+esfg+gwv+d++k+lklkdv +l+a+yg++pdl+k d++ d+vftwngt lcl|NCBI__GCF_000015165.1:WP_012042058.1 78 AVEMALWSLLGARPVTTIAWESFGEGWVSDIVKELKLKDVTKLHAGYGEIPDLSKADPATDIVFTWNGT 146 ********************************************************************* PP TIGR01365 139 tsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarle 207 tsgvrvpn+d+i+a reglticdatsaafaq ld+ kldvvtfswqk+lgge ahg+lilsprav+rle lcl|NCBI__GCF_000015165.1:WP_012042058.1 147 TSGVRVPNADWISASREGLTICDATSAAFAQALDWPKLDVVTFSWQKALGGEAAHGMLILSPRAVERLE 215 ********************************************************************* PP TIGR01365 208 sytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavle 276 +y+pawplpkifrltkggkl+ +ifegetintpsml+ved+ldal+w +sigglkal+arad+n +vl+ lcl|NCBI__GCF_000015165.1:WP_012042058.1 216 TYKPAWPLPKIFRLTKGGKLNAGIFEGETINTPSMLCVEDYLDALNWGKSIGGLKALIARADANTKVLA 284 ********************************************************************* PP TIGR01365 277 afvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapa 345 ++ a+++w+dfla+ ++irsntsvclkvvdp+++al +daqa+fak+lvs++eke++ +d yrdapa lcl|NCBI__GCF_000015165.1:WP_012042058.1 285 DWKARTPWIDFLAQDPAIRSNTSVCLKVVDPAITALSADAQAEFAKKLVSLVEKENAGFDFAHYRDAPA 353 ********************************************************************* PP TIGR01365 346 glriwcgatveksdleallewldwafa 372 glriwcgatve+sd+ l++w+dwafa lcl|NCBI__GCF_000015165.1:WP_012042058.1 354 GLRIWCGATVEASDVALLTQWIDWAFA 380 **************************8 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: 8.51 // [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