Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_026605825.1 METAC_RS0102515 phosphoserine transaminase
Query= metacyc::MONOMER-15918 (370 letters) >NCBI__GCF_000427445.1:WP_026605825.1 Length = 390 Score = 456 bits (1173), Expect = e-133 Identities = 216/378 (57%), Positives = 272/378 (71%), Gaps = 10/378 (2%) Query: 3 PTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPDD 62 P P P FS GPC KHPG+ ++ L+ GRSHRSK GK KL AI TR++L +P D Sbjct: 6 PAARPATPNFSCGPCTKHPGWKIQNLQGPTVGRSHRSKVGKAKLKLAIDLTREILQVPPD 65 Query: 63 YFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEYG 122 + + IVP SDTGA E+ LWSMLG RGV+V+ WESFS+GW D+ + L++K+ R A+YG Sbjct: 66 HRIAIVPGSDTGAVELALWSMLGQRGVEVIAWESFSEGWVIDVVEHLQIKNARAQVADYG 125 Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKLD 182 ++ DL +DF NDVVF WNGTTSGV+VPNADWIP DR+G+T+CDATSA FA + + KLD Sbjct: 126 EIVDLASLDFDNDVVFAWNGTTSGVRVPNADWIPADRKGLTICDATSAAFAQRLDWAKLD 185 Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGSTI 242 V+TFSWQKVLGGE AHGMLIL PRAV+RL SYTPAWPLPK+FRLT+GGKL + IF G TI Sbjct: 186 VVTFSWQKVLGGEAAHGMLILGPRAVERLTSYTPAWPLPKLFRLTEGGKLIESIFEGETI 245 Query: 243 NTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRSS 302 NTPSML ED++ L WA+S+GGL+ L+ R + N +V + WI FLA+ +RS+ Sbjct: 246 NTPSMLCVEDYIDALSWAKSIGGLEALMARADANSKALSEWVVRTPWIDFLAKDPTVRSN 305 Query: 303 TSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEK 352 TS+C K+ E K ++ LE EK+AYDIG+YRDAP GLRIWCGATVE Sbjct: 306 TSICLKIVDPLILAHGLKAEAEFAKSIVDMLEAEKIAYDIGAYRDAPPGLRIWCGATVET 365 Query: 353 EDLECLCEWIEWAYNLVK 370 D+E L W+++AY +K Sbjct: 366 SDIEALTLWLDYAYQKLK 383 Lambda K H 0.319 0.136 0.430 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: 485 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_026605825.1 METAC_RS0102515 (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.19524.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-200 650.7 0.6 4.2e-200 650.5 0.6 1.0 1 lcl|NCBI__GCF_000427445.1:WP_026605825.1 METAC_RS0102515 phosphoserine tr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026605825.1 METAC_RS0102515 phosphoserine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 650.5 0.6 4.2e-200 4.2e-200 1 372 [. 9 380 .. 9 382 .. 1.00 Alignments for each domain: == domain 1 score: 650.5 bits; conditional E-value: 4.2e-200 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 rpa p+fs gpc+k+pg+ +++l+ ++grshrsk+gk+klk ai+ tre+l+vp d++i iv++sdtg lcl|NCBI__GCF_000427445.1:WP_026605825.1 9 RPATPNFSCGPCTKHPGWKIQNLQGPTVGRSHRSKVGKAKLKLAIDLTREILQVPPDHRIAIVPGSDTG 77 79******************************************************************* PP TIGR01365 70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngt 138 ave+alws+lg+rgv+++a+esf++gwv dv+ l++k+ r a+yg++ dl+ +df++dvvf+wngt lcl|NCBI__GCF_000427445.1:WP_026605825.1 78 AVELALWSMLGQRGVEVIAWESFSEGWVIDVVEHLQIKNARAQVADYGEIVDLASLDFDNDVVFAWNGT 146 ********************************************************************* PP TIGR01365 139 tsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarle 207 tsgvrvpn+d+ipadr+glticdatsaafaq+ld+ kldvvtfswqkvlgge ahg+lil prav+rl lcl|NCBI__GCF_000427445.1:WP_026605825.1 147 TSGVRVPNADWIPADRKGLTICDATSAAFAQRLDWAKLDVVTFSWQKVLGGEAAHGMLILGPRAVERLT 215 ********************************************************************* PP TIGR01365 208 sytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavle 276 sytpawplpk+frlt+ggkl+++ifegetintpsml+ved++dal wa+siggl+al+arad+n + l+ lcl|NCBI__GCF_000427445.1:WP_026605825.1 216 SYTPAWPLPKLFRLTEGGKLIESIFEGETINTPSMLCVEDYIDALSWAKSIGGLEALMARADANSKALS 284 ********************************************************************* PP TIGR01365 277 afvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapa 345 ++v +++w+dfla+ + +rsnts+clk+vdp + a +a+a+fak +v++le e++aydig+yrdap+ lcl|NCBI__GCF_000427445.1:WP_026605825.1 285 EWVVRTPWIDFLAKDPTVRSNTSICLKIVDPLILAHGLKAEAEFAKSIVDMLEAEKIAYDIGAYRDAPP 353 ********************************************************************* PP TIGR01365 346 glriwcgatveksdleallewldwafa 372 glriwcgatve+sd+eal+ wld+a++ lcl|NCBI__GCF_000427445.1:WP_026605825.1 354 GLRIWCGATVETSDIEALTLWLDYAYQ 380 *************************97 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.04 // [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