Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate CCNA_03323 CCNA_03323 phosphoserine aminotransferase
Query= metacyc::MONOMER-15918 (370 letters) >FitnessBrowser__Caulo:CCNA_03323 Length = 396 Score = 461 bits (1187), Expect = e-134 Identities = 230/383 (60%), Positives = 275/383 (71%), Gaps = 15/383 (3%) Query: 2 KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61 KP P P FSSGPCAK PG++ E L++ GRSHRSK GK +L AI +TR++L +P Sbjct: 7 KPAIRPARPEFSSGPCAKRPGWTPENLRNAVLGRSHRSKLGKARLKAAIDQTREVLEVPA 66 Query: 62 DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121 D+ +GIV SDTGA EM +WSMLG R V +L +ESF K W TD+TKQLKL D V A Y Sbjct: 67 DFLIGIVAGSDTGAVEMAMWSMLGARPVQLLAFESFGKDWVTDVTKQLKLPDVEVLSAPY 126 Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181 G+LPD KVD D+VF WNGTTSGV+VPNAD+I DREG+T+CDATSA FA D+ + KL Sbjct: 127 GQLPDTSKVDPAKDLVFTWNGTTSGVRVPNADFISADREGITICDATSAAFAQDLDWTKL 186 Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTK-----GGKLNKDI 236 DV+TFSWQK LGGEGAHG+LILSPRAV RLESYTPAWP+PK+FR+TK G K++ DI Sbjct: 187 DVVTFSWQKALGGEGAHGVLILSPRAVARLESYTPAWPMPKLFRMTKANKDGGNKVSLDI 246 Query: 237 FAGSTINTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAET 296 F G+TINTPSML ED L LKWA S+GGL+ + R ++NL V +VAK W+ FLA T Sbjct: 247 FEGATINTPSMLCVEDALDALKWASSIGGLQAMQARADQNLKVLADWVAKTPWVDFLAAT 306 Query: 297 KEIRSSTSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWC 346 EIRS+TSVC KV D + K+L LEKE A DIG YRDAP+GLRIWC Sbjct: 307 PEIRSNTSVCLKVVDPAICALPEDAQADFAKKLASLLEKEGAALDIGGYRDAPAGLRIWC 366 Query: 347 GATVEKEDLECLCEWIEWAYNLV 369 GATVE DLE L W++WA+ V Sbjct: 367 GATVEASDLEALTPWLDWAFATV 389 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: 494 Number of extensions: 17 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: 396 Length adjustment: 30 Effective length of query: 340 Effective length of database: 366 Effective search space: 124440 Effective search space used: 124440 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 CCNA_03323 CCNA_03323 (phosphoserine aminotransferase)
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.21315.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-234 763.8 1.5 1.7e-234 763.6 1.5 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_03323 CCNA_03323 phosphoserine aminotr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_03323 CCNA_03323 phosphoserine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 763.6 1.5 1.7e-234 1.7e-234 1 374 [] 11 389 .. 11 389 .. 1.00 Alignments for each domain: == domain 1 score: 763.6 bits; conditional E-value: 1.7e-234 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 rpa+pefssgpcakrpg+++e+l+na+lgrshrsklgk++lk+ai++trevlevpad+ligiva+sdtgavem lcl|FitnessBrowser__Caulo:CCNA_03323 11 RPARPEFSSGPCAKRPGWTPENLRNAVLGRSHRSKLGKARLKAAIDQTREVLEVPADFLIGIVAGSDTGAVEM 83 7************************************************************************ PP TIGR01365 74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146 a+ws+lgar+v+llafesfgk+wvtdvtkqlkl+dv+vl+a+yg+lpd++kvd++kd+vftwngttsgvrvpn lcl|FitnessBrowser__Caulo:CCNA_03323 84 AMWSMLGARPVQLLAFESFGKDWVTDVTKQLKLPDVEVLSAPYGQLPDTSKVDPAKDLVFTWNGTTSGVRVPN 156 ************************************************************************* PP TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219 +dfi+adreg+ticdatsaafaqdld++kldvvtfswqk+lggegahgvlilspravarlesytpawp+pk+f lcl|FitnessBrowser__Caulo:CCNA_03323 157 ADFISADREGITICDATSAAFAQDLDWTKLDVVTFSWQKALGGEGAHGVLILSPRAVARLESYTPAWPMPKLF 229 ************************************************************************* PP TIGR01365 220 rltk.....ggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdf 287 r+tk g+k+s difeg+tintpsml+vedaldalkwa+siggl+a++arad+nl+vl+++vak++wvdf lcl|FitnessBrowser__Caulo:CCNA_03323 230 RMTKankdgGNKVSLDIFEGATINTPSMLCVEDALDALKWASSIGGLQAMQARADQNLKVLADWVAKTPWVDF 302 ********99*************************************************************** PP TIGR01365 288 laatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdl 360 laat+eirsntsvclkvvdp+++al+edaqadfak+l+s+lekeg+a+dig+yrdapaglriwcgatve+sdl lcl|FitnessBrowser__Caulo:CCNA_03323 303 LAATPEIRSNTSVCLKVVDPAICALPEDAQADFAKKLASLLEKEGAALDIGGYRDAPAGLRIWCGATVEASDL 375 ************************************************************************* PP TIGR01365 361 eallewldwafalv 374 eal++wldwafa+v lcl|FitnessBrowser__Caulo:CCNA_03323 376 EALTPWLDWAFATV 389 ***********986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (374 nodes) Target sequences: 1 (396 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.90 // [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