Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate SMc00640 SMc00640 phosphoserine aminotransferase
Query= metacyc::MONOMER-15918 (370 letters) >FitnessBrowser__Smeli:SMc00640 Length = 392 Score = 484 bits (1247), Expect = e-141 Identities = 237/379 (62%), Positives = 280/379 (73%), Gaps = 10/379 (2%) Query: 2 KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61 KP P N FSSGPCAK PG+++E L D P GRSHR+K GK KL +AI TR++L +P Sbjct: 6 KPAMRPANTHFSSGPCAKRPGWTLEALSDAPLGRSHRAKIGKTKLKQAIDLTREILEVPA 65 Query: 62 DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121 DY +GIVPASDTGA EM LWS+LG RGVD+L WESF GW TD+ KQLKL D R EA+Y Sbjct: 66 DYRIGIVPASDTGAVEMALWSLLGARGVDMLAWESFGAGWVTDVVKQLKLSDVRRLEADY 125 Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181 G+LPDL KVDF DVVF WNGTTSGV+VPNAD+IP DR+G+T+CDATSA FA + + KL Sbjct: 126 GELPDLSKVDFDRDVVFTWNGTTSGVRVPNADFIPADRKGLTICDATSAAFAQALDFAKL 185 Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGST 241 DV+TFSWQKVLGGEGAHG+LILSPRAV+RLE+Y PAWPLPKIFR+TKGGKL + IF G T Sbjct: 186 DVVTFSWQKVLGGEGAHGVLILSPRAVERLETYVPAWPLPKIFRMTKGGKLIEGIFTGET 245 Query: 242 INTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRS 301 INTPSML ED++ L WA+SVGGL+ L+ R + N V FVA N+WI LA E RS Sbjct: 246 INTPSMLCVEDYIDALLWAKSVGGLEGLMARADANAEVIHRFVAANDWIANLAVKPETRS 305 Query: 302 STSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVE 351 +TSVC K+ D K ++ LEKE VA+DIG YRDAPSGLRIW GAT+E Sbjct: 306 NTSVCLKIADNDVSALDADAQAAFAKGVVALLEKEGVAFDIGHYRDAPSGLRIWAGATIE 365 Query: 352 KEDLECLCEWIEWAYNLVK 370 D+E L W+ WA+ K Sbjct: 366 TSDMEALMPWLAWAFETQK 384 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: 491 Number of extensions: 19 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: 392 Length adjustment: 30 Effective length of query: 340 Effective length of database: 362 Effective search space: 123080 Effective search space used: 123080 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 SMc00640 SMc00640 (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.7591.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-219 713.2 1.1 4.3e-219 713.0 1.1 1.0 1 lcl|FitnessBrowser__Smeli:SMc00640 SMc00640 phosphoserine aminotran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc00640 SMc00640 phosphoserine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 713.0 1.1 4.3e-219 4.3e-219 1 373 [. 10 382 .. 10 383 .. 1.00 Alignments for each domain: == domain 1 score: 713.0 bits; conditional E-value: 4.3e-219 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavemal 75 rpan +fssgpcakrpg+++e+l +a+lgrshr+k+gk+klk+ai+ tre+levpady+igiv+asdtgavemal lcl|FitnessBrowser__Smeli:SMc00640 10 RPANTHFSSGPCAKRPGWTLEALSDAPLGRSHRAKIGKTKLKQAIDLTREILEVPADYRIGIVPASDTGAVEMAL 84 79************************************************************************* PP TIGR01365 76 wsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpngdfi 150 wsllgargvd+la+esfg gwvtdv+kqlkl dvr+lea+yg+lpdl+kvdf++dvvftwngttsgvrvpn+dfi lcl|FitnessBrowser__Smeli:SMc00640 85 WSLLGARGVDMLAWESFGAGWVTDVVKQLKLSDVRRLEADYGELPDLSKVDFDRDVVFTWNGTTSGVRVPNADFI 159 *************************************************************************** PP TIGR01365 151 padreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkifrltkgg 225 padr+glticdatsaafaq ld+ kldvvtfswqkvlggegahgvlilsprav+rle+y pawplpkifr+tkgg lcl|FitnessBrowser__Smeli:SMc00640 160 PADRKGLTICDATSAAFAQALDFAKLDVVTFSWQKVLGGEGAHGVLILSPRAVERLETYVPAWPLPKIFRMTKGG 234 *************************************************************************** PP TIGR01365 226 klskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatkeirsntsv 300 kl+++if getintpsml+ved++dal wa+s+ggl+ l+arad+n++v++ fva ++w+ la+++e+rsntsv lcl|FitnessBrowser__Smeli:SMc00640 235 KLIEGIFTGETINTPSMLCVEDYIDALLWAKSVGGLEGLMARADANAEVIHRFVAANDWIANLAVKPETRSNTSV 309 *************************************************************************** PP TIGR01365 301 clkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdleallewldwafal 373 clk++d dv+ald+daqa fak++v +lekegva+dig yrdap+glriw gat+e+sd+eal++wl waf++ lcl|FitnessBrowser__Smeli:SMc00640 310 CLKIADNDVSALDADAQAAFAKGVVALLEKEGVAFDIGHYRDAPSGLRIWAGATIETSDMEALMPWLAWAFET 382 ***********************************************************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (374 nodes) Target sequences: 1 (392 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.88 // [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