Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate Ga0059261_2265 Ga0059261_2265 phosphoserine aminotransferase apoenzyme (EC 2.6.1.52)
Query= metacyc::MONOMER-15918 (370 letters) >FitnessBrowser__Korea:Ga0059261_2265 Length = 378 Score = 457 bits (1177), Expect = e-133 Identities = 220/369 (59%), Positives = 267/369 (72%), Gaps = 2/369 (0%) Query: 3 PTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPDD 62 P P P FSSGPCAK PG+S ++L GRSHRSK GK +L AI R+ML LPD Sbjct: 8 PATKPARPYFSSGPCAKPPGWSADKLHTEVLGRSHRSKLGKTRLQYAIDLMREMLKLPDT 67 Query: 63 YFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEYG 122 + +GIVP SDTGAFEM +W+MLG RGV L WESF +GW TD KQLKL D V A+YG Sbjct: 68 HRIGIVPGSDTGAFEMAMWTMLGARGVTTLAWESFGEGWVTDAVKQLKL-DPTVIRADYG 126 Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKLD 182 +LPDL +VDF +DV+F WNGTTSGV+VPN DWIPDDREG+T D+TSA+FA D+P+ K+D Sbjct: 127 QLPDLSQVDFADDVLFTWNGTTSGVRVPNGDWIPDDREGLTFADSTSAVFAYDLPWDKID 186 Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGSTI 242 V TFSWQKVLGGEG HG+LIL PRAV+RLE YTPAWPLPK+FRL GKL + +F G TI Sbjct: 187 VATFSWQKVLGGEGGHGVLILGPRAVERLEQYTPAWPLPKVFRLMAKGKLAEGVFKGETI 246 Query: 243 NTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRSS 302 NTPSMLA ED + L+WA+ +GGL LI R++ N A + VA+ +W+ LA + RS Sbjct: 247 NTPSMLAVEDAIFALEWAKGLGGLDGLIARSDANAAALDKIVAERDWLGHLAADEATRSK 306 Query: 303 TSVCFKVDLSDEK-LKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLECLCEW 361 TSVC V+ +DE +K LEK AYD+ YRDAP+GLRIWCGATV+ D+E L W Sbjct: 307 TSVCLTVEGADEAFIKTFASLLEKADAAYDVAGYRDAPAGLRIWCGATVDTADIEALGPW 366 Query: 362 IEWAYNLVK 370 ++WAY K Sbjct: 367 LDWAYASAK 375 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: 503 Number of extensions: 20 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: 378 Length adjustment: 30 Effective length of query: 340 Effective length of database: 348 Effective search space: 118320 Effective search space used: 118320 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 Ga0059261_2265 Ga0059261_2265 (phosphoserine aminotransferase apoenzyme (EC 2.6.1.52))
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.14279.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-183 593.5 0.5 1e-182 593.2 0.5 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_2265 Ga0059261_2265 phosphoserine ami Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_2265 Ga0059261_2265 phosphoserine aminotransferase apoenzyme (EC 2.6.1.52) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 593.2 0.5 1e-182 1e-182 1 373 [. 11 373 .. 11 374 .. 0.98 Alignments for each domain: == domain 1 score: 593.2 bits; conditional E-value: 1e-182 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 +pa+p fssgpcak pg+s ++l+ +lgrshrsklgk++l+ ai+ re+l++p+ ++igiv++sdtg lcl|FitnessBrowser__Korea:Ga0059261_2265 11 KPARPYFSSGPCAKPPGWSADKLHTEVLGRSHRSKLGKTRLQYAIDLMREMLKLPDTHRIGIVPGSDTG 79 69******************************************************************* PP TIGR01365 70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngt 138 a+ema+w++lgargv la+esfg+gwvtd +kqlkl d v+ a+yg+lpdl++vdf+ dv+ftwngt lcl|FitnessBrowser__Korea:Ga0059261_2265 80 AFEMAMWTMLGARGVTTLAWESFGEGWVTDAVKQLKL-DPTVIRADYGQLPDLSQVDFADDVLFTWNGT 147 ************************************9.6789*************************** PP TIGR01365 139 tsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarle 207 tsgvrvpngd+ip+dreglt+ d+tsa+fa dl+++k+dv tfswqkvlggeg hgvlil prav+rle lcl|FitnessBrowser__Korea:Ga0059261_2265 148 TSGVRVPNGDWIPDDREGLTFADSTSAVFAYDLPWDKIDVATFSWQKVLGGEGGHGVLILGPRAVERLE 216 ********************************************************************* PP TIGR01365 208 sytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavle 276 ytpawplpk+frl gkl++++f+getintpsmlaveda+ al+wa+ +ggl+ l+ar+d+n+a l+ lcl|FitnessBrowser__Korea:Ga0059261_2265 217 QYTPAWPLPKVFRLMAKGKLAEGVFKGETINTPSMLAVEDAIFALEWAKGLGGLDGLIARSDANAAALD 285 ********************************************************************* PP TIGR01365 277 afvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapa 345 + va +w+++laa +++rs+tsvcl v e a+ f+k ++s+lek ++ayd+ +yrdapa lcl|FitnessBrowser__Korea:Ga0059261_2265 286 KIVAERDWLGHLAADEATRSKTSVCLTV---------EGADEAFIKTFASLLEKADAAYDVAGYRDAPA 345 ***************************9.........444456************************** PP TIGR01365 346 glriwcgatveksdleallewldwafal 373 glriwcgatv++ d+eal +wldwa+a lcl|FitnessBrowser__Korea:Ga0059261_2265 346 GLRIWCGATVDTADIEALGPWLDWAYAS 373 **************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (374 nodes) Target sequences: 1 (378 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: 8.07 // [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