Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_019556287.1 F612_RS0103100 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_000381085.1:WP_019556287.1 Length = 364 Score = 377 bits (969), Expect = e-109 Identities = 189/364 (51%), Positives = 245/364 (67%), Gaps = 4/364 (1%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 MA+ FNFS+GPAMLP V+++A E DWN G SVME+SHR KE++ VA + E D R++ Sbjct: 1 MARAFNFSAGPAMLPEAVMRKASAEFLDWNHAGMSVMEMSHRSKEYMSVAHKIEADLREV 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 + +P NYKVLF HGG QF+A+PLN+ + T DY + G W+ AIKEA +Y N+ Sbjct: 61 MAIPDNYKVLFLHGGASMQFSAIPLNLTQEGDTVDYFNTGVWSDKAIKEASRYVNVNIVT 120 Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETP---DFGADVVVAADFSS 177 D + + EW SD+A Y+H C NETI G+ E F V AD SS Sbjct: 121 GG-EADNPTEIPDVAEWSFSDDAKYIHLCTNETITGLEFQEDQLEHVFAQGKPVIADMSS 179 Query: 178 TILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSM 237 I+ RPIDVSRY +IYAGAQKNIGPAGL+I+I+R+DL+G A P++L+++ +N SM Sbjct: 180 NIMCRPIDVSRYAIIYAGAQKNIGPAGLSIMIIRDDLVGHAREITPTLLNWATYANNESM 239 Query: 238 FNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSR 297 FNTP T+AWYL+GLVF+WLKANGGV + +NQ+KA+ LY IDNS FY N + RS Sbjct: 240 FNTPATYAWYLAGLVFEWLKANGGVEAIASVNQRKAQKLYDYIDNSPFYYNTIKPTQRSW 299 Query: 298 MNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEF 357 MNV F L ++ L+ F++ S AAGL +LKGH+ GGMRASIYNAMP EGV L FM +F Sbjct: 300 MNVTFYLTNNELESEFVQASKAAGLLSLKGHKAFGGMRASIYNAMPEEGVDTLIAFMEQF 359 Query: 358 ERRH 361 + H Sbjct: 360 AKTH 363 Lambda K H 0.319 0.136 0.405 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: 393 Number of extensions: 16 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: 362 Length of database: 364 Length adjustment: 29 Effective length of query: 333 Effective length of database: 335 Effective search space: 111555 Effective search space used: 111555 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_019556287.1 F612_RS0103100 (3-phosphoserine/phosphohydroxythreonine transaminase)
to HMM TIGR01364 (serC: phosphoserine transaminase (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/TIGR01364.hmm # target sequence database: /tmp/gapView.10032.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01364 [M=358] Accession: TIGR01364 Description: serC_1: phosphoserine transaminase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-156 504.6 0.1 7.7e-156 504.4 0.1 1.0 1 lcl|NCBI__GCF_000381085.1:WP_019556287.1 F612_RS0103100 3-phosphoserine/p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000381085.1:WP_019556287.1 F612_RS0103100 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 504.4 0.1 7.7e-156 7.7e-156 2 358 .] 5 363 .. 4 363 .. 0.98 Alignments for each domain: == domain 1 score: 504.4 bits; conditional E-value: 7.7e-156 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 +nFsaGPa+lpe+v++ka +e+ld+n+ g+svme+sHRske+++v+++ e dlre++ ipdny+vlfl lcl|NCBI__GCF_000381085.1:WP_019556287.1 5 FNFSAGPAMLPEAVMRKASAEFLDWNHAGMSVMEMSHRSKEYMSVAHKIEADLREVMAIPDNYKVLFLH 73 8******************************************************************** PP TIGR01364 71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139 GGa+ qf+a+plnl++e++++dy +tG+ws+ka+kea+++++ v++v+ e ++ ++ipd e+++++d lcl|NCBI__GCF_000381085.1:WP_019556287.1 74 GGASMQFSAIPLNLTQEGDTVDYFNTGVWSDKAIKEASRYVN-VNIVTGGEADNPTEIPDVAEWSFSDD 141 ****************************************99.************************** PP TIGR01364 140 aayvylcanetieGvefkelpevkk....aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvv 204 a+y++lc+neti+G+ef+e + +p++aD+ss+i+ r+idvs+y++iyaGaqKniGpaG++++ lcl|NCBI__GCF_000381085.1:WP_019556287.1 142 AKYIHLCTNETITGLEFQEDQLEHVfaqgKPVIADMSSNIMCRPIDVSRYAIIYAGAQKNIGPAGLSIM 210 ******************765444345679*************************************** PP TIGR01364 205 ivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllY 273 i+r+dl+++a++++p++l++++ a+n+s++ntp+t+a+y++glv++wlk++GGv++++ nq+Ka+ lY lcl|NCBI__GCF_000381085.1:WP_019556287.1 211 IIRDDLVGHAREITPTLLNWATYANNESMFNTPATYAWYLAGLVFEWLKANGGVEAIASVNQRKAQKLY 279 ********************************************************************* PP TIGR01364 274 eaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalple 342 ++id+s fy n++++++Rs+mnv+F l+++ele+eF++ ++++gl+slkGh++ GG+RasiYna+p e lcl|NCBI__GCF_000381085.1:WP_019556287.1 280 DYIDNSP-FYYNTIKPTQRSWMNVTFYLTNNELESEFVQASKAAGLLSLKGHKAFGGMRASIYNAMPEE 347 ****997.************************************************************* PP TIGR01364 343 evqaLvdfmkeFekkh 358 +v +L++fm++F+k+h lcl|NCBI__GCF_000381085.1:WP_019556287.1 348 GVDTLIAFMEQFAKTH 363 *************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (364 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: 7.89 // [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