Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_024851080.1 N745_RS0105245 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_000526715.1:WP_024851080.1 Length = 354 Score = 392 bits (1007), Expect = e-114 Identities = 194/357 (54%), Positives = 251/357 (70%), Gaps = 7/357 (1%) Query: 5 FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64 FNFS+GPAM+P EV+++AQ E DW G SVMEVSHR KEF+ +A + E+D RD++++P Sbjct: 4 FNFSAGPAMMPEEVMRKAQAEFLDWQNTGMSVMEVSHRSKEFMALAHKTERDLRDIMHIP 63 Query: 65 SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124 NYKVLF HGG QFA++P+N+ + T DYV+ G W+ AIKEA +Y NV T Sbjct: 64 DNYKVLFVHGGASLQFASIPMNLSNENDTVDYVNTGVWSTKAIKEASRYVNVNVVSTSET 123 Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184 ++ E S +A Y+H C NETI G+ P D ++ +DFSSTILSRPI Sbjct: 124 -----SIPDYAEMNFSPDAKYIHICQNETITGVEFQNLPK--TDKIIVSDFSSTILSRPI 176 Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244 V YGVIYAGAQKNIGPAGL IVIVREDL+G A P+++++ NDN SMFNTP T+ Sbjct: 177 RVEDYGVIYAGAQKNIGPAGLAIVIVREDLIGHARPDTPTLMNWQTYNDNESMFNTPSTY 236 Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304 AWYL+ LVF+W+K GGV ++ +IN++KA LY +ID SDFY N++ + RS MNV F+L Sbjct: 237 AWYLASLVFEWIKEKGGVEKIAEINKRKASKLYDLIDASDFYYNEIEPSVRSWMNVTFKL 296 Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRH 361 ++ LD FLEES AAGL +LKGH+V GGMRASIYNAMP EG+ AL FM FE+++ Sbjct: 297 KNTDLDAAFLEESKAAGLLSLKGHKVYGGMRASIYNAMPEEGIDALVAFMKAFEQKY 353 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: 396 Number of extensions: 10 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: 354 Length adjustment: 29 Effective length of query: 333 Effective length of database: 325 Effective search space: 108225 Effective search space used: 108225 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_024851080.1 N745_RS0105245 (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.8707.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-157 509.8 0.3 2e-157 509.6 0.3 1.0 1 lcl|NCBI__GCF_000526715.1:WP_024851080.1 N745_RS0105245 3-phosphoserine/p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000526715.1:WP_024851080.1 N745_RS0105245 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 509.6 0.3 2e-157 2e-157 2 358 .] 4 353 .. 3 353 .. 0.98 Alignments for each domain: == domain 1 score: 509.6 bits; conditional E-value: 2e-157 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 +nFsaGPa++peev++kaq+e+ld++++g+svme+sHRskef+++++++e+dlr++++ipdny+vlf+ lcl|NCBI__GCF_000526715.1:WP_024851080.1 4 FNFSAGPAMMPEEVMRKAQAEFLDWQNTGMSVMEVSHRSKEFMALAHKTERDLRDIMHIPDNYKVLFVH 72 8******************************************************************** PP TIGR01364 71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139 GGa+ qfa++p+nl +e++++dy++tG+ws+ka+kea+++++ v+vv+++e ++ipd e+++++d lcl|NCBI__GCF_000526715.1:WP_024851080.1 73 GGASLQFASIPMNLSNENDTVDYVNTGVWSTKAIKEASRYVN-VNVVSTSE----TSIPDYAEMNFSPD 136 ****************************************98.99888875....78************ PP TIGR01364 140 aayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrk 208 a+y+++c+neti+Gvef++lp ++++++v+D+ss ilsr+i v++yg+iyaGaqKniGpaG+++vivr+ lcl|NCBI__GCF_000526715.1:WP_024851080.1 137 AKYIHICQNETITGVEFQNLP-KTDKIIVSDFSSTILSRPIRVEDYGVIYAGAQKNIGPAGLAIVIVRE 204 *********************.678899***************************************** PP TIGR01364 209 dllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaid 277 dl+++a+ ++p+++++++ +n+s++ntp+t+a+y+++lv++w+kekGGv+k+++ n++Ka+ lY++id lcl|NCBI__GCF_000526715.1:WP_024851080.1 205 DLIGHARPDTPTLMNWQTYNDNESMFNTPSTYAWYLASLVFEWIKEKGGVEKIAEINKRKASKLYDLID 273 ********************************************************************* PP TIGR01364 278 esegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqa 346 +s+ fy n++e++ Rs+mnv+F+lk+++l++ Fl+e++++gl+slkGh++ GG+RasiYna+p e++ a lcl|NCBI__GCF_000526715.1:WP_024851080.1 274 ASD-FYYNEIEPSVRSWMNVTFKLKNTDLDAAFLEESKAAGLLSLKGHKVYGGMRASIYNAMPEEGIDA 341 996.***************************************************************** PP TIGR01364 347 LvdfmkeFekkh 358 Lv+fmk Fe+k+ lcl|NCBI__GCF_000526715.1:WP_024851080.1 342 LVAFMKAFEQKY 353 *********997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (354 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: 6.93 // [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