Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_018945974.1 B1A74_RS01035 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_001995255.1:WP_018945974.1 Length = 360 Score = 407 bits (1046), Expect = e-118 Identities = 204/361 (56%), Positives = 262/361 (72%), Gaps = 2/361 (0%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 M++I+NFS+GPA LP VL++A+ E+ D++G G SVME+SHRGK F++VAE+AE D R L Sbjct: 1 MSRIWNFSAGPAALPQAVLERARDEMLDFHGTGMSVMEMSHRGKPFMEVAEKAEADLRKL 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 + +P +Y VLF GG GQF+A+P+N+ DY+D G W+ AIKEA+K N+ Sbjct: 61 MGIPDDYAVLFLQGGATGQFSAIPMNLQPGGQPMDYIDTGAWSGKAIKEAQKVGPVNIV- 119 Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180 A +G ++ W+L NAAY+HY PNETI G+ E PD G D + AD SSTIL Sbjct: 120 ASSQAEGYASIPERSTWKLDPNAAYVHYTPNETIGGVEFHEVPDVG-DKPLVADMSSTIL 178 Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240 SRPIDVS++GVIYAGAQKNIGPAG+T+VIVR+DLL + P++LD+ + DN SM+NT Sbjct: 179 SRPIDVSKFGVIYAGAQKNIGPAGVTVVIVRKDLLEREKGQVPAVLDWKLQADNDSMYNT 238 Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNV 300 PPTF WY +GLVF+WL GG+ +M +INQ+KA+ LY IDNS FYRN V + RS MNV Sbjct: 239 PPTFGWYFAGLVFEWLLEQGGLEKMAEINQRKADKLYRFIDNSAFYRNPVEPSARSWMNV 298 Query: 301 PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360 PF LAD +LD FL+E+ AAGL +LKGHR VGGMRASIYNA+P E V AL +FM +FE R Sbjct: 299 PFILADDSLDGPFLKEADAAGLSSLKGHRSVGGMRASIYNAVPEEAVDALIEFMADFEER 358 Query: 361 H 361 H Sbjct: 359 H 359 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: 431 Number of extensions: 15 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: 360 Length adjustment: 29 Effective length of query: 333 Effective length of database: 331 Effective search space: 110223 Effective search space used: 110223 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_018945974.1 B1A74_RS01035 (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.12827.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-165 534.5 0.0 6e-165 534.4 0.0 1.0 1 lcl|NCBI__GCF_001995255.1:WP_018945974.1 B1A74_RS01035 3-phosphoserine/ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001995255.1:WP_018945974.1 B1A74_RS01035 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 534.4 0.0 6e-165 6e-165 2 358 .] 5 359 .. 4 359 .. 0.99 Alignments for each domain: == domain 1 score: 534.4 bits; conditional E-value: 6e-165 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 nFsaGPaalp++vle+a++e+ldf+g+g+svme+sHR k f++v+e+ae dlr+L+ ipd+y+vlflq lcl|NCBI__GCF_001995255.1:WP_018945974.1 5 WNFSAGPAALPQAVLERARDEMLDFHGTGMSVMEMSHRGKPFMEVAEKAEADLRKLMGIPDDYAVLFLQ 73 7******************************************************************** PP TIGR01364 71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139 GGat+qf+a+p+nl ++ dyi tGaws ka+kea+k++ v++vas++ + y +ip++++++l+++ lcl|NCBI__GCF_001995255.1:WP_018945974.1 74 GGATGQFSAIPMNLQPGGQPMDYIDTGAWSGKAIKEAQKVGP-VNIVASSQAEGYASIPERSTWKLDPN 141 ****************************************99.************************** PP TIGR01364 140 aayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrk 208 aayv+++ neti Gvef+e+p+v ++plvaD+ss ilsr+idvsk+g+iyaGaqKniGpaGvtvvivrk lcl|NCBI__GCF_001995255.1:WP_018945974.1 142 AAYVHYTPNETIGGVEFHEVPDVGDKPLVADMSSTILSRPIDVSKFGVIYAGAQKNIGPAGVTVVIVRK 210 ********************************************************************* PP TIGR01364 209 dllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaid 277 dller+k ++p vld+k +a+nds+yntpptf++y +glv++wl+e+GG++k+++ nq+Ka+ lY id lcl|NCBI__GCF_001995255.1:WP_018945974.1 211 DLLEREKGQVPAVLDWKLQADNDSMYNTPPTFGWYFAGLVFEWLLEQGGLEKMAEINQRKADKLYRFID 279 ********************************************************************* PP TIGR01364 278 esegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqa 346 +s fy+n+ve++aRs+mnv+F l+++ l+ Flkea ++gl slkGhrsvGG+RasiYna+p e+v a lcl|NCBI__GCF_001995255.1:WP_018945974.1 280 NSA-FYRNPVEPSARSWMNVPFILADDSLDGPFLKEADAAGLSSLKGHRSVGGMRASIYNAVPEEAVDA 347 995.***************************************************************** PP TIGR01364 347 LvdfmkeFekkh 358 L++fm +Fe++h lcl|NCBI__GCF_001995255.1:WP_018945974.1 348 LIEFMADFEERH 359 *********987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (360 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.41 // [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