Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_092991515.1 BLP65_RS00440 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_900102855.1:WP_092991515.1 Length = 357 Score = 402 bits (1034), Expect = e-117 Identities = 209/364 (57%), Positives = 262/364 (71%), Gaps = 9/364 (2%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 MA++FNFS+GPAMLP V+++A++E+ DW G G SVME+SHRGKEF+ +A +AE D R+L Sbjct: 1 MARVFNFSAGPAMLPQVVIERAREEMLDWQGSGMSVMEMSHRGKEFMSIAAKAEADLREL 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNV-F 119 + +PSNYKVLF GG QFA VP+N+L K ADY++ G W+ AI EAK+Y N+ Sbjct: 61 MGIPSNYKVLFLQGGASSQFAMVPMNLLPGKGRADYINTGSWSKKAIAEAKRYGQVNLAA 120 Query: 120 DAKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTI 179 + +T A+ QLS +AAY+HY PNETI G+ P+ G D+ + AD SSTI Sbjct: 121 ETSMTCPAQDAL------QLSADAAYVHYTPNETIQGVEFPYVPETG-DIPLVADMSSTI 173 Query: 180 LSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFN 239 LSRPIDVSR+GVIYAGAQKNIGPAGLT+VIVREDL+G+ PS+ Y D SM+N Sbjct: 174 LSRPIDVSRFGVIYAGAQKNIGPAGLTVVIVREDLIGECLEGTPSMFQYKTHVDADSMYN 233 Query: 240 TPPTFAWYLSGLVFKWLKAN-GGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRM 298 TPPT+AWYLSGLVF WLK + GG+ +M +IN++KA+ LY +D S FY N V + RS M Sbjct: 234 TPPTYAWYLSGLVFDWLKNDIGGLDKMAEINERKAKKLYDAVDGSGFYANPVEPSCRSWM 293 Query: 299 NVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFE 358 NVPF LA++ LD FLEE+ L LKGHR VGGMRASIYNAMP EGV AL FM +FE Sbjct: 294 NVPFTLANADLDATFLEEAGKQRLTTLKGHRSVGGMRASIYNAMPEEGVDALVAFMADFE 353 Query: 359 RRHG 362 +RHG Sbjct: 354 KRHG 357 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: 12 Number of successful extensions: 4 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: 357 Length adjustment: 29 Effective length of query: 333 Effective length of database: 328 Effective search space: 109224 Effective search space used: 109224 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_092991515.1 BLP65_RS00440 (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.25047.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-161 522.3 0.0 3.1e-161 522.2 0.0 1.0 1 lcl|NCBI__GCF_900102855.1:WP_092991515.1 BLP65_RS00440 3-phosphoserine/ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900102855.1:WP_092991515.1 BLP65_RS00440 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 522.2 0.0 3.1e-161 3.1e-161 1 358 [] 4 356 .. 4 356 .. 0.98 Alignments for each domain: == domain 1 score: 522.2 bits; conditional E-value: 3.1e-161 TIGR01364 1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 ++nFsaGPa+lp+ v+e+a++e+ld++g+g+svme+sHR kef++++ +ae dlreL+ ip+ny+vlfl lcl|NCBI__GCF_900102855.1:WP_092991515.1 4 VFNFSAGPAMLPQVVIERAREEMLDWQGSGMSVMEMSHRGKEFMSIAAKAEADLRELMGIPSNYKVLFL 72 58******************************************************************* PP TIGR01364 70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelke 138 qGGa++qfa+vp+nll k adyi+tG+wskka++eak++++ v+ +a++ + p ++ l+l+ lcl|NCBI__GCF_900102855.1:WP_092991515.1 73 QGGASSQFAMVPMNLLPGKGRADYINTGSWSKKAIAEAKRYGQ-VNLAAET----SMTCPAQDALQLSA 136 *****************************************99.8888877....4789********** PP TIGR01364 139 daayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivr 207 daayv+++ neti+Gvef +pe+ ++plvaD+ss ilsr+idvs++g+iyaGaqKniGpaG+tvvivr lcl|NCBI__GCF_900102855.1:WP_092991515.1 137 DAAYVHYTPNETIQGVEFPYVPETGDIPLVADMSSTILSRPIDVSRFGVIYAGAQKNIGPAGLTVVIVR 205 ********************************************************************* PP TIGR01364 208 kdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkek.GGvkklekknqeKakllYea 275 +dl++++ + +ps+++Yk++++ ds+yntppt+a+y++glv++wlk+ GG++k+++ n++Kak lY+a lcl|NCBI__GCF_900102855.1:WP_092991515.1 206 EDLIGECLEGTPSMFQYKTHVDADSMYNTPPTYAWYLSGLVFDWLKNDiGGLDKMAEINERKAKKLYDA 274 *********************************************9855******************** PP TIGR01364 276 idesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleev 344 +d s gfy n+ve+++Rs+mnv+Ftl++++l+++Fl+ea +++l++lkGhrsvGG+RasiYna+p e+v lcl|NCBI__GCF_900102855.1:WP_092991515.1 275 VDGS-GFYANPVEPSCRSWMNVPFTLANADLDATFLEEAGKQRLTTLKGHRSVGGMRASIYNAMPEEGV 342 **99.6*************************************************************** PP TIGR01364 345 qaLvdfmkeFekkh 358 aLv+fm +Fek+h lcl|NCBI__GCF_900102855.1:WP_092991515.1 343 DALVAFMADFEKRH 356 ***********997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (357 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: 6.54 // [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