Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_011764801.1 AZO_RS05410 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_000061505.1:WP_011764801.1 Length = 365 Score = 399 bits (1026), Expect = e-116 Identities = 200/366 (54%), Positives = 259/366 (70%), Gaps = 5/366 (1%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 M +++NF++GPA LPAEVL+QA +E+ DW G G VME+SHR KEF+ +AE+AE D R+L Sbjct: 1 MTRVWNFAAGPAALPAEVLQQAAEEMLDWRGAGVGVMEMSHRSKEFVSIAEQAEADLREL 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 + +P+NY+VLF GG + A +P+N++G++ ADYV G W+ + KEA+KY N+ Sbjct: 61 MAIPANYRVLFMQGGAIAENAIIPMNLMGEEKRADYVVTGSWSVKSQKEARKYGEVNIA- 119 Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFG----ADVVVAADFS 176 A G V PM EW+LS +Y+ C NETI G+ PD A+V V AD S Sbjct: 120 ATSEASGYTTVPPMSEWKLSARPSYLFTCTNETIGGVEYPFEPDLARIGRAEVPVVADVS 179 Query: 177 STILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGS 236 S ILSRP DV++YG+++ GAQKNIGPAGLTIVIVR+DLLG+A CP+ DY + DNGS Sbjct: 180 SHILSRPFDVTKYGLLFGGAQKNIGPAGLTIVIVRDDLLGRAAPFCPTAFDYRTVADNGS 239 Query: 237 MFNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRS 296 M+NTPPT+A Y++GLVF+WLK GGVA ++ N KAELLYG +D+ FY N + A RS Sbjct: 240 MYNTPPTYAIYIAGLVFQWLKRKGGVAGIEAQNIAKAELLYGFLDDCPFYENRIDPACRS 299 Query: 297 RMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVE 356 RMNVPF L D +L+ FL + AGL LKGH+ VGGMRASIYNAMPLEGV+AL D+M + Sbjct: 300 RMNVPFFLKDESLNDRFLAGAKDAGLVQLKGHKSVGGMRASIYNAMPLEGVQALVDYMRD 359 Query: 357 FERRHG 362 F RHG Sbjct: 360 FALRHG 365 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: 419 Number of extensions: 14 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: 365 Length adjustment: 29 Effective length of query: 333 Effective length of database: 336 Effective search space: 111888 Effective search space used: 111888 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_011764801.1 AZO_RS05410 (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.18835.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-156 504.7 0.0 7e-156 504.5 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011764801.1 AZO_RS05410 3-phosphoserine/phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011764801.1 AZO_RS05410 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 504.5 0.0 7e-156 7e-156 2 358 .] 5 364 .. 4 364 .. 0.98 Alignments for each domain: == domain 1 score: 504.5 bits; conditional E-value: 7e-156 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 nF+aGPaalp evl++a++e+ld++g g++vme+sHRskef +++e+ae dlreL+ ip ny+vlf+q lcl|NCBI__GCF_000061505.1:WP_011764801.1 5 WNFAAGPAALPAEVLQQAAEEMLDWRGAGVGVMEMSHRSKEFVSIAEQAEADLRELMAIPANYRVLFMQ 73 7******************************************************************** PP TIGR01364 71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139 GGa + a +p+nl+ e+k ady+vtG+ws k+ kea+k+++ v+++a++e + y+++p +e++l+ + lcl|NCBI__GCF_000061505.1:WP_011764801.1 74 GGAIAENAIIPMNLMGEEKRADYVVTGSWSVKSQKEARKYGE-VNIAATSEASGYTTVPPMSEWKLSAR 141 ****************************************98.************************** PP TIGR01364 140 aayvylcanetieGvefkelpevkk.....aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtv 203 +y++ c+neti Gve+ +p+ ++ +p+vaD+ss+ilsr++dv+kygl+++GaqKniGpaG+t+ lcl|NCBI__GCF_000061505.1:WP_011764801.1 142 PSYLFTCTNETIGGVEYPFEPDLARigraeVPVVADVSSHILSRPFDVTKYGLLFGGAQKNIGPAGLTI 210 *********************9987777889************************************** PP TIGR01364 204 vivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakll 272 vivr+dll+ra +p+ +dY+++a+n s+yntppt+aiy++glv++wlk+kGGv+ +e++n +Ka+ll lcl|NCBI__GCF_000061505.1:WP_011764801.1 211 VIVRDDLLGRAAPFCPTAFDYRTVADNGSMYNTPPTYAIYIAGLVFQWLKRKGGVAGIEAQNIAKAELL 279 ********************************************************************* PP TIGR01364 273 YeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpl 341 Y +d+ fy+n++++++Rs+mnv+F lk+e l+++Fl+ a+++glv+lkGh+svGG+RasiYna+pl lcl|NCBI__GCF_000061505.1:WP_011764801.1 280 YGFLDDCP-FYENRIDPACRSRMNVPFFLKDESLNDRFLAGAKDAGLVQLKGHKSVGGMRASIYNAMPL 347 *****996.************************************************************ PP TIGR01364 342 eevqaLvdfmkeFekkh 358 e+vqaLvd+m++F+ +h lcl|NCBI__GCF_000061505.1:WP_011764801.1 348 EGVQALVDYMRDFALRH 364 *************8765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (365 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: 10.09 // [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