Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_004299033.1 C665_RS02130 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_000310185.1:WP_004299033.1 Length = 365 Score = 397 bits (1020), Expect = e-115 Identities = 204/366 (55%), Positives = 256/366 (69%), Gaps = 5/366 (1%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 M++++NFS+GPA+LP EVL+QA E+ DW+G G VME+SHRGKEF +A +AE D R+L Sbjct: 1 MSRVWNFSAGPAVLPEEVLRQAADEMLDWHGSGMGVMEMSHRGKEFTAIAAQAEADLREL 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 L VP+ Y+VLF GG + A +P+N++GD+ ADYV G W+ + KEA+KY N+ Sbjct: 61 LAVPAGYRVLFMQGGAIAENAIIPMNLMGDRRVADYVVTGSWSQKSQKEARKYAEVNIA- 119 Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFG----ADVVVAADFS 176 A G V M EW+LS + AY+ C NETI G+ PD +V V AD S Sbjct: 120 ASSEAGGFTTVPAMAEWKLSADPAYVFTCTNETIGGLEYPFEPDLAQIGRGEVPVVADMS 179 Query: 177 STILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGS 236 S ILSR IDVS+YG+I+ GAQKNIGPAGLTIVIVREDLLG+A CP+ D+ + DNGS Sbjct: 180 SHILSRVIDVSKYGLIFGGAQKNIGPAGLTIVIVREDLLGRAMPHCPTAFDFKTVADNGS 239 Query: 237 MFNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRS 296 M+NTPPT+ Y++GLVF+WLK GGVA ++ N KA+LLY +D SDFY N + A RS Sbjct: 240 MYNTPPTYGIYIAGLVFQWLKRQGGVAAIEAQNVAKAKLLYDFLDASDFYENRIDPACRS 299 Query: 297 RMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVE 356 RMNVPF L D AL+ FL E+ AAGL LKGH+ VGGMRASIYNAMPL GV+AL DFM + Sbjct: 300 RMNVPFFLKDEALNDAFLAEAKAAGLVQLKGHKSVGGMRASIYNAMPLAGVQALVDFMRD 359 Query: 357 FERRHG 362 F R G Sbjct: 360 FAARRG 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: 412 Number of extensions: 11 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_004299033.1 C665_RS02130 (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.4012.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-159 516.2 0.0 2.2e-159 516.1 0.0 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004299033.1 C665_RS02130 3-phosphoserine/pho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_004299033.1 C665_RS02130 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 516.1 0.0 2.2e-159 2.2e-159 2 357 .. 5 363 .. 4 364 .. 0.99 Alignments for each domain: == domain 1 score: 516.1 bits; conditional E-value: 2.2e-159 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 nFsaGPa+lpeevl++a++e+ld++g+g++vme+sHR kef++++ +ae dlreLl +p y+vlf+q lcl|NCBI__GCF_000310185.1:WP_004299033.1 5 WNFSAGPAVLPEEVLRQAADEMLDWHGSGMGVMEMSHRGKEFTAIAAQAEADLRELLAVPAGYRVLFMQ 73 7******************************************************************** PP TIGR01364 71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139 GGa + a +p+nl+ +++vady+vtG+ws+k+ kea+k+ + v+++as+e + ++++p e++l+ d lcl|NCBI__GCF_000310185.1:WP_004299033.1 74 GGAIAENAIIPMNLMGDRRVADYVVTGSWSQKSQKEARKYAE-VNIAASSEAGGFTTVPAMAEWKLSAD 141 ****************************************88.************************** PP TIGR01364 140 aayvylcanetieGvefkelpevkk.....aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtv 203 ayv+ c+neti G+e+ +p+ ++ +p+vaD+ss+ilsr idvskygli++GaqKniGpaG+t+ lcl|NCBI__GCF_000310185.1:WP_004299033.1 142 PAYVFTCTNETIGGLEYPFEPDLAQigrgeVPVVADMSSHILSRVIDVSKYGLIFGGAQKNIGPAGLTI 210 *********************9998888889************************************** PP TIGR01364 204 vivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakll 272 vivr+dll+ra ++p+ +d+k++a+n s+yntppt++iy++glv++wlk++GGv+++e++n +Kakll lcl|NCBI__GCF_000310185.1:WP_004299033.1 211 VIVREDLLGRAMPHCPTAFDFKTVADNGSMYNTPPTYGIYIAGLVFQWLKRQGGVAAIEAQNVAKAKLL 279 ********************************************************************* PP TIGR01364 273 YeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpl 341 Y+ +d+s+ fy+n++++++Rs+mnv+F lk+e l++ Fl+ea+++glv+lkGh+svGG+RasiYna+pl lcl|NCBI__GCF_000310185.1:WP_004299033.1 280 YDFLDASD-FYENRIDPACRSRMNVPFFLKDEALNDAFLAEAKAAGLVQLKGHKSVGGMRASIYNAMPL 347 *****996.************************************************************ PP TIGR01364 342 eevqaLvdfmkeFekk 357 ++vqaLvdfm++F+++ lcl|NCBI__GCF_000310185.1:WP_004299033.1 348 AGVQALVDFMRDFAAR 363 *************875 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.56 // [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