Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_050463940.1 AKL27_RS16295 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_001189915.1:WP_050463940.1 Length = 365 Score = 392 bits (1008), Expect = e-114 Identities = 199/365 (54%), Positives = 255/365 (69%), Gaps = 7/365 (1%) Query: 4 IFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNV 63 ++NFS+GPA+LP EVL+QA E+ DW+G G SVME+SHRGKE++ + E A +D R+L +V Sbjct: 2 VYNFSAGPAVLPKEVLQQAADEMLDWHGSGMSVMEMSHRGKEYMSIIETALRDMRELFSV 61 Query: 64 PSNYKVLFCHGGGRGQFAAVPLNIL---GDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 P NYK+LF GG + A +P+N+ G ADY++ G W+ +IKEA++YC NV Sbjct: 62 PDNYKILFMQGGAIAENAIIPMNLAALRGQVGVADYINTGSWSTKSIKEARRYCEVNVA- 120 Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADV---VVAADFSS 177 A + +W+LS NAAY+H C NETIDG+ TP+ AD + AD SS Sbjct: 121 ASSEAGKFARIPDRADWRLSRNAAYVHVCTNETIDGVEYQFTPEVAADTDNAPLVADMSS 180 Query: 178 TILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSM 237 ILSR +DVS+YGVIY GAQKNIGPAGLTIVIVR+DLLG A CPS D+ + DN SM Sbjct: 181 HILSRAVDVSKYGVIYGGAQKNIGPAGLTIVIVRDDLLGHALPICPSAFDWKTVADNDSM 240 Query: 238 FNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSR 297 +NTPPT+A Y++GLVF+WLK GGV EM++ N KA LLY +D++ FYR +A RSR Sbjct: 241 YNTPPTYAIYIAGLVFQWLKRQGGVPEMERRNIAKAALLYDYLDSTGFYRTRIASECRSR 300 Query: 298 MNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEF 357 MNVPF L D AL+ FL + GL LKGH+ VGGMRASIYNAMPLEGV+AL ++ EF Sbjct: 301 MNVPFYLHDEALNDAFLAGAKEHGLLQLKGHKSVGGMRASIYNAMPLEGVQALVHYLQEF 360 Query: 358 ERRHG 362 ER++G Sbjct: 361 ERQNG 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: 413 Number of extensions: 16 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: 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_050463940.1 AKL27_RS16295 (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.22497.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-162 524.1 0.0 8.6e-162 524.0 0.0 1.0 1 lcl|NCBI__GCF_001189915.1:WP_050463940.1 AKL27_RS16295 3-phosphoserine/ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001189915.1:WP_050463940.1 AKL27_RS16295 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 524.0 0.0 8.6e-162 8.6e-162 1 357 [. 2 363 .. 2 364 .. 0.98 Alignments for each domain: == domain 1 score: 524.0 bits; conditional E-value: 8.6e-162 TIGR01364 1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 ++nFsaGPa+lp+evl++a++e+ld++g+g+svme+sHR ke+++++e+a +d+reL+++pdny++lf+ lcl|NCBI__GCF_001189915.1:WP_050463940.1 2 VYNFSAGPAVLPKEVLQQAADEMLDWHGSGMSVMEMSHRGKEYMSIIETALRDMRELFSVPDNYKILFM 70 59******************************************************************* PP TIGR01364 70 qGGattqfaavplnllk...ekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeele 135 qGGa + a +p+nl++ + vadyi+tG+ws+k++kea+++++ v+v+as+e +k+ +ipd+ +++ lcl|NCBI__GCF_001189915.1:WP_050463940.1 71 QGGAIAENAIIPMNLAAlrgQVGVADYINTGSWSTKSIKEARRYCE-VNVAASSEAGKFARIPDRADWR 138 ****************97555559********************99.********************** PP TIGR01364 136 lkedaayvylcanetieGvefkelpevkk....aplvaDlssdilsrkidvskygliyaGaqKniGpaG 200 l+ +aayv++c+neti+Gve++ +pev+ aplvaD+ss+ilsr +dvskyg+iy+GaqKniGpaG lcl|NCBI__GCF_001189915.1:WP_050463940.1 139 LSRNAAYVHVCTNETIDGVEYQFTPEVAAdtdnAPLVADMSSHILSRAVDVSKYGVIYGGAQKNIGPAG 207 ************************9987666779*********************************** PP TIGR01364 201 vtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKa 269 +t+vivr+dll++a ++ps +d+k++a+nds+yntppt+aiy++glv++wlk++GGv ++e++n +Ka lcl|NCBI__GCF_001189915.1:WP_050463940.1 208 LTIVIVRDDLLGHALPICPSAFDWKTVADNDSMYNTPPTYAIYIAGLVFQWLKRQGGVPEMERRNIAKA 276 ********************************************************************* PP TIGR01364 270 kllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYna 338 +llY+++d++ gfy+++++ ++Rs+mnv+F l++e l++ Fl+ a+e+gl++lkGh+svGG+RasiYna lcl|NCBI__GCF_001189915.1:WP_050463940.1 277 ALLYDYLDST-GFYRTRIASECRSRMNVPFYLHDEALNDAFLAGAKEHGLLQLKGHKSVGGMRASIYNA 344 ********65.8********************************************************* PP TIGR01364 339 lpleevqaLvdfmkeFekk 357 +ple+vqaLv++++eFe++ lcl|NCBI__GCF_001189915.1:WP_050463940.1 345 MPLEGVQALVHYLQEFERQ 363 ****************987 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: 8.39 // [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