Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_041755522.1 PST_RS11800 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_000013785.1:WP_041755522.1 Length = 361 Score = 415 bits (1066), Expect = e-120 Identities = 208/358 (58%), Positives = 257/358 (71%), Gaps = 2/358 (0%) Query: 5 FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64 FNF +GPA LP VL++AQ EL DW+G G SVME+SHR ++ +A++AE+D RDLL +P Sbjct: 6 FNFCAGPAALPEAVLQRAQAELLDWHGKGLSVMEMSHRSDDYTAIAKKAEQDLRDLLAIP 65 Query: 65 SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124 SNYKVLF GG QFA +PLN+L + ADYVD G W+ AI+EA+++ N+ Sbjct: 66 SNYKVLFLQGGASQQFAEIPLNLLPEGGVADYVDTGIWSRKAIEEARRFGHVNIAATAKP 125 Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184 D A+ +WQLSD AAY+HY NETI G+ D P+ G D + D SS ILSRPI Sbjct: 126 YDYF-AIPGQNDWQLSDGAAYLHYASNETIGGLQFDWVPELG-DTPLVVDMSSDILSRPI 183 Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244 DVS++G+IYAGAQKNIGP+GL +VIVREDLLG A CP++LDY I DNGSM+NTP TF Sbjct: 184 DVSKFGLIYAGAQKNIGPSGLVVVIVREDLLGHARSVCPTMLDYKIAADNGSMYNTPATF 243 Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304 +WYLSGLVF+WLK GGV M+K N+ K ++LYG ID SDFY N +A RS MNVPF+L Sbjct: 244 SWYLSGLVFEWLKEQGGVEAMEKRNRAKKDMLYGAIDASDFYTNPIAVNARSWMNVPFRL 303 Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362 AD LDK FL + A GL LKGHR VGGMRASIYNA+ L+ V+AL +M EFE+ HG Sbjct: 304 ADERLDKAFLAGADARGLLNLKGHRSVGGMRASIYNAVGLDAVEALVAYMAEFEKEHG 361 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: 423 Number of extensions: 12 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: 361 Length adjustment: 29 Effective length of query: 333 Effective length of database: 332 Effective search space: 110556 Effective search space used: 110556 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_041755522.1 PST_RS11800 (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.29967.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-167 541.5 0.0 4.5e-167 541.3 0.0 1.0 1 lcl|NCBI__GCF_000013785.1:WP_041755522.1 PST_RS11800 3-phosphoserine/phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013785.1:WP_041755522.1 PST_RS11800 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 541.3 0.0 4.5e-167 4.5e-167 2 358 .] 6 360 .. 5 360 .. 0.99 Alignments for each domain: == domain 1 score: 541.3 bits; conditional E-value: 4.5e-167 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 +nF+aGPaalpe+vl++aq+elld++g+glsvme+sHRs+++++++++ae+dlr+Ll ip+ny+vlflq lcl|NCBI__GCF_000013785.1:WP_041755522.1 6 FNFCAGPAALPEAVLQRAQAELLDWHGKGLSVMEMSHRSDDYTAIAKKAEQDLRDLLAIPSNYKVLFLQ 74 8******************************************************************** PP TIGR01364 71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139 GGa++qfa++plnll e+ vady+ tG ws+ka++ea+++++ v+++a+++ +y +ip +++++l++ lcl|NCBI__GCF_000013785.1:WP_041755522.1 75 GGASQQFAEIPLNLLPEGGVADYVDTGIWSRKAIEEARRFGH-VNIAATAKPYDYFAIPGQNDWQLSDG 142 ****************************************99.************************** PP TIGR01364 140 aayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrk 208 aay+++++neti G++f+++pe ++plv+D+ssdilsr+idvsk+gliyaGaqKniGp+G++vvivr+ lcl|NCBI__GCF_000013785.1:WP_041755522.1 143 AAYLHYASNETIGGLQFDWVPELGDTPLVVDMSSDILSRPIDVSKFGLIYAGAQKNIGPSGLVVVIVRE 211 ********************************************************************* PP TIGR01364 209 dllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaid 277 dll++a++++p++ldYki+a+n s+yntp+tf++y++glv++wlke+GGv+++ek+n++K+++lY aid lcl|NCBI__GCF_000013785.1:WP_041755522.1 212 DLLGHARSVCPTMLDYKIAADNGSMYNTPATFSWYLSGLVFEWLKEQGGVEAMEKRNRAKKDMLYGAID 280 ********************************************************************* PP TIGR01364 278 esegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqa 346 +s+ fy+n+++ +aRs+mnv+F+l++e+l+k Fl+ a ++gl++lkGhrsvGG+RasiYna+ l++v+a lcl|NCBI__GCF_000013785.1:WP_041755522.1 281 ASD-FYTNPIAVNARSWMNVPFRLADERLDKAFLAGADARGLLNLKGHRSVGGMRASIYNAVGLDAVEA 348 996.***************************************************************** PP TIGR01364 347 LvdfmkeFekkh 358 Lv++m eFek+h lcl|NCBI__GCF_000013785.1:WP_041755522.1 349 LVAYMAEFEKEH 360 *********997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (361 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: 7.75 // [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