Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_013835369.1 THICY_RS04230 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_000214825.1:WP_013835369.1 Length = 357 Score = 391 bits (1005), Expect = e-113 Identities = 196/361 (54%), Positives = 249/361 (68%), Gaps = 5/361 (1%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 M + FNFS+GPAMLP V++QAQ E DW+G G SVME+SHR ++++ +A AE+ R++ Sbjct: 1 MTRTFNFSAGPAMLPEPVMQQAQSEFLDWHGTGMSVMEMSHRSQDYMAMAHHAEQTLREI 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 + +P NYKVLF HGG QF+A+PLN+ DY + G W+A AIKEA +Y NV Sbjct: 61 MAIPDNYKVLFVHGGASMQFSAIPLNLADTGDVVDYFNTGVWSAKAIKEASRYAQVNV-- 118 Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180 D + EW+ S NA Y+HY NETI G+ P+ + + AD SSTIL Sbjct: 119 ---VCDNHAMIPDESEWKFSANAKYIHYTTNETIGGVEFLNQPNVPEGIPLIADMSSTIL 175 Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240 SRPIDVS++G+IYAGAQKNIGPAGL IVIVR+DL+G A P++L++ +N SMFNT Sbjct: 176 SRPIDVSQFGMIYAGAQKNIGPAGLAIVIVRDDLVGSARDITPTLLNWQTYAENDSMFNT 235 Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNV 300 P T++WYL+GLVF W+K GGVA M + NQ KA LY ID+ DFY N V K+ RS MNV Sbjct: 236 PSTYSWYLAGLVFDWIKEQGGVAAMAEHNQTKAHRLYQAIDSIDFYTNPVPKSQRSWMNV 295 Query: 301 PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360 PF L D++LD FL+ES AGL LKGH++VGGMRASIYNAMP EGV AL DFM +F R Sbjct: 296 PFTLQDASLDSTFLKESKDAGLLNLKGHKLVGGMRASIYNAMPQEGVDALIDFMRDFANR 355 Query: 361 H 361 + Sbjct: 356 Y 356 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: 417 Number of extensions: 24 Number of successful extensions: 2 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_013835369.1 THICY_RS04230 (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.31830.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-158 511.0 0.0 8.5e-158 510.8 0.0 1.0 1 lcl|NCBI__GCF_000214825.1:WP_013835369.1 THICY_RS04230 3-phosphoserine/ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214825.1:WP_013835369.1 THICY_RS04230 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 510.8 0.0 8.5e-158 8.5e-158 2 358 .] 5 356 .. 4 356 .. 0.98 Alignments for each domain: == domain 1 score: 510.8 bits; conditional E-value: 8.5e-158 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 +nFsaGPa+lpe v+++aq+e+ld++g+g+svme+sHRs+++++++++ae+ lre++ ipdny+vlf+ lcl|NCBI__GCF_000214825.1:WP_013835369.1 5 FNFSAGPAMLPEPVMQQAQSEFLDWHGTGMSVMEMSHRSQDYMAMAHHAEQTLREIMAIPDNYKVLFVH 73 8******************************************************************** PP TIGR01364 71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139 GGa+ qf+a+plnl+++++v+dy +tG+ws+ka+kea+++ + v+vv ++ + ipde+e++++ + lcl|NCBI__GCF_000214825.1:WP_013835369.1 74 GGASMQFSAIPLNLADTGDVVDYFNTGVWSAKAIKEASRYAQ-VNVVCDN----HAMIPDESEWKFSAN 137 ****************************************98.9999877....589************ PP TIGR01364 140 aayvylcanetieGvefkelpevkk.aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivr 207 a+y+++++neti Gvef ++p+v + +pl+aD+ss ilsr+idvs++g+iyaGaqKniGpaG+++vivr lcl|NCBI__GCF_000214825.1:WP_013835369.1 138 AKYIHYTTNETIGGVEFLNQPNVPEgIPLIADMSSTILSRPIDVSQFGMIYAGAQKNIGPAGLAIVIVR 206 **********************98889****************************************** PP TIGR01364 208 kdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeai 276 +dl+++a++++p++l++++ aends++ntp+t+++y++glv++w+ke+GGv++++++nq+Ka+ lY+ai lcl|NCBI__GCF_000214825.1:WP_013835369.1 207 DDLVGSARDITPTLLNWQTYAENDSMFNTPSTYSWYLAGLVFDWIKEQGGVAAMAEHNQTKAHRLYQAI 275 ********************************************************************* PP TIGR01364 277 desegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevq 345 d+ +fy+n+v k++Rs+mnv+Ftl+++ l+++Flke++++gl++lkGh+ vGG+RasiYna+p e+v lcl|NCBI__GCF_000214825.1:WP_013835369.1 276 DSI-DFYTNPVPKSQRSWMNVPFTLQDASLDSTFLKESKDAGLLNLKGHKLVGGMRASIYNAMPQEGVD 343 *77.5**************************************************************** PP TIGR01364 346 aLvdfmkeFekkh 358 aL+dfm++F++++ lcl|NCBI__GCF_000214825.1:WP_013835369.1 344 ALIDFMRDFANRY 356 *********9886 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.11 // [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