Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_041102150.1 SUTH_RS09890 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_000828635.1:WP_041102150.1 Length = 360 Score = 399 bits (1024), Expect = e-116 Identities = 204/362 (56%), Positives = 255/362 (70%), Gaps = 2/362 (0%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 MA+IFNFS+GPA LP VL+QA E+ DW+G GTSVME+SHRGKEF+ +A +AE D R+L Sbjct: 1 MARIFNFSAGPAALPEAVLQQAADEMLDWHGSGTSVMEMSHRGKEFMGIAAQAEADLREL 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 + +P+NYKVLF GG QF +P+N+L K ADYV G WA AIK AK + NV Sbjct: 61 MAIPANYKVLFLQGGASAQFEMIPINLLRGKGAADYVHTGEWAKKAIKAAKAFGNVNVV- 119 Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180 A W+L NAAY+HY NETI G+ TPD G DV + D SS IL Sbjct: 120 ASAEDKAFTYAPAQASWKLDKNAAYVHYTANETIGGVEFHWTPDTG-DVPLVCDMSSNIL 178 Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240 S+P+DVS++G+IYAGAQKNIGPAGLTIVI+R+DL+G A P++LDY D SM+NT Sbjct: 179 SKPVDVSKFGLIYAGAQKNIGPAGLTIVIIRDDLVGHAQPTPPAMLDYKTHVDAESMYNT 238 Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNV 300 PPT+A Y++GLVF+WLK NGGVA M++ N KA LLY + +DFYRN V K +RSRMNV Sbjct: 239 PPTYAIYIAGLVFQWLKKNGGVAAMERQNIAKANLLYDYLATTDFYRNPVRKEDRSRMNV 298 Query: 301 PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360 PF L D+ALD+ FL+ + + G+ LKGHR VGGMRASIYNAMP+ GV+AL +M EF + Sbjct: 299 PFTLKDAALDEEFLKGAKSRGMAQLKGHRSVGGMRASIYNAMPVAGVEALVAYMKEFAAQ 358 Query: 361 HG 362 G Sbjct: 359 KG 360 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: 414 Number of extensions: 10 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: 360 Length adjustment: 29 Effective length of query: 333 Effective length of database: 331 Effective search space: 110223 Effective search space used: 110223 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_041102150.1 SUTH_RS09890 (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.4538.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-167 542.8 0.0 1.8e-167 542.6 0.0 1.0 1 lcl|NCBI__GCF_000828635.1:WP_041102150.1 SUTH_RS09890 3-phosphoserine/pho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000828635.1:WP_041102150.1 SUTH_RS09890 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 542.6 0.0 1.8e-167 1.8e-167 1 357 [. 4 358 .. 4 359 .. 0.99 Alignments for each domain: == domain 1 score: 542.6 bits; conditional E-value: 1.8e-167 TIGR01364 1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 i+nFsaGPaalpe+vl++a++e+ld++g+g+svme+sHR kef+ ++ +ae dlreL+ ip ny+vlfl lcl|NCBI__GCF_000828635.1:WP_041102150.1 4 IFNFSAGPAALPEAVLQQAADEMLDWHGSGTSVMEMSHRGKEFMGIAAQAEADLRELMAIPANYKVLFL 72 68******************************************************************* PP TIGR01364 70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelke 138 qGGa+ qf ++p+nll+ k ady+ tG+w+kka+k ak +++ v+vvas+e+k ++ p + +++l++ lcl|NCBI__GCF_000828635.1:WP_041102150.1 73 QGGASAQFEMIPINLLRGKGAADYVHTGEWAKKAIKAAKAFGN-VNVVASAEDKAFTYAPAQASWKLDK 140 *****************************************99.************************* PP TIGR01364 139 daayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivr 207 +aayv+++aneti Gvef+++p++ ++plv+D+ss+ils+++dvsk+gliyaGaqKniGpaG+t+vi+r lcl|NCBI__GCF_000828635.1:WP_041102150.1 141 NAAYVHYTANETIGGVEFHWTPDTGDVPLVCDMSSNILSKPVDVSKFGLIYAGAQKNIGPAGLTIVIIR 209 ********************************************************************* PP TIGR01364 208 kdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeai 276 +dl+++a+ + p +ldYk++++ +s+yntppt+aiy++glv++wlk++GGv+++e++n +Ka+llY+++ lcl|NCBI__GCF_000828635.1:WP_041102150.1 210 DDLVGHAQPTPPAMLDYKTHVDAESMYNTPPTYAIYIAGLVFQWLKKNGGVAAMERQNIAKANLLYDYL 278 ********************************************************************* PP TIGR01364 277 desegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevq 345 +++ fy+n+v+k++Rs+mnv+Ftlk++ l++eFlk a+++g+ +lkGhrsvGG+RasiYna+p+++v+ lcl|NCBI__GCF_000828635.1:WP_041102150.1 279 ATTD-FYRNPVRKEDRSRMNVPFTLKDAALDEEFLKGAKSRGMAQLKGHRSVGGMRASIYNAMPVAGVE 346 9885.**************************************************************** PP TIGR01364 346 aLvdfmkeFekk 357 aLv++mkeF+++ lcl|NCBI__GCF_000828635.1:WP_041102150.1 347 ALVAYMKEFAAQ 358 *********975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (360 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: 00:00:00.06 # Mc/sec: 1.95 // [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