Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate AO353_10515 AO353_10515 3-phosphoserine/phosphohydroxythreonine aminotransferase
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10515 Length = 360 Score = 362 bits (929), Expect = e-105 Identities = 187/363 (51%), Positives = 247/363 (68%), Gaps = 4/363 (1%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 MA+ NFS+GP LP EVL QA +E D+ G G SVME+SHR + F++VA + E+D RD+ Sbjct: 1 MARSHNFSAGPTALPMEVLTQAHEEFFDFAGTGMSVMEISHRCEVFMEVAYQTERDLRDI 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 L VPS YKVLF GG QFA VP+N+LG+K TADY+ G W+ AI+ A++YC + Sbjct: 61 LQVPSEYKVLFLQGGASLQFAQVPMNLLGNKRTADYLHTGLWSGKAIEAARRYCDVRIV- 119 Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180 A G + + +W L+ NAAY+HY NET+ G+ + PD A +V D S++L Sbjct: 120 ASGKESGFDRIPDVSDWNLNPNAAYLHYTENETVHGVQFVDAPDGLAPLV--CDACSSLL 177 Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240 S+PIDV+++G++YA AQKN+G AGLT+VI+ LL A P IL+Y+ + D SM NT Sbjct: 178 SKPIDVAKHGLVYAAAQKNMGVAGLTVVIIDPALLDGAQAFTPDILNYARITDAQSMLNT 237 Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSD-FYRNDVAKANRSRMN 299 P TF WYL+GL KW+K GG+ + ++NQ KAELLY ID+SD FYRN V RS N Sbjct: 238 PATFPWYLTGLTLKWIKRRGGLEALHRLNQTKAELLYRTIDDSDGFYRNSVRAPFRSINN 297 Query: 300 VPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFER 359 VPF LAD+AL+K F++ + AGL+ LKGH VGG+RAS+YNA+ LE V+ALTDFM F R Sbjct: 298 VPFVLADAALEKTFVQLAEQAGLNGLKGHASVGGIRASLYNAVTLEAVEALTDFMKGFVR 357 Query: 360 RHG 362 HG Sbjct: 358 VHG 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: 380 Number of extensions: 18 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: 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 AO353_10515 AO353_10515 (3-phosphoserine/phosphohydroxythreonine aminotransferase)
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.29880.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-147 474.9 0.0 8.1e-147 474.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 AO353_10515 3-phosphoserine/phos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 AO353_10515 3-phosphoserine/phosphohydroxythreonine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 474.7 0.0 8.1e-147 8.1e-147 2 357 .. 5 358 .. 4 359 .. 0.99 Alignments for each domain: == domain 1 score: 474.7 bits; conditional E-value: 8.1e-147 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyev 66 +nFsaGP+alp evl++a++e++df g+g+svmeisHR + f++v+ ++e+dlr++l++p++y+v lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 5 HNFSAGPTALPMEVLTQAHEEFFDFAGTGMSVMEISHRCEVFMEVAYQTERDLRDILQVPSEYKV 69 7**************************************************************** PP TIGR01364 67 lflqGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipde 131 lflqGGa+ qfa+vp+nll +k++ady+ tG ws ka++ a+++++ v++vas +e+ +++ipd lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 70 LFLQGGASLQFAQVPMNLLGNKRTADYLHTGLWSGKAIEAARRYCD-VRIVASGKESGFDRIPDV 133 *********************************************9.****************** PP TIGR01364 132 eelelkedaayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKni 196 ++++l+++aay+++++net++Gv+f ++p aplv+D s++ls++idv+k+gl+ya aqKn+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 134 SDWNLNPNAAYLHYTENETVHGVQFVDAP-DGLAPLVCDACSSLLSKPIDVAKHGLVYAAAQKNM 197 *****************************.6789******************************* PP TIGR01364 197 GpaGvtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkkl 261 G+aG+tvvi+ ll+ a++ +p++l+Y+ +++ +s++ntp+tf +y++gl+lkw+k++GG+++l lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 198 GVAGLTVVIIDPALLDGAQAFTPDILNYARITDAQSMLNTPATFPWYLTGLTLKWIKRRGGLEAL 262 ***************************************************************** PP TIGR01364 262 ekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhr 326 ++ nq+Ka+llY +id+s+gfy+n+v++ Rs+ nv+F l+++ lek+F++ ae++gl +lkGh lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 263 HRLNQTKAELLYRTIDDSDGFYRNSVRAPFRSINNVPFVLADAALEKTFVQLAEQAGLNGLKGHA 327 ***************************************************************** PP TIGR01364 327 svGGiRasiYnalpleevqaLvdfmkeFekk 357 svGGiRas+Yna++le+v+aL dfmk F + lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 328 SVGGIRASLYNAVTLEAVEALTDFMKGFVRV 358 ***************************9875 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.06 // [ok]
This GapMind analysis is from Apr 09 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