Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_086508941.1 BZY95_RS05315 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_002151265.1:WP_086508941.1 Length = 361 Score = 368 bits (945), Expect = e-106 Identities = 192/363 (52%), Positives = 245/363 (67%), Gaps = 3/363 (0%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 M + +NF +GPA LP VL++A++EL D+ G G SVME+SHR EF+ +AE+AE D R+L Sbjct: 1 MTRHYNFCAGPAALPTPVLERAREELLDYQGRGLSVMEMSHRSPEFVAIAEQAEADLREL 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 L VP NYKVLF GG QF+ VP+N+LG A+++ G W A+ EA++ Sbjct: 61 LAVPENYKVLFLQGGASLQFSMVPMNLLGQGGAANFLYTGIWGKKALAEARQLGFAVHMA 120 Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180 G V + LS +AAY+HY NETI G+ D PD G +V D+SS+IL Sbjct: 121 GSSEPSGHAEVPTQADIALSADAAYLHYTANETIGGLEFDYIPDVGVPLV--CDYSSSIL 178 Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240 + P+DVSR+GVIYAGAQKNIGPAGLT+V+VR+DLL + PS+ DY + + GSM NT Sbjct: 179 AEPLDVSRFGVIYAGAQKNIGPAGLTLVLVRDDLLDRRCPRIPSLFDYQAMAEAGSMVNT 238 Query: 241 PPTFAWYLSGLVFKWLKAN-GGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMN 299 PPT+AWYL+GLVF+WLK + GG+ M IN +KA LY ID S FY N +A NRSRMN Sbjct: 239 PPTYAWYLAGLVFQWLKHDIGGLEAMATINARKAAKLYAAIDASGFYSNPIAPRNRSRMN 298 Query: 300 VPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFER 359 VPF LAD++LDK FL E+ AGL L GHR VGGMRAS+YNA+P V L DFM +FE+ Sbjct: 299 VPFVLADASLDKTFLAEAEQAGLLNLAGHRSVGGMRASLYNAVPEAAVDTLIDFMADFEQ 358 Query: 360 RHG 362 R G Sbjct: 359 RRG 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: 383 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: 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_086508941.1 BZY95_RS05315 (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.8749.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-149 483.2 0.0 2.5e-149 483.0 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508941.1 BZY95_RS05315 3-phosphoserine/ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508941.1 BZY95_RS05315 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 483.0 0.0 2.5e-149 2.5e-149 2 357 .. 5 359 .. 4 360 .. 0.98 Alignments for each domain: == domain 1 score: 483.0 bits; conditional E-value: 2.5e-149 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 +nF+aGPaalp+ vle+a++elld++g+glsvme+sHRs ef +++e+ae dlreLl +p+ny+vlflq lcl|NCBI__GCF_002151265.1:WP_086508941.1 5 YNFCAGPAALPTPVLERAREELLDYQGRGLSVMEMSHRSPEFVAIAEQAEADLRELLAVPENYKVLFLQ 73 8******************************************************************** PP TIGR01364 71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139 GGa+ qf++vp+nll ++ a+++ tG w+kkal+ea++l+ v+++ s+e + + ++p + ++ l+ d lcl|NCBI__GCF_002151265.1:WP_086508941.1 74 GGASLQFSMVPMNLLGQGGAANFLYTGIWGKKALAEARQLGFAVHMAGSSEPSGHAEVPTQADIALSAD 142 ********************************************************************* PP TIGR01364 140 aayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrk 208 aay++++aneti G+ef+ +p+ +plv+D ss+il++++dvs++g+iyaGaqKniGpaG+t+v+vr+ lcl|NCBI__GCF_002151265.1:WP_086508941.1 143 AAYLHYTANETIGGLEFDYIPD-VGVPLVCDYSSSILAEPLDVSRFGVIYAGAQKNIGPAGLTLVLVRD 210 *********************5.579******************************************* PP TIGR01364 209 dllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlke.kGGvkklekknqeKakllYeai 276 dll+r +ps++dY+ +ae s+ ntppt+a+y++glv++wlk+ GG+++++ n +Ka+ lY ai lcl|NCBI__GCF_002151265.1:WP_086508941.1 211 DLLDRRCPRIPSLFDYQAMAEAGSMVNTPPTYAWYLAGLVFQWLKHdIGGLEAMATINARKAAKLYAAI 279 ********************************************9626********************* PP TIGR01364 277 desegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevq 345 d+s gfy n++++++Rs+mnv+F l+++ l+k+Fl+eae++gl++l GhrsvGG+Ras+Yna+p ++v lcl|NCBI__GCF_002151265.1:WP_086508941.1 280 DAS-GFYSNPIAPRNRSRMNVPFVLADASLDKTFLAEAEQAGLLNLAGHRSVGGMRASLYNAVPEAAVD 347 *99.6**************************************************************** PP TIGR01364 346 aLvdfmkeFekk 357 +L+dfm +Fe++ lcl|NCBI__GCF_002151265.1:WP_086508941.1 348 TLIDFMADFEQR 359 *********986 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: 9.93 // [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