Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_066919888.1 ACG33_RS07085 3-phosphoserine/phosphohydroxythreonine transaminase
Query= BRENDA::P23721 (362 letters) >NCBI__GCF_001579945.1:WP_066919888.1 Length = 360 Score = 427 bits (1097), Expect = e-124 Identities = 211/361 (58%), Positives = 261/361 (72%), Gaps = 2/361 (0%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 M ++FNFS+GPA+LP EVL+QA+ E+ DW+G G SVME+SHRGK F+ +A +AE D R+L Sbjct: 1 MMRVFNFSAGPAVLPLEVLEQARDEMLDWHGTGMSVMEMSHRGKAFVSIAAQAEADLREL 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 L VP+NYKVLF GG QFAA+P+N+ G + DYV G W+ AI EAK+Y NV Sbjct: 61 LQVPANYKVLFLQGGATAQFAAIPMNLAGPDSVVDYVHTGAWSKKAIGEAKRYANVNV-- 118 Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180 A + ++ WQ S NAAY+HY PNETI G+ PD A+V + AD SSTIL Sbjct: 119 AANAGEPYASIPAQESWQRSPNAAYLHYTPNETIGGVEFHFIPDTNAEVPLVADLSSTIL 178 Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240 SRP+DVS++G+IYAGAQKNIGPAGL +VIVREDLLG+A P+ILD++ + +GSM NT Sbjct: 179 SRPLDVSKFGLIYAGAQKNIGPAGLALVIVREDLLGRARAGTPTILDFAAMAKDGSMLNT 238 Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNV 300 PPT+AWY++GLVF+WL+ GG+ M K NQ KA LY ID+S FY N VAK RS MNV Sbjct: 239 PPTYAWYVAGLVFQWLRRQGGLEAMGKRNQAKAAKLYEAIDDSSFYANPVAKGARSWMNV 298 Query: 301 PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360 PF LA LDK F+ E+ AGL L+GHR VGGMRAS+YNAMP+EGV AL FM EFERR Sbjct: 299 PFTLARPELDKTFIAEAREAGLVTLEGHRSVGGMRASLYNAMPMEGVDALVGFMREFERR 358 Query: 361 H 361 H Sbjct: 359 H 359 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: 422 Number of extensions: 14 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: 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_066919888.1 ACG33_RS07085 (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.4217.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-160 520.4 0.0 1.2e-160 520.2 0.0 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066919888.1 ACG33_RS07085 3-phosphoserine/ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066919888.1 ACG33_RS07085 3-phosphoserine/phosphohydroxythreonine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 520.2 0.0 1.2e-160 1.2e-160 1 358 [] 4 359 .. 4 359 .. 0.98 Alignments for each domain: == domain 1 score: 520.2 bits; conditional E-value: 1.2e-160 TIGR01364 1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 ++nFsaGPa+lp evle+a++e+ld++g+g+svme+sHR k+f +++ +ae dlreLl++p ny+vlfl lcl|NCBI__GCF_001579945.1:WP_066919888.1 4 VFNFSAGPAVLPLEVLEQARDEMLDWHGTGMSVMEMSHRGKAFVSIAAQAEADLRELLQVPANYKVLFL 72 58******************************************************************* PP TIGR01364 70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelke 138 qGGat qfaa+p+nl+ ++v+dy+ tGawskka+ eak++ + v+v+a++ + y +ip +e+++ ++ lcl|NCBI__GCF_001579945.1:WP_066919888.1 73 QGGATAQFAAIPMNLAGPDSVVDYVHTGAWSKKAIGEAKRYAN-VNVAANA-GEPYASIPAQESWQRSP 139 *****************************************98.9988887.689************** PP TIGR01364 139 daayvylcanetieGvefkelpevkk.aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvviv 206 +aay++++ neti Gvef+ +p+++ +plvaDlss ilsr++dvsk+gliyaGaqKniGpaG+++viv lcl|NCBI__GCF_001579945.1:WP_066919888.1 140 NAAYLHYTPNETIGGVEFHFIPDTNAeVPLVADLSSTILSRPLDVSKFGLIYAGAQKNIGPAGLALVIV 208 **********************876559***************************************** PP TIGR01364 207 rkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYea 275 r+dll+ra++ +p++ld++ +a+ s++ntppt+a+yv+glv++wl+++GG++++ k+nq+Ka+ lYea lcl|NCBI__GCF_001579945.1:WP_066919888.1 209 REDLLGRARAGTPTILDFAAMAKDGSMLNTPPTYAWYVAGLVFQWLRRQGGLEAMGKRNQAKAAKLYEA 277 ********************************************************************* PP TIGR01364 276 idesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleev 344 id+s+ fy n+v+k aRs+mnv+Ftl+ el+k+F++ea+e+glv+l GhrsvGG+Ras+Yna+p+e+v lcl|NCBI__GCF_001579945.1:WP_066919888.1 278 IDDSS-FYANPVAKGARSWMNVPFTLARPELDKTFIAEAREAGLVTLEGHRSVGGMRASLYNAMPMEGV 345 **996.*************************************************************** PP TIGR01364 345 qaLvdfmkeFekkh 358 aLv fm+eFe++h lcl|NCBI__GCF_001579945.1:WP_066919888.1 346 DALVGFMREFERRH 359 ***********987 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.59 // [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