Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 6937577 Sama_1732 phosphoserine aminotransferase (RefSeq)
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__SB2B:6937577 Length = 364 Score = 406 bits (1043), Expect = e-118 Identities = 207/364 (56%), Positives = 262/364 (71%), Gaps = 5/364 (1%) Query: 1 MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60 M+ ++NF +GPAMLPA V+K+AQ EL DWNG G SVMEVSHRG FIQ+A+++E D R+L Sbjct: 1 MSAVYNFCAGPAMLPAAVMKKAQAELLDWNGQGVSVMEVSHRGAPFIQLAKDSEADLREL 60 Query: 61 LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120 +N+P NY VLF HGGGRGQF+AV N LGD A Y+ +G W+ +A +EAKK N D Sbjct: 61 MNIPDNYHVLFMHGGGRGQFSAVVNNFLGDNGKALYLVSGQWSKAATEEAKKLAGDNSID 120 Query: 121 AKVTVDGLRAVKPMREWQLSDNAA---YMHYCPNETIDGIAIDETPDFGADVVVAADFSS 177 V+ + + + LS N + Y+HYCPNET+DGI I + D + + AD SS Sbjct: 121 VINVVEKVNGLNKVVIPALSGNGSEYRYLHYCPNETVDGIEIFD--DIDSPWPIVADMSS 178 Query: 178 TILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSM 237 I+SR IDVSR+ +IYAGAQKNIGP+GL+IVIVR+D+L + SI+DY + +N SM Sbjct: 179 NIMSREIDVSRFALIYAGAQKNIGPSGLSIVIVRKDMLELPQLTQSSIMDYRLTAENDSM 238 Query: 238 FNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSR 297 +NTPPTFAWYL+ VFKWLK+ GG+ M ++N +KA LY ID+ DFY+N VA NRS+ Sbjct: 239 YNTPPTFAWYLAAEVFKWLKSVGGIKGMAEVNAEKARRLYACIDSLDFYKNGVAPQNRSQ 298 Query: 298 MNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEF 357 MNV FQLAD +LDK FL+E+ A GL ALKGHR+VGGMRASIYNAMPLEGV AL FM F Sbjct: 299 MNVTFQLADESLDKDFLKEAEALGLVALKGHRIVGGMRASIYNAMPLEGVDALVSFMRSF 358 Query: 358 ERRH 361 +H Sbjct: 359 AAKH 362 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: 395 Number of extensions: 18 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: 364 Length adjustment: 29 Effective length of query: 333 Effective length of database: 335 Effective search space: 111555 Effective search space used: 111555 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 6937577 Sama_1732 (phosphoserine aminotransferase (RefSeq))
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.23880.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-148 480.1 0.0 2.1e-148 479.9 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6937577 Sama_1732 phosphoserine aminotra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937577 Sama_1732 phosphoserine aminotransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 479.9 0.0 2.1e-148 2.1e-148 1 358 [] 4 362 .. 4 362 .. 0.94 Alignments for each domain: == domain 1 score: 479.9 bits; conditional E-value: 2.1e-148 TIGR01364 1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqf 77 ++nF+aGPa+lp +v++kaq+elld+ng+g+svme+sHR f ++++++e dlreL+nipdny+vlf+ GG+++qf lcl|FitnessBrowser__SB2B:6937577 4 VYNFCAGPAMLPAAVMKKAQAELLDWNGQGVSVMEVSHRGAPFIQLAKDSEADLRELMNIPDNYHVLFMHGGGRGQF 80 59*************************************************************************** PP TIGR01364 78 aavplnllkekkvadyivtGawskkalkeakkltk..evkvvase.eekkyskipdeeelelkedaayvylcaneti 151 +av n+l ++ +a y+v+G+wsk a++eakkl +++v++ + + +k+ + ++ y+++c net+ lcl|FitnessBrowser__SB2B:6937577 81 SAVVNNFLGDNGKALYLVSGQWSKAATEEAKKLAGdnSIDVINVVeKVNGLNKVVIPALSGNGSEYRYLHYCPNETV 157 *********************************9877444433332334445554446666668899********** PP TIGR01364 152 eGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkila 228 +G+e+ + + p+vaD+ss+i+sr+idvs+++liyaGaqKniGp+G+++vivrkd+le + + +s++dY+ +a lcl|FitnessBrowser__SB2B:6937577 158 DGIEIFDDI-DSPWPIVADMSSNIMSREIDVSRFALIYAGAQKNIGPSGLSIVIVRKDMLELPQLTQSSIMDYRLTA 233 ******998.7889*************************************************************** PP TIGR01364 229 endslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkee 305 ends+yntpptfa+y+++ v+kwlk+ GG+k +++ n eKa+ lY +id+ +fykn v++++Rs+mnv+F+l++e lcl|FitnessBrowser__SB2B:6937577 234 ENDSMYNTPPTFAWYLAAEVFKWLKSVGGIKGMAEVNAEKARRLYACIDSL-DFYKNGVAPQNRSQMNVTFQLADES 309 *************************************************77.6************************ PP TIGR01364 306 lekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358 l+k Flkeae+ glv+lkGhr+vGG+RasiYna+ple+v aLv+fm++F++kh lcl|FitnessBrowser__SB2B:6937577 310 LDKDFLKEAEALGLVALKGHRIVGGMRASIYNAMPLEGVDALVSFMRSFAAKH 362 **************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (364 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: 00:00:00.01 # Mc/sec: 11.62 // [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