Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate GFF1394 HP15_1361 phosphoserine aminotransferase
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__Marino:GFF1394 Length = 347 Score = 380 bits (977), Expect = e-110 Identities = 192/349 (55%), Positives = 242/349 (69%), Gaps = 2/349 (0%) Query: 14 LPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVPSNYKVLFCH 73 +P VL+QA+ E+ DW G G SVME+SHR EF+Q+AE AEKD R+L V +Y VLF Sbjct: 1 MPESVLRQARDEMLDWRGTGMSVMEMSHRSDEFVQIAETAEKDLRELAGVSDDYAVLFMQ 60 Query: 74 GGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVTVDGLRAVKP 133 GG QF+ +PLN+LG+K +ADYV+ G W+ AI EA +Y NV A G + Sbjct: 61 GGASSQFSTIPLNLLGEKGSADYVNTGIWSKKAIAEASRYGKVNVV-ASSEDSGFTTIPD 119 Query: 134 MREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPIDVSRYGVIY 193 WQ S +AAYMHY PNETI G+ D P+ +VA D SS++LSRP+DVSR+GVIY Sbjct: 120 QSSWQTSADAAYMHYTPNETIGGLEFDFIPESPTAPLVA-DMSSSMLSRPVDVSRFGVIY 178 Query: 194 AGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTFAWYLSGLVF 253 AGAQKNIGP+GL +VI+R+DLLGKA P++++Y ++ DNGSM+NTP T++WYL+GLVF Sbjct: 179 AGAQKNIGPSGLVVVIIRKDLLGKARKETPTMMNYQVIADNGSMYNTPATYSWYLAGLVF 238 Query: 254 KWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQLADSALDKLF 313 KWLK GGV M +IN +KA LY ID ++FY N + RS MNVPF LAD AL+ F Sbjct: 239 KWLKEQGGVKAMGEINLRKARKLYDFIDTNEFYANPIDPRFRSWMNVPFTLADDALNGEF 298 Query: 314 LEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362 L+ + A GL L GHR VGGMRASIYNAMP GV AL D+M EF + G Sbjct: 299 LKGANARGLLNLAGHRSVGGMRASIYNAMPEAGVDALIDYMTEFAKERG 347 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: 14 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: 347 Length adjustment: 29 Effective length of query: 333 Effective length of database: 318 Effective search space: 105894 Effective search space used: 105894 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 GFF1394 HP15_1361 (phosphoserine 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.10767.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-156 505.9 0.0 3e-156 505.7 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF1394 HP15_1361 phosphoserine aminotra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1394 HP15_1361 phosphoserine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 505.7 0.0 3e-156 3e-156 11 357 .. 1 345 [. 1 346 [. 0.99 Alignments for each domain: == domain 1 score: 505.7 bits; conditional E-value: 3e-156 TIGR01364 11 lpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqfaavplnll 85 +pe+vl++a++e+ld++g+g+svme+sHRs+ef +++e+ae+dlreL ++d+y+vlf+qGGa++qf+++plnll lcl|FitnessBrowser__Marino:GFF1394 1 MPESVLRQARDEMLDWRGTGMSVMEMSHRSDEFVQIAETAEKDLRELAGVSDDYAVLFMQGGASSQFSTIPLNLL 75 89************************************************************************* PP TIGR01364 86 kekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylcanetieGvefkelp 160 ek ady++tG wskka++ea++++k v+vvas+e++ +++ipd+++++++ daay++++ neti G+ef+ +p lcl|FitnessBrowser__Marino:GFF1394 76 GEKGSADYVNTGIWSKKAIAEASRYGK-VNVVASSEDSGFTTIPDQSSWQTSADAAYMHYTPNETIGGLEFDFIP 149 *************************99.*********************************************** PP TIGR01364 161 evkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkilaendslyn 235 e+ +aplvaD+ss++lsr++dvs++g+iyaGaqKniGp+G++vvi+rkdll++a+ke+p++++Y+++a+n s+yn lcl|FitnessBrowser__Marino:GFF1394 150 ESPTAPLVADMSSSMLSRPVDVSRFGVIYAGAQKNIGPSGLVVVIIRKDLLGKARKETPTMMNYQVIADNGSMYN 224 *************************************************************************** PP TIGR01364 236 tpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeF 310 tp+t+++y++glv+kwlke+GGvk++ + n +Ka+ lY+ id++ +fy n+++++ Rs+mnv+Ftl+++ l+ eF lcl|FitnessBrowser__Marino:GFF1394 225 TPATYSWYLAGLVFKWLKEQGGVKAMGEINLRKARKLYDFIDTN-EFYANPIDPRFRSWMNVPFTLADDALNGEF 298 ******************************************77.5***************************** PP TIGR01364 311 lkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekk 357 lk a+++gl++l GhrsvGG+RasiYna+p ++v aL+d+m eF+k+ lcl|FitnessBrowser__Marino:GFF1394 299 LKGANARGLLNLAGHRSVGGMRASIYNAMPEAGVDALIDYMTEFAKE 345 ********************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (347 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: 7.97 // [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