Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate GFF1940 Psest_1983 phosphoserine aminotransferase
Query= BRENDA::P23721 (362 letters) >FitnessBrowser__psRCH2:GFF1940 Length = 361 Score = 416 bits (1068), Expect = e-121 Identities = 208/358 (58%), Positives = 260/358 (72%), Gaps = 2/358 (0%) Query: 5 FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64 FNF +GPA LP VL++AQ EL DW+G G SVME+SHR E+ +AE+AE+D RDLL +P Sbjct: 6 FNFCAGPAALPEAVLQRAQAELLDWHGKGLSVMEMSHRSDEYTAIAEKAEQDLRDLLAIP 65 Query: 65 SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124 SNYKVLF GG QFA +PLN+L + ADY+D G W+ AI+EA+++ NV + Sbjct: 66 SNYKVLFLQGGASQQFAEIPLNLLPEDGVADYIDTGIWSRKAIEEARRFGNVNVAASAKP 125 Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184 +D A+ +WQLS+ AAY+HY NETI G+ D P+ G D + D SS ILSR I Sbjct: 126 LDYF-AIPGQNDWQLSERAAYLHYASNETIGGLQFDWVPEVG-DTPLVVDMSSDILSRTI 183 Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244 DVS++G+IYAGAQKNIGP+GL +VIVREDLLG+A ACP++LDY I DNGSM+NTP TF Sbjct: 184 DVSKFGLIYAGAQKNIGPSGLVVVIVREDLLGRARSACPTMLDYKIAADNGSMYNTPATF 243 Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304 +WYLSGLVF+WLK GGV M++ N+ K ++LYG ID SDFY N +A RS MNVPF+L Sbjct: 244 SWYLSGLVFEWLKEQGGVEAMEQRNRAKKDMLYGAIDASDFYTNPIAVNARSWMNVPFRL 303 Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362 AD LDK FL + A GL LKGHR VGGMRASIYNA+ L+ V+AL +M EFE+ HG Sbjct: 304 ADERLDKSFLAGADARGLLNLKGHRSVGGMRASIYNAVGLDAVEALVAYMAEFEKEHG 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: 421 Number of extensions: 13 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: 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 GFF1940 Psest_1983 (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.22849.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-168 544.3 0.0 6.4e-168 544.1 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF1940 Psest_1983 phosphoserine aminotr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1940 Psest_1983 phosphoserine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 544.1 0.0 6.4e-168 6.4e-168 2 358 .] 6 360 .. 5 360 .. 0.99 Alignments for each domain: == domain 1 score: 544.1 bits; conditional E-value: 6.4e-168 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattq 76 +nF+aGPaalpe+vl++aq+elld++g+glsvme+sHRs+e+++++e+ae+dlr+Ll ip+ny+vlflqGGa++q lcl|FitnessBrowser__psRCH2:GFF1940 6 FNFCAGPAALPEAVLQRAQAELLDWHGKGLSVMEMSHRSDEYTAIAEKAEQDLRDLLAIPSNYKVLFLQGGASQQ 80 8************************************************************************** PP TIGR01364 77 faavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylcaneti 151 fa++plnll e+ vadyi tG ws+ka++ea+++++ v+v+as++ +y +ip +++++l+e+aay+++++neti lcl|FitnessBrowser__psRCH2:GFF1940 81 FAEIPLNLLPEDGVADYIDTGIWSRKAIEEARRFGN-VNVAASAKPLDYFAIPGQNDWQLSERAAYLHYASNETI 154 **********************************99.************************************** PP TIGR01364 152 eGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYki 226 G++f+++pev ++plv+D+ssdilsr+idvsk+gliyaGaqKniGp+G++vvivr+dll+ra++ +p++ldYki lcl|FitnessBrowser__psRCH2:GFF1940 155 GGLQFDWVPEVGDTPLVVDMSSDILSRTIDVSKFGLIYAGAQKNIGPSGLVVVIVREDLLGRARSACPTMLDYKI 229 *************************************************************************** PP TIGR01364 227 laendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtl 301 +a+n s+yntp+tf++y++glv++wlke+GGv+++e++n++K+++lY aid+s+ fy+n+++ +aRs+mnv+F+l lcl|FitnessBrowser__psRCH2:GFF1940 230 AADNGSMYNTPATFSWYLSGLVFEWLKEQGGVEAMEQRNRAKKDMLYGAIDASD-FYTNPIAVNARSWMNVPFRL 303 ***************************************************996.******************** PP TIGR01364 302 kkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358 ++e+l+k+Fl+ a ++gl++lkGhrsvGG+RasiYna+ l++v+aLv++m eFek+h lcl|FitnessBrowser__psRCH2:GFF1940 304 ADERLDKSFLAGADARGLLNLKGHRSVGGMRASIYNAVGLDAVEALVAYMAEFEKEH 360 ******************************************************997 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.99 // [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