Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate CA265_RS03895 CA265_RS03895 phosphoserine transaminase
Query= SwissProt::Q9RME2 (361 letters) >FitnessBrowser__Pedo557:CA265_RS03895 Length = 365 Score = 320 bits (820), Expect = 4e-92 Identities = 165/353 (46%), Positives = 235/353 (66%), Gaps = 4/353 (1%) Query: 7 NFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPN 66 NF AGP LP +E+A + ++N+ +S++E+SHRS +E+V + Q L+RELL +PN Sbjct: 6 NFGAGPCILPSSVMEQAAQAVINWGGMGLSILEVSHRSPEFEDVVLKTQLLVRELLSVPN 65 Query: 67 DYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKAN 126 Y +LFLQGGAS QF M+ MN L+ G Y+ TG +++KA+KEAKL GE + AS+K Sbjct: 66 HYSVLFLQGGASTQFAMVAMNFLSAGKKAAYLDTGYFAQKAIKEAKLFGEVELVASSKDK 125 Query: 127 SYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVN 186 Y IPD +F +++ AY+H TSNNTI GT+ +F N P++ DMSSDI SR + V+ Sbjct: 126 DYAYIPD--QFNVDQESAYIHYTSNNTIEGTEIFDFSP-NGVPVVCDMSSDIFSRKINVS 182 Query: 187 QFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTPPTFSIY 246 F +IYAGAQKN+GP+G+T+VI K + LN +++P+M+ Y + S+YNTPP FSIY Sbjct: 183 DFDLIYAGAQKNMGPAGMTLVIAKNEFLNQAKKEIPSMMDYRIFRDNMSMYNTPPVFSIY 242 Query: 247 MLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRN 306 + L W+KD GG I ++N EKAK++Y ID + FY G A+ RS MNVTF N Sbjct: 243 VAMLNLLWLKDQGGVSGIEQRNIEKAKLLYAEIDRNPLFY-GTADVAHRSRMNVTFLAVN 301 Query: 307 EELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKE 359 +++ FL A +QG VG+ G+R+VGG RAS+YNA+P+ + L M F++ Sbjct: 302 KDVEGGFLKFAADQGIVGIKGYRTVGGFRASLYNALPLSSVEVLVNAMASFEK 354 Lambda K H 0.316 0.132 0.372 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: 350 Number of extensions: 10 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: 361 Length of database: 365 Length adjustment: 29 Effective length of query: 332 Effective length of database: 336 Effective search space: 111552 Effective search space used: 111552 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate CA265_RS03895 CA265_RS03895 (phosphoserine 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.26688.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-141 456.3 0.4 3.6e-141 456.1 0.4 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS03895 CA265_RS03895 phosphoserine tran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS03895 CA265_RS03895 phosphoserine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 456.1 0.4 3.6e-141 3.6e-141 2 357 .. 5 355 .. 4 356 .. 0.98 Alignments for each domain: == domain 1 score: 456.1 bits; conditional E-value: 3.6e-141 TIGR01364 2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 +nF+aGP++lp++v+e+a++ ++++ g+gls++e+sHRs efe+vv +++ +reLl++p++y+vlfl lcl|FitnessBrowser__Pedo557:CA265_RS03895 5 HNFGAGPCILPSSVMEQAAQAVINWGGMGLSILEVSHRSPEFEDVVLKTQLLVRELLSVPNHYSVLFL 72 8******************************************************************* PP TIGR01364 70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelk 137 qGGa+tqfa+v++n+l+++k+a+y+ tG++++ka+keak +++ v+ vas+++k+y ip ++++++ lcl|FitnessBrowser__Pedo557:CA265_RS03895 73 QGGASTQFAMVAMNFLSAGKKAAYLDTGYFAQKAIKEAKLFGE-VELVASSKDKDYAYIP--DQFNVD 137 *****************************************88.****************..789999 PP TIGR01364 138 edaayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvi 205 +++ay+++++n+tieG+e+ + + +p+v+D+ssdi+srki+vs+++liyaGaqKn+GpaG+t+vi lcl|FitnessBrowser__Pedo557:CA265_RS03895 138 QESAYIHYTSNNTIEGTEIFDFS-PNGVPVVCDMSSDIFSRKINVSDFDLIYAGAQKNMGPAGMTLVI 204 99****************99765.6889**************************************** PP TIGR01364 206 vrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllY 273 +++ l++akke+ps++dY+i +n s+yntpp+f+iyv+ l l wlk++GGv+ +e++n eKakllY lcl|FitnessBrowser__Pedo557:CA265_RS03895 205 AKNEFLNQAKKEIPSMMDYRIFRDNMSMYNTPPVFSIYVAMLNLLWLKDQGGVSGIEQRNIEKAKLLY 272 ******************************************************************** PP TIGR01364 274 eaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpl 341 id++ ++ ++++ ++Rs+mnv+F ++++e Flk a+++g+v++kG+r+vGG+Ras+Ynalpl lcl|FitnessBrowser__Pedo557:CA265_RS03895 273 AEIDRNP-LFYGTADVAHRSRMNVTFLAVNKDVEGGFLKFAADQGIVGIKGYRTVGGFRASLYNALPL 339 ****997.666889****************************************************** PP TIGR01364 342 eevqaLvdfmkeFekk 357 +v+ Lv+ m +Fek lcl|FitnessBrowser__Pedo557:CA265_RS03895 340 SSVEVLVNAMASFEKI 355 *************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (358 nodes) Target sequences: 1 (365 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: 9.73 // [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