Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate AZOBR_RS16425 AZOBR_RS16425 branched-chain amino acid aminotransferase
Query= reanno::psRCH2:GFF445 (307 letters) >lcl|FitnessBrowser__azobra:AZOBR_RS16425 AZOBR_RS16425 branched-chain amino acid aminotransferase Length = 290 Score = 242 bits (618), Expect = 7e-69 Identities = 130/290 (44%), Positives = 176/290 (60%), Gaps = 7/290 (2%) Query: 5 DRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTDRLFD 64 DRDGVIWYDG LV WRDA HVL+H LHY VFEG R YN GT +F+L H++RL Sbjct: 8 DRDGVIWYDGALVPWRDANLHVLSHGLHYASCVFEGERVYN---GT-VFKLTEHSERLAA 63 Query: 65 SAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHVIVAA 124 SA I+ +PYS EI+ AT V+ AY+RP+ + GSE MG+ A ++HV +A Sbjct: 64 SARILGFELPYSVAEIDAATNETVKAMGFTDAYVRPVAWRGSEMMGVAAQASRIHVAIAV 123 Query: 125 WHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGADEAL 184 W W +Y EA GIK+ S + R ++ T +K+ G Y+ L+ EA + G +AL Sbjct: 124 WQWPSYFSPEAKMAGIKLTWSRWRRPAPDMAPTASKAAGLYMICTLSKHEAEAEGYQDAL 183 Query: 185 MLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKRITRD 244 MLD GY+AE +G N+F++ DG I+TP+ L+GITR TV+ LA G++++E+ I D Sbjct: 184 MLDYRGYLAEATGANLFLVMDGKIHTPKPDCFLDGITRRTVIDLAKARGIEVIERHIQPD 243 Query: 245 EVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTG 294 E+ E F TGTAAEVTP+ ++ GR + E L K Y LV G Sbjct: 244 ELANTQEVFLTGTAAEVTPVGQIGDHRFTPGR---VCETLVKDYDALVRG 290 Lambda K H 0.319 0.135 0.400 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: 266 Number of extensions: 6 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: 307 Length of database: 290 Length adjustment: 27 Effective length of query: 280 Effective length of database: 263 Effective search space: 73640 Effective search space used: 73640 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: 48 (23.1 bits)
Align candidate AZOBR_RS16425 AZOBR_RS16425 (branched-chain amino acid aminotransferase)
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))
# 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/TIGR01122.hmm # target sequence database: /tmp/gapView.8311.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01122 [M=298] Accession: TIGR01122 Description: ilvE_I: branched-chain amino acid aminotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-90 289.6 0.0 1.4e-90 289.5 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS16425 AZOBR_RS16425 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS16425 AZOBR_RS16425 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 289.5 0.0 1.4e-90 1.4e-90 1 285 [. 14 289 .. 14 290 .] 0.96 Alignments for each domain: == domain 1 score: 289.5 bits; conditional E-value: 1.4e-90 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w+dG lv+++da++hvl+h+lhY + vfeG R+Y++ ++f+l+eh eRl sa+il +e+pys e lcl|FitnessBrowser__azobra:AZOBR_RS16425 14 WYDGALVPWRDANLHVLSHGLHYASCVFEGERVYNG----TVFKLTEHSERLAASARILGFELPYSVAE 78 9***********************************....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 + +t+e++++ ++++aY+Rp++++G+e +g+ ++++ +++v+ia+w+w+ y+ ea Gik + s + lcl|FitnessBrowser__azobra:AZOBR_RS16425 79 IDAATNETVKAMGFTDAYVRPVAWRGSEMMGVAAQAS-RIHVAIAVWQWPSYFSPEAKMAGIKLTWSRW 146 **********************************655.9****************************** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr a+++ pt+ kaag Y+ +l k+ea ++Gy++a++Ld Gy+ae +G n+f+v dg++ tP+ + lcl|FitnessBrowser__azobra:AZOBR_RS16425 147 RRPAPDMAPTASKAAGLYMICTLSKHEAEAEGYQDALMLDYRGYLAEATGANLFLVMDGKIHTPKP-DC 214 *****************************************************************9.99 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 L+gitr +vi+lak +giev e++i +el + evfltGtaaevtP+ ++ + + G v ++l lcl|FitnessBrowser__azobra:AZOBR_RS16425 215 FLDGITRRTVIDLAKARGIEVIERHIQPDELANTQEVFLTGTAAEVTPVGQIGDHRFTP---GRVCETL 280 ****************************************************9998866...5567777 PP TIGR01122 277 qeaffdlve 285 + + lv+ lcl|FitnessBrowser__azobra:AZOBR_RS16425 281 VKDYDALVR 289 777777665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (290 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: 00:00:00.00 # Mc/sec: 9.98 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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