Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate 8501549 DvMF_2268 branched-chain amino acid aminotransferase (RefSeq)
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >FitnessBrowser__Miya:8501549 Length = 307 Score = 357 bits (915), Expect = e-103 Identities = 170/302 (56%), Positives = 219/302 (72%) Query: 3 MADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKR 62 M + IW DGK + W +A +HVLTHTLHYG+GVFEG+RAYK ADGG+A+FRL+EH +R Sbjct: 1 MVQKAETIWFDGKQVPWDEANVHVLTHTLHYGVGVFEGIRAYKCADGGSAVFRLREHMQR 60 Query: 63 LLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVA 122 LLNSAKI +M +P+ + L A E ++ NKL Y+RP+ +VG+ +GV N + Sbjct: 61 LLNSAKILRMVIPYTVDQLVDAVEETLKRNKLAEGYIRPLSFVGAGAMGVYPGDNPVQTI 120 Query: 123 IAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYD 182 IA WPWGAYLG + + GIRVKTSSF RHHVN M +AKA G YVNS+LA EA ADGYD Sbjct: 121 IATWPWGAYLGAEALEHGIRVKTSSFCRHHVNAMMTKAKACGNYVNSVLAKMEAKADGYD 180 Query: 183 EALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRI 242 E L+LD G+VSE +GEN F+V + T L+S LDGITR+++ITLAR+ G +V+E++ Sbjct: 181 EGLMLDTQGFVSEATGENIFIVRGKLIKTTPLTSVLDGITRNSLITLARELGYEVVEQQF 240 Query: 243 TRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKYAN 302 TRDE+Y DEAFF GTAAE+TPIRE+D R IG G GP+T+ LQ +F V G++ YA+ Sbjct: 241 TRDELYIADEAFFCGTAAELTPIREVDLRVIGQGTAGPVTKHLQGEYFKAVKGENPAYAH 300 Query: 303 WL 304 WL Sbjct: 301 WL 302 Lambda K H 0.319 0.136 0.411 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: 334 Number of extensions: 6 Number of successful extensions: 1 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: 307 Length adjustment: 27 Effective length of query: 280 Effective length of database: 280 Effective search space: 78400 Effective search space used: 78400 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 8501549 DvMF_2268 (branched-chain amino acid aminotransferase (RefSeq))
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.10797.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-133 430.4 0.0 1.8e-133 430.2 0.0 1.0 1 lcl|FitnessBrowser__Miya:8501549 DvMF_2268 branched-chain amino a Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501549 DvMF_2268 branched-chain amino acid aminotransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 430.2 0.0 1.8e-133 1.8e-133 1 296 [. 9 303 .. 9 305 .. 0.99 Alignments for each domain: == domain 1 score: 430.2 bits; conditional E-value: 1.8e-133 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipyskeelvevtke 76 w+dG+ v++++a+vhvlth+lhYG gvfeGiRaY+ + g+a+frl+eh++Rl++sakilr+ ipy+ ++lv+++ e lcl|FitnessBrowser__Miya:8501549 9 WFDGKQVPWDEANVHVLTHTLHYGVGVFEGIRAYKCADgGSAVFRLREHMQRLLNSAKILRMVIPYTVDQLVDAVEE 85 9**********************************866599************************************ PP TIGR01122 77 vlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaa 153 +l++n+l + YiRpl +vGa+ +g++p d +v+ iia+w+wgaylg+eale+Gi+vk+ssf r++vn+++tkaka lcl|FitnessBrowser__Miya:8501549 86 TLKRNKLAEGYIRPLSFVGAGAMGVYP-GDNPVQTIIATWPWGAYLGAEALEHGIRVKTSSFCRHHVNAMMTKAKAC 161 ***************************.999********************************************** PP TIGR01122 154 gnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievke 230 gnY+ns+lak+ea++ Gyde+++Ld++G+v+e +Genifiv+ ++t p+ +s+L+gitr+++i+la+elg+ev+e lcl|FitnessBrowser__Miya:8501549 162 GNYVNSVLAKMEAKADGYDEGLMLDTQGFVSEATGENIFIVRGKLIKTTPL-TSVLDGITRNSLITLARELGYEVVE 237 **************************************************9.78*********************** PP TIGR01122 231 erisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewlt 296 ++++r+ely+aDe+f+ Gtaae+tPirevD r ig+g++Gpvtk+lq ++f+ v+g+++++++wl+ lcl|FitnessBrowser__Miya:8501549 238 QQFTRDELYIADEAFFCGTAAELTPIREVDLRVIGQGTAGPVTKHLQGEYFKAVKGENPAYAHWLH 303 ****************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (307 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: 00:00:00.04 # Mc/sec: 2.01 // [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