Align branched-chain-amino-acid aminotransferase subunit (EC 2.6.1.6; EC 2.6.1.42) (characterized)
to candidate Dsui_2030 Dsui_2030 branched-chain amino acid aminotransferase, group I
Query= metacyc::MONOMER-11691 (307 letters) >FitnessBrowser__PS:Dsui_2030 Length = 308 Score = 372 bits (956), Expect = e-108 Identities = 180/304 (59%), Positives = 225/304 (74%) Query: 1 MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYDTPQGTAIFRLQAHTD 60 MSM +RDG IW DG + WRDA HVL+HTLHYG G FEG+RAY TP+G AIFRL+ H Sbjct: 1 MSMENRDGFIWLDGHWLPWRDAKVHVLSHTLHYGYGCFEGIRAYATPRGPAIFRLEEHLR 60 Query: 61 RLFDSAHIMNMQIPYSRDEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120 RL DSAHI+ + +P+SR E+ + R AV N L+SAYIRP+VF G E +G+ +G + HV Sbjct: 61 RLADSAHILAIDLPWSRAELAQVCREAVSRNGLDSAYIRPLVFLGPEKVGVDPAGAQTHV 120 Query: 121 IIAAWSWGAYMGEEALQQGIKVRTSSFTRHHVNISMTRAKSNGAYINSMLALQEAISGGA 180 ++AAW WGAY+G +AL+QGI+VR SS+ RHH N+ M RAK+ Y NS+LA++EA G Sbjct: 121 MVAAWPWGAYLGGDALEQGIRVRISSYARHHPNVQMCRAKAISTYSNSILAVREARRDGY 180 Query: 181 DEAMMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRNTILTLAAEHGFKLVEKR 240 DEA++LD EGYVAEGSGEN+F+++DG + PE T+ L+GITR +I LA E G L KR Sbjct: 181 DEALLLDTEGYVAEGSGENLFLVRDGELLEPETTSALDGITRRSIHVLAREAGLTLRAKR 240 Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRKIGAGRRGPVTEKLQKAYFDLVSGKTEAHA 300 ITRDEVY ADE F TGTAAEVTP+ EVD R IG G+ GPVT LQ+ YF V G+ EAHA Sbjct: 241 ITRDEVYCADEVFLTGTAAEVTPVVEVDRRSIGTGQPGPVTRLLQQRYFACVRGEDEAHA 300 Query: 301 EWRT 304 +W T Sbjct: 301 DWLT 304 Lambda K H 0.319 0.134 0.394 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: 383 Number of extensions: 9 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: 308 Length adjustment: 27 Effective length of query: 280 Effective length of database: 281 Effective search space: 78680 Effective search space used: 78680 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 Dsui_2030 Dsui_2030 (branched-chain amino acid aminotransferase, group I)
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.carbon/TIGR01122.hmm # target sequence database: /tmp/gapView.21050.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-130 418.4 0.0 8.3e-130 418.2 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_2030 Dsui_2030 branched-chain amino a Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_2030 Dsui_2030 branched-chain amino acid aminotransferase, group I # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 418.2 0.0 8.3e-130 8.3e-130 1 297 [. 11 305 .. 11 306 .. 0.99 Alignments for each domain: == domain 1 score: 418.2 bits; conditional E-value: 8.3e-130 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtkev 77 wldG+ ++++dakvhvl+h+lhYG g feGiRaY t++g+aifrl+eh+ Rl dsa+il +++p+s+ el +v++e+ lcl|FitnessBrowser__PS:Dsui_2030 11 WLDGHWLPWRDAKVHVLSHTLHYGYGCFEGIRAYATPRGPAIFRLEEHLRRLADSAHILAIDLPWSRAELAQVCREA 87 9**************************************************************************** PP TIGR01122 78 lrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaag 154 + +n+l+saYiRplv++G e++g++p ++++++v++aaw+wgaylg +ale+Gi+v++ss++r+++n+ + +aka + lcl|FitnessBrowser__PS:Dsui_2030 88 VSRNGLDSAYIRPLVFLGPEKVGVDP-AGAQTHVMVAAWPWGAYLGGDALEQGIRVRISSYARHHPNVQMCRAKAIS 163 **************************.999*********************************************** PP TIGR01122 155 nYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkee 231 +Y ns+la ea+r Gydea+lLd+eGyvaeGsGen+f+v+dg+ll P++ +s+L+gitr ++ la+e g++++ + lcl|FitnessBrowser__PS:Dsui_2030 164 TYSNSILAVREARRDGYDEALLLDTEGYVAEGSGENLFLVRDGELLEPET-TSALDGITRRSIHVLAREAGLTLRAK 239 *************************************************9.78************************ PP TIGR01122 232 risreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewlty 297 ri+r+e+y aDevfltGtaaevtP++evD r+ig g+ Gpvt+ lq+++f v+g++e++++wlt+ lcl|FitnessBrowser__PS:Dsui_2030 240 RITRDEVYCADEVFLTGTAAEVTPVVEVDRRSIGTGQPGPVTRLLQQRYFACVRGEDEAHADWLTP 305 ****************************************************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (308 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: 6.57 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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:
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