Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate N515DRAFT_0573 N515DRAFT_0573 branched-chain amino acid aminotransferase
Query= reanno::Dyella79:N515DRAFT_2015 (305 letters) >FitnessBrowser__Dyella79:N515DRAFT_0573 Length = 313 Score = 383 bits (984), Expect = e-111 Identities = 185/300 (61%), Positives = 234/300 (78%), Gaps = 3/300 (1%) Query: 8 WIWQNGQIKPWREATTHVMSHALHYGSSVFEGIRSYATPDGAAIFRLTDHLKRLYQSAKI 67 ++W NGQIKPW EAT HV +HALHYGSSVFEG R YATP G A FRL DH +RL++SA++ Sbjct: 5 FLWHNGQIKPWTEATVHVSTHALHYGSSVFEGERVYATPQGPAYFRLADHTRRLFESARV 64 Query: 68 YDMVLPYSQDQIAAACRDVIKQNGLGAAYLRPVAYRGLGGFGLSAE--TPIDVAVAAWPM 125 Y++ + YS+D+I AAC +VI+ N +G+AY+RP+ +RG GG G+ A+ P+DVA+ A Sbjct: 65 YEIEVGYSEDEINAACMEVIRANRMGSAYVRPIVFRGAGGLGVLAKPGAPVDVAIMAMEW 124 Query: 126 GPYLGPEALESGIDACVSSWQRFAPNTIPAGAKAGGNYLSGQLIAREARRLGFGEGIALA 185 G YLG +A E G D CVSSWQR APNT+P+ AKAGGNYLS QLI EARR G+ EGIAL Sbjct: 125 GAYLG-DAREQGADVCVSSWQRPAPNTVPSWAKAGGNYLSSQLIGLEARRGGYAEGIALG 183 Query: 186 NTGLLSEGAGENLFLVFDGVLHTTPASASILTGITRHTLITLAREDGIEVIERDIPREYL 245 + GLLSEGAGEN+F+V +G L T P SA IL GITR T++TLA + GI+V ERD+PRE L Sbjct: 184 HNGLLSEGAGENVFVVKNGKLLTPPTSAGILAGITRDTVMTLAEDLGIKVEERDLPREAL 243 Query: 246 YLCDELLMCGTAAEITPIRSVDGKKIGSGKAGRVTRRMQELFFGLFNGKTNDQWGWLEPV 305 Y DE+ M GTAAEITP+RSVD K +G+G+ G +TR +Q+ FFGLF+G+T+D+WGWL PV Sbjct: 244 YTADEVFMTGTAAEITPVRSVDRKPVGTGRPGPITRALQDAFFGLFDGRTDDRWGWLAPV 303 Lambda K H 0.320 0.138 0.425 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: 353 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: 305 Length of database: 313 Length adjustment: 27 Effective length of query: 278 Effective length of database: 286 Effective search space: 79508 Effective search space used: 79508 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 N515DRAFT_0573 N515DRAFT_0573 (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.10696.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-125 403.0 0.0 4.2e-125 402.8 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 N515DRAFT_0573 branched-chain am Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 N515DRAFT_0573 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 402.8 0.0 4.2e-125 4.2e-125 1 298 [] 7 303 .. 7 303 .. 0.99 Alignments for each domain: == domain 1 score: 402.8 bits; conditional E-value: 4.2e-125 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipys 66 w +G++ ++ +a+vhv thalhYG++vfeG R+Y t++g+a frl +h+ Rl++sa+++++e+ ys lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 7 WHNGQIKPWTEATVHVSTHALHYGSSVFEGERVYATPQGPAYFRLADHTRRLFESARVYEIEVGYS 72 99**************************************************************** PP TIGR01122 67 keelvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGik 132 ++e++ +++ev+r+n + saY+Rp+v++Ga++lg+ +k +++v+v+i+a+ewgaylg+ a e+G + lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 73 EDEINAACMEVIRANRMGSAYVRPIVFRGAGGLGVLAKPGAPVDVAIMAMEWGAYLGD-AREQGAD 137 *********************************************************6.9****** PP TIGR01122 133 vkvssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgv 198 v vss++r a+n++p+ aka+gnYl+s+l++ ea+r Gy e+i+L ++G ++eG+Gen+f+vk+g+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 138 VCVSSWQRPAPNTVPSWAKAGGNYLSSQLIGLEARRGGYAEGIALGHNGLLSEGAGENVFVVKNGK 203 ****************************************************************** PP TIGR01122 199 lltPpvsesiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrki 264 lltPp+s iL gitrd+v++la++lgi+v+e+ + re+lytaDevf+tGtaae+tP+r+vD + + lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 204 LLTPPTSAGILAGITRDTVMTLAEDLGIKVEERDLPREALYTADEVFMTGTAAEITPVRSVDRKPV 269 ****************************************************************** PP TIGR01122 265 gegkrGpvtkklqeaffdlvegktekkeewltyv 298 g g+ Gp+t+ lq+aff l+ g+t+++++wl +v lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 270 GTGRPGPITRALQDAFFGLFDGRTDDRWGWLAPV 303 ******************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (313 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: 00:00:00.00 # Mc/sec: 11.61 // [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