Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate GFF448 HP15_436 branched-chain-amino-acid aminotransferase
Query= reanno::psRCH2:GFF445 (307 letters) >FitnessBrowser__Marino:GFF448 Length = 308 Score = 474 bits (1219), Expect = e-138 Identities = 230/307 (74%), Positives = 261/307 (85%) Query: 1 MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTD 60 MSMADRDGVIW DGE+V WRDA THVLTHTLHYG+G FEGVRAYNT +G AIFRL+ HTD Sbjct: 1 MSMADRDGVIWMDGEMVPWRDAKTHVLTHTLHYGLGCFEGVRAYNTANGPAIFRLKEHTD 60 Query: 61 RLFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120 RLF SAHI+NM MP+SK+EINEA RAAVRENNL+ AY+RPM F GSEGMGLRA LKVHV Sbjct: 61 RLFRSAHILNMKMPFSKDEINEAQRAAVRENNLDEAYLRPMAFLGSEGMGLRADNLKVHV 120 Query: 121 IVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGA 180 +VAAW W +YM EA E+GIKVRTSS+TRHHVNITM +AK+NG YINSMLAL EAISGGA Sbjct: 121 MVAAWSWPSYMSPEAKEMGIKVRTSSYTRHHVNITMCKAKANGNYINSMLALNEAISGGA 180 Query: 181 DEALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKR 240 +EAL+LD EGYVAEGSGENIFI++DGV++TPE+T+CL GITR T++ A E + I E+R Sbjct: 181 EEALLLDNEGYVAEGSGENIFIMRDGVLHTPELTSCLEGITRATIMDFARELNIPIKERR 240 Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHA 300 ITRDEVYIADEAFFTGTAAEV PIRE+DGR IG G+RGP+TEKLQ YFD V GK H+ Sbjct: 241 ITRDEVYIADEAFFTGTAAEVLPIRELDGRVIGAGKRGPVTEKLQAMYFDAVKGKLAEHS 300 Query: 301 EWRTLVK 307 W T VK Sbjct: 301 GWLTHVK 307 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: 419 Number of extensions: 12 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 GFF448 HP15_436 (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.30725.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-135 437.7 0.0 1.1e-135 437.5 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF448 HP15_436 branched-chain-amino-ac Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF448 HP15_436 branched-chain-amino-acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 437.5 0.0 1.1e-135 1.1e-135 1 298 [] 11 306 .. 11 306 .. 0.99 Alignments for each domain: == domain 1 score: 437.5 bits; conditional E-value: 1.1e-135 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtke 76 w+dGe+v+++dak+hvlth+lhYG g feG+RaY+t +g+aifrlkeh++Rl+ sa+il++++p+sk+e++e+++ lcl|FitnessBrowser__Marino:GFF448 11 WMDGEMVPWRDAKTHVLTHTLHYGLGCFEGVRAYNTANGPAIFRLKEHTDRLFRSAHILNMKMPFSKDEINEAQRA 86 9*************************************************************************** PP TIGR01122 77 vlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkaka 152 ++r+nnl++aY+Rp++++G+e++gl++ +lkv+v++aaw+w+ y+ ea e Gikv++ss++r++vn+ + kaka lcl|FitnessBrowser__Marino:GFF448 87 AVRENNLDEAYLRPMAFLGSEGMGLRA-DNLKVHVMVAAWSWPSYMSPEAKEMGIKVRTSSYTRHHVNITMCKAKA 161 ***************************.899********************************************* PP TIGR01122 153 agnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgiev 228 +gnY+ns+la ea++ G++ea+lLd+eGyvaeGsGenifi++dgvl tP++ +s+L+gitr +++++a+el i + lcl|FitnessBrowser__Marino:GFF448 162 NGNYINSMLALNEAISGGAEEALLLDNEGYVAEGSGENIFIMRDGVLHTPEL-TSCLEGITRATIMDFARELNIPI 236 ****************************************************.78********************* PP TIGR01122 229 keerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewltyv 298 ke+ri+r+e+y+aDe+f+tGtaaev Pire+Dgr ig+gkrGpvt+klq +fd v+gk ++++wlt+v lcl|FitnessBrowser__Marino:GFF448 237 KERRITRDEVYIADEAFFTGTAAEVLPIRELDGRVIGAGKRGPVTEKLQAMYFDAVKGKLAEHSGWLTHV 306 *******************************************************************987 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: 00:00:00.00 # Mc/sec: 9.33 // [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