Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_027459212.1 K420_RS0117620 branched-chain amino acid transaminase
Query= reanno::psRCH2:GFF445 (307 letters) >NCBI__GCF_000519045.1:WP_027459212.1 Length = 306 Score = 448 bits (1153), Expect = e-131 Identities = 210/306 (68%), Positives = 254/306 (83%) Query: 1 MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTD 60 MSM+DRDG IW DG+LV WRDATTHVLTH+LHYGMGVFEGVRAY T GTAIFRL+ HT+ Sbjct: 1 MSMSDRDGFIWQDGKLVPWRDATTHVLTHSLHYGMGVFEGVRAYKTERGTAIFRLKEHTE 60 Query: 61 RLFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120 RLF SAHI M MPYS EE+NEA + +R NNLES Y+RP+ FYGSE MG+ G KVHV Sbjct: 61 RLFRSAHIFQMAMPYSAEELNEAQKEVIRANNLESGYLRPLAFYGSEKMGVSPKGAKVHV 120 Query: 121 IVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGA 180 I+AAW WGAY+G+E ++ GI+++TSS+TRHHVNITM RAK++G Y+NS+LA EA G Sbjct: 121 IIAAWPWGAYLGEEGMQRGIRIKTSSYTRHHVNITMVRAKASGNYMNSILANNEATGDGY 180 Query: 181 DEALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKR 240 DEAL+LDPEGYV EG+GENIFI+K+G +YTP++TACL GITR TV+ LA E G++++EKR Sbjct: 181 DEALLLDPEGYVCEGAGENIFIVKNGKLYTPDLTACLEGITRATVMQLAGELGIEVIEKR 240 Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHA 300 ITRDEVY ADEAFFTGTAAEVTPIRE+D R IG G RGPIT+ LQ+ YFD+V G++ AHA Sbjct: 241 ITRDEVYCADEAFFTGTAAEVTPIRELDNRQIGPGHRGPITKALQEKYFDVVYGRSAAHA 300 Query: 301 EWRTLV 306 +W +V Sbjct: 301 DWLAVV 306 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: 384 Number of extensions: 11 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: 306 Length adjustment: 27 Effective length of query: 280 Effective length of database: 279 Effective search space: 78120 Effective search space used: 78120 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 WP_027459212.1 K420_RS0117620 (branched-chain amino acid transaminase)
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.3379.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-143 462.5 0.0 3.1e-143 462.3 0.0 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027459212.1 K420_RS0117620 branched-chain am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027459212.1 K420_RS0117620 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 462.3 0.0 3.1e-143 3.1e-143 1 298 [] 11 306 .] 11 306 .] 0.99 Alignments for each domain: == domain 1 score: 462.3 bits; conditional E-value: 3.1e-143 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w dG+lv+++da++hvlth+lhYG+gvfeG+RaY+t++g+aifrlkeh+eRl+ sa+i+++ +pys+ee lcl|NCBI__GCF_000519045.1:WP_027459212.1 11 WQDGKLVPWRDATTHVLTHSLHYGMGVFEGVRAYKTERGTAIFRLKEHTERLFRSAHIFQMAMPYSAEE 79 99******************************************************************* PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l+e++kev+r+nnl+s Y+Rpl+++G+e++g++p ++kv+viiaaw+wgaylgee++++Gi++k+ss+ lcl|NCBI__GCF_000519045.1:WP_027459212.1 80 LNEAQKEVIRANNLESGYLRPLAFYGSEKMGVSP-KGAKVHVIIAAWPWGAYLGEEGMQRGIRIKTSSY 147 **********************************.6779****************************** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r++vn+ + +aka+gnY+ns+la+ ea+ Gydea+lLd eGyv eG+Genifivk+g+l+tP++ ++ lcl|NCBI__GCF_000519045.1:WP_027459212.1 148 TRHHVNITMVRAKASGNYMNSILANNEATGDGYDEALLLDPEGYVCEGAGENIFIVKNGKLYTPDL-TA 215 ******************************************************************.78 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L+gitr +v++la elgiev e+ri+r+e+y aDe+f+tGtaaevtPire+D+r+ig g+rGp+tk l lcl|NCBI__GCF_000519045.1:WP_027459212.1 216 CLEGITRATVMQLAGELGIEVIEKRITRDEVYCADEAFFTGTAAEVTPIRELDNRQIGPGHRGPITKAL 284 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewltyv 298 qe++fd+v+g+ ++++wl v lcl|NCBI__GCF_000519045.1:WP_027459212.1 285 QEKYFDVVYGRSAAHADWLAVV 306 ******************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (306 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: 7.58 // [ok]
This GapMind analysis is from Apr 10 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