Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_028489329.1 Q394_RS0110920 branched-chain amino acid transaminase
Query= BRENDA::O86428 (307 letters) >NCBI__GCF_000621325.1:WP_028489329.1 Length = 306 Score = 445 bits (1145), Expect = e-130 Identities = 208/306 (67%), Positives = 259/306 (84%) Query: 1 MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYDTPQGTAIFRLQAHTD 60 MSM+DRDG+IW DGE+V WR+A HVLTHTLHYGMGVFEGVRAY T QGTAIFRLQ HTD Sbjct: 1 MSMSDRDGLIWLDGEMVPWREAKVHVLTHTLHYGMGVFEGVRAYKTDQGTAIFRLQEHTD 60 Query: 61 RLFDSAHIMNMQIPYSRDEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120 RLF+SA IM M +PYS+D + EA +AAVR+N+L+SAYIRPM FYGSEGMGLRA L+ H Sbjct: 61 RLFNSAKIMRMAMPYSKDVLMEAQKAAVRDNDLDSAYIRPMCFYGSEGMGLRADNLETHA 120 Query: 121 IIAAWSWGAYMGEEALQQGIKVRTSSFTRHHVNISMTRAKSNGAYINSMLALQEAISGGA 180 ++AAW+W AY+G E +++GI+++TS+FTRHHVNI+M +AK+NG Y+NSMLAL+EA+ G Sbjct: 121 MVAAWTWSAYLGAENMEKGIRIKTSTFTRHHVNITMCKAKANGNYMNSMLALREALDDGY 180 Query: 181 DEAMMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRNTILTLAAEHGFKLVEKR 240 DEA++LD +GYVAEGS EN F++KDG+IYTP++T+ L+GITR TIL LA + G ++ EKR Sbjct: 181 DEALLLDVDGYVAEGSAENFFLVKDGIIYTPDLTSALDGITRKTILRLATDLGIEVREKR 240 Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRKIGAGRRGPVTEKLQKAYFDLVSGKTEAHA 300 ITRDEVYIADEAFF+GTAAEVTPIRE+D R IG+G RGP+TEKLQ YFD+V G+ E + Sbjct: 241 ITRDEVYIADEAFFSGTAAEVTPIRELDRRSIGSGTRGPITEKLQSLYFDVVYGRAEKYR 300 Query: 301 EWRTLV 306 +W T V Sbjct: 301 DWLTYV 306 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: 390 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: 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_028489329.1 Q394_RS0110920 (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.25444.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-141 456.9 0.1 1.6e-141 456.7 0.1 1.0 1 lcl|NCBI__GCF_000621325.1:WP_028489329.1 Q394_RS0110920 branched-chain am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000621325.1:WP_028489329.1 Q394_RS0110920 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 456.7 0.1 1.6e-141 1.6e-141 1 298 [] 11 306 .] 11 306 .] 0.99 Alignments for each domain: == domain 1 score: 456.7 bits; conditional E-value: 1.6e-141 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 wldGe+v++++akvhvlth+lhYG+gvfeG+RaY+td+g+aifrl+eh++Rl++saki+r+ +pysk+ lcl|NCBI__GCF_000621325.1:WP_028489329.1 11 WLDGEMVPWREAKVHVLTHTLHYGMGVFEGVRAYKTDQGTAIFRLQEHTDRLFNSAKIMRMAMPYSKDV 79 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l+e++k ++r n+l+saYiRp+ ++G+e++gl++ +l+++ ++aaw+w aylg+e +ekGi++k+s+f lcl|NCBI__GCF_000621325.1:WP_028489329.1 80 LMEAQKAAVRDNDLDSAYIRPMCFYGSEGMGLRA-DNLETHAMVAAWTWSAYLGAENMEKGIRIKTSTF 147 **********************************.899******************************* PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r++vn+ + kaka+gnY+ns+la eal Gydea+lLd +GyvaeGs en+f+vkdg ++tP++ +s lcl|NCBI__GCF_000621325.1:WP_028489329.1 148 TRHHVNITMCKAKANGNYMNSMLALREALDDGYDEALLLDVDGYVAEGSAENFFLVKDGIIYTPDL-TS 215 ******************************************************************.78 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L+gitr ++++la++lgiev+e+ri+r+e+y+aDe+f++GtaaevtPire+D r+ig+g+rGp+t+kl lcl|NCBI__GCF_000621325.1:WP_028489329.1 216 ALDGITRKTILRLATDLGIEVREKRITRDEVYIADEAFFSGTAAEVTPIRELDRRSIGSGTRGPITEKL 284 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewltyv 298 q+ +fd+v+g+ ek+ +wltyv lcl|NCBI__GCF_000621325.1:WP_028489329.1 285 QSLYFDVVYGRAEKYRDWLTYV 306 ********************98 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.30 // [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