Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_029933850.1 N746_RS0102835 branched-chain amino acid transaminase
Query= BRENDA::O86428 (307 letters) >NCBI__GCF_000711195.1:WP_029933850.1 Length = 308 Score = 476 bits (1224), Expect = e-139 Identities = 226/306 (73%), Positives = 265/306 (86%) Query: 2 SMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYDTPQGTAIFRLQAHTDR 61 +M+DRDG+IW DG++V WR+A THVLTHTLHYGMGVFEGVRAYD QGTAIFRL+AHTDR Sbjct: 3 TMSDRDGLIWMDGQMVPWREANTHVLTHTLHYGMGVFEGVRAYDAEQGTAIFRLEAHTDR 62 Query: 62 LFDSAHIMNMQIPYSRDEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHVI 121 LF+SA IMNM +P+ + +NEA RAAVREN L+SAYIRPMV+YGSEGMGLRA LK HVI Sbjct: 63 LFNSAKIMNMPMPFDKTTLNEAQRAAVRENGLKSAYIRPMVYYGSEGMGLRADNLKTHVI 122 Query: 122 IAAWSWGAYMGEEALQQGIKVRTSSFTRHHVNISMTRAKSNGAYINSMLALQEAISGGAD 181 IAAW WGAYMGEE L +GIKV TSS+TRHHVNI+MT+AK+NGAY+NSMLALQEA+S G D Sbjct: 123 IAAWEWGAYMGEENLTRGIKVATSSYTRHHVNITMTKAKANGAYMNSMLALQEAVSHGCD 182 Query: 182 EAMMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRNTILTLAAEHGFKLVEKRI 241 EA++LD EGYV EGSGEN F+I+DGVIYTPE+TA L+GITR T++ LA E G+++VEKRI Sbjct: 183 EALLLDTEGYVCEGSGENFFMIRDGVIYTPELTAALDGITRKTVMQLARECGYEVVEKRI 242 Query: 242 TRDEVYIADEAFFTGTAAEVTPIREVDGRKIGAGRRGPVTEKLQKAYFDLVSGKTEAHAE 301 TRDEVYIADEAFFTGTAAEVTPIRE+D R IG G RGP+TE+LQ YFD+V G++ AH + Sbjct: 243 TRDEVYIADEAFFTGTAAEVTPIRELDNRPIGQGSRGPITERLQSLYFDVVHGRSAAHLD 302 Query: 302 WRTLVK 307 W VK Sbjct: 303 WLATVK 308 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: 434 Number of extensions: 7 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 WP_029933850.1 N746_RS0102835 (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.9289.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-140 451.9 0.1 5.4e-140 451.7 0.1 1.0 1 lcl|NCBI__GCF_000711195.1:WP_029933850.1 N746_RS0102835 branched-chain am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711195.1:WP_029933850.1 N746_RS0102835 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.7 0.1 5.4e-140 5.4e-140 1 298 [] 12 307 .. 12 307 .. 0.99 Alignments for each domain: == domain 1 score: 451.7 bits; conditional E-value: 5.4e-140 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w+dG++v++++a++hvlth+lhYG+gvfeG+RaY++++g+aifrl+ h++Rl++saki+++++p+ k + lcl|NCBI__GCF_000711195.1:WP_029933850.1 12 WMDGQMVPWREANTHVLTHTLHYGMGVFEGVRAYDAEQGTAIFRLEAHTDRLFNSAKIMNMPMPFDKTT 80 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l+e+++ ++r+n+lksaYiRp+vy+G+e++gl++ +lk++viiaawewgay+gee l +Gikv +ss+ lcl|NCBI__GCF_000711195.1:WP_029933850.1 81 LNEAQRAAVRENGLKSAYIRPMVYYGSEGMGLRA-DNLKTHVIIAAWEWGAYMGEENLTRGIKVATSSY 148 **********************************.899******************************* PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r++vn+ +tkaka+g+Y+ns+la +ea+++G dea+lLd+eGyv eGsGen+f+++dgv++tP++ ++ lcl|NCBI__GCF_000711195.1:WP_029933850.1 149 TRHHVNITMTKAKANGAYMNSMLALQEAVSHGCDEALLLDTEGYVCEGSGENFFMIRDGVIYTPEL-TA 216 ******************************************************************.77 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L+gitr +v++la+e g+ev+e+ri+r+e+y+aDe+f+tGtaaevtPire+D+r ig+g+rGp+t++l lcl|NCBI__GCF_000711195.1:WP_029933850.1 217 ALDGITRKTVMQLARECGYEVVEKRITRDEVYIADEAFFTGTAAEVTPIRELDNRPIGQGSRGPITERL 285 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewltyv 298 q+ +fd+v+g+ ++ +wl +v lcl|NCBI__GCF_000711195.1:WP_029933850.1 286 QSLYFDVVHGRSAAHLDWLATV 307 ******************9876 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: 7.63 // [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