Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_019868366.1 METMI_RS0121515 branched-chain amino acid transaminase
Query= reanno::psRCH2:GFF445 (307 letters) >NCBI__GCF_000384075.1:WP_019868366.1 Length = 307 Score = 440 bits (1132), Expect = e-128 Identities = 209/306 (68%), Positives = 253/306 (82%) Query: 1 MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTD 60 M+M DRDGVIW DG+ V+WR+A HVLTHTLHYG+GVFEG+RAY+ GTA+FR+Q HTD Sbjct: 1 MTMDDRDGVIWLDGKWVEWREAKVHVLTHTLHYGLGVFEGIRAYHATQGTAVFRMQEHTD 60 Query: 61 RLFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120 RLF SAHIMNM MP++K+EIN A R A+ +N L+SAYIR M FYGSEGMGLRA LKVHV Sbjct: 61 RLFRSAHIMNMLMPFTKDEINRAQRDALVKNQLDSAYIRTMCFYGSEGMGLRADNLKVHV 120 Query: 121 IVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGA 180 +VAAW WGAY+G E++E GI++RTSS+TR+H N TM +AK+NG YINS+LALQEA+S G Sbjct: 121 MVAAWPWGAYLGAESIEKGIRIRTSSYTRNHHNSTMCKAKANGNYINSILALQEALSNGY 180 Query: 181 DEALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKR 240 DEALMLD EG+ AEGS EN+FI++DG IYTPE T+ L GITR TV+ +A E G +++EKR Sbjct: 181 DEALMLDHEGFAAEGSAENLFIVRDGKIYTPETTSALEGITRDTVMKIAHEQGYEVIEKR 240 Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHA 300 ITRDE+Y ADEAFFTG+AAEVTPIRE+D R IG G RGPIT++LQ YFD V G+ DAHA Sbjct: 241 ITRDEIYCADEAFFTGSAAEVTPIRELDNRVIGSGSRGPITQQLQSLYFDAVHGRGDAHA 300 Query: 301 EWRTLV 306 +W T V Sbjct: 301 DWLTYV 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: 383 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: 307 Length adjustment: 27 Effective length of query: 280 Effective length of database: 280 Effective search space: 78400 Effective search space used: 78400 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_019868366.1 METMI_RS0121515 (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.22680.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-138 444.3 0.1 1.1e-137 444.1 0.1 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019868366.1 METMI_RS0121515 branched-chain a Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_019868366.1 METMI_RS0121515 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 444.1 0.1 1.1e-137 1.1e-137 1 298 [] 11 306 .. 11 306 .. 0.99 Alignments for each domain: == domain 1 score: 444.1 bits; conditional E-value: 1.1e-137 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 wldG+ v++++akvhvlth+lhYG gvfeGiRaY++ +g+a+fr++eh++Rl+ sa+i+++ +p++k+e lcl|NCBI__GCF_000384075.1:WP_019868366.1 11 WLDGKWVEWREAKVHVLTHTLHYGLGVFEGIRAYHATQGTAVFRMQEHTDRLFRSAHIMNMLMPFTKDE 79 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 ++ +++++l kn+l+saYiR + ++G+e++gl++ +lkv+v++aaw+wgaylg+e++ekGi++++ss+ lcl|NCBI__GCF_000384075.1:WP_019868366.1 80 INRAQRDALVKNQLDSAYIRTMCFYGSEGMGLRA-DNLKVHVMVAAWPWGAYLGAESIEKGIRIRTSSY 147 **********************************.899******************************* PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r+++ns + kaka+gnY+ns+la +eal++Gydea++Ld+eG+ aeGs en+fiv+dg+++tP++ +s lcl|NCBI__GCF_000384075.1:WP_019868366.1 148 TRNHHNSTMCKAKANGNYINSILALQEALSNGYDEALMLDHEGFAAEGSAENLFIVRDGKIYTPET-TS 215 *****************************************************************9.78 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L+gitrd+v+k+a+e+g+ev e+ri+r+e+y aDe+f+tG+aaevtPire+D+r ig+g+rGp+t++l lcl|NCBI__GCF_000384075.1:WP_019868366.1 216 ALEGITRDTVMKIAHEQGYEVIEKRITRDEIYCADEAFFTGSAAEVTPIRELDNRVIGSGSRGPITQQL 284 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewltyv 298 q+ +fd v+g+ +++++wltyv lcl|NCBI__GCF_000384075.1:WP_019868366.1 285 QSLYFDAVHGRGDAHADWLTYV 306 ********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (307 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.38 // [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