Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_022948950.1 H035_RS0110590 branched-chain amino acid transaminase
Query= reanno::psRCH2:GFF445 (307 letters) >NCBI__GCF_000421465.1:WP_022948950.1 Length = 309 Score = 421 bits (1083), Expect = e-123 Identities = 201/302 (66%), Positives = 241/302 (79%) Query: 1 MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTD 60 M M D+DG IW DGE + WR+A HVLTHTLHYG GVFEG+RAY GTAIFRLQ HTD Sbjct: 1 MPMHDKDGEIWLDGEWLPWREAKVHVLTHTLHYGAGVFEGLRAYYGQRGTAIFRLQEHTD 60 Query: 61 RLFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120 RLF SAHIM M +PY KE +N AV N L+SAYIRPM FYG+EGMGLRA L++HV Sbjct: 61 RLFRSAHIMRMTIPYPKETLNRIQCEAVFRNGLDSAYIRPMCFYGAEGMGLRADNLELHV 120 Query: 121 IVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGA 180 +VAAW WGAY+G E LE GI+VRTSSFTR+H+N M +AK+NG Y+NSMLALQEA+ G Sbjct: 121 MVAAWEWGAYLGAENLEKGIRVRTSSFTRNHINSLMCKAKANGNYVNSMLALQEAVDTGF 180 Query: 181 DEALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKR 240 DEAL+LD +G +AEGSGENIF+++ G +YTP++T+ L GITR TV+T+A E GL+++EKR Sbjct: 181 DEALLLDHQGNIAEGSGENIFLVRSGKLYTPDLTSVLEGITRDTVMTIAREMGLEVIEKR 240 Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHA 300 +TRD+VY+ADEAFFTGTAAE+TPIREVDGR IG G RGP+TEKLQ YFD V G+ H Sbjct: 241 LTRDDVYVADEAFFTGTAAEITPIREVDGRQIGGGTRGPVTEKLQSLYFDYVHGRRSDHP 300 Query: 301 EW 302 EW Sbjct: 301 EW 302 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: 376 Number of extensions: 10 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: 309 Length adjustment: 27 Effective length of query: 280 Effective length of database: 282 Effective search space: 78960 Effective search space used: 78960 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_022948950.1 H035_RS0110590 (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.227423.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-136 439.5 0.0 3.1e-136 439.4 0.0 1.0 1 NCBI__GCF_000421465.1:WP_022948950.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000421465.1:WP_022948950.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 439.4 0.0 3.1e-136 3.1e-136 1 298 [] 11 306 .. 11 306 .. 0.99 Alignments for each domain: == domain 1 score: 439.4 bits; conditional E-value: 3.1e-136 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 wldGe +++++akvhvlth+lhYG gvfeG+RaY +++g+aifrl+eh++Rl+ sa+i+r+ ipy ke+l+ + NCBI__GCF_000421465.1:WP_022948950.1 11 WLDGEWLPWREAKVHVLTHTLHYGAGVFEGLRAYYGQRGTAIFRLQEHTDRLFRSAHIMRMTIPYPKETLNRI 83 9************************************************************************ PP TIGR01122 74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146 + e++ +n+l+saYiRp+ ++Gae++gl++ +l+ +v++aawewgaylg+e lekGi+v++ssf+r++ ns+ NCBI__GCF_000421465.1:WP_022948950.1 84 QCEAVFRNGLDSAYIRPMCFYGAEGMGLRA-DNLELHVMVAAWEWGAYLGAENLEKGIRVRTSSFTRNHINSL 155 ******************************.899*************************************** PP TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219 + kaka+gnY+ns+la +ea+ +G+dea+lLd++G++aeGsGenif+v+ g+l+tP++ +s+L+gitrd+v++ NCBI__GCF_000421465.1:WP_022948950.1 156 MCKAKANGNYVNSMLALQEAVDTGFDEALLLDHQGNIAEGSGENIFLVRSGKLYTPDL-TSVLEGITRDTVMT 227 **********************************************************.78************ PP TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekke 292 +a+e+g+ev e+r++r+++y+aDe+f+tGtaae+tPirevDgr+ig g+rGpvt+klq+ +fd v+g+ ++ NCBI__GCF_000421465.1:WP_022948950.1 228 IAREMGLEVIEKRLTRDDVYVADEAFFTGTAAEITPIREVDGRQIGGGTRGPVTEKLQSLYFDYVHGRRSDHP 300 ************************************************************************* PP TIGR01122 293 ewltyv 298 ewl +v NCBI__GCF_000421465.1:WP_022948950.1 301 EWLVPV 306 **9765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (309 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: 14.33 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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