Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_010532003.1 ON01_RS15935 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_000224785.1:WP_010532003.1 Length = 369 Score = 505 bits (1300), Expect = e-148 Identities = 240/360 (66%), Positives = 296/360 (82%), Gaps = 1/360 (0%) Query: 3 KQTIRVELTSTKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAM 62 +Q IR E+ S+ K KP +QL FG +FTDHMF+MDY ADKGW+DPRI+PY+PL+++P+AM Sbjct: 5 QQGIRTEICSSGKEKPKSDQLEFGTIFTDHMFMMDYTADKGWHDPRIVPYEPLNIEPSAM 64 Query: 63 VYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVA 122 V+HYGQ+VFEG+KAY++ D LFRP++N R+N SN RLCIP IDE L+ LKQLV Sbjct: 65 VFHYGQSVFEGMKAYLTSDGDAQLFRPQRNFSRMNHSNSRLCIPPIDEAFALKALKQLVG 124 Query: 123 IDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVE 182 ++KDWIP AEGTSLYIRPFII+TE FLGVA S YK +IILSPVG+YYKEGI PVKIAVE Sbjct: 125 LEKDWIPEAEGTSLYIRPFIISTEAFLGVAPSSHYKFIIILSPVGAYYKEGINPVKIAVE 184 Query: 183 SEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFK 242 ++VR VKGGTG AKT GNYA+SLKAQ++A E G +QVLWLDG+E+KYIEEVGSMN+FFK Sbjct: 185 HDYVRTVKGGTGEAKTGGNYAASLKAQEMAAE-GIAQVLWLDGVERKYIEEVGSMNVFFK 243 Query: 243 INGEIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTG 302 I+G +VTP LNGSILEG+TRNSVI LLK+W + V ERK++++EVIQAHKDG LEEAFG G Sbjct: 244 IDGTVVTPALNGSILEGVTRNSVIQLLKYWNVPVEERKLSMEEVIQAHKDGKLEEAFGAG 303 Query: 303 TAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEVAALTES 362 TAAVISP+GEL+ ++ + IN G TG IAK+LYDT+TGIQ G + D F W +V L ++ Sbjct: 304 TAAVISPIGELVRGEKHIEINEGNTGAIAKRLYDTLTGIQYGKIEDPFDWVEKVKDLKQT 363 Lambda K H 0.316 0.135 0.390 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: 510 Number of extensions: 16 Number of successful extensions: 2 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: 363 Length of database: 369 Length adjustment: 30 Effective length of query: 333 Effective length of database: 339 Effective search space: 112887 Effective search space used: 112887 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_010532003.1 ON01_RS15935 (branched-chain amino acid aminotransferase)
to HMM TIGR01123 (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/TIGR01123.hmm # target sequence database: /tmp/gapView.1898044.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01123 [M=313] Accession: TIGR01123 Description: ilvE_II: 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-123 396.9 0.0 3.1e-123 396.7 0.0 1.0 1 NCBI__GCF_000224785.1:WP_010532003.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010532003.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 396.7 0.0 3.1e-123 3.1e-123 1 313 [] 46 357 .. 46 357 .. 0.98 Alignments for each domain: == domain 1 score: 396.7 bits; conditional E-value: 3.1e-123 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 W++++++++++l+++++++v+hYgq vfeG+kay t+dG + lfRp++n R+++s +rl +P ++e+ l+a NCBI__GCF_000224785.1:WP_010532003.1 46 WHDPRIVPYEPLNIEPSAMVFHYGQSVFEGMKAYLTSDGDAQLFRPQRNFSRMNHSNSRLCIPPIDEAFALKA 118 ************************************************************************* PP TIGR01123 74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146 lkqlv ++kdw+p+a+ ++sLY+RPf+i+te+ lGv+++++y f++++sPvGaY+k+g++pv+i ve +yvR+ NCBI__GCF_000224785.1:WP_010532003.1 119 LKQLVGLEKDWIPEAE-GTSLYIRPFIISTEAFLGVAPSSHYKFIIILSPVGAYYKEGINPVKIAVEHDYVRT 190 *************988.******************************************************** PP TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219 +++GtG +k+gGnYaasl+aq++aa +g+++v++ld ve+k+ieevG++n+f+ ++ g++vt++l +siLegv NCBI__GCF_000224785.1:WP_010532003.1 191 VKGGTGEAKTGGNYAASLKAQEMAA-EGIAQVLWLDGVERKYIEEVGSMNVFFKID-GTVVTPALNGSILEGV 261 ********************88775.69************************9775.9*************** PP TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290 tr+s+++l k +++ veer+++++e+ +a + G++ +f++Gtaavi+P+gel ++k++e++++++G ++k+ NCBI__GCF_000224785.1:WP_010532003.1 262 TRNSVIQLLKYWNVPVEERKLSMEEVIQAHKDGKLeeAFGAGTAAVISPIGELVRGEKHIEINEGNTGAIAKR 334 *********************************9889************************************ PP TIGR01123 291 lrdeltdiqyGkledkegWivev 313 l+d+lt+iqyGk+ed+++W+ +v NCBI__GCF_000224785.1:WP_010532003.1 335 LYDTLTGIQYGKIEDPFDWVEKV 357 *******************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (369 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: 17.75 // [ok]
This GapMind analysis is from Jul 26 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