Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_011187437.1 DP_RS00965 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_000025945.1:WP_011187437.1 Length = 360 Score = 399 bits (1025), Expect = e-116 Identities = 190/342 (55%), Positives = 248/342 (72%) Query: 15 KPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFEGL 74 K KP L FG FTDHMF M ++ + GW+D +I PY L +DPAAMV+HYGQ +FEG+ Sbjct: 18 KEKPSSENLCFGSDFTDHMFAMTWSRENGWHDAKICPYHNLVLDPAAMVFHYGQAIFEGM 77 Query: 75 KAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAEGT 134 K Y +D +FRP N+ER+NQS RLC+P++ ++VL+ LK L+ ++KDWIP A G+ Sbjct: 78 KGYKGKDGQTYMFRPTDNLERMNQSAVRLCMPRLPVDKVLKSLKALLYLEKDWIPEAPGS 137 Query: 135 SLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEFVRAVKGGTG 194 SLYIRP +IA EP LGV S Y +I+SPVG+YYKEG P KI V E RAV GG G Sbjct: 138 SLYIRPTMIAVEPSLGVRPSEKYYFFVIMSPVGAYYKEGCNPTKIYVSDEQARAVPGGVG 197 Query: 195 NAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKINGEIVTPMLNG 254 N KTAGNYA+SL ++A +KG SQVLWLD E KY+EEVG+ NIFF+I E++TP L G Sbjct: 198 NIKTAGNYAASLYTAEIARKKGCSQVLWLDAKEFKYVEEVGTSNIFFRIGDELITPPLGG 257 Query: 255 SILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPVGELI 314 SIL GITR+S++ L + WGL VSERKI I+EV++A +DG L E+FGTGTAAVISPVGE++ Sbjct: 258 SILGGITRDSILKLARSWGLNVSERKITIEEVLRASEDGTLLESFGTGTAAVISPVGEIV 317 Query: 315 WQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356 ++D++ IN G+ GE++++LY + GIQ G + D F W V Sbjct: 318 YKDKSYIINAGKAGELSQRLYAELQGIQYGELEDPFKWVERV 359 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: 402 Number of extensions: 11 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: 363 Length of database: 360 Length adjustment: 29 Effective length of query: 334 Effective length of database: 331 Effective search space: 110554 Effective search space used: 110554 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_011187437.1 DP_RS00965 (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.26052.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-125 401.9 0.0 9.8e-125 401.6 0.0 1.1 1 lcl|NCBI__GCF_000025945.1:WP_011187437.1 DP_RS00965 branched-chain amino Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025945.1:WP_011187437.1 DP_RS00965 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 401.6 0.0 9.8e-125 9.8e-125 1 313 [] 47 359 .. 47 359 .. 0.99 Alignments for each domain: == domain 1 score: 401.6 bits; conditional E-value: 9.8e-125 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++a++ ++++l ld++++v+hYgq++feG+k y+ +dG+ ++fRp++n +R+++sa rl +P+l+ + lcl|NCBI__GCF_000025945.1:WP_011187437.1 47 WHDAKICPYHNLVLDPAAMVFHYGQAIFEGMKGYKGKDGQTYMFRPTDNLERMNQSAVRLCMPRLPVDK 115 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 +l++lk l+ ++kdw+p+a ++sLY+RP++ia+e++lGv+++++y f+v++sPvGaY+k+g +p++i+ lcl|NCBI__GCF_000025945.1:WP_011187437.1 116 VLKSLKALLYLEKDWIPEAP-GSSLYIRPTMIAVEPSLGVRPSEKYYFFVIMSPVGAYYKEGCNPTKIY 183 *****************888.9*********************************************** PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v++e +Ra+p+G+G++k++GnYaasl + ++a+++g+++v++ld++e k++eevG++nif+ ++d el+ lcl|NCBI__GCF_000025945.1:WP_011187437.1 184 VSDEQARAVPGGVGNIKTAGNYAASLYTAEIARKKGCSQVLWLDAKEFKYVEEVGTSNIFFRIGD-ELI 251 ****************************************************************9.*** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t+pl +siL g+tr+s+l+la+++gl+v+er+i+i+e+ +a+e G + f++Gtaavi+Pvge+ ++ lcl|NCBI__GCF_000025945.1:WP_011187437.1 252 TPPLGGSILGGITRDSILKLARSWGLNVSERKITIEEVLRASEDGTLleSFGTGTAAVISPVGEIVYKD 320 *********************************************99999******************* PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313 k++++++++ Ge++++l+ el +iqyG+led+++W+ +v lcl|NCBI__GCF_000025945.1:WP_011187437.1 321 KSYIINAGKAGELSQRLYAELQGIQYGELEDPFKWVERV 359 ***********************************9776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (360 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: 12.77 // [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