Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_012609538.1 G491_RS0128675 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_000429905.1:WP_012609538.1 Length = 354 Score = 433 bits (1114), Expect = e-126 Identities = 207/351 (58%), Positives = 264/351 (75%) Query: 6 IRVELTSTKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYH 65 I+V S KP P ++L FG++FTDHMF MDYA KGW+DPRI PY LS DPA +V+H Sbjct: 3 IKVTKASNLKPHPADDKLGFGKIFTDHMFNMDYAEGKGWFDPRIEPYAALSCDPAMLVFH 62 Query: 66 YGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDK 125 YGQ +FEGLKAY + +V LFRP+ N R N+S LCIP DE + L+ L+QL++++K Sbjct: 63 YGQAIFEGLKAYRTPKGNVQLFRPQANFARFNRSASMLCIPNFDEAEALDHLRQLISVEK 122 Query: 126 DWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEF 185 DW+P++ GTSLYIRP IIAT+ +LGVAAS TY+ ILSPVG+YY EG P+KI V +E Sbjct: 123 DWVPSSPGTSLYIRPTIIATDNYLGVAASQTYRFFTILSPVGAYYAEGFAPIKILVTTEH 182 Query: 186 VRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKING 245 VRA + G G AKTA NYA+SL A A + G++QVLWLD +E+KY+EEVGSMNIFF I+G Sbjct: 183 VRASRQGIGEAKTAANYAASLLAGHKAAKAGYTQVLWLDAVERKYVEEVGSMNIFFVIDG 242 Query: 246 EIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAA 305 E+VTP LNGSIL GITR+SV+ + +HWGL VSER I+I+E+ +A+++G LEE FGTGTAA Sbjct: 243 EVVTPELNGSILPGITRDSVLTMARHWGLPVSERHISIEEIFEANENGKLEECFGTGTAA 302 Query: 306 VISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356 VISPVGEL + + ++I N E G +++KLYD ITGIQ G D FGW V Sbjct: 303 VISPVGELRYDERVITIRNNEVGPLSQKLYDAITGIQFGEKEDPFGWIVPV 353 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: 433 Number of extensions: 14 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: 354 Length adjustment: 29 Effective length of query: 334 Effective length of database: 325 Effective search space: 108550 Effective search space used: 108550 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_012609538.1 G491_RS0128675 (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.19777.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-125 403.2 0.0 3.7e-125 403.0 0.0 1.0 1 lcl|NCBI__GCF_000429905.1:WP_012609538.1 G491_RS0128675 branched-chain am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429905.1:WP_012609538.1 G491_RS0128675 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 403.0 0.0 3.7e-125 3.7e-125 1 313 [] 41 353 .. 41 353 .. 0.99 Alignments for each domain: == domain 1 score: 403.0 bits; conditional E-value: 3.7e-125 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W +++++++a+l+ d++ v+hYgq++feGlkayRt +G++ lfRp+an +R++rsa+ l +P+ +e+ lcl|NCBI__GCF_000429905.1:WP_012609538.1 41 WFDPRIEPYAALSCDPAMLVFHYGQAIFEGLKAYRTPKGNVQLFRPQANFARFNRSASMLCIPNFDEAE 109 8899***************************************************************** PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 l+ l+ql+ ++kdwvp+ ++sLY+RP++iat+++lGv+a+++y+f+ ++sPvGaY+++g ap++i+ lcl|NCBI__GCF_000429905.1:WP_012609538.1 110 ALDHLRQLISVEKDWVPSSP-GTSLYIRPTIIATDNYLGVAASQTYRFFTILSPVGAYYAEGFAPIKIL 177 *****************888.************************************************ PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v+te+vRa +G+G +k++ nYaaslla +kaa+ g+ +v++ld+ve+k++eevG++nif++++ ge+v lcl|NCBI__GCF_000429905.1:WP_012609538.1 178 VTTEHVRASRQGIGEAKTAANYAASLLAGHKAAKAGYTQVLWLDAVERKYVEEVGSMNIFFVID-GEVV 245 **************************************************************97.8*** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t++l +siL+g+tr+s+l++a+++gl v+er+i+i+e+ +a e+G++ f++Gtaavi+Pvgel+ ++ lcl|NCBI__GCF_000429905.1:WP_012609538.1 246 TPELNGSILPGITRDSVLTMARHWGLPVSERHISIEEIFEANENGKLeeCFGTGTAAVISPVGELRYDE 314 *********************************************9889******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313 + ++++++evG++++kl+d++t+iq+G++ed++gWiv v lcl|NCBI__GCF_000429905.1:WP_012609538.1 315 RVITIRNNEVGPLSQKLYDAITGIQFGEKEDPFGWIVPV 353 ************************************965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (354 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: 7.27 // [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