Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_011940734.1 GURA_RS20105 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_000016745.1:WP_011940734.1 Length = 357 Score = 401 bits (1031), Expect = e-116 Identities = 192/339 (56%), Positives = 251/339 (74%) Query: 19 DPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFEGLKAYV 78 D +QL FGR+FTD M ++++ A KGW D RI PY P +DPA +V+HY Q +FEGLKAY Sbjct: 19 DESQLGFGRIFTDRMLMVEWKAGKGWVDARIEPYAPFVLDPACLVFHYAQEIFEGLKAYK 78 Query: 79 SEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAEGTSLYI 138 D V LFRPE N R N S DRLC+P + EE L+G+++LV ++KDW+P+AEGTSLYI Sbjct: 79 WTDGTVALFRPEMNARRFNLSADRLCMPTVPEELFLKGIEELVQLEKDWVPSAEGTSLYI 138 Query: 139 RPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEFVRAVKGGTGNAKT 198 RP +IA EP LGV S Y +I+SPVG+YY G KPVKI VE +FVRA GGTG AKT Sbjct: 139 RPAMIAVEPVLGVKPSDHYYFYVIMSPVGAYYASGFKPVKIMVEDKFVRATPGGTGEAKT 198 Query: 199 AGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKINGEIVTPMLNGSILE 258 GNYASSLKA A++KGF QVLWLDG+ K+YIEEVG+MN+FF +VT L GSIL Sbjct: 199 GGNYASSLKAGLEAKKKGFDQVLWLDGVHKRYIEEVGAMNMFFAYEDRVVTAPLEGSILH 258 Query: 259 GITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPVGELIWQDE 318 GITR+SV+ L+ +GL+V ERKI + E++ + G ++EAFG+GTAAV++PVG L ++DE Sbjct: 259 GITRDSVLKLVASFGLKVEERKIDVIELMNDIRSGKVKEAFGSGTAAVVTPVGALSYKDE 318 Query: 319 TLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEVA 357 L++++GE G++ +KLYDT+T IQ G + D FGW ++A Sbjct: 319 CLTVDDGEVGKLTQKLYDTLTAIQYGKMEDSFGWIKKIA 357 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: 465 Number of extensions: 20 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: 357 Length adjustment: 29 Effective length of query: 334 Effective length of database: 328 Effective search space: 109552 Effective search space used: 109552 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_011940734.1 GURA_RS20105 (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.24488.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-127 409.3 0.0 5.1e-127 409.1 0.0 1.0 1 lcl|NCBI__GCF_000016745.1:WP_011940734.1 GURA_RS20105 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016745.1:WP_011940734.1 GURA_RS20105 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 409.1 0.0 5.1e-127 5.1e-127 1 312 [. 44 355 .. 44 356 .. 0.99 Alignments for each domain: == domain 1 score: 409.1 bits; conditional E-value: 5.1e-127 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W +a+++++a++ ld++ v+hY+qe+feGlkay++ dG + lfRp+ na+R++ sa+rl +P ++eel lcl|NCBI__GCF_000016745.1:WP_011940734.1 44 WVDARIEPYAPFVLDPACLVFHYAQEIFEGLKAYKWTDGTVALFRPEMNARRFNLSADRLCMPTVPEEL 112 999****************************************************************** PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 fl+ +++lv+++kdwvp+a+ ++sLY+RP +ia+e++lGvk++ +y f+v++sPvGaY+++g +pv+i+ lcl|NCBI__GCF_000016745.1:WP_011940734.1 113 FLKGIEELVQLEKDWVPSAE-GTSLYIRPAMIAVEPVLGVKPSDHYYFYVIMSPVGAYYASGFKPVKIM 180 *****************999.************************************************ PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 ve+++vRa+p+GtG +k+gGnYa+sl+a +a+++g+d+v++ld v+k++ieevGa+n+f+ ++d ++v lcl|NCBI__GCF_000016745.1:WP_011940734.1 181 VEDKFVRATPGGTGEAKTGGNYASSLKAGLEAKKKGFDQVLWLDGVHKRYIEEVGAMNMFFAYED-RVV 248 *****************************************************************.*** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t pl +siL+g+tr+s+l+l+ + gl+veer+i++ el + +G++ +f++Gtaav+tPvg l+ ++ lcl|NCBI__GCF_000016745.1:WP_011940734.1 249 TAPLEGSILHGITRDSVLKLVASFGLKVEERKIDVIELMNDIRSGKVkeAFGSGTAAVVTPVGALSYKD 317 *********************************************9999******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWive 312 + ++v+++evG++t+kl+d+lt iqyGk+ed +gWi + lcl|NCBI__GCF_000016745.1:WP_011940734.1 318 ECLTVDDGEVGKLTQKLYDTLTAIQYGKMEDSFGWIKK 355 ***********************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (357 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: 8.75 // [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