Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_073040767.1 BUB04_RS14560 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_900129305.1:WP_073040767.1 Length = 356 Score = 396 bits (1018), Expect = e-115 Identities = 188/343 (54%), Positives = 252/343 (73%), Gaps = 1/343 (0%) Query: 14 KKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFEG 73 ++P+P +QL FGR+F+DHMF MDY + W +PR+IPY PL +DPAAMV HYGQ +FEG Sbjct: 13 RRPRPADDQLVFGRIFSDHMFRMDYQ-EGAWQNPRVIPYGPLELDPAAMVLHYGQGIFEG 71 Query: 74 LKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAEG 133 LKAY D + LFRP KNMER N+S R+C+P++D + LE ++ LV +D +WIP + G Sbjct: 72 LKAYRCADGRIHLFRPLKNMERFNRSVRRMCMPEVDAQLHLEAIEALVRLDVEWIPRSVG 131 Query: 134 TSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEFVRAVKGGT 193 SLYIRP +IA+EP LGV + Y II PVG+YY EG P+KI V ++VRAV+GG Sbjct: 132 ASLYIRPTMIASEPHLGVRPAAEYIHYIITGPVGAYYPEGFNPIKIYVSDQYVRAVRGGV 191 Query: 194 GNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKINGEIVTPMLN 253 G AKT NYA+SL A ++A++KG++QVLWLD +E++Y+EEVG+MNIFF++ E+VTP L+ Sbjct: 192 GEAKTMANYAASLFAAELAKKKGYTQVLWLDAVERRYVEEVGTMNIFFRLKDELVTPPLS 251 Query: 254 GSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPVGEL 313 GSIL G+TR SVI L KHWG+ V+ER + IDEVI G L+E FGTGTAAVISPVGE+ Sbjct: 252 GSILPGVTRESVIDLAKHWGIAVNERPVTIDEVIDGIASGDLKEIFGTGTAAVISPVGEV 311 Query: 314 IWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356 +++++ + +G GE +++ YD I GIQ G D FGW +V Sbjct: 312 FYKEKSYVVQDGSVGEWSRRFYDEIVGIQYGEKEDPFGWIHQV 354 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: 411 Number of extensions: 14 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: 356 Length adjustment: 29 Effective length of query: 334 Effective length of database: 327 Effective search space: 109218 Effective search space used: 109218 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_073040767.1 BUB04_RS14560 (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.20205.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-128 412.3 0.0 6.3e-128 412.1 0.0 1.0 1 lcl|NCBI__GCF_900129305.1:WP_073040767.1 BUB04_RS14560 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900129305.1:WP_073040767.1 BUB04_RS14560 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.1 0.0 6.3e-128 6.3e-128 1 313 [] 42 354 .. 42 354 .. 0.99 Alignments for each domain: == domain 1 score: 412.1 bits; conditional E-value: 6.3e-128 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++++++++++leld++++vlhYgq +feGlkayR+adG+i lfRp +n++R++rs +r+ +Pe++ +l lcl|NCBI__GCF_900129305.1:WP_073040767.1 42 WQNPRVIPYGPLELDPAAMVLHYGQGIFEGLKAYRCADGRIHLFRPLKNMERFNRSVRRMCMPEVDAQL 110 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 lea++ lv++d +w+p +asLY+RP++ia e++lGv++a ey++++++ PvGaY+ +g +p++i+ lcl|NCBI__GCF_900129305.1:WP_073040767.1 111 HLEAIEALVRLDVEWIPRSV-GASLYIRPTMIASEPHLGVRPAAEYIHYIITGPVGAYYPEGFNPIKIY 178 *****************665.************************************************ PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v+++yvRa+ +G+G +k+ nYaasl a + a+++g+ +v++ld+ve++++eevG++nif+ +kd elv lcl|NCBI__GCF_900129305.1:WP_073040767.1 179 VSDQYVRAVRGGVGEAKTMANYAASLFAAELAKKKGYTQVLWLDAVERRYVEEVGTMNIFFRLKD-ELV 246 *****************************************************************.*** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t+pls+siL+gvtres++ lak++g++v+er ++ide+ + ++G++ +f++Gtaavi+Pvge+ ++ lcl|NCBI__GCF_900129305.1:WP_073040767.1 247 TPPLSGSILPGVTRESVIDLAKHWGIAVNERPVTIDEVIDGIASGDLkeIFGTGTAAVISPVGEVFYKE 315 *********************************************9999******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313 k+++v+++ vGe +++++de+++iqyG++ed++gWi +v lcl|NCBI__GCF_900129305.1:WP_073040767.1 316 KSYVVQDGSVGEWSRRFYDEIVGIQYGEKEDPFGWIHQV 354 ************************************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (356 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: 8.36 // [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