Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_072907398.1 BUB13_RS07340 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_900142125.1:WP_072907398.1 Length = 354 Score = 379 bits (972), Expect = e-110 Identities = 184/352 (52%), Positives = 242/352 (68%), Gaps = 3/352 (0%) Query: 6 IRVELTSTKKPKP---DPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAM 62 + +E+ KP D N L+FG+ FTD MFVM++ KGW+ RI PY P ++DPAAM Sbjct: 1 MNLEILPVSDLKPAIEDENNLAFGKSFTDRMFVMEFDRAKGWHSARIQPYAPFTLDPAAM 60 Query: 63 VYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVA 122 V HY Q +FEGLKA+ ED + LFRP N+ R NQS R+C+P++DE+ L+ + +L+ Sbjct: 61 VLHYSQEIFEGLKAFRREDGSIALFRPADNVARFNQSARRMCMPEVDEKFFLDSMLELIR 120 Query: 123 IDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVE 182 +++ W+P AEGTSLYIRP +IATEP LGV + Y +IL PVG+YYK GI PVKI + Sbjct: 121 MEERWVPKAEGTSLYIRPTMIATEPMLGVRPADQYLCYVILCPVGAYYKGGIAPVKIWIS 180 Query: 183 SEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFK 242 FVRA +GGTG AKT GNYA+SL A + A KG+ QVLWLD EKKY+EEVGSMN+ F Sbjct: 181 DHFVRAAEGGTGEAKTGGNYAASLYAAREASLKGYDQVLWLDAKEKKYVEEVGSMNMLFH 240 Query: 243 INGEIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTG 302 + +IVT L G++L+GITR S + LL G Q+ ER + +DEV++ ++G L+EAFGTG Sbjct: 241 YDDKIVTSPLKGTVLDGITRRSALKLLSEMGYQIEERALTVDEVMEGAQNGRLKEAFGTG 300 Query: 303 TAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTT 354 TA VISPVG +QDE + + NGE GE+ KLY+ +T IQ G D W T Sbjct: 301 TAVVISPVGSFCYQDECVQLGNGEPGELTMKLYNQLTAIQYGRQPDPHNWIT 352 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: 430 Number of extensions: 18 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_072907398.1 BUB13_RS07340 (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.17544.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-129 415.5 0.0 6.5e-129 415.3 0.0 1.0 1 lcl|NCBI__GCF_900142125.1:WP_072907398.1 BUB13_RS07340 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900142125.1:WP_072907398.1 BUB13_RS07340 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.3 0.0 6.5e-129 6.5e-129 1 312 [. 42 353 .. 42 354 .] 0.99 Alignments for each domain: == domain 1 score: 415.3 bits; conditional E-value: 6.5e-129 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++a+++++a+++ld++++vlhY+qe+feGlka+R +dG+i lfRp +n++R+++sa+r+ +Pe++e+ lcl|NCBI__GCF_900142125.1:WP_072907398.1 42 WHSARIQPYAPFTLDPAAMVLHYSQEIFEGLKAFRREDGSIALFRPADNVARFNQSARRMCMPEVDEKF 110 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 fl+++ +l++++++wvpka+ ++sLY+RP++iate+ lGv++a +yl +v+++PvGaY+kgg+apv+i+ lcl|NCBI__GCF_900142125.1:WP_072907398.1 111 FLDSMLELIRMEERWVPKAE-GTSLYIRPTMIATEPMLGVRPADQYLCYVILCPVGAYYKGGIAPVKIW 178 *****************999.************************************************ PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 +++++vRaa++GtG +k+gGnYaasl a ++a+ +g+d+v++ld++ekk++eevG++n+++ ++d ++v lcl|NCBI__GCF_900142125.1:WP_072907398.1 179 ISDHFVRAAEGGTGEAKTGGNYAASLYAAREASLKGYDQVLWLDAKEKKYVEEVGSMNMLFHYDD-KIV 246 ****************************************************************9.*** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t+pl + +L+g+tr+s+l+l ++g+++eer +++de+ + +++G + +f++Gta vi+Pvg++ ++ lcl|NCBI__GCF_900142125.1:WP_072907398.1 247 TSPLKGTVLDGITRRSALKLLSEMGYQIEERALTVDEVMEGAQNGRLkeAFGTGTAVVISPVGSFCYQD 315 *********************************************9999******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWive 312 + v++ ++e+Ge+t+kl+++lt iqyG++ d+++Wi+ lcl|NCBI__GCF_900142125.1:WP_072907398.1 316 ECVQLGNGEPGELTMKLYNQLTAIQYGRQPDPHNWITT 353 ************************************86 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: 7.31 // [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