Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_004514563.1 GMET_RS14295 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_000012925.1:WP_004514563.1 Length = 357 Score = 380 bits (976), Expect = e-110 Identities = 183/345 (53%), Positives = 244/345 (70%), Gaps = 1/345 (0%) Query: 14 KKPK-PDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFE 72 KKPK D +QL FG++FTD MF++++ +GW D RI PY P +DPA V HY Q +FE Sbjct: 13 KKPKYTDESQLGFGKLFTDRMFMVEWKIGQGWVDARIEPYAPFVLDPACSVLHYAQEIFE 72 Query: 73 GLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAE 132 GLKAY D + LFRPE N R N S DRLC+P++ EE L+G+++LVA+++DWIP++E Sbjct: 73 GLKAYKWADGTITLFRPEMNARRFNHSADRLCMPEVPEELFLDGIEKLVALERDWIPSSE 132 Query: 133 GTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEFVRAVKGG 192 GTSLYIRP +I +P LGV + Y +ILSPVG+YY G P+KI VE ++VR+V GG Sbjct: 133 GTSLYIRPTMIGVDPVLGVKPADHYYFYVILSPVGAYYSAGFNPIKIMVEDQYVRSVPGG 192 Query: 193 TGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKINGEIVTPML 252 TG AKT GNYA SLKA A++KG+ QVLWLDG+ ++YIEEVG+MN+ F IVT L Sbjct: 193 TGEAKTGGNYACSLKAGLEAKKKGYDQVLWLDGVHRRYIEEVGAMNMLFAYGKTIVTASL 252 Query: 253 NGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPVGE 312 G+IL G+TR+S + L G + ER I ++E++ + G + EAFG+GTAAVISPVG Sbjct: 253 TGTILNGVTRDSTLKLAASLGYTIEERLIDVNELMADIRAGKVTEAFGSGTAAVISPVGV 312 Query: 313 LIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEVA 357 L ++DE ++ NG G I ++LYDT+TGIQ G V D FGWT ++A Sbjct: 313 LAYKDEVCTVGNGGVGPITQQLYDTLTGIQTGKVPDTFGWTRKIA 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: 459 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: 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_004514563.1 GMET_RS14295 (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.13650.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-124 399.1 0.0 6.6e-124 398.9 0.0 1.0 1 lcl|NCBI__GCF_000012925.1:WP_004514563.1 GMET_RS14295 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012925.1:WP_004514563.1 GMET_RS14295 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 398.9 0.0 6.6e-124 6.6e-124 1 312 [. 44 355 .. 44 356 .. 0.99 Alignments for each domain: == domain 1 score: 398.9 bits; conditional E-value: 6.6e-124 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W +a+++++a++ ld++ +vlhY+qe+feGlkay++adG i+lfRp+ na+R+++sa+rl +Pe++eel lcl|NCBI__GCF_000012925.1:WP_004514563.1 44 WVDARIEPYAPFVLDPACSVLHYAQEIFEGLKAYKWADGTITLFRPEMNARRFNHSADRLCMPEVPEEL 112 999****************************************************************** PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 fl+ +++lv++++dw+p+ + ++sLY+RP++i+++++lGvk+a +y f+v++sPvGaY+ g +p++i+ lcl|NCBI__GCF_000012925.1:WP_004514563.1 113 FLDGIEKLVALERDWIPSSE-GTSLYIRPTMIGVDPVLGVKPADHYYFYVILSPVGAYYSAGFNPIKIM 180 *****************988.************************************************ PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 ve++yvR++p+GtG +k+gGnYa sl+a +a+++g+d+v++ld v++++ieevGa+n+++ ++ ++v lcl|NCBI__GCF_000012925.1:WP_004514563.1 181 VEDQYVRSVPGGTGEAKTGGNYACSLKAGLEAKKKGYDQVLWLDGVHRRYIEEVGAMNMLFAYGK-TIV 248 ****************************************************************8.*** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t +l++ iL+gvtr+s l+la +lg+++eer i+++el a aG++ +f++Gtaavi+Pvg l+ ++ lcl|NCBI__GCF_000012925.1:WP_004514563.1 249 TASLTGTILNGVTRDSTLKLAASLGYTIEERLIDVNELMADIRAGKVteAFGSGTAAVISPVGVLAYKD 317 *********************************************9999******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWive 312 + ++v ++ vG++t++l+d+lt+iq+Gk+ d++gW+ + lcl|NCBI__GCF_000012925.1:WP_004514563.1 318 EVCTVGNGGVGPITQQLYDTLTGIQTGKVPDTFGWTRK 355 ***********************************976 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: 7.23 // [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