Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_022529386.1 L248_RS06710 branched-chain amino acid aminotransferase
Query= BRENDA::Q8DTW7 (341 letters) >NCBI__GCF_000469325.1:WP_022529386.1 Length = 345 Score = 466 bits (1200), Expect = e-136 Identities = 223/336 (66%), Positives = 269/336 (80%), Gaps = 2/336 (0%) Query: 5 LDWKNLGFEYHKLPFRYISYYKDGKWDDGKLTEDATLHISESSPALHYGQEAFEGLKAYR 64 +DW++LGFEY + P+R+ ++++DG W+ G+LT+D + ++ESSP LHYGQ AFEG+KAYR Sbjct: 8 IDWQHLGFEYMQTPYRFEAHWRDGAWEPGQLTKDPNMTMNESSPILHYGQGAFEGMKAYR 67 Query: 65 TKDGSVQLFRPNMNAERLQRTADRLLMPQVPTDKFIDAAKQVVRANEEYVPPYGTGATLY 124 KDG + LFRP+ NA+RLQ +ADRLLMP+ PTD F++A K VV AN +YVPPYGTGATLY Sbjct: 68 AKDGRILLFRPDQNAQRLQHSADRLLMPEYPTDDFLNAVKLVVAANADYVPPYGTGATLY 127 Query: 125 LRPLLIGVGDVIGVHPADEYIFTIFAMPVGNYFKGGLAPTNFLIQDDYDRAAPHGTGAAK 184 +RPLLIGVG+ IGVHPA EY+ IFAMPVG YFKGGL PT+FL+ DYDRAA +GTG +K Sbjct: 128 IRPLLIGVGENIGVHPAPEYVLRIFAMPVGPYFKGGLTPTSFLVV-DYDRAAHNGTGQSK 186 Query: 185 VGGNYAASLLPGKVAHERQFSDVIYLDPATHTKIEEVGSANFFGITKDNEFI-TPLSPSI 243 VGGNYAASLL G+ AH FSD IYLDP H IEEVGSANF TKD + + TP SPSI Sbjct: 187 VGGNYAASLLAGQEAHTHHFSDAIYLDPVHHRYIEEVGSANFLAFTKDGKTLKTPKSPSI 246 Query: 244 LPSVTKYSLLYLAEHRFGMKAIEGDVCVDELDKFVEAGACGTAAVISPIGGVQHGDDFHV 303 LPS+TKYS LYLAEH GMK E + +DELD+F EA ACGTAAVISPI G+Q+GD +HV Sbjct: 247 LPSITKYSSLYLAEHVLGMKTEETRISIDELDEFGEAAACGTAAVISPIAGIQYGDHYHV 306 Query: 304 FYSETEVGPVTHKLYDELTGIQFGDVKAPEGWIYKV 339 FY E +VGP+THKLYD LTGIQFGDV P GW+ +V Sbjct: 307 FYDEKKVGPITHKLYDLLTGIQFGDVDGPAGWVQEV 342 Lambda K H 0.319 0.139 0.423 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: 501 Number of extensions: 23 Number of successful extensions: 3 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: 341 Length of database: 345 Length adjustment: 29 Effective length of query: 312 Effective length of database: 316 Effective search space: 98592 Effective search space used: 98592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_022529386.1 L248_RS06710 (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.carbon/TIGR01123.hmm # target sequence database: /tmp/gapView.1265673.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-127 409.2 0.0 5.5e-127 409.0 0.0 1.0 1 NCBI__GCF_000469325.1:WP_022529386.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000469325.1:WP_022529386.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 409.0 0.0 5.5e-127 5.5e-127 1 313 [] 33 342 .. 33 342 .. 0.99 Alignments for each domain: == domain 1 score: 409.0 bits; conditional E-value: 5.5e-127 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 W+ ++l+++ +++++e+s +lhYgq feG+kayR +dG+illfRpd+na+Rl++sa+rll+Pe +++ fl+a NCBI__GCF_000469325.1:WP_022529386.1 33 WEPGQLTKDPNMTMNESSPILHYGQGAFEGMKAYRAKDGRILLFRPDQNAQRLQHSADRLLMPEYPTDDFLNA 105 9************************************************************************ PP TIGR01123 74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146 +k +v+a++d+vp+++++a+LY+RP+li++++n+Gv++a+ey++ ++a PvG+Yfkggl+p + f+ +y+Ra NCBI__GCF_000469325.1:WP_022529386.1 106 VKLVVAANADYVPPYGTGATLYIRPLLIGVGENIGVHPAPEYVLRIFAMPVGPYFKGGLTP-TSFLVVDYDRA 177 *************************************************************.99999****** PP TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219 a +GtG+ kvgGnYaaslla ++a+ ++++d++yldpv++++ieevG+an+++ tkdg+++ tp+s+siL+++ NCBI__GCF_000469325.1:WP_022529386.1 178 AHNGTGQSKVGGNYAASLLAGQEAHTHHFSDAIYLDPVHHRYIEEVGSANFLAFTKDGKTLKTPKSPSILPSI 250 ************************************************************************* PP TIGR01123 220 tresllelakd.lgleveereiaidelkaaveaGeivfacGtaavitPvgelkiegkevevkse.evGevtkk 290 t++s l la++ lg++ ee +i+idel+++ ea acGtaavi+P+++++ +++ +++++e +vG++t+k NCBI__GCF_000469325.1:WP_022529386.1 251 TKYSSLYLAEHvLGMKTEETRISIDELDEFGEAA----ACGTAAVISPIAGIQYGDHYHVFYDEkKVGPITHK 319 *******************************999....***********************99989******* PP TIGR01123 291 lrdeltdiqyGkledkegWivev 313 l+d lt+iq+G+++++ gW+ ev NCBI__GCF_000469325.1:WP_022529386.1 320 LYDLLTGIQFGDVDGPAGWVQEV 342 *******************9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (345 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 23.15 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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