Align Branched-chain-amino-acid transaminase 1; BCAT 1; EC 2.6.1.42 (characterized)
to candidate WP_011610681.1 TERY_RS04180 branched-chain amino acid aminotransferase
Query= SwissProt::O31461 (356 letters) >NCBI__GCF_000014265.1:WP_011610681.1 Length = 355 Score = 311 bits (798), Expect = 1e-89 Identities = 158/357 (44%), Positives = 225/357 (63%), Gaps = 6/357 (1%) Query: 1 MNKLIEREKTVYYKEKP-DPSSLGFGQYFTDYMFVMDYEEGIGWHHPRIAPYAPLTLDPS 59 +N I EKT + + K D ++ FG+ F+D+M V Y W +I PY +++ PS Sbjct: 4 VNSQISIEKTSHSRIKEQDINNTPFGKVFSDHMLVATYANN-SWQEVKITPYGNISIRPS 62 Query: 60 SSVFHYGQAVFEGLKAYRTDDGRVLLFRPDQNIKRLNRSCERMSMPPLDEELVLEALTQL 119 SV HYGQAVFEGLKAY+ G+ +LFR + N KR+N S R+ MP + +E+ ++ L +L Sbjct: 63 LSVLHYGQAVFEGLKAYKNYQGKPVLFRLEANYKRINNSAFRLCMPSIPKEIFIDGLKEL 122 Query: 120 VELEKDWVPKEKGTSLYIRPFVIATEPSLGVKASRSYTFMIVLSPVGSYYGDDQLKPVRI 179 + L+ DW+P + ++LYIRP AT+ S+G+K + SY F+I+ SP G++Y PV++ Sbjct: 123 IRLDTDWIPTKSDSALYIRPIYFATDESVGLKPANSYKFIILSSPTGTFYS----APVKL 178 Query: 180 YVEDEYVRAVNGGVGFAKTAGNYAASLQAQRKANELGYDQVLWLDAIEKKYVEEVGSMNI 239 V D+YVRA GG G AK AGNYA S A ++A E GYD VLWLD EKKY+EE G+MN+ Sbjct: 179 IVTDKYVRASEGGTGAAKCAGNYAGSFLADKEAKEQGYDNVLWLDGKEKKYIEECGTMNV 238 Query: 240 FFVINGEAVTPALSGSILSGVTRASAIELIRSWGIPVREERISIDEVYAASARGELTEVF 299 FVIN +TP L+GSIL G+TR SA+ L R G+ V E ISIDEV A G ++E F Sbjct: 239 AFVINDVLITPKLTGSILGGITRDSALTLFRDMGVKVEERLISIDEVAKAYEAGNISEAF 298 Query: 300 GTGTAAVVTPVGELNIHGKTVIVGDGQIGDLSKKLYETITDIQLGKVKGPFNWTVEV 356 G GTAA + + +N GK +I+ + ++ + + DI+ GKV P+ W ++ Sbjct: 299 GMGTAATIAHISVINYQGKDMILPPVDERKYASQVLQKLEDIKTGKVTDPYGWICQL 355 Lambda K H 0.317 0.137 0.400 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: 365 Number of extensions: 17 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: 356 Length of database: 355 Length adjustment: 29 Effective length of query: 327 Effective length of database: 326 Effective search space: 106602 Effective search space used: 106602 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_011610681.1 TERY_RS04180 (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.7841.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-106 341.9 0.0 1.7e-106 341.7 0.0 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011610681.1 TERY_RS04180 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011610681.1 TERY_RS04180 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 341.7 0.0 1.7e-106 1.7e-106 1 312 [. 46 354 .. 46 355 .] 0.98 Alignments for each domain: == domain 1 score: 341.7 bits; conditional E-value: 1.7e-106 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W+e ++++++++++ ++ +vlhYgq+vfeGlkay+ +Gk +lfR +an kR+++sa rl +P +++e+ lcl|NCBI__GCF_000014265.1:WP_011610681.1 46 WQEVKITPYGNISIRPSLSVLHYGQAVFEGLKAYKNYQGKPVLFRLEANYKRINNSAFRLCMPSIPKEI 114 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 f++ lk+l+++d dw+p +ks+++LY+RP+ +at++++G k+a++y f++l sP G+++ apv+ lcl|NCBI__GCF_000014265.1:WP_011610681.1 115 FIDGLKELIRLDTDWIP-TKSDSALYIRPIYFATDESVGLKPANSYKFIILSSPTGTFYS---APVKLI 179 *****************.677**************************************7...57778* PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v+++yvRa ++GtGa+k++GnYa s+la k+a+eqg+d+v++ld +ekk+iee G++n+ ++++d l+ lcl|NCBI__GCF_000014265.1:WP_011610681.1 180 VTDKYVRASEGGTGAAKCAGNYAGSFLADKEAKEQGYDNVLWLDGKEKKYIEECGTMNVAFVIND-VLI 247 *****************************************************************.9** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t++l++siL g+tr+s+l+l +d+g++veer i+ide+ +a eaG+i +f+ Gtaa i+ ++ ++ +g lcl|NCBI__GCF_000014265.1:WP_011610681.1 248 TPKLTGSILGGITRDSALTLFRDMGVKVEERLISIDEVAKAYEAGNIseAFGMGTAATIAHISVINYQG 316 **********************************************999******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWive 312 k +++ + + + ++ ++l di++Gk+ d++gWi + lcl|NCBI__GCF_000014265.1:WP_011610681.1 317 KDMILPPVDERKYASQVLQKLEDIKTGKVTDPYGWICQ 354 *****999999*************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (355 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: 7.95 // [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