Align Branched-chain-amino-acid transaminase 1; BCAT 1; EC 2.6.1.42 (characterized)
to candidate 5207757 Shew_0278 branched-chain amino acid aminotransferase (RefSeq)
Query= SwissProt::O31461 (356 letters) >FitnessBrowser__PV4:5207757 Length = 363 Score = 295 bits (756), Expect = 1e-84 Identities = 152/343 (44%), Positives = 221/343 (64%), Gaps = 5/343 (1%) Query: 16 KPDPSSLGFGQYFTDYMFVMDYEEGIGWHHPRIAPYAPLTLDPSSSVFHYGQAVFEGLKA 75 KP+ +++GFG TD+MF+MDY +G W PR+ PY P + P + HYGQ++FEG KA Sbjct: 19 KPE-TNVGFGNLRTDHMFLMDYRDG-EWRDPRVVPYGPFEMAPGAMALHYGQSIFEGAKA 76 Query: 76 YRTDDGRVLLFRPDQNIKRLNRSCERMSMPPLDEELVLEALTQLVELEKDWVPKEKGTSL 135 + DDG + FR ++N +RLN S E + +PP+ E + L + L+++++ W P + G L Sbjct: 77 FMHDDGEIYTFRLNKNAERLNLSGEVVCIPPVPEAMQLAGINALIDVDRLWFPMQDGACL 136 Query: 136 YIRPFVIATEPSLGVKASRSYTFMIVLSPVGSYYGDDQLKPVRIYVEDEYVRAVNGGVGF 195 YIRPFV ATE L V S+ YTF ++LSP G+YY D K +R+ + + + RAV+GG G Sbjct: 137 YIRPFVFATEDRLSVSPSQQYTFCVMLSPSGAYYADGFDKAIRLLITERFHRAVSGGTGA 196 Query: 196 AKTAGNYAASLQAQRKANELGYDQVLWLDAIEKKYVEEVGSMNIFFVI-NGEAVTPALSG 254 +K AGNYAASL+A + A E G QVL+LDA K +EEVG+MN F V+ +G + P + Sbjct: 197 SKAAGNYAASLRAGKAAAEYGAAQVLYLDA-NNKQIEEVGAMNHFHVLKDGTIIIPKFTD 255 Query: 255 SILSGVTRASAIELIRSWGIPVREERISIDEVYAASARGELTEVFGTGTAAVVTPVGELN 314 +IL +T S +EL + G VR+E + +D+ A GE+ E G GTAAVV+PVG Sbjct: 256 TILKSITSQSIMELGEALGCEVRQETVMLDQFIADIESGEIVEAGGFGTAAVVSPVGSYI 315 Query: 315 IHGKTVI-VGDGQIGDLSKKLYETITDIQLGKVKGPFNWTVEV 356 V+ VGDGQ+G+ ++++Y+ +TDIQ GK +GP W +V Sbjct: 316 FEDHRVLTVGDGQVGEHTRRIYQVLTDIQKGKRQGPEGWMQKV 358 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: 359 Number of extensions: 27 Number of successful extensions: 5 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: 363 Length adjustment: 29 Effective length of query: 327 Effective length of database: 334 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 5207757 Shew_0278 (branched-chain amino acid aminotransferase (RefSeq))
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.31499.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-104 334.1 0.0 4e-104 333.9 0.0 1.0 1 lcl|FitnessBrowser__PV4:5207757 Shew_0278 branched-chain amino a Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5207757 Shew_0278 branched-chain amino acid aminotransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 333.9 0.0 4e-104 4e-104 1 313 [] 44 358 .. 44 358 .. 0.96 Alignments for each domain: == domain 1 score: 333.9 bits; conditional E-value: 4e-104 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkqlv 78 W ++++++++++e+++g+++lhYgq +feG ka+ ++dG+i++fR ++na+Rl+ s e + +P ++e++ l ++ l+ lcl|FitnessBrowser__PV4:5207757 44 WRDPRVVPYGPFEMAPGAMALHYGQSIFEGAKAFMHDDGEIYTFRLNKNAERLNLSGEVVCIPPVPEAMQLAGINALI 121 99**************************************************************************** PP TIGR01123 79 kadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglap.vsifveteyvRaapkGtGavk 155 +d+ w p ++ +a LY+RPf++ated l v ++++y+f+v++sP GaY+++g ++ ++ ++++ + Ra+ +GtGa k lcl|FitnessBrowser__PV4:5207757 122 DVDRLWFPMQD-GACLYIRPFVFATEDRLSVSPSQQYTFCVMLSPSGAYYADGFDKaIRLLITERFHRAVSGGTGASK 198 ********888.*****************************************887589999**************** PP TIGR01123 156 vgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresllelakdlgl 233 +GnYaasl+a k aae g ++v+yld+++k +ieevGa+n f ++kdg++++++ ++ iL+++t +s++el + lg lcl|FitnessBrowser__PV4:5207757 199 AAGNYAASLRAGKAAAEYGAAQVLYLDANNK-QIEEVGAMNHFHVLKDGTIIIPKFTDTILKSITSQSIMELGEALGC 275 ****************************987.9********************************************* PP TIGR01123 234 eveereiaidelkaaveaGei..vfacGtaavitPvgelkiegke.vevkseevGevtkklrdeltdiqyGkledkeg 308 ev+ + + +d++ a e+Gei + + Gtaav++Pvg+ e++ ++v +++vGe t+++++ ltdiq Gk +++eg lcl|FitnessBrowser__PV4:5207757 276 EVRQETVMLDQFIADIESGEIveAGGFGTAAVVSPVGSYIFEDHRvLTVGDGQVGEHTRRIYQVLTDIQKGKRQGPEG 353 *********************4444568*********988777651578899************************** PP TIGR01123 309 Wivev 313 W+ +v lcl|FitnessBrowser__PV4:5207757 354 WMQKV 358 **987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (363 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 12.40 // [ok]
This GapMind analysis is from Apr 09 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