Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate 199535 SO0340 branched-chain amino acid aminotransferase (NCBI ptt file)
Query= SwissProt::P39576 (363 letters) >FitnessBrowser__MR1:199535 Length = 363 Score = 288 bits (737), Expect = 2e-82 Identities = 153/347 (44%), Positives = 218/347 (62%), Gaps = 6/347 (1%) Query: 13 TKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFE 72 T++ KP+ N + FG + TDHMF+MDY D W DPRI+PY P M P AM HYGQ++FE Sbjct: 15 TEQFKPEGN-VGFGSLRTDHMFLMDYH-DGEWRDPRIVPYGPFEMAPGAMALHYGQSIFE 72 Query: 73 GLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAE 132 G KA++ ED + FR KN ER+N+S D +CIP IDE+ ++ + L+ +D+ W P E Sbjct: 73 GAKAFMHEDGEIYTFRINKNAERMNRSADIVCIPNIDEQMQIDAINALIDVDRLWFPMQE 132 Query: 133 GTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGI-KPVKIAVESEFVRAVKG 191 G LYIRPFI ATE L V+ S Y ++LSP G+YY G+ K +++ + + RAV G Sbjct: 133 GACLYIRPFIFATEDRLSVSPSSRYTFCVVLSPSGAYYAAGVNKGIRLLISKTYHRAVSG 192 Query: 192 GTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKI-NGEIVTP 250 GTG +K AGNYA+SL+A + A + G SQVL+LD + IEE G+MN F + +G ++ P Sbjct: 193 GTGASKAAGNYAASLRAGKAAAQFGASQVLYLDA-NNQQIEEAGAMNHFHILKDGTVIIP 251 Query: 251 MLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPV 310 +IL+ IT S++ L + G +V + + +D+ I + G + EA G GTAAV+S V Sbjct: 252 TFTDTILKSITSQSIMELSELLGCEVRQETVMLDKFIADIESGEIIEAGGFGTAAVVSAV 311 Query: 311 GELIWQD-ETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356 G I++D +++ NGE GE +++Y T IQKG V GW V Sbjct: 312 GSYIFEDGRVVTVGNGEVGEHIQRIYKLYTDIQKGHVQGPEGWVKRV 358 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: 359 Number of extensions: 14 Number of successful extensions: 4 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: 363 Length adjustment: 29 Effective length of query: 334 Effective length of database: 334 Effective search space: 111556 Effective search space used: 111556 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 199535 SO0340 (branched-chain amino acid aminotransferase (NCBI ptt file))
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.14576.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-102 326.7 0.1 7.1e-102 326.5 0.1 1.0 1 lcl|FitnessBrowser__MR1:199535 SO0340 branched-chain amino acid Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:199535 SO0340 branched-chain amino acid aminotransferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 326.5 0.1 7.1e-102 7.1e-102 1 313 [] 44 358 .. 44 358 .. 0.96 Alignments for each domain: == domain 1 score: 326.5 bits; conditional E-value: 7.1e-102 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkqlvk 79 W ++++++++++e+++g+++lhYgq +feG ka+ ++dG+i++fR ++na+R++rsa+++ +P+++e++ ++a++ l+ lcl|FitnessBrowser__MR1:199535 44 WRDPRIVPYGPFEMAPGAMALHYGQSIFEGAKAFMHEDGEIYTFRINKNAERMNRSADIVCIPNIDEQMQIDAINALID 122 99***************************************************************************** PP TIGR01123 80 adkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglap.vsifveteyvRaapkGtGavkvg 157 +d+ w p ++ +a LY+RPf++ated l v ++++y+f+v++sP GaY++ g+++ ++ ++++ y Ra+ +GtGa k + lcl|FitnessBrowser__MR1:199535 123 VDRLWFPMQE-GACLYIRPFIFATEDRLSVSPSSRYTFCVVLSPSGAYYAAGVNKgIRLLISKTYHRAVSGGTGASKAA 200 *******777.*****************************************99978999******************* PP TIGR01123 158 GnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresllelakdlgleve 236 GnYaasl+a k aa+ g ++v+yld++++ +iee+Ga+n f i+kdg+++++ ++ iL+++t +s++el + lg ev+ lcl|FitnessBrowser__MR1:199535 201 GNYAASLRAGKAAAQFGASQVLYLDANNQ-QIEEAGAMNHFHILKDGTVIIPTFTDTILKSITSQSIMELSELLGCEVR 278 **************************998.9************************************************ PP TIGR01123 237 ereiaidelkaaveaGei..vfacGtaavitPvge.lkiegkevevkseevGevtkklrdeltdiqyGkledkegWive 312 + + +d++ a e+Gei + + Gtaav++ vg+ + +g+ v+v ++evGe +++++ tdiq G+++++egW+ + lcl|FitnessBrowser__MR1:199535 279 QETVMLDKFIADIESGEIieAGGFGTAAVVSAVGSyIFEDGRVVTVGNGEVGEHIQRIYKLYTDIQKGHVQGPEGWVKR 357 *****************96566679********9835566788899999***************************987 PP TIGR01123 313 v 313 v lcl|FitnessBrowser__MR1:199535 358 V 358 6 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.85 // [ok]
This GapMind analysis is from Sep 17 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