Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate 6939205 Sama_3299 branched-chain amino acid aminotransferase (RefSeq)
Query= SwissProt::P39576 (363 letters) >FitnessBrowser__SB2B:6939205 Length = 361 Score = 280 bits (716), Expect = 4e-80 Identities = 144/344 (41%), Positives = 214/344 (62%), Gaps = 4/344 (1%) Query: 15 KPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFEGL 74 +P + FG++ TDHMF+MDY D W + RI+PY P M P AM HYGQ++FEG Sbjct: 16 EPFEPQGDVGFGKLRTDHMFMMDYK-DGQWQNARILPYGPFEMMPGAMALHYGQSIFEGA 74 Query: 75 KAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAEGT 134 KA++ +D + FR +KN +RLN+S D +CIP I E LE + L+ +D+ W P EG Sbjct: 75 KAFMHDDGEIYTFRLDKNAQRLNRSADIVCIPNIPEAVQLEAINALIDVDRLWFPRQEGA 134 Query: 135 SLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEFVRAVKGGTG 194 LYIRPF+ ATE L V+ ++ Y ++LSP G+YY + + +++ + ++F RAV GGTG Sbjct: 135 CLYIRPFVFATEDRLSVSPANQYTFCVVLSPSGAYYGKNLNAIRLLITTQFHRAVSGGTG 194 Query: 195 NAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIF-FKINGEIVTPMLN 253 +K AGNYA+SL+A + A E G +QVL+LD +YIEEVG+MN F + +G ++ P Sbjct: 195 ASKAAGNYAASLRAGKAAAEHGAAQVLYLDS-TNQYIEEVGAMNHFHIRKDGTLIIPEFT 253 Query: 254 GSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPVGEL 313 +IL IT S++AL + G +V + + + + I + G + EA G GTAAV+SPVG Sbjct: 254 DTILRSITSESILALGEELGCEVRQETVKLSDFIADIEAGEIVEAGGFGTAAVVSPVGSY 313 Query: 314 IWQD-ETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356 I++D +++ +G+ GE +Y T +QKG GW +V Sbjct: 314 IFEDGRIVTVGDGKVGERISHIYKVYTEMQKGLRPAPEGWVRKV 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: 334 Number of extensions: 17 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: 361 Length adjustment: 29 Effective length of query: 334 Effective length of database: 332 Effective search space: 110888 Effective search space used: 110888 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 6939205 Sama_3299 (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.26915.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-104 334.4 0.0 3.2e-104 334.2 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6939205 Sama_3299 branched-chain amino a Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6939205 Sama_3299 branched-chain amino acid aminotransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 334.2 0.0 3.2e-104 3.2e-104 1 313 [] 44 357 .. 44 357 .. 0.97 Alignments for each domain: == domain 1 score: 334.2 bits; conditional E-value: 3.2e-104 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkql 77 W++a++ +++++e+ +g+++lhYgq +feG ka+ ++dG+i++fR d+na+Rl+rsa+++ +P+++e++ lea++ l lcl|FitnessBrowser__SB2B:6939205 44 WQNARILPYGPFEMMPGAMALHYGQSIFEGAKAFMHDDGEIYTFRLDKNAQRLNRSADIVCIPNIPEAVQLEAINAL 120 ***************************************************************************** PP TIGR01123 78 vkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkGtGav 154 + +d+ w p ++ +a LY+RPf++ated l v +a++y+f+v++sP GaY+ ++l+ ++ +++t++ Ra+ +GtGa lcl|FitnessBrowser__SB2B:6939205 121 IDVDRLWFPRQE-GACLYIRPFVFATEDRLSVSPANQYTFCVVLSPSGAYYGKNLNAIRLLITTQFHRAVSGGTGAS 196 *********888.**************************************************************** PP TIGR01123 155 kvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresllelakdl 231 k +GnYaasl+a k aae+g ++v+yld++++ +ieevGa+n f i kdg+l++++ ++ iL ++t es+l l ++l lcl|FitnessBrowser__SB2B:6939205 197 KAAGNYAASLRAGKAAAEHGAAQVLYLDSTNQ-YIEEVGAMNHFHIRKDGTLIIPEFTDTILRSITSESILALGEEL 272 ****************************9887.******************************************** PP TIGR01123 232 gleveereiaidelkaaveaGei..vfacGtaavitPvge.lkiegkevevkseevGevtkklrdeltdiqyGkled 305 g ev+ + +++ ++ a eaGei + + Gtaav++Pvg+ + +g+ v+v +++vGe+ ++++ t++q G + lcl|FitnessBrowser__SB2B:6939205 273 GCEVRQETVKLSDFIADIEAGEIveAGGFGTAAVVSPVGSyIFEDGRIVTVGDGKVGERISHIYKVYTEMQKGLRPA 349 ***********************4444568********9835566788999999*********************** PP TIGR01123 306 kegWivev 313 +egW+ +v lcl|FitnessBrowser__SB2B:6939205 350 PEGWVRKV 357 ****9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (361 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: 00:00:00.01 # Mc/sec: 9.94 // [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