Align Branched-chain-amino-acid transaminase 1; BCAT 1; EC 2.6.1.42 (characterized)
to candidate Echvi_1626 Echvi_1626 branched-chain amino acid aminotransferase, group II
Query= SwissProt::O31461 (356 letters) >FitnessBrowser__Cola:Echvi_1626 Length = 355 Score = 276 bits (705), Expect = 8e-79 Identities = 147/332 (44%), Positives = 203/332 (61%), Gaps = 12/332 (3%) Query: 24 FGQYFTDYMFVMDYEEGIGWHHPRIAPYAPLTLDPSSSVFHYGQAVFEGLKAYRTDDGRV 83 FG TD+M V Y +G WH I PY L L P + HYGQ VFEGLKAYR +D + Sbjct: 23 FGVEATDHMLVARYSDG-HWHSATIQPYEQLVLSPLAMCLHYGQTVFEGLKAYRQEDDTI 81 Query: 84 LLFRPDQNIKRLNRSCERMSMPPLDEELVLEALTQLVELEKDWVPKEKGTSLYIRPFVIA 143 +FR ++ +R+N+S RM+MP + EEL + +LV+LE++W+ +G SLYIRPFVIA Sbjct: 82 SIFRLARHHERINQSLRRMAMPEIPEELFETGIRELVDLEQEWIRGGEGNSLYIRPFVIA 141 Query: 144 TEPSLGVKASRSYTFMIVLSPVGSYYGDDQLKPVRIYVEDEYVRAVNGGVGFAKTAGNYA 203 TE LGV S Y FM+V +P+ +YY KP+++ VE Y RAV GGVG AK GNY Sbjct: 142 TEARLGVSISTDYLFMVVCTPMAAYYA----KPLKVKVERHYTRAVPGGVGAAKNGGNYG 197 Query: 204 ASLQAQRKANELGYDQVLWLDAIEKKYVEEVGSMNIFFVINGEAVTPALSGSILSGVTRA 263 A+ A + G+DQV+W DA + ++VEE G+MN+ F+I+G +TP ++L+GVTR Sbjct: 198 AAYYPAHLAQQAGFDQVIWTDARDHQFVEESGTMNLMFIIDGVLLTPPAGETVLAGVTRD 257 Query: 264 SAIELIRSWGIPVREERISIDEVYAASARGELTEVFGTGTAAVVTPVGELNIHG---KTV 320 S + + R G PV E IS+ E+ A + G+ E FG GTAAVV P+ + I G + Sbjct: 258 SLLSIARDMGWPVEERPISLKELEEAFSTGKKVEAFGAGTAAVVAPLELIQIDGQDFRPY 317 Query: 321 IVGDGQIGDLSKKLYETITDIQLGKVKGPFNW 352 I D Q+ L +L + I+ GK K P+ W Sbjct: 318 IAEDAQMYQLKARL----SAIRAGKEKDPYAW 345 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: 334 Number of extensions: 10 Number of successful extensions: 2 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 Echvi_1626 Echvi_1626 (branched-chain amino acid aminotransferase, group II)
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.190793.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-97 310.2 0.0 8e-97 309.9 0.0 1.0 1 FitnessBrowser__Cola:Echvi_1626 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Cola:Echvi_1626 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 309.9 0.0 8e-97 8e-97 1 310 [. 41 346 .. 41 349 .. 0.97 Alignments for each domain: == domain 1 score: 309.9 bits; conditional E-value: 8e-97 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkqlv 78 W++a+++++++l l++ ++ lhYgq vfeGlkayR++d i +fR + +R+++s +r+++Pe++eelf +++lv FitnessBrowser__Cola:Echvi_1626 41 WHSATIQPYEQLVLSPLAMCLHYGQTVFEGLKAYRQEDDTISIFRLARHHERINQSLRRMAMPEIPEELFETGIRELV 118 ****************************************************************************** PP TIGR01123 79 kadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkGtGavkv 156 ++++w+ + ++sLY+RPf+iate+ lGv +++ylf+v+++P+ aY+++ l++ ve +y+Ra+p+G+Ga+k FitnessBrowser__Cola:Echvi_1626 119 DLEQEWIRGGE-GNSLYIRPFVIATEARLGVSISTDYLFMVVCTPMAAYYAKPLKV---KVERHYTRAVPGGVGAAKN 192 *******9776.9*************************************998877...89***************** PP TIGR01123 157 gGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresllelakdlgle 234 gGnY a+ + + a++ g+d+v++ d+ +++ +ee G++n+++i++ g l+t+p e +L gvtr+sll++a+d+g FitnessBrowser__Cola:Echvi_1626 193 GGNYGAAYYPAHLAQQAGFDQVIWTDARDHQFVEESGTMNLMFIID-GVLLTPPAGETVLAGVTRDSLLSIARDMGWP 269 ********************************************97.8****************************** PP TIGR01123 235 veereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkklrdeltdiqyGkledkegWi 310 veer i++ el++a +G+ +f++Gtaav++P++ ++i+g+ ++ + +e ++l+ l i Gk +d++ W FitnessBrowser__Cola:Echvi_1626 270 VEERPISLKELEEAFSTGKKveAFGAGTAAVVAPLELIQIDGQDFRPYIAE-DAQMYQLKARLSAIRAGKEKDPYAWN 346 ******************98789********************99988774.456799*******************6 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 20.94 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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