Align branched-chain-amino-acid aminotransferase subunit (EC 2.6.1.42) (characterized)
to candidate 3609919 Dshi_3301 branched-chain amino acid aminotransferase (RefSeq)
Query= metacyc::MONOMER-11914 (306 letters) >FitnessBrowser__Dino:3609919 Length = 289 Score = 214 bits (545), Expect = 2e-60 Identities = 116/294 (39%), Positives = 175/294 (59%), Gaps = 14/294 (4%) Query: 4 EASGKIWLNGEMVEWEEATVHVLSHVVHYGSSVFEGIRCYRNSKGSAIFRLREHVKRLFD 63 + G IW++G++V+W A VH+L+H +HY SSVFEG R Y IF R H +RL Sbjct: 7 DRDGTIWMDGKLVDWRAANVHILTHAMHYASSVFEGERAYNGK----IFESRRHSERLHF 62 Query: 64 SAKIYRMDIPYTQEQICDAIVETVRENGLEECYIRPVVFRGYG-EMGVHPVNCPVDVAVA 122 SA ++IP+T ++I A E ++ NGL + Y+R V +RG G +MGV PV +A+A Sbjct: 63 SAGELDIEIPFTVDEIEAAKYEVMKVNGLSDAYVRAVAWRGAGPDMGVASARNPVHLAIA 122 Query: 123 AWEWGAYLGAEALEVGVDAGVSTWRRMAPNTMPNMAKAGGNYLNSQLAKMEAVRHGYDEA 182 WEWG+Y G +A G ++ W+R +P T+P AKA G Y+ +K A G +A Sbjct: 123 CWEWGSYYG-DAKTRGAKLDIAKWKRPSPETIPVHAKAAGLYMICTTSKHAAEAKGCSDA 181 Query: 183 IMLDYHGYISEGSGENIFLVSEGEIYTPPVSSSLLRGITRDSVIKIARTEGVTVHEEPIT 242 + +DY GY++E +G NIF V +GE++TP L GITR +VI + R + V VHE I Sbjct: 182 LFMDYRGYVAEATGANIFFVKDGEVHTPD-PDCFLNGITRQTVIGMLRDKQVKVHERHIM 240 Query: 243 REMLYIADEAFFTGTAAEITPIRSVD--GIEIGAGRRGPVTKLLQDEFFRIIRA 294 E L ++ + TGTAAE+TP+ + E+GA +T+ + + + +++RA Sbjct: 241 PEELEGFEQCWLTGTAAEVTPVGQIGTYNFEVGA-----LTRDIAESYEQLVRA 289 Lambda K H 0.320 0.136 0.414 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: 286 Number of extensions: 16 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: 306 Length of database: 289 Length adjustment: 26 Effective length of query: 280 Effective length of database: 263 Effective search space: 73640 Effective search space used: 73640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate 3609919 Dshi_3301 (branched-chain amino acid aminotransferase (RefSeq))
to HMM TIGR01122 (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/TIGR01122.hmm # target sequence database: /tmp/gapView.7416.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01122 [M=298] Accession: TIGR01122 Description: ilvE_I: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-84 267.5 0.0 7.9e-84 267.3 0.0 1.0 1 lcl|FitnessBrowser__Dino:3609919 Dshi_3301 branched-chain amino a Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3609919 Dshi_3301 branched-chain amino acid aminotransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 267.3 0.0 7.9e-84 7.9e-84 1 285 [. 13 288 .. 13 289 .] 0.98 Alignments for each domain: == domain 1 score: 267.3 bits; conditional E-value: 7.9e-84 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtkev 77 w+dG+lvd++ a+vh+ltha+hY ++vfeG RaY++ if + h eRl+ sa l++eip++ +e+ + ev lcl|FitnessBrowser__Dino:3609919 13 WMDGKLVDWRAANVHILTHAMHYASSVFEGERAYNG----KIFESRRHSERLHFSAGELDIEIPFTVDEIEAAKYEV 85 9***********************************....9************************************ PP TIGR01122 78 lrknnlksaYiRplvyvGae.dlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaa 153 +++n+l++aY+R ++++Ga+ d+g+ + +v+++ia wewg y+g+ a +G k ++ ++r ++++ip +akaa lcl|FitnessBrowser__Dino:3609919 86 MKVNGLSDAYVRAVAWRGAGpDMGVAS-ARNPVHLAIACWEWGSYYGD-AKTRGAKLDIAKWKRPSPETIPVHAKAA 160 ******************9769*****.888****************6.89************************** PP TIGR01122 154 gnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievke 230 g Y+ + k+ a ++G +a+++d Gyvae +G nif vkdg++ tP+ + L+gitr++vi +++++ ++v+e lcl|FitnessBrowser__Dino:3609919 161 GLYMICTTSKHAAEAKGCSDALFMDYRGYVAEATGANIFFVKDGEVHTPDP-DCFLNGITRQTVIGMLRDKQVKVHE 236 ***************************************************.99*********************** PP TIGR01122 231 erisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlve 285 ++i eel + +ltGtaaevtP+ ++ + ++G +t+ + e++ +lv+ lcl|FitnessBrowser__Dino:3609919 237 RHIMPEELEGFEQCWLTGTAAEVTPVGQIGTY---NFEVGALTRDIAESYEQLVR 288 ***************************99876...568999**********9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (289 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.59 // [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