Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate YP_004141379.1 Mesci_2177 branched-chain amino acid aminotransferase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000185905.1:YP_004141379.1 Length = 297 Score = 228 bits (581), Expect = 1e-64 Identities = 116/262 (44%), Positives = 165/262 (62%), Gaps = 5/262 (1%) Query: 7 DGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLNS 66 DG IWM+G+ + W DAKIHVLTH LHY VFEG RAY G IF+L EHT+RL S Sbjct: 10 DGFIWMNGEFVQWGDAKIHVLTHGLHYASAVFEGERAY-----GGEIFKLNEHTERLHES 64 Query: 67 AKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIAAW 126 A++ +P+ L A ++++ + Y+RPI W GSE++GVSA+ N I+ AIA W Sbjct: 65 ARLLGFKIPYSVAELNDASSTLLKKQGFQDAYVRPIAWRGSEQMGVSAQNNRINCAIAIW 124 Query: 127 PWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALL 186 W +Y KGIR+ + + R + ++KA+G Y+ ++ A A GY +A++ Sbjct: 125 QWPSYFDPAQKLKGIRLDVAEWRRPDPRTAPSKSKAAGLYMICTMSKHAAEAKGYADAMM 184 Query: 187 LDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRDE 246 LD G V+E +G N F V +GK++TP LDGITR TVI LA+D G++VIE+ I +E Sbjct: 185 LDWRGQVAEATGANIFFVKDGKIHTPKPDCFLDGITRRTVIGLAKDRGLEVIERAILPEE 244 Query: 247 VYTCDEAFFTGTAAEVTPIREL 268 + + ++ F TGTAAEVTP+ E+ Sbjct: 245 LESFEQCFLTGTAAEVTPVSEI 266 Lambda K H 0.319 0.136 0.411 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: 266 Number of extensions: 9 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: 307 Length of database: 297 Length adjustment: 27 Effective length of query: 280 Effective length of database: 270 Effective search space: 75600 Effective search space used: 75600 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 YP_004141379.1 Mesci_2177 (branched-chain amino acid aminotransferase)
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.aa/TIGR01122.hmm # target sequence database: /tmp/gapView.23971.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-90 288.9 0.0 2.2e-90 288.8 0.0 1.0 1 lcl|NCBI__GCF_000185905.1:YP_004141379.1 Mesci_2177 branched-chain amino Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185905.1:YP_004141379.1 Mesci_2177 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 288.8 0.0 2.2e-90 2.2e-90 1 287 [. 14 291 .. 14 297 .] 0.97 Alignments for each domain: == domain 1 score: 288.8 bits; conditional E-value: 2.2e-90 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w++Ge+v++ dak+hvlth+lhY ++vfeG RaY + if+l+eh+eRl++sa+ l ++ipys e lcl|NCBI__GCF_000185905.1:YP_004141379.1 14 WMNGEFVQWGDAKIHVLTHGLHYASAVFEGERAYGG----EIFKLNEHTERLHESARLLGFKIPYSVAE 78 9*********************************99....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l+++ +l+k+++++aY+Rp++++G+e++g+++ + +++ +ia w+w+ y++ kGi+ v+ + lcl|NCBI__GCF_000185905.1:YP_004141379.1 79 LNDASSTLLKKQGFQDAYVRPIAWRGSEQMGVSA-QNNRINCAIAIWQWPSYFDPAQKLKGIRLDVAEW 146 **********************************.6669****************9999********** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr ++ + p+k kaag Y+ ++ k+ a ++Gy +a++Ld G vae +G nif vkdg++ tP+ + lcl|NCBI__GCF_000185905.1:YP_004141379.1 147 RRPDPRTAPSKSKAAGLYMICTMSKHAAEAKGYADAMMLDWRGQVAEATGANIFFVKDGKIHTPKP-DC 214 *****************************************************************9.99 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 L+gitr +vi lak++g+ev e+ i eel + fltGtaaevtP+ e+ + ++G++ k+l lcl|NCBI__GCF_000185905.1:YP_004141379.1 215 FLDGITRRTVIGLAKDRGLEVIERAILPEELESFEQCFLTGTAAEVTPVSEIGPYRF---EVGEIAKNL 280 ***************************************************998876...789****** PP TIGR01122 277 qeaffdlvegk 287 ++ ++ v+ k lcl|NCBI__GCF_000185905.1:YP_004141379.1 281 MNDYSAAVQPK 291 ****9999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (297 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: 9.90 // [ok]
This GapMind analysis is from Apr 10 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