Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_020174241.1 A3OQ_RS0104865 branched-chain amino acid aminotransferase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000385335.1:WP_020174241.1 Length = 295 Score = 218 bits (556), Expect = 1e-61 Identities = 118/272 (43%), Positives = 164/272 (60%), Gaps = 5/272 (1%) Query: 6 RDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLN 65 RDG IWM+G+L+ W+DAK+HVL+H LHY VFEG RAY G IF+ EH++R Sbjct: 9 RDGFIWMNGELVPWKDAKLHVLSHGLHYASCVFEGERAY-----GGRIFKSSEHSERFRT 63 Query: 66 SAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIAA 125 SA + ++P+ L A + VV +N SCY+RP+ W GSE + V+A+ +TI+VAIAA Sbjct: 64 SAALLDFEIPYSVADLDAFKQLVVDKNNFTSCYVRPVAWRGSEMMAVAAQNSTINVAIAA 123 Query: 126 WPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEAL 185 W W + + KGIR+ + + R + AKA+G Y+ ++ A GY +A+ Sbjct: 124 WNWPSMFDVNEKMKGIRLDIADYRRPDPMTAPSGAKAAGLYMICTISKHRAERRGYADAM 183 Query: 186 LLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRD 245 +LD G V+E +G N F G ++TP LDGITR TVI LAR G++VIE+RI + Sbjct: 184 MLDWLGRVAECTGANIFFTAKGVVHTPIADCFLDGITRKTVIDLARRRGLEVIERRIMPE 243 Query: 246 EVYTCDEAFFTGTAAEVTPIRELDNRTIGSGA 277 E+ DEAF GT AEVTP+ E+ GA Sbjct: 244 ELAGFDEAFICGTGAEVTPVSEIGPYKFTPGA 275 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: 278 Number of extensions: 8 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: 295 Length adjustment: 27 Effective length of query: 280 Effective length of database: 268 Effective search space: 75040 Effective search space used: 75040 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 WP_020174241.1 A3OQ_RS0104865 (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.22645.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-80 255.6 0.0 3.3e-80 255.4 0.0 1.0 1 lcl|NCBI__GCF_000385335.1:WP_020174241.1 A3OQ_RS0104865 branched-chain am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000385335.1:WP_020174241.1 A3OQ_RS0104865 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 255.4 0.0 3.3e-80 3.3e-80 1 285 [. 14 289 .. 14 295 .] 0.96 Alignments for each domain: == domain 1 score: 255.4 bits; conditional E-value: 3.3e-80 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w++Gelv+++dak+hvl+h+lhY + vfeG RaY + +if+ +eh eR+ +sa l++eipys + lcl|NCBI__GCF_000385335.1:WP_020174241.1 14 WMNGELVPWKDAKLHVLSHGLHYASCVFEGERAYGG----RIFKSSEHSERFRTSAALLDFEIPYSVAD 78 9*********************************99....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l + v+ knn++s+Y+Rp++++G+e + + + + +++v+iaaw+w+ +++ + kGi+ ++ + lcl|NCBI__GCF_000385335.1:WP_020174241.1 79 LDAFKQLVVDKNNFTSCYVRPVAWRGSEMMAVAA-QNSTINVAIAAWNWPSMFDVNEKMKGIRLDIADY 146 **********************************.7779****************************** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr ++ + p+ akaag Y+ ++ k+ a r+Gy +a++Ld G vae +G nif +gv+ tP + lcl|NCBI__GCF_000385335.1:WP_020174241.1 147 RRPDPMTAPSGAKAAGLYMICTISKHRAERRGYADAMMLDWLGRVAECTGANIFFTAKGVVHTPIA-DC 214 ****************************************************************98.99 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 L+gitr +vi+la+++g+ev e+ri eel De+f+ Gt aevtP+ e+ k G + + l lcl|NCBI__GCF_000385335.1:WP_020174241.1 215 FLDGITRKTVIDLARRRGLEVIERRIMPEELAGFDEAFICGTGAEVTPVSEIGPYKFT---PGAISRAL 280 ****************************************************998875...56778888 PP TIGR01122 277 qeaffdlve 285 + ++ v+ lcl|NCBI__GCF_000385335.1:WP_020174241.1 281 IDDYSAEVQ 289 888776665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (295 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.24 // [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