Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_085773086.1 B1812_RS19650 branched-chain amino acid aminotransferase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_002117405.1:WP_085773086.1 Length = 294 Score = 216 bits (550), Expect = 5e-61 Identities = 113/262 (43%), Positives = 156/262 (59%), Gaps = 5/262 (1%) Query: 6 RDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLN 65 RDG IW +G L WR+AK+HVL+H LHY VFEG RAY G IF+ +EH++R Sbjct: 9 RDGVIWFNGALTPWREAKLHVLSHGLHYASAVFEGERAY-----GGKIFKSREHSERFRR 63 Query: 66 SAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIAA 125 SA++ ++P+ L AA+ VV+ N ++ CY+RPI W GSE + V+A+ +TIH AIA Sbjct: 64 SAQLLDFEIPYSVAELEAAKDAVVKANGMQDCYVRPIAWRGSEMMAVAAQNSTIHTAIAV 123 Query: 126 WPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEAL 185 W W + + KGIR+ + + R AKA+G Y+ ++ A GY +AL Sbjct: 124 WDWPSMFDVETKMKGIRLDIAEYRRPDPRTEPSLAKAAGLYMICTISKHRAERRGYADAL 183 Query: 186 LLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRD 245 + D G V+E +G N F V +G L+TP LDGITR TVI LA+ G+ V E+RI + Sbjct: 184 MYDWLGRVAECTGANVFFVKDGALHTPIADCFLDGITRQTVIELAKRRGVAVFERRIMPE 243 Query: 246 EVYTCDEAFFTGTAAEVTPIRE 267 E+ E F GT AEVTP+ E Sbjct: 244 ELTGFSECFICGTGAEVTPVSE 265 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: 279 Number of extensions: 11 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: 294 Length adjustment: 27 Effective length of query: 280 Effective length of database: 267 Effective search space: 74760 Effective search space used: 74760 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_085773086.1 B1812_RS19650 (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.24512.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-78 248.3 0.0 5.3e-78 248.2 0.0 1.0 1 lcl|NCBI__GCF_002117405.1:WP_085773086.1 B1812_RS19650 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002117405.1:WP_085773086.1 B1812_RS19650 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 248.2 0.0 5.3e-78 5.3e-78 1 262 [. 14 269 .. 14 293 .. 0.95 Alignments for each domain: == domain 1 score: 248.2 bits; conditional E-value: 5.3e-78 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w++G l ++++ak+hvl+h+lhY ++vfeG RaY + if+ +eh eR+ sa+ l++eipys e lcl|NCBI__GCF_002117405.1:WP_085773086.1 14 WFNGALTPWREAKLHVLSHGLHYASAVFEGERAYGG----KIFKSREHSERFRRSAQLLDFEIPYSVAE 78 9*********************************99....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l + v+++n+++++Y+Rp++++G+e + + + + +++ +ia+w+w+ +++ e+ kGi+ ++ + lcl|NCBI__GCF_002117405.1:WP_085773086.1 79 LEAAKDAVVKANGMQDCYVRPIAWRGSEMMAVAA-QNSTIHTAIAVWDWPSMFDVETKMKGIRLDIAEY 146 **********************************.7779****************************** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr ++ + p+ akaag Y+ ++ k+ a r+Gy +a++ d G vae +G n+f vkdg+l tP + lcl|NCBI__GCF_002117405.1:WP_085773086.1 147 RRPDPRTEPSLAKAAGLYMICTISKHRAERRGYADALMYDWLGRVAECTGANVFFVKDGALHTPIA-DC 214 ****************************************************************98.99 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgr 262 L+gitr++vi+lak++g+ v e+ri eel e f+ Gt aevtP+ e lcl|NCBI__GCF_002117405.1:WP_085773086.1 215 FLDGITRQTVIELAKRRGVAVFERRIMPEELTGFSECFICGTGAEVTPVSEAGPY 269 *************************************************986555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (294 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.60 // [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