Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_043743277.1 AMB_RS02850 branched-chain amino acid aminotransferase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000009985.1:WP_043743277.1 Length = 290 Score = 239 bits (609), Expect = 7e-68 Identities = 124/289 (42%), Positives = 177/289 (61%), Gaps = 8/289 (2%) Query: 5 DRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLL 64 DRDG +W DGKL+ WRDAKIHVLTH LHYG VFEG R Y G +F+L+EH++RL+ Sbjct: 8 DRDGFLWFDGKLVPWRDAKIHVLTHGLHYGSCVFEGERVY-----GGKVFKLREHSQRLI 62 Query: 65 NSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIA 124 +S +I +VP+ E + A V+ N + Y+RP+ W GSE +GV+A+ I A+A Sbjct: 63 DSGRILGFEVPWTVEEIDEATMATVKANNIVDGYVRPVAWRGSEMMGVAAQTTKIRFAVA 122 Query: 125 AWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEA 184 W W +Y + KGIR+ S++ R H + +KA+G Y+ ++ +A DGY+++ Sbjct: 123 TWSWPSYWSPEARMKGIRLNISTWKRPHPETAPTASKAAGLYMICTMSKHKAEGDGYEDS 182 Query: 185 LLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITR 244 L+LD G V+E +G N F V +L+TP L+GITR TVI LA+ GI V+E+ I Sbjct: 183 LMLDWRGQVAEATGANIFFVFGNELHTPTPDCFLNGITRQTVIALAKKRGITVVERAIFP 242 Query: 245 DEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIV 293 +E+ E F TGTAAEVTP+RE+ T G IT +L + + +V Sbjct: 243 EEMTKASECFLTGTAAEVTPVREIGPYTF---TPGDITRQLITDYDALV 288 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: 286 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: 290 Length adjustment: 27 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 WP_043743277.1 AMB_RS02850 (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.1323.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-91 292.9 0.0 1.4e-91 292.8 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_043743277.1 AMB_RS02850 branched-chain amino Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_043743277.1 AMB_RS02850 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 292.8 0.0 1.4e-91 1.4e-91 1 285 [. 14 289 .. 14 290 .] 0.98 Alignments for each domain: == domain 1 score: 292.8 bits; conditional E-value: 1.4e-91 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w+dG+lv+++dak+hvlth+lhYG+ vfeG R+Y + +f+l+eh +Rl ds +il +e+p++ ee lcl|NCBI__GCF_000009985.1:WP_043743277.1 14 WFDGKLVPWRDAKIHVLTHGLHYGSCVFEGERVYGG----KVFKLREHSQRLIDSGRILGFEVPWTVEE 78 9*********************************99....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 + e+t+ ++++nn+ + Y+Rp++++G+e +g+ + +k++ ++a+w+w+ y ea kGi+ ++s++ lcl|NCBI__GCF_000009985.1:WP_043743277.1 79 IDEATMATVKANNIVDGYVRPVAWRGSEMMGVAA-QTTKIRFAVATWSWPSYWSPEARMKGIRLNISTW 146 **********************************.6679****************************** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r ++++ pt+ kaag Y+ ++ k++a Gy+++++Ld G vae +G nif v ++l tP + lcl|NCBI__GCF_000009985.1:WP_043743277.1 147 KRPHPETAPTASKAAGLYMICTMSKHKAEGDGYEDSLMLDWRGQVAEATGANIFFVFGNELHTPTP-DC 214 *****************************************************************9.99 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 L+gitr++vi lak++gi+v+e+ i ee+ a e fltGtaaevtP+re+ + + G++t++l lcl|NCBI__GCF_000009985.1:WP_043743277.1 215 FLNGITRQTVIALAKKRGITVVERAIFPEEMTKASECFLTGTAAEVTPVREIGPYTF---TPGDITRQL 280 ****************************************************99887...5689***** PP TIGR01122 277 qeaffdlve 285 + + lv+ lcl|NCBI__GCF_000009985.1:WP_043743277.1 281 ITDYDALVR 289 ***999886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (290 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: 11.03 // [ok]
This GapMind analysis is from Apr 09 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