Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_013459094.1 SULKU_RS01180 branched-chain amino acid transaminase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000183725.1:WP_013459094.1 Length = 306 Score = 320 bits (820), Expect = 3e-92 Identities = 160/300 (53%), Positives = 218/300 (72%), Gaps = 3/300 (1%) Query: 10 IWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLNSAKI 69 IWM+GKL+ W DAKIHVL+HTLHYG G EG +AYKT G AIFRL +HTKRL+ SAK+ Sbjct: 7 IWMNGKLLPWHDAKIHVLSHTLHYGNGAIEGTKAYKTPKG-YAIFRLNDHTKRLIESAKM 65 Query: 70 FQMDVPFDHETLAAAQCEVVRENKL--ESCYLRPIIWVGSEKLGVSAKGNTIHVAIAAWP 127 ++VP+ E L AQ E+++ N+ E+ YLRPI+++G +GV K + VA++AW Sbjct: 66 TLINVPYTVEELNHAQIELLKANEFTGENVYLRPIVYLGYGVMGVYHKEAPVEVAVSAWE 125 Query: 128 WGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALLL 187 WGAYLGE+G+ KGIR+K SSF+R + +M +AKA Y+NS +A EA+ GYDEALLL Sbjct: 126 WGAYLGEEGMKKGIRLKISSFSRPNNKSNMGKAKAVANYLNSQMAKFEAVEAGYDEALLL 185 Query: 188 DVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRDEV 247 D +GYV+E SG +FF++ +G++ TP + L IT+ TVI +A G V +RI+R+E+ Sbjct: 186 DDEGYVAEASGASFFMIKDGEIITPPNDNSLASITQKTVIEMAEKMGYTVSRRRISREEI 245 Query: 248 YTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKYANWLTKI 307 Y DEAF TGTAAE+TP+RE+D R +G+G RGPITEK+QS +FDIV G++ Y ++LT I Sbjct: 246 YIADEAFLTGTAAEITPVREVDARVLGAGGRGPITEKIQSSYFDIVYGRNPDYDHYLTYI 305 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: 307 Number of extensions: 12 Number of successful extensions: 3 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: 306 Length adjustment: 27 Effective length of query: 280 Effective length of database: 279 Effective search space: 78120 Effective search space used: 78120 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_013459094.1 SULKU_RS01180 (branched-chain amino acid transaminase)
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.14048.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-126 406.9 0.3 2.6e-126 406.8 0.3 1.0 1 lcl|NCBI__GCF_000183725.1:WP_013459094.1 SULKU_RS01180 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183725.1:WP_013459094.1 SULKU_RS01180 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.8 0.3 2.6e-126 2.6e-126 1 298 [] 8 305 .. 8 305 .. 0.99 Alignments for each domain: == domain 1 score: 406.8 bits; conditional E-value: 2.6e-126 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w++G+l++++dak+hvl+h+lhYG+g eG++aY+t+kg aifrl++h++Rl +sak++ +++py+ ee lcl|NCBI__GCF_000183725.1:WP_013459094.1 8 WMNGKLLPWHDAKIHVLSHTLHYGNGAIEGTKAYKTPKGYAIFRLNDHTKRLIESAKMTLINVPYTVEE 76 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlks..aYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvs 136 l+++++e+l++n+++ +Y+Rp+vy+G++ +g+++ +++vev++ awewgaylgee+++kGi+ k+s lcl|NCBI__GCF_000183725.1:WP_013459094.1 77 LNHAQIELLKANEFTGenVYLRPIVYLGYGVMGVYH-KEAPVEVAVSAWEWGAYLGEEGMKKGIRLKIS 144 **************6445******************.788***************************** PP TIGR01122 137 sfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvs 205 sf r +++s + kaka++nYlns++ak+ea++aGydea+lLd+eGyvae sG ++f++kdg+++tPp+ lcl|NCBI__GCF_000183725.1:WP_013459094.1 145 SFSRPNNKSNMGKAKAVANYLNSQMAKFEAVEAGYDEALLLDDEGYVAEASGASFFMIKDGEIITPPN- 212 *******************************************************************9. PP TIGR01122 206 esiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtk 274 +++L +it+ +vi++a+++g++v ++risree+y+aDe+fltGtaae+tP+revD+r +g+g rGp+t+ lcl|NCBI__GCF_000183725.1:WP_013459094.1 213 DNSLASITQKTVIEMAEKMGYTVSRRRISREEIYIADEAFLTGTAAEITPVREVDARVLGAGGRGPITE 281 889****************************************************************** PP TIGR01122 275 klqeaffdlvegktekkeewltyv 298 k+q+++fd+v+g++++++++lty+ lcl|NCBI__GCF_000183725.1:WP_013459094.1 282 KIQSSYFDIVYGRNPDYDHYLTYI 305 *********************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (306 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: 6.72 // [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