Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_019557720.1 F612_RS0110445 branched-chain amino acid transaminase
Query= reanno::psRCH2:GFF445 (307 letters) >NCBI__GCF_000381085.1:WP_019557720.1 Length = 308 Score = 456 bits (1172), Expect = e-133 Identities = 218/305 (71%), Positives = 253/305 (82%) Query: 2 SMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTDR 61 +M DRDGVIW DGE++ WR+A HVLTHTLHYGMGVFEGVRAY G +IFRL AHT R Sbjct: 3 TMDDRDGVIWLDGEMIPWREAKVHVLTHTLHYGMGVFEGVRAYEAEQGPSIFRLDAHTKR 62 Query: 62 LFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHVI 121 L +SA IMNM MPY K ++ A A VRENNL+SAYIRPM FYGSEGMGLRA LK HV+ Sbjct: 63 LTNSAKIMNMAMPYDKATLDAAQCAVVRENNLKSAYIRPMAFYGSEGMGLRADNLKTHVM 122 Query: 122 VAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGAD 181 VAAW WGAYMG+E L GIK+ TSS+TRHHVNITMT+AKSNG+Y+NSMLALQEA+S G D Sbjct: 123 VAAWEWGAYMGEENLTRGIKIATSSYTRHHVNITMTKAKSNGSYMNSMLALQEAVSHGCD 182 Query: 182 EALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKRI 241 EAL+LD +GYVAEGSGEN F++ DGV+YTPE+T CL+GITR T++T+A E GL+++EKRI Sbjct: 183 EALLLDVDGYVAEGSGENFFMVTDGVLYTPELTCCLDGITRKTIMTMAKEIGLEVIEKRI 242 Query: 242 TRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHAE 301 TRDEVYIADEAFFTGTAAEV PIRE+D R IG G RGPITEKLQ YFD+V G++ AH + Sbjct: 243 TRDEVYIADEAFFTGTAAEVMPIRELDNRPIGTGSRGPITEKLQTMYFDIVHGRSPAHMD 302 Query: 302 WRTLV 306 W T V Sbjct: 303 WLTTV 307 Lambda K H 0.319 0.135 0.400 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: 404 Number of extensions: 6 Number of successful extensions: 1 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: 308 Length adjustment: 27 Effective length of query: 280 Effective length of database: 281 Effective search space: 78680 Effective search space used: 78680 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_019557720.1 F612_RS0110445 (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.12282.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-138 445.7 0.1 4.1e-138 445.5 0.1 1.0 1 lcl|NCBI__GCF_000381085.1:WP_019557720.1 F612_RS0110445 branched-chain am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000381085.1:WP_019557720.1 F612_RS0110445 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 445.5 0.1 4.1e-138 4.1e-138 1 298 [] 12 307 .. 12 307 .. 0.99 Alignments for each domain: == domain 1 score: 445.5 bits; conditional E-value: 4.1e-138 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 wldGe++++++akvhvlth+lhYG+gvfeG+RaYe+++g+ ifrl+ h++Rl +saki+++ +py k + lcl|NCBI__GCF_000381085.1:WP_019557720.1 12 WLDGEMIPWREAKVHVLTHTLHYGMGVFEGVRAYEAEQGPSIFRLDAHTKRLTNSAKIMNMAMPYDKAT 80 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l ++ v+r+nnlksaYiRp++++G+e++gl++ +lk++v++aawewgay+gee l +Gik+ +ss+ lcl|NCBI__GCF_000381085.1:WP_019557720.1 81 LDAAQCAVVRENNLKSAYIRPMAFYGSEGMGLRA-DNLKTHVMVAAWEWGAYMGEENLTRGIKIATSSY 148 **********************************.899******************************* PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r++vn+ +tkak++g+Y+ns+la +ea+++G dea+lLd +GyvaeGsGen+f+v dgvl+tP++ + lcl|NCBI__GCF_000381085.1:WP_019557720.1 149 TRHHVNITMTKAKSNGSYMNSMLALQEAVSHGCDEALLLDVDGYVAEGSGENFFMVTDGVLYTPEL-TC 216 ******************************************************************.88 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L+gitr +++++ake g+ev e+ri+r+e+y+aDe+f+tGtaaev Pire+D+r ig g+rGp+t+kl lcl|NCBI__GCF_000381085.1:WP_019557720.1 217 CLDGITRKTIMTMAKEIGLEVIEKRITRDEVYIADEAFFTGTAAEVMPIRELDNRPIGTGSRGPITEKL 285 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewltyv 298 q+ +fd+v+g+ +++++wlt+v lcl|NCBI__GCF_000381085.1:WP_019557720.1 286 QTMYFDIVHGRSPAHMDWLTTV 307 *******************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (308 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: 00:00:00.00 # Mc/sec: 11.49 // [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