Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate CA265_RS15785 CA265_RS15785 branched-chain-amino-acid transaminase
Query= reanno::psRCH2:GFF445 (307 letters) >FitnessBrowser__Pedo557:CA265_RS15785 Length = 296 Score = 196 bits (497), Expect = 7e-55 Identities = 113/297 (38%), Positives = 168/297 (56%), Gaps = 6/297 (2%) Query: 1 MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTD 60 M + + +I+ DG+ + +++T + +LHYG FEG+RAY T +G IF+ AH D Sbjct: 1 MKYYNSNTIIYLDGQFEKAVNSSTDLYGQSLHYGYAAFEGIRAYKTHNGNRIFKAAAHFD 60 Query: 61 RLFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120 RL S + N+P P+ K+E+ AT ++ N L+ AYIRP+VF SG V + Sbjct: 61 RLERSCQLANIPFPWDKQELIAATYKLLQLNKLKDAYIRPLVFCHPNMKLNEPSG--VSI 118 Query: 121 IVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGA 180 ++ AW W AY G++ L+L + S + R + AK +G Y+NS+LA A G Sbjct: 119 LICAWEWDAYSGNKLLKLTV----SDYERPNPKSIPMEAKLSGNYVNSILATTAANIKGY 174 Query: 181 DEALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKR 240 DEAL+LD G+VAE SG NIF+ KDG ++TP + L GITR TV L ++ +EK+ Sbjct: 175 DEALLLDMHGFVAEASGANIFLEKDGKLFTPSLGNILPGITRATVKELCTVLDIECIEKK 234 Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTD 297 +T +++ AD AF GTA E+ I +D R I +Q+AY +LV K + Sbjct: 235 LTIEDLKNADSAFLCGTATEIAGIASIDDIVYRPIWRESIGYTIQRAYKNLVLEKVN 291 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: 205 Number of extensions: 5 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: 296 Length adjustment: 27 Effective length of query: 280 Effective length of database: 269 Effective search space: 75320 Effective search space used: 75320 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 CA265_RS15785 CA265_RS15785 (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.32303.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-79 251.0 0.0 8.3e-79 250.8 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS15785 CA265_RS15785 branched-chain-ami Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS15785 CA265_RS15785 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 250.8 0.0 8.3e-79 8.3e-79 1 288 [. 11 290 .. 11 295 .. 0.97 Alignments for each domain: == domain 1 score: 250.8 bits; conditional E-value: 8.3e-79 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyske 68 +ldG++ + ++ + + ++lhYG + feGiRaY+t++g +if++ h++Rl s + +++ p+ k+ lcl|FitnessBrowser__Pedo557:CA265_RS15785 11 YLDGQFEKAVNSSTDLYGQSLHYGYAAFEGIRAYKTHNGNRIFKAAAHFDRLERSCQLANIPFPWDKQ 78 89****************************************************************** PP TIGR01122 69 elvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvs 136 el+ +t ++l+ n+lk+aYiRplv+ + +++l+++++ v+++i awew ay g+ k +k +vs lcl|FitnessBrowser__Pedo557:CA265_RS15785 79 ELIAATYKLLQLNKLKDAYIRPLVF-CHPNMKLNEPSG--VSILICAWEWDAYSGN----KLLKLTVS 139 *************************.7899****9666..99*************6....7899**** PP TIGR01122 137 sfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpv 204 ++r +++sip +ak +gnY+ns+la + a+ +Gydea+lLd +G+vae sG nif+ kdg+l+tP++ lcl|FitnessBrowser__Pedo557:CA265_RS15785 140 DYERPNPKSIPMEAKLSGNYVNSILATTAANIKGYDEALLLDMHGFVAEASGANIFLEKDGKLFTPSL 207 ******************************************************************** PP TIGR01122 205 sesiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpv 272 +iL gitr +v +l + l ie e++++ e+l aD +fl Gta e++ i ++D++ r ++ lcl|FitnessBrowser__Pedo557:CA265_RS15785 208 -GNILPGITRATVKELCTVLDIECIEKKLTIEDLKNADSAFLCGTATEIAGIASIDDIVYRPIWRESI 274 .66***************************************************************** PP TIGR01122 273 tkklqeaffdlvegkt 288 ++q a+++lv +k+ lcl|FitnessBrowser__Pedo557:CA265_RS15785 275 GYTIQRAYKNLVLEKV 290 ***********98775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (296 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: 00:00:00.01 # Mc/sec: 7.13 // [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