Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate PfGW456L13_3544 Branched-chain amino acid aminotransferase (EC 2.6.1.42)
Query= reanno::pseudo5_N2C3_1:AO356_22970 (339 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3544 Length = 339 Score = 657 bits (1695), Expect = 0.0 Identities = 315/339 (92%), Positives = 331/339 (97%) Query: 1 MGNESINWDKLGFDYIKTDKRYLSHWRDGAWDAGTLTDDNVLHISEGSTALHYGQQCFEG 60 MGNESINWDKLGFDYIKTDKRYLS++R+G WD GTLT+DNVLHISEGSTALHYGQQCFEG Sbjct: 1 MGNESINWDKLGFDYIKTDKRYLSYFRNGEWDKGTLTEDNVLHISEGSTALHYGQQCFEG 60 Query: 61 LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPQVETEQFVEACKQVVRANERFIPPYGT 120 +KAYRCKDGSINLFRPDQNA RMQRSCARLLMPQVETEQF+EACK+VVRANERFIPPYGT Sbjct: 61 MKAYRCKDGSINLFRPDQNALRMQRSCARLLMPQVETEQFIEACKEVVRANERFIPPYGT 120 Query: 121 GGALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYFKGGLTPHNFLISSFDRAAPQGT 180 GGALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYFKGGLTPHNFLISS+DRAAPQGT Sbjct: 121 GGALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYFKGGLTPHNFLISSYDRAAPQGT 180 Query: 181 GAAKVGGNYAASLMPGSQAKKASFADCIYLDPMTHSKIEEVGSANFFGITHDNTFVTPRS 240 GAAKVGGNYAASLMPGSQAKKA FADCIYLDP+TH+KIEEVGSANFFGITHDN FVTP S Sbjct: 181 GAAKVGGNYAASLMPGSQAKKAHFADCIYLDPLTHTKIEEVGSANFFGITHDNKFVTPNS 240 Query: 241 PSVLPGITRLSLIELAKSRLGLEVIEGDVFIDKLSDFKEAGACGTAAVITPIGGISYKDK 300 PSVLPGITRLSLIELA+SRLGL+V+EGDVFIDKL+DFKEAGACGTAAVITPIGGI+Y D Sbjct: 241 PSVLPGITRLSLIELARSRLGLDVVEGDVFIDKLADFKEAGACGTAAVITPIGGINYNDH 300 Query: 301 LHVFHSETEVGPITQKLYKELTGVQTGDVEAPAGWIVKV 339 LHVFHSETEVGPITQKLYKELTGVQTGD+EAPAGWIVKV Sbjct: 301 LHVFHSETEVGPITQKLYKELTGVQTGDIEAPAGWIVKV 339 Lambda K H 0.320 0.138 0.422 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: 561 Number of extensions: 14 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: 339 Length of database: 339 Length adjustment: 28 Effective length of query: 311 Effective length of database: 311 Effective search space: 96721 Effective search space used: 96721 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: 49 (23.5 bits)
Align candidate PfGW456L13_3544 (Branched-chain amino acid aminotransferase (EC 2.6.1.42))
to HMM TIGR01123 (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/TIGR01123.hmm # target sequence database: /tmp/gapView.19106.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01123 [M=313] Accession: TIGR01123 Description: ilvE_II: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-141 456.6 0.0 2.1e-141 456.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3544 Branched-chain amino acid aminot Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3544 Branched-chain amino acid aminotransferase (EC 2.6.1.42) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 456.4 0.0 2.1e-141 2.1e-141 1 313 [] 31 339 .] 31 339 .] 0.99 Alignments for each domain: == domain 1 score: 456.4 bits; conditional E-value: 2.1e-141 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrr 55 Wd+++l++++ l+++egs++lhYgq++feG+kayR++dG+i+lfRpd+na R++r lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3544 31 WDKGTLTEDNVLHISEGSTALHYGQQCFEGMKAYRCKDGSINLFRPDQNALRMQR 85 ******************************************************* PP TIGR01123 56 saerlllPeleeelflealkqlvkadkdwvpkakseasLYlRPfliatednlGvk 110 s+ rll+P++e+e+f+ea+k++v+a+++++p+++++ +LYlRPf+i+++dn+Gv+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3544 86 SCARLLMPQVETEQFIEACKEVVRANERFIPPYGTGGALYLRPFVIGVGDNIGVR 140 ******************************************************* PP TIGR01123 111 aakeylflvlasPvGaYfkgglapvsifveteyvRaapkGtGavkvgGnYaasll 165 +a+e++f++++ PvGaYfkggl+p ++f+ + y+Raap+GtGa+kvgGnYaasl+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3544 141 TAPEFIFSIFCIPVGAYFKGGLTP-HNFLISSYDRAAPQGTGAAKVGGNYAASLM 194 ************************.99**************************** PP TIGR01123 166 aqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvt 220 + ++a++ +++d++yldp +++kieevG+an+f+it+d ++++tp+s+s+L+g+t lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3544 195 PGSQAKKAHFADCIYLDPLTHTKIEEVGSANFFGITHD-NKFVTPNSPSVLPGIT 248 **************************************.**************** PP TIGR01123 221 resllelakd.lgleveereiaidelkaaveaGeivfacGtaavitPvgelkieg 274 r sl+ela++ lgl v e+++ id+l +++eaG acGtaavitP+g+++ ++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3544 249 RLSLIELARSrLGLDVVEGDVFIDKLADFKEAG----ACGTAAVITPIGGINYND 299 **********9**********************....****************** PP TIGR01123 275 kevevkse.evGevtkklrdeltdiqyGkledkegWivev 313 + ++++se evG++t+kl++elt++q+G++e++ gWiv+v lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3544 300 HLHVFHSEtEVGPITQKLYKELTGVQTGDIEAPAGWIVKV 339 ******999*****************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (339 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.88 // [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