Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate PP_3511 PP_3511 Branched-chain-amino-acid aminotransferase
Query= reanno::pseudo5_N2C3_1:AO356_22970 (339 letters) >FitnessBrowser__Putida:PP_3511 Length = 339 Score = 585 bits (1507), Expect = e-172 Identities = 283/339 (83%), Positives = 308/339 (90%), Gaps = 1/339 (0%) Query: 1 MGNESINWDKLGFDYIKTDKRYLSHWRDGAWDAGTLTDDNVLHISEGSTALHYGQQCFEG 60 M NESINWDKLGFDYIKTDKRYLS WR+G WD GTLT+DNVLHISEGSTALHYGQQCFEG Sbjct: 1 MSNESINWDKLGFDYIKTDKRYLSVWRNGEWDKGTLTEDNVLHISEGSTALHYGQQCFEG 60 Query: 61 LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPQVETEQFVEACKQVVRANERFIPPYGT 120 LKAYRCKDGSINLFRPDQNAARMQRSCARLLMP V T+ F+EACKQVV+ANE+F+PP+G Sbjct: 61 LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPHVPTDVFIEACKQVVKANEKFVPPHGK 120 Query: 121 GGALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYFKGGLTPHNFLISSFDRAAPQGT 180 G ALYLRPFVIG GDNIGVRTAPEFIFS+F IPVG+YFKGG+ PHNF ISSFDRAAPQGT Sbjct: 121 G-ALYLRPFVIGTGDNIGVRTAPEFIFSVFAIPVGSYFKGGMKPHNFQISSFDRAAPQGT 179 Query: 181 GAAKVGGNYAASLMPGSQAKKASFADCIYLDPMTHSKIEEVGSANFFGITHDNTFVTPRS 240 GAAKVGGNYAASL PG++AKKA+FAD IYLDP+TH+KIEEVGSANFFGIT +N FVTP+S Sbjct: 180 GAAKVGGNYAASLQPGAEAKKANFADAIYLDPLTHTKIEEVGSANFFGITANNEFVTPKS 239 Query: 241 PSVLPGITRLSLIELAKSRLGLEVIEGDVFIDKLSDFKEAGACGTAAVITPIGGISYKDK 300 SVLPGITRLSL+ELA+SRLG+ VIEGDV I KL F EAGACGTAAVITPIGGI Y K Sbjct: 240 ASVLPGITRLSLMELAQSRLGMTVIEGDVEISKLDRFVEAGACGTAAVITPIGGIEYNGK 299 Query: 301 LHVFHSETEVGPITQKLYKELTGVQTGDVEAPAGWIVKV 339 LHVFH +VGP+TQKLY ELTG+Q+GDVEAPAGWIVKV Sbjct: 300 LHVFHDLEKVGPVTQKLYNELTGIQSGDVEAPAGWIVKV 338 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: 505 Number of extensions: 16 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: 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 PP_3511 PP_3511 (Branched-chain-amino-acid aminotransferase)
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.carbon/TIGR01123.hmm # target sequence database: /tmp/gapView.10878.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-138 447.1 0.0 1.6e-138 447.0 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_3511 PP_3511 Branched-chain-amino-aci Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3511 PP_3511 Branched-chain-amino-acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 447.0 0.0 1.6e-138 1.6e-138 1 313 [] 31 338 .. 31 338 .. 0.99 Alignments for each domain: == domain 1 score: 447.0 bits; conditional E-value: 1.6e-138 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealk 75 Wd+++l++++ l+++egs++lhYgq++feGlkayR++dG+i+lfRpd+na+R++rs+ rll+P++++++f+ea+k lcl|FitnessBrowser__Putida:PP_3511 31 WDKGTLTEDNVLHISEGSTALHYGQQCFEGLKAYRCKDGSINLFRPDQNAARMQRSCARLLMPHVPTDVFIEACK 105 *************************************************************************** PP TIGR01123 76 qlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkG 150 q+vka++++vp+++ + +LYlRPf+i+t+dn+Gv++a+e++f+v+a PvG+Yfkgg++p ++f + ++Raap+G lcl|FitnessBrowser__Putida:PP_3511 106 QVVKANEKFVPPHG-KGALYLRPFVIGTGDNIGVRTAPEFIFSVFAIPVGSYFKGGMKP-HNFQISSFDRAAPQG 178 ***********998.999*****************************************.999999********* PP TIGR01123 151 tGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresll 225 tGa+kvgGnYaasl++ ++a++ +++d++yldp +++kieevG+an+f+it + + ++tp+s s+L+g+tr sl+ lcl|FitnessBrowser__Putida:PP_3511 179 TGAAKVGGNYAASLQPGAEAKKANFADAIYLDPLTHTKIEEVGSANFFGITAN-NEFVTPKSASVLPGITRLSLM 252 ****************************************************8.99******************* PP TIGR01123 226 elakd.lgleveereiaidelkaaveaGeivfacGtaavitPvgelkiegkevevkse.evGevtkklrdeltdi 298 ela++ lg++v e++++i +l+++veaG acGtaavitP+g+++ +gk +++++ +vG+vt+kl++elt+i lcl|FitnessBrowser__Putida:PP_3511 253 ELAQSrLGMTVIEGDVEISKLDRFVEAG----ACGTAAVITPIGGIEYNGKLHVFHDLeKVGPVTQKLYNELTGI 323 *****9**********************....***********************99769*************** PP TIGR01123 299 qyGkledkegWivev 313 q G++e++ gWiv+v lcl|FitnessBrowser__Putida:PP_3511 324 QSGDVEAPAGWIVKV 338 *************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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.06 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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