Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_012971296.1 ALVIN_RS10480 branched-chain amino acid transaminase
Query= reanno::psRCH2:GFF445 (307 letters) >NCBI__GCF_000025485.1:WP_012971296.1 Length = 307 Score = 452 bits (1163), Expect = e-132 Identities = 217/305 (71%), Positives = 255/305 (83%) Query: 2 SMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTDR 61 +MADRDG+IW DGE+V WR+A THVLTHTLHYGMGVFEGVRAY T GTAIFRL+ HT R Sbjct: 3 TMADRDGLIWLDGEMVPWREAKTHVLTHTLHYGMGVFEGVRAYPTARGTAIFRLEEHTRR 62 Query: 62 LFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHVI 121 LF+SAHI+ MPM + +E IN+A R VREN LESAYIRPM FYG+EGMGLRA L+VH + Sbjct: 63 LFNSAHILGMPMRWDQETINQAQRDVVRENGLESAYIRPMCFYGAEGMGLRADNLQVHCM 122 Query: 122 VAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGAD 181 VAAW WGAY+G+E + GI+++ SSFTRHHVN TM RAK+NG Y+NSM+ALQEA+ G D Sbjct: 123 VAAWSWGAYLGEENMRNGIRIKVSSFTRHHVNTTMCRAKANGNYMNSMMALQEALRDGYD 182 Query: 182 EALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKRI 241 EAL+LD G+V EGSGENIFI++DGV+YTP++T+ L+GITR TV+TL E GLK+VEKRI Sbjct: 183 EALLLDAAGFVMEGSGENIFIVRDGVLYTPDLTSALDGITRRTVMTLCEELGLKVVEKRI 242 Query: 242 TRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHAE 301 TRDEVYIADEAFFTGTAAEVTPIRE+DGRAIG G RGPITE+LQ YFD V G+ + H E Sbjct: 243 TRDEVYIADEAFFTGTAAEVTPIREIDGRAIGSGTRGPITERLQTLYFDQVHGRREQHPE 302 Query: 302 WRTLV 306 W LV Sbjct: 303 WLALV 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: 413 Number of extensions: 11 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: 307 Length adjustment: 27 Effective length of query: 280 Effective length of database: 280 Effective search space: 78400 Effective search space used: 78400 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_012971296.1 ALVIN_RS10480 (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.9146.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-138 445.7 0.0 4e-138 445.6 0.0 1.0 1 lcl|NCBI__GCF_000025485.1:WP_012971296.1 ALVIN_RS10480 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025485.1:WP_012971296.1 ALVIN_RS10480 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 445.6 0.0 4e-138 4e-138 1 298 [] 12 307 .] 12 307 .] 0.99 Alignments for each domain: == domain 1 score: 445.6 bits; conditional E-value: 4e-138 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 wldGe+v++++ak+hvlth+lhYG+gvfeG+RaY t +g+aifrl+eh+ Rl++sa+il +++ + +e+ lcl|NCBI__GCF_000025485.1:WP_012971296.1 12 WLDGEMVPWREAKTHVLTHTLHYGMGVFEGVRAYPTARGTAIFRLEEHTRRLFNSAHILGMPMRWDQET 80 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 +++++++v+r+n+l+saYiRp+ ++Gae++gl++ +l+v+ ++aaw+wgaylgee + +Gi++kvssf lcl|NCBI__GCF_000025485.1:WP_012971296.1 81 INQAQRDVVRENGLESAYIRPMCFYGAEGMGLRA-DNLQVHCMVAAWSWGAYLGEENMRNGIRIKVSSF 148 **********************************.899******************************* PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r++vn+ + +aka+gnY+ns++a +ealr Gydea+lLd G+v eGsGenifiv+dgvl+tP++ +s lcl|NCBI__GCF_000025485.1:WP_012971296.1 149 TRHHVNTTMCRAKANGNYMNSMMALQEALRDGYDEALLLDAAGFVMEGSGENIFIVRDGVLYTPDL-TS 216 ******************************************************************.78 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L+gitr +v++l +elg++v+e+ri+r+e+y+aDe+f+tGtaaevtPire+Dgr ig+g+rGp+t++l lcl|NCBI__GCF_000025485.1:WP_012971296.1 217 ALDGITRRTVMTLCEELGLKVVEKRITRDEVYIADEAFFTGTAAEVTPIREIDGRAIGSGTRGPITERL 285 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewltyv 298 q+ +fd v+g+ e++ ewl v lcl|NCBI__GCF_000025485.1:WP_012971296.1 286 QTLYFDQVHGRREQHPEWLALV 307 ******************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (307 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: 8.58 // [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