Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012040942.1 BBTA_RS02885 branched-chain amino acid aminotransferase
Query= BRENDA::P9WQ75 (368 letters) >NCBI__GCF_000015165.1:WP_012040942.1 Length = 363 Score = 291 bits (745), Expect = 2e-83 Identities = 149/339 (43%), Positives = 209/339 (61%), Gaps = 6/339 (1%) Query: 30 GFGKYHTDHMVSIDYAEGRGWHNARVIPYGPIELDPSAIVLHYAQEVFEGLKAYRWADGS 89 GFGKY T+ MV Y++G GW ++PYG + DP A+VLHY Q ++EG+KAYR D S Sbjct: 18 GFGKYMTNAMVLCRYSDGTGWEKPSLVPYGTLAFDPCALVLHYGQAIYEGMKAYRSPDAS 77 Query: 90 IVSFRADANAARLRSSARRLAIPELPDAVFIESLRQLIAVDKAWVPGAGGEEALYLRPFI 149 I FR D NAAR R+SARR+ + E+P+ +FIE++ L+ + WVP AG E +LYLRP + Sbjct: 78 IALFRPDRNAARFRASARRMEMAEMPEGLFIEAVSTLVDAQRDWVP-AGAESSLYLRPVM 136 Query: 150 FATEPGLGVRPATQYRYLLIASPAGAYFKGGIAPVSVWVSTEYVRACPGGTGAAKFGGNY 209 A E GVR +T Y + ++A+P A ++ G+AP + VS ++ RA PGG G AK GNY Sbjct: 137 VADEAAFGVRRSTTYLFFIVATPVDALYRDGMAPFRLMVSEDFARAAPGGGGDAKTSGNY 196 Query: 210 AASLLAQAEAAENGCDQVVWLDAVERRYIEEMGGMNIFFVLGSGGSARLVTPELSGSLLP 269 +L+A A +G + V+WLD VER +IEE G N+F G L+TP L+G +LP Sbjct: 197 GRTLIALEAARRSGFNNVLWLDPVEREFIEEAGITNVFVRRGRD----LLTPPLNGRILP 252 Query: 270 GITRDSLLQLAIDAGFAVEERRIDIDEWQKKAAAGEITEVFACGTAAVITPVARVRHGAS 329 G+ R+++LQ+A D G + ER I + E AG++ EVF GTA + PV + Sbjct: 253 GVMRETILQVARDWGLSAIEREISVTELLSGIDAGDVDEVFLSGTAVHVAPVGVIARRGR 312 Query: 330 EFRI-ADGQPGEVTMALRDTLTGIQRGTFADTHGWMARL 367 E R+ A G+ + L ++ IQRG ADT GWM R+ Sbjct: 313 EHRLAAAGEAQSLAKRLSQAISEIQRGLVADTRGWMRRV 351 Lambda K H 0.320 0.136 0.412 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: 357 Number of extensions: 17 Number of successful extensions: 4 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: 368 Length of database: 363 Length adjustment: 30 Effective length of query: 338 Effective length of database: 333 Effective search space: 112554 Effective search space used: 112554 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 WP_012040942.1 BBTA_RS02885 (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.aa/TIGR01123.hmm # target sequence database: /tmp/gapView.18863.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-99 318.2 0.0 2.8e-99 318.0 0.0 1.0 1 lcl|NCBI__GCF_000015165.1:WP_012040942.1 BBTA_RS02885 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015165.1:WP_012040942.1 BBTA_RS02885 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 318.0 0.0 2.8e-99 2.8e-99 1 313 [] 38 351 .. 38 351 .. 0.98 Alignments for each domain: == domain 1 score: 318.0 bits; conditional E-value: 2.8e-99 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W+++ l+++++l +d+ + vlhYgq+++eG+kayR+ d +i lfRpd+na+R+r sa+r+ + e++e l lcl|NCBI__GCF_000015165.1:WP_012040942.1 38 WEKPSLVPYGTLAFDPCALVLHYGQAIYEGMKAYRSPDASIALFRPDRNAARFRASARRMEMAEMPEGL 106 9******************************************************************** PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 f+ea+ lv a++dwvp a++e+sLYlRP+++a e+ Gv+ +++ylf+++a+Pv a +++g+ap + + lcl|NCBI__GCF_000015165.1:WP_012040942.1 107 FIEAVSTLVDAQRDWVP-AGAESSLYLRPVMVADEAAFGVRRSTTYLFFIVATPVDALYRDGMAPFRLM 174 *****************.889************************************************ PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v+++++Raap+G G +k++GnY +l a + a+++g+++v++ldpve++ iee+G +n+f+ + +l+ lcl|NCBI__GCF_000015165.1:WP_012040942.1 175 VSEDFARAAPGGGGDAKTSGNYGRTLIALEAARRSGFNNVLWLDPVEREFIEEAGITNVFVRRGR-DLL 242 ***********************************************************988776.9** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t+pl + iL+gv re +l++a+d+gl++ erei++ el +aG++ vf++Gta ++Pvg ++ g lcl|NCBI__GCF_000015165.1:WP_012040942.1 243 TPPLNGRILPGVMRETILQVARDWGLSAIEREISVTELLSGIDAGDVdeVFLSGTAVHVAPVGVIARRG 311 *********************************************9999******************** PP TIGR01123 275 kevevkse.evGevtkklrdeltdiqyGkledkegWivev 313 +e++++++ e ++k+l +++ +iq+G ++d+ gW+ +v lcl|NCBI__GCF_000015165.1:WP_012040942.1 312 REHRLAAAgEAQSLAKRLSQAISEIQRGLVADTRGWMRRV 351 ****998879999************************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (363 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: 10.24 // [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