Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_084056807.1 B9A12_RS05115 branched-chain amino acid aminotransferase
Query= BRENDA::A0A2Z4MEX9 (357 letters) >NCBI__GCF_900176285.1:WP_084056807.1 Length = 356 Score = 390 bits (1003), Expect = e-113 Identities = 187/355 (52%), Positives = 249/355 (70%), Gaps = 1/355 (0%) Query: 1 MECQLTITRTEQKKEKPASDKLGFGVHFTDHMFTMDYTEGKGWHDPQIVPYSPLTLDPAA 60 ME L EQ+K P D+L FG F+DHMF MDY EG+ WH+P++VPY L +DPAA Sbjct: 1 MEISLQPVAPEQRKTPPPDDQLVFGKIFSDHMFRMDYGEGR-WHNPRVVPYGTLEMDPAA 59 Query: 61 MVFHYGQAVFEGLKAYRNQEGKVRLFRPDQNFKRMNRSLERMSMPLIDEEFMVEALKQLV 120 MV HYGQ +FEGLKAYR +G++ LFRP +N +R NRS RM MP +D +F +EA++ L+ Sbjct: 60 MVLHYGQGIFEGLKAYRCADGRIHLFRPLKNMERFNRSARRMCMPEVDVQFHLEAIETLI 119 Query: 121 AVDKEWIPTESGQSLYIRPFVIATEPCFGVRASHTYKLVIVLSPVGAYYAGGMKPVKIYV 180 +D WIP G SLYIRP +IA+EP GVR + Y ++ PVGAYY G P+KIYV Sbjct: 120 RLDAAWIPHSVGASLYIRPTMIASEPHLGVRPALEYIHYVITGPVGAYYPEGFNPIKIYV 179 Query: 181 ENNYVRAVRGGTGNAKVAGNYAGSLKAQVEAKEKGYEQVLWLDGVENKYIEEVGSMNVFF 240 + YVRAVRGG G AK NYA SL A +AK+KGY QVLWLD VE +Y+EEVG+MN+FF Sbjct: 180 SDQYVRAVRGGVGEAKTMANYAASLYAAEQAKKKGYTQVLWLDAVERRYVEEVGTMNIFF 239 Query: 241 KVKGEVWTPALNGSILEGITRDSTIQLLKDWGIPVVEKRISMEDLHTAYVNGELEEAFGT 300 ++ E+ TP L+GSIL G+TR+S I L + WGI V E+ I+++++ +G+L+E FG+ Sbjct: 240 RIDDELVTPPLSGSILPGVTRESVIDLARHWGITVKERPITIDEVIDRIASGDLKEIFGS 299 Query: 301 GTAAVISPVGDLNWNGHQMIINGEKTGELTTRLYDEMTGIQYGDREDKFGWSVEV 355 GTAAVISPVG++ + ++ K GE + R +DE+ GIQYG+R+D FGW +V Sbjct: 300 GTAAVISPVGEVFYKERSYVVQDGKVGEWSRRFHDEIVGIQYGERDDPFGWVHQV 354 Lambda K H 0.317 0.136 0.406 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: 423 Number of extensions: 15 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: 357 Length of database: 356 Length adjustment: 29 Effective length of query: 328 Effective length of database: 327 Effective search space: 107256 Effective search space used: 107256 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_084056807.1 B9A12_RS05115 (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.7338.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-126 406.8 0.0 2.9e-126 406.6 0.0 1.0 1 lcl|NCBI__GCF_900176285.1:WP_084056807.1 B9A12_RS05115 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176285.1:WP_084056807.1 B9A12_RS05115 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.6 0.0 2.9e-126 2.9e-126 1 313 [] 42 354 .. 42 354 .. 0.99 Alignments for each domain: == domain 1 score: 406.6 bits; conditional E-value: 2.9e-126 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++++++++++le+d++++vlhYgq +feGlkayR+adG+i lfRp +n++R++rsa+r+ +Pe++ + lcl|NCBI__GCF_900176285.1:WP_084056807.1 42 WHNPRVVPYGTLEMDPAAMVLHYGQGIFEGLKAYRCADGRIHLFRPLKNMERFNRSARRMCMPEVDVQF 110 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 lea++ l+++d++w+p+ +asLY+RP++ia e++lGv++a ey+++v++ PvGaY+ +g +p++i+ lcl|NCBI__GCF_900176285.1:WP_084056807.1 111 HLEAIETLIRLDAAWIPHSV-GASLYIRPTMIASEPHLGVRPALEYIHYVITGPVGAYYPEGFNPIKIY 178 *****************655.************************************************ PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v+++yvRa+ +G+G +k+ nYaasl a ++a+++g+ +v++ld+ve++++eevG++nif+ ++d elv lcl|NCBI__GCF_900176285.1:WP_084056807.1 179 VSDQYVRAVRGGVGEAKTMANYAASLYAAEQAKKKGYTQVLWLDAVERRYVEEVGTMNIFFRIDD-ELV 246 ****************************************************************9.*** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t+pls+siL+gvtres++ la+++g++v+er i+ide+ + ++G++ +f++Gtaavi+Pvge+ ++ lcl|NCBI__GCF_900176285.1:WP_084056807.1 247 TPPLSGSILPGVTRESVIDLARHWGITVKERPITIDEVIDRIASGDLkeIFGSGTAAVISPVGEVFYKE 315 *********************************************9999******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313 ++++v++++vGe +++++de+++iqyG+ +d++gW+ +v lcl|NCBI__GCF_900176285.1:WP_084056807.1 316 RSYVVQDGKVGEWSRRFHDEIVGIQYGERDDPFGWVHQV 354 ***********************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (356 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: 10.88 // [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