Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_086508101.1 BZY95_RS00615 branched-chain amino acid aminotransferase
Query= BRENDA::A0R066 (368 letters) >NCBI__GCF_002151265.1:WP_086508101.1 Length = 358 Score = 413 bits (1062), Expect = e-120 Identities = 207/355 (58%), Positives = 253/355 (71%), Gaps = 7/355 (1%) Query: 16 PATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDPSAIVLHYGQE 75 P +R ILANPGFG ++TDHM + +T D GWH +V PYGP+ LDP+A VLHYGQE Sbjct: 7 PTAANIRADILANPGFGLHFTDHMAHVRWTADAGWHGHEVRPYGPLTLDPAAAVLHYGQE 66 Query: 76 IFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQLIAVDEKWVP 135 IFEG+KAYR ADGS+ SFRPE NA R + SARRLA+PEL +E F+ESLR L+ +D+ WVP Sbjct: 67 IFEGIKAYRHADGSVWSFRPEKNAERFRRSARRLALPELDDETFVESLRALMQLDQGWVP 126 Query: 136 P---AGGEESLYLRPFVIATEPGLGVRPSNEYRYLLIASPAGAYFKGGIKPVSVWLSHEY 192 AG E SLYLRPF+IA+E LGVRP+ E Y +IASPAGAYFKGGI PVS+WLS Y Sbjct: 127 TPKNAGDESSLYLRPFMIASEKFLGVRPAKEVDYYVIASPAGAYFKGGIAPVSIWLSSHY 186 Query: 193 VRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGMNLFFVFGS 252 RA+PGGTG AK GGNYAASL AQ +A + GC QV +LDA E +++EE+GGMNLFFV+ Sbjct: 187 KRAAPGGTGFAKCGGNYAASLAAQKEAEKHGCSQVAFLDAAENKWIEELGGMNLFFVYKD 246 Query: 253 GGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAGEITEVFAC 312 G RLVTP L+ ++L G+TRDS+L L D G EER I +DEW+ +G+I EVFAC Sbjct: 247 G---RLVTPRLTDTILEGVTRDSVLTLGRDEGLTPEERAISIDEWRDGVASGDIAEVFAC 303 Query: 313 GTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGWMARL 367 GTAAVITPV + +G + D EI LR L +Q G D HGW+ +L Sbjct: 304 GTAAVITPVGQLVTEEGTVQMPDA-GNEIAKRLRGKLLDLQYGRAEDKHGWLTKL 357 Lambda K H 0.318 0.135 0.409 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: 470 Number of extensions: 18 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: 358 Length adjustment: 29 Effective length of query: 339 Effective length of database: 329 Effective search space: 111531 Effective search space used: 111531 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_086508101.1 BZY95_RS00615 (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.31946.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-133 430.4 0.0 2e-133 430.2 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508101.1 BZY95_RS00615 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508101.1 BZY95_RS00615 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 430.2 0.0 2e-133 2e-133 1 313 [] 41 357 .. 41 357 .. 0.98 Alignments for each domain: == domain 1 score: 430.2 bits; conditional E-value: 2e-133 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W+ e++++++l+ld+++avlhYgqe+feG+kayR+adG++++fRp++na+R+rrsa+rl+lPel++e lcl|NCBI__GCF_002151265.1:WP_086508101.1 41 WHGHEVRPYGPLTLDPAAAVLHYGQEIFEGIKAYRHADGSVWSFRPEKNAERFRRSARRLALPELDDET 109 9******************************************************************** PP TIGR01123 70 flealkqlvkadkdwvpk...akseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapv 135 f+e+l+ l+++d+ wvp+ a+ e+sLYlRPf+ia e+ lGv++ake+ ++v+asP+GaYfkgg+apv lcl|NCBI__GCF_002151265.1:WP_086508101.1 110 FVESLRALMQLDQGWVPTpknAGDESSLYLRPFMIASEKFLGVRPAKEVDYYVIASPAGAYFKGGIAPV 178 ****************9622245689******************************************* PP TIGR01123 136 sifveteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdg 204 si+++++y+Raap+GtG++k+gGnYaasl aqk+a+++g+++v +ld++e+k iee+G++n+f+++kdg lcl|NCBI__GCF_002151265.1:WP_086508101.1 179 SIWLSSHYKRAAPGGTGFAKCGGNYAASLAAQKEAEKHGCSQVAFLDAAENKWIEELGGMNLFFVYKDG 247 ********************************************************************* PP TIGR01123 205 elvttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelk 271 +lvt+ l++ iLegvtr+s+l+l +d gl+ eer i+ide+++ v++G+i vfacGtaavitPvg+l lcl|NCBI__GCF_002151265.1:WP_086508101.1 248 RLVTPRLTDTILEGVTRDSVLTLGRDEGLTPEERAISIDEWRDGVASGDIaeVFACGTAAVITPVGQLV 316 *************************************************999***************** PP TIGR01123 272 iegkevevkseevGevtkklrdeltdiqyGkledkegWivev 313 +e+ +v++ ++ e++k+lr +l+d+qyG++edk+gW++++ lcl|NCBI__GCF_002151265.1:WP_086508101.1 317 TEEGTVQMPDA-GNEIAKRLRGKLLDLQYGRAEDKHGWLTKL 357 ********999.679************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (358 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: 10.34 // [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