Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012853862.1 TCUR_RS17465 branched-chain amino acid aminotransferase
Query= BRENDA::A0R066 (368 letters) >NCBI__GCF_000024385.1:WP_012853862.1 Length = 367 Score = 447 bits (1151), Expect = e-130 Identities = 216/366 (59%), Positives = 274/366 (74%), Gaps = 2/366 (0%) Query: 3 SGPLEFTVSANTNPATDAVRESILANPGFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQ 62 S L+F + + NP RE ILANPG+G+++TDHM++I Y+ D GWH+A++ PYGPI Sbjct: 2 SSTLDFDIKLSQNPTPQQERERILANPGWGQHFTDHMITIRYSADRGWHDARLEPYGPIT 61 Query: 63 LDPSAIVLHYGQEIFEGLKAYRWADGSIVSFRPEANAARLQSSARRLAIPELPEEVFIES 122 LDP+ V HY QEIFEG KAY ADGSIV+FRP +NAAR SARR+A+PE+PEE+F+ S Sbjct: 62 LDPATQVFHYAQEIFEGTKAYAQADGSIVTFRPYSNAARFNRSARRMAMPEIPEELFVRS 121 Query: 123 LRQLIAVDEKWVPPAGGEESLYLRPFVIATEPGLGV-RPSNEYRYLLIASPAGAYFKGGI 181 L L++ D WVP G SLYLRPF+ AT LGV RPS EY +++IASP+G Y+ GI Sbjct: 122 LELLVSTDRDWVPRTEGY-SLYLRPFMFATSRALGVQRPSQEYLFMVIASPSGLYYPQGI 180 Query: 182 KPVSVWLSHEYVRASPGGTGAAKFGGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEM 241 KPV+VW+S +Y RA+PGGTG AK GGNYAAS QA+A E GCDQVVWLDA ERR+VEE+ Sbjct: 181 KPVTVWISTDYTRAAPGGTGEAKCGGNYAASFAGQAEALEHGCDQVVWLDAAERRWVEEV 240 Query: 242 GGMNLFFVFGSGGSARLVTPELSGSLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKA 301 G MNL FV+GSG AR++TP L+G+LLPG+TRDSLL+LA D G VEE KI +D+W+ Sbjct: 241 GSMNLMFVYGSGPDARILTPALTGTLLPGVTRDSLLKLAPDLGIPVEEGKISIDQWEADC 300 Query: 302 GAGEITEVFACGTAAVITPVSHVKHHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTH 361 +G+ITEVF CGTAA+I+PV VK E+ I DG+PG I+M LR+ L GIQ GT D + Sbjct: 301 ASGKITEVFGCGTAAIISPVGGVKGPGREWKIGDGEPGPISMRLREELIGIQYGTRPDPY 360 Query: 362 GWMARL 367 GW+ ++ Sbjct: 361 GWVHKI 366 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: 516 Number of extensions: 17 Number of successful extensions: 3 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: 367 Length adjustment: 30 Effective length of query: 338 Effective length of database: 337 Effective search space: 113906 Effective search space used: 113906 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_012853862.1 TCUR_RS17465 (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.2851.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-128 413.7 0.0 2.3e-128 413.5 0.0 1.0 1 lcl|NCBI__GCF_000024385.1:WP_012853862.1 TCUR_RS17465 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_012853862.1 TCUR_RS17465 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 413.5 0.0 2.3e-128 2.3e-128 1 312 [. 49 365 .. 49 366 .. 0.99 Alignments for each domain: == domain 1 score: 413.5 bits; conditional E-value: 2.3e-128 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++a+l+++++++ld++++v+hY+qe+feG kay +adG+i++fRp na+R++rsa+r+++Pe++eel lcl|NCBI__GCF_000024385.1:WP_012853862.1 49 WHDARLEPYGPITLDPATQVFHYAQEIFEGTKAYAQADGSIVTFRPYSNAARFNRSARRMAMPEIPEEL 117 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGv.kaakeylflvlasPvGaYfkgglapvsi 137 f+++l+ lv +d+dwvp ++ + sLYlRPf++at lGv ++++eylf+v+asP G Y+ +g++pv++ lcl|NCBI__GCF_000024385.1:WP_012853862.1 118 FVRSLELLVSTDRDWVPRTE-GYSLYLRPFMFATSRALGVqRPSQEYLFMVIASPSGLYYPQGIKPVTV 185 *****************888.9*****************956899************************ PP TIGR01123 138 fveteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdg.. 204 +++t+y+Raap+GtG +k+gGnYaas+ q++a e+g+d+vv+ld++e++ +eevG++n+++++++g lcl|NCBI__GCF_000024385.1:WP_012853862.1 186 WISTDYTRAAPGGTGEAKCGGNYAASFAGQAEALEHGCDQVVWLDAAERRWVEEVGSMNLMFVYGSGpd 254 *****************************************************************9998 PP TIGR01123 205 .elvttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgel 270 +++t++l++ +L+gvtr+sll+la dlg+ vee++i+id+++a ++G+i vf+cGtaa+i+Pvg++ lcl|NCBI__GCF_000024385.1:WP_012853862.1 255 aRILTPALTGTLLPGVTRDSLLKLAPDLGIPVEEGKISIDQWEADCASGKIteVFGCGTAAIISPVGGV 323 899***********************************************999**************** PP TIGR01123 271 kiegkevevkseevGevtkklrdeltdiqyGkledkegWive 312 k g+e ++ ++e+G+++++lr+el++iqyG+ d++gW+ + lcl|NCBI__GCF_000024385.1:WP_012853862.1 324 KGPGREWKIGDGEPGPISMRLREELIGIQYGTRPDPYGWVHK 365 ***************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (367 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: 00:00:00.00 # Mc/sec: 12.73 // [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