Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012976015.1 AZL_RS18510 branched-chain amino acid aminotransferase
Query= BRENDA::A0R066 (368 letters) >NCBI__GCF_000010725.1:WP_012976015.1 Length = 366 Score = 225 bits (573), Expect = 2e-63 Identities = 133/338 (39%), Positives = 185/338 (54%), Gaps = 15/338 (4%) Query: 30 GFGKYYTDHMVSIDYTVDEGWHNAQVIPYGPIQLDPSAIVLHYGQEIFEGLKAYRWA--- 86 GFG+ + + D W ++ P+ L P LHYGQ IFEG+KAYR Sbjct: 31 GFGRIMAPVVAKAVFR-DGAWEAPRLTALEPMGLYPETQALHYGQAIFEGMKAYRNLGEI 89 Query: 87 -DGSIVSFRPEANAARLQSSARRLAIPELPEEVFIESLRQLIAVDEKWVPPAGGEESLYL 145 + + FRP +A R SA RL +PE PE+V++++L +L+A ++ +P A G+ SLYL Sbjct: 90 FEAPALLFRPRDHARRFNRSAARLGMPEFPEDVYVDTLVRLVAHLDRLIPDAPGQ-SLYL 148 Query: 146 RPFVIATEPGLGVRPSNEYRYLLIASPAGAYFKGGIKPVSVWLSHEYVRASPGGTGAAKF 205 RPF+ P L V PS EY +L+ A+P+ +F P++ W+ Y RA PGGTG+ K Sbjct: 149 RPFMFGATPSLSVVPSTEYVFLVCATPSDVFFT---TPINAWIERGYCRAGPGGTGSIKA 205 Query: 206 GGNYAASLLAQAQAAEMGCDQVVWLDAIERRYVEEMGGMNLFFVFGSGGSARLVTPELSG 265 GNYAAS A A+ G Q++WLDA+ERR +EE MN+ G RL+TP L+ Sbjct: 206 AGNYAASFPAAAKLQGNGFQQLLWLDAVERRKLEEFTAMNVAVRIGD----RLLTPALTD 261 Query: 266 SLLPGITRDSLLQLATDAGFAVEERKIDVDEWQKKAGAGEITEVFACGTAAVITPVSHVK 325 ++LPGITRDSLL+LAT G + E I+++E +G E+F CGT +V+ PV + Sbjct: 262 TILPGITRDSLLRLATSFGMPMHEATIEIEEVLDAIRSGGDVELFGCGTGSVVAPVKTLG 321 Query: 326 HHDGEFTIADGQPGEITMALRDTLTGIQRGTFADTHGW 363 G D I R L IQ G GW Sbjct: 322 DESG--LRLDLPSQRIAGMFRRKLLDIQHGLAPAPAGW 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: 437 Number of extensions: 23 Number of successful extensions: 5 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: 366 Length adjustment: 30 Effective length of query: 338 Effective length of database: 336 Effective search space: 113568 Effective search space used: 113568 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_012976015.1 AZL_RS18510 (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.14241.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-85 272.6 0.0 2.2e-85 272.4 0.0 1.0 1 lcl|NCBI__GCF_000010725.1:WP_012976015.1 AZL_RS18510 branched-chain amino Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010725.1:WP_012976015.1 AZL_RS18510 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 272.4 0.0 2.2e-85 2.2e-85 1 312 [. 50 360 .. 50 361 .. 0.93 Alignments for each domain: == domain 1 score: 272.4 bits; conditional E-value: 2.2e-85 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRta....dGkillfRpdanakRlrrsaerlllPel 65 W++++l++ +++ l + +++lhYgq++feG+kayR + +llfRp + a+R++rsa rl +Pe lcl|NCBI__GCF_000010725.1:WP_012976015.1 50 WEAPRLTALEPMGLYPETQALHYGQAIFEGMKAYRNLgeifEAPALLFRPRDHARRFNRSAARLGMPEF 118 9**********************************75222256678*********************** PP TIGR01123 66 eeelflealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglap 134 +e++++++l +lv+ ++ +p+a ++sLYlRPf+++ ++l v +++ey+flv a+P +f + ++ lcl|NCBI__GCF_000010725.1:WP_012976015.1 119 PEDVYVDTLVRLVAHLDRLIPDAP-GQSLYLRPFMFGATPSLSVVPSTEYVFLVCATPSDVFFTTPINA 186 *********************998.9*************************************987776 PP TIGR01123 135 vsifveteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkd 203 ++e y Ra p+GtG +k +GnYaas+ a +k + +g+++ ++ld+ve++k+ee a+n+ + ++d lcl|NCBI__GCF_000010725.1:WP_012976015.1 187 ---WIERGYCRAGPGGTGSIKAAGNYAASFPAAAKLQGNGFQQLLWLDAVERRKLEEFTAMNVAVRIGD 252 ...*****************************************************************9 PP TIGR01123 204 gelvttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgel 270 +l+t++l++ iL+g+tr+sll+la + g+ ++e i+i+e+ +a +G f+cGt +v++Pv+ l lcl|NCBI__GCF_000010725.1:WP_012976015.1 253 -RLLTPALTDTILPGITRDSLLRLATSFGMPMHEATIEIEEVLDAIRSGGDveLFGCGTGSVVAPVKTL 320 .****************************************9888877755489*************99 PP TIGR01123 271 kie.gkevevkseevGevtkklrdeltdiqyGkledkegWive 312 e g + + s+ ++ +r +l+diq+G + ++ gW v lcl|NCBI__GCF_000010725.1:WP_012976015.1 321 GDEsGLRLDLPSQ---RIAGMFRRKLLDIQHGLAPAPAGWQVP 360 6541445555555...899999******************886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (366 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: 10.25 // [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