Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_028997153.1 H537_RS0105945 branched-chain amino acid aminotransferase
Query= BRENDA::A0A2Z4MEX9 (357 letters) >NCBI__GCF_000430725.1:WP_028997153.1 Length = 353 Score = 299 bits (765), Expect = 9e-86 Identities = 150/344 (43%), Positives = 218/344 (63%), Gaps = 3/344 (0%) Query: 9 RTEQKKEKPASDKLGFGVHFTDHMFTMDY-TEGKGWHDPQIVPYSPLTLDPAAMVFHYGQ 67 R E+K++ PA+ + GFG +DHM M Y + GW+ P+I PY +L+P A+V HYGQ Sbjct: 8 RAERKEKLPAA-QFGFGEKVSDHMLVMTYDADAGGWNRPEIKPYQSFSLEPRALVLHYGQ 66 Query: 68 AVFEGLKAYRNQEGKVRLFRPDQNFKRMNRSLERMSMPLIDEEFMVEALKQLVAVDKEWI 127 ++FEGLKA+R +G + LFRP+QN +RMN S +M+MP I E ++AL +LV ++++W+ Sbjct: 67 SIFEGLKAFRRPDGHIALFRPEQNIRRMNASARKMAMPEIPEALFMDALLKLVDIERDWV 126 Query: 128 PTESGQSLYIRPFVIATEPCFGVRASHTYKLVIVLSPVGAYYAGGMKPVKIYVENNYVRA 187 P E+G SLYIRP + ++ GVRA+ Y L ++LSPV Y+ G KP K+ + R Sbjct: 127 PAEAGASLYIRPLMFGSDAVLGVRAASRYILCVMLSPVPPYFVPGGKPFKLLAREDCART 186 Query: 188 VRGGTGNAKVAGNYAGSLKAQVEAKEKGYEQVLWLDGVENKYIEEVGSMNVFFKVKGEVW 247 V GGTG+AK A NY SL A+ +GY+ +LWLD +++++EE G NVF + V Sbjct: 187 VAGGTGDAKTAANYGRSLVPLDAARREGYDNLLWLDSEQHRFVEEAGITNVFVQYADRVV 246 Query: 248 TPALNGSILEGITRDSTIQLLKDWGIPVVEKRISMEDLHTAYVNGELEEAFGTGTAAVIS 307 TP L+G IL GITRDS I+LL+D G V+E+ + DL +G + E F TGTA V++ Sbjct: 247 TPPLSGRILPGITRDSVIRLLRDEGRTVLEQETDIGDLVRDIDDGRVHEIFLTGTATVVA 306 Query: 308 PVGDLNWNGHQMIINGEKTGELTTRLYDEMTGIQYGDREDKFGW 351 PV ++ + G + + G L LY ++T IQYG D+ GW Sbjct: 307 PVDEIGFRGRRHALQIRDDG-LALSLYRQLTQIQYGLAPDRHGW 349 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: 294 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 357 Length of database: 353 Length adjustment: 29 Effective length of query: 328 Effective length of database: 324 Effective search space: 106272 Effective search space used: 106272 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_028997153.1 H537_RS0105945 (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.772866.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-103 331.3 0.0 2.9e-103 331.1 0.0 1.0 1 NCBI__GCF_000430725.1:WP_028997153.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000430725.1:WP_028997153.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 331.1 0.0 2.9e-103 2.9e-103 1 311 [. 42 351 .. 42 353 .] 0.98 Alignments for each domain: == domain 1 score: 331.1 bits; conditional E-value: 2.9e-103 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 W+++e++++++++l++ + vlhYgq +feGlka+R dG+i lfRp++n++R++ sa+++++Pe++e+lf++a NCBI__GCF_000430725.1:WP_028997153.1 42 WNRPEIKPYQSFSLEPRALVLHYGQSIFEGLKAFRRPDGHIALFRPEQNIRRMNASARKMAMPEIPEALFMDA 114 9************************************************************************ PP TIGR01123 74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146 l +lv +++dwvp a+++asLY+RP++++ +++lGv+aa++y+++v++sPv +Yf g +p + + ++++R+ NCBI__GCF_000430725.1:WP_028997153.1 115 LLKLVDIERDWVP-AEAGASLYIRPLMFGSDAVLGVRAASRYILCVMLSPVPPYFVPGGKPFKLLAREDCART 186 *************.667******************************************************** PP TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219 + +GtG +k++ nY sl + a+++g+d+ ++ld+ +++ +ee+G +n+f+ + d ++vt+pls+ iL+g+ NCBI__GCF_000430725.1:WP_028997153.1 187 VAGGTGDAKTAANYGRSLVPLDAARREGYDNLLWLDSEQHRFVEEAGITNVFVQYAD-RVVTPPLSGRILPGI 258 ********************************************************9.*************** PP TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290 tr+s+++l +d g +v e+e +i +l + + G + +f++Gta v++Pv e+ g+ + ++ + G ++ + NCBI__GCF_000430725.1:WP_028997153.1 259 TRDSVIRLLRDEGRTVLEQETDIGDLVRDIDDGRVheIFLTGTATVVAPVDEIGFRGRRHALQIRDDG-LALS 330 *********************************9999**********************999988665.89** PP TIGR01123 291 lrdeltdiqyGkledkegWiv 311 l+ +lt+iqyG + d++gW+ NCBI__GCF_000430725.1:WP_028997153.1 331 LYRQLTQIQYGLAPDRHGWMR 351 *******************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (353 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 15.57 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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