Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_066324126.1 BLR17_RS08000 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_900100165.1:WP_066324126.1 Length = 355 Score = 295 bits (754), Expect = 2e-84 Identities = 151/358 (42%), Positives = 221/358 (61%), Gaps = 8/358 (2%) Query: 2 TKQTIRVELT---STKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMD 58 T Q ++E+ +TK + D + L+FG VFTDH+F DY D W +P I PY P MD Sbjct: 3 TTQANKIEIIKAPNTKINEVDFDNLNFGSVFTDHLFECDYK-DGEWQNPTIKPYAPFMMD 61 Query: 59 PAAMVYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLK 118 P++ V+HYGQ +FEG+KAY +++ + LFRP++N++R N S R+ +P+I E +EGL Sbjct: 62 PSSRVFHYGQAIFEGMKAYKDDNNDIWLFRPDENVKRFNSSAVRMAMPEIPESLFMEGLN 121 Query: 119 QLVAIDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVK 178 QL+ +D+ WI G SLYIRPF+IAT + S+ YK +IILSP +YY VK Sbjct: 122 QLLKLDEAWIKKGLGNSLYIRPFMIATGYGVVANPSNEYKFMIILSPAKAYYS---GEVK 178 Query: 179 IAVESEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMN 238 + + F RA GG G AKTAGNYA +A + GF Q++W D +EE G+MN Sbjct: 179 VIIAEHFSRAANGGIGAAKTAGNYAGQFYPTSLANKDGFQQIIWTDDATHTKLEEAGTMN 238 Query: 239 IFFKINGEIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEA 298 +FF+IN +VT + IL+G+TR S+IA+ K G+ + ER + + E+I+ K+G L+E Sbjct: 239 VFFRINDTLVTAPTSERILDGVTRKSIIAMAKKEGIAIEERPVLVSELIEGIKNGSLKEI 298 Query: 299 FGTGTAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356 FG GTAAV+SP+ +++E + E +A +L + +T IQ D FGWT ++ Sbjct: 299 FGAGTAAVVSPIKGFAYKNEYFELPEIE-NSVALQLKEKLTNIQHKLAEDPFGWTVKI 355 Lambda K H 0.316 0.135 0.390 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: 416 Number of extensions: 27 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: 363 Length of database: 355 Length adjustment: 29 Effective length of query: 334 Effective length of database: 326 Effective search space: 108884 Effective search space used: 108884 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_066324126.1 BLR17_RS08000 (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.255206.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-101 325.9 0.0 1.3e-101 325.7 0.0 1.0 1 NCBI__GCF_900100165.1:WP_066324126.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066324126.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 325.7 0.0 1.3e-101 1.3e-101 1 313 [] 47 355 .] 47 355 .] 0.98 Alignments for each domain: == domain 1 score: 325.7 bits; conditional E-value: 1.3e-101 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 W++++++++a++ +d++s v+hYgq++feG+kay+ ++ i+lfRpd+n+kR+++sa r+++Pe++e lf+e NCBI__GCF_900100165.1:WP_066324126.1 47 WQNPTIKPYAPFMMDPSSRVFHYGQAIFEGMKAYKDDNNDIWLFRPDENVKRFNSSAVRMAMPEIPESLFMEG 119 ************************************************************************* PP TIGR01123 74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146 l+ql+k+d++w+ ++ ++sLY+RPf+iat+ + ++++ey f++++sP+ aY+ g++++ + +++ Ra NCBI__GCF_900100165.1:WP_066324126.1 120 LNQLLKLDEAWIK-KGLGNSLYIRPFMIATGYGVVANPSNEYKFMIILSPAKAYYSGEVKV---IIAEHFSRA 188 ************9.566****************************************9888...99******* PP TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219 a++G+Ga+k++GnYa + + + a+++g++++++ d ++++k+ee+G++n+f+ ++d +lvt p se iL+gv NCBI__GCF_900100165.1:WP_066324126.1 189 ANGGIGAAKTAGNYAGQFYPTSLANKDGFQQIIWTDDATHTKLEEAGTMNVFFRIND-TLVTAPTSERILDGV 260 ********************************************************9.*************** PP TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290 tr+s++ +ak+ g+++eer + + el + ++G++ +f++Gtaav++P+++++ +++ +e+ + v+ + NCBI__GCF_900100165.1:WP_066324126.1 261 TRKSIIAMAKKEGIAIEERPVLVSELIEGIKNGSLkeIFGAGTAAVVSPIKGFAYKNEYFELPEI-ENSVALQ 332 *********************************9999**********************999887.678**** PP TIGR01123 291 lrdeltdiqyGkledkegWivev 313 l+++lt+iq+ +ed++gW+v++ NCBI__GCF_900100165.1:WP_066324126.1 333 LKEKLTNIQHKLAEDPFGWTVKI 355 ********************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (355 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 29.90 // [ok]
This GapMind analysis is from Jul 26 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