Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_013841684.1 DESRU_RS08430 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_000215085.1:WP_013841684.1 Length = 358 Score = 375 bits (964), Expect = e-109 Identities = 193/357 (54%), Positives = 245/357 (68%), Gaps = 4/357 (1%) Query: 6 IRVELTSTKKPKP---DPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAM 62 I VE + ++ KP D +QL FGR+FTD MF M Y D W D +I Y+ S+DP+A Sbjct: 3 INVEPIADQELKPLYQDASQLGFGRIFTDRMFTMRYT-DGRWTDAKIEKYKNFSLDPSAC 61 Query: 63 VYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVA 122 V+HY Q +FEG+KAY +ED+ +LLFRPE+N+ R+N+S +RL +P I EE +L+ +++LV Sbjct: 62 VFHYSQEIFEGMKAYAAEDNRLLLFRPEQNVRRMNRSAERLVMPAIPEETMLQAIEELVL 121 Query: 123 IDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVE 182 +K WIP A GTSLYIRP +IA EPFLGV S Y IILSPVG+YYK G +PV + VE Sbjct: 122 TEKRWIPKAPGTSLYIRPTMIAAEPFLGVHPSAEYIFFIILSPVGAYYKGGFQPVPLYVE 181 Query: 183 SEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFK 242 +VRA GG G+ KT GNYA+SL A A++KGFSQVLWLD E+KYIEEVG+MN+FF Sbjct: 182 DTYVRAAVGGVGDIKTGGNYAASLLAGYQAQKKGFSQVLWLDARERKYIEEVGAMNMFFV 241 Query: 243 INGEIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTG 302 ++VTP L GSIL GITR SV+ L H GL ER I IDEVI+ + G + EAFG+G Sbjct: 242 FGNKLVTPALTGSILPGITRASVLELAAHLGLTTEERAITIDEVIEGIQTGEITEAFGSG 301 Query: 303 TAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEVAAL 359 TAAVISPVG L +Q + IN+ G +KLYDT+ IQ G D FGW + L Sbjct: 302 TAAVISPVGSLFFQGKDYVINHNRVGSATQKLYDTLVDIQYGKAEDPFGWVKVIGEL 358 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: 432 Number of extensions: 19 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: 363 Length of database: 358 Length adjustment: 29 Effective length of query: 334 Effective length of database: 329 Effective search space: 109886 Effective search space used: 109886 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_013841684.1 DESRU_RS08430 (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.379293.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-128 411.7 0.0 9.5e-128 411.5 0.0 1.0 1 NCBI__GCF_000215085.1:WP_013841684.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013841684.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 411.5 0.0 9.5e-128 9.5e-128 1 310 [. 43 352 .. 43 355 .. 0.99 Alignments for each domain: == domain 1 score: 411.5 bits; conditional E-value: 9.5e-128 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 W +a+++++++++ld+++ v+hY+qe+feG+kay +d ++llfRp++n++R++rsaerl++P ++ee +l+a NCBI__GCF_000215085.1:WP_013841684.1 43 WTDAKIEKYKNFSLDPSACVFHYSQEIFEGMKAYAAEDNRLLLFRPEQNVRRMNRSAERLVMPAIPEETMLQA 115 9************************************************************************ PP TIGR01123 74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146 +++lv ++k+w+pka ++sLY+RP++ia e+ lGv+++ ey+f++++sPvGaY+kgg +pv +ve+ yvRa NCBI__GCF_000215085.1:WP_013841684.1 116 IEELVLTEKRWIPKAP-GTSLYIRPTMIAAEPFLGVHPSAEYIFFIILSPVGAYYKGGFQPVPLYVEDTYVRA 187 *************999.******************************************************** PP TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219 a +G+G +k+gGnYaaslla +a+++g+++v++ld+ e+k+ieevGa+n+f++ ++ +lvt++l++siL+g+ NCBI__GCF_000215085.1:WP_013841684.1 188 AVGGVGDIKTGGNYAASLLAGYQAQKKGFSQVLWLDARERKYIEEVGAMNMFFVFGN-KLVTPALTGSILPGI 259 ********************************************************8.*************** PP TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290 tr+s+lela +lgl+ eer i+ide+ + ++Gei +f++Gtaavi+Pvg+l +gk +++++++vG t+k NCBI__GCF_000215085.1:WP_013841684.1 260 TRASVLELAAHLGLTTEERAITIDEVIEGIQTGEIteAFGSGTAAVISPVGSLFFQGKDYVINHNRVGSATQK 332 **********************************999************************************ PP TIGR01123 291 lrdeltdiqyGkledkegWi 310 l+d+l+diqyGk+ed++gW+ NCBI__GCF_000215085.1:WP_013841684.1 333 LYDTLVDIQYGKAEDPFGWV 352 *******************8 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 29.92 // [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