Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_092349638.1 BLU87_RS13210 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_900107645.1:WP_092349638.1 Length = 354 Score = 373 bits (957), Expect = e-108 Identities = 173/347 (49%), Positives = 248/347 (71%) Query: 8 VELTSTKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYG 67 + LT+ K+ D ++L+FGR ++D M +M+Y + KGW+ RI PY PLS+DPAAMV+HY Sbjct: 6 IPLTAPKEKYKDEDKLAFGRQYSDRMLIMEYDSGKGWHSARIQPYGPLSLDPAAMVFHYS 65 Query: 68 QTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDW 127 Q +FEG+K + D + +FRP N+ R N+S +R+C+P++DE+ L+ + +L+ ++ DW Sbjct: 66 QEIFEGMKVFRRADGTLSMFRPADNITRFNRSAERMCMPKVDEKFFLDAILKLIRMEADW 125 Query: 128 IPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEFVR 187 +P++EGTSLYIRP +IATEP LGV ++ Y +ILSPVG YYK GI PVKI + +VR Sbjct: 126 VPHSEGTSLYIRPTMIATEPMLGVRPANQYLCYVILSPVGPYYKGGIAPVKIWISDFYVR 185 Query: 188 AVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKINGEI 247 A +GGTG AKT GNYA+SL A + A EKG+ QVLWLD EK+++EEVGSMN+ F +G+I Sbjct: 186 ATEGGTGEAKTGGNYAASLYAAKEAAEKGYDQVLWLDAKEKRFVEEVGSMNMLFLYDGKI 245 Query: 248 VTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVI 307 VT L+G++L+GITR S + LLK G +V ER +++DE+I+ +G L+EAFGTGTA VI Sbjct: 246 VTSPLHGTVLDGITRRSALTLLKEMGYEVEERALSVDEIIEGANNGRLQEAFGTGTAVVI 305 Query: 308 SPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTT 354 SPVG ++D + + +G+ G++ +LY +T IQ G D W T Sbjct: 306 SPVGSFCYKDTCVQLGDGQPGKLTMELYHKLTAIQYGKEPDNHNWVT 352 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: 403 Number of extensions: 17 Number of successful extensions: 1 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: 354 Length adjustment: 29 Effective length of query: 334 Effective length of database: 325 Effective search space: 108550 Effective search space used: 108550 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_092349638.1 BLU87_RS13210 (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.carbon/TIGR01123.hmm # target sequence database: /tmp/gapView.3698113.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-126 405.5 0.0 7.4e-126 405.3 0.0 1.0 1 NCBI__GCF_900107645.1:WP_092349638.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900107645.1:WP_092349638.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.3 0.0 7.4e-126 7.4e-126 1 311 [. 42 352 .. 42 354 .] 0.99 Alignments for each domain: == domain 1 score: 405.3 bits; conditional E-value: 7.4e-126 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 W++a+++++++l+ld++++v+hY+qe+feG+k +R adG + +fRp +n+ R++rsaer+ +P+++e+ fl+a NCBI__GCF_900107645.1:WP_092349638.1 42 WHSARIQPYGPLSLDPAAMVFHYSQEIFEGMKVFRRADGTLSMFRPADNITRFNRSAERMCMPKVDEKFFLDA 114 ************************************************************************* PP TIGR01123 74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146 + +l+++++dwvp+ + ++sLY+RP++iate+ lGv++a++yl +v++sPvG+Y+kgg+apv+i++++ yvRa NCBI__GCF_900107645.1:WP_092349638.1 115 ILKLIRMEADWVPHSE-GTSLYIRPTMIATEPMLGVRPANQYLCYVILSPVGPYYKGGIAPVKIWISDFYVRA 186 *************888.******************************************************** PP TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219 +++GtG +k+gGnYaasl a k+aae+g+d+v++ld++ek+ +eevG++n++++++ g++vt+pl + +L+g+ NCBI__GCF_900107645.1:WP_092349638.1 187 TEGGTGEAKTGGNYAASLYAAKEAAEKGYDQVLWLDAKEKRFVEEVGSMNMLFLYD-GKIVTSPLHGTVLDGI 258 *****************************************************987.9*************** PP TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290 tr+s+l+l k++g+eveer +++de+ + +++G + +f++Gta vi+Pvg++ +++ v++ ++++G++t++ NCBI__GCF_900107645.1:WP_092349638.1 259 TRRSALTLLKEMGYEVEERALSVDEIIEGANNGRLqeAFGTGTAVVISPVGSFCYKDTCVQLGDGQPGKLTME 331 *********************************9899************************************ PP TIGR01123 291 lrdeltdiqyGkledkegWiv 311 l+++lt iqyGk d+++W++ NCBI__GCF_900107645.1:WP_092349638.1 332 LYHKLTAIQYGKEPDNHNWVT 352 *******************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (354 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: 24.77 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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