Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_012283532.1 HM1_RS11370 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_000019165.1:WP_012283532.1 Length = 355 Score = 434 bits (1116), Expect = e-126 Identities = 201/351 (57%), Positives = 274/351 (78%) Query: 6 IRVELTSTKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYH 65 +++ L +K KP ++L FG +FTDHMFVMDY+ ++GW++ +I+PY PL ++P+ MV+H Sbjct: 5 LQINLAQARKEKPAADKLGFGTIFTDHMFVMDYSVEQGWHNAQIMPYGPLLLEPSIMVFH 64 Query: 66 YGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDK 125 YGQ VFEG+KA+ ++D+ V+LFRPE+ + R++ S +LCIP DE V++ +K LV I++ Sbjct: 65 YGQAVFEGMKAFRTKDERVVLFRPERYIRRMSYSIQKLCIPAFDEAFVVDAIKTLVDIER 124 Query: 126 DWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEF 185 DW+ AEGT+LYIRPFIIAT+P+LGV S+TYK ++ILSPVG+YYKEG PVKI + EF Sbjct: 125 DWVYGAEGTALYIRPFIIATDPYLGVRPSNTYKFMVILSPVGAYYKEGFNPVKIYITDEF 184 Query: 186 VRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKING 245 RA K G G+ KT NYA+SL A + A++ GF+QVLWLD IEKKYIEEVG+MN+FFKI+G Sbjct: 185 TRAAKQGLGDVKTPANYAASLYAGEQAKKMGFTQVLWLDPIEKKYIEEVGTMNVFFKIDG 244 Query: 246 EIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAA 305 E+VTP L+GSIL G+TR+SV+ +LK WG+ VSER I++DE+ A+ +G LEE FGTGTAA Sbjct: 245 EVVTPALSGSILSGVTRDSVLQVLKSWGIAVSERAISVDEIFAAYDEGRLEEVFGTGTAA 304 Query: 306 VISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356 VISPVG L + +SIN G TGE++ +L+D ITG+Q G +D+FGW EV Sbjct: 305 VISPVGLLRHGEREISINGGVTGELSARLFDAITGMQYGKCSDDFGWIVEV 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: 432 Number of extensions: 9 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: 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_012283532.1 HM1_RS11370 (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.5298.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-123 396.4 0.0 4.4e-123 396.2 0.0 1.0 1 lcl|NCBI__GCF_000019165.1:WP_012283532.1 HM1_RS11370 branched-chain amino Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019165.1:WP_012283532.1 HM1_RS11370 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 396.2 0.0 4.4e-123 4.4e-123 1 313 [] 43 355 .] 43 355 .] 0.99 Alignments for each domain: == domain 1 score: 396.2 bits; conditional E-value: 4.4e-123 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++a+++++++l l+++ +v+hYgq+vfeG+ka+Rt+d +++lfRp++ ++R+ s ++l +P +e+ lcl|NCBI__GCF_000019165.1:WP_012283532.1 43 WHNAQIMPYGPLLLEPSIMVFHYGQAVFEGMKAFRTKDERVVLFRPERYIRRMSYSIQKLCIPAFDEAF 111 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 +++a+k lv +++dwv a+ +++LY+RPf+iat+++lGv+++++y f+v++sPvGaY+k+g +pv+i+ lcl|NCBI__GCF_000019165.1:WP_012283532.1 112 VVDAIKTLVDIERDWVYGAE-GTALYIRPFIIATDPYLGVRPSNTYKFMVILSPVGAYYKEGFNPVKIY 179 *****************999.9*********************************************** PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 +++e++Raa++G+G vk+ nYaasl a ++a++ g+ +v++ldp+ekk+ieevG++n+f+ ++ ge+v lcl|NCBI__GCF_000019165.1:WP_012283532.1 180 ITDEFTRAAKQGLGDVKTPANYAASLYAGEQAKKMGFTQVLWLDPIEKKYIEEVGTMNVFFKID-GEVV 247 ************************************************************9775.9*** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t++ls+siL+gvtr+s+l++ k++g++v+er i++de+ aa ++G + vf++Gtaavi+Pvg l++++ lcl|NCBI__GCF_000019165.1:WP_012283532.1 248 TPALSGSILSGVTRDSVLQVLKSWGIAVSERAISVDEIFAAYDEGRLeeVFGTGTAAVISPVGLLRHGE 316 *********************************************8888******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313 +e++++ + +Ge++ +l+d++t++qyGk d +gWivev lcl|NCBI__GCF_000019165.1:WP_012283532.1 317 REISINGGVTGELSARLFDAITGMQYGKCSDDFGWIVEV 355 *************************************97 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.68 // [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