Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_035238892.1 Q366_RS10700 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_000745975.1:WP_035238892.1 Length = 353 Score = 384 bits (985), Expect = e-111 Identities = 186/340 (54%), Positives = 243/340 (71%), Gaps = 1/340 (0%) Query: 17 KPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFEGLKA 76 KPD + L FG +FTDHMF +DY +KGW++ RI P+Q PA MV HYGQ +FEGLKA Sbjct: 14 KPDGSTLGFGNIFTDHMFNLDYNPEKGWHNARIEPFQKFEFSPATMVLHYGQAIFEGLKA 73 Query: 77 YVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAEGTSL 136 Y ++ +LLFR + N +RLN S LCIP++D + +++ L +L+ ++KDW+P A GTSL Sbjct: 74 YKNDKKDILLFRVKDNFKRLNNSAKGLCIPELDSDFLIKALHKLLKLEKDWVPEAPGTSL 133 Query: 137 YIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEFVRAVKGGTGNA 196 YIRP IIAT+P + + S TY+ +ILSPVG+YY EG KPV I V ++ RA+ GG G Sbjct: 134 YIRPAIIATDPSIDLRPSETYRYFVILSPVGAYY-EGFKPVNIWVSKDYTRAIPGGVGEF 192 Query: 197 KTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKINGEIVTPMLNGSI 256 KTAGNYA+SL A A E G++QVLWLD +EKKYIEEVGSMNIFF I EIVTP L GSI Sbjct: 193 KTAGNYAASLFAATEAAENGYNQVLWLDAVEKKYIEEVGSMNIFFVIGDEIVTPKLTGSI 252 Query: 257 LEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPVGELIWQ 316 L GITR+SVI L +WG ++SER+I+IDE+++AH G L+E FG+GT ISPVG++ Sbjct: 253 LPGITRSSVIDLSNNWGFKISERRISIDEILEAHDSGDLKEVFGSGTGVGISPVGKIGLD 312 Query: 317 DETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356 D L+IN + GE+A K + +TGI+ G D+F W T V Sbjct: 313 DTELTINGNKPGELAVKFDEELTGIKLGNREDKFNWVTPV 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: 447 Number of extensions: 17 Number of successful extensions: 2 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: 353 Length adjustment: 29 Effective length of query: 334 Effective length of database: 324 Effective search space: 108216 Effective search space used: 108216 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_035238892.1 Q366_RS10700 (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.26681.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-115 368.9 0.0 1.1e-114 368.7 0.0 1.0 1 lcl|NCBI__GCF_000745975.1:WP_035238892.1 Q366_RS10700 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745975.1:WP_035238892.1 Q366_RS10700 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 368.7 0.0 1.1e-114 1.1e-114 1 312 [. 41 351 .. 41 352 .. 0.99 Alignments for each domain: == domain 1 score: 368.7 bits; conditional E-value: 1.1e-114 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++a++++ +++e++++++vlhYgq++feGlkay+ ++ illfR ++n kRl++sa+ l +Pel+++ lcl|NCBI__GCF_000745975.1:WP_035238892.1 41 WHNARIEPFQKFEFSPATMVLHYGQAIFEGLKAYKNDKKDILLFRVKDNFKRLNNSAKGLCIPELDSDF 109 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 +++al++l+k++kdwvp+a ++sLY+RP +iat++++ +++++y+++v++sPvGaY++ g +pv+i+ lcl|NCBI__GCF_000745975.1:WP_035238892.1 110 LIKALHKLLKLEKDWVPEAP-GTSLYIRPAIIATDPSIDLRPSETYRYFVILSPVGAYYE-GFKPVNIW 176 *****************888.**************************************6.8999**** PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v+++y+Ra+p+G+G k++GnYaasl a ++aae+g+++v++ld+vekk+ieevG++nif++++d e+v lcl|NCBI__GCF_000745975.1:WP_035238892.1 177 VSKDYTRAIPGGVGEFKTAGNYAASLFAATEAAENGYNQVLWLDAVEKKYIEEVGSMNIFFVIGD-EIV 244 *****************************************************************.*** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t++l++siL+g+tr+s++ l +++g++++er+i+ide+ +a ++G++ vf++Gt i+Pvg++ ++ lcl|NCBI__GCF_000745975.1:WP_035238892.1 245 TPKLTGSILPGITRSSVIDLSNNWGFKISERRISIDEILEAHDSGDLkeVFGSGTGVGISPVGKIGLDD 313 *********************************************9999******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWive 312 +e++++ +++Ge++ k+ +elt+i++G+ edk++W++ lcl|NCBI__GCF_000745975.1:WP_035238892.1 314 TELTINGNKPGELAVKFDEELTGIKLGNREDKFNWVTP 351 ***********************************985 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 9.85 // [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