Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate Echvi_2202 Echvi_2202 branched-chain amino acid aminotransferase, group II
Query= SwissProt::P39576 (363 letters) >FitnessBrowser__Cola:Echvi_2202 Length = 355 Score = 334 bits (857), Expect = 2e-96 Identities = 172/356 (48%), Positives = 239/356 (67%), Gaps = 8/356 (2%) Query: 5 TIRVELTSTKKPK---PDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAA 61 TI +++ T + K D LSFG+V +DHMFV DY + W D RI PY PLS++PA Sbjct: 4 TIDIQIKQTSQSKLQGTDFENLSFGQVMSDHMFVADYKNGE-WQDFRIEPYAPLSLNPAN 62 Query: 62 MVYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLV 121 HYGQ+VFEGLKAY E ++VL+FRP+ N +RLN+S DRLCIPQ+ EE +EGL++L+ Sbjct: 63 ATLHYGQSVFEGLKAYKDEHNNVLIFRPDANQQRLNESADRLCIPQLPEEIFMEGLRKLL 122 Query: 122 AIDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAV 181 A+D+DWIPN G SLYIRPFI AT+ +LG+ S TYK +I PVG YY KPV + V Sbjct: 123 AVDRDWIPNKPGCSLYIRPFIFATDDYLGIRPSATYKFMIFTCPVGHYY---AKPVSVKV 179 Query: 182 ESEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFF 241 E+++ RA +GGTG AK AGNYA SL Q+A+++G+ Q+LW DG + IEE G+MN+ F Sbjct: 180 ETKYTRAAEGGTGQAKAAGNYAGSLYPAQIAQKQGYDQLLWTDGKNHENIEESGTMNVMF 239 Query: 242 KINGEIVT-PMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFG 300 IN ++T P G+IL+GITR+SV+ L K GL+VSER + + E+ +A ++ L+EAFG Sbjct: 240 IINNTLITAPTSKGTILKGITRDSVLTLAKEKGLKVSERFLTVTELKEALENNTLQEAFG 299 Query: 301 TGTAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356 TGTAA I+ + ++ D + + ++ +T+ I+ G D GW T+V Sbjct: 300 TGTAATIAHIYKINVGDTDYDLPEKPADSFSYQVLETLDAIKYGRQEDTHGWITKV 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: 377 Number of extensions: 14 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 Echvi_2202 Echvi_2202 (branched-chain amino acid aminotransferase, group II)
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.2614539.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-107 345.6 0.0 1.3e-107 345.4 0.0 1.0 1 FitnessBrowser__Cola:Echvi_2202 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Cola:Echvi_2202 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 345.4 0.0 1.3e-107 1.3e-107 1 313 [] 45 355 .] 45 355 .] 0.97 Alignments for each domain: == domain 1 score: 345.4 bits; conditional E-value: 1.3e-107 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkqlv 78 W++ +++++a+l+l+++ a lhYgq vfeGlkay+ + ++l+fRpdan +Rl++sa+rl +P+l+ee+f+e l++l+ FitnessBrowser__Cola:Echvi_2202 45 WQDFRIEPYAPLSLNPANATLHYGQSVFEGLKAYKDEHNNVLIFRPDANQQRLNESADRLCIPQLPEEIFMEGLRKLL 122 9***************************************************************************** PP TIGR01123 79 kadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkGtGavkv 156 ++d+dw+p++ + sLY+RPf++at+d+lG++++ +y f+++++PvG+Y+++ pvs+ vet+y+Raa++GtG++k FitnessBrowser__Cola:Echvi_2202 123 AVDRDWIPNKP-GCSLYIRPFIFATDDYLGIRPSATYKFMIFTCPVGHYYAK---PVSVKVETKYTRAAEGGTGQAKA 196 ********777.**************************************86...56679****************** PP TIGR01123 157 gGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttpls.esiLegvtresllelakdlgl 233 +GnYa sl + ++a++qg+d+ ++ d +++++iee G++n+++i+++ +l+t p s + iL+g+tr+s+l+lak+ gl FitnessBrowser__Cola:Echvi_2202 197 AGNYAGSLYPAQIAQKQGYDQLLWTDGKNHENIEESGTMNVMFIINN-TLITAPTSkGTILKGITRDSVLTLAKEKGL 273 **********************************************9.88888877368******************* PP TIGR01123 234 eveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkklrdeltdiqyGkledkegW 309 +v+er +++ elk+a e+ + +f++Gtaa i+ + +++++++ + + +++ ++++ ++l i+yG++ed++gW FitnessBrowser__Cola:Echvi_2202 274 KVSERFLTVTELKEALENNTLqeAFGTGTAATIAHIYKINVGDTDYDLPEKPADSFSYQVLETLDAIKYGRQEDTHGW 351 ******************98888******************************************************* PP TIGR01123 310 ivev 313 i++v FitnessBrowser__Cola:Echvi_2202 352 ITKV 355 *997 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: 00:00:00.00 # Mc/sec: 20.73 // [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