Align Branched-chain-amino-acid transaminase 1; BCAT 1; EC 2.6.1.42 (characterized)
to candidate WP_017549722.1 C792_RS0112120 branched-chain amino acid aminotransferase
Query= SwissProt::O31461 (356 letters) >NCBI__GCF_000330705.1:WP_017549722.1 Length = 355 Score = 414 bits (1064), Expect = e-120 Identities = 205/356 (57%), Positives = 257/356 (72%), Gaps = 1/356 (0%) Query: 1 MNKLIEREKTVYYKEKPDPSSLGFGQYFTDYMFVMDYEEGIGWHHPRIAPYAPLTLDPSS 60 M++ ++ E+ K KPD S++ FG FTDYMF Y GW I PY L L PS+ Sbjct: 1 MSQTLQIERANELKHKPDVSTVQFGTVFTDYMFTNRYTPEYGWSGASIVPYQNLQLSPSA 60 Query: 61 SVFHYGQAVFEGLKAYRTDDGRVLLFRPDQNIKRLNRSCERMSMPPLDEELVLEALTQLV 120 HYGQ+VFEGLKAY+ D +LLFRPDQN KR+N S R+SMP ++EE L AL +L+ Sbjct: 61 QAIHYGQSVFEGLKAYKQGDD-ILLFRPDQNFKRMNESLSRLSMPEINEENALNALYELL 119 Query: 121 ELEKDWVPKEKGTSLYIRPFVIATEPSLGVKASRSYTFMIVLSPVGSYYGDDQLKPVRIY 180 ++E+DWVP +G SLYIRPFV A EP LGV+ S +Y F I+LSPVG YYG QL P IY Sbjct: 120 KVERDWVPDGEGQSLYIRPFVFADEPFLGVRPSETYQFNIILSPVGGYYGATQLNPTSIY 179 Query: 181 VEDEYVRAVNGGVGFAKTAGNYAASLQAQRKANELGYDQVLWLDAIEKKYVEEVGSMNIF 240 VED++VR+V GGVGFAK +GNYAASL AQ+KANELGY+QVLWLD +E+KYVEEVGSMNIF Sbjct: 180 VEDDFVRSVRGGVGFAKVSGNYAASLLAQKKANELGYEQVLWLDGVEQKYVEEVGSMNIF 239 Query: 241 FVINGEAVTPALSGSILSGVTRASAIELIRSWGIPVREERISIDEVYAASARGELTEVFG 300 FV +GE +TP L+GSIL G+TR S IEL + G V+EE+I ID++ G +TEVFG Sbjct: 240 FVRDGELITPQLNGSILPGITRKSIIELAKHKGYTVKEEKIHIDDLVEDIHGGRVTEVFG 299 Query: 301 TGTAAVVTPVGELNIHGKTVIVGDGQIGDLSKKLYETITDIQLGKVKGPFNWTVEV 356 GTAAV+ PVG+LNIHG IV D Q+G++S L+ +TDIQ G+ + PF W V + Sbjct: 300 AGTAAVIAPVGKLNIHGIDYIVNDNQVGEVSLDLFNDLTDIQYGRKEDPFGWVVRL 355 Lambda K H 0.317 0.137 0.400 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: 463 Number of extensions: 11 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: 356 Length of database: 355 Length adjustment: 29 Effective length of query: 327 Effective length of database: 326 Effective search space: 106602 Effective search space used: 106602 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_017549722.1 C792_RS0112120 (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.2386735.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-124 399.6 0.0 4.5e-124 399.4 0.0 1.0 1 NCBI__GCF_000330705.1:WP_017549722.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330705.1:WP_017549722.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.4 0.0 4.5e-124 4.5e-124 1 313 [] 43 355 .] 43 355 .] 0.98 Alignments for each domain: == domain 1 score: 399.4 bits; conditional E-value: 4.5e-124 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 W+ a ++++++l+l+++++++hYgq vfeGlkay++ d illfRpd+n kR+++s +rl++Pe++ee l+a NCBI__GCF_000330705.1:WP_017549722.1 43 WSGASIVPYQNLQLSPSAQAIHYGQSVFEGLKAYKQGD-DILLFRPDQNFKRMNESLSRLSMPEINEENALNA 114 999********************************988.7********************************* PP TIGR01123 74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgg.lapvsifveteyvR 145 l +l+k+++dwvp+ + ++sLY+RPf++a e+ lGv+++++y f +++sPvG Y+ l+p+si+ve+++vR NCBI__GCF_000330705.1:WP_017549722.1 115 LYELLKVERDWVPDGE-GQSLYIRPFVFADEPFLGVRPSETYQFNIILSPVGGYYGATqLNPTSIYVEDDFVR 186 *************666.9*************************************87669************* PP TIGR01123 146 aapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLeg 218 ++ +G+G++kv+GnYaasllaqkka+e g+++v++ld ve+k++eevG++nif++ + gel+t++l +siL+g NCBI__GCF_000330705.1:WP_017549722.1 187 SVRGGVGFAKVSGNYAASLLAQKKANELGYEQVLWLDGVEQKYVEEVGSMNIFFVRD-GELITPQLNGSILPG 258 ******************************************************976.9************** PP TIGR01123 219 vtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtk 289 +tr+s++elak+ g++v+e++i+id+l + + G + vf++Gtaavi+Pvg+l+i+g ++v++++vGev+ NCBI__GCF_000330705.1:WP_017549722.1 259 ITRKSIIELAKHKGYTVKEEKIHIDDLVEDIHGGRVteVFGAGTAAVIAPVGKLNIHGIDYIVNDNQVGEVSL 331 **********************************9999*********************************** PP TIGR01123 290 klrdeltdiqyGkledkegWivev 313 l++ ltdiqyG++ed++gW+v++ NCBI__GCF_000330705.1:WP_017549722.1 332 DLFNDLTDIQYGRKEDPFGWVVRL 355 *********************985 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 14.78 // [ok]
This GapMind analysis is from Jul 26 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