Align Branched-chain-amino-acid transaminase 1; BCAT 1; EC 2.6.1.42 (characterized)
to candidate WP_013011212.1 DACET_RS09770 branched-chain amino acid aminotransferase
Query= SwissProt::O31461 (356 letters) >NCBI__GCF_000025725.1:WP_013011212.1 Length = 367 Score = 274 bits (700), Expect = 3e-78 Identities = 145/341 (42%), Positives = 210/341 (61%), Gaps = 4/341 (1%) Query: 18 DPSSLGFGQYFTDYMFVMDYEEGIGWHHPRIAPYAPLTLDPSSSVFHYGQAVFEGLKAYR 77 D SL FG+ +D+M ++DY +G+ W RI PY L++ P + HYGQ++FEG KA+ Sbjct: 20 DAESLPFGKLRSDHMLLIDYAKGV-WKDARIVPYGSLSIMPGAVALHYGQSIFEGAKAFM 78 Query: 78 TDDGRVLLFRPDQNIKRLNRSCERMSMPPLDEELVLEALTQLVELEKDWVPKEKGTSLYI 137 +DG + FR ++N KRLN S ++ MP + ++ +E + +L+++E+ W P + +SLY+ Sbjct: 79 HEDGELYAFRLEENAKRLNVSANQLCMPEIPVDVQVEGMMKLLDVERKWCPMQPESSLYV 138 Query: 138 RPFVIATEPSLGVKASRSYTFMIVLSPVGSYYGDDQLKPVRIYVEDEYVRAVNGGVGFAK 197 RPF+I TE +LG+ S +YTF ++LSP G+YY VR+ V + Y RAV+GG G AK Sbjct: 139 RPFMIGTEDALGMAPSSTYTFCVLLSPSGAYYSGGFKHAVRLLVTERYHRAVSGGTGSAK 198 Query: 198 TAGNYAASLQAQRKANELGYDQVLWLDAIEKKYVEEVGSMNIFFVINGEAVT-PALSGSI 256 GNY + QA R + + QVL+LDA +Y+EEVGSMN F + + V P + SI Sbjct: 199 CCGNYGQAFQAARFSKKYDASQVLYLDA-SNQYIEEVGSMNHFHITKDKTVVIPEFTDSI 257 Query: 257 LSGVTRASAIELIRSWGIPVREERISIDEVYAASARGELTEVFGTGTAAVVTPVGE-LNI 315 L +T S +EL+ S G VR+ER+ I E GE+ E G GTAAVVTPV E + Sbjct: 258 LRSITSLSVMELLPSLGYKVRQERVKITEFLDGIRSGEIIEAGGFGTAAVVTPVSEYIFE 317 Query: 316 HGKTVIVGDGQIGDLSKKLYETITDIQLGKVKGPFNWTVEV 356 +G + VGDG IG+ ++K+YE T IQ GK W +V Sbjct: 318 NGDILTVGDGGIGENTRKIYEAYTAIQTGKAADKLGWLQKV 358 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: 355 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: 356 Length of database: 367 Length adjustment: 29 Effective length of query: 327 Effective length of database: 338 Effective search space: 110526 Effective search space used: 110526 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_013011212.1 DACET_RS09770 (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.21170.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-102 328.1 0.0 2.8e-102 327.9 0.0 1.0 1 lcl|NCBI__GCF_000025725.1:WP_013011212.1 DACET_RS09770 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025725.1:WP_013011212.1 DACET_RS09770 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 327.9 0.0 2.8e-102 2.8e-102 1 313 [] 44 358 .. 44 358 .. 0.97 Alignments for each domain: == domain 1 score: 327.9 bits; conditional E-value: 2.8e-102 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++a+++++++l++ +g+ +lhYgq +feG ka+ ++dG+++ fR ++nakRl+ sa++l +Pe++ ++ lcl|NCBI__GCF_000025725.1:WP_013011212.1 44 WKDARIVPYGSLSIMPGAVALHYGQSIFEGAKAFMHEDGELYAFRLEENAKRLNVSANQLCMPEIPVDV 112 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglap.vsi 137 +e +++l+ ++++w p + e+sLY+RPf+i+ted lG++++++y+f+vl+sP GaY+ gg + v+ lcl|NCBI__GCF_000025725.1:WP_013011212.1 113 QVEGMMKLLDVERKWCPMQP-ESSLYVRPFMIGTEDALGMAPSSTYTFCVLLSPSGAYYSGGFKHaVRL 180 *****************776.*****************************************8876999 PP TIGR01123 138 fveteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgel 206 +v++ y Ra+ +GtG +k+ GnY +++a + ++ ++v+yld+ ++ +ieevG++n f itkd ++ lcl|NCBI__GCF_000025725.1:WP_013011212.1 181 LVTERYHRAVSGGTGSAKCCGNYGQAFQAARFSKKYDASQVLYLDASNQ-YIEEVGSMNHFHITKDKTV 248 **********************************************988.******************* PP TIGR01123 207 vttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvge.lki 272 v+++ ++siL ++t s++el +lg++v+ ++++i e+ + +Gei + + Gtaav+tPv+e + lcl|NCBI__GCF_000025725.1:WP_013011212.1 249 VIPEFTDSILRSITSLSVMELLPSLGYKVRQERVKITEFLDGIRSGEIieAGGFGTAAVVTPVSEyIFE 317 ***********************************************96566679********984567 PP TIGR01123 273 egkevevkseevGevtkklrdeltdiqyGkledkegWivev 313 +g+ ++v ++ +Ge t+k++++ t iq+Gk++dk gW+ +v lcl|NCBI__GCF_000025725.1:WP_013011212.1 318 NGDILTVGDGGIGENTRKIYEAYTAIQTGKAADKLGWLQKV 358 889999*******************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (367 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: 10.78 // [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