Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_035238991.1 Q366_RS11460 branched-chain amino acid aminotransferase
Query= SwissProt::P39576 (363 letters) >NCBI__GCF_000745975.1:WP_035238991.1 Length = 354 Score = 421 bits (1083), Expect = e-122 Identities = 207/349 (59%), Positives = 262/349 (75%), Gaps = 2/349 (0%) Query: 6 IRVELTSTKKP--KPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMV 63 + V++T +P +P L FG VFTDHMFVMDY DKGW++ RI PY SM PA+MV Sbjct: 1 MEVKVTRVSEPGTRPKDEDLGFGTVFTDHMFVMDYEKDKGWFNARIEPYGDFSMSPASMV 60 Query: 64 YHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAI 123 HYGQ VFEGLKAY ++D + L+R N R+N+S+ LCIP+ID + V++ LK+L+ + Sbjct: 61 LHYGQAVFEGLKAYKTKDGKIQLYRARDNFARMNRSSQGLCIPEIDIDFVMDALKKLIKL 120 Query: 124 DKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVES 183 ++ WIP GTSLYIRP ++AT+PFLGV AS+TYK IILSPVGSYY +G++PVKI V Sbjct: 121 EQAWIPETMGTSLYIRPTLVATDPFLGVRASYTYKFFIILSPVGSYYAQGLQPVKIWVCE 180 Query: 184 EFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKI 243 + VRAV+GG G KT GNYA+SL A + A+++G++QVLWLDGIE KYIEEVG+MNIFF I Sbjct: 181 DHVRAVRGGVGEFKTPGNYAASLLAGEKAKKEGYNQVLWLDGIELKYIEEVGAMNIFFLI 240 Query: 244 NGEIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGT 303 N E+VTPMLNGSIL GITR SVI L K WG++VSERKI+IDEVI A +G L+E FG+GT Sbjct: 241 NDELVTPMLNGSILPGITRFSVIELAKKWGMKVSERKISIDEVIAAADNGTLQEMFGSGT 300 Query: 304 AAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGW 352 AAV+SPVGEL ++D + I NGE GE+ K Y+ +T IQ G D GW Sbjct: 301 AAVVSPVGELRYKDRVIHIGNGEPGEVCMKFYNAVTAIQYGNAEDTEGW 349 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: 451 Number of extensions: 12 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: 354 Length adjustment: 29 Effective length of query: 334 Effective length of database: 325 Effective search space: 108550 Effective search space used: 108550 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_035238991.1 Q366_RS11460 (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.16014.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-124 400.6 0.0 2.3e-124 400.4 0.0 1.0 1 lcl|NCBI__GCF_000745975.1:WP_035238991.1 Q366_RS11460 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745975.1:WP_035238991.1 Q366_RS11460 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 400.4 0.0 2.3e-124 2.3e-124 1 311 [. 41 351 .. 41 353 .. 0.99 Alignments for each domain: == domain 1 score: 400.4 bits; conditional E-value: 2.3e-124 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W +a+++++++++++++s+vlhYgq+vfeGlkay+t+dGki l+R+ +n +R++rs++ l +Pe++ + lcl|NCBI__GCF_000745975.1:WP_035238991.1 41 WFNARIEPYGDFSMSPASMVLHYGQAVFEGLKAYKTKDGKIQLYRARDNFARMNRSSQGLCIPEIDIDF 109 999****************************************************************** PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 +++alk+l+k++++w+p++ ++sLY+RP+l+at++ lGv+a+ +y f++++sPvG+Y+++gl+pv+i+ lcl|NCBI__GCF_000745975.1:WP_035238991.1 110 VMDALKKLIKLEQAWIPETM-GTSLYIRPTLVATDPFLGVRASYTYKFFIILSPVGSYYAQGLQPVKIW 177 *****************666.************************************************ PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v +++vRa+ +G+G k+ GnYaaslla +ka+++g+++v++ld +e k+ieevGa+nif++++d elv lcl|NCBI__GCF_000745975.1:WP_035238991.1 178 VCEDHVRAVRGGVGEFKTPGNYAASLLAGEKAKKEGYNQVLWLDGIELKYIEEVGAMNIFFLIND-ELV 245 *****************************************************************.*** PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t+ l +siL+g+tr s++elak++g++v+er+i+ide+ aa+++G + +f++Gtaav++Pvgel+ ++ lcl|NCBI__GCF_000745975.1:WP_035238991.1 246 TPMLNGSILPGITRFSVIELAKKWGMKVSERKISIDEVIAAADNGTLqeMFGSGTAAVVSPVGELRYKD 314 *********************************************9899******************** PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWiv 311 + +++ ++e+Gev +k+++++t iqyG++ed+egWi lcl|NCBI__GCF_000745975.1:WP_035238991.1 315 RVIHIGNGEPGEVCMKFYNAVTAIQYGNAEDTEGWIE 351 ***********************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (354 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: 11.00 // [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