Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate CA265_RS22650 CA265_RS22650 branched chain amino acid aminotransferase
Query= BRENDA::A0A2Z4MEX9 (357 letters) >FitnessBrowser__Pedo557:CA265_RS22650 Length = 354 Score = 312 bits (800), Expect = 8e-90 Identities = 148/349 (42%), Positives = 228/349 (65%), Gaps = 5/349 (1%) Query: 5 LTITRTEQKKEKPAS-DKLGFGVHFTDHMFTMDYTEGKGWHDPQIVPYSPLTLDPAAMVF 63 + IT+ +Q + +L FG FTDHMFT DY +G+ W + QI+PY P+ + PA Sbjct: 7 IKITKADQTRLTVTDFSQLPFGKVFTDHMFTADYEDGE-WKNLQILPYGPIPMSPAISAL 65 Query: 64 HYGQAVFEGLKAYRNQEGKVRLFRPDQNFKRMNRSLERMSMPLIDEEFMVEALKQLVAVD 123 HYGQA+FEGLKAYR +GK+ +FR D+NF+R N+S RMSMP I EE ++ L L+ VD Sbjct: 66 HYGQAIFEGLKAYRQPDGKISVFRADKNFERFNKSAARMSMPGIPEEIFMQGLAALINVD 125 Query: 124 KEWIPTESGQSLYIRPFVIATEPCFGVRASHTYKLVIVLSPVGAYYAGGMKPVKIYVENN 183 ++W+P + +LYIRP + A +P GV+AS TYK ++ +P G YY+ +K + +E Sbjct: 126 EKWVPNQEDYALYIRPVMFAMDPYLGVKASDTYKFALLTTPTGPYYSSALK---VKIETE 182 Query: 184 YVRAVRGGTGNAKVAGNYAGSLKAQVEAKEKGYEQVLWLDGVENKYIEEVGSMNVFFKVK 243 + RA GG G AK AGNYA SL +AK++GY+Q++W D V +++IEE G+ N+ F + Sbjct: 183 FTRADEGGVGFAKTAGNYARSLYPFEQAKKEGYDQLIWTDSVTHEFIEEAGTANLLFVIN 242 Query: 244 GEVWTPALNGSILEGITRDSTIQLLKDWGIPVVEKRISMEDLHTAYVNGELEEAFGTGTA 303 G++ TP++ ++L+G+TRD+ I+L KD G+ V E+R+S++++ NG L EAF GTA Sbjct: 243 GKLVTPSVRSTVLDGVTRDTIIKLAKDAGVEVEERRVSVKEVIEGIENGSLTEAFAAGTA 302 Query: 304 AVISPVGDLNWNGHQMIINGEKTGELTTRLYDEMTGIQYGDREDKFGWS 352 A ++ VG++ +NG + T ++ + ++ I+YG D+FGW+ Sbjct: 303 ATVTHVGEMGYNGQIYKLTDPSTRHISNGIAKKLNDIRYGLAPDEFGWN 351 Lambda K H 0.317 0.136 0.406 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: 393 Number of extensions: 17 Number of successful extensions: 3 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: 357 Length of database: 354 Length adjustment: 29 Effective length of query: 328 Effective length of database: 325 Effective search space: 106600 Effective search space used: 106600 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 CA265_RS22650 CA265_RS22650 (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.10057.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-103 329.8 0.0 8e-103 329.6 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS22650 CA265_RS22650 branched chain ami Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS22650 CA265_RS22650 branched chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 329.6 0.0 8e-103 8e-103 1 309 [. 45 350 .. 45 354 .] 0.99 Alignments for each domain: == domain 1 score: 329.6 bits; conditional E-value: 8e-103 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleee 68 W++ ++ +++++ ++++ ++lhYgq++feGlkayR+ dGki +fR+d+n +R+++sa r+++P ++ee lcl|FitnessBrowser__Pedo557:CA265_RS22650 45 WKNLQILPYGPIPMSPAISALHYGQAIFEGLKAYRQPDGKISVFRADKNFERFNKSAARMSMPGIPEE 112 999***************************************************************** PP TIGR01123 69 lflealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvs 136 +f++ l+ l+++d++wvp+++ + +LY+RP+++a++++lGvka+ +y f +l++P G+Y+ + l++ lcl|FitnessBrowser__Pedo557:CA265_RS22650 113 IFMQGLAALINVDEKWVPNQE-DYALYIRPVMFAMDPYLGVKASDTYKFALLTTPTGPYYSSALKV-- 177 ******************888.9**************************************99988.. PP TIGR01123 137 ifveteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdg 204 +ete++Ra ++G+G++k++GnYa sl + ++a+++g+d+ ++ d+v+++ iee+G+an++++++ g lcl|FitnessBrowser__Pedo557:CA265_RS22650 178 -KIETEFTRADEGGVGFAKTAGNYARSLYPFEQAKKEGYDQLIWTDSVTHEFIEEAGTANLLFVIN-G 243 .79**************************************************************9.8 PP TIGR01123 205 elvttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgel 270 +lvt++ +L+gvtr+ +++lakd+g+eveer++++ e+ + e+G++ +fa+Gtaa +t vge+ lcl|FitnessBrowser__Pedo557:CA265_RS22650 244 KLVTPSVRSTVLDGVTRDTIIKLAKDAGVEVEERRVSVKEVIEGIENGSLteAFAAGTAATVTHVGEM 311 ************************************************9999**************** PP TIGR01123 271 kiegkevevkseevGevtkklrdeltdiqyGkledkegW 309 +g+ +++++ + ++++ + ++l di yG + d++gW lcl|FitnessBrowser__Pedo557:CA265_RS22650 312 GYNGQIYKLTDPSTRHISNGIAKKLNDIRYGLAPDEFGW 350 *************************************** 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 12.51 // [ok]
This GapMind analysis is from Apr 09 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