Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate RR42_RS25890 RR42_RS25890 branched-chain amino acid aminotransferase
Query= reanno::Cup4G11:RR42_RS25890 (363 letters) >FitnessBrowser__Cup4G11:RR42_RS25890 Length = 363 Score = 736 bits (1899), Expect = 0.0 Identities = 363/363 (100%), Positives = 363/363 (100%) Query: 1 MTQQTTFSLEPNPNALDAATRDALMRDPAFGRVFTDHMVTITWREGQGWQDAKVTARKPF 60 MTQQTTFSLEPNPNALDAATRDALMRDPAFGRVFTDHMVTITWREGQGWQDAKVTARKPF Sbjct: 1 MTQQTTFSLEPNPNALDAATRDALMRDPAFGRVFTDHMVTITWREGQGWQDAKVTARKPF 60 Query: 61 SIDPACSVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESLFLE 120 SIDPACSVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESLFLE Sbjct: 61 SIDPACSVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESLFLE 120 Query: 121 AIEQLVRIDQAWVPHGSGSLYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKA 180 AIEQLVRIDQAWVPHGSGSLYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKA Sbjct: 121 AIEQLVRIDQAWVPHGSGSLYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKA 180 Query: 181 VSVWVSENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGG 240 VSVWVSENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGG Sbjct: 181 VSVWVSENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGG 240 Query: 241 MNIFFVMDDGTLVTPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRL 300 MNIFFVMDDGTLVTPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRL Sbjct: 241 MNIFFVMDDGTLVTPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRL 300 Query: 301 AEAFVCGTAATLVAIGEVRSARTRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWVHH 360 AEAFVCGTAATLVAIGEVRSARTRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWVHH Sbjct: 301 AEAFVCGTAATLVAIGEVRSARTRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWVHH 360 Query: 361 VAL 363 VAL Sbjct: 361 VAL 363 Lambda K H 0.321 0.135 0.415 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: 647 Number of extensions: 11 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: 363 Length adjustment: 29 Effective length of query: 334 Effective length of database: 334 Effective search space: 111556 Effective search space used: 111556 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
Align candidate RR42_RS25890 RR42_RS25890 (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.24802.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-124 399.3 0.0 5.8e-124 399.1 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS25890 RR42_RS25890 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS25890 RR42_RS25890 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.1 0.0 5.8e-124 5.8e-124 1 313 [] 49 361 .. 49 361 .. 0.99 Alignments for each domain: == domain 1 score: 399.1 bits; conditional E-value: 5.8e-124 TIGR01123 1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 W++a++++ +++++d++ +vlhYgqe+feG+kayR adG ++lfRp +na+R++ sa+r+++P l+e l lcl|FitnessBrowser__Cup4G11:RR42_RS25890 49 WQDAKVTARKPFSIDPACSVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESL 117 ********************************************************************* PP TIGR01123 70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138 flea++qlv++d++wvp ++ sLYlRPf++a e lG+k+a+e++f+v+a+PvG+Yfkgg + vs++ lcl|FitnessBrowser__Cup4G11:RR42_RS25890 118 FLEAIEQLVRIDQAWVP--HGSGSLYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKAVSVW 184 *****************..5579********************************************** PP TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207 v+++y+Raap+GtG +k+gGnYa sl aq++a+++g+d+vv+ld++e++ +ee+G++nif++++dg+lv lcl|FitnessBrowser__Cup4G11:RR42_RS25890 185 VSENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGGMNIFFVMDDGTLV 253 ********************************************************************* PP TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274 t+pls+siL+g+tr+s++ela+++g+ veer+ + e++a +++G + +f cGtaa + +ge++ lcl|FitnessBrowser__Cup4G11:RR42_RS25890 254 TPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRLaeAFVCGTAATLVAIGEVRSAR 322 *********************************************98889******************* PP TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313 + + + ++ G+ k lrd l++iq+ +++++ gW+ +v lcl|FitnessBrowser__Cup4G11:RR42_RS25890 323 TRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWVHHV 361 ***********************************9765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (313 nodes) Target sequences: 1 (363 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.68 // [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