Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate Ga0059261_3317 Ga0059261_3317 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >FitnessBrowser__Korea:Ga0059261_3317 Length = 486 Score = 156 bits (395), Expect = 1e-42 Identities = 112/372 (30%), Positives = 180/372 (48%), Gaps = 13/372 (3%) Query: 30 LKVTEKPGIISLAGGLPSPKTFPVSAFAAA--SAAVLANDGPAALQYAASEGYAPLRQAI 87 L + PG+ L G P + FP A A SAA A+ QY G LR++I Sbjct: 120 LALPSGPGL-KLDEGAPDGRLFPADLLARAYRSAAHRASR-ENRFQYGNPRGTPALRESI 177 Query: 88 ADFLPWD----VDADQILITTGSQQALDLIAKVLIDENSRVLVETPTYLGALQAFTPMEP 143 A L V A+ I IT GSQ + L A+VL+ V+VE TY A+ AF + Sbjct: 178 ATMLKSQRGLPVTAENICITRGSQNGIFLAAQVLVRPGDTVIVEALTYEPAVAAFRALGA 237 Query: 144 SVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEARRAALVKAAAEL 203 ++VAV D++G+ ID ++ A +A ++V P+ Q PT ++ RR L++ + + Sbjct: 238 NIVAVGLDEDGIDIDAVEHACRRNAVRA--VFVTPHHQFPTTVSLRPERRLRLLELSHQF 295 Query: 204 NLPLVEDNPYGDLWFDNPPPAPLTARNPEGCIYMGSFSKVLAPGLRLGFVVAPKAVYPKL 263 ++ED+ + F++ P P+ P IY+GS SK+L P LR+G+V AP V + Sbjct: 296 GFAIIEDDYDHEFHFESQPLLPMAGYGPGHVIYVGSMSKLLLPALRIGYVAAPPPVIDAI 355 Query: 264 LQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLAALTQEMAGLGVE 323 D + AE+++ L RH +R +Y ++ E A + + + + V+ Sbjct: 356 AHMVSLTDGMGNALTEDAAAELIENGELRRHARKVRQVYAKRRENFAAEIDRTLGDI-VD 414 Query: 324 WNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADPRTLRLSFVTSTVE 383 + PDGG+ W+R + A+E +A + F +F + PR LR+ F + Sbjct: 415 YKMPDGGLAFWLRFHTDLDAME--ARAAAMGLRFAASRSFMTRDDAPRGLRIGFASLNEH 472 Query: 384 QIATGIAALAAA 395 + T +AAL A Sbjct: 473 EAKTAVAALREA 484 Lambda K H 0.318 0.134 0.392 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: 402 Number of extensions: 23 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: 401 Length of database: 486 Length adjustment: 32 Effective length of query: 369 Effective length of database: 454 Effective search space: 167526 Effective search space used: 167526 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 (21.7 bits) S2: 51 (24.3 bits)
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