Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate GFF1057 HP15_1036 transcriptional regulator, GntR family with aminotransferase domain protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >FitnessBrowser__Marino:GFF1057 Length = 480 Score = 144 bits (363), Expect = 5e-39 Identities = 118/387 (30%), Positives = 179/387 (46%), Gaps = 14/387 (3%) Query: 14 LARRAERMNPSVIREI---LKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPA 70 + R R P RE+ L E+ ++ LA +P P P+ S A G Sbjct: 88 MRRHRSRPVPVSAREMALDLCADEQKRMVPLATAIPHPDYLPLRQIQH-STLWAARRGLE 146 Query: 71 ALQYAASEGYAPLRQAIAD---FLPWDVDADQILITTGSQQALDLIAKVLIDENSRVLVE 127 L YA G R+ IA L V D +L T G+Q+A+ L + + V VE Sbjct: 147 TLDYAFP-GKESFRRQIAQRMATLGVPVTPDDVLATNGAQEAIILALRAVTQPGDIVAVE 205 Query: 128 TPTYLGALQAFTPMEPSVVAVASD-DEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGR 186 +P++ G LQA + V+ + + EG+ ++ L+ + KA V+ N NP G Sbjct: 206 SPSFPGILQALEVVGLKVIEIPTHPSEGLSLEGLQLALEQWPLKA--CVVVTNHSNPMGA 263 Query: 187 TMTEARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARN-PEGCIYMGSFSKVLA 245 M++ R+ LV A +PL+ED+ YGDL P P A + + IY SFSK ++ Sbjct: 264 QMSDERKKQLVSMLAAAAVPLIEDDIYGDLHHTGDRPKPAKAFDRADNVIYCSSFSKTIS 323 Query: 246 PGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQ 305 PGLRLG++V P Q K +L T Q VA ++ DR++ + R Y++ Sbjct: 324 PGLRLGWMV-PGRHMASARQHKYFVNLATSSIPQMAVAHFLEQGGYDRYLRSARQHYREA 382 Query: 306 CEAMLAALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYA 365 E M A+ + G +RP GG LWV+LP+G+S E+ +A ++ PG F Sbjct: 383 TERMRTAVARAFPE-GTAVSRPQGGFVLWVQLPDGVSGTEVYHRARAEDINVAPGLMFST 441 Query: 366 DNADPRTLRLSFVTSTVEQIATGIAAL 392 + LRL+ E+I +A L Sbjct: 442 ADKYDNCLRLNSANPWSERIEHAVARL 468 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: 454 Number of extensions: 24 Number of successful extensions: 5 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: 480 Length adjustment: 32 Effective length of query: 369 Effective length of database: 448 Effective search space: 165312 Effective search space used: 165312 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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