Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate GFF1728 HP15_1687 transcriptional regulator, GntR family with aminotransferase domain protein
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__Marino:GFF1728 Length = 480 Score = 161 bits (407), Expect = 4e-44 Identities = 117/378 (30%), Positives = 183/378 (48%), Gaps = 12/378 (3%) Query: 37 LLKLVESSDVISLAGGLPAPETFP--VEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLA 94 LL +++ + L L A E P V + I + + + A Y G LR Sbjct: 109 LLDIMDRNAAFDLLPKLHAGELPPGIVSLNRAIGRALRRQRGADFQYYDKPAGDLKLREQ 168 Query: 95 LAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYE 154 L + KR P++ ++ ITSG Q AL L GD+V VE+P + LQ + Sbjct: 169 LGLLLAKR-GWPVTPDELCITSGCQHALFLALMACCQRGDVVAVESPGFYGVLQLLEQLG 227 Query: 155 PEFVQIPLDD-EGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLE 213 + ++IP GM +D LEE L ++ P F P G MSE R+RL+ Sbjct: 228 LQVMEIPTSTASGMDMDALEEALGRWN-----IQACVVSPAFATPGGALMSEAPRRRLMA 282 Query: 214 LASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEP 273 LA +YD ++ED+ Y E +S P +KA D+ RV++ +FSK+L+ R+GWI+ Sbjct: 283 LAEKYDLAVIEDDIYAESGFSRVP-DTLKALDENNRVIHCSSFSKVLSRDLRLGWISGAR 341 Query: 274 HLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFM 333 R L + K L ++ + Q Y+E G L H+ + +RD +L +L + Sbjct: 342 WHQRILHL-KMVTQLASSRYLQQGVAAYMEEGELSAHLRRQRKVLSEQRDRLLASLLAW- 399 Query: 334 PEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLNFT 393 P VR T P+GG+ VW+ LP +DT + KA+ GV PG F A N +R++F+ Sbjct: 400 PVSVRVTAPQGGLAVWLELPATVDTLAVYPKALDAGVVITPGPLFSASGKYGNCLRISFS 459 Query: 394 YVPEEKIREGIKRLAETI 411 + +E+ + +L E + Sbjct: 460 HPWDERRIRALNQLPELL 477 Lambda K H 0.318 0.137 0.398 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: 417 Length of database: 480 Length adjustment: 33 Effective length of query: 384 Effective length of database: 447 Effective search space: 171648 Effective search space used: 171648 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