Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate GFF1690 HP15_1649 transcriptional regulator, GntR family with aminotransferase domain protein
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__Marino:GFF1690 Length = 466 Score = 134 bits (336), Expect = 7e-36 Identities = 115/423 (27%), Positives = 188/423 (44%), Gaps = 52/423 (12%) Query: 25 KALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGT 84 +ALG+ + R +V + + G P P+ ++++ ++++ + AA L Sbjct: 55 EALGLIEARERSGFFVVPPQNKFEVPGQAPTPDEPKPVSVSQVFQDIMTRSAAFDLLPAC 114 Query: 85 TK-----GFTPLRLALAEWMRKR------YDIPISKV--------------------DIM 113 + G L ++ +R++ YD P D Sbjct: 115 NRDEPPPGIIQLNRSIGRALRRQSTRFQYYDEPAGDQELRNQIALRAARRGWIAQADDFC 174 Query: 114 ITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQIPLDDE-GMRVDLL 172 ITSG QQ+L L GD+V VE P + LQ + + ++IP E GM V L Sbjct: 175 ITSGCQQSLFLALMAVCKSGDVVAVETPGFYGVLQLLEQLQLRVIEIPASPESGMNVSAL 234 Query: 173 EEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGELR 232 E+ L+ + VK P F P G M + R+ LL LA +D I+ED+ Y E Sbjct: 235 EDVLKVWD-----VKACVVSPAFATPTGSVMPTEARRGLLALADRHDVAIIEDDIYAESG 289 Query: 233 YSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAE--PHLIRKLEIAKQSVDLCT 290 + P +KA D RV++ +FSK+L+ R+GW++ I KL++ Q L + Sbjct: 290 WLNVP-DTLKAIDTSARVIHCSSFSKVLSRDLRLGWVSGGRWHDEILKLKLTSQ---LAS 345 Query: 291 NPFSQV-IAWKYVEGGH---LDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGM 346 + F Q +A EGG+ L H ++ + RRD +L+ L + +R T P GG+ Sbjct: 346 SRFLQEGVAGFIAEGGYASFLRRHRQDL----RRRRDQLLELLSGW-NVSLRVTTPHGGL 400 Query: 347 FVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKR 406 +WV L E +DT + +A+ +G+ PG F N +R++F + +KR Sbjct: 401 ALWVELQEDVDTLRLYGRALQEGIVITPGNLFSVSGKFSNCLRISFAHPWNAARVSALKR 460 Query: 407 LAE 409 L E Sbjct: 461 LPE 463 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: 462 Number of extensions: 33 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 417 Length of database: 466 Length adjustment: 32 Effective length of query: 385 Effective length of database: 434 Effective search space: 167090 Effective search space used: 167090 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