Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 207560 DVU2086 transcriptional regulator, GntR family
Query= BRENDA::A0A060PQX5 (417 letters) >MicrobesOnline__882:207560 Length = 480 Score = 150 bits (379), Expect = 8e-41 Identities = 112/372 (30%), Positives = 178/372 (47%), Gaps = 10/372 (2%) Query: 44 SDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLALAEWMRKRY 103 S V+S G+PA + FP E A + V AL+Y G LR A+A ++R+ Sbjct: 106 SGVVSFRSGIPALDVFPREEWARTYQRVCAALPDDALRYSAPAGVWALREAIAGYLRRTR 165 Query: 104 DIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQIPLD 163 I +MITSG+ Q L ++ R+ G +V+ E P + + + +P+D Sbjct: 166 GIRCHAERVMITSGATQGLRIMSRLLQRSGGVVLAEDPAHAGLREVLEVTGLRVEGVPVD 225 Query: 164 DEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIV 223 D GM +L +E + G V VY P+ Q P G + +RR+ L+ A E + LIV Sbjct: 226 DRGMDTGML-PSAEEARRAG--VAFVYVTPSHQYPLGGILPVQRRQALVRFAREAECLIV 282 Query: 224 EDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAK 283 ED+ GE R+ G PV + E V+YLG+FSK+LAP R+G+ L+ K Sbjct: 283 EDDYDGEFRHEGSPVGTLHELAPES-VVYLGSFSKVLAPALRLGFAILPARLLAAWHREK 341 Query: 284 QSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPE 343 D+ T+ SQ ++ G L+ HI + + Y+ RR ++K+L + V Sbjct: 342 LYSDVHTDALSQHALASFIGSGALERHIWRMKKLYRRRRAFLVKSLMRHFGDAVGIRGHA 401 Query: 344 GGMFVWVTLPEGI--DTKLMLEKAVAKGVAYVPGEAFFAHR--DVKNTMRLNFTYVPEEK 399 G+ + V G+ D K+M E A GV P A+ D N + L + ++ EE Sbjct: 402 TGLHL-VAAFTGVRFDDKVMSELA-RGGVEATPVHAYALQHGDDHVNELILGYAHLSEEA 459 Query: 400 IREGIKRLAETI 411 + +G++ L + + Sbjct: 460 MEQGVRLLKQVL 471 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: 453 Number of extensions: 21 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: 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 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