Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate PP_3544 PP_3544 Transcriptional regulator, GntR family
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__Putida:PP_3544 Length = 469 Score = 194 bits (494), Expect = 4e-54 Identities = 116/381 (30%), Positives = 202/381 (53%), Gaps = 10/381 (2%) Query: 34 VRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRL 93 V +L ++ + I+ P+PE FP++ ++ + + + G LR Sbjct: 95 VFSILDSIKDPNTIAFGSAFPSPELFPLQRLSRSLASASRSMDPRMVVTDLSPGNPQLRR 154 Query: 94 ALA-EWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKY 152 +A +M +P+ +++IT+G+ +AL+L + PGD+V +EAP + A LQ + Sbjct: 155 QIALRYMVGGLMLPME--ELLITNGALEALNLCLQAVTQPGDLVAIEAPAFYACLQVLER 212 Query: 153 YEPEFVQIPLDD-EGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRL 211 + + V+IP+ EGM + +L + L E VK V+ + FQNP G +M E +++ + Sbjct: 213 LKLKAVEIPVHPREGMDLGVLAQTL-----EMHPVKAVWCMTNFQNPVGASMPEAKKQAM 267 Query: 212 LELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAA 271 +EL + + ++ED+ Y EL YS + KP KA+D +G VM+ G+F+K LAPG+RIGW+AA Sbjct: 268 VELLARHQVPLIEDDVYAELYYSQQAPKPAKAFDTQGLVMHCGSFAKSLAPGYRIGWVAA 327 Query: 272 EPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEE 331 +K+E K LC + +Q Y++ G D H+ + + ++ ML A+ Sbjct: 328 -GRFAQKIERLKLMTSLCASMPAQAAIADYLQHGGYDRHLRKLRYALEGQQANMLAAIAR 386 Query: 332 FMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLN 391 P R ++P GG F+W+ LPE +D + A+A+G++ PG F R N +RLN Sbjct: 387 HFPAQTRVSQPSGGYFLWLELPEQMDALKLFHMALAQGISIAPGPIFSPTRRFGNCIRLN 446 Query: 392 FTYVPEEKIREGIKRLAETIK 412 + + + ++ L I+ Sbjct: 447 YGSPWHDGAEQAMETLGRIIR 467 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: 440 Number of extensions: 15 Number of successful extensions: 4 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: 469 Length adjustment: 32 Effective length of query: 385 Effective length of database: 437 Effective search space: 168245 Effective search space used: 168245 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