Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__MR1:200454 Length = 425 Score = 177 bits (449), Expect = 6e-49 Identities = 141/421 (33%), Positives = 210/421 (49%), Gaps = 44/421 (10%) Query: 47 NPGFLEYRKSVTAGGDYGAVE--WQAGSLNTLV-DTQGQEFIDCLGGFGIFNVGHRNPVV 103 N + R++ AGG G + + A + N V D +G+EFID GG + N GH +P V Sbjct: 5 NDSLMARRQAAVAGG-VGQIHPIFTARAENASVWDVEGREFIDFAGGIAVLNTGHLHPKV 63 Query: 104 VSAVQNQLAKQPLHSQELLDPLRAML--AKTLAALTPGKL-KYSFFCNSGTESVEAALKL 160 +AV QL + H+ ++ + + + L L PG K + SG+E+VE A+K+ Sbjct: 64 KAAVAAQL-EDFSHTCFMVLGYESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAVKV 122 Query: 161 AKAYQSPRGKFTFIATSGAFHGKSLGALSATAK-------------STFRKPFMPLLPGF 207 A+AY G F TSG +HG+++ AL+ T K + FR F L G Sbjct: 123 ARAYTKRAGVIAF--TSG-YHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGV 179 Query: 208 RHVPFGNIEAMRTALNECKKTGD--DVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFG 265 + +AM + K + D+AA+ILEP+QGEGG P ++ +R LCD G Sbjct: 180 -----SDDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAVSPAFMQRLRALCDREG 234 Query: 266 ALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDN 325 ++I DEVQTG GRTG FA E V DI AK++ GG P+ +V + Sbjct: 235 IMLIADEVQTGAGRTGTFFAMEQMGVSADITTFAKSIAGG-FPLSGITGRAQVMDAI--G 291 Query: 326 PFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEAR 385 P T+GGNPLACAAALA + V E+ L +A GD + + E+P + + R Sbjct: 292 PGGLGGTYGGNPLACAAALAVLEVFEEEKLLERANAIGDRIKSALNTMQVEHPQ-IADVR 350 Query: 386 GKGMLMAIEFV-DNEIGYNFASEMFRQR------VLVAGTLNNAKTIRIEPPLTLTIEQC 438 G G + AIE + D + + +++ + +L GT N +RI PLT++ Q Sbjct: 351 GLGAMNAIELMEDGKPAPQYCAQILAEARNRGLILLSCGTYGN--VLRILVPLTVSDTQL 408 Query: 439 E 439 + Sbjct: 409 D 409 Lambda K H 0.320 0.135 0.393 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: 417 Number of extensions: 17 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: 459 Length of database: 425 Length adjustment: 32 Effective length of query: 427 Effective length of database: 393 Effective search space: 167811 Effective search space used: 167811 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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