Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate SM_b21186 SM_b21186 4-aminobutyrate aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Smeli:SM_b21186 Length = 422 Score = 192 bits (487), Expect = 2e-53 Identities = 126/349 (36%), Positives = 187/349 (53%), Gaps = 23/349 (6%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLR--AMLAKTLAA 135 D +G +ID G + N GHR+P V++AV+ QL + H+ + P LA+ L A Sbjct: 34 DKEGNRYIDFAAGIAVVNTGHRHPKVIAAVKAQLDRFT-HTCHQVVPYENYVHLAERLNA 92 Query: 136 LTPGKL-KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKS 194 + PG K + F +G E+VE A+K+A+A G+ +A G FHG++ ++ T K Sbjct: 93 IVPGDFAKKTIFVTTGAEAVENAVKIARA---ATGRQAVVAFGGGFHGRTFMGMALTGKV 149 Query: 195 TFRKPFMPLLPG-FRHVPFG------NIEAMRTALNECKKTGDD---VAAVILEPIQGEG 244 K +P H PF +E +AL + D VAA+I+EP+QGEG Sbjct: 150 VPYKVGFGAMPADVFHAPFPIELHGVTVEQSLSALKKLFAADVDPARVAAIIIEPVQGEG 209 Query: 245 GVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGG 304 G P ++ A+R++CD+ G L+I DEVQTG RTGK+FA EH V PD+ +AK+L G Sbjct: 210 GFYPVPTAFMKALREVCDQHGILLIADEVQTGFARTGKLFAMEHHGVAPDLTTMAKSLAG 269 Query: 305 GVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGD 364 G P+ A E+ P T+GGNPL AAA A ++V+ E+NL +A Q G+ Sbjct: 270 G-FPLAAVTGRAEIMDA--PGPGGLGGTYGGNPLGIAAAHAVLDVIAEENLCERANQLGN 326 Query: 365 MLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRV 413 L + + P++V + RG G + A+EF N++ N S F +V Sbjct: 327 RLKQRLAAIREKAPEIV-DIRGPGFMNAVEF--NDVRTNLPSAEFANKV 372 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: 446 Number of extensions: 17 Number of successful extensions: 6 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: 422 Length adjustment: 32 Effective length of query: 427 Effective length of database: 390 Effective search space: 166530 Effective search space used: 166530 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