Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate RR42_RS26160 RR42_RS26160 4-aminobutyrate aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Cup4G11:RR42_RS26160 Length = 424 Score = 189 bits (480), Expect = 2e-52 Identities = 142/402 (35%), Positives = 204/402 (50%), Gaps = 32/402 (7%) Query: 75 TLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM--LAKT 132 TL D +G+++ D G + N GHR+P V+ AV QL + H+ + P + LA+ Sbjct: 33 TLWDVEGRQYTDFACGIAVLNTGHRHPRVMQAVIAQLERFT-HTAYQIVPYESYVALAER 91 Query: 133 LAALTP-GKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSAT 191 + AL P LK + +G E+VE A+K+A+A+ G IA SG FHG++L ++ T Sbjct: 92 INALVPIDGLKKTALFTTGAEAVENAVKIARAHTGRPG---VIAFSGGFHGRTLLGMALT 148 Query: 192 AK-STFRKPFMPLLPGFRHVPFG------NIEAMRTALNECKKTGDD---VAAVILEPIQ 241 K + ++ F P H PF + E AL KT D VAA+I+EP+Q Sbjct: 149 GKVAPYKVGFGPFPSDIYHAPFPCDLHGVSTEQSIQALESLFKTDIDPQRVAAIIIEPVQ 208 Query: 242 GEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKA 301 GEGG P ++ +R LCD+ G L+I DEVQTG GRTGK+FA H V PD++ +AK+ Sbjct: 209 GEGGFHPAPVDFMQTLRALCDKHGILLIADEVQTGFGRTGKLFAMSHYPVAPDLITMAKS 268 Query: 302 LGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQ 361 L GG MP+ A + P T+ GNPLA AAA A I + ++ L +A Sbjct: 269 LAGG-MPLSAVCGRASIMDAPL--PGGLGGTYAGNPLAVAAAHAVIETIEQERLCERATA 325 Query: 362 KGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQR--------- 412 G L +Q ++ P + + RG G ++A+EF D G A R + Sbjct: 326 LGKQLKAALQQASQTCPG-IADIRGLGSMVAVEFHDPATGQPSAELAKRVQLRAMEAGLI 384 Query: 413 VLVAGTLNNAKTIRIEPPLTLTIEQCELVIKAARKALAAMRV 454 +L GT N TIR PLT+ Q + + K LA + V Sbjct: 385 LLTCGTYGN--TIRFLYPLTIPQAQFDAALVVLTKVLAGIAV 424 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: 416 Number of extensions: 22 Number of successful extensions: 5 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: 424 Length adjustment: 32 Effective length of query: 427 Effective length of database: 392 Effective search space: 167384 Effective search space used: 167384 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