Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Dino:3608039 Length = 444 Score = 185 bits (469), Expect = 3e-51 Identities = 121/352 (34%), Positives = 183/352 (51%), Gaps = 24/352 (6%) Query: 70 AGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPL-HSQELLDPLRAM 128 AG+ ++D G+ ++D GG + +GH +P V +A+ Q+ K H+ + Sbjct: 18 AGAGCYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGFFTSEPAEV 77 Query: 129 LAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSL 185 L L A P ++ + + G+ESVEAALKLA+ + G + IA ++HG +L Sbjct: 78 LCDALIAAAPKGIEKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHGNTL 137 Query: 186 GALSATAKSTFRKPFMPLLP---------GFRHVPFGNIEAM--RTALN----ECKKTGD 230 GAL+A + R+ + PLL +RH G +A R A + E ++ G Sbjct: 138 GALAAGGNAWRREKYAPLLVETYHIDPCYAYRHQAVGESDAAYGRRAADALRTEIERLGP 197 Query: 231 D-VAAVILEPIQGE-GGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEH 288 + V A I EP+ G G + P PGY +R++CDE+G L+ILDEV GMGRTG +FACE Sbjct: 198 ETVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFACEQ 257 Query: 289 ENVQPDILCLAKALGGGVMPIGATIATEEVFSVLF--DNPFLHTTTFGGNPLACAAALAT 346 + + PDI+ +AK LG G PIGA +A+ ++ + F H T+ G+PLA AAA A Sbjct: 258 DGISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGSGSFQHGHTYHGHPLAAAAAGAV 317 Query: 347 INVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDN 398 + L AQ KG L ++ V + RG+G+ IE V++ Sbjct: 318 VETLRAPGTMAQVRAKGATLQSRLEAALGQHSH-VGDIRGRGLFRGIELVED 368 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: 489 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: 444 Length adjustment: 33 Effective length of query: 426 Effective length of database: 411 Effective search space: 175086 Effective search space used: 175086 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