Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate RR42_RS26850 RR42_RS26850 hypothetical protein
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Cup4G11:RR42_RS26850 Length = 447 Score = 199 bits (507), Expect = 1e-55 Identities = 124/350 (35%), Positives = 186/350 (53%), Gaps = 24/350 (6%) Query: 70 AGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPL-HSQELLDPLRAM 128 AG LVD+ G+ +ID GG + +GH +P V+ A++ Q H+ + Sbjct: 18 AGKGIELVDSNGKHYIDASGGAAVSCLGHGHPRVIEAIKQQADSLAYAHTSFFTTEVSEE 77 Query: 129 LAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFT---FIATSGAFHGKSL 185 LA+TLA PG L + +F + G+E+VEAALKLA+ Y G+ FIA ++HG +L Sbjct: 78 LARTLAQAAPGDLNHVYFVSGGSEAVEAALKLARQYFVEIGQTQRRHFIARRQSYHGNTL 137 Query: 186 GALSATAKSTFRKPFMPLLPGFRHVP----FGNIEAMRTALNECKKTGDDVAAVILE--- 238 GAL+ + R+PF+PLL HV + + EA T ++ D++ A ILE Sbjct: 138 GALAIGGNAWRREPFLPLLVPAHHVAPCYAYRDQEAGETDQQYAQRLADELEAKILELGP 197 Query: 239 ----------PIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEH 288 + G + P YL VR +CD++G L+ILDE+ +GMGRTG +FACE Sbjct: 198 HSVAAFVAETVVGATAGAVPPVADYLRRVRAVCDKYGVLLILDEIMSGMGRTGYLFACEE 257 Query: 289 ENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDNP--FLHTTTFGGNPLACAAALAT 346 + V PDI+ +AK L G PIGA I++ ++ + F H T+ G+ ACAAALA Sbjct: 258 DGVVPDIVTIAKGLAAGYQPIGAMISSSRIYDAVVGGSGFFQHGHTYIGHATACAAALAV 317 Query: 347 INVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFV 396 + E L +G L R+ ++P+ V + RG+G+ + +EFV Sbjct: 318 QRTIAEDCLLENVLARGGQLRARLRETLGDHPN-VGDIRGRGLFVGVEFV 366 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: 519 Number of extensions: 29 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: 447 Length adjustment: 33 Effective length of query: 426 Effective length of database: 414 Effective search space: 176364 Effective search space used: 176364 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