Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Marino:GFF3766 Length = 425 Score = 184 bits (468), Expect = 4e-51 Identities = 121/339 (35%), Positives = 185/339 (54%), Gaps = 25/339 (7%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM--LAKTL 133 L D G+ ID GG G+ N+GHR+P VV AV+ QL K +H+ + + P LA+ L Sbjct: 34 LWDADGKRMIDFAGGIGVLNIGHRHPKVVEAVKAQLDKL-MHTCQTVMPYEGYVKLAEKL 92 Query: 134 AALTP--GKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSAT 191 + + P G K NSG E++E A+K+A+A GK I G +HG++ ++ Sbjct: 93 SGVVPVRGHAKV-MLANSGAEALENAMKIARA---ATGKTNVICFDGGYHGRTFYTMAMN 148 Query: 192 AKST-FRKPFMPLLPGFRH-----VPFGNI---EAMRTALNECK--KTGDDVAAVILEPI 240 K+ ++ F P+ PG + VP+ + EA+R K + AA+++EP+ Sbjct: 149 GKAAPYQTDFGPM-PGTVYRAPYPVPYHGVSEDEALRGLKMAMKADSPAHNTAAIVIEPV 207 Query: 241 QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK 300 GEGG P +L +RK+CDE LMI DEVQ+G GRTGKMFA EH V+PD++ +AK Sbjct: 208 LGEGGFYAAPTSFLKEIRKICDENDILMIADEVQSGFGRTGKMFAIEHSGVEPDLMTMAK 267 Query: 301 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE 360 ++ G MPI A + T++ P T+ G+P ACAAALA +V E+++ +++ Sbjct: 268 SMADG-MPISAIVGTDKYMDA--SGPNSLGGTYTGSPTACAAALAVFDVFKEEDILGKSQ 324 Query: 361 QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNE 399 G+ L F Q ++ V R G + A E V+++ Sbjct: 325 ALGEKLKQRFSQWQEQFAH-VDNVRNLGPMAAFELVESK 362 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: 390 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: 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