Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_008507916.1 BIBO1_RS13055 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000182725.1:WP_008507916.1 Length = 403 Score = 221 bits (564), Expect = 3e-62 Identities = 136/395 (34%), Positives = 215/395 (54%), Gaps = 20/395 (5%) Query: 65 AVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD- 123 A+ ++ G L+ G+ +ID G + ++GH +P +V ++ Q A++ H + + Sbjct: 18 ALRFERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQ-AEKLWHLSNIYEI 76 Query: 124 PLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAF 180 P + L + L T FF NSG E++E A+K A+ YQ G +F I GAF Sbjct: 77 PAQEKLGRRLVENTFADKV--FFTNSGAEALECAIKTARRYQYVSGHPERFRIITFEGAF 134 Query: 181 HGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPI 240 HG++L ++A ++ + + F P + GF VPFG+ A+R A+ + A ++LEPI Sbjct: 135 HGRTLATIAAGGQAKYLEGFGPKVEGFDQVPFGDEAALRAAITP------ETAGILLEPI 188 Query: 241 QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK 300 QGEGG+ P +L VR++CDE G L++LDEVQTG+GRTGK FA E ++PDI+ +AK Sbjct: 189 QGEGGLRAFPEEFLRLVRQICDENGLLLLLDEVQTGVGRTGKFFAHEWAGIRPDIMAIAK 248 Query: 301 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE 360 +GGG PIGA +AT E + +H TT+GGNPL A A ++V+L + Sbjct: 249 GIGGG-FPIGACLATAEAAKGM--TAGMHGTTYGGNPLGMAVGNAVLDVVLADGFMENVQ 305 Query: 361 QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLN 420 ++ G L YP++V E RG+G+LM ++ V + + + VL G + Sbjct: 306 ATALVMKQGLASLVDRYPNVVSEIRGRGLLMGLKCVVPNT--SLIQALRDEHVLSVGAGD 363 Query: 421 NAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVS 455 N +R+ PPL T E+ +K A+ + ++ Sbjct: 364 N--VVRLLPPLITTPEEAREALKHIETAVERLSIA 396 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: 426 Number of extensions: 25 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: 403 Length adjustment: 32 Effective length of query: 427 Effective length of database: 371 Effective search space: 158417 Effective search space used: 158417 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 24 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