Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_053937056.1 WG78_RS06780 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_001294205.1:WP_053937056.1 Length = 400 Score = 191 bits (486), Expect = 3e-53 Identities = 134/390 (34%), Positives = 201/390 (51%), Gaps = 25/390 (6%) Query: 71 GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130 G+ + + D G+E+ID GG + ++GH +P +V+A+ Q K S + LA Sbjct: 26 GAGSRVWDQAGKEYIDFGGGIAVNSLGHCHPELVAALTEQGNKLWHISNVFTNEPALALA 85 Query: 131 KTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPR---GKFTFIATSGAFHGKSLGA 187 KTL T + FFCNSG E+ EAALKLA+ + K ++ +FHG++ Sbjct: 86 KTLVEHTFAERV--FFCNSGAEANEAALKLARRASIEKYGERKNKVLSALNSFHGRTFFT 143 Query: 188 LSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVI 247 +S + + F P G H + ++ ++ ++ DD A VI+EPIQGEGGV Sbjct: 144 VSVGGQPKYSDGFGPKPAGIEHFKYNDLASLEALID------DDTACVIIEPIQGEGGVT 197 Query: 248 LPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVM 307 +L VR LCD+F AL+I DEVQ+G GRTG ++A V PDIL AK LGGG Sbjct: 198 PATQEFLQGVRALCDKFNALLIFDEVQSGNGRTGSLYAYMDFGVVPDILSTAKGLGGG-F 256 Query: 308 PIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLL 367 PIGA + TE+V L H TT+GGNPLA A A I+++ + + K + + Sbjct: 257 PIGAMLTTEKVAKHLVAG--THGTTYGGNPLATAVAGTAISIITRPETLSGVKAKSERIR 314 Query: 368 DGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIG-----YNFASEMFRQRVLVAGTLNNA 422 G + +A +YP +V E RG G+L+ ++ G N A+E + VLV Sbjct: 315 AGLQAIADKYP-VVAEIRGMGLLIGVQLKAEYAGRSRDVLNAAAE---EGVLVLAA--GP 368 Query: 423 KTIRIEPPLTLTIEQCELVIKAARKALAAM 452 +R P L ++ ++ + + KA A + Sbjct: 369 DVVRFAPSLVISDDEIDAGLARVEKAFARL 398 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: 417 Number of extensions: 21 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: 400 Length adjustment: 32 Effective length of query: 427 Effective length of database: 368 Effective search space: 157136 Effective search space used: 157136 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