Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_010961322.1 MCA_RS10180 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000008325.1:WP_010961322.1 Length = 391 Score = 248 bits (634), Expect = 2e-70 Identities = 151/370 (40%), Positives = 215/370 (58%), Gaps = 18/370 (4%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAA 135 L DT+G+ ++D + G + ++GH +P V A+ +Q + S L+ LAK L Sbjct: 24 LFDTEGKRYLDAVSGVAVCSLGHAHPAVAKALCDQAGRLVHCSNLYRIGLQEDLAKQLCD 83 Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFT--FIATSGAFHGKSLGALSATAK 193 L+ + +FFCNSG E+ EAALK+A+ Y RG T + G+FHG++L LSAT Sbjct: 84 LSG--MDNAFFCNSGAEANEAALKIARRYGHHRGIDTPKIVVMEGSFHGRTLATLSATGN 141 Query: 194 STFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGY 253 ++ F PL+ GF +P+G+ EA+ DV AV++EP+QGEGGV +PP Y Sbjct: 142 PKVQEGFAPLVGGFVRLPYGDAEAVAAV------DDPDVVAVLVEPVQGEGGVRIPPDDY 195 Query: 254 LTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATI 313 L ++ LC+ G L++LDEVQTGMGRTG+MF +H V PD++ LAKALG GV PIGA + Sbjct: 196 LARLKSLCERRGWLLMLDEVQTGMGRTGRMFGHQHTGVTPDVMALAKALGNGV-PIGACL 254 Query: 314 ATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQL 373 A +L H +TFGGNPLACAAALA I+ L Q+L +AE G LLDGFR Sbjct: 255 ARGVAAEMLTAGK--HGSTFGGNPLACAAALAVIDTLTRQSLAQRAEILGQRLLDGFRTR 312 Query: 374 AREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTL 433 P ++ E RG G+++ +E Q +L+ T +T+R+ PPL L Sbjct: 313 LSGRPGVI-EIRGLGLMIGLEL--ERPCTRLVGMALEQGLLINVTAE--RTVRLLPPLIL 367 Query: 434 TIEQCELVIK 443 T Q + +++ Sbjct: 368 TDAQADDLVE 377 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: 425 Number of extensions: 14 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: 391 Length adjustment: 32 Effective length of query: 427 Effective length of database: 359 Effective search space: 153293 Effective search space used: 153293 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