Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate CCNA_00620 CCNA_00620 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Caulo:CCNA_00620 Length = 392 Score = 211 bits (537), Expect = 3e-59 Identities = 137/381 (35%), Positives = 204/381 (53%), Gaps = 24/381 (6%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQEL--LDPLRAMLAKTL 133 L D G++++D G + +GH +P +V A++ Q A H+ L L A+ K Sbjct: 23 LYDQDGRDYLDLAAGVAVNTLGHGDPRLVQALKTQ-ADILWHASNLYRLPAQEALATKLT 81 Query: 134 AALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGK---FTFIATSGAFHGKSLGALSA 190 A ++ FF NSG E+VEAA+K A+ +Q +G+ + + AFHG++L +SA Sbjct: 82 DATFADRV---FFANSGAEAVEAAIKTARRWQGAKGRPERYRVLTFGNAFHGRTLATISA 138 Query: 191 TAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPP 250 T + R+ F PL F PF +IE A+ AA+++EPIQGEGG+ Sbjct: 139 TDQMKVREGFTPLYDAFDTTPFNDIEGAARAITP------QTAAILVEPIQGEGGLTPAT 192 Query: 251 PGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIG 310 PG+L +R LCD+ L+ILDEVQTG+GRTG +FA E V+PDI+ +AK LGGG PIG Sbjct: 193 PGFLAGLRALCDQHDLLLILDEVQTGIGRTGHLFAHELYGVRPDIIAVAKGLGGG-FPIG 251 Query: 311 ATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGF 370 A +ATE+ S + P H +T+GGNPLACA A A ++ +L ++ ++ Sbjct: 252 ACLATEDAASGM--TPGSHGSTYGGNPLACAVASAVLDAVLAPGFLETVRERAALVDALL 309 Query: 371 RQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPP 430 +L R + DL A+G G++ ++ + F + AG A +R+ PP Sbjct: 310 ERLLRRHSDLFVRAQGHGLMRGLQVRASARDVVAHLRDFGVMTVAAG----ADVVRLLPP 365 Query: 431 LTLTIEQCELVIKAARKALAA 451 LTI + E+ AR AA Sbjct: 366 --LTISELEIAEAEARLLRAA 384 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: 386 Number of extensions: 17 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: 392 Length adjustment: 32 Effective length of query: 427 Effective length of database: 360 Effective search space: 153720 Effective search space used: 153720 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