Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Dsui_3250 Dsui_3250 acetylornithine/succinylornithine aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__PS:Dsui_3250 Length = 390 Score = 223 bits (567), Expect = 1e-62 Identities = 146/384 (38%), Positives = 214/384 (55%), Gaps = 24/384 (6%) Query: 66 VEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD-P 124 V + G N + DT G+ ++D L G + +GH +P +V+A+ +Q A+ LH+ L P Sbjct: 13 VAFSHGEGNRIYDTDGKCYLDALSGIAVNTLGHNHPKLVNAIASQAARV-LHTSNLYRIP 71 Query: 125 LRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFT--FIATSGAFHG 182 L+ LA LA L+ +++ FFCNSG E+ EAA+KLA+ + +G I AFHG Sbjct: 72 LQEELADRLAGLS--RMEEVFFCNSGCEANEAAIKLARFFGHQKGVDAPVIIVMEKAFHG 129 Query: 183 KSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQG 242 ++L LSAT + F PL+ GF VP+ +++A+R A + +V AV+LE +QG Sbjct: 130 RTLATLSATGNRKAQAGFEPLVSGFVRVPYNDLDAIRAAA----ELNPNVVAVLLEMVQG 185 Query: 243 EGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKAL 302 EGG+ + P + +R LCDE L++ DEVQ GMGRTG F +H + PD+ LAK L Sbjct: 186 EGGIHVADPEFQRGLRSLCDEKDWLLMCDEVQCGMGRTGTWFGFQHAGILPDVATLAKGL 245 Query: 303 GGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQK 362 G GV PIGA + + + P H +TFGGNPLACAAAL TI + E+ L A + Sbjct: 246 GSGV-PIGACMTAGKAAGLF--KPGNHGSTFGGNPLACAAALTTIACIEEEKLRENAVAQ 302 Query: 363 GDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA 422 G+ + G + LV E RGKG+++ IE +D G A + L AG L N Sbjct: 303 GEAIRRGLSEALAGVGGLV-EIRGKGLMLGIE-LDRPCGELVA------KGLEAGLLINV 354 Query: 423 ---KTIRIEPPLTLTIEQCELVIK 443 K +R+ P LT + + +++ Sbjct: 355 TAEKVVRLLPALTFSAADTQELVQ 378 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: 393 Number of extensions: 17 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: 390 Length adjustment: 32 Effective length of query: 427 Effective length of database: 358 Effective search space: 152866 Effective search space used: 152866 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: 50 (23.9 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