Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate Dsui_3250 Dsui_3250 acetylornithine/succinylornithine aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__PS:Dsui_3250 Length = 390 Score = 187 bits (474), Expect = 6e-52 Identities = 143/410 (34%), Positives = 202/410 (49%), Gaps = 45/410 (10%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P+ SHG ++DTDGK Y+D + GI V LGH +P +V AI +QA R+ H + + Sbjct: 12 PVAFSHGEGNRIYDTDGKCYLDALSGIAVNTLGHNHPKLVNAIASQAARVLHTS-----N 66 Query: 75 GPYLALMEQLS-QFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRA-----IIAFDGG 128 + L E+L+ + +S NSG EA E A+K+AR ++ II + Sbjct: 67 LYRIPLQEELADRLAGLSRMEEVFFCNSGCEANEAAIKLARFFGHQKGVDAPVIIVMEKA 126 Query: 129 FHGRTLATLNLNGKVAPYKQRVGELP--GPVYHLPYPSADTGVTCEQALKAMDRLFSVEL 186 FHGRTLATL+ G K + G P +PY D A++A L Sbjct: 127 FHGRTLATLSATGN---RKAQAGFEPLVSGFVRVPYNDLD-------AIRAAAELNP--- 173 Query: 187 AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246 +V A + E VQGEGG DP F + LR CDE+ L++ DE+Q G GRTG F F Sbjct: 174 ---NVVAVLLEMVQGEGGIHVADPEFQRGLRSLCDEKDWLLMCDEVQCGMGRTGTWFGFQ 230 Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306 GI PD+ LAK + G+P+GA + + G G T+ GNP++CAAAL ++A + Sbjct: 231 HAGILPDVATLAKGLGSGVPIGACMTAGKAAGLFKPGNHGSTFGGNPLACAAALTTIACI 290 Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYIG--RLTGVGAMRGIEFANADGSPAPAQL 364 +E L Q +AI R + L+ G + G G M GIE P + Sbjct: 291 EEEKLRENAVAQGEAI----RRGLSEALAGVGGLVEIRGKGLMLGIEL----DRPCGELV 342 Query: 365 AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414 AK +EA GLL+ + A ++RLL LT A +E + L + E Sbjct: 343 AKGLEA----GLLI--NVTAEKVVRLLPALTFSAADTQELVQRLAALIKE 386 Lambda K H 0.320 0.137 0.402 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: 408 Number of extensions: 21 Number of successful extensions: 4 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: 416 Length of database: 390 Length adjustment: 31 Effective length of query: 385 Effective length of database: 359 Effective search space: 138215 Effective search space used: 138215 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