Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__PS:Dsui_0023 Length = 396 Score = 198 bits (503), Expect = 3e-55 Identities = 147/410 (35%), Positives = 211/410 (51%), Gaps = 51/410 (12%) Query: 16 ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHY--AFNAAP 73 + + GR + + D GKRY+DFV G V LGH +PA+VEA+ +QA +L + AF P Sbjct: 23 LVFAEGRGSWLVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGKLINPSPAFYNEP 82 Query: 74 HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG-----ATGKRAIIAFDGG 128 A + S F V + ++GAEA E A+K+AR G II F GG Sbjct: 83 SLKLAAGLAAHSCFDRVFF------ASTGAEANEGAIKLARKWGQKHKGGAHEIITFAGG 136 Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188 FHGRTLAT++ +GK ++PG +P A L +D + + L Sbjct: 137 FHGRTLATMSASGKPGWDTLFAPQVPG------FPKAQ--------LNDLDSVAA--LIN 180 Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248 E A + EP+QGEGG + F Q LR+ CD+RG+L+I+DE+Q+G GRTG+ FA Sbjct: 181 ERTVAIMLEPIQGEGGVVPASAEFLQLLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHA 240 Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308 GIEPD++ L K I GG+PL A++ KE + G GGTY+GNP+ A A L +T Sbjct: 241 GIEPDIMTLGKGIGGGVPLSALLA-KESVCCFEAGDQGGTYNGNPLMTAVGAAVLEVLTA 299 Query: 309 ENLATWGERQEQAIVSRYERWKASGLSPYIGRL-----TGVGAMRGIEFANADGSPAPAQ 363 A V+ + +GL RL G G +R + A+ G PA Sbjct: 300 PGFL--------AEVAAKGEYLGAGLQRLSDRLGLRGERGQGLLRALLLADERG-PA--- 347 Query: 364 LAKVMEAARARGLL-LMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 ++EAAR RG L+ + H++R + LT+ E +++ L LE+ L Sbjct: 348 ---IVEAARERGPEGLLLNAPRPHLLRFMPSLTVSREEIDQMLAWLEELL 394 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: 496 Number of extensions: 24 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: 416 Length of database: 396 Length adjustment: 31 Effective length of query: 385 Effective length of database: 365 Effective search space: 140525 Effective search space used: 140525 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