Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase
Query= SwissProt::Q88FI7 (416 letters) >FitnessBrowser__Dyella79:N515DRAFT_3308 Length = 411 Score = 202 bits (513), Expect = 2e-56 Identities = 140/406 (34%), Positives = 203/406 (50%), Gaps = 33/406 (8%) Query: 16 ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75 + L HG+ A VWDT+G+ Y+D GI V LGH +P +V+A+ QA +L H + N Sbjct: 27 VVLDHGKGARVWDTEGRDYVDLGAGIAVNALGHQDPDLVDALVTQARKLWHSS-NVFYTE 85 Query: 76 PYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG-------ATGKRAIIAFDGG 128 P L L E+L Q + L NSG EA E A+K+ R A +R I+ F G Sbjct: 86 PPLHLAEELVQ--ASGFAERVFLCNSGTEANEAAIKLVRKWAASKGRAPEQRVILTFRGS 143 Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188 FHGRTLA + + Y++ LPG +L + + ++ F A Sbjct: 144 FHGRTLAAVTATAQ-PKYQENYEPLPGGFRYLDFND----------VAGLEAAF----AQ 188 Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248 DVAA + EPVQGEGG L PAF + R CD L+++DEIQ G GRTG FA + Sbjct: 189 GDVAAVMLEPVQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTGTLFAHAQD 248 Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308 G+ PD++ LAK++ G P+GA++ ++ + G G T+ GNP++ A A +L ++ Sbjct: 249 GVTPDIVTLAKALGCGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALRKLAS 308 Query: 309 ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVM 368 L +Q QA+ R G + G G M G A A + +V+ Sbjct: 309 AELMANVAKQAQAL--RDGLAAIDGELKLFAEVRGRGLMLGAVLAEA----YKGRAGEVL 362 Query: 369 EAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414 + A A GLL++ +G ++R + PL I L EGL L LA+ Sbjct: 363 DHAAAHGLLVLQAGP--DVLRFVPPLNITDADLAEGLARLRAALAD 406 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: 435 Number of extensions: 23 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: 416 Length of database: 411 Length adjustment: 31 Effective length of query: 385 Effective length of database: 380 Effective search space: 146300 Effective search space used: 146300 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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