Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_027489558.1 LRK54_RS06590 acetylornithine/succinylornithine family transaminase
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_021560695.1:WP_027489558.1 Length = 408 Score = 213 bits (542), Expect = 8e-60 Identities = 146/406 (35%), Positives = 213/406 (52%), Gaps = 33/406 (8%) Query: 16 ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75 + L HG+ A VWDT+G+ Y+DF GI V LGH +P ++ A+ AQA +L H + N Sbjct: 25 LVLDHGKGARVWDTEGRDYVDFGAGIAVNALGHQDPDLLAALAAQAHKLWHSS-NVFYTE 83 Query: 76 PYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG-------ATGKRAIIAFDGG 128 P L L E+L + L NSGAEA E A+K+ R A +R I+ F+G Sbjct: 84 PPLRLAEELVH--ASGFAERVFLCNSGAEANEAAIKLVRKWAAAQGRAPERRVIVTFNGS 141 Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188 FHGRTLAT+ + A Y+Q LP +L + A+ A++ F A Sbjct: 142 FHGRTLATVTATAQ-AKYQQGYEPLPEGFRYLDFNDAE----------ALEATF----AA 186 Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248 DVAA + EPVQGEGG L P F + +R CD+ L+++DEIQ G GRTG FA Sbjct: 187 GDVAAVMLEPVQGEGGVLPAAPGFLKRVRELCDQHDALLVLDEIQCGMGRTGTLFAHVHD 246 Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308 + PD++ LAK++ GG P+GA++ ++ + G G T+ GNP++ A A +LA+++ Sbjct: 247 HVVPDIVTLAKALGGGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALAKLSS 306 Query: 309 ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVM 368 + ERQ + + R + + G G M G A+A A A V+ Sbjct: 307 PAVLMNVERQANDLRAGLAR--INHELQLFAEVRGRGLMIGAVLADAYKGKAGA----VL 360 Query: 369 EAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414 + A RGLLL+ +G ++R + PLTI E L +GL L L++ Sbjct: 361 DHAATRGLLLLQAGP--DVLRFVPPLTITDEELADGLARLHAALSD 404 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: 419 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: 408 Length adjustment: 31 Effective length of query: 385 Effective length of database: 377 Effective search space: 145145 Effective search space used: 145145 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 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