Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Keio:15866 Length = 406 Score = 194 bits (492), Expect = 5e-54 Identities = 130/398 (32%), Positives = 194/398 (48%), Gaps = 34/398 (8%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P G + +WD GK YIDF GGI V LGH +P + EA+ QA++ H N + Sbjct: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTG-NGYTN 80 Query: 75 GPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG------ATGKRAIIAFDGG 128 P L L ++L + ++ NSGAEA E ALK+AR + K I+AF Sbjct: 81 EPVLRLAKKL---IDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137 Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188 FHGRTL T++ G+ A Y Q LP + H Y ++ L Sbjct: 138 FHGRTLFTVSAGGQPA-YSQDFAPLPADIRHAAYNDINSASA---------------LID 181 Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248 + A I EP+QGEGG + AF Q LR C+ L+I DE+Q+G GRTG+ +A+ Sbjct: 182 DSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHY 241 Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308 G+ PDLL AK++ GG P+GA++ +E + G G TY GNP++ A A L + Sbjct: 242 GVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINT 301 Query: 309 ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVM 368 + +++ V R + + G+G + G NAD + Q+++ Sbjct: 302 PEMLNGVKQRHDWFVERLN--TINHRYGLFSEVRGLGLLIGC-VLNADYAGQAKQISQ-- 356 Query: 369 EAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLD 406 EAA+A ++L+ G +++R L + E + GLD Sbjct: 357 EAAKAGVMVLIAGG---NVVRFAPALNVSEEEVTTGLD 391 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: 428 Number of extensions: 14 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: 406 Length adjustment: 31 Effective length of query: 385 Effective length of database: 375 Effective search space: 144375 Effective search space used: 144375 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