Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Koxy:BWI76_RS11670 Length = 406 Score = 198 bits (503), Expect = 3e-55 Identities = 133/401 (33%), Positives = 193/401 (48%), Gaps = 46/401 (11%) Query: 21 GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80 G + +WD GK YIDF GGI V LGH +P +V+A+ QA + H N + P L L Sbjct: 28 GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTG-NGYTNEPVLRL 86 Query: 81 MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG------ATGKRAIIAFDGGFHGRTL 134 +QL + ++ NSGAEA E ALK+AR + K I+AF FHGRTL Sbjct: 87 AKQL---IDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTL 143 Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAF 194 T++ G+ A Y Q LP + H Y D+ L ++ A Sbjct: 144 FTVSAGGQPA-YSQDFAPLPPQIQHAIYNDLDSAKA---------------LIDDNTCAV 187 Query: 195 IFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDL 254 I EP+QGEGG + D F + LR CD L+I DE+Q+G GRTG+ +A+ G+ PDL Sbjct: 188 IVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDL 247 Query: 255 LLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATW 314 L AK++ GG P+GA++ + + + G G TY GNP++CA A E AT Sbjct: 248 LSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVA--------GEVFATI 299 Query: 315 GERQEQAIVSRYERWKASGLSPYIGR------LTGVGAMRGIEFANADGSPAPAQLAKVM 368 R+ V + +W L+ R + G+G + G + A A + Sbjct: 300 NTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKA----IS 355 Query: 369 EAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILE 409 A GL+++ +G +++R L I + + GLD E Sbjct: 356 NQAAEEGLMILIAG--ANVVRFAPALIISEDEVNSGLDRFE 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: 412 Number of extensions: 17 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