Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 8499751 DvMF_0516 aminotransferase class-III (RefSeq)
Query= curated2:Q8ZV07 (383 letters) >FitnessBrowser__Miya:8499751 Length = 459 Score = 132 bits (331), Expect = 3e-35 Identities = 126/425 (29%), Positives = 198/425 (46%), Gaps = 66/425 (15%) Query: 15 IVKGFMQYVWDDKGQRYIDCNTNHGV--VFLGHANPKIVEAVKKQVEEIWAVPLNFATPA 72 +V+G + D G+ Y+D T+ GV V +G+ +I AV +Q++ A+P AT Sbjct: 38 VVEGEGLTLRDINGKEYLDA-TSGGVWCVNVGYGRERIARAVYEQMK---AMPYYAATAG 93 Query: 73 RERFIEEFSKLLPPKFGVV--FLQNTGTEAVEVAIKIAKKVTR------KPTIVAFTNSF 124 +IE KLL G+ +L N+G+EA E A K+ + + K I+ + Sbjct: 94 NIPYIEFAQKLLAHMPGLTRAYLSNSGSEANEKAYKMVRSLAHLSGNPAKKKILFRARDY 153 Query: 125 HGRTMGSLSITWNEKYKKAFEPL------YPHV-----RFGK------FNVPHEVDKLI- 166 HG T+G+LS T + K+ F PL +PH F K + V+++I Sbjct: 154 HGTTLGALSSTGQAERKEWFGPLVPGFVEFPHACCYRCAFNKTYPGCDIDCARAVERIIE 213 Query: 167 --GEDTCC-VVVEPIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWA 223 G +T ++VEPI GGV P E+ L + +R G LLI DEV G GRTG ++ Sbjct: 214 QEGPETVGGLIVEPITAGGGVIPPVAEYYTVLADICRRHGVLLIMDEVVCGMGRTGTMFG 273 Query: 224 FQKYGVEPDIFTAGKPVAGG-LPIGLAVAREDFGDVF--EPGEHG------STFAGNAVV 274 +Q YGV PDI T K VA +PI + E+ F +P + ST+ G A Sbjct: 274 YQHYGVTPDIVTMAKGVASAYMPISVTATTEEVFKAFLNDPADKMAYFRDISTYGGCAAG 333 Query: 275 MAAAAAASRLLREEDVPGRAERIGAELAKALGDTGSRLAV-RVKGMGLMLGLEL------ 327 +AA ++ EE + +G L L + G V V+G GL+ G+EL Sbjct: 334 CSAALENMAIIEEEKLLDNVNAMGDYLLAGLKELGDLPYVGDVRGKGLLCGIELVQDKAG 393 Query: 328 --RVKADQFIQPLLERGVMALTAG---------VNTLRFLPPYMISKEDVEVV----HAA 372 + + IQ + E A+ G N + P Y++++++++V+ AA Sbjct: 394 KKPMAEGKVIQVVGEMAANAVLVGRTNRSLPGFNNIINIAPAYVVTRDNIDVILRTLRAA 453 Query: 373 VTEVL 377 + +VL Sbjct: 454 LVKVL 458 Lambda K H 0.320 0.138 0.408 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: 401 Number of extensions: 22 Number of successful extensions: 2 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: 383 Length of database: 459 Length adjustment: 32 Effective length of query: 351 Effective length of database: 427 Effective search space: 149877 Effective search space used: 149877 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 Aug 03 2021. The underlying query database was built on Aug 03 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