Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate Synpcc7942_0031 Synpcc7942_0031 aminotransferase
Query= curated2:Q8ZV07 (383 letters) >FitnessBrowser__SynE:Synpcc7942_0031 Length = 424 Score = 161 bits (408), Expect = 3e-44 Identities = 129/394 (32%), Positives = 193/394 (48%), Gaps = 52/394 (13%) Query: 28 GQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAVPL-NFATPARERFIEEFSKLLPP 86 G+ IDC ++ V GHA+ +IVEA+ +Q + V F+ ER E K+LP Sbjct: 36 GRELIDCISSWWVNLHGHAHLRIVEAIAQQAATLEHVIFAGFSHEPAERLAMELCKILPE 95 Query: 87 KFGVVFLQNTGTEAVEVAIKIAKKVTR-----KPTIVAFTNSFHGRTMGSLSITWNEKYK 141 K VF + G+ AVEVA+K+A + + I+AF ++HG T G++S+ + Sbjct: 96 KLTRVFFSDNGSTAVEVALKMALQYWHNLDQPRSRILAFDGAYHGDTFGAMSVGERSLFN 155 Query: 142 KAFEPL--------YPHVRFGKFNVPHEV--------DKLIGEDTCCVVVEP-IQGEGGV 184 FE L YP +G V + L D V++EP +QG GG+ Sbjct: 156 APFEKLLFSVEFLPYPETWWGDETVEAKEAAAIAAVEQALAAGDVAAVIIEPLVQGAGGM 215 Query: 185 NPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKYGVEPDIFTAGKPVAGG- 243 A P+FL+ L Q G+LLI DEV TGFGRTGA +A Q+ G++PD+ K + GG Sbjct: 216 RMARPQFLQQLAARVQAAGSLLIADEVMTGFGRTGAWFACQRAGIQPDLICLSKGLTGGF 275 Query: 244 LPIGLAVAREDFGDVFEPGE------HGSTFAGNAVVMAAAAAASRLLREED--VPG--R 293 LP+ + VA E D F G HG ++ N + AAA A+ LL + + V G Sbjct: 276 LPLSITVATEVIYDTFCSGNPDHTFYHGHSYTANPLGCAAAIASLELLLDSEAIVQGLED 335 Query: 294 AERIGAE-LAKALGDTGSRLAVRVKGMGLM---------LGLELRVKADQFIQPLLERGV 343 A G E LA+ T RL + L+ +GL +R Q + RG+ Sbjct: 336 AHLPGLELLAQHPKVTRPRLTGGIAACDLVSDRGGYLDPIGLRVR-------QAAIARGL 388 Query: 344 MALTAGVNTLRFLPPYMISKEDVEVVHAAVTEVL 377 + G N L LPPY ++ +++ ++AA+ ++L Sbjct: 389 LLRPLG-NVLYLLPPYCLTPTELQDIYAAIADLL 421 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: 394 Number of extensions: 23 Number of successful extensions: 6 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: 424 Length adjustment: 31 Effective length of query: 352 Effective length of database: 393 Effective search space: 138336 Effective search space used: 138336 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