Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate AO356_02850 AO356_02850 2,4-diaminobutyrate 4-aminotransferase
Query= curated2:Q8ZV07 (383 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_02850 Length = 470 Score = 203 bits (517), Expect = 7e-57 Identities = 138/434 (31%), Positives = 222/434 (51%), Gaps = 74/434 (17%) Query: 7 YYREYGIRIVKGFMQYVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQV-EEIWAVP 65 Y R + + + YV D +G+ +IDC G + LGH +P +++A+++ + +E+ Sbjct: 45 YPRRIPLALKRAKGLYVEDVEGRTFIDCLAGAGTLALGHNHPVVIDAIQQVLADELPLHT 104 Query: 66 LNFATPARERFIEEFSKLLPPKFG----VVFLQNTGTEAVEVAIKIAKKVTRKPTIVAFT 121 L+ TP ++RF+++ LLP + + F TGT+AVE A+K+ + T + T+++F Sbjct: 105 LDLTTPVKDRFVQDLFGLLPVELAAEAKIQFCGPTGTDAVEAALKLVRTATGRSTVLSFQ 164 Query: 122 NSFHGRTMGSLSITWNEKYKKAFEPL---------YPH---VRFGKFNVP------HEVD 163 +HG + G+LS+ + KK L YP+ FG V H ++ Sbjct: 165 GGYHGMSQGALSLMGSLGPKKPLGALLSSGVQFMPYPYNYRCPFGLGGVEGVKANLHYLE 224 Query: 164 KLIGEDTC------CVVVEPIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGR 217 L+ + V+VE +QGEGGV PA ++L+ LR ++ G LI DE+Q+GFGR Sbjct: 225 NLLNDPEAGVQLPAAVIVEVVQGEGGVIPADLDWLRGLRRITEQAGVALIVDEIQSGFGR 284 Query: 218 TGAVWAFQKYGVEPDIFTAGKPVAGGLPIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAA 277 TG ++AF+ G+ PD+ K + G LP+ + V R D+ D + PG H TF GN + MAA Sbjct: 285 TGKMFAFEHAGIIPDVVVLSKAIGGSLPLAVVVYR-DWLDTWLPGAHAGTFRGNQMAMAA 343 Query: 278 AAAASRLLREEDVPGRAERIGAELAK----------ALGDTGSRLAVRVKGMGLMLGLEL 327 +A R LRE D+P A +G L++ LGD ++G GLMLG+EL Sbjct: 344 GSAVMRYLREHDLPAHAAAMGERLSEHLHILQRDYPQLGD--------IRGRGLMLGVEL 395 Query: 328 ----------------RVKADQFIQPLLERGVMALTAG--VNTLRFLPPYMISKEDVE-- 367 A + + L+RG++ G +RFLPP +I++ +++ Sbjct: 396 VDPAGKPDAQGHPPVHAQLAPRLQRECLKRGLILELGGRQGGVVRFLPPLIITRAEIDRV 455 Query: 368 ------VVHAAVTE 375 +HAAVTE Sbjct: 456 AEIFGRALHAAVTE 469 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: 439 Number of extensions: 22 Number of successful extensions: 7 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: 470 Length adjustment: 32 Effective length of query: 351 Effective length of database: 438 Effective search space: 153738 Effective search space used: 153738 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: 51 (24.3 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