Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate AO356_24295 AO356_24295 2,4-diaminobutyrate 4-aminotransferase
Query= curated2:Q8ZV07 (383 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24295 Length = 457 Score = 204 bits (520), Expect = 3e-57 Identities = 129/400 (32%), Positives = 208/400 (52%), Gaps = 57/400 (14%) Query: 22 YVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAVP---LNFATPARERFIE 78 YV D +GQ ++DC G + LGH +P I+EA+ + + VP L+ TP ++ F++ Sbjct: 46 YVQDSRGQVFVDCLAGAGTLALGHNHPVIIEAITQVMAA--GVPMHTLDLMTPVKDAFVQ 103 Query: 79 EFSKLLPPKFG----VVFLQNTGTEAVEVAIKIAKKVTRKPTIVAFTNSFHGRTMGSLSI 134 E LP +F + F +G +AVE A+K+ + T + +++AF ++HG T+G+L+I Sbjct: 104 EIFACLPSEFARHARIQFCGPSGADAVEAALKLTRTATGRHSVLAFEGAYHGMTLGTLAI 163 Query: 135 TWNEKYKKAFEPLYPHVRFGKFNVPHE-------------------VDKLIGEDT----- 170 + N K A L P V+ + PH+ ++ L+ + Sbjct: 164 SGNLSPKNALGALMPGVQ--RLPFPHDYRCPFGVAGDQAVTLNVRYLEHLLNDPESGVTA 221 Query: 171 -CCVVVEPIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKYGV 229 +++EPIQGEGGV A +L+ LR Q G LI DE+Q G R+G ++ F++ G+ Sbjct: 222 PAAMILEPIQGEGGVIAAPDRWLQELRRLTQAHGIPLIVDEIQCGIARSGRMFGFEQSGI 281 Query: 230 EPDIFTAGKPVAGGLPIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASRLLREED 289 PD+ T K + GGLP+ + V E DV++PG H TF GN + MAA A R +R++ Sbjct: 282 TPDVITLSKAIGGGLPLSVMVYHESL-DVWQPGAHAGTFRGNQLAMAAGTATLRFIRDQG 340 Query: 290 VPGRAERIGAELAKALGDTGSRL--AVRVKGMGLMLGLEL----------------RVKA 331 + AE +GA L K L + V+G GLMLG+E+ +A Sbjct: 341 LVQHAETVGAHLQKQLQALQNEFDWIGDVRGRGLMLGMEIVDPQGTPDVQGHPPVDTARA 400 Query: 332 DQFIQPLLERGVMALTAGVN--TLRFLPPYMISKEDVEVV 369 F Q L+ G++ G + T+RFLPP +I++++++ V Sbjct: 401 KAFQQACLKHGLIVELGGRHGATVRFLPPLIITEQEIDFV 440 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: 403 Number of extensions: 21 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: 457 Length adjustment: 32 Effective length of query: 351 Effective length of database: 425 Effective search space: 149175 Effective search space used: 149175 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