Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate AO356_25480 AO356_25480 amidase
Query= curated2:Q6MRL7 (490 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25480 Length = 485 Score = 175 bits (443), Expect = 4e-48 Identities = 152/495 (30%), Positives = 228/495 (46%), Gaps = 48/495 (9%) Query: 11 ISEAVNNRSISAKEVTLHFLKRIENLNPKLNAFTSLNPQAVQEAEAVDARIANGEDVGLL 70 ++E V + E+ ++R+E + P+LNA + ++A A ++ G LL Sbjct: 18 LAEWVRRGEVQPGELLETAIERLERVEPQLNAVAERLYDSARQA-ARTPQVGQG----LL 72 Query: 71 AGVPFGIKEMFC-TKGLTTTAGSKILENFVPPYDATAVARLKKSGIVVMGKLNQDEFAMG 129 AGVP IK++F G T GS+ L +F +++ V RL+++G VMG EF Sbjct: 73 AGVPTLIKDLFSPVHGAAMTNGSRALGDFRADFESEVVTRLRRAGCQVMGTSTSPEFGTS 132 Query: 130 SSNETSFHGVVKNPWDLERVPGGSSGGSAAAQASRLVAGTLGTDTGGSIRQPASFCGIVG 189 S E++ G +NPW E GGSSGG+AA A+R+V G D GGS+R PAS CG+ G Sbjct: 133 YSTESARFGATRNPWSSEHSAGGSSGGAAALVAARVVPFAHGNDGGGSLRVPASCCGVFG 192 Query: 190 VKPTYGRVSRYGIVAYA-SSLDQAGPMVSSVRDAALTLEVISGFDPQDSTTTQKQVPAWS 248 KP+ G + IV + + + SVRD+A L+ +G D Q ++ Sbjct: 193 FKPSRGLMPSGPIVGEGWAGMGTPHAITLSVRDSAALLDATAGMDLGAPYAAPVQALPYT 252 Query: 249 QNLKADVKGMKIGLMKEYMTGALDPDVQKTVENSVDTLKQLGAEIVEVSVP--MTAFAVP 306 ++AD K ++I L+++ P + V + + LG + V++P + F Sbjct: 253 MAVQADPKPLRIALVEQLGPWPTAPQSLQAVGEAARLCEALGHRVEPVNLPVGLLEFLDH 312 Query: 307 VYYLVAASEASSNLSRYDGVKYGYRAEFKNLSAVDLEEFYSQTRG---QAFGAEVKRRIM 363 V+ ++ AS SR+ VDL Q RG QA EV+ RI+ Sbjct: 313 VFTIIGAS------SRH---------------YVDL---LGQMRGFAVQAEELEVRTRII 348 Query: 364 LGTYCLSSGYYDAFYNKAGQVRRLIMEQYLEAFKKCDVILSPVTTAPAFKIGERVSDPLA 423 L SG A Y A + + Q + DVIL+PV T IGE + Sbjct: 349 LRDKGNVSG---AQYAAAVEWIHALGRQLAVFMQDYDVILTPVLTREPVLIGELDLQDVC 405 Query: 424 MYLNDI---------FTTSTNLAGLPGMSVPFGQSQSGLPIGIQLTAGHFEEQKMLNVAF 474 M L+ + FT N +G P MSVP S +GLP+G EE +L +A Sbjct: 406 MSLDQLIERYHSYSPFTALFNASGQPAMSVPLSWSANGLPMGAHFAGRFGEENTLLALAA 465 Query: 475 ALEGASLVKGKHPHV 489 LE A +G+ P V Sbjct: 466 QLERAQPWRGRVPAV 480 Lambda K H 0.316 0.132 0.372 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: 513 Number of extensions: 32 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 490 Length of database: 485 Length adjustment: 34 Effective length of query: 456 Effective length of database: 451 Effective search space: 205656 Effective search space used: 205656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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