Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011951593.1 SWIT_RS03805 amidase
Query= curated2:Q2FQM9 (431 letters) >NCBI__GCF_000016765.1:WP_011951593.1 Length = 382 Score = 184 bits (467), Expect = 4e-51 Identities = 143/404 (35%), Positives = 194/404 (48%), Gaps = 52/404 (12%) Query: 30 SGVTVAVKDNISTKGIETTCASKILKGYIPPYDAH--VVTLLKNAGAAIVGKTNMDEFGM 87 +G TVAVKD I G T+ S+ L PP AH VV L GA IVGKTNM EF Sbjct: 28 AGPTVAVKDCIDIAGKRTSVGSEALSE-APPAAAHAAVVAALIAGGARIVGKTNMHEFAY 86 Query: 88 GTTTENSAYGPTLNPLDHQRVPGGSSGGSAAAVAAGLVDCAIGSDTGGSIRCPAAFCGIV 147 G T N G +NP +PGGSS GSAAAVAAGLV+ AIG+DTGGSIR PA CG+ Sbjct: 87 GVTGVNRWLGTPVNPNYPGLIPGGSSSGSAAAVAAGLVEIAIGTDTGGSIRMPATCCGVF 146 Query: 148 GLKPTYGRVSRFGLIAYANSLEQIGPMARDVQTLSNLYSVIAGHDSRDATSVDKPYKHNP 207 GLKP++GRVSR G I +SL+ +GP ARDV + ++I D T V P Sbjct: 147 GLKPSFGRVSREGCIPADSSLDCVGPFARDVAGIETAMALI------DPTFV-------P 193 Query: 208 VSDITGLKIGVPDEFFGEGVNPNVAEVVRQAIDTLESMGATAVPCTIPSMKYALSAYYVT 267 ++IG + + AE+ + L GA VP +P + A A Sbjct: 194 AGRPASVRIGWVE-------SSADAEIAEAVLAELRRSGADVVPVDLPGLGQAFEAGITI 246 Query: 268 CTSEASSNLARFDGVRYGPAVGTLKSWHDAYSEQRKAGFGKEVRRRIILGTFSLAAGYYG 327 +EA S ++ D + R G +VR R +LG ++A Sbjct: 247 MAAEAWS------------------TFGDLVEDPR---IGADVRAR-LLGASKVSAAQLA 284 Query: 328 RYYQKAQTARQMVRDDFERIFRDVDVIAGPTMPDIAFKLGEKSDPLQMYLSDILTVPANL 387 +A+ R ++ VD +A P +P + L + D +M L P N+ Sbjct: 285 ----EAEKVRTRFVAAVDQALAGVDALALPALPALPPALDDLGDAARMLRLTSLIRPFNV 340 Query: 388 AGVPALSVPCGKINSMPVGLQLIGRYFEDERIIDTAYAYEQGRA 431 +G PAL++P + P+ +QL+GR +DE + EQG A Sbjct: 341 SGHPALAIP---LAGRPIAIQLVGRRNDDETLCAVGARIEQGLA 381 Lambda K H 0.318 0.135 0.399 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: 421 Number of extensions: 24 Number of successful extensions: 5 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: 431 Length of database: 382 Length adjustment: 31 Effective length of query: 400 Effective length of database: 351 Effective search space: 140400 Effective search space used: 140400 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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