Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_015931094.1 MNOD_RS21620 amidase
Query= curated2:Q72L58 (471 letters) >NCBI__GCF_000022085.1:WP_015931094.1 Length = 414 Score = 172 bits (435), Expect = 2e-47 Identities = 155/459 (33%), Positives = 224/459 (48%), Gaps = 58/459 (12%) Query: 5 EIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLNERLLEEAEAVDPGLPLAGLVVA 64 ++R R+ G ++P + + DP +GA + RL A D G PLAG+ V Sbjct: 6 DLRDRIGAGRLTPQGAVSLAREAIANRDPEVGAIV----RLDPAAPVPDEG-PLAGIAVG 60 Query: 65 VKDNIATRGLRTTAGSRLLENFVPPYEATAVARLKALGALVLGKTNLDEFGMGSSTEHSA 124 +KD I T L T GS L + P +A VARLK LGA+ L KT F TE Sbjct: 61 LKDIIDTADLPTEMGSPLYAGWRPRADAPVVARLKRLGAVPLAKTTTTAFAFLDPTE--- 117 Query: 125 FFPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFCGVYGLKPTYGR 184 T+NP + PGGSS GSAAA+AA + PLALG+ TGGSV +PAAFCGV G+KP++ Sbjct: 118 ---TRNPRNLAHTPGGSSAGSAAAVAAGMLPLALGTQTGGSVIRPAAFCGVVGVKPSFRL 174 Query: 185 VSRFGLIAYASSLDQIGPMARSVRDLALLMDAVAGPDPLDATSLDLPPRFQEALEGPLPP 244 + G+ ++ +LD +G A V D A + +A D ++DLP A + LP Sbjct: 175 LPTVGVKCFSWALDTVGLFAARVADAAHALALLA-----DRPAIDLP-----AGDPGLP- 223 Query: 245 LRLGVVREAL-AGNSPGVERALEEALKVFRELGLSVREVSWPSL-PQALAAYYILAPAEA 302 R+G++R+ A +P ALE A G VR++ P + +A A + ++ EA Sbjct: 224 -RIGLLRQDFCAPPAPEALAALERAAAAAERAGAQVRDLDLPPIFAEAFARHPVIQDFEA 282 Query: 303 SSNLA-RYDGTLYGRRAEGEEVEGMMEATRALFGLEVKRRVLVGTFVLSSGYYEAYYGRA 361 + LA YD + R A + ++ + + E Y+A A Sbjct: 283 AQALAWEYD---HHRNALPPLLRAQLDGAQRVGPAE----------------YDASRRIA 323 Query: 362 QAFRRRLKAEAQALFRE--VDLLLLPTTPHPAFPFGARRDPLAMYREDLYTVGANLTGLP 419 RR LK +F E VD++L + P PA P G A + L+T L G+P Sbjct: 324 HQARRSLK----DVFGEEGVDVILTLSAPGPA-PEGLASTGDARFNR-LWT----LMGVP 373 Query: 420 ALSFPAGFEGH-LPVGLQLLAPWGEDERLLRAALAFEEA 457 ++ P LP+G+Q++A +G+D R L AA E A Sbjct: 374 CVTVPVETTAEGLPLGVQVIARFGDDGRALAAARLIERA 412 Lambda K H 0.319 0.137 0.395 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: 533 Number of extensions: 35 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: 471 Length of database: 414 Length adjustment: 32 Effective length of query: 439 Effective length of database: 382 Effective search space: 167698 Effective search space used: 167698 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 (21.7 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