Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_009545287.1 CCE_RS16755 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
Query= curated2:A6TTJ8 (491 letters) >NCBI__GCF_000017845.1:WP_009545287.1 Length = 456 Score = 281 bits (718), Expect = 4e-80 Identities = 168/486 (34%), Positives = 265/486 (54%), Gaps = 36/486 (7%) Query: 1 MKIEEMTIMDIRKGYVQKQFTVKDVVQGYIDRIKELDGKINAFITLCEESALMEAAVLDE 60 M I + + + + K+ + +V+ + D I++ + +N F + + A+ EA +D+ Sbjct: 1 MNINSLDAIALSQKIKNKEISASEVITQFTDNIEQQNLTLNCFTAILKNQAVEEAKNIDQ 60 Query: 61 KLSRGEEIGLLGGIPVAIKDNMCTQGIKTSCASEMLADFIPPYD-ATIVKKLRAAGAIII 119 K+++GE IG+L G+P A+K+ +GI T S++ P + AT +KKL AAGAI++ Sbjct: 61 KIAKGETIGILAGVPFAVKNLFDIEGIITLAGSKINQKNTPAAENATAIKKLNAAGAILV 120 Query: 120 GKTNMDEFAMGSSTENSAFKVTKNPWDLTKVPGGSSGGSAAALAAGFAPLTIGSDTGGSI 179 G NMDE+A G TENS + T NP DL+++ GGSSGGSAAA+AA P T+GSDT GS+ Sbjct: 121 GALNMDEYAYGFVTENSHYGATPNPHDLSRISGGSSGGSAAAVAANLVPFTLGSDTNGSV 180 Query: 180 RQPAAFCGTVGLKPTYGLVSRFGLIAFASSLDQIGPFTKTVKDCALSLQVMQGNDPLDST 239 R PAA CG +GLKPTYG +SR G + F++SLD IG FT++V+D A V+QG D D Sbjct: 181 RVPAALCGVLGLKPTYGRLSRAGTVLFSNSLDHIGGFTRSVRDMAAIFDVLQGEDKTDPV 240 Query: 240 SIQQEPMDDYVKDLDKGVKGLKVGIPKEFFQEGLNIEISDSIKEAIKVLEQLGAVVEEFS 299 P + K L+ + LK+ + E+FQ+G E +++ K+L + E + Sbjct: 241 CTSLAPQLCFDK-LNGDISRLKIAVAGEYFQKGAETEALKAVETVAKILN----IKETIN 295 Query: 300 LPVTDSGLSAYYIISSAEASSNLARYDGVRYGHRAAVYEGIEEMMLNSRSEGFGKEVKRR 359 +P +A YII++ E S+ L R + F + R Sbjct: 296 IPEAHRARAAAYIITACEGSN-------------------FHIKNLRLRPQDFDTATRDR 336 Query: 360 IMLGTYVLSSGYYDAYYKKAMDFRKKTRNVFKKAFESYDVILTPTSPVLPFTIGEKT--- 416 + G ++ ++ +Y +A FR+ R+ K+ F+ DVI+ PT+P + +G++T Sbjct: 337 FLAGAFIPNT-----WYIQAQRFRRWYRDQVKQIFQKVDVIIAPTTPCVATPLGQETMNI 391 Query: 417 --GDPLEMYLADIYTVNVNIAGVPAISIPCGFSKEKLPIGLQLIGDHYSEKKLLQAAYGL 474 + L +T ++ G+P +S P KLP+G+QLI Y E K+LQ A L Sbjct: 392 NGEEILIRPNLGRFTQPLSFIGLPVLSFPI-LRPNKLPLGVQLIAAPYQELKILQVAAFL 450 Query: 475 EQELGI 480 E++L I Sbjct: 451 EEKLNI 456 Lambda K H 0.317 0.136 0.382 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: 506 Number of extensions: 22 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: 491 Length of database: 456 Length adjustment: 33 Effective length of query: 458 Effective length of database: 423 Effective search space: 193734 Effective search space used: 193734 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: 51 (24.3 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