Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF3456 PS417_17690 amidase
Query= curated2:Q6A8P5 (501 letters) >FitnessBrowser__WCS417:GFF3456 Length = 467 Score = 196 bits (498), Expect = 1e-54 Identities = 159/482 (32%), Positives = 224/482 (46%), Gaps = 43/482 (8%) Query: 1 MNELLTLTAAELGERIAARQISSEEVTQAHLDRISEVDGDIHAFLLVDHAGALDAARRID 60 M+E+ LTA +L + + +S +VT+ L RI + ++A+ VD GAL+AAR + Sbjct: 1 MSEIGQLTAVQLLQHFRDKTLSPVDVTEDALLRIERYNPVVNAYCHVDPEGALNAARASE 60 Query: 61 ARIADGEHLGPLAGVPLAVKDLFCTKGIATTASSQMLEGWIP-PYDSTIVTRCKDAGMVI 119 R +G+ G L GVP ++KDL T G+ T S+ P D+ + AG V+ Sbjct: 61 QRWLNGQPCGALDGVPASIKDLTLTVGMPTRKGSRTTSAEGPWDVDAPFTAFMRKAGAVL 120 Query: 120 LGKTNLDEFAMGSSTETSAFGPTHNPWDLERVPGGSGGGSAASLASFQAPLALGTDTGGS 179 LGKT EF T+ +G T NPWD GGS GG+ A+ A L G+D GGS Sbjct: 121 LGKTTTPEFGWKGVTDNPLYGITRNPWDTRTTAGGSSGGAGAAAALNLGVLHQGSDAGGS 180 Query: 180 IRQPGAVTGTVGIKPTYGSTSRYGVIAMASSLDTPGPCARTVLDAALLHQAIAGHDAMDQ 239 IR P A TGT GIKPT+G ++ AM + L GP R V D+ L+ Q IA DA D Sbjct: 181 IRIPCAFTGTFGIKPTFGYVPQWPASAM-TLLSHLGPMTRKVEDSVLMLQTIAQPDARD- 238 Query: 240 TTINQP--TPAVVEAARQTDVSGVRIGVVTELSGQVYDPQVEARFHEAVEMLIEAGAEVV 297 I P TP + TD++G+R+ DPQV +AV L++ GA V Sbjct: 239 GLIGAPRTTPWLTPG---TDLNGLRVAYSPNFGYVDVDPQVAKVVAQAVAGLVQLGAHVE 295 Query: 298 EVSCPNFDLALPAYYLIQPAEVSSNLARYDAMRYGLRVNDDGEHSAEQ--VMRATRGAGL 355 ++ P F P EV S L A R +ND + + + A RG L Sbjct: 296 QID-PGFS---------DPLEVFSTLWAAGAARLTRPMNDAQKQLLDPGLLRIAQRGERL 345 Query: 356 GAEAKRRIILGTYALSAGYYDAYYGSAQKVRTLIQRDFEKAWQMCDVLVSPATPTTAFRL 415 + + +A + R + + DVLVSP P TAF Sbjct: 346 SLDD-------------------FNAALEARAALVARMAAFHEHYDVLVSPMMPITAFDA 386 Query: 416 GERTADPMAMY---RSDLCTVPANMAGSPAGSFPIGLSETDGMPVGMQVMAPIMADDRIY 472 G + + T P N+ PA S P GL+ T+G+PVG+ V+ AD+++ Sbjct: 387 GHDVPPGSGLQEWTQWTPFTYPFNLTQQPAASVPCGLA-TNGLPVGLHVVGARFADEQVL 445 Query: 473 RV 474 RV Sbjct: 446 RV 447 Lambda K H 0.317 0.133 0.387 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: 564 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: 501 Length of database: 467 Length adjustment: 34 Effective length of query: 467 Effective length of database: 433 Effective search space: 202211 Effective search space used: 202211 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: 52 (24.6 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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