Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012049314.1 SWIT_RS15760 amidase
Query= curated2:A6TTJ8 (491 letters) >NCBI__GCF_000016765.1:WP_012049314.1 Length = 521 Score = 206 bits (523), Expect = 2e-57 Identities = 149/487 (30%), Positives = 237/487 (48%), Gaps = 32/487 (6%) Query: 2 KIEEMTIMDIRKGYVQKQFTVKDVVQGYIDRIKELDGKINAFITLCEESALMEAA-VLDE 60 +I T D+ + + ++V+ ++D I + +NA ++ E AL+ AA D Sbjct: 47 EIVTWTAADLAARIRSRAVSCREVMTAHLDWIDRANPALNAIVSRVERPALLAAADEADR 106 Query: 61 KLSRGEEIGLLGGIPVAIKDNMCTQGIKTSCASEMLADFIPPYDATIVKKLRAAGAIIIG 120 +++ G G + G+P A+KD T+GI+T+ S + AD +P D V++LRAAGAI+IG Sbjct: 107 EIAAGRHRGWMHGLPHAVKDLAATRGIRTTMGSPIFADNVPKADEIFVERLRAAGAILIG 166 Query: 121 KTNMDEFAMGSSTENSAFKVTKNPWDLTKVPGGSSGGSAAALAAGFAPLTIGSDTGGSIR 180 KTN+ EF +GS + N F VT+N +D ++ GGSSGG+AAALAA P+ GSD GS+R Sbjct: 167 KTNVPEFGLGSQSYNPVFGVTRNAYDPSRTAGGSSGGAAAALAARMVPVADGSDFAGSLR 226 Query: 181 QPAAFCGTVGLKPTYGLVSRFGL-IAFASSLDQIGPFTKTVKDCALSLQVMQGNDPLDST 239 PA + G +P+ G V F ++ GP +TV D AL L VM G D Sbjct: 227 NPAGWNNIFGFRPSAGRVPHGPTNELFVQNIGYEGPMARTVGDLALLLSVMAGYDARTPL 286 Query: 240 SIQQEPMDDYVKDLDKGVKGLKVGIPKEFFQEGLNIEISDSIKEAIKVLEQLGAVVEEFS 299 S+ +P + LD+ +KG+++G + + + D ++ LE G V+E S Sbjct: 287 SLDGDPA-VFAGPLDRDMKGVRIGWLGDLGGVPMAPGMLDLCLSGLRRLEAAGCVIEPVS 345 Query: 300 LPVTDSGLSAYYIISSAEASSNLARYDGVRYGHRAAVYEGIEEMMLN-SRSEGFGKEVKR 358 L + L ++ +R G A G+ + + +R + E Sbjct: 346 LDIDHDTLWKAFV--------------QLRQGFLAG---GLGPLYADPARRKLLKPEAVW 388 Query: 359 RIMLGTYVLSSGYYDAYYKKAMDFRKKTRNVFKKAFESYDVILTPTSPVLPFTIG----- 413 I G + + Y+A R + ++KAFE +D + P++ + PF Sbjct: 389 EIENGMKLSAVDLYNASV-----VRSRVYEAYRKAFERHDFLALPSAQLFPFDADLHWPK 443 Query: 414 EKTGDPLEMYLADIYTV-NVNIAGVPAISIPCGFSKEKLPIGLQLIGDHYSEKKLLQAAY 472 E G ++ Y + V ++ G PA+ +P GF E LP GLQL+G + +LQ Sbjct: 444 EIAGVAMDSYHRWMEIVAGPSLTGCPALCVPAGFGPEGLPSGLQLVGPSRQDLAVLQLGR 503 Query: 473 GLEQELG 479 EQ G Sbjct: 504 AYEQVAG 510 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: 498 Number of extensions: 25 Number of successful extensions: 4 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: 521 Length adjustment: 34 Effective length of query: 457 Effective length of database: 487 Effective search space: 222559 Effective search space used: 222559 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 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