Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_046008778.1 OLEAN_RS07920 hypothetical protein
Query= curated2:Q1J0C2 (483 letters) >NCBI__GCF_000967895.1:WP_046008778.1 Length = 491 Score = 151 bits (382), Expect = 4e-41 Identities = 145/486 (29%), Positives = 215/486 (44%), Gaps = 50/486 (10%) Query: 1 MSECSTATDLARAVQARETTPQALLEAARRRAEAARD-LNALISLNDRADEQAARVQVRL 59 M +C A+ LA+ + +E + + +AA RAE LNA+++ Q + L Sbjct: 14 MGDCD-ASGLAKRIANKEVSIAEVTDAAIARAEQINPKLNAIVTDCFDLARQNTK-NATL 71 Query: 60 DAGETLPLAGVPIVVKDNLNVIGTRTTCGSRILANYVSPYDATAVERLTGAGAVIIGKAN 119 +G T GVP VKDN +V G T GSR + N + + +++ G I+GK+ Sbjct: 72 KSGSTAAFEGVPTFVKDNTDVKGLPTLFGSRAVLNRPAKRNGEFTDQMLSTGLTILGKST 131 Query: 120 MDEFAMGSSTESSAWGPTLNPWDRERVPGGSSGGSAVAVAANLTPVALGSDTGGSVRQPA 179 + EF + +TES A G T NPW+ GGSSGG+A VA+ P+A G+D GGS+R PA Sbjct: 132 LPEFGIPPTTESLAQGATCNPWNTNHSSGGSSGGAAALVASGAVPIAHGNDGGGSIRIPA 191 Query: 180 AFTGIYGLKPTYGR-VSRYGLVAYASSLDQIGPFARSAADLALLMNVLAGHDPRDATSLD 238 A G+ GLKPT R V+ +G A ++ G RS D AL M H R+ + Sbjct: 192 AACGLVGLKPTRNRLVNMHGTEALPINVGHEGVITRSVRDTALFMAEAEKHF-RNTKLVS 250 Query: 239 APPAFRPGTPDDLQGLRVGVIREALEGNT--PGVEAALNATLDALRGAGATVREVSVPSV 296 PG + LR+G++ AL+G P V+ LN T G +V EV+ P Sbjct: 251 LGHIQAPGK----KRLRIGLVTGALKGINVQPDVQRTLNETGLLCESLGHSVEEVAFPFA 306 Query: 297 QHAIAAYYLIATPEASSNLARYDGMVYGERVSAPDAVSSMTLTREQGFGREVKRRIMLGT 356 IA +L ++ R+ V G GF ++ Sbjct: 307 DQ-IADDFLTYYSFLFFSMHRFGKFVIG-----------------PGFDSSKVEKLCA-- 346 Query: 357 YALSSGYYDAYYSKAMKVRRL-----IAQDFARAFGNVDVLVTPTSPFPAFRRGEKTQDP 411 LS+ + +RRL I Q+ + + DVL+ PT A + Sbjct: 347 -HLSNSFIGNIGKLPFVIRRLKNTINITQELHKHY---DVLLCPTLSSSAPKNNYMLNQA 402 Query: 412 LAMYAADVDTVAI-------NLAGLPALSVPAGFERVDGVRLPVGVQLIAPPLQDERLVA 464 L A + + N+ G PA+S+P G LP+G+Q A +D+ L+ Sbjct: 403 LPASAMVKNMMEFAPFAALQNITGEPAISLPMG---TSDNGLPIGMQFSAGYGEDKTLLE 459 Query: 465 LAGGLE 470 LA LE Sbjct: 460 LAFELE 465 Lambda K H 0.316 0.132 0.375 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: 490 Number of extensions: 27 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 483 Length of database: 491 Length adjustment: 34 Effective length of query: 449 Effective length of database: 457 Effective search space: 205193 Effective search space used: 205193 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