Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate SMc03245 SMc03245 amidase
Query= curated2:A6TTJ8 (491 letters) >FitnessBrowser__Smeli:SMc03245 Length = 435 Score = 172 bits (435), Expect = 3e-47 Identities = 145/456 (31%), Positives = 224/456 (49%), Gaps = 49/456 (10%) Query: 33 IKELDGKIN---AFITLCEESALMEAAVLDEKLSRGEEIGLLGGIPVAIKDNMCTQGIKT 89 + LDG+ N ++ L E+A EA D + G+ +G L G V+IKD G T Sbjct: 16 LARLDGRRNDERVYVKLYPETARAEADAADGRRREGKSLGPLDGRIVSIKDLFDIAGEPT 75 Query: 90 SCASEMLADFIPPY--DATIVKKLRAAGAIIIGKTNMDEFAMGSSTENSAFKVTKNPWDL 147 A ++ PP DA IV++LRAAGA+IIGK++M EFA + N + V N D Sbjct: 76 -LAGSIIRRAAPPATADAAIVRRLRAAGAVIIGKSHMTEFAFTAVGLNPHYPVPGNAIDP 134 Query: 148 TKVPGGSSGGSAAALAAGFAPLTIGSDTGGSIRQPAAFCGTVGLKPTYGLVSRFGLIAFA 207 + +PGGSS G+A + A G + + IGSD+GGS+R PAA G VG KPT +S G + Sbjct: 135 SLIPGGSSSGAAVSAAEGTSEIAIGSDSGGSVRIPAALQGLVGFKPTARRISLEGAFPLS 194 Query: 208 SSLDQIGPFTKTVKDCALSLQVMQGNDPLDSTSIQQEPMDDYVKDLDKGVKGLKVGIPKE 267 SLD IGP +TV CA + VM G+ P +++ P+ GLK+GIP+ Sbjct: 195 PSLDSIGPLARTVAGCAAADAVMAGDTP---RPLERMPL-----------AGLKLGIPEG 240 Query: 268 FFQEGLNIEISDSIKEAIKVLEQLGAVVEEFSLPVTDSGLSAYYIISSAEASSNLARYDG 327 EGL EI+ + + +++ + GA + + D L+ + + A A +LA + Sbjct: 241 ALLEGLAPEIAAAFERSLQAFSRAGAKLAACGI---DDLLARF---AEATAIGSLAGLEA 294 Query: 328 VRYGHRAAVYEGIEEMMLNSRSEGFGKEVKRRIMLGTYVLSSGYYDAYYKKAMDFRKKTR 387 R H + + + + RS ++RR+ + DA + + R++ Sbjct: 295 SRV-HADWLLDDNAPVDIRVRS-----TLRRRLTVP---------DAAIEDLLRTRQELM 339 Query: 388 NVFKKAFESYDVILTPTSPVLPFTIGEKTGDPLE-MYLADIYTVNVNIAG---VPAISIP 443 + +D+ L PT+P+ +I D E + D+ N +A + AIS+P Sbjct: 340 RAMDERLAPFDLTLLPTTPIPAVSIASVEEDRAEYRRVEDLLLRNTQVANQFDLTAISLP 399 Query: 444 -CGFSKEKLPIGLQLIGDHYSEKKLLQAAYGLEQEL 478 G S+ P GL L+G H ++ LL AA +E L Sbjct: 400 MAGTSR---PAGLMLMGRHGADAMLLGAAAAMEDLL 432 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: 417 Number of extensions: 15 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: 435 Length adjustment: 33 Effective length of query: 458 Effective length of database: 402 Effective search space: 184116 Effective search space used: 184116 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 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