Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF1044 HP15_1023 6-aminohexanoate-cyclic-dimer hydrolase
Query= curated2:Q67KJ2 (488 letters) >FitnessBrowser__Marino:GFF1044 Length = 498 Score = 157 bits (397), Expect = 8e-43 Identities = 140/478 (29%), Positives = 209/478 (43%), Gaps = 63/478 (13%) Query: 15 ELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAGDTELGPLAGVPIA 74 E+S E+ ++A++R VEP + + D I A KLDA + G L GVP Sbjct: 31 EISVTELTQTAIARAQAVEPLLHGLASANYDQAIRTASKLDAADQTGSFPL--FRGVPTL 88 Query: 75 VKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANMDEFAMGSSGESSA 134 +KDN SGM T S + + + +L A G + +GK+ + EF ++ E + Sbjct: 89 IKDNTNVSGMTTRHGSLAVPSVPASDTSPFARQLLAQGFLCLGKSTLPEFGFNATTEPAH 148 Query: 135 FGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAAFTGIVGLKPTYG- 193 T NPW+L G SS GSAA VAAG P+A D GGSIR PAA G+VGLKPT G Sbjct: 149 APATCNPWNLAYSSGASSGGSAALVAAGVVPIAHANDGGGSIRIPAACCGLVGLKPTRGR 208 Query: 194 YVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGRTP--PALKFGGEP 251 + + ++ G + R V D A FE A R P PA+ P Sbjct: 209 LIDNEAAASLPINIISEGVVTRSVRDTANFFE--------QAETYFRNPGLPAIGKMEGP 260 Query: 252 SLSGVRLG-VPKELLGPGIDPGVKARVEEAIAQLEELGATVEECSLP-----STEYALSA 305 S +R+G V + G D + VEE +LE++G +E +P ++AL Sbjct: 261 SGRPLRIGLVLDSINGHKTDDITRRTVEETALRLEKMGHRIEPVPVPVHSTFPDDFAL-- 318 Query: 306 YYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIMLGTYVLSA 365 Y+ + + +G RA LH + K + +G + R + L Sbjct: 319 YWAL--------------LAFGIRANGRKLLHPAFDKHKTDGLTNGLDRMFRRQFWRLPT 364 Query: 366 GHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIG------------EKVD 413 A +R + D+ A +DA++TP T +G E++ Sbjct: 365 ----ALWRLKRS-----WHDYAHAMAGFDAVLTPVLGHTTPALGHLSPAVPFDTLFERLR 415 Query: 414 DPVSMYLGDICTIPVNLAGLPAVSVPCGFV-DGLPVGMQLIGKPFADTQILQIAWAYQ 470 + VS T N G PA+S+P G D LPV +Q +G+ + +L IA+ + Sbjct: 416 EYVSF------TPLANATGAPAISLPMGHTPDQLPVSVQFMGRHGGERTLLDIAFTLE 467 Lambda K H 0.318 0.135 0.391 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: 618 Number of extensions: 41 Number of successful extensions: 3 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: 488 Length of database: 498 Length adjustment: 34 Effective length of query: 454 Effective length of database: 464 Effective search space: 210656 Effective search space used: 210656 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 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