Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_013721506.1 ALIDE2_RS04670 amidase
Query= curated2:B8HY89 (482 letters) >NCBI__GCF_000204645.1:WP_013721506.1 Length = 468 Score = 210 bits (534), Expect = 1e-58 Identities = 166/491 (33%), Positives = 239/491 (48%), Gaps = 44/491 (8%) Query: 3 SIRELHQQLVSKERSAKEITQDALEKIQQLEPKVHAFLTLTAEQALAQAERVDQQIATGT 62 S EL ++ S E TQ L+ I + EP +HA L E+ALAQA + + G Sbjct: 8 SASELLAAYRARSLSPVEATQSVLDHIARWEPHLHATYLLRPEEALAQARASEARWLRGA 67 Query: 63 EIGLLAGIPIAIKDNLCTKGIPTTCGSKILQGFIPPYESTVTSRLAAAGAVMVGKTNLDE 122 G L G+P +KDN+ T+G PT G+ P ++ +RL AGAV+V KT + + Sbjct: 68 PCGPLDGVPATVKDNIATRGDPTPLGTAATPLMPAPADAPPAARLREAGAVIVCKTTMPD 127 Query: 123 FAMGSSTENSAYQLTANPWDLQRVPGGSSGGSAAAVAAGETLIALGSDTGGSIRQPASFC 182 + M SS +S + L NPWDL R PGGSS G+ AA AAG + +G+D GGSIR PA +C Sbjct: 128 YGMLSSGLSSFHALARNPWDLSRGPGGSSAGAGAAAAAGYGPLHVGTDIGGSIRLPAGWC 187 Query: 183 GVVGLKPTYGLVSRYGLVAYASSLDQIGPFATNVEDAALLLGAIAGHDPQDSTSLNV-PI 241 GV GLKP+ G + + + GP V+DAAL++ ++ D +DS SL PI Sbjct: 188 GVFGLKPSLGRIP----IDPPYTGRAAGPMTRTVQDAALMMQVLSAPDARDSMSLPAQPI 243 Query: 242 --PDYTQFLIPDLKGKKIGIIQET-YGEGLDPQVEQVTHKAIQQLEELGAEVREISCPRF 298 D+ Q L+G +IG++ + G +DPQV A + E+ GA + + Sbjct: 244 AWDDFGQG-PGRLRGLRIGLLLDAGCGLPVDPQVRAAVEAAARLFEQAGAAIEPMPPFLT 302 Query: 299 RYGLPTYYIIAPSEASANLARYDGVKYGFRSPDPENLLSMYTRTRAEGFGPEVKRRIMIG 358 R+ L DG+ + +R + + + T T G + K I Sbjct: 303 RHML------------------DGMDHFWRM---RSFMDLRTLTP----GQQGKVLPFIR 337 Query: 359 TYALSAGYYDA-YYLKAQKVRTLIKQDFEAAFEQVDVLVCPTAPTTAFAA--GAKTADPL 415 +A+SA D +A + + A D ++ P AP AFAA A T DPL Sbjct: 338 DWAMSAAGLDGPQVFEASQQFHATRVATVHACAPFDYVLSPVAPMPAFAAELPAPTDDPL 397 Query: 416 SMYLSDLMTIPVNLAGLPGLSLPCGFDQQGLPIGLQLIGNVLREDLVFQVAYAYEQ---- 471 T+P N++ P S+ CG+ GLPIGLQ+ G + V Q+A+A+EQ Sbjct: 398 RPLEHIAFTVPFNMSEQPAASVNCGYTGGGLPIGLQIAGRRFDDLGVLQMAHAFEQLRGP 457 Query: 472 ATPW---HDRH 479 PW DRH Sbjct: 458 QRPWPEPPDRH 468 Lambda K H 0.317 0.134 0.388 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: 562 Number of extensions: 30 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: 482 Length of database: 468 Length adjustment: 33 Effective length of query: 449 Effective length of database: 435 Effective search space: 195315 Effective search space used: 195315 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 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