Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_106719629.1 CU100_RS26290 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_003010935.1:WP_106719629.1 Length = 492 Score = 213 bits (541), Expect = 2e-59 Identities = 163/483 (33%), Positives = 237/483 (49%), Gaps = 39/483 (8%) Query: 15 MLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARRAAGDASPLLG- 73 M A G+ISS E+T A L+RIA + K+ A++ V AR A + D L G Sbjct: 1 MRAAGQISSAEITHAYLSRIAKFDGKLNAYVEVYEQEARFAATSLDTGSNGRIEGGLAGG 60 Query: 74 IPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLNCDEFAMGSST 133 IP+ +KD++ G TT S A+ RL A+G++ILGK E A Sbjct: 61 IPIALKDLLEVDGKITTAGSAHFRGRRSRVTASLATRLIASGSIILGKTQTVELAYSGWG 120 Query: 134 ENSAFQQTRNPWN--LERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPAALCGITGL 191 N NPW+ ++R PGGSS GSA AV+AG AP A+GTDTGGS+R PAA CGITGL Sbjct: 121 INPQMGTPWNPWDEDIQRDPGGSSSGSAVAVSAGLAPWAVGTDTGGSVRLPAAFCGITGL 180 Query: 192 KPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTDYPAPDYEAA 251 K T G+++ G++ + + D GP+ R+V D AI+ ++ G+ A + A Sbjct: 181 KTTAGQIATDGIIPLSKTFDTPGPITRSVLDAAILYNLMLGSKSQFAFGSG-TVSGISRA 239 Query: 252 LTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPHTPYALPVYYL 311 L G ++GL++G + G++PDV A ++E L GA++ EI+LP + L Sbjct: 240 LEGGVQGLKLGSLPKAEREGVEPDVLGAYDRSLETLSNLGADIVEINLP--------FRL 291 Query: 312 IAPAEASANLARFDGVRYGLRV--PGESYFDELERTRGAGFGPEVRRRIMLGTYALSAGY 369 A + + + Y V G S DE R+ G G R + ++L A Sbjct: 292 NDCRTAHSTIINSEAYSYFYDVIEDGSSLIDESTRS-GISTG-----RTISPQHSLDA-- 343 Query: 370 YDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGA--HTDDPLAMYLEDVCT 427 +K+ ++++ I A VD + PTT +VA + T P T Sbjct: 344 ----FKQIWRLKSQI----SGALLNVDALLTPTTESVAIPVEGLDRTKSPARF------T 389 Query: 428 LPLNLAGLPGLVVPCG-FAEGLPIGLQLIGRAFDEESLLRVGDAYQRVTDWHTRMPEVRE 486 +N G+ GL +P G AE LP LQ++ R E LR+G A+Q TDWH P + Sbjct: 390 RFVNALGMCGLAIPNGKSAEALPTSLQIVCRQHQERLALRIGLAFQNATDWHLGYPPMCR 449 Query: 487 DGS 489 D + Sbjct: 450 DAA 452 Lambda K H 0.320 0.136 0.398 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: 499 Number of extensions: 21 Number of successful extensions: 5 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: 490 Length of database: 492 Length adjustment: 34 Effective length of query: 456 Effective length of database: 458 Effective search space: 208848 Effective search space used: 208848 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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