Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011842024.1 RSPH17029_RS15190 amidase
Query= curated2:Q67KJ2 (488 letters) >NCBI__GCF_000015985.1:WP_011842024.1 Length = 452 Score = 221 bits (562), Expect = 5e-62 Identities = 179/481 (37%), Positives = 241/481 (50%), Gaps = 56/481 (11%) Query: 2 LSAARLNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAG 61 L+ A L +G + AVE+ E+ L++IA EP V A+ + DH + +A+ LDARR++G Sbjct: 13 LTGAELAERLASGAVRAVELVEACLAQIAAREPEVQAWAFLDGDHAMAQARALDARRQSG 72 Query: 62 DTELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANM 121 LGPL G+P+ VKD I GM T G V+ DA V RLRAAGA+++GK Sbjct: 73 -AALGPLHGLPVGVKDVIDVRGMPTGLGLAGGAGRVAQADAFVAARLRAAGAILMGKTAT 131 Query: 122 DEFAMGSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAA 181 E A TRNP D R PGGSSSGSAAAVAAG PLA+GT TGGS+ +PAA Sbjct: 132 AEAAFLEPA------ATRNPHDPARTPGGSSSGSAAAVAAGMVPLAIGTQTGGSVIRPAA 185 Query: 182 FTGIVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGRT 241 F GI G KP++G + R GV+ + SLD +G GR V DVA L E +AG D D + + Sbjct: 186 FCGIAGFKPSFGLIPRSGVLTQSPSLDTMGVFGRSVADVALLAEALAGHDPADPASLLQP 245 Query: 242 PPALKFGGEPSLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEECSLPSTEY 301 P L E + S + + P PG +A EE L+EL + L Sbjct: 246 APRLP---ETAASDPPVTPTLAFVRP---PGWEAAHEEMRLALQELAELLGRDCL----- 294 Query: 302 ALSAYYVIAVAEASSNLARFDGV-----RYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRI 356 A + AV A+++L R + Y A +A L + S+ EG RRI Sbjct: 295 ---ALELPAVFGAAADLRRRINLAEMAHHYAGLAGRA-ALSPLLSEALAEG------RRI 344 Query: 357 MLGTYVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKVDDPV 416 Y+ A + RT + E F R DA++ P P A D + Sbjct: 345 PAADYL-----------AALEARTALRAGLEPIFHRCDAILCPAAPGPA-PDRATTGDAI 392 Query: 417 SMYLGDICTIPVNLAGLPAVSVPCGFV--DGLPVGMQLIGKPFADTQILQIA-WAYQKVT 473 L C GLPAV++P FV DGLP+G QL+G P D ++L+ A W Q++ Sbjct: 393 FNGLWTFC-------GLPAVTLPL-FVSSDGLPMGAQLVGPPGGDARLLRTARWLVQRLA 444 Query: 474 K 474 + Sbjct: 445 Q 445 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: 589 Number of extensions: 32 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: 488 Length of database: 452 Length adjustment: 33 Effective length of query: 455 Effective length of database: 419 Effective search space: 190645 Effective search space used: 190645 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: 51 (24.3 bits)
This GapMind analysis is from Apr 16 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