Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_015927249.1 MNOD_RS02450 amidase
Query= curated2:Q72L58 (471 letters) >NCBI__GCF_000022085.1:WP_015927249.1 Length = 481 Score = 228 bits (580), Expect = 4e-64 Identities = 180/486 (37%), Positives = 239/486 (49%), Gaps = 45/486 (9%) Query: 2 LAHEIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLN--ERLLEEAEAVDPGL--- 56 LA IR+R VS EV QA+L ++ +P + A +SL E LL EAEA D L Sbjct: 15 LAQAIRSRA----VSAREVMQAHLDQIARFNPAVTAIVSLRDPELLLAEAEAADRDLAAG 70 Query: 57 ----PLAGLVVAVKDNIATRGLRTTAGSRLLENFVPPYEATAVARLKALGALVLGKTNLD 112 PL GL AVKD +G+ T GS + + +P +A VARL+ GA+++GKTN+ Sbjct: 71 RWRGPLHGLPHAVKDTSPAQGMPWTQGSPVFRSRMPEADAPYVARLRQAGAILIGKTNVP 130 Query: 113 EFGMGSSTEHSAFFPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAF 172 EFG+GS T + F PT+N +DP R GGSSGG+A ALA + PLA GSD GS+R PAA+ Sbjct: 131 EFGLGSHTVNPVFGPTRNAYDPGRSAGGSSGGAAVALALRMLPLADGSDHAGSLRNPAAW 190 Query: 173 CGVYGLKPTYGRVSRFGLIAYASSLDQIGPMARSVRDLALLMDAVAGPDP-LDATSLDLP 231 GV GL+P+ GRV + L GPMAR DL LL+ +AGPDP L + P Sbjct: 191 NGVLGLRPSPGRVPLRTDEVFLPDLTVAGPMARCTADLGLLLSVMAGPDPRLPQAIQEDP 250 Query: 232 PRFQEALEGPLPPLRLGVVRE--ALAGNSPGVERALEEALKVFRELGLSVREVSWPSLPQ 289 F LP LR+G + + PGV E+ L V G V ++ P+ Sbjct: 251 APFARPQPRDLPGLRVGWLGDCGGHLATEPGVLDLCEQGLAVLEARGARVEPLALGLDPE 310 Query: 290 AL-AAYYILAPAEASSNLARYDGTLYGRRAEGEEVEGMMEATRALFGLEVKRRVLVGTFV 348 + A+ +L A G +A A + EV+ + + F Sbjct: 311 EVWQAWRVLRAWLAG-----------GAQAPLWRDPQTRAALKPEAAWEVEEGLKLDAFA 359 Query: 349 LSSGYYEAYYGRAQAFRRRLKAEAQALFREVDLLLLPTTPHPAFPFG-------ARRDPL 401 + A A R R A+ LF VDLL LP FP A RD Sbjct: 360 IL---------EASAMRSRWYAQVLRLFETVDLLALPAAQVFPFPIEEAWPRRIAGRDMD 410 Query: 402 AMYREDLYTVGANLTGLPALSFPAG-FEGHLPVGLQLLAPWGEDERLLRAALAFEEATAR 460 +R T+ A + G PA+S PAG +G LP+GLQL+AP + LL A A+EEATA Sbjct: 411 TYHRWMEVTIPATMAGCPAISLPAGRNQGGLPMGLQLIAPHRGEAALLSVAAAYEEATAF 470 Query: 461 AHLKAP 466 + P Sbjct: 471 DRMLPP 476 Lambda K H 0.319 0.137 0.395 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: 636 Number of extensions: 31 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 471 Length of database: 481 Length adjustment: 33 Effective length of query: 438 Effective length of database: 448 Effective search space: 196224 Effective search space used: 196224 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 (21.7 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