Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate AO353_25440 AO353_25440 amidase
Query= curated2:Q72L58 (471 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25440 Length = 483 Score = 191 bits (486), Expect = 4e-53 Identities = 160/481 (33%), Positives = 228/481 (47%), Gaps = 48/481 (9%) Query: 3 AHEIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLN--ERLLEEAEAVDPGLP--- 57 AHE+ + +VS EV QAYL ++ +P + A +SL E LL +A+ D L Sbjct: 14 AHELADCIRLRQVSCREVMQAYLSHIERFNPWVNALISLQAPEDLLAQADQRDAELASGL 73 Query: 58 ----LAGLVVAVKDNIATRGLRTTAGSRLLENFVPPYEATAVARLKALGALVLGKTNLDE 113 + GL A+KD TRG+RTT GS L E+F+P + R+KA GA+++GKTN E Sbjct: 74 YRGWMHGLPHAIKDLSLTRGIRTTFGSPLFEDFLPDRDGIMCERIKAAGAIIIGKTNTPE 133 Query: 114 FGMGSSTEHSAFFPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFC 173 FG+GS T + F T +DP + GGSSGG+A+ALA L P+A GSD GS+R PAAF Sbjct: 134 FGLGSQTYNPLFGATGCAYDPSKTAGGSSGGAASALAMHLVPVADGSDMMGSLRNPAAFN 193 Query: 174 GVYGLKPTYGRVS-RFGLIAYASSLDQIGPMARSVRDLALLMDAVAGPDPLDATSL-DLP 231 V+G +P+ GRV + L GPM R VRD ALL+ AG D S+ + Sbjct: 194 NVFGFRPSQGRVPFDDSADLFIDQLGYEGPMGRCVRDAALLLSVQAGADARAPLSIAESG 253 Query: 232 PRFQEALEGPLPPLRLGVVREALAGNSP---GVERALEEALKVFRELGLSVREVSWPSLP 288 F LE RLG + + G P G+ ++A F LG S+ S P Sbjct: 254 AAFAAPLERDFSGTRLGWLGD-FNGYLPMEKGILDLCQKAFTDFESLGCSIEPASVDFAP 312 Query: 289 QAL-AAYYILAPAEASSNLARYDGTLYGRRAEGEEVEGMMEATRALFGLEVKRRVLVGTF 347 + L ++ L + +L G+ Y ++ RA E V G Sbjct: 313 EQLWNSWRTLRHWMVAGSL----GSAYANPSQ-----------RARLKEEACWEVENGLR 357 Query: 348 VLSSGYYEAYYGRAQAFRRRLKAEAQALFREVDLLLLPTT---------PHPAFPFGARR 398 + +S + A R+ +R LF+ D LLLPT P P G Sbjct: 358 LSASDVFAASVARSHWYR-----AISNLFKRFDYLLLPTAQVFPFDKNLPWPTSIEGVSM 412 Query: 399 DPLAMYREDLYTVGANLTGLPALSFPAGFEGH-LPVGLQLLAPWGEDERLLRAALAFEEA 457 D + E + L+G P + GF + LP+GLQ++ D +L+ A A+E+A Sbjct: 413 DTYHRWME--VVIPGTLSGCPVANVQVGFNRNGLPMGLQIIGKHQADFAVLQLAHAYEQA 470 Query: 458 T 458 + Sbjct: 471 S 471 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: 520 Number of extensions: 31 Number of successful extensions: 4 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: 471 Length of database: 483 Length adjustment: 33 Effective length of query: 438 Effective length of database: 450 Effective search space: 197100 Effective search space used: 197100 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 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