Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012536352.1 AFE_RS03690 AtzE family amidohydrolase
Query= curated2:Q2IH94 (492 letters) >NCBI__GCF_000021485.1:WP_012536352.1 Length = 465 Score = 252 bits (643), Expect = 2e-71 Identities = 178/473 (37%), Positives = 248/473 (52%), Gaps = 44/473 (9%) Query: 27 STELVEASLARIQATDGKLGAFLAVCADRARAAAKAADARAARGERRSELDGVPVAVKDL 86 + E+V+ +L I A +G++ AF V RA A+A D + ARGE L GVP AVK+L Sbjct: 25 AVEVVQDTLRHIHARNGEINAFTCVTEARALREAEAVDQKVARGEDPGPLAGVPFAVKNL 84 Query: 87 FVTKGVPTTAGSRI-LEGYLPPYDATVVERLEAAGAVIVGKLNMDEFAMGSSNENSAYKP 145 F +G T AGS+I + L DAT V RL AAGAV+VG LNM E+A + EN Y P Sbjct: 85 FDLQGEITLAGSKINRKDALAVADATAVRRLTAAGAVLVGALNMGEYAYDFTGENIHYGP 144 Query: 146 CHNPWDLSRTPGGSSGGSAASVAAGQVHASLGTDTGGSIREPAAFCGVVGVKPTYGRVSR 205 NP D R GGSSGGS A+VAAG V +LG+DT GSIR P++ CG+ G+KPTYGR+SR Sbjct: 145 SRNPHDRLRMTGGSSGGSGAAVAAGMVPIALGSDTNGSIRVPSSLCGIFGLKPTYGRLSR 204 Query: 206 YGVVAFASSLDQVGPLAREVGDAALVLRTIAGHDPRDMTSSTRPVDDYLGPLEEGARGLR 265 G F SLD VGPLAR V D AL + G D D + R + G L +G GL+ Sbjct: 205 AGAFPFCPSLDHVGPLARSVADLALAYDAMQGADAADPVCADRATEPVSGSLADGVAGLK 264 Query: 266 VGVPREWLSGGLDAGVEAAIRAALDTYRRLGATL--VD-VSLPHSKYGIGAYYLIAPAEA 322 + + + ++ A AA R+ A L D V +P + A YLI AE Sbjct: 265 IAIAAGYF-------MQQATSAAEQALARVAAALNVTDLVEIPGTAQARAAAYLITNAE- 316 Query: 323 SSNLARYDGVRYGLRAEGAKGLKEMYAESREQGLGAEPKRRIMLGTYALSSGYYDAYYLR 382 SSNL D +R+ + + R++ GT +S + ++ Sbjct: 317 SSNL-HLDRLRH-----------------HAADYDPDVRDRMLAGTLLPAS-----WNIQ 353 Query: 383 AQKVRTLIRRDFDEAFRGCDVIAGPVTPSVAFALGER--TGDPLQMYL---ADIFTITCN 437 AQ+ R R + + F D++ P TP A A+G+R D QM + ++T + Sbjct: 354 AQRFRRWYRAEVLKVFARYDLLLAPATPMSAPAIGQRYMELDGEQMMVRPHLGLYTQPLS 413 Query: 438 LAALPGLSVPCGLEAASGLPVGLQLVGRPFDEATLFRAARALERE--LGPLPA 488 LP + VP + +A +P+G+Q++ P+ EA +F+ AR LE P+PA Sbjct: 414 FIGLPVVVVP--VASAGAMPIGVQIIAAPWQEARIFKVARELELHGFTSPIPA 464 Lambda K H 0.317 0.135 0.393 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: 517 Number of extensions: 27 Number of successful extensions: 4 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: 492 Length of database: 465 Length adjustment: 34 Effective length of query: 458 Effective length of database: 431 Effective search space: 197398 Effective search space used: 197398 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