Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate PfGW456L13_1565 probable amidase
Query= curated2:Q72L58 (471 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1565 Length = 484 Score = 191 bits (484), Expect = 6e-53 Identities = 158/486 (32%), Positives = 226/486 (46%), Gaps = 58/486 (11%) Query: 3 AHEIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLN--ERLLEEAEAVDPGLP--- 57 AHE+ R+ +VS EV Q YL ++ +P + A +SL + LL +A+ D L Sbjct: 14 AHELAERIRLRQVSCREVMQTYLAHIERFNPKINALVSLQAPQDLLAQADIRDAELAKGQ 73 Query: 58 ----LAGLVVAVKDNIATRGLRTTAGSRLLENFVPPYEATAVARLKALGALVLGKTNLDE 113 + GL A+KD TRG+RTT GS L ++F+P + V R+KA GA+++GK+N E Sbjct: 74 YRGWMHGLPHAIKDLSLTRGIRTTLGSPLYKDFIPERDGIMVERIKAAGAIIIGKSNTPE 133 Query: 114 FGMGSSTEHSAFFPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFC 173 FG+GS + + F T +DP + GGSSGG+AAALA L P+A GSD GS+R PAAF Sbjct: 134 FGLGSQSYNPLFGATGCAYDPSKTAGGSSGGAAAALAMHLVPVADGSDMMGSLRNPAAFN 193 Query: 174 GVYGLKPTYGRVS-RFGLIAYASSLDQIGPMARSVRDLALLMDAVAGPDPLDATSL-DLP 231 ++G +P+ GRV + L GPMARSVRD ALL+ AG D S+ + Sbjct: 194 NIFGFRPSQGRVPFDDSADLFIDQLGYEGPMARSVRDAALLLSVQAGADARAPLSIAESG 253 Query: 232 PRFQEALEGPLPPLRLGVVREALAGNSP---GVERALEEALKVFRELGLSVREVSWPSLP 288 F L+ RLG + + G P G+ E+A F LG + V P Sbjct: 254 SAFAAPLDRDFKGTRLGWLGD-FNGYLPMEKGILSLCEKAFADFESLGCRIEPVQCEFAP 312 Query: 289 QALAAYYILAPAEASSNLARYDGTLYGRRAEGEEVEGMMEAT------RALFGLEVKRRV 342 + L + + R V G + AT RAL E V Sbjct: 313 EKLWSSW--------------------RTLRHWMVAGSLGATYADPQKRALLKPEACWEV 352 Query: 343 LVGTFVLSSGYYEAYYGRAQAFRRRLKAEAQALFREVDLLLLP---------TTPHPAFP 393 G + ++ + A R+ +R LF + D LLLP T P P Sbjct: 353 ENGLKLSATDVFAASVTRSDWYR-----AISRLFEKYDYLLLPSAQVFPFDKTQPWPTTI 407 Query: 394 FGARRDPLAMYREDLYTVGANLTGLPALSFPAGFEGH-LPVGLQLLAPWGEDERLLRAAL 452 G D + E + L+G P + GF LP+GLQ++ D +L+ A Sbjct: 408 EGVTMDTYHRWME--VVIPGTLSGCPVANVQVGFSASGLPMGLQIIGKHQADFAVLQLAH 465 Query: 453 AFEEAT 458 +E+A+ Sbjct: 466 TYEQAS 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: 504 Number of extensions: 21 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: 484 Length adjustment: 34 Effective length of query: 437 Effective length of database: 450 Effective search space: 196650 Effective search space used: 196650 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