Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate PfGW456L13_3622 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)
Query= curated2:Q72L58 (471 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3622 Length = 474 Score = 191 bits (486), Expect = 3e-53 Identities = 147/466 (31%), Positives = 233/466 (50%), Gaps = 35/466 (7%) Query: 9 RVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLNERLLEEAEAVDPGL-PLAGLVVAVKD 67 R+ GEV+PLE+ + ++ DP LGA ++++ + A A+DP PLAG+ + +KD Sbjct: 17 RLKSGEVTPLELVNLAAREIEIQDPALGAVVAIDIEGAQRA-ALDPKAGPLAGVPILIKD 75 Query: 68 -NIATRGLRTTAGSRLLENFVPPY-EATAVARLKALGALVLGKTNLDEFGMGSSTEHSAF 125 NI +G T GSRL E+ VP ++ V+RL+ GA++LGKT EF TE Sbjct: 76 TNIDVKGFATRHGSRLYEDAVPAQVDSEFVSRLRNAGAIILGKTKTPEFAGDFVTEPEWQ 135 Query: 126 FPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFCGVYGLKPTYGRV 185 P +NP +P GGSSGGSA A+ A + P+A G+D GGS+R PA+ CGV GLKP+ GR Sbjct: 136 GPCRNPRNPQYASGGSSGGSACAVGAGMVPVAHGTDCGGSIRVPASVCGVVGLKPSRGRT 195 Query: 186 SRFGLIA-YASSLDQIGPMARSVRDLALLMDAVAGPDP-LDATSLDLPPRFQEALEGPLP 243 + + LD + R+VRD ALL+D ++G +P + PP + E L+ P Sbjct: 196 PVGPHVGEFVGGLDSEHVLTRTVRDSALLLDVLSGYEPGAPYAAPPAPPSWLECLKTRSP 255 Query: 244 PLRLGVVREALAGNS--PGVERALEEALKVFRELGLSVREVSWPSLPQALAAYYILAPAE 301 L++ G+S + +A+ A+ + G +R +WP + +A AA + E Sbjct: 256 RLKIAFACARPDGSSIDETIHKAILNAVDFLSKDGHELRPFNWPDMTKAGAAAALFWQME 315 Query: 302 ASSNLARYDGTLYGRRAEGEEVEGMMEATRALFGLEVKRRVLVGTFVLSSGYYEAYYGRA 361 + L + G ++VE + T + +R L + ++ RA Sbjct: 316 IEA-LMEHKAQTRGYPISVQDVEWI---TYEFYKCSTQRTAL-----------DVHHARA 360 Query: 362 QAFRRRLKAEAQALFREVDLLLLPTTPHP-----AFPFGARRDPLAMYRE----DLYTVG 412 + ++ + F ++D+L+ PT F R Y+ +T Sbjct: 361 T--QNKVSHDMADSFTDIDVLITPTVALAPPLIGGFVATGERHLDEWYKNAYAFSPFTEV 418 Query: 413 ANLTGLPALSFPAG-FEGHLPVGLQLLAPWGEDERLLRAALAFEEA 457 NLTG PA+S P G E LP+G+Q++ +G++E +LR A E + Sbjct: 419 FNLTGQPAISIPVGIMENGLPIGMQIVGKFGDEETILRLASEVERS 464 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: 476 Number of extensions: 22 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: 471 Length of database: 474 Length adjustment: 33 Effective length of query: 438 Effective length of database: 441 Effective search space: 193158 Effective search space used: 193158 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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