Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate Pf1N1B4_4165 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)
Query= curated2:Q7UT33 (499 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4165 Length = 478 Score = 176 bits (446), Expect = 2e-48 Identities = 153/490 (31%), Positives = 216/490 (44%), Gaps = 51/490 (10%) Query: 14 SGEVTAVEVIAQSLAAIRASQPTINAFTHVAEETAMQAAEAVDADRKAGKTLGPLAGLPV 73 +GEVT+ E+ ++AA++ P INA V E + E GPLAG+P Sbjct: 20 TGEVTSAELAELAIAAVQQVNPQINA---VIEHWSPTVTEGT----------GPLAGVPF 66 Query: 74 AIKDVLCTS-DMPTTCSSKMLEGFVPPYDATVVARLKSAGAIVVGKTNMDEFAMGASTET 132 IKD+ TS S++ +G V D+ ++ R +AG +G+T E A TE+ Sbjct: 67 LIKDLAITSAGRRVELGSRLAQGLVAESDSYLMQRFNAAGLATLGRTTTPEMAFSTETES 126 Query: 133 SAMGVTGNPWDTTKTPGGSSGGAAAAVAAGAVPLSLGTDTGGSIRQPAAFCGITGLKPTY 192 G T NPWDT + GGSSGG+ AAVAAG VP++ TD GSIR PA++ G+ GLKPT Sbjct: 127 VLQGPTRNPWDTRLSAGGSSGGSGAAVAAGIVPIAHATDAAGSIRVPASYNGLVGLKPTR 186 Query: 193 GRVSRYGLV--AFASSLDQAGPMGWSVDDVAIGLQAMAGYDPRDSTSVNAEVPDFTPAMA 250 GR S + FA Q G + +V D A + + GY P D A F A Sbjct: 187 GRASNGPALDEVFAGFGVQLG-LSRTVRDSAALMDIVQGYAPGDPYYTAAPDEGFL-AQV 244 Query: 251 AEDVRGMRIGVLREGLDQDGISPAVRDALATAESVFREQGAEIVEVELPHSKYWVPTYYV 310 D +RIG+L + + P + +A G + V P W Sbjct: 245 GRDPGRLRIGLLDTPWNGAALDPEIAEATLAVARELEALGHRVERVIAPLGTSWDSFVQA 304 Query: 311 IAPCEASSNLSRFDGAHYGYRVADAEIAAADSGPLEAMYSLSRAGGFGSEVKRRIMVGTY 370 A ++ + DG +AAA S P++ + +L A + Y Sbjct: 305 NAHIWCATLVRWIDG-----------LAAATSRPID-LSTLEPA-----------TLACY 341 Query: 371 ALSEGYYDAYYNQALKVRRLIRNDYDAAFQQVDLMLGPVTPSPAFALN-----EKTDDPI 425 A + AL+VR LI F D++L P P AL+ +T D + Sbjct: 342 AYGLEARAVEFAGALEVRNLIARSVAGWFDDFDVLLTPTLPRLPHALDTYSRGAQTMDGL 401 Query: 426 ----AMYLCDLFTVGANLAGVPAISLPGGFD-AVGLPVGVQLQAPVMEETRLLRAGNVFQ 480 ++ FT N+AG PA+SLP GLP+G+Q A E LLR + Sbjct: 402 QWTARVFEHSPFTPVFNVAGTPAMSLPLAMSREQGLPIGLQFAARFGAEEVLLRLAGQLE 461 Query: 481 MASDFHTRRP 490 A +H RRP Sbjct: 462 QALPWHERRP 471 Lambda K H 0.316 0.132 0.381 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: 567 Number of extensions: 33 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: 499 Length of database: 478 Length adjustment: 34 Effective length of query: 465 Effective length of database: 444 Effective search space: 206460 Effective search space used: 206460 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: 52 (24.6 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