Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate Pf6N2E2_1873 Amidase
Query= curated2:Q2S4S2 (514 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1873 Length = 476 Score = 161 bits (408), Expect = 4e-44 Identities = 149/510 (29%), Positives = 220/510 (43%), Gaps = 77/510 (15%) Query: 3 YPTFTDARRALDAGETSCEALVSSFLERIDARDNEINAFTSVDQDGALNHARYLDSQRER 62 Y T T+A A S ++ + + RI+A ++++NA T D AL A+ + R Sbjct: 10 YLTATEAVAQFKAKTLSPVDVLRAQIARIEAVNSKLNAITYTHFDRALKEAQVAEGLYMR 69 Query: 63 G-NPRPLAGLVLAVKDNICIRGYPVSCGSKMLADFSSLYDATVIDRLRDAGAIFIGKTNC 121 G RPL G+ A+KD I+G ++ GSK ADF A ++RL DAGAI +T Sbjct: 70 GVATRPLEGVTCAIKDGNPIKGEIMTVGSKAFADFIPDESAPTVERLIDAGAIVHCRTTM 129 Query: 122 DEFAMGSSNETSHFGPVRNPHAPEYVPGGSSGGSAAAVAAGLCHAALGSDTGGSVRQPAA 181 EF + ++ +G RN PEY GGSSGG+ +A+AAG+ A G+D GGS+R PAA Sbjct: 130 SEFGHSAITKSPLWGVTRNAWNPEYSSGGSSGGAGSALAAGMTTLADGTDGGGSIRVPAA 189 Query: 182 FCGTVGLKPTYGRVSRSGLVAFASSLDVIGPLTRSAEDAATILNVIAGEDERDSTSAPVD 241 G G KP +GR + ++ +L GPL RS D A + NV++G+ +D S P Sbjct: 190 LGGLFGYKPPFGR-NPVDTLSPGETLMHYGPLARSVADCALMQNVMSGQHPKDLYSLPDQ 248 Query: 242 VPDYTEGLGDGVEGLRLGLPEEYFAEGLDDDIRRMVTEQVDRLDDAGATVEEVSLPHTEY 301 V T G+ + G R+ L + ++R + G VEE+ LP Sbjct: 249 VVLPT--FGESLRGRRIALSMNLGFYEVSKEVRENTLAAAEVFRGLGCIVEEIQLPWERA 306 Query: 302 GVATYYLVATAEASSNLARYDGIRYGHRADLQETKQALQERREELKEELASARAQGDEAR 361 V +L+ ++ + + DL L E R +L Sbjct: 307 SVEDAWLI----------KWQALLWAQCGDL------LPEFRNDL--------------- 335 Query: 362 ADTLEAQLDDEQSTLDALYTRSRTEGFGDEVKRRIMLGTYALSAGYYDKYYEKAQRVRTL 421 D +L ++ S LD L RT ++ K + A +GY Sbjct: 336 -DPFVVELMEQGSHLD-LRRFYRT----NQTKHEMHQALVAAMSGY-------------- 375 Query: 422 IRHDFERAFEDVDALITPTTPTPPFRLGEKTDDPL--------EMYLNDIYTVTAN-LAG 472 D LI PTT T DPL Y+ + T N L+ Sbjct: 376 ------------DLLIAPTTATTQIPADRHDADPLLINGKAIDRPYVGWLLTTPFNLLSQ 423 Query: 473 LPGLTVPIGEHPDTPGLPVGLQVLGPHFDE 502 P +VP G T +P GLQ++GP +D+ Sbjct: 424 YPVFSVPSGV-DQTTSIPTGLQIIGPAYDD 452 Lambda K H 0.316 0.135 0.386 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: 510 Number of extensions: 22 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 514 Length of database: 476 Length adjustment: 34 Effective length of query: 480 Effective length of database: 442 Effective search space: 212160 Effective search space used: 212160 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