Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate PP_0613 PP_0613 Amidase family protein
Query= curated2:Q1DCA3 (486 letters) >FitnessBrowser__Putida:PP_0613 Length = 469 Score = 240 bits (613), Expect = 7e-68 Identities = 171/488 (35%), Positives = 236/488 (48%), Gaps = 35/488 (7%) Query: 5 DLTMLELAAKLAAGEASSEEATRASLARIQQVDPKVRAFLRVDEAGALAAARASDARRKS 64 +LT +EL + S E LARI +P V AF VD GA AAARAS+ R + Sbjct: 9 ELTAVELLELYHRRQLSPVEVVDDVLARIDLHNPAVNAFCHVDGEGARAAARASEQRWQR 68 Query: 65 GSPASALDGVPLGLKDIFLTEGVETTAGSRILEGFVP-PYDATVVRLLKEAGLPLVGKLN 123 G P LDGVP +KD+ LT G+ T GSR G P DA ++EAG LVGK Sbjct: 69 GQPCGRLDGVPASIKDLTLTRGMPTRKGSRTTSGAGPWEIDAPFSAFMREAGAVLVGKTT 128 Query: 124 MDEFAMGSSNESSAFFPSHNPWDVSRTPGGSSGGSAAAVAAREVFGALGTDTGGSIRQPA 183 EF ++ + + NPWD T GGSSGG+AAA A G+D GGSIR P Sbjct: 129 TPEFGWKGVTDNPLYGITRNPWDTRLTAGGSSGGAAAAAALNLGVLHQGSDAGGSIRIPC 188 Query: 184 ALTNTVGLKPTYGRVSRFGVIAFASSLDQPGPMTRTVADAAALLQVIARPDAQDATSADA 243 A T T G+KPT+G V ++ A + L GPMTRTV D+ +L +ARPDA+D A A Sbjct: 189 AFTGTFGIKPTFGYVPQWPASAM-TVLSHLGPMTRTVDDSVLMLDCVARPDARDGL-AGA 246 Query: 244 PVPDYSADLEAGVRGLKLGVPREYFTEGMDPEVEAAVREALREYERLGATLVDVSLPHTK 303 P + + GL++ + +DP+++A V +A++ RLGA + +V Sbjct: 247 PRQAPWLSQQQDLSGLRIAYSANFGYVQVDPQIQALVAQAVQRLARLGAQVEEVD----- 301 Query: 304 YALATYYLIAPAEASSNLARYDGVRFGLRAKDARSLRDVYALTREQGFG--AEVKRRIML 361 S L ++ + F A+ A +L D + G AE +I L Sbjct: 302 -----------PGFSDPLETFNTLWFAGAARLASALSDEQKALLDPGLRWIAEQGAQISL 350 Query: 362 GTFALSSGYYDAHYLRAQKVRTLIREDFTRAFQQVDALLSPTSPVPAFKLGEKVEDPLSM 421 G Y +A + R + Q+ D L+SP P+ AF+ G V M Sbjct: 351 G-----------EYTQALEARAELIAKMNAFHQRYDVLVSPMLPLVAFEAGHNVPPGSGM 399 Query: 422 YLMDIYT---LPCNLAGLPGLSVPCGFTKAGLPVGLQILGRPFDEAGLLRIARAYEREHD 478 +T P NL P SVPCGFT+ GLPVGLQ++ F + +LR+ + YE+ + Sbjct: 400 AQWMEWTPLSYPFNLTQQPAASVPCGFTREGLPVGLQVVAGRFADEQVLRVCKVYEQHYP 459 Query: 479 FFRRSAPL 486 AP+ Sbjct: 460 SRHLQAPI 467 Lambda K H 0.318 0.134 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: 553 Number of extensions: 37 Number of successful extensions: 7 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: 486 Length of database: 469 Length adjustment: 34 Effective length of query: 452 Effective length of database: 435 Effective search space: 196620 Effective search space used: 196620 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 (21.7 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