Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate H281DRAFT_05429 H281DRAFT_05429 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit
Query= curated2:A8F5H6 (467 letters) >FitnessBrowser__Burk376:H281DRAFT_05429 Length = 432 Score = 166 bits (421), Expect = 1e-45 Identities = 140/450 (31%), Positives = 209/450 (46%), Gaps = 66/450 (14%) Query: 10 CLSKESDLINLSLERIKCIDSAVKSFITVVDKQEEL------EGPYKGIPIAIKDNITTK 63 C+S+E+ L RI +D V++ + ++ + GP G+P+A+KD T Sbjct: 28 CISEEA------LGRIDDVDPHVRAMTAIARREAVVAASASASGPLAGLPVAVKDIFDTS 81 Query: 64 NIRTTCGSKMLENYTPPYDATCVKRLKNYGFAIVGKTNLDEFAMGSSTERSAFFVTRNPW 123 ++ T+ GS + E Y P DAT V L+ G IVGKT EFA + T TRNP Sbjct: 82 DLVTSFGSPIYEGYQPRSDATIVTLLRRNGGTIVGKTVTSEFAYMAPTG------TRNPC 135 Query: 124 DLDYVAGGSSGGSAAAVASGEVVAALGSDTGGSVRQPAAFCGIVGFKPTYGLVSRYGLVA 183 D+ AGGSS GSAAAVA+G V A+GS TGGS +PA+FCGI G+KPT GL+ G+ Sbjct: 136 DIGRTAGGSSSGSAAAVAAGMVPFAIGSQTGGSTIRPASFCGIAGYKPTLGLLPTVGMKC 195 Query: 184 FASSLDQIGPMTKSVRDAALIMEVIAGKDPMDSTTVSKKLDFLTHIEDGISGMKFAVPEE 243 F+ S D IG VRD A + +V++G+ ++ + F VP+ Sbjct: 196 FSWSFDTIGLFAAGVRDVAYLAQVLSGR--------------RLAVDVAPASPVFGVPDG 241 Query: 244 VYKYEQLDREVSDRFEEALKTAEKLGAKVSRVKIPT-IKYAVATYYIIAPAEASSNLARY 302 Y + + A+++ E+ G +V V+ T + + + I EA L Sbjct: 242 -YPWTGASANATTALGTAVRSIERAGGRVRPVRFSTWMTDMIDAHETIQSFEAYQTL--- 297 Query: 303 DGVKYGLRIEEPGLMDTYMKTRNVGFGEEVRRRIFLGTFTLSAAYYEAYFGKAQKVRKLL 362 G +Y D + + E + R L T T A + KVR Sbjct: 298 -GYEY----------DHHRAELSAKLSEFLDRASALDTATYVNA---CALMEQAKVR--- 340 Query: 363 SDDLNRVLADFDAILTPTSPSPA-FKIGSVADPLTYYLMDIFTIPANLSGLPAISVP-FG 420 L+ + D +LTP++ A +GS DP F L G P ++VP Sbjct: 341 ---LSELFEGIDVLLTPSARDEAPDGLGSTGDP-------AFNRNWTLLGCPCVNVPGLW 390 Query: 421 FAKNLPVGLQIMGRRFDDPKVLAIARAFEK 450 A+ P+G+Q++GR +D + LA A E+ Sbjct: 391 GARGGPIGVQVIGRPGEDARSLAAAAFVEQ 420 Lambda K H 0.319 0.136 0.390 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: 416 Number of extensions: 22 Number of successful extensions: 3 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: 467 Length of database: 432 Length adjustment: 33 Effective length of query: 434 Effective length of database: 399 Effective search space: 173166 Effective search space used: 173166 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