Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate H281DRAFT_01567 H281DRAFT_01567 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit
Query= curated2:Q7UT33 (499 letters) >FitnessBrowser__Burk376:H281DRAFT_01567 Length = 513 Score = 204 bits (519), Expect = 6e-57 Identities = 166/496 (33%), Positives = 231/496 (46%), Gaps = 41/496 (8%) Query: 3 HSASEILKQLDSGEVTAVEVIAQSLAAIRASQPTINAFTHVAEETAMQAAEAVDADRKAG 62 HSA + L + E++AVE++ +A I A P +NA T + E A A A DA Sbjct: 10 HSAVALRALLQAREISAVELLDACIARIEALNPYVNAITATSFERARLEARAADAAFARS 69 Query: 63 KTLGPLAGLPVAIKDVLCTSDMPTTCSSKMLEGFVPPYDATVVARLKSAGAIVVGKTNMD 122 TLGPL GLP+AIKD+ T + TT S + VP D T+V RL++AGAIVVGKTN+ Sbjct: 70 ATLGPLHGLPIAIKDLEETEGILTTYGSPLYRANVPARDNTLVRRLRAAGAIVVGKTNVP 129 Query: 123 EFAMGASTETSAMGVTGNPWDTTKTPGGSSGGAAAAVAAGAVPLSLGTDTGGSIRQPAAF 182 E GA++ G TGNP+D GGSSGG+AAA+A VPL+ G+DTGGS+R PAA Sbjct: 130 ELGAGANSFNPVWGATGNPFDPRLNAGGSSGGSAAALALDMVPLASGSDTGGSLRIPAAK 189 Query: 183 CGITGLKPTYGRVSRYGLVAFASSLDQAGPMGWSVDDVAIGLQAMAGYDPRDSTSVNAEV 242 CG+ GL+ + G V + + GPMG +V+D + L A G D + Sbjct: 190 CGVVGLRTSPGLVPSDRKPLGWTPIAVVGPMGRNVEDTWLQLAATVGQSDSDPLGYPFTM 249 Query: 243 PDFTPAMAAEDVRGMRIGVLREGLDQDGISPAVRDALATAESVFREQGAEIVEVELPHSK 302 A D+ +RIG + V + +VFR + +E H Sbjct: 250 APTMDGRALTDLSKLRIGYTEDF--------GVCEVDDEIRAVFRRK----IEFLRGH-- 295 Query: 303 YWVPTYYVIAPCEASSNLSRFDGAHYGYRVADAEIAAADSGPLEAMYSLSRAGGFGSEVK 362 +A CE F+GAH + V AE A L+ Y + G + Sbjct: 296 --------VAVCEPVE--VDFEGAHRCFDVLRAEAFVAG---LQKAYE-TNPELLGPNPR 341 Query: 363 RRIMVGTYALSEGYYDAYYNQALKVRRLIRNDYDAAFQQVDLMLGPVTPSPAFALNE--- 419 +G + G D A + R + + F + DL+L P TP F + Sbjct: 342 ANYEMG---IGMGLADCVRAHADQTR--LFRQFQTLFDRYDLILSPTTPVSPFPWTQPYL 396 Query: 420 KTDDPIAM---YLCDLFTVGANLAGVPAISLPGGFDAVGLPVGVQLQAPVMEETRLLRAG 476 K+ + + + Y T LA PA+SLP G D G+P G+Q+ + LL A Sbjct: 397 KSVNGVELENYYRWLALTYVVTLATNPALSLPCGVDHRGMPFGLQMIGAFRGDLTLLDAA 456 Query: 477 NVFQ--MASDFHTRRP 490 F+ AS TRRP Sbjct: 457 RAFETLFASSDETRRP 472 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: 598 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 499 Length of database: 513 Length adjustment: 34 Effective length of query: 465 Effective length of database: 479 Effective search space: 222735 Effective search space used: 222735 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 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