Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate BWI76_RS11360 BWI76_RS11360 L-asparaginase
Query= curated2:Q18GL3 (442 letters) >FitnessBrowser__Koxy:BWI76_RS11360 Length = 347 Score = 101 bits (251), Expect = 4e-26 Identities = 107/350 (30%), Positives = 158/350 (45%), Gaps = 47/350 (13%) Query: 93 SAVAF-DESLPTVSLISTGGTIAS-------TVDYRTGAVTAQFDAEDVLRAVPDLAGRA 144 SA AF D LP + +++TGGTIA T Y+ GA+ Q ++ AVP+++ A Sbjct: 15 SAFAFSDTRLPHIVILATGGTIAGSAASNTQTTGYKAGAIGVQ----TLINAVPEMSKVA 70 Query: 145 NYRGRVVRNILSENMTPAVWQDLAAAVADEI-RAGADGVVVMHGTDTMQYSASALSYMLD 203 G V NI SENMT + L+ V + + R DGVV+ HGTDT+ + L+ + Sbjct: 71 RVDGEQVANIGSENMTSDIILKLSKRVNELLARDDVDGVVITHGTDTLDETPYFLNLTVK 130 Query: 204 TPVPVVFTGSQRSADRPSSDNVMNAVCAVEAAT---ADISGVFVCMHASTADDTCALHRG 260 + PVVFT + R A S+D MN + AV A A GV V ++ + Sbjct: 131 SNKPVVFTAAMRPATAISADGPMNLLEAVTVAADPQAKGRGVMVVLND-------RIGAA 183 Query: 261 TRVRKNHTSRRDAFKT-----VGATPIGKIEYDTETVSFHRDHAARESTELNLTSELNED 315 V K + + D FK +G GK +++T H + + +LN L + Sbjct: 184 RFVTKTNATTLDTFKAPEEGYLGVIVSGKPQFETRVDKIHTVRSVFDVRQLN---ALPKV 240 Query: 316 VMLLTF--TPGMNIDRQTAFLTDSTPDGLIIAGTGLGHVHTEFIPTVAELVADGVVVAMT 373 V++ + P D A DG+I AGTG G V + + G+VV Sbjct: 241 VIIYGYQDDPEYMYDAAIAHHV----DGIIYAGTGAGSVSVRSAAGIEKAEKAGIVVVRA 296 Query: 374 SQCIEGRVCDRVYDTGRDLLEAGVVEAGDTL-PGTAKVKLMWALANHPDP 422 S+ G V D G + G+V D+L P A++ LM AL +P Sbjct: 297 SRTGSGVV---PVDDG----QPGLV--SDSLNPAKARILLMTALTQTKNP 337 Lambda K H 0.315 0.129 0.370 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: 397 Number of extensions: 26 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: 442 Length of database: 347 Length adjustment: 31 Effective length of query: 411 Effective length of database: 316 Effective search space: 129876 Effective search space used: 129876 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: 50 (23.9 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