Align glutamine-tRNA ligase (EC 6.1.1.18); glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate 5210072 Shew_2516 glutaminyl-tRNA synthetase (RefSeq)
Query= BRENDA::P00962 (554 letters) >FitnessBrowser__PV4:5210072 Length = 556 Score = 830 bits (2144), Expect = 0.0 Identities = 400/550 (72%), Positives = 456/550 (82%), Gaps = 4/550 (0%) Query: 3 EAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQC 62 + E RP+NFIR IIDEDL SGKHT VHTRFPPEPNGYLHIGHAKSICLNFG+AQDYKG C Sbjct: 5 DTEVRPSNFIRNIIDEDLESGKHTRVHTRFPPEPNGYLHIGHAKSICLNFGLAQDYKGLC 64 Query: 63 NLRFDDTNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYV 122 NLRFDDTNP KEDI+YV SI+ DV WLGF W G +RYSS+YFDQLH YA+ELINKGLAYV Sbjct: 65 NLRFDDTNPEKEDIDYVNSIQADVHWLGFQWDGEIRYSSNYFDQLHQYAVELINKGLAYV 124 Query: 123 DELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASP 182 L EQ REYRGTL +PGKNSPYRD VEENL LFEKMR G F+EG+ LRAKIDMASP Sbjct: 125 CFLNGEQTREYRGTLKEPGKNSPYRDTFVEENLELFEKMRKGEFKEGECALRAKIDMASP 184 Query: 183 FIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYD 242 F+ MRDPV+YRI+FA HHQTG+KWCIYPMYDFTHCISDALE ITHSLCTLEFQDNRRLYD Sbjct: 185 FMCMRDPVIYRIRFAHHHQTGDKWCIYPMYDFTHCISDALEDITHSLCTLEFQDNRRLYD 244 Query: 243 WVLDNI---TIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRR 299 WVLDN+ P RQYEFSRLNLEYT+MSKRKLN LV V GWDDPRMPTI+GLRR Sbjct: 245 WVLDNLDDFQAPNRTRQYEFSRLNLEYTLMSKRKLNDLVVRGLVSGWDDPRMPTIAGLRR 304 Query: 300 RGYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENY-Q 358 RGYT A+IREFC+RIGVTKQ+N +E++ L++CIRE+LNE+APRAMAVI+PVK++IENY + Sbjct: 305 RGYTPAAIREFCRRIGVTKQENMVEVSMLDACIREELNEHAPRAMAVINPVKVIIENYPE 364 Query: 359 GEGEMVTMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVI 418 G+ E ++ P HP MG R++ F E++ID DFREEANK+YKRL+ GKEVRLRNAYVI Sbjct: 365 GQVEKLSAPAHPTIESMGERELVFGRELYIDADDFREEANKKYKRLIQGKEVRLRNAYVI 424 Query: 419 KAERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFS 478 KAER +KD GN+TTI+CTYD TL K+PADGRKVKGVIHWV A A+P E RLYDRLF+ Sbjct: 425 KAERCDKDEAGNVTTIYCTYDDQTLGKNPADGRKVKGVIHWVEATSAVPAEFRLYDRLFN 484 Query: 479 VPNPGAADDFLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPV 538 PNP AA+ V+NP+SLV+K G EP L +A A KA+QFEREGYFC DS+ S+ E V Sbjct: 485 QPNPAAAETVDEVLNPKSLVVKHGLVEPGLVNAEAEKAYQFEREGYFCADSKDSSPEHLV 544 Query: 539 FNRTVGLRDT 548 FN TV LRD+ Sbjct: 545 FNLTVALRDS 554 Lambda K H 0.319 0.137 0.416 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: 1078 Number of extensions: 40 Number of successful extensions: 3 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: 554 Length of database: 556 Length adjustment: 36 Effective length of query: 518 Effective length of database: 520 Effective search space: 269360 Effective search space used: 269360 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 (21.8 bits) S2: 53 (25.0 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