Align glutamine-tRNA ligase (EC 6.1.1.18); glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate 208462 DVU2951 glutaminyl-tRNA synthetase
Query= BRENDA::P00962 (554 letters) >MicrobesOnline__882:208462 Length = 570 Score = 654 bits (1687), Expect = 0.0 Identities = 328/554 (59%), Positives = 398/554 (71%), Gaps = 8/554 (1%) Query: 5 EARP-TNFIRQIIDEDLASGKHT-TVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQC 62 EA P +F+R + D +G+ VHTRFPPEPNGYLHIGHAKSICLNFGIA +Y G+C Sbjct: 14 EATPGLDFVRSRVVADNRTGRFDGRVHTRFPPEPNGYLHIGHAKSICLNFGIANEYGGKC 73 Query: 63 NLRFDDTNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYV 122 NLRFDDTNPVKE EYV+SI+ DV W+GF W Y+S+YF+QL+ +A +LI G AYV Sbjct: 74 NLRFDDTNPVKESREYVDSIRTDVAWMGFSWDDREFYASNYFEQLYQFAEQLIMAGKAYV 133 Query: 123 DELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASP 182 D L+ E+IR +RGTLTQPG SPYR+RSVEENL LF +MRAG F +G LRAKIDMASP Sbjct: 134 DSLSAEEIRAHRGTLTQPGTESPYRNRSVEENLDLFRRMRAGEFADGTHVLRAKIDMASP 193 Query: 183 FIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYD 242 +VMRDP LYRI+ A HH+TG+ WCIYPMYDFTHCISD+LEGITHS+CTLEF++NR LYD Sbjct: 194 NVVMRDPTLYRIRHAHHHRTGDAWCIYPMYDFTHCISDSLEGITHSICTLEFENNRELYD 253 Query: 243 WVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRRGY 302 W LD + + HP+Q EF+RLNL YTV+SKRKL LV V+GWDDPRMPTISGLRRRG Sbjct: 254 WTLDALGV-YHPQQIEFARLNLTYTVLSKRKLIQLVEGGFVKGWDDPRMPTISGLRRRGV 312 Query: 303 TAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENY-QGEG 361 ++REFC RIGV K D+T++ E CIRE LN PR M V+DP+++VIENY +G+ Sbjct: 313 PPEALREFCARIGVAKADSTVDYGLFEFCIRERLNATTPRVMGVLDPIRVVIENYPEGQV 372 Query: 362 EMVTMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVIKAE 421 E MP HP GSR VPFS ++I+R DFRE+ K++ RL G EVRLR AY I Sbjct: 373 EEFDMPYHPEDASFGSRIVPFSRVLYIERDDFREDPPKKFFRLAPGAEVRLRYAYYITCR 432 Query: 422 RVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFSVPN 481 V KD GNI + CTYD ++ DGRKVKG +HWVSAAHA+ E+RLY++LF+V + Sbjct: 433 EVVKDEAGNIVELRCTYDPESRGGSSPDGRKVKGTLHWVSAAHAVESEVRLYEQLFAVSD 492 Query: 482 PGAADD---FLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPV 538 P + F +NP+SL + + EPSL G QFER GYFC D S PV Sbjct: 493 PDDVPEGGVFTDNLNPDSLKVVRAMLEPSLGGIEPGTKVQFERMGYFCADP-DSVPGAPV 551 Query: 539 FNRTVGLRDTWAKV 552 FNRTV L+DTWAK+ Sbjct: 552 FNRTVTLKDTWAKL 565 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: 1019 Number of extensions: 45 Number of successful extensions: 5 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: 570 Length adjustment: 36 Effective length of query: 518 Effective length of database: 534 Effective search space: 276612 Effective search space used: 276612 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