Align glutamine-tRNA ligase (EC 6.1.1.18); glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate BPHYT_RS14000 BPHYT_RS14000 glutaminyl-tRNA synthetase
Query= BRENDA::P00962 (554 letters) >FitnessBrowser__BFirm:BPHYT_RS14000 Length = 569 Score = 626 bits (1614), Expect = 0.0 Identities = 314/557 (56%), Positives = 399/557 (71%), Gaps = 15/557 (2%) Query: 9 TNFIRQIIDEDLASGKH-TTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRFD 67 +NFIR IID+D +GK V TRFPPEPNGYLHIGHAKSICLNFG+A+ Y G C+LRFD Sbjct: 12 SNFIRNIIDDDNRTGKWGQRVETRFPPEPNGYLHIGHAKSICLNFGVARSYGGVCHLRFD 71 Query: 68 DTNPVKEDIEYVESIKNDVEWLGFHWS----GNVRYSSDYFDQLHAYAIELINKGLAYVD 123 DTNP KE +EYV+SI + V WLGF W + Y+SDY+D+L+ +A LI +G AYVD Sbjct: 72 DTNPEKESVEYVDSIIDAVRWLGFEWEKDGKAELYYASDYYDKLYEFAELLIERGKAYVD 131 Query: 124 ELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASPF 183 + E++R RG+ T+ G S +R+RSV+ENL LF +M+AG F+EG+ LRAKIDM+SP Sbjct: 132 SQSAEEMRANRGSATEVGTPSRFRERSVQENLDLFRRMKAGEFQEGEHVLRAKIDMSSPN 191 Query: 184 IVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYDW 243 MRDPV+YRI+FA H++TG+KWCIYPMYD+THCISDALE ITHSLCTLEF+D+R LYDW Sbjct: 192 FNMRDPVIYRIRFAHHYRTGDKWCIYPMYDYTHCISDALENITHSLCTLEFEDHRPLYDW 251 Query: 244 VLDNI------TIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGL 297 +L+ + T P+ P+Q EFSRLNL Y + SKRKL LVT+ HV+GWDDPRMPTI G+ Sbjct: 252 ILNELAEAGVFTRPL-PQQIEFSRLNLTYAITSKRKLLQLVTEGHVDGWDDPRMPTIVGV 310 Query: 298 RRRGYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENY 357 RRRG+T SI+ FC+RIGVTK D+ I+M+ E +R+DL+E APR AV+DPVKL+I+N+ Sbjct: 311 RRRGFTPESIQLFCERIGVTKVDSWIDMSVFEGALRDDLDEKAPRTAAVLDPVKLIIDNF 370 Query: 358 -QGEGEMVTMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAY 416 +G E P HP+ PEMG R+ P S E+WI+R D+ E K Y RL G +VRLR Y Sbjct: 371 PEGVTEPCNAPVHPHHPEMGVREFPISRELWIERDDYNETPPKGYFRLFPGNKVRLRYGY 430 Query: 417 VIKAERVEKDAEGNITTIFCTYDADTLS-KDPADGRKVKGVIHWVSAAHALPVEIRLYDR 475 VI+ +KD +GNI + C Y D+ S + A+ KVKG IHWVSAA A P E+R+YDR Sbjct: 431 VIECIGADKDEKGNIVAVHCNYFPDSKSGTEGANNYKVKGNIHWVSAAAACPAEVRIYDR 490 Query: 476 LFSVPNPGAAD-DFLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTA 534 LF P P A DFL +NP+S + + EP ++A+ + +QFER GYF D S Sbjct: 491 LFKEPQPDAGGRDFLEALNPDSKRVVNAYLEPGAREALPEQRYQFERHGYFVADRVDSKP 550 Query: 535 EKPVFNRTVGLRDTWAK 551 KPVFNR V LRD+W K Sbjct: 551 GKPVFNRIVSLRDSWGK 567 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: 1032 Number of extensions: 46 Number of successful extensions: 7 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: 569 Length adjustment: 36 Effective length of query: 518 Effective length of database: 533 Effective search space: 276094 Effective search space used: 276094 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