Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate SMc03172 SMc03172 glutamyl-tRNA synthetase
Query= metacyc::MONOMER-13959 (483 letters) >FitnessBrowser__Smeli:SMc03172 Length = 485 Score = 337 bits (864), Expect = 5e-97 Identities = 187/480 (38%), Positives = 276/480 (57%), Gaps = 17/480 (3%) Query: 5 VRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLK 64 VRVR APSPTG H+G A ALFNYLFA+ GGKFI+R+EDTD R+ E+ L+ LK Sbjct: 6 VRVRIAPSPTGEPHVGTAYIALFNYLFAKKHGGKFILRIEDTDATRSTPEFEKKVLDALK 65 Query: 65 WLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIA 124 W G++W E D+GG YGPYRQS+R DIYK Y E+++ G ++C+CT E LE+ RE Q A Sbjct: 66 WCGLEWSEGPDIGGPYGPYRQSDRKDIYKPYVEKIVANGHGFRCFCTPERLEQMREAQRA 125 Query: 125 RGEMPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEISFESDGIGD 184 G+ P+Y G L+ EE + G +R ++P F D V G++ + + Sbjct: 126 AGKPPKYDGLCLSLSAEEVTSRVDAGEPHVVRMKIPTEGSCKFRDGVYGDVEIPWEAVDM 185 Query: 185 FVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTL 244 V++K DG PTY+ A +DD+LMK+THV RGE+ +++ PK I+IYQ G + P F H++L Sbjct: 186 QVLLKADGMPTYHMANVVDDHLMKITHVARGEEWLASVPKHILIYQYLGLEPPVFMHLSL 245 Query: 245 IVNESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLGWSPVGEEELFTKEQFIEIF 304 + N + KLSKR I Y LGYLPEAL NF+GL EEL T E+ E F Sbjct: 246 MRNADKSKLSKRKNP--TSISYYTALGYLPEALMNFLGLFFIQIAEGEELLTMEELAEKF 303 Query: 305 DVNRLSKSPALFDMHKLKWVNNQYVK-KLDLDQVVELTLPHLQKAGKVGTELSAEEQEWV 363 D LSK+ A+FD+ KL W+N ++++ KL ++ L A + E + Sbjct: 304 DPENLSKAGAIFDIQKLDWLNARWIREKLSEEEFAARVLAW------------AMDNERL 351 Query: 364 RKLISLYHEQLSYGAEIVELTDLFFTDEIEYNQEAKAVLE--EEQVPEVLSTFAAKLEEL 421 ++ + L ++S E+ +L F ++ A A ++ E++ ++L+T LE++ Sbjct: 352 KEGLKLSQTRISKLGELPDLAAFLFKSDLGLQPAAFAGVKASPEEMLKILNTVQPDLEKI 411 Query: 422 EEFTPDNIKASIKAVQKETGHKGKKLFMPIRVAVTGQTHGPELPQSIELIGKETAIQRLK 481 E+ D+I+ ++A + G K K + P+ VA +G L S+EL+G+ QRLK Sbjct: 412 LEWNKDSIETELRASAERMGKKLKAVVAPLFVACSGSQRSLPLFDSMELLGRSVVRQRLK 471 Lambda K H 0.316 0.137 0.394 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: 655 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: 483 Length of database: 485 Length adjustment: 34 Effective length of query: 449 Effective length of database: 451 Effective search space: 202499 Effective search space used: 202499 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