Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate AO356_21340 AO356_21340 glutamate--tRNA ligase
Query= metacyc::MONOMER-13959 (483 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_21340 Length = 493 Score = 343 bits (879), Expect = 1e-98 Identities = 182/479 (37%), Positives = 285/479 (59%), Gaps = 16/479 (3%) Query: 5 VRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLK 64 VR R APSPTG H+G A ALFNY FA+ GG+FI+R+EDTD+ R+ EQ + L+ Sbjct: 4 VRTRIAPSPTGDPHVGTAYIALFNYCFAKQHGGEFILRIEDTDQLRSTRESEQQIFDALR 63 Query: 65 WLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIA 124 WLGIDW E DVGG +GPYRQSER DIYK Y ++L++ G A+ C+CT EEL++ R EQ+A Sbjct: 64 WLGIDWSEGPDVGGPHGPYRQSERGDIYKQYCQQLVDMGHAFPCFCTAEELDQMRAEQMA 123 Query: 125 RGEMPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEISFESDGIGD 184 RGE PRY G+ L++EE + +A G IR +VP V D+++G++ D + Sbjct: 124 RGETPRYDGRALLLSKEEVARRLAAGEPHVIRMKVPSEGVCVVPDMLRGDVEIPWDRMDM 183 Query: 185 FVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTL 244 V++K DG PTY A +DD+LM +THVLRGE+ + + PK I++Y+ FGW+ PQ +M L Sbjct: 184 QVLMKTDGLPTYFLANVVDDHLMGITHVLRGEEWLPSAPKLILLYEYFGWEQPQLCYMPL 243 Query: 245 IVNESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLGWSPVGEEELFTKEQFIEIF 304 + N + KLSKR + Y+ +G++PEA+ N++G +GWS E E F+ ++ +E F Sbjct: 244 LRNPDKSKLSKRKNP--TSVTFYERMGFMPEAMLNYLGRMGWSMPDEREKFSLQEMVEHF 301 Query: 305 DVNRLSKSPALFDMHKLKWVNNQYVKKLDLDQVVELTLPHLQKAGKVGTELSAEEQEWVR 364 D++R+S +FD+ KL W+N Q+++ L +++ A +V + A E++ Sbjct: 302 DLSRVSLGGPIFDIEKLSWLNGQWLRDLPVEEF----------AARV--QKWALNPEYMM 349 Query: 365 KLISLYHEQLSYGAEIVELTDLFFTDEIEYNQE--AKAVLEEEQVPEVLSTFAAKLEELE 422 K+ ++ ++I L FF + + + L +QV +++ KLE L Sbjct: 350 KIAPHVQGRVETFSQIAPLAGFFFAGGVTPDAKLFESKKLSGDQVRQLMQLILWKLESLR 409 Query: 423 EFTPDNIKASIKAVQKETGHKGKKLFMPIRVAVTGQTHGPELPQSIELIGKETAIQRLK 481 ++ D+I A+I+AV + K + + A+TGQ + ++E++G + RL+ Sbjct: 410 QWEKDSITATIQAVVESLELKLRDAMPLMFAAITGQASSVSVLDAMEILGPDLTRFRLR 468 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: 623 Number of extensions: 27 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: 493 Length adjustment: 34 Effective length of query: 449 Effective length of database: 459 Effective search space: 206091 Effective search space used: 206091 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