Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate Pf1N1B4_24 Glutamyl-tRNA synthetase (EC 6.1.1.17)
Query= metacyc::MONOMER-13959 (483 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_24 Length = 437 Score = 310 bits (794), Expect = 6e-89 Identities = 165/437 (37%), Positives = 261/437 (59%), Gaps = 20/437 (4%) Query: 26 LFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLKWLGIDWDESVDVGGEYGPYRQ 85 LFNY FA+ GG+FI+R+EDTD+ R+ EQ + L+WLGIDW E DVGG +GPYRQ Sbjct: 1 LFNYCFAKQHGGEFILRIEDTDQLRSTRESEQQIFDALRWLGIDWSEGPDVGGPHGPYRQ 60 Query: 86 SERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIARGEMPRYSGKHRDLTQEEQEK 145 SER DIY+ Y ++L++ G A+ C+CT EEL++ R EQ+ARGE PRY G+ L++EE + Sbjct: 61 SERGDIYQKYCQQLVDMGHAFPCFCTAEELDQMRAEQMARGETPRYDGRALLLSKEEVAR 120 Query: 146 FIAEGRKPSIRFRVPEGKVIAFNDIVKGEISFESDGIGDFVIVKKDGTPTYNFAVAIDDY 205 +A G IR +VP V D+++G++ D + V++K DG PTY A +DD+ Sbjct: 121 RLAAGEPHVIRMKVPTEGVCVVPDMLRGDVEIPWDRMDMQVLMKTDGLPTYFLANVVDDH 180 Query: 206 LMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTLIVNESRKKLSKRDESIIQFIE 265 LM +THVLRGE+ + + PK I++Y+ FGW+ PQ +M L+ N + KLSKR + Sbjct: 181 LMGITHVLRGEEWLPSAPKLILLYEYFGWEQPQLCYMPLLRNPDKSKLSKRKNP--TSVT 238 Query: 266 QYKELGYLPEALFNFIGLLGWSPVGEEELFTKEQFIEIFDVNRLSKSPALFDMHKLKWVN 325 Y+ +G++PEA+ N++G +GWS E E F+ ++ ++ FD++R+S +FD+ KL W+N Sbjct: 239 FYERMGFMPEAMLNYLGRMGWSMPDEREKFSLQEMVDNFDLSRVSLGGPIFDIEKLSWLN 298 Query: 326 NQYVKKLDLDQVVELTLPHLQKAGKVGTELSAEEQEWVRKLISLYHEQLSYGAEIVELTD 385 Q+++ L +++ LQK A E++ K+ ++ +++ L Sbjct: 299 GQWLRDLPVEEFA----ARLQK--------WALNPEYMMKIAPHVQGRVETFSQVAPLAG 346 Query: 386 LFFTDEIEYNQEAKAV----LEEEQVPEVLSTFAAKLEELEEFTPDNIKASIKAVQKETG 441 FF + N +AK L +QV +++ KLE L ++ D+I A+I+AV + Sbjct: 347 FFFAGGV--NPDAKLFESKKLSGDQVRQLMQLILWKLESLRQWEKDSITATIQAVVESLE 404 Query: 442 HKGKKLFMPIRVAVTGQ 458 K + + A+TG+ Sbjct: 405 LKLRDAMPLMFAAITGR 421 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: 554 Number of extensions: 25 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: 437 Length adjustment: 33 Effective length of query: 450 Effective length of database: 404 Effective search space: 181800 Effective search space used: 181800 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: 51 (24.3 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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