Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate 352275 BT2748 glutamyl-tRNA synthetase (NCBI ptt file)
Query= metacyc::MONOMER-13959 (483 letters) >FitnessBrowser__Btheta:352275 Length = 504 Score = 325 bits (834), Expect = 2e-93 Identities = 180/499 (36%), Positives = 290/499 (58%), Gaps = 27/499 (5%) Query: 4 EVRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYL 63 +VRVR+APSPTG LHIG RTAL+NYLFAR GG I R+EDTD R + G E+ L Sbjct: 5 KVRVRFAPSPTGALHIGGVRTALYNYLFARQHGGDLIFRIEDTDSNRFVPGAEEYILESF 64 Query: 64 KWLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQI 123 KWLGI +DE V GGE+GPYRQSER +IYK Y + LL+ AY + T EEL+ +R E Sbjct: 65 KWLGIHFDEGVSFGGEHGPYRQSERREIYKKYVQILLDNDKAYIAFDTPEELDAKRAEIA 124 Query: 124 ARGEMPRYSGKHRD---LTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEISFESD 180 G R+ +++EE + IAEG++ +RF++ + + ND+++GE+ S Sbjct: 125 NFQYDASTRGMMRNSLTMSKEEVDALIAEGKQYVVRFKIEPNEDVHVNDLIRGEVVINSS 184 Query: 181 GIGDFVIVKK-DGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWD--IP 237 + D V+ K D PTY+ A +DD+LM+++HV+RGE+ + + P +++Y+AFGW+ +P Sbjct: 185 ILDDKVLYKSADELPTYHLANIVDDHLMEVSHVIRGEEWLPSAPLHVLLYRAFGWEDTMP 244 Query: 238 QFGHMTLIVN-ESRKKLSKRDESIIQF--------------IEQYKELGYLPEALFNFIG 282 +F H+ L++ E KLSKRD + F Y+E GYLPEA+ NF+ Sbjct: 245 EFAHLPLLLKPEGNGKLSKRDGDRLGFPVFPLEWRPESGEVSSGYRESGYLPEAVINFLA 304 Query: 283 LLGWSPVGEEELFTKEQFIEIFDVNRLSKSPALFDMHKLKWVNNQYVKKLDLDQVVELTL 342 LLGW+P ++E+ + ++ I++FD++R SKS A FD K W N+QY++ +++ EL L Sbjct: 305 LLGWNPGNDQEVMSMDEMIKLFDIHRCSKSGAKFDYKKGIWFNHQYIQLKPNEEIAELFL 364 Query: 343 PHLQKAGKVGTELSAEEQEWVRKLISLYHEQLSYGAEIVELTDLFFTDEIEYNQEAKAVL 402 P L++ G E E+ V ++ + +++S+ E+ ++ FF EY+++ Sbjct: 365 PVLKEH---GVEAPFEK---VVTVVGMMKDRVSFIKELWDVCSFFFVAPAEYDEKTVKKR 418 Query: 403 EEEQVPEVLSTFAAKLEELEEFTPDNIKASIKAVQKETGHKGKKLFMPIRVAVTGQTHGP 462 +E + ++ A + +E+F+ + + + E G+ + R+ + G+ GP Sbjct: 419 WKEDSAKCMTELAEVIAGIEDFSIEGQEKVVMDWIAEKGYHTGNIMNAFRLTLVGEGKGP 478 Query: 463 ELPQSIELIGKETAIQRLK 481 + ++GKE + R+K Sbjct: 479 HMFDISWVLGKEETLARMK 497 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: 699 Number of extensions: 39 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: 483 Length of database: 504 Length adjustment: 34 Effective length of query: 449 Effective length of database: 470 Effective search space: 211030 Effective search space used: 211030 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