Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate AZOBR_RS04235 AZOBR_RS04235 glutamyl-tRNA synthetase
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__azobra:AZOBR_RS04235 Length = 452 Score = 265 bits (676), Expect = 3e-75 Identities = 183/464 (39%), Positives = 237/464 (51%), Gaps = 40/464 (8%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 M+V VR APSPTG LH+G R A+ NWL+AR GG F+LR++DTD ERS+PEY E I Sbjct: 1 MSVAVRFAPSPTGLLHVGNVRLALVNWLFARKAGGNFLLRLDDTDEERSKPEYAEGIERD 60 Query: 61 LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120 L WLGLTWD +SDR Y + L G Y CY TPEEL RA ++G+ P Sbjct: 61 LTWLGLTWDRFAR-ESDRYGRYDEVAAALKASGRLYPCYETPEELNLKRASLVSQGRPPI 119 Query: 121 YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIAR 180 YD L ++A E+ GR P RFK+E +EW DLVRG V ++GA L ++I Sbjct: 120 YDRAALRLGDADRARLESEGRKPHWRFKLE-HTPVEWTDLVRGPVHFEGAALSDPVLIR- 177 Query: 181 AAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEAL-----GATPPNF 235 E G PLY L VVDD + IT VIRGEDH+ NT QI ++EAL G P F Sbjct: 178 -----EDGRPLYTLTSVVDDADLAITHVIRGEDHVANTAVQIQIFEALTNSEGGGVVPVF 232 Query: 236 AHTPLILNSTGQKLSKRDGVTSISDFRAMGYLAP-ALANYMTLLGWSPPEGVGELFTLDL 294 AH PL+ ++TGQ LSKR G S++ R + P ALA+ + LG S + + TLD Sbjct: 233 AHLPLLTDATGQGLSKRLGSLSVASLREEEGIEPMALASLLAKLGTS--DAIEPRLTLDE 290 Query: 295 AAKHFSFERINKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDRP 354 F ++++A +FD ++L LN + + L E EL A D+ Sbjct: 291 LVAEFDIAKVSRATPKFDPEELLRLNARILHLLPFERVAGEL------AALGLDDADAAF 344 Query: 355 WLFDLAQLLQPGLNTLREAIDQGAVFFIPSVTFDSEAMAQLGQPQSATILAYLLEHLPAE 414 W + ++P L+ + EA D AV P LA LP E Sbjct: 345 W-----EAVRPNLSRVAEARDWWAVTHAPVAP----------AADDPAFLAEAAALLPEE 389 Query: 415 PALTVAMGQQLIQQAAKAAGVKKGATM-RTLRAALTGAVHGPDL 457 P G A KA +KG + LR ALTG HGP+L Sbjct: 390 PWDLSTWGTW--TGAVKAKTGRKGKDLFLPLRRALTGRDHGPEL 431 Lambda K H 0.320 0.136 0.418 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: 630 Number of extensions: 35 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: 485 Length of database: 452 Length adjustment: 33 Effective length of query: 452 Effective length of database: 419 Effective search space: 189388 Effective search space used: 189388 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: 51 (24.3 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