Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate WP_012974856.1 AZL_RS12200 glutamate--tRNA ligase
Query= SwissProt::Q8DLI5 (485 letters) >NCBI__GCF_000010725.1:WP_012974856.1 Length = 447 Score = 254 bits (649), Expect = 4e-72 Identities = 179/461 (38%), Positives = 233/461 (50%), Gaps = 39/461 (8%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 M+ VR APSPTG +H+G R A+ NWL+AR GG F+ R++DTD ERS E+ + I Sbjct: 1 MSTAVRFAPSPTGRIHVGNVRQALVNWLFARKTGGSFLFRLDDTDEERSTREFADAIAAD 60 Query: 61 LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120 L WLGLTWD +SDR Y +A L G Y CY TPEEL RA ++G+ P Sbjct: 61 LTWLGLTWDRFAR-ESDRYPRYDEATAALKAAGRLYPCYETPEELNLKRASLVSQGRPPI 119 Query: 121 YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIAR 180 YD LT E++A E GR RFK+ +EW DLVRG V ++G L ++I Sbjct: 120 YDRAALRLTDEDRARLEGEGRKAHWRFKL-TPTPVEWTDLVRGPVRFEGTALSDPVLIR- 177 Query: 181 AAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPL 240 E G PLY L VVDD+ IT VIRGEDH+ NT QI ++EA+GA P FAH PL Sbjct: 178 -----EDGRPLYTLTSVVDDVDFAITHVIRGEDHVANTAVQIQIFEAMGAAVPVFAHLPL 232 Query: 241 ILNSTGQKLSKRDGVTSISDFRAMGYLAP-ALANYMTLLGWSPPEGVGELFTLDLAAKHF 299 + ++ GQ LSKR G S+ R + P A+ + + LG S P + TLD A F Sbjct: 233 LTDAGGQGLSKRLGSLSVGSLRDEDGIEPMAVNSLLAKLGTSDP--IEARLTLDELAAEF 290 Query: 300 SFERINKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPL--WQGAGYAFDEERDRPWLF 357 ++ + +FD ++L LN + I L P E +A + GA AF W Sbjct: 291 DLSKVARGTPKFDPEELGRLNAR-ILHLTPFEAVASRLEALGLTGADAAF-------W-- 340 Query: 358 DLAQLLQPGLNTLREAIDQGAVFFIPSVTFDSEAMAQLGQPQSATILAYLLEHLPAEPAL 417 + ++P L L +A D AV P + A LA LP EP Sbjct: 341 ---EAVRPNLARLDDARDWWAVTHAPVAPL----------VEDAGFLAQAAALLPDEPWD 387 Query: 418 TVAMGQQLIQQAAKAAGVKKGATM-RTLRAALTGAVHGPDL 457 G A K A +KG + LR ALTG HGP+L Sbjct: 388 LGTWGAW--TNAVKGATGRKGKELFLPLRRALTGRDHGPEL 426 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: 633 Number of extensions: 39 Number of successful extensions: 6 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: 447 Length adjustment: 33 Effective length of query: 452 Effective length of database: 414 Effective search space: 187128 Effective search space used: 187128 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 10 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