Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate WP_012566189.1 RC1_RS04625 glutamate--tRNA ligase 1
Query= SwissProt::Q8DLI5 (485 letters) >NCBI__GCF_000016185.1:WP_012566189.1 Length = 451 Score = 246 bits (629), Expect = 9e-70 Identities = 177/466 (37%), Positives = 228/466 (48%), Gaps = 45/466 (9%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 MTV VR APSPTG LHIG R A+ NWL+AR GG F+ R++DTD ERS PE+ I E Sbjct: 1 MTVAVRFAPSPTGLLHIGNLRAALTNWLFARKAGGSFLFRLDDTDEERSTPEFAAAIEED 60 Query: 61 LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120 L+WLGL WD +SDR Y A+ L G Y CY T EEL RA ++G+ P Sbjct: 61 LRWLGLDWDRFAR-ESDRYGRYDAAVAALKRAGRLYPCYETAEELALKRAALLSQGRPPI 119 Query: 121 YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIAR 180 YD L ++A EA GR P RF++E +I W DL++G S+Q ADL ++I Sbjct: 120 YDRAALRLGDADRARLEAEGRRPHWRFRLEPG-EIVWDDLIQGHKSFQAADLSDPVLIR- 177 Query: 181 AAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATP-----PNF 235 E G PLY L VVDD IT +IRGEDH+ NT Q+ L++AL P F Sbjct: 178 -----EDGRPLYTLTSVVDDQDFAITHIIRGEDHVTNTAVQVQLFQALAEAEGQGGVPVF 232 Query: 236 AHTPLILNSTGQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPPEGVGELFTLDLA 295 AH PLI + G+ LSKR G S+ R G AL +YM LG S + + +L Sbjct: 233 AHFPLIAGAEGEGLSKRLGSFSLRSLREQGVEPLALCSYMAKLGTS--DAIEARLSLAEL 290 Query: 296 AKHFSFERINKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDRPW 355 A F R+ + RFD ++L LN Q + +P + E + D D W Sbjct: 291 AAEFDLARMGRGTPRFDPEELARLNAQ-VLHAQPFAAVQERL-----RALGLDGADDAFW 344 Query: 356 LFDLAQLLQPGLNTLREAIDQGAVFFIPSVTFDSEAMAQLGQPQSATILAYLLEHLPAEP 415 L ++P L L +A+D V P +G A A LL P P Sbjct: 345 L-----AVRPNLTRLADALDWWQVAHAPLTPV-------IGDTAFAAAAAELLPSEPWGP 392 Query: 416 ----ALTVAMGQQLIQQAAKAAGVKKGATMRTLRAALTGAVHGPDL 457 A T A+ ++ G K A LR ALT HGP+L Sbjct: 393 ETWGAWTAAVKER--------TGAKGKALFLPLRLALTAREHGPEL 430 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: 597 Number of extensions: 40 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: 451 Length adjustment: 33 Effective length of query: 452 Effective length of database: 418 Effective search space: 188936 Effective search space used: 188936 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