Align Glutamate--tRNA ligase; Glutamyl-tRNA synthetase; GluRS; EC 6.1.1.17 (characterized)
to candidate Synpcc7942_2393 Synpcc7942_2393 glutamyl-tRNA synthetase
Query= SwissProt::Q8DLI5 (485 letters) >FitnessBrowser__SynE:Synpcc7942_2393 Length = 481 Score = 614 bits (1583), Expect = e-180 Identities = 309/482 (64%), Positives = 366/482 (75%), Gaps = 2/482 (0%) Query: 1 MTVRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEG 60 ++VRVR+APSPTGNLHIGTARTAVFNWL+AR G+FILRIEDTD ERSR EYT+NIL G Sbjct: 1 VSVRVRIAPSPTGNLHIGTARTAVFNWLFARRHQGQFILRIEDTDLERSRSEYTDNILTG 60 Query: 61 LQWLGLTWDEGPYFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKAKGQAPR 120 LQWLGL WDEGP++Q+ RLDLY+ A+Q LLD G AY CYCT ELEALR Q+A+ +APR Sbjct: 61 LQWLGLNWDEGPFYQTQRLDLYKAAVQQLLDSGKAYRCYCTEAELEALRESQRARNEAPR 120 Query: 121 YDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGGDMVIAR 180 YDNRHR LTPE++AAF+A GR VIRF+I+DDR+I W DLVR RV W+G+DLGGDMVIAR Sbjct: 121 YDNRHRDLTPEQEAAFQAEGREAVIRFRIDDDREIAWTDLVRDRVVWKGSDLGGDMVIAR 180 Query: 181 AAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPNFAHTPL 240 +P G IG PLYNL VVVDDI M I+ VIRGEDHI NT KQILLYEALGA P FAHTPL Sbjct: 181 RSPAGTIGQPLYNLAVVVDDIDMTISHVIRGEDHIANTAKQILLYEALGAAVPEFAHTPL 240 Query: 241 ILNSTGQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPPEGVGELFTLDLAAKHFS 300 ILN G+KLSKRDGVTSISDF+ +GYL A+ANYMTLLGWSP EG+ E F+L AA F Sbjct: 241 ILNKEGRKLSKRDGVTSISDFQNLGYLPEAIANYMTLLGWSPVEGMDERFSLAEAATVFD 300 Query: 301 FERINKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDRPWLFDLA 360 F+R+NKAGA+FDWDKLNWLN Q I++ E +A L P W AG WL +LA Sbjct: 301 FDRVNKAGAKFDWDKLNWLNSQVIKEKSASELVALLQPFWSKAG-VDTAAYPAAWLEELA 359 Query: 361 QLLQPGLNTLREAIDQGAVFFIPSVTFDSEAMAQLGQPQSATILAYLLEHLPAEPALTVA 420 LL P L TL + + Q +FF + +A+AQLGQ S +L +LE LP+E ALT+ Sbjct: 360 TLLGPSLVTLTDIVGQSQLFFSQGIELQEDAIAQLGQAGSKAVLQQILEALPSE-ALTLE 418 Query: 421 MGQQLIQQAAKAAGVKKGATMRTLRAALTGAVHGPDLMAAWQILHQRGWDEPRLAAALKQ 480 + + LI QA KAAGVKKG MR+LRAAL G++ GPDL+ +W +LHQ G +PRL AA+ Sbjct: 419 VAKGLIDQAVKAAGVKKGIGMRSLRAALMGSMQGPDLLTSWVLLHQAGQAQPRLQAAIAA 478 Query: 481 AQ 482 AQ Sbjct: 479 AQ 480 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: 740 Number of extensions: 30 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: 485 Length of database: 481 Length adjustment: 34 Effective length of query: 451 Effective length of database: 447 Effective search space: 201597 Effective search space used: 201597 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: 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