Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate 8500239 DvMF_0996 glutamyl-tRNA synthetase (RefSeq)
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__Miya:8500239 Length = 464 Score = 360 bits (925), Expect = e-104 Identities = 208/465 (44%), Positives = 266/465 (57%), Gaps = 8/465 (1%) Query: 7 TGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEG 66 T VVTRFAPSPTG LHIGGARTA+FNWL ARH GG FL+R+EDTD+ERS + +I Sbjct: 2 TKVVTRFAPSPTGHLHIGGARTAIFNWLLARHFGGTFLLRIEDTDQERSLQEYTDSILAS 61 Query: 67 LDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR 126 + WLGL D ++I+Q R + + +L G AY C + EE+E RE AR G + Sbjct: 62 MRWLGLDWDGDLIYQSRRFDIYNGYIDRMLETGHAYWCECTPEEVEQMRETARERGLKPK 121 Query: 127 SPWRDAPEGDLSAP-HVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTYN 185 R G P V+R K PL G + D+VKG + F ELDD+VL R+DG PTYN Sbjct: 122 YDGRCRERGLGPGPGRVVRLKAPLTGRVVFEDVVKGTLAFDAAELDDMVLRRSDGTPTYN 181 Query: 186 LAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRH 245 +AVVVDD MGVTHV+RGDDH++N +Q LIYQA+ +P F H+P+I GPD KLSKRH Sbjct: 182 MAVVVDDATMGVTHVLRGDDHVSNTPKQVLIYQALGLPLPIFGHVPMILGPDKKKLSKRH 241 Query: 246 GAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWAK 305 GA+AV E+ G +P+ + NYL RLGW GD E+F ++ + F ++ APA D K Sbjct: 242 GARAVIEYEQDGLLPQALVNYLVRLGWSFGDQEIFALQELVEKFTTDNLNSAPAAFDPDK 301 Query: 306 LNHINAQHLRKADDARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAKTILELVDH 365 L +NA +LR+ L LA + G + A ER+A VP +E A + +L Sbjct: 302 LQWLNAHYLRETPVDELARLAAPFVKAEGFDV---APERLATLVPLFRERASNLADLARV 358 Query: 366 CAFALKTRPLALEE---KTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAESE 422 F L ALE K LT E + LR L A FD A LE V+ + E Sbjct: 359 MRFML-VDATALEHDPAAVAKALTAEGKAHVAALRGLLEQADPFDKAALEKVVHDYVEQG 417 Query: 423 GVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDALA 467 G+ F + GP LR L G P L + M L R E + RLD A A Sbjct: 418 GLKFKQVGPPLRVALAGSLGGPGLPEIMEVLGRAETLARLDRAAA 462 Lambda K H 0.319 0.135 0.405 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: 675 Number of extensions: 37 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: 470 Length of database: 464 Length adjustment: 33 Effective length of query: 437 Effective length of database: 431 Effective search space: 188347 Effective search space used: 188347 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 (21.7 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