Align Glutamate--tRNA ligase; EC 6.1.1.17 (characterized, see rationale)
to candidate 5208954 Shew_1449 glutamyl-tRNA synthetase (RefSeq)
Query= uniprot:A0A0H3C8P5_CAUVN (470 letters) >FitnessBrowser__PV4:5208954 Length = 469 Score = 337 bits (863), Expect = 7e-97 Identities = 184/460 (40%), Positives = 267/460 (58%), Gaps = 4/460 (0%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 + TRFAPSPTGFLH+GGARTAL++WLYAR G+F++R+EDTD ERST A AAI EG++ Sbjct: 3 IKTRFAPSPTGFLHVGGARTALYSWLYARANQGEFVLRIEDTDLERSTPEACAAILEGME 62 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIRSP 128 WLGL D+ +Q R R+ E++ ++L +G AY+C+ S E +E RE+ A+G + Sbjct: 63 WLGLNWDEGPYYQTKRFDRYNEIIAQMLEQGTAYKCYCSRERIEAMREEQAAKGEQQKYD 122 Query: 129 W--RDAPEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTYNL 186 RD D P V+RFK P +G + +D V+G + N LDDL++ R DG PTYN Sbjct: 123 GCCRDKAPRDTDEPFVVRFKNPTEGSVVFDDHVRGRIEISNELLDDLIIARTDGTPTYNF 182 Query: 187 AVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRHG 246 VVVDD DMG+T V+RG+DH+NN RQ I +A++ VP +AH+ +I G DGAKLSKRHG Sbjct: 183 CVVVDDWDMGITCVVRGEDHINNTPRQINILKALNAPVPEYAHVAMILGDDGAKLSKRHG 242 Query: 247 AQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWAKL 306 A V ++ D GY+PE + NYL RLGW HGD EVF+ E+ +F + D+ KA + + KL Sbjct: 243 AVGVMQYRDDGYLPEALLNYLVRLGWSHGDQEVFSIEEMKQYFKLDDINKAASAFNTEKL 302 Query: 307 NHINAQHLRKADDARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAKTILELVDHC 366 +N QH K A L + + + +A V + E AKT+ EL Sbjct: 303 IWLN-QHYMKELAPEYVAKHL-EWHMQDQNIDTANGPALAEVVSALAERAKTLKELAASS 360 Query: 367 AFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAESEGVGF 426 + + E +K L +E L+ L+ + A +++ + +++ A +G Sbjct: 361 RYFYEDFAEFDETAAKKHLRGVALEPLQLLQKKFAELSEWNVEAIHQAIEATAAELELGM 420 Query: 427 GKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466 GK G LR +TG +P ++ T + + R+ A+ Sbjct: 421 GKVGMPLRVAVTGAGMSPAVDLTAFLVGKARCEQRISKAI 460 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: 642 Number of extensions: 31 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: 469 Length adjustment: 33 Effective length of query: 437 Effective length of database: 436 Effective search space: 190532 Effective search space used: 190532 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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