Align Glutamate--tRNA ligase; EC 6.1.1.17 (characterized, see rationale)
to candidate 16503 b2400 glutamyl-tRNA synthetase (NCBI)
Query= uniprot:A0A0H3C8P5_CAUVN (470 letters) >FitnessBrowser__Keio:16503 Length = 471 Score = 353 bits (907), Expect = e-102 Identities = 190/466 (40%), Positives = 280/466 (60%), Gaps = 15/466 (3%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 + TRFAPSPTG+LH+GGARTAL++WL+AR+ GG+F++R+EDTD ERST A+ AI +G++ Sbjct: 3 IKTRFAPSPTGYLHVGGARTALYSWLFARNHGGEFVLRIEDTDLERSTPEAIEAIMDGMN 62 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIRSP 128 WL L+ D+ +Q R R+ V+ ++L +G AY+C+ S E LE RE+ A+G R Sbjct: 63 WLSLEWDEGPYYQTKRFDRYNAVIDQMLEEGTAYKCYCSKERLEALREEQMAKGEKPRYD 122 Query: 129 WRDAPEGDLSA---PHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTYN 185 R + A P V+RF P +G + +D ++GP+ F N ELDDL++ R DG+PTYN Sbjct: 123 GRCRHSHEHHADDEPCVVRFANPQEGSVVFDDQIRGPIEFSNQELDDLIIRRTDGSPTYN 182 Query: 186 LAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRH 245 VVVDD DM +THVIRG+DH+NN RQ I +A+ VP +AH+ +I+G DG KLSKRH Sbjct: 183 FCVVVDDWDMEITHVIRGEDHINNTPRQINILKALKAPVPVYAHVSMINGDDGKKLSKRH 242 Query: 246 GAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPA-----R 300 GA +V ++ D GY+PE + NYL RLGW HGD E+FT E+ I +F + V K+ + + Sbjct: 243 GAVSVMQYRDDGYLPEALLNYLVRLGWSHGDQEIFTREEMIKYFTLNAVSKSASAFNTDK 302 Query: 301 LDWAKLNHINAQHLRKADDARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAKTIL 360 L W ++INA + +TR P AD + + E KT+ Sbjct: 303 LLWLNHHYINALPPEYVATHLQWHIEQENIDTRNGPQLADLVKLLG-------ERCKTLK 355 Query: 361 ELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAE 420 E+ C + + + +K L + L+ +RD+LAA D+ A + +++ A+ Sbjct: 356 EMAQSCRYFYEDFAEFDADAAKKHLRPVARQPLEVVRDKLAAITDWTAENVHHAIQATAD 415 Query: 421 SEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466 VG GK G LR +TG Q+P L+ T+ A+ + +I R++ AL Sbjct: 416 ELEVGMGKVGMPLRVAVTGAGQSPALDVTVHAIGKTRSIERINKAL 461 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: 661 Number of extensions: 28 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: 471 Length adjustment: 33 Effective length of query: 437 Effective length of database: 438 Effective search space: 191406 Effective search space used: 191406 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