Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_028321419.1 H567_RS0110855 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_000422285.1:WP_028321419.1 Length = 469 Score = 360 bits (924), Expect = e-104 Identities = 208/470 (44%), Positives = 275/470 (58%), Gaps = 17/470 (3%) Query: 5 TPTGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIF 64 T +VTRF PSPTG+LHIGGARTALFNWL+AR GG F++R+EDTD+ RST+ A AI Sbjct: 2 TEQKIVTRFPPSPTGYLHIGGARTALFNWLFARRHGGTFILRIEDTDQARSTDEAAQAII 61 Query: 65 EGLDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRA 124 E + WLGL D FQ R + + +LLA+G+AY C S E LE R A+A G Sbjct: 62 ESMQWLGLDWDAGPYFQSRRYDLYNRAIDQLLAEGKAYHCHCSPELLEEKRSAAKARGL- 120 Query: 125 IRSPWRDAPEGDLS---AP-HVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADG 180 P D DL AP V+R K P G T +DL+KGP+ N ELDDL+L R+DG Sbjct: 121 --KPKYDGTCRDLGLGPAPGSVVRLKCPATGTTHFDDLIKGPIRISNEELDDLILRRSDG 178 Query: 181 APTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAK 240 +PTY++AVV DD D+G+THVIRGDDH+NN RQ IY A+ P +AH+P+I GPD + Sbjct: 179 SPTYHMAVVADDIDLGITHVIRGDDHVNNTPRQIQIYNALGVPTPYYAHVPMILGPDKTR 238 Query: 241 LSKRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPAR 300 LSKRHGA +V + D+GY+P + N L RLGW HGD E FT E+ I F + +V K+ Sbjct: 239 LSKRHGAMSVLAYRDMGYLPHALLNALVRLGWSHGDQEKFTREELIETFSLENVGKSAGV 298 Query: 301 LDWAKLNHINAQHLRKADD---ARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAK 357 + KL +NAQ++R+ D A L A L A RG P A ++ V +K ++ Sbjct: 299 FNLEKLIDLNAQYIRETSDQDLAGLLAPFLDAIGIRGVP-----ARQLEAAVATLKPRSR 353 Query: 358 TILELVDHCAFALKTRPLALEEKTQKQ-LTEETVERLKRLRDQLAAAPDFDAATLETVLK 416 T++E+ D A LA EEK K+ L E + L+ L +L F A LE V + Sbjct: 354 TLVEMAD-AARMYFDETLAYEEKGDKKFLVPEVLPHLEDLARRLKVMGTFTEAALEDVFR 412 Query: 417 SFAESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466 ++ G+ + LR LTG +P L + M L RDE + R+D L Sbjct: 413 AYLGERGIKLKEVAQPLRLALTGRTASPGLFEVMVVLGRDEVLRRIDRVL 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: 629 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: 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 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