Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate N515DRAFT_0134 N515DRAFT_0134 glutamyl-tRNA synthetase (EC 6.1.1.17)
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__Dyella79:N515DRAFT_0134 Length = 466 Score = 375 bits (963), Expect = e-108 Identities = 209/468 (44%), Positives = 283/468 (60%), Gaps = 17/468 (3%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 V TRFAPSPTGFLHIGGARTAL+ WL AR GG+F++R+EDTDRERST+ AV AI +G+ Sbjct: 3 VRTRFAPSPTGFLHIGGARTALYCWLEARRRGGQFVLRIEDTDRERSTQEAVQAILDGMS 62 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR-- 126 WLGL D+ ++Q R R+ +V ELL G+AY + S EE+E RE A A G R Sbjct: 63 WLGLVHDEGPVYQTHRLDRYKQVADELLKAGKAYYAYESKEEIEAMREAAMARGEKPRYN 122 Query: 127 SPWRDAPEGDLSAPH-VIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTYN 185 +RD E P+ VIRFK PL+G + +D VKG V + N ELDDLV+ R+DG PTYN Sbjct: 123 GYYRDRNESFREDPNRVIRFKNPLEGSVVFDDKVKGRVEWANAELDDLVIFRSDGWPTYN 182 Query: 186 LAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRH 245 AVVVDD DMG+T VIRGDDH+NN RQ IY+A+D VP FAH+P+I GPDG KLSKRH Sbjct: 183 FAVVVDDIDMGITEVIRGDDHVNNTPRQINIYKALDKPVPEFAHLPMILGPDGQKLSKRH 242 Query: 246 GAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWAK 305 GA +V ++ D G++P + NYL RLGW HGD E+F+ ++ I FD+ DV KA +R D K Sbjct: 243 GAVSVMQYRDDGFLPHALLNYLVRLGWSHGDQEIFSPQEMIELFDIGDVNKAASRFDVTK 302 Query: 306 LNHINAQHLRKADDARLTA------LALAAAETRGEPLPADAAERIARTVPEVKEGAKTI 359 L+ +N QH K D+ + A L LA + PLPAD + +++ +T+ Sbjct: 303 LSWLN-QHYLKTDEPQAIAPEFEYQLQLAGIDYSKGPLPAD-------VIVALRDRVQTL 354 Query: 360 LELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFA 419 E+ + ++ K L + + L AA ++ + ++ A Sbjct: 355 KEMAERAKIWYGPIVEWDDKAVAKHLQNDGAVAVLEEAKALFAACEWTPEAIHQAVEQIA 414 Query: 420 ESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDALA 467 +G GK LR +TG +P ++ T+ R+EA+ R+DDA+A Sbjct: 415 ARLELGMGKIAQPLRVAMTGTQVSPSIDHTVYLAGREEALKRIDDAIA 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: 664 Number of extensions: 31 Number of successful extensions: 4 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: 466 Length adjustment: 33 Effective length of query: 437 Effective length of database: 433 Effective search space: 189221 Effective search space used: 189221 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