Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate BPHYT_RS12355 BPHYT_RS12355 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__BFirm:BPHYT_RS12355 Length = 469 Score = 337 bits (863), Expect = 7e-97 Identities = 189/469 (40%), Positives = 267/469 (56%), Gaps = 12/469 (2%) Query: 7 TGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEG 66 T V TRFAPSPTGF+H+G R+AL+ W +AR G F++R+EDTD ERST +V AI EG Sbjct: 3 TSVRTRFAPSPTGFIHLGNIRSALYPWAFARKMKGTFVLRIEDTDVERSTSESVDAILEG 62 Query: 67 LDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR 126 + WLGL D+ +Q R R+ EV+ ++ G Y C+MS EEL+ RE+ R G R Sbjct: 63 MAWLGLDFDEGPFYQMQRMDRYREVLKQMQDAGLVYPCYMSTEELDALRERQREAGEKPR 122 Query: 127 --SPWRDAPEGDLSAPH-----VIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRAD 179 WR P L P V+RF+ PL G +D VKG + N ELDDLV+ R D Sbjct: 123 YDGTWRPEPGKVLPEPPAGVQPVLRFRNPLTGVVAWDDAVKGRIEISNEELDDLVIARPD 182 Query: 180 GAPTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGA 239 G PTYN VVVDD DM +THVIRGDDH+NN RQ I +A+ P +AH+P + G Sbjct: 183 GTPTYNFCVVVDDLDMRITHVIRGDDHVNNTPRQINILRALGGEPPVYAHLPTVLNEQGE 242 Query: 240 KLSKRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPA 299 K+SKRHGA +V + D G++PE + NYLARLGW HGD E+F+ EQ + WFD+ + K+PA Sbjct: 243 KMSKRHGAMSVVGYRDAGFLPEAVVNYLARLGWSHGDAEIFSREQFVEWFDLEHLGKSPA 302 Query: 300 RLDWAKLNHINAQHLRKADDARLTALALAAAETRG--EPLPADAAERIARTVPEVKEGAK 357 + D KL +NA ++++AD+ARL LA G E A A+ +A V +K+ A Sbjct: 303 QYDHDKLAWLNAHYIKEADNARLAELAKPFFAELGIDEAALAQGAD-LAAVVGLLKDRAS 361 Query: 358 TILELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKS 417 T+ E+ ++ A +T P E + +T+ L L L ++ + LK+ Sbjct: 362 TVKEIAENAAMFYRT-PAPDAESLAQHVTDVVRPALADLAAALKTV-EWTKEAIAAALKA 419 Query: 418 FAESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466 + + + +R ++ G P ++ + RD +GR++ AL Sbjct: 420 TLGAHKLKMPQLAMPVRLLVAGTTHTPSIDSVLMLFGRDVVVGRIEKAL 468 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: 611 Number of extensions: 33 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 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