Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate YP_426688.1 Rru_A1601 glutamyl-tRNA synthetase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_000013085.1:YP_426688.1 Length = 468 Score = 481 bits (1238), Expect = e-140 Identities = 247/462 (53%), Positives = 310/462 (67%), Gaps = 5/462 (1%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 VVTRFAPSPTGFLHIGGARTALFNWL+ARH GG+FL+R+EDTDR RST AVAAIF+GL+ Sbjct: 3 VVTRFAPSPTGFLHIGGARTALFNWLFARHHGGRFLLRIEDTDRVRSTPEAVAAIFDGLE 62 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR-- 126 WLGL D+E FQ RA RH E HEL+AKG AYRC+ + +EL RE+ +A+G R Sbjct: 63 WLGLDWDEEPTFQFARAARHAEAAHELVAKGLAYRCYCTPDELTAMREEQKAKGLPPRYN 122 Query: 127 SPWRDAPEGDLSA--PHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTY 184 WRD + A VIR K P DGET + D V+G VT N +LDD++LLR+DG PTY Sbjct: 123 GLWRDRDPSEAPAGVAPVIRLKAPQDGETTITDSVQGAVTVANNQLDDMILLRSDGTPTY 182 Query: 185 NLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKR 244 L+VVVDDHDMGVTHVIRGDDHL NA RQT +Y A+ W P FAHIPLIHG DGAKLSKR Sbjct: 183 MLSVVVDDHDMGVTHVIRGDDHLTNAFRQTQLYWALGWETPVFAHIPLIHGADGAKLSKR 242 Query: 245 HGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWA 304 HGA + D+G++PE +RNYL RLGW HGDDEVFT EQA+ WF + + ++P+R D Sbjct: 243 HGALGAEAYRDMGFLPEALRNYLVRLGWAHGDDEVFTTEQAVEWFSLESIGRSPSRFDMQ 302 Query: 305 KLNHINAQHLRKADDARLTALALAAAE-TRGEPLPADAAERIARTVPEVKEGAKTILELV 363 KL +N ++R+ DD RLTAL + E T G +PA + + +KE AKT++EL Sbjct: 303 KLTALNGSYMRETDDDRLTALLVPRLESTLGLDIPAAGHALLRAGMAGLKERAKTLVELA 362 Query: 364 DHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAESEG 423 D AF ++ RPLA++ K +K L +E L L D+L + +LE + + +E G Sbjct: 363 DLAAFYVRPRPLAIDAKAEKALDDEGRTILAALIDKLDDFSPWTRDSLENLARVMSEERG 422 Query: 424 VGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDA 465 V GK +R LTG +P + + M L DE +GRL DA Sbjct: 423 VKLGKVAQPIRAALTGSTVSPPIFEVMEILGPDETLGRLRDA 464 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: 738 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: 468 Length adjustment: 33 Effective length of query: 437 Effective length of database: 435 Effective search space: 190095 Effective search space used: 190095 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