Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate 6938086 Sama_2207 glutamyl-tRNA synthetase (RefSeq)
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__SB2B:6938086 Length = 469 Score = 348 bits (893), Expect = e-100 Identities = 188/460 (40%), Positives = 274/460 (59%), Gaps = 4/460 (0%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 V TRFAPSPTGFLH+GGARTAL++WL+AR G+F++R+EDTD ERST+ AV AI EG++ Sbjct: 3 VKTRFAPSPTGFLHVGGARTALYSWLHARANQGEFVLRIEDTDLERSTQEAVDAILEGME 62 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIRSP 128 WL L D+ +Q R R+ E++ ++L G AY+C+ S E LE RE+ A+G + Sbjct: 63 WLNLNWDEGPYYQTKRFDRYNEIIDQMLKAGTAYKCYCSKERLEAVREEQAAKGERQKYD 122 Query: 129 W--RDAPEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTYNL 186 R A PHV+RF P G + +D V+G + N ELDDL++ R DG+PTYN Sbjct: 123 GCCRGAAPRAEGEPHVVRFLNPQGGSVVFDDHVRGRIEIANEELDDLIIRRTDGSPTYNF 182 Query: 187 AVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRHG 246 VVVDD DMG+THV+RG+DH+NN RQ I +A+ +P +AH+ +I G DGAKLSKRHG Sbjct: 183 CVVVDDWDMGITHVVRGEDHINNTPRQINILKALGAPIPEYAHVSMILGDDGAKLSKRHG 242 Query: 247 AQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWAKL 306 A +V ++ D GY+PE + NYL RLGW HGD E+F+ ++ + +F + D+ KA + + KL Sbjct: 243 AVSVMQYRDDGYLPEALLNYLVRLGWSHGDQEIFSMDELVEFFRLDDINKAASAFNSEKL 302 Query: 307 NHINAQHLRKADDARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAKTILELVDHC 366 +N QH KA D A L + + + +A V + E AKT+ EL Sbjct: 303 LWLN-QHYIKALDPEYVAKHL-EWHMKDQGIDTSNGPALADVVTALSERAKTLKELAASS 360 Query: 367 AFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAESEGVGF 426 + + ++ +K L +E LK ++ +LAA ++ + ++ A VG Sbjct: 361 RYFYEDFEEFDADQAKKHLRGVALEPLKLVQQKLAALTEWTREAIHQAIEETATELEVGM 420 Query: 427 GKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466 GK G LR +TG Q+P L+ T+ + + + R+ A+ Sbjct: 421 GKVGMPLRVAVTGAGQSPGLDITLELIGKARSEQRISKAV 460 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: 630 Number of extensions: 29 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