Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate 7024217 Shewana3_1418 glutamyl-tRNA synthetase (RefSeq)
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__ANA3:7024217 Length = 469 Score = 350 bits (897), Expect = e-101 Identities = 189/458 (41%), Positives = 272/458 (59%), Gaps = 4/458 (0%) Query: 11 TRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLDWL 70 TRFAPSPTGFLH+GGARTAL++WL AR G+F++R+EDTD ERST+AA AI EG++WL Sbjct: 5 TRFAPSPTGFLHVGGARTALYSWLQARANNGEFVLRIEDTDIERSTQAACDAILEGMNWL 64 Query: 71 GLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIRSPW- 129 GL D+ +Q R R+ E++ ++L +G AY+C+ S E ++ RE A G A + Sbjct: 65 GLTWDEGPYYQTKRFDRYNEIIAQMLEQGTAYKCYCSRERIDALREAQAANGEAQKYDGC 124 Query: 130 -RDAPEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTYNLAV 188 RD P D P V+RFK P+ G + +D V+G + F N LDDL++ R DG PTYN V Sbjct: 125 CRDLPARDTDEPFVVRFKNPIGGSVVFDDHVRGRIEFSNDALDDLIIARTDGVPTYNFCV 184 Query: 189 VVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRHGAQ 248 VVDD DMG+T V+RG+DH+NN RQ I +A+ +P +AH+ +I G DGAKLSKRHGA Sbjct: 185 VVDDWDMGITCVVRGEDHINNTPRQINILKALGAPIPEYAHVSMILGDDGAKLSKRHGAV 244 Query: 249 AVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWAKLNH 308 +V ++ D GY+PE + NYL RLGW HGD EVF+ E+ F + D+ KAP+ + KL Sbjct: 245 SVMQYRDDGYLPEALLNYLVRLGWSHGDQEVFSLEEMKQLFKLDDINKAPSAFNTEKLVW 304 Query: 309 INAQHLRKADDARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAKTILELVDHCAF 368 +N QH K D A L + + ++ V + E AKT+ EL + Sbjct: 305 LN-QHYIKTLDPEYVASHL-QWHMDDQKIDTSNGPALSAVVTALAERAKTLKELAASSRY 362 Query: 369 ALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAESEGVGFGK 428 + E+ +K L +E L+ ++ +LAA ++ + +++ A VG GK Sbjct: 363 FYEDFAEFDAEQAKKHLRGVALEPLQLVQQKLAALTEWTVEAIHQAIEATATELEVGMGK 422 Query: 429 FGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466 G LR +TG Q+P L+ T+ + + + R+ A+ Sbjct: 423 VGMPLRVAVTGAGQSPGLDITLFLIGKARSEQRISKAI 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: 622 Number of extensions: 24 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