Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate Dsui_2789 Dsui_2789 glutamyl-tRNA synthetase
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__PS:Dsui_2789 Length = 463 Score = 374 bits (959), Expect = e-108 Identities = 209/463 (45%), Positives = 278/463 (60%), Gaps = 19/463 (4%) Query: 11 TRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLDWL 70 TRFAPSPTG+LHIGGARTALF+W YAR GGKF++R+EDTD RST AV AI +G++WL Sbjct: 4 TRFAPSPTGYLHIGGARTALFSWAYARRHGGKFVLRIEDTDVARSTPEAVQAIIDGMNWL 63 Query: 71 GLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR--SP 128 GL+ D+ +Q R R+ EV+ ++L G AY C+ S EELE RE RA+G R Sbjct: 64 GLEHDEGPFYQMQRIYRYKEVIQQMLEAGTAYHCYTSPEELEQIREAQRAKGEKPRYDGR 123 Query: 129 WRDAPEGDLSAPH-----VIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPT 183 WR P L P V+RFK P+DG +DLVKG + N ELDD ++ RADG PT Sbjct: 124 WRPEPGKTLPTPPSGIQPVVRFKNPVDGVVTWDDLVKGRIEISNSELDDFIIARADGTPT 183 Query: 184 YNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSK 243 YN VVVDD DMG+T VIRGDDH+NN RQ + QA+ +VP +AH+ +I G DG KLSK Sbjct: 184 YNFCVVVDDWDMGITQVIRGDDHVNNTPRQINVLQALGASVPQYAHLSMILGDDGQKLSK 243 Query: 244 RHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDW 303 RHGA +V ++ + GY+PE + NYL RLGW HGDDEVF+ EQ WFD+ + + A+ + Sbjct: 244 RHGAVSVMQYDEDGYLPEAVLNYLGRLGWSHGDDEVFSMEQFCQWFDLDHITPSAAQFNT 303 Query: 304 AKLNHINAQHLRKADDARLTALALAAAETRG-EPLPADAAERIARTVPEVKEGAKTILEL 362 KLN +NA ++++AD+ RL L RG P P A E I + KE T+ EL Sbjct: 304 EKLNWLNAHYIKQADNGRLADLVRPRLAARGITPAPVPALESI---IALYKERVHTLNEL 360 Query: 363 VDHC-AFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAP--DFDAATLETVLKSFA 419 D F + P A E + L+EE L D +A +++A + ++K Sbjct: 361 ADAAEVFYIDIHPNA--ELLAQHLSEEA---KPALADFIAGVQGVNWEAPAIGALIKETV 415 Query: 420 ESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRL 462 G+ K LR +LTG AQ P ++ +A R++ + RL Sbjct: 416 AKHGLKMPKLAMPLRVLLTGQAQTPSVDAVVALFPREKVLARL 458 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: 656 Number of extensions: 39 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: 463 Length adjustment: 33 Effective length of query: 437 Effective length of database: 430 Effective search space: 187910 Effective search space used: 187910 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