Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_041099473.1 SUTH_RS11795 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_000828635.1:WP_041099473.1 Length = 472 Score = 368 bits (945), Expect = e-106 Identities = 205/473 (43%), Positives = 274/473 (57%), Gaps = 15/473 (3%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 V TRFAPSPTGFLHIGGARTALF+W YAR GG F++R+EDTD RST AV AI +G+ Sbjct: 3 VRTRFAPSPTGFLHIGGARTALFSWAYARRHGGSFILRIEDTDVARSTPEAVQAIIDGMQ 62 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR-- 126 WLGL D+ +Q R R+ EV+ ++L G AY C+M EEL+ RE RA G R Sbjct: 63 WLGLAHDEGPFYQMQRMYRYKEVIQQMLEVGTAYHCYMPSEELDQLREAQRARGEKPRYD 122 Query: 127 SPWRDA---------PEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLR 177 WR + P V+RF+ PLDG +DLVKG + F N ELDD ++ R Sbjct: 123 GRWRPSLANEAGKALPTPPSGVQPVVRFRNPLDGVVAWDDLVKGRIEFANEELDDFIIAR 182 Query: 178 ADGAPTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPD 237 ADG PTYN VVVDD DM +THVIRGDDH+NN RQ + +A+ AVP +AH+ +I G D Sbjct: 183 ADGTPTYNFCVVVDDRDMEITHVIRGDDHVNNTPRQINLLRALGAAVPEYAHLSMILGDD 242 Query: 238 GAKLSKRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKA 297 G KLSKRHGA +V ++ + GY+PE + NYLARLGW HGD+EVF EQ + WFD+ + + Sbjct: 243 GQKLSKRHGAVSVMQYDEDGYLPEAVLNYLARLGWSHGDEEVFGMEQFVQWFDLDHITAS 302 Query: 298 PARLDWAKLNHINAQHLRKADDARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAK 357 A+ + KLN +NA +L+ AD RL A A +G + +A+ V ++ A Sbjct: 303 AAQFNTEKLNWLNAHYLKLADPQRLAAEATRRLAAQG--VAVAGGPEMAKLVALYRDRAG 360 Query: 358 TILELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKS 417 + EL D P EE + TE ++ L+ L +L+A ++ AA L +K Sbjct: 361 NLNELAD-AVHPFHVAPKPTEELRAQHFTEAALKGLRLLHQRLSAC-NWQAAELGQAVKQ 418 Query: 418 FAESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDALAPRA 470 A G+ + LR L G Q+P ++ + L R+ + RL L A Sbjct: 419 SAAESGLKMPQLAIPLRVALLGLPQSPSIDAVLEVLGRERVLARLAAVLPAEA 471 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: 670 Number of extensions: 40 Number of successful extensions: 2 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: 472 Length adjustment: 33 Effective length of query: 437 Effective length of database: 439 Effective search space: 191843 Effective search space used: 191843 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