Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_011385181.1 AMB_RS14100 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_000009985.1:WP_011385181.1 Length = 477 Score = 492 bits (1267), Expect = e-143 Identities = 245/464 (52%), Positives = 319/464 (68%), Gaps = 6/464 (1%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 VVTRFAPSPTGFLHIGG RTALFNWL+ARH GGKFL+R+EDTDR RST+AAV AIF+G+ Sbjct: 3 VVTRFAPSPTGFLHIGGGRTALFNWLFARHHGGKFLLRIEDTDRARSTDAAVEAIFDGIK 62 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIRSP 128 WLGL D E + Q RA RH EV +LL +G+AYRC+ + +EL RE+ +A+G+ +R P Sbjct: 63 WLGLDWDGEAVMQFARACRHAEVARQLLDEGKAYRCYCTQDELTAIREEQKAKGQPMRYP 122 Query: 129 --WRDAPEGDL--SAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTY 184 WRD P D AP V+R K P +GET++ DLV+G V N +LDD+VLLRADG PTY Sbjct: 123 GIWRDRPATDAPEGAPFVVRLKAPAEGETIIADLVQGDVRVANDQLDDMVLLRADGTPTY 182 Query: 185 NLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKR 244 L+VVVDDHDMG+THVIRGDDHL NA RQ +Y+A W VP FAHIPLIHGPDGAKLSKR Sbjct: 183 MLSVVVDDHDMGITHVIRGDDHLTNAFRQYQLYKACGWEVPTFAHIPLIHGPDGAKLSKR 242 Query: 245 HGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWA 304 HGA V + D+G++PE MRNYL RLGW HGDDE+ + EQA+ WF + V ++P+R D+ Sbjct: 243 HGALGVDAYRDMGFLPEAMRNYLLRLGWSHGDDEIISTEQAVEWFTLDSVGRSPSRFDFV 302 Query: 305 KLNHINAQHLRKADDARLTALALAAAETR-GEPLPADAAERIARTVPEVKEGAKTILELV 363 KL ++N ++R ADD RLT + + E + G+ L ++ R+ + +KE AKT++EL Sbjct: 303 KLTNLNGHYMRGADDGRLTEVLVPLLEAKTGKALSGESVARLRTGMTGLKERAKTMVELA 362 Query: 364 DHCAFALKTRPLALEEKTQKQLTEETVER-LKRLRDQLAAAPDFDAATLETVLKSFAESE 422 D F + RPLAL+EK K + +ET L R ++ + TLE + AE+ Sbjct: 363 DSALFYVAERPLALDEKAAKTMADETATADLAAYRTEVKELGAWTRDTLEDAARRLAEAR 422 Query: 423 GVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466 G GK LR L G + +P + + M L R+E++GR++DAL Sbjct: 423 GQKLGKIAQPLRAALAGSSVSPPIFEVMEVLGREESLGRIEDAL 466 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: 718 Number of extensions: 33 Number of successful extensions: 4 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: 477 Length adjustment: 33 Effective length of query: 437 Effective length of database: 444 Effective search space: 194028 Effective search space used: 194028 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