Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate 3608405 Dshi_1805 glutamyl-tRNA synthetase (RefSeq)
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__Dino:3608405 Length = 471 Score = 456 bits (1173), Expect = e-133 Identities = 247/471 (52%), Positives = 307/471 (65%), Gaps = 9/471 (1%) Query: 1 MSNPTPTGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAV 60 MS + VVTRFAPSPTG+LHIGGARTALFNWLYAR GGKFL+R+EDTD+ RST A Sbjct: 1 MSPTDASPVVTRFAPSPTGYLHIGGARTALFNWLYARGRGGKFLLRIEDTDKARSTAEAT 60 Query: 61 AAIFEGLDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARA 120 AIF GL WLGL D + + Q A RH +V L G+AY+C+ + +E+ RE ARA Sbjct: 61 EAIFAGLRWLGLDWDGDAVSQAEGAARHAQVARALQEAGKAYKCFTTQDEIAAFREAARA 120 Query: 121 EGRA--IRSPWRDA-PEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLR 177 EGR+ RSPWRDA P AP+VIR K P +G T++ D V+G V +N +LDD++LLR Sbjct: 121 EGRSTLFRSPWRDADPASHPDAPYVIRIKAPQEGTTVIADQVQGDVRIRNDQLDDMILLR 180 Query: 178 ADGAPTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPD 237 +DG+P Y LAVVVDDHDMGVTHVIRGDDHLNNAARQ +IY AM W +P FAHIPLIHGPD Sbjct: 181 SDGSPVYMLAVVVDDHDMGVTHVIRGDDHLNNAARQMMIYDAMGWDMPVFAHIPLIHGPD 240 Query: 238 GAKLSKRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKA 297 G KLSKRHGA V E+ +GY + MRNYLARLGW HGDDE F D QA +WFD+ + K+ Sbjct: 241 GKKLSKRHGALGVEEYQAMGYPAQAMRNYLARLGWSHGDDEFFGDAQAQAWFDLDGIGKS 300 Query: 298 PARLDWAKLNHINAQHLRKADDARLTALALAAAETRGEPLPADAAER-IARTVPEVKEGA 356 PARLD KL++++ QHL D + A A G P +A E ++R + +K+ A Sbjct: 301 PARLDLKKLDNLSGQHLGVMADEAIVAGAQGYLAATGAPPLTEAQETGLSRAMYCLKDRA 360 Query: 357 KTILELVDHCAFALKTRPLALEEKTQKQLTEETVER--LKRLRDQLAAAPDFDAATLETV 414 K +L++ F L +RP+ + K K L +TV R L L QL A + TLE V Sbjct: 361 KKFPDLLEKAHFILASRPIDPDPKAAKSL--DTVSRGILAELTPQLQNA-SWTRDTLEGV 417 Query: 415 LKSFAESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDA 465 + AE+ G+G GK LR L G + P + M L RDE + RL DA Sbjct: 418 VGGLAEAHGLGLGKLAAPLRAALAGRSATPSVFDMMLVLGRDETLARLSDA 468 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: 710 Number of extensions: 34 Number of successful extensions: 5 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: 471 Length adjustment: 33 Effective length of query: 437 Effective length of database: 438 Effective search space: 191406 Effective search space used: 191406 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