Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate GFF1673 PGA1_c16960 glutamyl-tRNA synthetase GltX
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__Phaeo:GFF1673 Length = 466 Score = 466 bits (1199), Expect = e-136 Identities = 250/468 (53%), Positives = 306/468 (65%), Gaps = 9/468 (1%) Query: 1 MSNPTPTGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAV 60 MS P VVTRFAPSPTG+LHIGGARTALFNWLYAR GGKFL+R+EDTDRERS A Sbjct: 1 MSKP----VVTRFAPSPTGYLHIGGARTALFNWLYARGRGGKFLLRIEDTDRERSNPEAT 56 Query: 61 AAIFEGLDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARA 120 AAI +G+ WLGL D EV+ Q A RH V ELL G+AY+C+ + EE+ R++A+A Sbjct: 57 AAILQGMAWLGLDHDGEVVSQFEGAERHAAVARELLEAGKAYKCFATQEEIAAFRDEAKA 116 Query: 121 EGRAI--RSPWRDAPEGDL-SAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLR 177 EG++ RSPWRDA + AP+VIR K P DG T++ D V+G VT KN +LDD+VLLR Sbjct: 117 EGKSTLYRSPWRDADDSSHPDAPYVIRIKAPQDGTTVIRDEVQGDVTIKNAQLDDMVLLR 176 Query: 178 ADGAPTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPD 237 +DG P Y LAVVVDDHDMGVTHVIRGDDHLNNAARQ +IY+AM W VP +AHIPLIHG D Sbjct: 177 SDGTPVYMLAVVVDDHDMGVTHVIRGDDHLNNAARQMMIYEAMGWDVPVWAHIPLIHGAD 236 Query: 238 GAKLSKRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKA 297 G KLSKRHGA E+ +GY GMRNYLARLGW HGDDE FTD QA WFD+ + K+ Sbjct: 237 GKKLSKRHGALGAQEYQAMGYPAAGMRNYLARLGWSHGDDEFFTDAQARDWFDLDGIGKS 296 Query: 298 PARLDWAKLNHINAQHLRKADDARLTALALAAAETRGEPLPADA-AERIARTVPEVKEGA 356 PAR D KL ++ QH+ +DDA L A G+P D + + R + +K+ A Sbjct: 297 PARFDTKKLENLCGQHIAISDDAALRNELQAYLAAAGKPQLNDVQSNDLERAMYCLKDRA 356 Query: 357 KTILELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLK 416 KT EL++ F L +RP+ ++K K L + L L QL A + LE +L Sbjct: 357 KTFPELLEKAHFILVSRPIEPDQKAAKALASVSDGILSELTPQLQNA-SWSRDDLEALLN 415 Query: 417 SFAESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDD 464 +FAE++ FGK LR L G A P + M L RDE + RL D Sbjct: 416 AFAEAQDTKFGKLAGPLRAALAGRAVTPSVFDMMLILGRDETLARLSD 463 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: 699 Number of extensions: 36 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: 466 Length adjustment: 33 Effective length of query: 437 Effective length of database: 433 Effective search space: 189221 Effective search space used: 189221 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