Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_106716609.1 CU100_RS10940 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_003010935.1:WP_106716609.1 Length = 474 Score = 483 bits (1244), Expect = e-141 Identities = 249/473 (52%), Positives = 317/473 (67%), Gaps = 16/473 (3%) Query: 7 TGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEG 66 + VVTRFAPSPTG+LHIGGARTALFNWLYA+HTGGK L+R+EDTDRERS+EAAV AI +G Sbjct: 3 SSVVTRFAPSPTGYLHIGGARTALFNWLYAKHTGGKMLLRIEDTDRERSSEAAVTAILDG 62 Query: 67 LDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR 126 L WLGL+ D + + Q+ RAPRH V EL++KG+AY C+ S ELE REKARAEGR R Sbjct: 63 LRWLGLEWDGDAVSQYERAPRHRAVAEELVSKGKAYYCYASQAELEEVREKARAEGRPPR 122 Query: 127 --SPWRD-----APEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRAD 179 WRD APEG VIR K P +GETLV D V+G V F N +LDD ++LR+D Sbjct: 123 YDGRWRDRDPSEAPEG---VKPVIRIKAPQEGETLVRDQVQGDVRFPNKDLDDFIILRSD 179 Query: 180 GAPTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGA 239 G PTY AVVVDDHDMGVTH+IRGDDHL NAARQT+IY AM W VP HIPLIHG DGA Sbjct: 180 GNPTYMHAVVVDDHDMGVTHIIRGDDHLTNAARQTVIYDAMGWEVPVMGHIPLIHGADGA 239 Query: 240 KLSKRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPA 299 KLSKRHGA V + +GY+P +RNYL RLGW HGDDE+ +DEQ I WF+++D+ + A Sbjct: 240 KLSKRHGALGVEAYRAMGYLPAALRNYLVRLGWSHGDDEIMSDEQMIQWFEISDINRGAA 299 Query: 300 RLDWAKLNHINAQHLRKADDARLT-ALALAAAETRG-----EPLPADAAERIARTVPEVK 353 R D+ KL IN ++R +DDA L A+ E G L + +++ +P +K Sbjct: 300 RFDFQKLEAINGHYMRMSDDAGLVQAMVDILPEIEGGAEMLSRLDGNTKKQLLAAMPGLK 359 Query: 354 EGAKTILELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLET 413 E AKT++EL D + RPL+L+EK L EE L + QLA+ ++ L+ Sbjct: 360 ERAKTLVELADSAKYLFAQRPLSLDEKAYGLLNEEGRSILSGVLPQLASVEQWEPGPLDA 419 Query: 414 VLKSFAESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466 ++++AE G+ GK LR LTG A +P + +A L R+E++GR+ D + Sbjct: 420 AVRAYAEETGLKLGKIAQPLRAALTGKATSPGVFDVLAVLGREESLGRIKDQI 472 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: 693 Number of extensions: 37 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: 474 Length adjustment: 33 Effective length of query: 437 Effective length of database: 441 Effective search space: 192717 Effective search space used: 192717 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 Jul 26 2024. The underlying query database was built on Jul 25 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