Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_020175690.1 A3OQ_RS0112285 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_000385335.1:WP_020175690.1 Length = 473 Score = 465 bits (1197), Expect = e-135 Identities = 250/474 (52%), Positives = 317/474 (66%), Gaps = 14/474 (2%) Query: 1 MSNPTPTGVVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAV 60 MS+P VVTRFAPSPTGFLHIGGARTALFNWLYA +TGGK L+R+EDTDRERST+AA+ Sbjct: 1 MSDP----VVTRFAPSPTGFLHIGGARTALFNWLYACNTGGKMLLRIEDTDRERSTDAAI 56 Query: 61 AAIFEGLDWLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARA 120 AAI +GL WLGL D +VI+Q RA RH EV LL G+AY C+ + +ELE REKARA Sbjct: 57 AAILDGLSWLGLTWDGDVIYQFQRAQRHREVAQSLLDTGKAYYCYATPKELEEMREKARA 116 Query: 121 EGRAIR--SPWRDAPEGDL--SAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLL 176 E R R WRD P D VIR K P +GET+V D V+G V++ N +LDDLVLL Sbjct: 117 ESRPPRYDGRWRDRPASDAPPDVKPVIRLKAPQEGETVVEDKVQGRVSWANKDLDDLVLL 176 Query: 177 RADGAPTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGP 236 R+DG PTY LAVVVDDHDMGVT +IRGDDHL NAARQ IY+A+ WAVPA AHIPLIHGP Sbjct: 177 RSDGTPTYMLAVVVDDHDMGVTQIIRGDDHLTNAARQMQIYEALGWAVPAMAHIPLIHGP 236 Query: 237 DGAKLSKRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVK 296 DGAKLSKRHGA V + +GY+P+ +RNYL RLGW GD E F+ ++ I FD+A V + Sbjct: 237 DGAKLSKRHGALGVDAYRAMGYLPDALRNYLVRLGWSQGDKEFFSTQEMIEAFDLAHVGR 296 Query: 297 APARLDWAKLNHINAQHLRKADDARLTALALAAAE--TRGEPL--PADAAER--IARTVP 350 + AR D+ KL +N ++R + D L AA EP+ DAA R + R +P Sbjct: 297 SAARFDFVKLESMNGHYMRSSPDEDLLKALNAALPFLPNAEPILQKYDAAMRAKLLRAMP 356 Query: 351 EVKEGAKTILELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAAT 410 +KE AKT++EL+D F RPL +++K + L+ + LK+L + AA PD+ AA Sbjct: 357 GLKERAKTLIELLDGANFLFAERPLPIDDKAKTILSPDGRTHLKQLIPRFAALPDWTAAA 416 Query: 411 LETVLKSFAESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDD 464 E V++++ E V G+ LR LTG + +P + + L R+E++ RL D Sbjct: 417 TEEVVRNYVEETKVKLGQVAQPLRAALTGRSTSPGIFDVLEVLGREESLSRLQD 470 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: 703 Number of extensions: 35 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: 473 Length adjustment: 33 Effective length of query: 437 Effective length of database: 440 Effective search space: 192280 Effective search space used: 192280 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