Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_018123799.1 B149_RS0103595 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_000375485.1:WP_018123799.1 Length = 467 Score = 422 bits (1084), Expect = e-122 Identities = 223/463 (48%), Positives = 298/463 (64%), Gaps = 5/463 (1%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 +V+RFAPSPTGFLHIGGARTALF+WL ARH+GGKFL+RVEDTDRERST+ A+ AI + + Sbjct: 3 IVSRFAPSPTGFLHIGGARTALFSWLLARHSGGKFLLRVEDTDRERSTQEAIDAILDAMK 62 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIRSP 128 WLGL+ D E+ +Q RA RH EV+ +L+ G AY C + E+++ REKARAEGR + Sbjct: 63 WLGLEHDGEITYQSERADRHNEVIDQLIEAGHAYYCDCTKEQVDAMREKARAEGRKPKYD 122 Query: 129 WRDAPEGDLSAP-HVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTYNLA 187 +G + P V+R K PLDG T +DLVKGP+ N E+DD++L R+DG+PTYNLA Sbjct: 123 GSCREKGLEAGPDRVVRLKAPLDGVTAYDDLVKGPIAVNNEEMDDMILRRSDGSPTYNLA 182 Query: 188 VVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRHGA 247 VVVDDHDMGV HV+RGDDH+NN RQ LIY+AM W VP F H+P+I GPD KLSKRHGA Sbjct: 183 VVVDDHDMGVNHVLRGDDHVNNTPRQILIYKAMGWEVPTFGHVPMILGPDKKKLSKRHGA 242 Query: 248 QAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWAKLN 307 +V E+ LGY+PE NYLARLGW HGD E+F+ ++ I FD A++ +P+ D K Sbjct: 243 LSVMEYEKLGYLPEAACNYLARLGWSHGDQEIFSRQEMIDLFDTANLGNSPSVFDLKKFE 302 Query: 308 HINAQHLRKADDARLTALAL-AAAETRGEPLPADA-AERIARTVPEVKEGAKTILELVDH 365 +NA +++AD RLT + + GE A A +++ VP ++ AK I E+V+ Sbjct: 303 WVNAHWIKEADPERLTDMVMDFIGRELGEEAAASAPRDKVLALVPHLQPRAKAIPEMVEQ 362 Query: 366 C-AFALKTRPLALEEK-TQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAESEG 423 F + L +EK K +TEE L+ + ++L A F +LE V K E Sbjct: 363 ARPFIVDAASLPYDEKAVTKFITEEAKPLLQDVLNRLEADETFTHDSLEAVCKGVLEERE 422 Query: 424 VGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466 + F LR +TG ++P + TM L R+E + R+ AL Sbjct: 423 LKFKVLAQPLRVAVTGTTKSPSIYDTMLVLGREETLARIRRAL 465 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: 642 Number of extensions: 33 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: 467 Length adjustment: 33 Effective length of query: 437 Effective length of database: 434 Effective search space: 189658 Effective search space used: 189658 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 10 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