Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_028486606.1 B076_RS0106510 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_000483485.1:WP_028486606.1 Length = 469 Score = 370 bits (950), Expect = e-107 Identities = 201/468 (42%), Positives = 283/468 (60%), Gaps = 21/468 (4%) Query: 11 TRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLDWL 70 TRFAPSPTG+LHIGG RTALF+WLYA+ GG+F++R+EDTD ERST+ +V AI EG+ WL Sbjct: 4 TRFAPSPTGYLHIGGVRTALFSWLYAKKLGGEFILRIEDTDLERSTQESVNAILEGMSWL 63 Query: 71 GLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIRSPWR 130 GL D +Q R R+ EV+ L KG AY C+ + EEL+ RE +A G R R Sbjct: 64 GLDYDQGPFYQTHRFERYKEVIDLLFEKGLAYYCYATPEELDEMREAQKAAGEKPRYDGR 123 Query: 131 ------DAPEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTY 184 +APEG VIRFK P +GE ++ND VKG V N ELDDL++ R+DG PTY Sbjct: 124 YRNFNGEAPEG---IKPVIRFKNPEEGEVVINDQVKGKVVIANKELDDLIIARSDGTPTY 180 Query: 185 NLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKR 244 NL VVVDD DMGVTHVIRGDDHLNN RQ +Y+A+ VP F+HIP++ G DG++LSKR Sbjct: 181 NLTVVVDDWDMGVTHVIRGDDHLNNTPRQINLYEAIGAEVPKFSHIPMVLGEDGSRLSKR 240 Query: 245 HGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWA 304 HGA +V ++ + G++PE + NYL RLGW +GD E+FT +Q I +FD+ V +P+ + Sbjct: 241 HGAVSVLQYKEQGFLPEALLNYLVRLGWSYGDQEIFTIDQMIEFFDLDSVNSSPSTFNTE 300 Query: 305 KLNHINAQHLRKADDARLTA-----LALAAAETRGEPLPADAAERIARTVPEVKEGAKTI 359 KL IN QH++ A L+ + + P AD A+ + ++ AKT Sbjct: 301 KLTWINEQHIKMAKPEHLSRHLAPFVTELGCDLNNGPDLADVADLL-------RDRAKTF 353 Query: 360 LELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFA 419 +E+ + + + +K L E L+ L ++L + ++ + T+ +++ A Sbjct: 354 IEMANSATYFYQDFEEFEAGAAKKHLRPVAEEPLQLLFNKLQSLDNWQSETIHEAIQAAA 413 Query: 420 ESEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDALA 467 E +G GK G LR +TGG Q+P ++ T + + + R+ ALA Sbjct: 414 EELELGMGKVGMPLRVAITGGGQSPAIDATAQLIGQKRCLERIKMALA 461 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: 603 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: 469 Length adjustment: 33 Effective length of query: 437 Effective length of database: 436 Effective search space: 190532 Effective search space used: 190532 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