Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_028988845.1 G579_RS0101950 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_000423825.1:WP_028988845.1 Length = 472 Score = 385 bits (988), Expect = e-111 Identities = 208/463 (44%), Positives = 291/463 (62%), Gaps = 10/463 (2%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 V TRFAPSPTG+LHIGGARTAL++WL+AR GG+F++R+EDTD ERST +V AI +G+ Sbjct: 3 VRTRFAPSPTGYLHIGGARTALYSWLHARSHGGQFVLRIEDTDLERSTPESVQAILDGMG 62 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIRSP 128 WL L D+ +Q R R+ EV+ +LL G+AY C+ + EEL+ RE+ RA G R Sbjct: 63 WLELDWDEGPYYQTQRFDRYREVIGQLLDAGQAYHCYCTREELDAMREEQRARGEKPRYD 122 Query: 129 WR----DAPEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTY 184 R AP + V+RF+ P +GET+V+DL+ G V F+N ELDDL++ R+DG+PTY Sbjct: 123 GRCRHRTAPREGVEP--VVRFRSPDEGETVVDDLIHGRVVFQNSELDDLIIARSDGSPTY 180 Query: 185 NLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKR 244 N VVVDD DMG+T VIRGDDHLNN RQ I QA+ P +AH+P+I GPD K+SKR Sbjct: 181 NFCVVVDDWDMGITDVIRGDDHLNNTPRQIQILQALGATPPRYAHVPMILGPDKQKMSKR 240 Query: 245 HGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWA 304 HGA +V ++ D GY+P+ + NYL RLGW HGD EVF+ E+ I +F + DV KA + + Sbjct: 241 HGAVSVVQYRDEGYLPDALLNYLVRLGWSHGDQEVFSREEMIRYFHIEDVNKAASVFNPE 300 Query: 305 KLNHINAQHLRKADDARLTALALAAAETRGEPLPADAAERIARTVPEVKEGAKTILELVD 364 KL +NA H++ +D A+L A + RG + +DA +A V +E A+T++E+ D Sbjct: 301 KLLWLNAHHIKHSDPAQLAARLRPFLQQRG--VDSDAGPALAEVVRTQQERARTLVEMAD 358 Query: 365 HCAFALKTRPLALEEK-TQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAESEG 423 + F + P A E K K LT + + L+ ++ A D+ A + ++ AE+ G Sbjct: 359 NSLFFYRA-PAAYEPKDAAKHLTADALPLLEAVQQAFEALEDWSAPAIHELVNRVAEAAG 417 Query: 424 VGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466 GK LR + G A +P ++ T+A L R E + RL AL Sbjct: 418 AKLGKLAQPLRVAIAGRAVSPPIDVTLALLGRAETLARLGRAL 460 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: 472 Length adjustment: 33 Effective length of query: 437 Effective length of database: 439 Effective search space: 191843 Effective search space used: 191843 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