Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_011840551.1 RSPH17029_RS03600 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_000015985.1:WP_011840551.1 Length = 471 Score = 489 bits (1259), Expect = e-143 Identities = 256/463 (55%), Positives = 312/463 (67%), Gaps = 5/463 (1%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 VVTRFAPSPTG+LHIGG RTALFNWLYAR G FL+R+EDTDRERST A AI GL Sbjct: 9 VVTRFAPSPTGYLHIGGGRTALFNWLYARGRKGTFLLRIEDTDRERSTPEATDAILRGLT 68 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRA--IR 126 WLGL D EV+ Q R RH EV E+LA+G AY+C+ + EE+E RE ARAEGR+ R Sbjct: 69 WLGLDWDGEVVSQFARKDRHAEVAREMLARGAAYKCFSTQEEIEAFREAARAEGRSTLFR 128 Query: 127 SPWRDA-PEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTYN 185 SPWRDA P AP VIR K P GET++ D V+G V F+N LDD+V+LR+DG PTY Sbjct: 129 SPWRDADPTSHPDAPFVIRMKAPRSGETVIEDEVQGTVRFQNETLDDMVVLRSDGTPTYM 188 Query: 186 LAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKRH 245 LAVVVDDHDMGVTHVIRGDDHLNNAARQT++Y+AM W VP +AHIPLIHGPDG KLSKRH Sbjct: 189 LAVVVDDHDMGVTHVIRGDDHLNNAARQTMVYEAMGWEVPVWAHIPLIHGPDGKKLSKRH 248 Query: 246 GAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWAK 305 GA V E+ +GY GMRNYLARLGW HGDDE FT EQA+ WFD+ + ++PARLD+ K Sbjct: 249 GALGVEEYQAMGYPAAGMRNYLARLGWSHGDDEFFTSEQAMDWFDLGGIGRSPARLDFKK 308 Query: 306 LNHINAQHLRKADDARL-TALALAAAETRGEPLPADAAERIARTVPEVKEGAKTILELVD 364 L + QH+ +DA L +A A R L AER+ + + +K+ AKT EL++ Sbjct: 309 LESVCGQHIAVMEDAELMREIAAYLAAARKPALTDLQAERLEKGLYALKDRAKTFPELLE 368 Query: 365 HCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAESEGV 424 FAL++RP+A ++ K L + L+ L L AA + LE +L +FA +G+ Sbjct: 369 KARFALESRPIAADDAAAKALDPVSRGILRELTPMLQAA-SWSKQDLEAILTAFASEKGM 427 Query: 425 GFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDALA 467 GFGK LR L G P + M + RDE I RL+DA A Sbjct: 428 GFGKLAAPLRTALAGRTVTPSVYDMMLVIGRDETIARLEDAAA 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: 690 Number of extensions: 35 Number of successful extensions: 5 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: 471 Length adjustment: 33 Effective length of query: 437 Effective length of database: 438 Effective search space: 191406 Effective search space used: 191406 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 16 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