Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate AZOBR_RS07420 AZOBR_RS07420 glutamyl-tRNA synthetase
Query= reanno::Caulo:CCNA_01982 (470 letters) >FitnessBrowser__azobra:AZOBR_RS07420 Length = 470 Score = 479 bits (1234), Expect = e-140 Identities = 244/462 (52%), Positives = 308/462 (66%), Gaps = 5/462 (1%) Query: 9 VVTRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLD 68 VVTRFAPSPTGFLHIGGARTALFNWLYAR GG +L+R+EDTDR+RST+AAV AI +GL Sbjct: 3 VVTRFAPSPTGFLHIGGARTALFNWLYARRNGGTYLLRIEDTDRQRSTDAAVDAILDGLS 62 Query: 69 WLGLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAEGRAIR-- 126 WLGL D + + Q R RH EV ++LA GRAY C+ S EELE R +A G+ +R Sbjct: 63 WLGLDWDGDAVSQFARKDRHAEVAQQMLAAGRAYYCYASPEELEEMRAAQKAAGQPVRYD 122 Query: 127 SPWRDAPEGDLSA--PHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGAPTY 184 WRD + A VIR K P +GET++ D V+G VT +N +LDDL+LLRADG PTY Sbjct: 123 GRWRDRDPSEAPAGVKPVIRLKAPQEGETVLKDRVQGEVTVQNAQLDDLILLRADGTPTY 182 Query: 185 NLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKLSKR 244 LAVVVDDHDMGVTHVIRGDDHL N RQ IY AM W +P F HIPLIHGPDGAKLSKR Sbjct: 183 LLAVVVDDHDMGVTHVIRGDDHLTNTFRQIQIYNAMGWDLPEFGHIPLIHGPDGAKLSKR 242 Query: 245 HGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARLDWA 304 HGA V + D+GY+PE +RNYL RLGWGHGDDE+ + EQA+ WF++ + ++P+R D+A Sbjct: 243 HGALGVDAYRDMGYLPEAIRNYLLRLGWGHGDDEIISTEQAVEWFNLEGIGRSPSRFDFA 302 Query: 305 KLNHINAQHLRKADDARLTALALAAAETR-GEPLPADAAERIARTVPEVKEGAKTILELV 363 KL ++NA ++R+ADDARL LA E G L + + R + +K+ A+T+++L Sbjct: 303 KLENLNAHYMRQADDARLVGLATPRLEAELGRALTESERDLLTRAMNGLKQRARTVVDLA 362 Query: 364 DHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAESEG 423 F L RPLA++EK L E+ L L + A DF AA LE ++++FAE G Sbjct: 363 QSARFYLAARPLAMDEKAAALLDEKGRGILTDLAARFEAEADFTAAALEGLVRAFAEERG 422 Query: 424 VGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDA 465 GK LR LTG +P + + L R E + R+ DA Sbjct: 423 EKLGKIAQPLRAALTGSTVSPPIFEVAEILGRAETLARMKDA 464 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: 681 Number of extensions: 32 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: 470 Length adjustment: 33 Effective length of query: 437 Effective length of database: 437 Effective search space: 190969 Effective search space used: 190969 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