Align glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24) (characterized)
to candidate WP_057507305.1 ABB28_RS03545 glutamate--tRNA ligase
Query= reanno::Caulo:CCNA_01982 (470 letters) >NCBI__GCF_001431535.1:WP_057507305.1 Length = 468 Score = 369 bits (946), Expect = e-106 Identities = 207/466 (44%), Positives = 277/466 (59%), Gaps = 19/466 (4%) Query: 11 TRFAPSPTGFLHIGGARTALFNWLYARHTGGKFLIRVEDTDRERSTEAAVAAIFEGLDWL 70 TRFAPSPTG+LHIGGARTAL+ WL ARH GG+F++R+EDTDRERST+ A+ AI E ++WL Sbjct: 5 TRFAPSPTGYLHIGGARTALYCWLEARHRGGEFVLRIEDTDRERSTQGAIDAILEAMEWL 64 Query: 71 GLKSDDEVIFQHTRAPRHVEVVHELLAKGRAYRCWMSIEELEVAREKARAE--------- 121 GL D+ I+Q R R++EV +L+A G+AY + + EEL+ RE A A+ Sbjct: 65 GLDYDEGPIYQTQRVARYLEVAQQLVADGKAYYAYETREELDAMREAAMAKQEKPRYNGA 124 Query: 122 GRAIRSPWRDAPEGDLSAPHVIRFKGPLDGETLVNDLVKGPVTFKNIELDDLVLLRADGA 181 R P+RD P VIRFK PLDG + +DL+KGP+ N ELDD+V+ R DG Sbjct: 125 AREQNLPYRDDPN------RVIRFKNPLDGTVVFDDLIKGPIEIANSELDDMVIFRPDGY 178 Query: 182 PTYNLAVVVDDHDMGVTHVIRGDDHLNNAARQTLIYQAMDWAVPAFAHIPLIHGPDGAKL 241 PTYN AVVVDD DMG+T VIRGDDH+NN RQ +Y + VP F H+P+I GAKL Sbjct: 179 PTYNFAVVVDDWDMGITEVIRGDDHINNTPRQINLYLGIGAPVPKFGHMPMILDEQGAKL 238 Query: 242 SKRHGAQAVGEFADLGYIPEGMRNYLARLGWGHGDDEVFTDEQAISWFDVADVVKAPARL 301 SKR GA V ++ D GY+PE + +YLARLGW HGD E+F+ ++ I FDV + ARL Sbjct: 239 SKRTGAADVMQYKDAGYLPEALLSYLARLGWSHGDQEIFSRQELIDLFDVTNCNSKAARL 298 Query: 302 DWAKLNHINAQHLRKADDARLTALALA-AAETRGEPLPADAAERIARTVPEVKEGAKTIL 360 D AKL +N QH K + A A AL E G L +A V ++E +T+ Sbjct: 299 DMAKLGWVN-QHFLKTEAAASIAPALVYQLEKLG--LDLNAGPSAEDVVVALRERVQTLK 355 Query: 361 ELVDHCAFALKTRPLALEEKTQKQLTEETVERLKRLRDQLAAAPDFDAATLETVLKSFAE 420 E+ + + E K L L + R+ LAA P + A ++ L A Sbjct: 356 EMAEKAVVWYQPLETYDEAAVAKHLKPGAELPLGKARELLAALPAWTAESVGVALHDAAA 415 Query: 421 SEGVGFGKFGPALRGVLTGGAQAPDLNKTMAALSRDEAIGRLDDAL 466 + +G GK LR +TG +PD+++T+ RDEA+ R+D A+ Sbjct: 416 ALEIGMGKVAQPLRVAITGTQVSPDISQTVYLAGRDEALKRIDVAI 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: 624 Number of extensions: 31 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: 468 Length adjustment: 33 Effective length of query: 437 Effective length of database: 435 Effective search space: 190095 Effective search space used: 190095 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