Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate WP_010531090.1 ON01_RS10970 aspartate--tRNA ligase
Query= BRENDA::Q9KDG1 (595 letters) >NCBI__GCF_000224785.1:WP_010531090.1 Length = 588 Score = 780 bits (2015), Expect = 0.0 Identities = 386/581 (66%), Positives = 467/581 (80%) Query: 9 GQLSEEQVNERVQLKGWVQRRRDLGQVIFVDLRDRSGVVQLVFNSDISQEALETAEKVRN 68 G LSE V++ V LKGWVQ RRDLG +IF+DLRDRSG+VQ+VFN D S+ ALE AE VR Sbjct: 8 GTLSENDVDQSVLLKGWVQTRRDLGGLIFIDLRDRSGLVQVVFNPDHSKAALEAAEAVRT 67 Query: 69 EYVLDVEGVVLKRDPSTVNDKIATGTIEVHVERLTILNKAKSLPFQIEANTDASEDIRLK 128 EYVL++ G V+KRD TVN + TG IEV + LTILNKAK+ PF I+ TD +ED+RLK Sbjct: 68 EYVLEITGSVVKRDEGTVNPAMGTGRIEVIAKDLTILNKAKTPPFLIQEETDVAEDLRLK 127 Query: 129 YRYLDLRRPDMQETMKLRHQTTKLIRDFLDGQEFFEIETPMLTKSTPEGARDYLVPSRVH 188 YRY+DLRR +QET K+RH+TT+ IR+FL+ F E+ETP+LTKSTPEGARDYLVPSRVH Sbjct: 128 YRYIDLRRNKLQETFKMRHRTTQAIRNFLNDDGFLEMETPILTKSTPEGARDYLVPSRVH 187 Query: 189 HGEFYALPQSPQIFKQLLMVSGFERYYQIVRCFRDEDLRADRQPEFTQIDIETSFMDKED 248 HG+FYALPQSPQ+FKQL+M+ GFE+YYQI RCFRDEDLRADRQPEFTQ+DIETSF+ ++ Sbjct: 188 HGQFYALPQSPQLFKQLIMMGGFEKYYQIARCFRDEDLRADRQPEFTQVDIETSFLTSDE 247 Query: 249 LLTMTENMMAKIMKEVKGLDVALPFPRMTYDDAMNRYGSDKPDTRFEMELIELSDIVKDS 308 ++ MTE MM ++KEVK +D++LP PRM YD+AM+R+GSDKPDTRF MELI +SDIVKDS Sbjct: 248 IMDMTEQMMRHVLKEVKNVDISLPLPRMPYDEAMSRFGSDKPDTRFGMELIHVSDIVKDS 307 Query: 309 DFKVFSSAIKSGGIVKGLNLKGGAGSLSRKEIDGLAEFVKPYGAKGLAWLKVEEGELKGP 368 FKVF A++SGG V LN KG A + SRK+ID L +FVK Y AKG+AWLKV+ G+L GP Sbjct: 308 SFKVFKGAVESGGKVCLLNAKGQAANYSRKDIDQLTDFVKIYDAKGMAWLKVDGGQLTGP 367 Query: 369 IAKFFAGETGAELQQAMGAEDGDLLFFAADKKEVVFDSLGALRLKLGKDFNLIDESKFNF 428 IAKF + + L + AEDGDLL F +DK VV+DSLGALRLKLG++ NLIDE+KFNF Sbjct: 368 IAKFLSDDETNGLIERSAAEDGDLLLFGSDKSSVVYDSLGALRLKLGRELNLIDETKFNF 427 Query: 429 LWVVDFPLVEYDEEAKRFVALHHPFTSPKQEDLTKLETDPASVRADAYDLVLNGYELGGG 488 LWV D+PL+EYDE+ +R+ A HHPFT P +EDL KL+ DP+ VRA+AYDLVLNGYELGGG Sbjct: 428 LWVTDWPLLEYDEDLERYFAAHHPFTMPVEEDLDKLDMDPSDVRANAYDLVLNGYELGGG 487 Query: 489 SQRIYQRPVQEKMFAALGFTEEAAQKEFGFLLEAFEYGTPPHGGIALGLDRLVMLLAGRL 548 S RI+++ Q KM LGFT+E A ++FGFLLEA EYG PPHGGIALGLDR+VMLLAG Sbjct: 488 SLRIHKKDQQMKMLDVLGFTQEEADEQFGFLLEALEYGAPPHGGIALGLDRIVMLLAGSS 547 Query: 549 NLRDTIAFPKTASASCLLTEAPGEVSLEQLLDLNLSIIGHK 589 NLRDTI FPKTASAS LLT+AP +VS QL +L + I K Sbjct: 548 NLRDTILFPKTASASDLLTDAPNDVSKGQLDELAIQINDEK 588 Lambda K H 0.319 0.138 0.393 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: 1025 Number of extensions: 35 Number of successful extensions: 1 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: 595 Length of database: 588 Length adjustment: 37 Effective length of query: 558 Effective length of database: 551 Effective search space: 307458 Effective search space used: 307458 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: 53 (25.0 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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