Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_011939082.1 GURA_RS11140 aspartate--tRNA ligase
Query= reanno::Miya:8501305 (614 letters) >NCBI__GCF_000016745.1:WP_011939082.1 Length = 593 Score = 718 bits (1853), Expect = 0.0 Identities = 346/588 (58%), Positives = 444/588 (75%), Gaps = 4/588 (0%) Query: 16 IEPLGDWVRSHDCATLTAADTGAEVCLMGWVQYRRDHGGLIFVDLRDRQGLTQIVFSPDV 75 I+ LG W R+H C LTA D G EV LMGW RRDHGGLIFVDLRDR+GL Q+VF PD Sbjct: 2 IDFLGGWKRTHYCGALTAGDIGKEVVLMGWAHRRRDHGGLIFVDLRDREGLAQVVFDPDN 61 Query: 76 NPAAHERAHIIRSEYVLAIRGTVRPRPEGMTNPGMKTGEIEVYVSEWKLLNTSKTPAFVI 135 +PAAH++A IR+EYV+AIRG V PRP+G N +KTGE+EV VSE K+LN SK F + Sbjct: 62 SPAAHKKAEAIRNEYVVAIRGKVIPRPDGTVNANLKTGEVEVLVSECKMLNRSKALPFTL 121 Query: 136 EDRTEASENLRLQYRYLDLRRPRMANNFIVRHKAAQATRRYLDELGFLEIETPYLTKSTP 195 +D + +ENLRL++RYLDLRRP + N I+R K AQ TR+YL GFLE+ETP+LTKSTP Sbjct: 122 DDYVDVAENLRLKHRYLDLRRPVLQENLILRSKVAQITRQYLTGNGFLELETPFLTKSTP 181 Query: 196 EGARDFLVPSRLNQGQFYALPQSPQLFKQLLMMSGMERYYQIVRCFRDEDMRADRQLEFT 255 EGARDFLVPSR+N+G+FYALPQSPQLFKQ+LM+SG +RY+Q+VRCFRDED+RADRQ EFT Sbjct: 182 EGARDFLVPSRINRGEFYALPQSPQLFKQILMVSGFDRYFQVVRCFRDEDLRADRQPEFT 241 Query: 256 QIDIEMSFVDEEQVMAMAEGLMARVFRDALDREIATPFPRMSYDDAMARYGVDKPDTRFG 315 QID EMSF+D E ++ + EGL+AR+F + + P PRM+Y +++ R+GVD PD RFG Sbjct: 242 QIDCEMSFIDREDIITVMEGLIARIFTETKGATVNLPIPRMTYAESIRRFGVDNPDLRFG 301 Query: 316 LELQDVTHIVRGSNFKLFAT----AELVKAMRVPGGETMTRKEIDEFTEFVKIYGAQGLA 371 LEL +++ IV+ + FK+FA +VK + G M+RKEID+ TEF KIYGA+GLA Sbjct: 302 LELVELSDIVKNAGFKVFADVVAGGGIVKGLNAKGCGGMSRKEIDDLTEFAKIYGAKGLA 361 Query: 372 WIKIRPDEWQSPIAKFLSDEERAGLKDALGLETGDIVFFQAGAPGMVNAALGNLRVRLGE 431 ++K+ + WQSPIAKF + EE + + A + GD++ F A P +VN +LG LR L + Sbjct: 362 YVKMTAEGWQSPIAKFFTAEEISAMDKAFDAKEGDLLLFVADKPKVVNDSLGKLRNHLAK 421 Query: 432 HLGLIDENAFNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHMDVMVENPAAARARAY 491 LGL+D++ FNF+W+TDFPL E+DEEEKR+ A HHPFT+P D ++ + +P RA+AY Sbjct: 422 SLGLLDKDTFNFVWITDFPLLEWDEEEKRWAAVHHPFTAPMDEDLEYVESDPGRCRAKAY 481 Query: 492 DMVLNGYELGGGSIRNHTAEKQRRMFAALGFSPEEAEAQFGFLTQALEMGAPPHGGIAFG 551 D+VLNG E+GGGSIR H + Q MF LG S E+A +FGFL A++ GAPPHGGIAFG Sbjct: 482 DLVLNGNEIGGGSIRIHQEKIQSLMFKMLGHSEEDARTKFGFLLDAMDYGAPPHGGIAFG 541 Query: 552 MDRLAMLLTGSSSIRDVIAFPKTQKATCLLTQAPDSVSARQLRDLGLR 599 +DRL MLLTGS SIRDVIAFPKTQK CL+++AP +V +QLR+LGL+ Sbjct: 542 LDRLIMLLTGSDSIRDVIAFPKTQKGACLMSEAPSAVDMKQLRELGLK 589 Lambda K H 0.321 0.137 0.407 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: 1001 Number of extensions: 27 Number of successful extensions: 2 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: 614 Length of database: 593 Length adjustment: 37 Effective length of query: 577 Effective length of database: 556 Effective search space: 320812 Effective search space used: 320812 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 (21.9 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 12 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