Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate CA265_RS19975 CA265_RS19975 aspartate--tRNA ligase
Query= uniprot:B8DMM5_DESVM (614 letters) >FitnessBrowser__Pedo557:CA265_RS19975 Length = 581 Score = 577 bits (1486), Expect = e-169 Identities = 289/580 (49%), Positives = 389/580 (67%), Gaps = 6/580 (1%) Query: 23 VRSHDCATLTAADTGAEVCLMGWVQYRRDHGGLIFVDLRDRQGLTQIVFSPDVNPAAHER 82 +R+ C L + G V L GWVQ RD GG+ F+D+RDR G+TQ+VF+ D N E Sbjct: 2 LRTVTCGALNLNNLGESVTLCGWVQKSRDLGGMTFIDIRDRYGITQLVFNMDDNRELCET 61 Query: 83 AHIIRSEYVLAIRGTVRPRPEGMTNPGMKTGEIEVYVSEWKLLNTSKTPAFVIEDRTEAS 142 A + E+V+ GTV R NP M TG++E+ +S ++LN +K P F+I+D T+ Sbjct: 62 ARTLGREFVIKAIGTVVERSN--KNPKMATGDVEIKISALEILNAAKLPPFMIDDETDGG 119 Query: 143 ENLRLQYRYLDLRRPRMANNFIVRHKAAQATRRYLDELGFLEIETPYLTKSTPEGARDFL 202 + LR++YRYLDLRR + NN ++RHK AQ+ RRYLD L F+E+ETP L KSTPEGARDF+ Sbjct: 120 DELRMKYRYLDLRRNPVRNNLVLRHKMAQSVRRYLDALDFIEVETPVLIKSTPEGARDFV 179 Query: 203 VPSRLNQGQFYALPQSPQLFKQLLMMSGMERYYQIVRCFRDEDMRADRQLEFTQIDIEMS 262 VPSR+N+G+FYALPQSPQ FKQLLM+SG +RY+QIV+CFRDED+RADRQ EFTQID EMS Sbjct: 180 VPSRMNEGEFYALPQSPQTFKQLLMVSGFDRYFQIVKCFRDEDLRADRQPEFTQIDCEMS 239 Query: 263 FVDEEQVMAMAEGLMARVFRDALDREIATPFPRMSYDDAMARYGVDKPDTRFGLELQDVT 322 F+++E ++ EGL+ +F++ + ++ PRM Y DAM YG DKPDTRF ++ ++ Sbjct: 240 FIEQEDILNTFEGLIRTLFKEVRNYDL-PEVPRMQYADAMRLYGSDKPDTRFAMQFVELN 298 Query: 323 HIVRGSNFKLFATAELVKAMRVPGGETMTRKEIDEFTEFVK--IYGAQGLAWIKIRPD-E 379 H+V+G F +F AELV + G + TRK++DE T+F+K GA GL + + D Sbjct: 299 HLVKGKGFPVFDNAELVVGINAKGAASYTRKQLDELTDFIKRPQIGATGLIYARHNEDGT 358 Query: 380 WQSPIAKFLSDEERAGLKDALGLETGDIVFFQAGAPGMVNAALGNLRVRLGEHLGLIDEN 439 +S + KF ++E+ +A G E GD++ AG+ V L LR+ +G LGL D+N Sbjct: 359 IKSSVDKFFNEEDLKQWSEAFGTEKGDLLLILAGSTDKVRKQLNELRLEMGSRLGLRDKN 418 Query: 440 AFNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHMDVMVENPAAARARAYDMVLNGYE 499 F+ LWV DFPL E+DEE +RY A HHPFTSPK + ++ +P RA AYDMV+NG E Sbjct: 419 TFSALWVLDFPLLEWDEETERYHAMHHPFTSPKPEDIALLDTDPKNVRANAYDMVINGTE 478 Query: 500 LGGGSIRNHTAEKQRRMFAALGFSPEEAEAQFGFLTQALEMGAPPHGGIAFGMDRLAMLL 559 +GGGSIR H Q MF LGFS EEA+ QFGFL A E GAPPHGGIAFG DRL + Sbjct: 479 VGGGSIRIHDRALQALMFKHLGFSAEEAQKQFGFLMDAFEFGAPPHGGIAFGFDRLTSIF 538 Query: 560 TGSSSIRDVIAFPKTQKATCLLTQAPDSVSARQLRDLGLR 599 G SIRDVIAFPK ++ +P ++ +QL++L ++ Sbjct: 539 AGLDSIRDVIAFPKNNSGRDVMIDSPSTIDEKQLKELKIK 578 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: 927 Number of extensions: 24 Number of successful extensions: 4 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: 581 Length adjustment: 37 Effective length of query: 577 Effective length of database: 544 Effective search space: 313888 Effective search space used: 313888 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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