Align aspartate-tRNA ligase (EC 6.1.1.12) (characterized)
to candidate WP_007474260.1 CMTB2_RS04165 aspartate--tRNA ligase
Query= BRENDA::P56459 (577 letters) >NCBI__GCF_000170735.1:WP_007474260.1 Length = 588 Score = 759 bits (1959), Expect = 0.0 Identities = 365/582 (62%), Positives = 471/582 (80%), Gaps = 5/582 (0%) Query: 1 MRSHFCTEISEKDVGKIVKVAGWCNTYRDHGGVVFIDLRDKSGLVQLVCDP--SSKAYEK 58 MRSH+C E++E +VG+ V++ GW N++RDHGGV+FIDLRD+SGL+Q+V DP S KA+E Sbjct: 1 MRSHYCAELNEFNVGEEVELVGWVNSHRDHGGVIFIDLRDRSGLIQIVADPADSKKAHEV 60 Query: 59 ALEVRSEFVLVAKGKVRLRGAGLENPKLKTGKIEIVLEELIIENKSATPPIEIGNKHVNE 118 A V+ E+V+ KGKVRLRG GLENPKLKTGKIE+V +E+ IENKS P +IG+K VNE Sbjct: 61 AERVKDEYVIKVKGKVRLRGEGLENPKLKTGKIEVVADEIEIENKSEVLPFQIGDKSVNE 120 Query: 119 DLRLKYRYLDLRSPNSYEIFKLRSEVALITRNTLAQKGFLEIETPILSKTTPEGARDYLV 178 +LRLKYRYLDLR NS E F LRS+V R+ ++GF+++ETPIL+K+TPEGARDYLV Sbjct: 121 ELRLKYRYLDLRDKNSLETFILRSKVVKAIRDYFDKEGFIDVETPILTKSTPEGARDYLV 180 Query: 179 PSRVHEGEFFALPQSPQLFKQLLMVGGMDRYFQIARCFRDEDLRADRQPEFTQIDAEMSF 238 PSR++ GEF+ALPQSPQLFKQ+LMV G D+Y+QIA+CFRDEDLRADRQPEFTQ+D EMSF Sbjct: 181 PSRIYPGEFYALPQSPQLFKQILMVAGFDKYYQIAKCFRDEDLRADRQPEFTQVDVEMSF 240 Query: 239 CDENDVMGVVEDLLQEIFKAVGHTISKPFKRMPYKEAMENYGSDKPDLRFELPLIEVGDC 298 ++DV+ +E +++E F+ G + P KR+ YKEAME YGSDKPDLRF+L +++V D Sbjct: 241 VTQDDVIKTIEGMIKEAFEVAGIKVDLPIKRISYKEAMEKYGSDKPDLRFDLAMVDVIDE 300 Query: 299 FRDSSNAIFSNTAKDPKNKRIKALNVKGADALFSRSVLKELEEFVRQFGAKGLAYLQIKE 358 F DS+N IFS AKD KN R KAL ++G D +SR LKELE FV++FGAKGLAY+Q+KE Sbjct: 301 FVDSNNEIFSEIAKDKKNNRFKALKIEGGDNFYSRKKLKELENFVKKFGAKGLAYIQVKE 360 Query: 359 DEIKGPLVKFLSEKGLKNILERTDAQVGDIVFFGAGDKKIVLDYMGRLRLKVAETLDLID 418 + +KGP++KF+SE+ L ++E+ + +VGDI+FFGAGDKK VLDYMGRLR+K+A+ + LI+ Sbjct: 361 ERLKGPILKFMSEESLNRLIEKLNPKVGDIIFFGAGDKKTVLDYMGRLRIKIAKDMGLIN 420 Query: 419 KDALNFLWVVNFPMFEKTENGYHA-AHHPFTMPK--NIECEDIEEVEAHAYDVVLNGVEL 475 +D NF+WVV+FPMFEK EN HHPFTMP + E+ E++ + AYD+VLNG E+ Sbjct: 421 EDEYNFVWVVDFPMFEKDENNNPTPLHHPFTMPDMGTWDEENFEDINSIAYDLVLNGYEI 480 Query: 476 GGGSIRIHKEEMQKKVFEKINIHEEEAQKKFGFLLEALKFGAPPHGGFAIGFDRLIMLMT 535 GGGSIRIHKEE+Q+KVF+ + I E EA++KFGFLL+ALKFGAPPHGGFA+G DR+IMLM Sbjct: 481 GGGSIRIHKEEIQEKVFKLLGIDEMEAREKFGFLLDALKFGAPPHGGFALGLDRVIMLMR 540 Query: 536 KSHSIRDVIAFPKTQKASCLLTNAPSPINEEQLRELHIRLRK 577 K+ +IRDVIAFPKTQKA CLLT AP +++ QL+ELHIR++K Sbjct: 541 KTDNIRDVIAFPKTQKAQCLLTGAPGEVDKSQLKELHIRIKK 582 Lambda K H 0.320 0.139 0.400 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: 1041 Number of extensions: 44 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: 577 Length of database: 588 Length adjustment: 36 Effective length of query: 541 Effective length of database: 552 Effective search space: 298632 Effective search space used: 298632 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 (21.8 bits) S2: 53 (25.0 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