Align aspartate-tRNA ligase (EC 6.1.1.12) (characterized)
to candidate WP_011372716.1 SUDEN_RS05705 aspartate--tRNA(Asp/Asn) ligase
Query= BRENDA::P56459 (577 letters) >NCBI__GCF_000012965.1:WP_011372716.1 Length = 580 Score = 781 bits (2018), Expect = 0.0 Identities = 379/580 (65%), Positives = 469/580 (80%), Gaps = 4/580 (0%) Query: 1 MRSHFCTEISEKDVGKIVKVAGWCNTYRDHGGVVFIDLRDKSGLVQLVCDP--SSKAYEK 58 MRSH+CTE+SE ++G+ V +AGW N+YRDHGG++FIDLRDKSGL+QL CDP S+ +++ Sbjct: 1 MRSHYCTELSEANIGQEVVLAGWANSYRDHGGIIFIDLRDKSGLIQLTCDPEDSASSHKI 60 Query: 59 ALEVRSEFVLVAKGKVRLRGAGLENPKLKTGKIEIVLEELIIENKSATPPIEIGNKHVNE 118 A +R EFVLVAKGKVRLRG GL NP+LKTG IEIV+ EL IEN+SA P IG+K+V E Sbjct: 61 ASSIRDEFVLVAKGKVRLRGEGLTNPRLKTGAIEIVVSELTIENRSAAVPFVIGDKNVGE 120 Query: 119 DLRLKYRYLDLRSPNSYEIFKLRSEVALITRNTLAQKGFLEIETPILSKTTPEGARDYLV 178 + RLKYRYL+LR P+ YE F+LRS+ A+ RN L + GFLE+ETPIL+K+TPEGARDYLV Sbjct: 121 ETRLKYRYLELRDPSMYETFRLRSKAAIAARNILDENGFLEVETPILTKSTPEGARDYLV 180 Query: 179 PSRVHEGEFFALPQSPQLFKQLLMVGGMDRYFQIARCFRDEDLRADRQPEFTQIDAEMSF 238 PSRVH GEF+ALPQSPQLFKQLLMVGG DRYFQIA+CFRDEDLRADRQPEFTQID EMSF Sbjct: 181 PSRVHSGEFYALPQSPQLFKQLLMVGGFDRYFQIAKCFRDEDLRADRQPEFTQIDVEMSF 240 Query: 239 CDENDVMGVVEDLLQEIFKAVGHTISKPFKRMPYKEAMENYGSDKPDLRFELPLIEVGDC 298 C++ DVM + E LL +F A G I PF R+ Y++AME YGSDKPDLR++L +++V D Sbjct: 241 CNQEDVMLIAEKLLVSMFGACGVEIKPPFNRIAYRDAMEWYGSDKPDLRYDLKMVDVIDI 300 Query: 299 FRDSSNAIFSNTAKDPKNKRIKALNVKGADALFSRSVLKELEEFVRQFGAKGLAYLQIKE 358 F N IF+N AK P RIKAL V GAD +FS+ +K E+FVRQFGA+GL Y Q+KE Sbjct: 301 FERCDNEIFTNIAKQPHKNRIKALRVPGADLVFSKREMKTFEDFVRQFGAQGLGYFQMKE 360 Query: 359 DEIKGPLVKFLSEKGLKNILERTDAQVGDIVFFGAGDKKIVLDYMGRLRLKVA--ETLDL 416 D +KGPL+KF S+ + +++R +VGD+VFFGAGDKK V DYMGRLR+ +A E ++L Sbjct: 361 DGLKGPLIKFFSDADIALLVDRLGMKVGDVVFFGAGDKKTVWDYMGRLRIFIAEHERMNL 420 Query: 417 IDKDALNFLWVVNFPMFEKTENGYHAAHHPFTMPKNIECEDIEEVEAHAYDVVLNGVELG 476 DKDA F+WVV+FPMFE + A HHPFT PK+ + +DIEE+++ AYD+VLNG ELG Sbjct: 421 ADKDAFEFVWVVDFPMFEVEDGRVKALHHPFTQPKDTDKDDIEEIDSIAYDIVLNGTELG 480 Query: 477 GGSIRIHKEEMQKKVFEKINIHEEEAQKKFGFLLEALKFGAPPHGGFAIGFDRLIMLMTK 536 GGSIRIHKEEMQ+++F+ + I EEEA++KFGFLL+ALKFGAPPHGGFAIGFDRL+ML++K Sbjct: 481 GGSIRIHKEEMQEEIFKLLGIGEEEAKEKFGFLLDALKFGAPPHGGFAIGFDRLMMLISK 540 Query: 537 SHSIRDVIAFPKTQKASCLLTNAPSPINEEQLRELHIRLR 576 SIRDVIAFPKTQKASC+LT APS ++ QLR+LHI+LR Sbjct: 541 KSSIRDVIAFPKTQKASCILTKAPSEVDATQLRDLHIKLR 580 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: 1017 Number of extensions: 48 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: 577 Length of database: 580 Length adjustment: 36 Effective length of query: 541 Effective length of database: 544 Effective search space: 294304 Effective search space used: 294304 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