Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate WP_012332324.1 M446_RS11745 aspartate--tRNA(Asp/Asn) ligase
Query= uniprot:A0A2I7KAZ8 (592 letters) >NCBI__GCF_000019365.1:WP_012332324.1 Length = 604 Score = 738 bits (1905), Expect = 0.0 Identities = 362/598 (60%), Positives = 448/598 (74%), Gaps = 12/598 (2%) Query: 1 MHDYRSHTCAELNKSNVGETVRLSGWVHRVRDHGGLLFIDLRDHYGVTQVMADPDSPVFA 60 MH YR+HTC L S+VG TVRLSGW HRVRDHGG+LFIDLRDHYGVTQ + D DS F Sbjct: 1 MHRYRTHTCGALRPSDVGATVRLSGWCHRVRDHGGVLFIDLRDHYGVTQCVVDADSAAFR 60 Query: 61 EIEKVRSEWCIRIDGNVKARDESLVNDKIPTGEIEVFIRDIEVLGKSEELPLMVFGEQEY 120 E VRSEW IR+DG V+ R E N +PTG +E++I D+EVLG++ ELP+ VFGE +Y Sbjct: 61 AAEAVRSEWVIRVDGRVRRRPEGTENADLPTGAVELYITDLEVLGQAVELPMPVFGELDY 120 Query: 121 PEETRLRYRYLDLRREKMQKNMLLRSNMIQSIRRRMWDKGFNEYQTPIITASSPEGARDF 180 PEETRLRYR+LDLRREK+ N++ R +I S+RRRM + GF E+QTPI+TASSPEGARDF Sbjct: 121 PEETRLRYRFLDLRREKLHANIMKRGAIIDSLRRRMREGGFFEFQTPILTASSPEGARDF 180 Query: 181 LVPSRLHPGKFYALPQAPQQFKQLMMVSGFDKYFQIAPCFRDEDPRADRSPTDFYQLDLE 240 LVPSRLHPGKFYALPQAPQQFKQL M++GFD+YFQIAPCFRDED RADRSP +FYQLD+E Sbjct: 181 LVPSRLHPGKFYALPQAPQQFKQLTMIAGFDRYFQIAPCFRDEDARADRSPGEFYQLDIE 240 Query: 241 MSFVTQQDVFDTIQPVMQGVFEEFGKGRKVDSEWPQISYKDAAKWYGTDKPDLRNPIKMQ 300 MSFVTQ+DVF ++PV++GVFEEF +G +V +P+I Y +A YG DKPDLRNP+ + Sbjct: 241 MSFVTQEDVFQAVEPVLRGVFEEFAEGWRVTGTFPRIPYAEAMLKYGVDKPDLRNPLIIV 300 Query: 301 DCSEHFRGSG--FAIFANLLENEGTEIRAIPAPKGGS--RKFCDRMNKFAQGEGLPGMGY 356 D ++ F F F +++ G +RAIPAP G+ R F DR+N +A+GEG PG+GY Sbjct: 301 DVTQEFSAEAVTFNAFKSVIRAGGV-VRAIPAPGAGAQPRSFFDRLNNWARGEGAPGLGY 359 Query: 357 IFWRDQGEGMEAAGPLAKNIGPERTEAIRQQLGLGVGDAAFFLGGKPKTFESVAGRARIV 416 I + ++G + GP+AK + PE AI + GL GDA FF G +AG+ARI Sbjct: 360 IVFEEEGGVLSGRGPIAKFVPPEVQAAIAAKAGLKAGDAVFFAAGVEAKAAGLAGKARIR 419 Query: 417 IGEELGLTDKDRFAFCWIVDFPIYEKDEETGKIDFEHNPFSMPQGGMDALLS-DP----- 470 IG++LGLTDKD+FAFCWI DFP+YE +E+ +IDF HNPFSMP D L DP Sbjct: 420 IGDDLGLTDKDQFAFCWITDFPMYEWNEDEKRIDFSHNPFSMPNYDHDGFLGLDPADAET 479 Query: 471 -LAVKGYQYDLACNGYELVSGAIRNHKPEIMFKAFEIAGYGKEEVEKRFGGMVNAFQYGA 529 L +K +QYD+ CNG EL SGAIRNH+P++M KAF IAGYG+E +E++FGGM+NA + GA Sbjct: 480 ILGIKAFQYDIVCNGIELSSGAIRNHRPDVMEKAFAIAGYGREVLEQKFGGMLNALRMGA 539 Query: 530 PPHGGCAAGIDRMVMLLADEANIREVIMFPMNQRAEDLMMAAPSEPMSDQLMELGLRV 587 PPHGG A G+DR+VMLL E NIREV++FPMNQRAEDLMM APSE QL EL +R+ Sbjct: 540 PPHGGIAPGVDRIVMLLCHEPNIREVVLFPMNQRAEDLMMGAPSEVTPKQLRELHIRL 597 Lambda K H 0.321 0.139 0.424 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: 1126 Number of extensions: 49 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: 592 Length of database: 604 Length adjustment: 37 Effective length of query: 555 Effective length of database: 567 Effective search space: 314685 Effective search space used: 314685 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