Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_036258034.1 DL86_RS01745 aspartate--tRNA ligase
Query= reanno::Caulo:CCNA_01969 (612 letters) >NCBI__GCF_000746085.1:WP_036258034.1 Length = 602 Score = 712 bits (1837), Expect = 0.0 Identities = 367/622 (59%), Positives = 447/622 (71%), Gaps = 34/622 (5%) Query: 4 MHAYRTHNCGALRASDTGAAVRLSGWIHRKRDHGGLVFIDLRDHYGLTQLVLHPETPGFN 63 MH YR+H CG LR + G +RLSGW HR RDHGG++FIDLRDHYG+TQ V+ P++ F Sbjct: 1 MHRYRSHTCGDLRETLAGETIRLSGWCHRIRDHGGVLFIDLRDHYGMTQCVVDPDSKAFA 60 Query: 64 VVERLRAESVIRVDGEVIARDASVVNPNLPTGEIEIRVSAVEVLSEAAELPLPVFGEPDY 123 + E+LR+E V+R+DG V R A N +PTG IE+ V+ +EVL AAELP+PVFGE +Y Sbjct: 61 LAEKLRSEWVVRIDGVVRQRPAGTENAEMPTGLIEVYVAEIEVLGPAAELPMPVFGEHNY 120 Query: 124 PEEIRLKHRYLDLRRETLHKNIVLRSRVIQSIRNRMFAQGFNEFQTPILTASSPEGARDF 183 PE+IRL++R+LDLRRE LH+NI+LR RVI S+R RM AQGF EFQTPILTASSPEGARDF Sbjct: 121 PEDIRLRYRFLDLRREKLHQNIMLRGRVIDSLRARMKAQGFFEFQTPILTASSPEGARDF 180 Query: 184 LVPSRLHPEKFYALPQAPQQFKQLLMVSGFDRYFQIAPCFRDEDLRADRSL-EFYQLDVE 242 LVPSRLHP KFYALPQAPQQFKQL+M +GFDRYFQIAPCFRDED RADRS EFYQLDVE Sbjct: 181 LVPSRLHPGKFYALPQAPQQFKQLVMAAGFDRYFQIAPCFRDEDARADRSPGEFYQLDVE 240 Query: 243 MSFVTQEDVFAAIEPVMHGVFEEFSNGKPVSPINGTHTFTNDFGQSFEHKGFERLTYAQS 302 MSFVTQEDVF A+EPV+ G+FEEF G+PV+ + F + YA++ Sbjct: 241 MSFVTQEDVFEAVEPVLRGIFEEFGGGQPVT------------------QKFPMIPYAEA 282 Query: 303 MAWYGSDKPDLRNPIKMANVSEHFR--DGGFGLFAKILGADAKNQVWAIPAPTGGS--RA 358 + YG+DKPDLRNP+ + +V++ F D F F ++ A V AIPA G+ R+ Sbjct: 283 LLKYGTDKPDLRNPLVIVDVTDEFSRDDVNFNAFKNVI--KAGGVVRAIPATGAGAQPRS 340 Query: 359 FCDRMNSWAQGEGQPGLGYVFW--SEDQGGWGGPIAKNLGEPTQ-ALMESLGLGAGDAAF 415 F D++N WA+GEG GLGYV + D GPIAK L Q + GL AGDA F Sbjct: 341 FFDKLNDWAKGEGAAGLGYVIFEGEGDSLAGKGPIAKFLPADVQKKIAAKAGLKAGDAVF 400 Query: 416 FVAGDPAVFAKFAGLARTRVGTELKLVDENQFKFCWIVDFPMFEWNEEEKKVDFSHNPFS 475 F AK AG AR R+G ELKL F+FCWIVDFPM+EWNE+EK++DFSHNPFS Sbjct: 401 FACDQEEKAAKLAGAARVRIGHELKLSKTGVFEFCWIVDFPMYEWNEDEKRIDFSHNPFS 460 Query: 476 MPQGGLEALETQDP------LTIRAYQYDIVCNGYELCSGAIRNHKPEIMLKAFATAGYG 529 MP EA DP ++A+QYDIVCNG EL SGAIRNH+P+IM KAFA AGYG Sbjct: 461 MPNFESEAFLALDPADEKTIFGMKAFQYDIVCNGVELSSGAIRNHRPDIMKKAFALAGYG 520 Query: 530 PEVVEEQFGGMLNAFRYGAPPHGGLAPGIDRIVMLLADQVAIREVIAFPLNQQGQDLLMN 589 +V+EE+FGGM AF+YGAPPHGG+APG+DRIVMLLA + +RE++ FP+NQ+ +DLLM Sbjct: 521 EDVLEEKFGGMYRAFQYGAPPHGGIAPGVDRIVMLLAGEENLREIVLFPMNQRAEDLLMG 580 Query: 590 APANVLDKQLKELHIRTAPPIK 611 AP+ V KQL+ELHIR P K Sbjct: 581 APSTVTPKQLRELHIRLNLPDK 602 Lambda K H 0.321 0.139 0.425 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: 1131 Number of extensions: 52 Number of successful extensions: 6 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: 612 Length of database: 602 Length adjustment: 37 Effective length of query: 575 Effective length of database: 565 Effective search space: 324875 Effective search space used: 324875 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