Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_012384393.1 BIND_RS07085 aspartate--tRNA(Asp/Asn) ligase
Query= reanno::Caulo:CCNA_01969 (612 letters) >NCBI__GCF_000019845.1:WP_012384393.1 Length = 597 Score = 718 bits (1854), Expect = 0.0 Identities = 371/614 (60%), Positives = 445/614 (72%), Gaps = 28/614 (4%) Query: 4 MHAYRTHNCGALRASDTGAAVRLSGWIHRKRDHGGLVFIDLRDHYGLTQLVLHPETPGFN 63 MH YRTH CG LR + RLSGW HR RDHGG++FIDLRDHYG+TQ V+ P++ F Sbjct: 1 MHRYRTHTCGDLREAQADETTRLSGWCHRIRDHGGVLFIDLRDHYGITQCVVDPDSKAFP 60 Query: 64 VVERLRAESVIRVDGEVIARDASVVNPNLPTGEIEIRVSAVEVLSEAAELPLPVFGEPDY 123 + E+LR+E V+R+DG V R + NP +PTG IEI V+ +EVL AAELP+PVFG+ DY Sbjct: 61 LAEKLRSEWVVRIDGLVRKRPSGTENPEMPTGFIEIYVTEIEVLGAAAELPMPVFGDIDY 120 Query: 124 PEEIRLKHRYLDLRRETLHKNIVLRSRVIQSIRNRMFAQGFNEFQTPILTASSPEGARDF 183 PE+IRLK+R+LDLRRE LHKNI+LR +VI S+R RM QGF EFQTPILTASSPEGARDF Sbjct: 121 PEDIRLKYRFLDLRREKLHKNIMLRGQVIDSLRRRMKEQGFFEFQTPILTASSPEGARDF 180 Query: 184 LVPSRLHPEKFYALPQAPQQFKQLLMVSGFDRYFQIAPCFRDEDLRADR-SLEFYQLDVE 242 LVPSR+H KFYALPQAPQQ+KQLLM++GFDRYFQIAPCFRDED RADR EFYQLDVE Sbjct: 181 LVPSRIHAGKFYALPQAPQQYKQLLMMAGFDRYFQIAPCFRDEDPRADRLPGEFYQLDVE 240 Query: 243 MSFVTQEDVFAAIEPVMHGVFEEFSNGKPVSPINGTHTFTNDFGQSFEHKGFERLTYAQS 302 MSF+TQEDVFAA+EPV+ G FEEF NG+PV+ + F R+ YA++ Sbjct: 241 MSFITQEDVFAAMEPVIRGAFEEFGNGQPVT------------------QTFPRIPYAEA 282 Query: 303 MAWYGSDKPDLRNPIKMANVSEHFR--DGGFGLFAKILGADAKNQVWAIPAPTGGS--RA 358 M YGSDKPDLRNP+ +A+V++ F D F F ++ V AIPA S R+ Sbjct: 283 MLKYGSDKPDLRNPLVIADVTDLFARDDVSFNAFKNVI--KKGGVVRAIPATGAASQPRS 340 Query: 359 FCDRMNSWAQGEGQPGLGYV-FWSEDQGGWG-GPIAKNL-GEPTQALMESLGLGAGDAAF 415 F D++N WA+ EG GLGYV F D+ G GPIAK L E A++ L AGDA F Sbjct: 341 FFDKLNDWAKSEGAAGLGYVIFEGSDEAPVGKGPIAKFLPAEVQAAIVTRADLKAGDAVF 400 Query: 416 FVAGDPAVFAKFAGLARTRVGTELKLVDENQFKFCWIVDFPMFEWNEEEKKVDFSHNPFS 475 F AK AG AR R+G EL L F+ CWIVDFPM+EWNE++K VDFSHNPFS Sbjct: 401 FACDIEEKAAKLAGAARLRIGHELGLSKTGVFELCWIVDFPMYEWNEDDKTVDFSHNPFS 460 Query: 476 MPQGGLEALETQDPLTIRAYQYDIVCNGYELCSGAIRNHKPEIMLKAFATAGYGPEVVEE 535 MPQGGLEAL+TQDPLTI+A+QYDI CNGYE+ SG IRNH+PE M+KAF AGYG E V E Sbjct: 461 MPQGGLEALQTQDPLTIKAFQYDIACNGYEIASGGIRNHRPEAMVKAFEIAGYGEETVVE 520 Query: 536 QFGGMLNAFRYGAPPHGGLAPGIDRIVMLLADQVAIREVIAFPLNQQGQDLLMNAPANVL 595 +FGGM AF+YGAPPHGG+A G+DRI+MLLA +RE+ FP+NQ+ +DLLM AP+ Sbjct: 521 RFGGMYRAFQYGAPPHGGMAAGVDRIIMLLAGVQNLREISLFPMNQKAEDLLMGAPSEAT 580 Query: 596 DKQLKELHIRTAPP 609 KQL+ELHIR P Sbjct: 581 TKQLRELHIRLNLP 594 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: 1146 Number of extensions: 51 Number of successful extensions: 5 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: 597 Length adjustment: 37 Effective length of query: 575 Effective length of database: 560 Effective search space: 322000 Effective search space used: 322000 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