Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_034995297.1 DL88_RS09765 aspartate--tRNA ligase
Query= reanno::Caulo:CCNA_01969 (612 letters) >NCBI__GCF_000745425.1:WP_034995297.1 Length = 597 Score = 721 bits (1861), Expect = 0.0 Identities = 371/615 (60%), Positives = 449/615 (73%), Gaps = 30/615 (4%) Query: 4 MHAYRTHNCGALRASDTGAAVRLSGWIHRKRDHGGLVFIDLRDHYGLTQLVLHPETPGFN 63 MH YR+H CG LR + +RLSGW HR RDHGG++FIDLRDHYG+TQ V+ P++ F Sbjct: 1 MHRYRSHTCGDLRETQADETIRLSGWCHRIRDHGGVLFIDLRDHYGMTQCVVDPDSAAFP 60 Query: 64 VVERLRAESVIRVDGEVIARDASVVNPNLPTGEIEIRVSAVEVLSEAAELPLPVFGEPDY 123 + E+LR+E V+++DG V R A NP +PTG IE+ V+ +EVL AAELP+PVFG+ DY Sbjct: 61 LAEKLRSEWVVKIDGLVRKRPAGTENPEMPTGLIEVYVTEIEVLGPAAELPMPVFGDVDY 120 Query: 124 PEEIRLKHRYLDLRRETLHKNIVLRSRVIQSIRNRMFAQGFNEFQTPILTASSPEGARDF 183 PE+IRLK+R+LDLRRE LHKNI+LR +V+ S+R RM QGF EFQTPILTASSPEGARDF Sbjct: 121 PEDIRLKYRFLDLRREKLHKNIMLRGKVVDSLRRRMKEQGFFEFQTPILTASSPEGARDF 180 Query: 184 LVPSRLHPEKFYALPQAPQQFKQLLMVSGFDRYFQIAPCFRDEDLRADR-SLEFYQLDVE 242 LVPSR+HP KFYALPQAPQQ+KQLLM++GFDRYFQIAPCFRDED RADR EFYQLD+E Sbjct: 181 LVPSRIHPGKFYALPQAPQQYKQLLMMAGFDRYFQIAPCFRDEDPRADRLPGEFYQLDIE 240 Query: 243 MSFVTQEDVFAAIEPVMHGVFEEFSNGKPVSPINGTHTFTNDFGQSFEHKGFERLTYAQS 302 MSFVTQED+FAA+EPV+ G FEEF NG+PV+ + F R+ YA++ Sbjct: 241 MSFVTQEDIFAAMEPVIRGAFEEFGNGQPVTQV------------------FPRIPYAEA 282 Query: 303 MAWYGSDKPDLRNPIKMANVSEHF--RDGGFGLFAKILGADAKNQVWAIPAPTGGS---R 357 M YGSDKPDLRNP+ +A+V++ F D F F ++ V AIPA TG + R Sbjct: 283 MLKYGSDKPDLRNPLVIADVTDLFGRDDVTFNAFKNVI--KKGGVVRAIPA-TGAAAQPR 339 Query: 358 AFCDRMNSWAQGEGQPGLGYV-FWSEDQGGWG-GPIAKNLGEPTQ-ALMESLGLGAGDAA 414 +F D++N WA+ EG GLGYV F D G G GPIAK L Q A++ L AGDA Sbjct: 340 SFFDKLNDWAKSEGAAGLGYVIFEGGDNGPVGKGPIAKFLPADVQAAIIARADLKAGDAV 399 Query: 415 FFVAGDPAVFAKFAGLARTRVGTELKLVDENQFKFCWIVDFPMFEWNEEEKKVDFSHNPF 474 FF AK AG AR R+G EL L F+ CWIVDFPM+EWNE++KKVDFSHNPF Sbjct: 400 FFACDIEEKAAKLAGAARLRIGHELGLSKTGVFELCWIVDFPMYEWNEDDKKVDFSHNPF 459 Query: 475 SMPQGGLEALETQDPLTIRAYQYDIVCNGYELCSGAIRNHKPEIMLKAFATAGYGPEVVE 534 SMPQGGLEAL+ QDPLTI+A+QYDI CNGYE+ SG IRNH+PE M+KAF AGYG E V Sbjct: 460 SMPQGGLEALQQQDPLTIKAFQYDIACNGYEIASGGIRNHRPEAMVKAFEIAGYGEETVV 519 Query: 535 EQFGGMLNAFRYGAPPHGGLAPGIDRIVMLLADQVAIREVIAFPLNQQGQDLLMNAPANV 594 E+FGGM AF+YGAPPHGG+A GIDRI+MLLA +RE+ FP+NQ+ +DLLM AP+ Sbjct: 520 ERFGGMYRAFQYGAPPHGGMAAGIDRIIMLLAGVQNLREISLFPMNQKAEDLLMGAPSEA 579 Query: 595 LDKQLKELHIRTAPP 609 KQL+ELHIR P Sbjct: 580 TTKQLRELHIRLNLP 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: 1161 Number of extensions: 55 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