Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_012974240.1 AZL_RS08600 aspartate--tRNA ligase
Query= reanno::Caulo:CCNA_01969 (612 letters) >NCBI__GCF_000010725.1:WP_012974240.1 Length = 608 Score = 721 bits (1861), Expect = 0.0 Identities = 372/610 (60%), Positives = 445/610 (72%), Gaps = 18/610 (2%) Query: 4 MHAYRTHNCGALRASDTGAAVRLSGWIHRKRDHGGLVFIDLRDHYGLTQLVLHPETPGFN 63 MH YRTH CG LR + G VRLSGW++RKRDHG L+FIDLRDHYGLTQ V+ P F Sbjct: 1 MHPYRTHTCGQLREENAGETVRLSGWMNRKRDHGQLLFIDLRDHYGLTQCVVDTSNPAFE 60 Query: 64 VVERLRAESVIRVDGEVIARDASVVNPNLPTGEIEIRVSAVEVLSEAAELPLPVFGEPDY 123 V RL+ ESVI V G+V+ R A +N LPTG IE++++ + V EA ++PL V + D Sbjct: 61 VANRLKLESVITVTGKVVKRTAETINDKLPTGRIEMQIAELAVEGEAEQIPLQVNQDTDA 120 Query: 124 PEEIRLKHRYLDLRRETLHKNIVLRSRVIQSIRNRMFAQGFNEFQTPILTASSPEGARDF 183 E++RL++R+LDLRRE +H+NI+LRSRVI S R RM QGF EFQTPILTASSPEGARD+ Sbjct: 121 GEDVRLRYRFLDLRRERIHENIMLRSRVIASARRRMIDQGFTEFQTPILTASSPEGARDY 180 Query: 184 LVPSRLHPEKFYALPQAPQQFKQLLMVSGFDRYFQIAPCFRDEDLRADRSL-EFYQLDVE 242 LVPSR HP KFYALPQAPQQFKQLLMV+GFDRYFQIAPCFRDED RADRS EFYQLD E Sbjct: 181 LVPSRNHPGKFYALPQAPQQFKQLLMVAGFDRYFQIAPCFRDEDARADRSPGEFYQLDFE 240 Query: 243 MSFVTQEDVFAAIEPVMHGVFEEFSNGKPVSPINGTHTFTNDFGQSFEHKGFERLTYAQS 302 MSFVTQEDVFAAIEPV+HG+F+EF F D + + F R++YA+S Sbjct: 241 MSFVTQEDVFAAIEPVLHGIFDEFGG------------FRRDSKPAIDGLPFRRISYAES 288 Query: 303 MAWYGSDKPDLRNPIKMANVSEHFR--DGGFGLFAKILGADAKNQVWAIPAPTGGSRAFC 360 M YG+DKPDLRNP+ + +V+E F+ D F F + L + P + R+F Sbjct: 289 MLKYGNDKPDLRNPLVITDVTEVFKRDDVEFRAFKQTLEKGGVVRAIRAPKVSDRPRSFF 348 Query: 361 DRMNSWAQGEGQPGLGYVFWSEDQGGWGGPIAKNLGEPTQ-ALMESLGLGAGDAAFFVAG 419 D++N WA+G G PGLGY+ + GG GPIAK + E Q AL E GL GDA FFV Sbjct: 349 DKLNDWARGLGAPGLGYIVM--EAGGGKGPIAKFVPEAAQAALRELAGLEDGDAIFFVCD 406 Query: 420 DPAVFAKFAGLARTRVGTELKLVDENQFKFCWIVDFPMFEWNEEEKKVDFSHNPFSMPQG 479 P AK AG ARTR+G EL L+++N F+FCWIVDFPM+E +EE KV FSHNPFSMPQG Sbjct: 407 QPGPAAKLAGFARTRIGEELDLIEKNAFRFCWIVDFPMYELDEETNKVIFSHNPFSMPQG 466 Query: 480 GLEALETQDPLTIRAYQYDIVCNGYELCSGAIRNHKPEIMLKAFATAGYGPEVVEEQFGG 539 GL+ALET +PL I+AYQYDIVCNG EL SGAIRNH PE+M KAF AGY PE +E +FGG Sbjct: 467 GLKALETMNPLDIKAYQYDIVCNGVELSSGAIRNHLPEVMYKAFEIAGYPPEELEARFGG 526 Query: 540 MLNAFRYGAPPHGGLAPGIDRIVMLLADQVAIREVIAFPLNQQGQDLLMNAPANVLDKQL 599 ML+AF+ GAPPHGG APGIDRIVMLLAD+ IREVIAFPLNQ+ +DLLM APA V +L Sbjct: 527 MLSAFKLGAPPHGGSAPGIDRIVMLLADEPNIREVIAFPLNQRAEDLLMQAPAPVDTARL 586 Query: 600 KELHIRTAPP 609 +ELH++ P Sbjct: 587 RELHLKLDLP 596 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: 1144 Number of extensions: 49 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: 608 Length adjustment: 37 Effective length of query: 575 Effective length of database: 571 Effective search space: 328325 Effective search space used: 328325 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