Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate Ga0059261_0221 Ga0059261_0221 aspartyl-tRNA synthetase, bacterial type
Query= uniprot:A0A0H3C7V8_CAUVN (612 letters) >FitnessBrowser__Korea:Ga0059261_0221 Length = 598 Score = 782 bits (2020), Expect = 0.0 Identities = 400/615 (65%), Positives = 471/615 (76%), Gaps = 29/615 (4%) Query: 4 MHAYRTHNCGALRASDTGAAVRLSGWIHRKRDHGGLVFIDLRDHYGLTQLVLHPETPGFN 63 MHAYR+H CG L A+ G VRLSGWIHRKRDHGG++F+DLRDHYG+TQ+V ++P Sbjct: 1 MHAYRSHTCGQLTAAQVGETVRLSGWIHRKRDHGGVLFVDLRDHYGVTQIVADSDSPALP 60 Query: 64 VVERLRAESVIRVDGEVIARDASVVNPNLPTGEIEIRVSAVEVLSEAAELPLPVFGEPDY 123 V+E LR ESV+ +DG V AR + VNPNL TGEIE+ V V S A ELP+PVFG+ +Y Sbjct: 61 VLEGLRVESVVTIDGVVKARSDATVNPNLSTGEIEVFAKGVTVQSAAQELPMPVFGDAEY 120 Query: 124 PEEIRLKHRYLDLRRETLHKNIVLRSRVIQSIRNRMFAQGFNEFQTPILTASSPEGARDF 183 PEEIRL++R+LDLRRE LH NI+LRS VI S+R RM QGF EFQTPILTASSPEGARD+ Sbjct: 121 PEEIRLRNRFLDLRREGLHANIMLRSHVIASLRRRMIDQGFTEFQTPILTASSPEGARDY 180 Query: 184 LVPSRLHPEKFYALPQAPQQFKQLLMVSGFDRYFQIAPCFRDEDLRADRSL-EFYQLDVE 242 LV SR+HP KFYALPQAPQ FKQLLMV+GFDRYFQIAPCFRDED RADRS EFYQLD E Sbjct: 181 LVASRVHPGKFYALPQAPQMFKQLLMVAGFDRYFQIAPCFRDEDARADRSPGEFYQLDFE 240 Query: 243 MSFVTQEDVFAAIEPVMHGVFEEFSN----GKPVSPINGTHTFTNDFGQSFEHKGFERLT 298 MS+VTQ+DVFAAIEPV+HGVFEEF++ G+ VSP+ F+R+ Sbjct: 241 MSYVTQDDVFAAIEPVLHGVFEEFADWQGKGRTVSPL-----------------PFKRIP 283 Query: 299 YAQSMAWYGSDKPDLRNPIKMANVSEHFRDGGFGLFAKILGADAKNQVWAIPAP--TGGS 356 Y +SM YG+DKPDLRNPI +++VS+HF GFG FA I+ +A + V AIPAP S Sbjct: 284 YRESMLKYGNDKPDLRNPILISDVSKHFEGSGFGRFASIV--EAGDVVRAIPAPGTAEKS 341 Query: 357 RAFCDRMNSWAQGEGQPGLGYVFWSEDQGGWGGPIAKNLGE-PTQALMESLGLGAGDAAF 415 R F D MN+WAQGEG GLGY + G WGGPIAKN GE AL + LGLG D F Sbjct: 342 RKFFDDMNAWAQGEGFAGLGYA--TRKGGEWGGPIAKNHGEDKMSALADELGLGPDDGIF 399 Query: 416 FVAGDPAVFAKFAGLARTRVGTELKLVDENQFKFCWIVDFPMFEWNEEEKKVDFSHNPFS 475 F AG A AK AGLARTRVG +L+L+D+N+F+FCWIVDFPMFE++E+ KK+DFSHNPFS Sbjct: 400 FAAGKEAQAAKLAGLARTRVGEQLELIDKNRFEFCWIVDFPMFEYDEDAKKIDFSHNPFS 459 Query: 476 MPQGGLEALETQDPLTIRAYQYDIVCNGYELCSGAIRNHKPEIMLKAFATAGYGPEVVEE 535 MPQG LEALET+DPL I A+QYDIVCNG EL SGAIRNH+PEIM KAF AGY E V+ Sbjct: 460 MPQGELEALETKDPLDILAWQYDIVCNGIELSSGAIRNHRPEIMYKAFEIAGYTQEQVDS 519 Query: 536 QFGGMLNAFRYGAPPHGGLAPGIDRIVMLLADQVAIREVIAFPLNQQGQDLLMNAPANVL 595 F GM+NAF++GAPPHGG APG+DRIVMLLADQ IREVI FP+NQ+ +DL+M AP+ V Sbjct: 520 NFAGMINAFKFGAPPHGGSAPGVDRIVMLLADQPNIREVIVFPMNQKAEDLMMQAPSFVS 579 Query: 596 DKQLKELHIRTAPPI 610 +KQLKELHIR AP + Sbjct: 580 EKQLKELHIRLAPGV 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: 1127 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: 598 Length adjustment: 37 Effective length of query: 575 Effective length of database: 561 Effective search space: 322575 Effective search space used: 322575 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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