Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_011385213.1 AMB_RS14265 aspartate--tRNA ligase
Query= reanno::Caulo:CCNA_01969 (612 letters) >NCBI__GCF_000009985.1:WP_011385213.1 Length = 598 Score = 737 bits (1903), Expect = 0.0 Identities = 376/611 (61%), Positives = 456/611 (74%), Gaps = 27/611 (4%) Query: 4 MHAYRTHNCGALRASDTGAAVRLSGWIHRKRDHGGLVFIDLRDHYGLTQLVLHPETPGFN 63 MH YR+H CG L+A+D G RLSGW+HRKRDHG L+F+DLRDHYG+TQ V+ +P F Sbjct: 1 MHVYRSHTCGQLKAADAGIQARLSGWVHRKRDHGNLLFVDLRDHYGITQCVIDVSSPVFA 60 Query: 64 VVERLRAESVIRVDGEVIARDASVVNPNLPTGEIEIRVSAVEVLSEAAELPLPVFGEPDY 123 +++ R ESVI V G+V+ R A +NP LPTGEIE++V+ VE+ S A LP+ V G+ +Y Sbjct: 61 ALDKARPESVITVTGKVVKRSAETINPRLPTGEIELQVAEVEIQSIADVLPIQVAGDQEY 120 Query: 124 PEEIRLKHRYLDLRRETLHKNIVLRSRVIQSIRNRMFAQGFNEFQTPILTASSPEGARDF 183 PE++RL++R+LDLRRE +H N++LRSRVI +R M QGF EFQTPILTASSPEGARD+ Sbjct: 121 PEDMRLRYRFLDLRREDVHANMMLRSRVIAYLRQAMIGQGFTEFQTPILTASSPEGARDY 180 Query: 184 LVPSRLHPEKFYALPQAPQQFKQLLMVSGFDRYFQIAPCFRDEDLRADRSL-EFYQLDVE 242 LVPSR+HP KFYALPQAPQQFKQLLMV+GFD+YFQIAPCFRDE RADRS EFYQLD E Sbjct: 181 LVPSRIHPGKFYALPQAPQQFKQLLMVAGFDKYFQIAPCFRDEAGRADRSPGEFYQLDFE 240 Query: 243 MSFVTQEDVFAAIEPVMHGVFEEFSNGKPVSPINGTHTFTNDFGQSFEHKGFERLTYAQS 302 MS+VTQ+DVFAAIEPV+ GVF+EF G+ V+P F R+TYA S Sbjct: 241 MSYVTQDDVFAAIEPVLEGVFKEFGKGRAVTP-----------------APFPRITYADS 283 Query: 303 MAWYGSDKPDLRNPIKMANVSEHFRDGGFGLFAKILGADAKNQVWAIPAP--TGGSRAFC 360 M YGSDKPDLRNPI +A+V+E FR GFGLFAK++ D V AIPAP G R++ Sbjct: 284 MLKYGSDKPDLRNPIIIADVTEPFRGSGFGLFAKLV--DKGAVVRAIPAPGAAGQPRSWF 341 Query: 361 DRMNSWAQGEGQPGLGYVFWSEDQGGWGGPIAKNLGEP--TQALMESLGLGAGDAAFFVA 418 D++N WA+ G GLGY+ ++ D G GPIAKNL EP +A+ + L GDA FF Sbjct: 342 DKLNDWARENGAGGLGYIQFAAD--GPKGPIAKNL-EPARVEAIKAAANLKDGDAVFFAC 398 Query: 419 GDPAVFAKFAGLARTRVGTELKLVDENQFKFCWIVDFPMFEWNEEEKKVDFSHNPFSMPQ 478 AKFAGL RT++G EL L++++ FKFCW VDFPM+E NEE V+FSHNPFSMPQ Sbjct: 399 DKALPAAKFAGLVRTKIGNELDLLEKDVFKFCWTVDFPMYEINEETGLVEFSHNPFSMPQ 458 Query: 479 GGLEALETQDPLTIRAYQYDIVCNGYELCSGAIRNHKPEIMLKAFATAGYGPEVVEEQFG 538 GG++AL QDPLTI AYQYDIVCNG EL SGAIRNH+P+IM KAF AGY VEE FG Sbjct: 459 GGMDALLNQDPLTINAYQYDIVCNGVELSSGAIRNHRPDIMYKAFEIAGYSAAHVEEHFG 518 Query: 539 GMLNAFRYGAPPHGGLAPGIDRIVMLLADQVAIREVIAFPLNQQGQDLLMNAPANVLDKQ 598 GMLNAF++GAPPHGG APG+DRIVMLLADQ IRE+I FP+NQQ QDLLM APA + ++ Sbjct: 519 GMLNAFKFGAPPHGGSAPGVDRIVMLLADQPNIREIILFPMNQQAQDLLMQAPAEIAMER 578 Query: 599 LKELHIRTAPP 609 L+ELHI+ P Sbjct: 579 LRELHIKVDLP 589 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: 1084 Number of extensions: 47 Number of successful extensions: 4 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 Apr 09 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