Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_011611941.1 TERY_RS11210 aspartate--tRNA ligase
Query= reanno::SynE:Synpcc7942_1313 (599 letters) >NCBI__GCF_000014265.1:WP_011611941.1 Length = 595 Score = 931 bits (2406), Expect = 0.0 Identities = 445/589 (75%), Positives = 520/589 (88%) Query: 1 MRTHYCGELRAEQVGTSVTLYGWVDRRRDHGGVIFVDLRDRTGTVQIVSDPERTPESYHQ 60 MRTHYCG++ + + +V L GWVDRRRDHGGVIF+DLRDR+G +QIVSDPERTP+SY Sbjct: 1 MRTHYCGQVNSNNIEETVNLCGWVDRRRDHGGVIFLDLRDRSGLIQIVSDPERTPDSYQI 60 Query: 61 AEGLRNEYVVKITGRVSGRPAESLNPKLPTGEVEIYADRIEILNAVRRQLPFQVSSADEE 120 A +RNEYVV+ITGRVS RP ESLNPKLPTGE+EIYAD I++LN + +QLPFQVS+A+ E Sbjct: 61 AGDIRNEYVVQITGRVSRRPEESLNPKLPTGEIEIYADDIQLLNGLGKQLPFQVSTAETE 120 Query: 121 TVREDLRLRYRYLDLRRDRMNRNLQLRHQVVKAIRRFLEDEEQFIEIETPVLTKSTPEGA 180 VRE+LRL+YRYLDLRR+RM RNL LRH+V+KAIRRFLEDE+ F+EIETP+LT+STPEGA Sbjct: 121 AVREELRLKYRYLDLRRERMTRNLLLRHEVIKAIRRFLEDEQNFVEIETPILTRSTPEGA 180 Query: 181 RDYLVPSRVNPGEWFALPQSPQLFKQLLMVSGFDRYYQIARCFRDEDLRADRQPEFTQLD 240 RDYLVPSRV+PGEWFALPQSPQLFKQ+LMVSGFDRYYQIARCFRDEDLRADRQPEFTQLD Sbjct: 181 RDYLVPSRVHPGEWFALPQSPQLFKQILMVSGFDRYYQIARCFRDEDLRADRQPEFTQLD 240 Query: 241 MEMSFLSQEEIIDLNERLIAHIFKTVKGIELPRPFPRLTYAEAMDRYGSDRPDTRFGLEL 300 MEMSF+SQEEI+ LNE+L+A+IF+ VKGI+LP PFPRLTY EAM+RYGSD+PD RFGLEL Sbjct: 241 MEMSFMSQEEILQLNEKLVAYIFQKVKGIDLPLPFPRLTYTEAMERYGSDKPDVRFGLEL 300 Query: 301 VDVSDVVADMGFKVFSGAVKSGGKVKILPIPDGNDRISNVRIKPGGDIFKEATEAGAAGL 360 VDVSD++ D GFKVFSGA+ GG VK+LPIP GND ISNVRIKPGGD+FKEA+E GA GL Sbjct: 301 VDVSDLMKDSGFKVFSGAIAKGGIVKVLPIPGGNDAISNVRIKPGGDLFKEASEVGAKGL 360 Query: 361 AYIRVRENGEIDTIGAIKDNLSDEQKAEILRRTQAQPGTLLLFGAGSTDIVNKSLDRVRQ 420 AY+RV+E G+IDTIGAIKDNL+DEQK E+L+RT AQPG LLLF A + VNK+LDR+R Sbjct: 361 AYVRVKEGGKIDTIGAIKDNLTDEQKQELLKRTNAQPGHLLLFAADDANTVNKTLDRLRL 420 Query: 421 FLGKELGLIDPEALNLLWVVDFPMVEWNADEKRYEALHHPFTAPNPQDLEDLTTARAQAY 480 +G++LGLID + ++LLWV DFPM EWN DE+R EALHHPFTAP+P D+ DL TARAQAY Sbjct: 421 VIGEQLGLIDQDKISLLWVTDFPMFEWNEDEQRLEALHHPFTAPHPDDINDLKTARAQAY 480 Query: 481 DIVLNGLEIGGGSLRIYQRDIQERVFETIGLSHEEAQAKFGFLLEAFDFGTPPHGGIAYG 540 D+V NG E+GGGSLRIYQRD+QE+VFE IGLS +EA KFGFLLEAF++GTPPHGGIAYG Sbjct: 481 DLVFNGYEVGGGSLRIYQRDVQEKVFEAIGLSAQEADNKFGFLLEAFEYGTPPHGGIAYG 540 Query: 541 LDRLVMLLTGEESIRDAIAFPKTQQARCLLTEAPADVSDRQLKELYVAS 589 LDRLVMLL EESIRD IAFPKTQQA+CLL AP++V +QLKEL+V+S Sbjct: 541 LDRLVMLLAVEESIRDVIAFPKTQQAKCLLANAPSEVDKKQLKELHVSS 589 Lambda K H 0.320 0.139 0.404 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: 1141 Number of extensions: 52 Number of successful extensions: 1 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: 599 Length of database: 595 Length adjustment: 37 Effective length of query: 562 Effective length of database: 558 Effective search space: 313596 Effective search space used: 313596 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