Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate Synpcc7942_1313 Synpcc7942_1313 aspartyl-tRNA synthetase
Query= reanno::SynE:Synpcc7942_1313 (599 letters) >FitnessBrowser__SynE:Synpcc7942_1313 Length = 599 Score = 1194 bits (3089), Expect = 0.0 Identities = 599/599 (100%), Positives = 599/599 (100%) Query: 1 MRTHYCGELRAEQVGTSVTLYGWVDRRRDHGGVIFVDLRDRTGTVQIVSDPERTPESYHQ 60 MRTHYCGELRAEQVGTSVTLYGWVDRRRDHGGVIFVDLRDRTGTVQIVSDPERTPESYHQ Sbjct: 1 MRTHYCGELRAEQVGTSVTLYGWVDRRRDHGGVIFVDLRDRTGTVQIVSDPERTPESYHQ 60 Query: 61 AEGLRNEYVVKITGRVSGRPAESLNPKLPTGEVEIYADRIEILNAVRRQLPFQVSSADEE 120 AEGLRNEYVVKITGRVSGRPAESLNPKLPTGEVEIYADRIEILNAVRRQLPFQVSSADEE Sbjct: 61 AEGLRNEYVVKITGRVSGRPAESLNPKLPTGEVEIYADRIEILNAVRRQLPFQVSSADEE 120 Query: 121 TVREDLRLRYRYLDLRRDRMNRNLQLRHQVVKAIRRFLEDEEQFIEIETPVLTKSTPEGA 180 TVREDLRLRYRYLDLRRDRMNRNLQLRHQVVKAIRRFLEDEEQFIEIETPVLTKSTPEGA Sbjct: 121 TVREDLRLRYRYLDLRRDRMNRNLQLRHQVVKAIRRFLEDEEQFIEIETPVLTKSTPEGA 180 Query: 181 RDYLVPSRVNPGEWFALPQSPQLFKQLLMVSGFDRYYQIARCFRDEDLRADRQPEFTQLD 240 RDYLVPSRVNPGEWFALPQSPQLFKQLLMVSGFDRYYQIARCFRDEDLRADRQPEFTQLD Sbjct: 181 RDYLVPSRVNPGEWFALPQSPQLFKQLLMVSGFDRYYQIARCFRDEDLRADRQPEFTQLD 240 Query: 241 MEMSFLSQEEIIDLNERLIAHIFKTVKGIELPRPFPRLTYAEAMDRYGSDRPDTRFGLEL 300 MEMSFLSQEEIIDLNERLIAHIFKTVKGIELPRPFPRLTYAEAMDRYGSDRPDTRFGLEL Sbjct: 241 MEMSFLSQEEIIDLNERLIAHIFKTVKGIELPRPFPRLTYAEAMDRYGSDRPDTRFGLEL 300 Query: 301 VDVSDVVADMGFKVFSGAVKSGGKVKILPIPDGNDRISNVRIKPGGDIFKEATEAGAAGL 360 VDVSDVVADMGFKVFSGAVKSGGKVKILPIPDGNDRISNVRIKPGGDIFKEATEAGAAGL Sbjct: 301 VDVSDVVADMGFKVFSGAVKSGGKVKILPIPDGNDRISNVRIKPGGDIFKEATEAGAAGL 360 Query: 361 AYIRVRENGEIDTIGAIKDNLSDEQKAEILRRTQAQPGTLLLFGAGSTDIVNKSLDRVRQ 420 AYIRVRENGEIDTIGAIKDNLSDEQKAEILRRTQAQPGTLLLFGAGSTDIVNKSLDRVRQ Sbjct: 361 AYIRVRENGEIDTIGAIKDNLSDEQKAEILRRTQAQPGTLLLFGAGSTDIVNKSLDRVRQ 420 Query: 421 FLGKELGLIDPEALNLLWVVDFPMVEWNADEKRYEALHHPFTAPNPQDLEDLTTARAQAY 480 FLGKELGLIDPEALNLLWVVDFPMVEWNADEKRYEALHHPFTAPNPQDLEDLTTARAQAY Sbjct: 421 FLGKELGLIDPEALNLLWVVDFPMVEWNADEKRYEALHHPFTAPNPQDLEDLTTARAQAY 480 Query: 481 DIVLNGLEIGGGSLRIYQRDIQERVFETIGLSHEEAQAKFGFLLEAFDFGTPPHGGIAYG 540 DIVLNGLEIGGGSLRIYQRDIQERVFETIGLSHEEAQAKFGFLLEAFDFGTPPHGGIAYG Sbjct: 481 DIVLNGLEIGGGSLRIYQRDIQERVFETIGLSHEEAQAKFGFLLEAFDFGTPPHGGIAYG 540 Query: 541 LDRLVMLLTGEESIRDAIAFPKTQQARCLLTEAPADVSDRQLKELYVASTWQPPIKERD 599 LDRLVMLLTGEESIRDAIAFPKTQQARCLLTEAPADVSDRQLKELYVASTWQPPIKERD Sbjct: 541 LDRLVMLLTGEESIRDAIAFPKTQQARCLLTEAPADVSDRQLKELYVASTWQPPIKERD 599 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: 1363 Number of extensions: 69 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: 599 Length adjustment: 37 Effective length of query: 562 Effective length of database: 562 Effective search space: 315844 Effective search space used: 315844 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