Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_041455911.1 AVA_RS01230 aspartate--tRNA ligase
Query= reanno::SynE:Synpcc7942_1313 (599 letters) >NCBI__GCF_000204075.1:WP_041455911.1 Length = 595 Score = 972 bits (2512), Expect = 0.0 Identities = 469/593 (79%), Positives = 538/593 (90%) Query: 1 MRTHYCGELRAEQVGTSVTLYGWVDRRRDHGGVIFVDLRDRTGTVQIVSDPERTPESYHQ 60 MRTHYCGELR + +G +VTLYGWVDRRRDHGGVIF+DLRDR+G VQ+VSDP+RTP+SY Sbjct: 1 MRTHYCGELRQKDIGETVTLYGWVDRRRDHGGVIFLDLRDRSGIVQVVSDPQRTPDSYEL 60 Query: 61 AEGLRNEYVVKITGRVSGRPAESLNPKLPTGEVEIYADRIEILNAVRRQLPFQVSSADEE 120 A LRNEYVV+ITGRV+ RP ESLN ++PTGEVEIYAD+IE+LN VR+QLPFQVS+AD E Sbjct: 61 ANSLRNEYVVEITGRVTQRPEESLNSRIPTGEVEIYADKIELLNGVRKQLPFQVSTADTE 120 Query: 121 TVREDLRLRYRYLDLRRDRMNRNLQLRHQVVKAIRRFLEDEEQFIEIETPVLTKSTPEGA 180 TVREDLRL+YRYLDLRRDRM RN+QLRHQVVKA+RR+LED E FIE+ETP+LT+STPEGA Sbjct: 121 TVREDLRLKYRYLDLRRDRMARNIQLRHQVVKAMRRYLEDVEGFIEVETPILTRSTPEGA 180 Query: 181 RDYLVPSRVNPGEWFALPQSPQLFKQLLMVSGFDRYYQIARCFRDEDLRADRQPEFTQLD 240 RDY++PSRVNPGEWFALPQSPQLFKQ+LMVSG DRYYQIARCFRDEDLRADRQPEFTQLD Sbjct: 181 RDYVLPSRVNPGEWFALPQSPQLFKQILMVSGMDRYYQIARCFRDEDLRADRQPEFTQLD 240 Query: 241 MEMSFLSQEEIIDLNERLIAHIFKTVKGIELPRPFPRLTYAEAMDRYGSDRPDTRFGLEL 300 MEMSF+S+EEII LNE+L+++IFKTVKG+ELP PFPRLTYAEAM+RYG D+PDTR+ L+L Sbjct: 241 MEMSFMSEEEIIQLNEKLVSYIFKTVKGVELPLPFPRLTYAEAMERYGCDKPDTRYDLQL 300 Query: 301 VDVSDVVADMGFKVFSGAVKSGGKVKILPIPDGNDRISNVRIKPGGDIFKEATEAGAAGL 360 V+VSDV+ D GFKVF AV +GG VKILPIP+GN++ISNVRIKPGGD+F+EA+EAGA GL Sbjct: 301 VNVSDVMKDSGFKVFRDAVANGGIVKILPIPNGNEQISNVRIKPGGDLFREASEAGAKGL 360 Query: 361 AYIRVRENGEIDTIGAIKDNLSDEQKAEILRRTQAQPGTLLLFGAGSTDIVNKSLDRVRQ 420 AYIRVRE+GEIDTIGAIKDNLS+EQK EIL+RT A+PG LLLFGAG VNK+LDR+RQ Sbjct: 361 AYIRVREDGEIDTIGAIKDNLSEEQKQEILQRTGAKPGHLLLFGAGDAATVNKTLDRLRQ 420 Query: 421 FLGKELGLIDPEALNLLWVVDFPMVEWNADEKRYEALHHPFTAPNPQDLEDLTTARAQAY 480 + KE GLIDP+ +NLLWVVDFPM EWNADEKR EALHHPFTAP+P DL DL TARAQAY Sbjct: 421 AIAKEFGLIDPDKINLLWVVDFPMFEWNADEKRLEALHHPFTAPHPDDLHDLKTARAQAY 480 Query: 481 DIVLNGLEIGGGSLRIYQRDIQERVFETIGLSHEEAQAKFGFLLEAFDFGTPPHGGIAYG 540 D+V NG E+GGGS RIYQR++QE+VFETIGLS EEAQ KFGFLLEAF++GTPPHGGIAYG Sbjct: 481 DLVFNGFEVGGGSRRIYQREVQEQVFETIGLSPEEAQNKFGFLLEAFEYGTPPHGGIAYG 540 Query: 541 LDRLVMLLTGEESIRDAIAFPKTQQARCLLTEAPADVSDRQLKELYVASTWQP 593 LDRLVML GEESIRD IAFPKTQQARCLLT+AP+ V +QLKEL+VAST++P Sbjct: 541 LDRLVMLFAGEESIRDVIAFPKTQQARCLLTDAPSGVDVKQLKELHVASTYKP 593 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: 1191 Number of extensions: 46 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 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