Align Homocysteine formation from aspartate semialdehyde (DUF39 component) (characterized)
to candidate WP_015739409.1 ADEG_RS07235 hypothetical protein
Query= reanno::Miya:8500721 (390 letters) >NCBI__GCF_000024605.1:WP_015739409.1 Length = 406 Score = 418 bits (1074), Expect = e-121 Identities = 206/382 (53%), Positives = 266/382 (69%), Gaps = 2/382 (0%) Query: 8 KTIAEINERIRQGKAVVLNAEEMTEAVRRMGKEKAAREIDVVTTGTFSPMCSSGLLFNIG 67 +T AEINE+I+ GK VV+ AEE+ V G ++ ARE+DVVTTGTF+PMCSSG FN G Sbjct: 5 RTFAEINEKIKAGKVVVVTAEELVSLVEEKGVKQVAREVDVVTTGTFAPMCSSGAFFNFG 64 Query: 68 QQDPPTLKTAKVWMNDVPAYAGLAAVDSYLGATEPTEDDPLNKVYPGRFKYGGGHVIEDL 127 P +K +VW+NDVPAYAGLAAVD++LGAT E DPLN PG F+YGGGHVIEDL Sbjct: 65 H-GAPRIKFFRVWLNDVPAYAGLAAVDAFLGATAVREGDPLNTDPPGEFRYGGGHVIEDL 123 Query: 128 VRGKAVHLRAEAYGTDCYPRKSLDKKITLSELPYAHLLNPRNCYQNYNAAVNLTSRIIYT 187 V + V LRA YGTDCYPR+ ++ ITL ++ A L NPRN YQNY AVN R +YT Sbjct: 124 VARRPVKLRAIGYGTDCYPRREIETVITLDDINEAFLFNPRNAYQNYACAVNTGDRTLYT 183 Query: 188 YMGPLKPNLRNVNFATAGRISPLFNDPLFRTIGLGTRIFLGGGTGYVLGAGTQHV-AAPK 246 YMG LKP L N +++T+G++SPL DP FRTIG+GTRIFLGGG GYV+ GTQH + P Sbjct: 184 YMGVLKPRLGNAHYSTSGQLSPLLKDPFFRTIGIGTRIFLGGGIGYVVNHGTQHFPSIPD 243 Query: 247 RTERGLPLSPAGTLMLKGDLKGMNARYLRGLSFLGYGCSLAVGVGIPIPILNEEIAWFTG 306 + + GTL + GDLK M+ R+LRG S LGYG SL+VG+G+ IPIL+EE+ ++ Sbjct: 244 LPAGAVRIPSGGTLAVMGDLKQMSPRWLRGTSMLGYGVSLSVGIGVAIPILDEEVCYYAS 303 Query: 307 VDDSDIQMPVKDYGHDYPNCLPRVIQHVTYEDLKSGEVEIMGKKVETVPMTSYPLSLEVA 366 D ++ P+ DY YP P + V+Y +L+SG++ I GK+V T ++SY + E+ Sbjct: 304 RPDRELYAPIVDYAEAYPQRRPGNLGWVSYAELRSGKITINGKEVPTASLSSYARAREIC 363 Query: 367 NTLKSWIEKGEFLLTEPVELLP 388 LK WI++G+FLLTEPV LP Sbjct: 364 QILKEWIQEGKFLLTEPVAPLP 385 Lambda K H 0.318 0.137 0.409 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: 523 Number of extensions: 22 Number of successful extensions: 3 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: 390 Length of database: 406 Length adjustment: 31 Effective length of query: 359 Effective length of database: 375 Effective search space: 134625 Effective search space used: 134625 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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