Align Homocysteine formation from aspartate semialdehyde (DUF39 component) (characterized)
to candidate 208448 DVU2938 conserved hypothetical protein
Query= reanno::Miya:8500721 (390 letters) >MicrobesOnline__882:208448 Length = 390 Score = 723 bits (1865), Expect = 0.0 Identities = 342/390 (87%), Positives = 378/390 (96%) Query: 1 MASFKVNKTIAEINERIRQGKAVVLNAEEMTEAVRRMGKEKAAREIDVVTTGTFSPMCSS 60 MA FKVNKTIAEINERI+QGKAVVLNAEEMTEAVRRMGKEKAARE+DVVTTGTFSPMCSS Sbjct: 1 MAHFKVNKTIAEINERIKQGKAVVLNAEEMTEAVRRMGKEKAAREVDVVTTGTFSPMCSS 60 Query: 61 GLLFNIGQQDPPTLKTAKVWMNDVPAYAGLAAVDSYLGATEPTEDDPLNKVYPGRFKYGG 120 GLLFNIGQQ+PPT+KT+KVW+N+VPAYAGLAAVD+Y+GATEPTEDDPLNKVYPGRFKYGG Sbjct: 61 GLLFNIGQQEPPTIKTSKVWLNNVPAYAGLAAVDAYIGATEPTEDDPLNKVYPGRFKYGG 120 Query: 121 GHVIEDLVRGKAVHLRAEAYGTDCYPRKSLDKKITLSELPYAHLLNPRNCYQNYNAAVNL 180 GHVIEDLVRGK+VHLRAEAYGTDCYPR+SLDK+ITL+E+P+A L NPRNCYQNYNAAVNL Sbjct: 121 GHVIEDLVRGKSVHLRAEAYGTDCYPRRSLDKQITLAEMPFAQLWNPRNCYQNYNAAVNL 180 Query: 181 TSRIIYTYMGPLKPNLRNVNFATAGRISPLFNDPLFRTIGLGTRIFLGGGTGYVLGAGTQ 240 TSRIIYTYMGPLKPN+RN+NFATAGR+SPLFNDP FRTIGLGTRIFLGG TGYV GAGTQ Sbjct: 181 TSRIIYTYMGPLKPNMRNINFATAGRLSPLFNDPYFRTIGLGTRIFLGGSTGYVTGAGTQ 240 Query: 241 HVAAPKRTERGLPLSPAGTLMLKGDLKGMNARYLRGLSFLGYGCSLAVGVGIPIPILNEE 300 HVAAPKRT+RGLPL+ AGTLM++GDLKGM+ARYLRGLSFLGYGC+LAVG+GIPIP+LNEE Sbjct: 241 HVAAPKRTDRGLPLTGAGTLMVQGDLKGMDARYLRGLSFLGYGCTLAVGIGIPIPVLNEE 300 Query: 301 IAWFTGVDDSDIQMPVKDYGHDYPNCLPRVIQHVTYEDLKSGEVEIMGKKVETVPMTSYP 360 IAWFTGVDDSDI MPV+DYGHDYPNCLPR+IQHV+YEDLKSGEVE+MGKKVE+VP+TSY Sbjct: 301 IAWFTGVDDSDILMPVRDYGHDYPNCLPRIIQHVSYEDLKSGEVEVMGKKVESVPLTSYS 360 Query: 361 LSLEVANTLKSWIEKGEFLLTEPVELLPSA 390 +SLE+A+ LKSWIEKG F LT+PVELLPSA Sbjct: 361 ISLEIADKLKSWIEKGTFTLTQPVELLPSA 390 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: 687 Number of extensions: 21 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: 390 Length of database: 390 Length adjustment: 31 Effective length of query: 359 Effective length of database: 359 Effective search space: 128881 Effective search space used: 128881 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 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