Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (uncharacterized)
to candidate SMa1871 SMa1871 cyclodeaminase
Query= curated2:Q59175 (359 letters) >FitnessBrowser__Smeli:SMa1871 Length = 330 Score = 114 bits (286), Expect = 3e-30 Identities = 74/217 (34%), Positives = 118/217 (54%), Gaps = 9/217 (4%) Query: 98 VLADVGSGYPMLLTEMTILTALRTAATSAVAAKHLAPKNARTMAIIGNGAQSEFQALAFK 157 +L D S + + + +++T LRT A+ AV+ K LA KNART+A IG G Q+ Q A Sbjct: 92 LLFDARSCALICIMDGSLITGLRTGASGAVSVKALARKNARTVASIGTGNQARMQIRAVN 151 Query: 158 AILGVDKLRLYDLDPQATAKCIRNLQGA-GFNIVACKSVEEAVEGADIITTVTADKANAT 216 I+ ++K+ + P++ ++ ++Q G ++ S +EAVE ADI+ T T K + Sbjct: 152 EIMKIEKIHAWSRTPESLSRYKTDIQREFGIPVIVASSKKEAVEQADILITTTRGK--GS 209 Query: 217 ILTDNMVGAGVHINAVGGDCSGKTELHGDILRRSDIFVEYPPQTRIEGEIQQ------LP 270 ++ + V G HI A+G D GK EL +I R + + V+ Q +GE + Sbjct: 210 LVEADWVKPGTHIVAIGTDQRGKQELDPEIFRNAKVVVDSVAQCTEKGETWHPLNKNIIT 269 Query: 271 EDYPVNELWEVITGRIAGRKDARQITLFDSVGFATED 307 +D E+ EV+ GR GR+ +IT+FDS G A +D Sbjct: 270 KDDIHGEIGEVLLGRKPGRESDDEITIFDSTGMAIQD 306 Lambda K H 0.318 0.135 0.389 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: 228 Number of extensions: 13 Number of successful extensions: 4 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: 359 Length of database: 330 Length adjustment: 29 Effective length of query: 330 Effective length of database: 301 Effective search space: 99330 Effective search space used: 99330 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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