Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate RR42_RS09460 RR42_RS09460 hypothetical protein
Query= curated2:O26344 (283 letters) >FitnessBrowser__Cup4G11:RR42_RS09460 Length = 271 Score = 169 bits (429), Expect = 5e-47 Identities = 106/273 (38%), Positives = 158/273 (57%), Gaps = 16/273 (5%) Query: 11 IMGHPLGHSLSPIMHNAAFRSLGMDWIYVPFPVKPENLKAAVEGLRALGVEGVNVTIPHK 70 IMG P ++ +HNAA+R+L +D+ +V F V +++ AV+ +RALGV G+NV++PHK Sbjct: 12 IMGEPFTFNVR--IHNAAYRALEIDYTFVCFGV--QDVPGAVQSIRALGVRGMNVSMPHK 67 Query: 71 EAVLEYIDDIHGTAALIGAVNTLKFDDGTVRGYNTDASGCLRALEEVTSVEGSSVLILGA 130 +AV+ ++D + TA IGAVNT+ DG + GYNTD G +RA +EVT ++G + +LGA Sbjct: 68 QAVIPHLDHLDETARAIGAVNTINNVDGVLTGYNTDCIGAVRAFQEVTELQGKRIALLGA 127 Query: 131 GGAARACAFQLAEKGASDITILNRTPEKARLLAEDMADKLGFEASYGGYELIQGSVKSAD 190 GGAARA A+ L E GA+ +T+ NRT + E++A LG +GG L D Sbjct: 128 GGAARAMAYGLREAGAA-VTLFNRTAAR----GEELAASLGLR--FGG-ALSDFRAADFD 179 Query: 191 ILIDTTPVGMHPHTDDRPLVGAELMHEGLVVHDLVYNPQRTVLLREAERASAIPVSGIRM 250 +L + T G D P+ G H L+V D + P R+ L+R+A + G RM Sbjct: 180 LLANATAAGFRA-PDVNPVAGQLAAH--LIVMDAAFIPVRSKLIRDAAELGCRTIDGTRM 236 Query: 251 LLYQGVEAFRIWTG-RDPPLDVMEDALKRVLNR 282 +L+Q +TG P++ ME AL + R Sbjct: 237 MLHQACAQVEFYTGCARAPIEAMEAALLEEIAR 269 Lambda K H 0.319 0.137 0.401 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: 226 Number of extensions: 14 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: 283 Length of database: 271 Length adjustment: 25 Effective length of query: 258 Effective length of database: 246 Effective search space: 63468 Effective search space used: 63468 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 (21.7 bits) S2: 47 (22.7 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