Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate CCNA_01345 CCNA_01345 short chain dehydrogenase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__Caulo:CCNA_01345 Length = 260 Score = 167 bits (423), Expect = 2e-46 Identities = 101/254 (39%), Positives = 146/254 (57%), Gaps = 14/254 (5%) Query: 13 LFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIA-----DLNPDVGEGAARELDGTFE 67 LF L GR A+VTGG++G+G +IAR LA+ GA V + +L+ V A Sbjct: 8 LFDLTGRVAIVTGGSRGLGLQIARALAEYGAAVALVARKQGELDAAVAALTAEGRTAVGL 67 Query: 68 RLNVTDADAVADLARRLPD----VDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFW 123 ++ A + DL R+ + +D+LVNNAG APAED P + W V+ +N+ G+F Sbjct: 68 VADLGQAGSAQDLTARVLERFGRIDILVNNAGAAWGAPAEDYPLEGWNKVMDLNVTGLFL 127 Query: 124 CCREFGR-TMLARGRGAIVSTASMSGLISNHPQPQA--AYNASKAAVIHLTRSLAGEWAS 180 + R L +G+GA+V+ AS+ GL +H AYN +K AVI++TR+LA EW Sbjct: 128 LTQAVAREAFLKQGKGAVVNVASIEGLQGHHHSQLGTIAYNTAKGAVINMTRALAAEWGP 187 Query: 181 RGVRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASF 240 R +RVNAVAPGY + +T L + + L++TPLG+L ++ L LASDA Sbjct: 188 RNIRVNAVAPGYFPSKMTMTTL--GQHGDDMLRQTPLGKLGGDTDLMGPALLLASDAGGH 245 Query: 241 VTGHTLVVDGGYTV 254 +TG +VVDGG T+ Sbjct: 246 ITGQIIVVDGGMTI 259 Lambda K H 0.319 0.134 0.408 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: 210 Number of extensions: 12 Number of successful extensions: 5 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: 255 Length of database: 260 Length adjustment: 24 Effective length of query: 231 Effective length of database: 236 Effective search space: 54516 Effective search space used: 54516 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: 47 (22.7 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