Align Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate 209413 DVU0477 isocitrate dehydrogenase, NADP-dependent
Query= SwissProt::Q02NB5 (418 letters) >MicrobesOnline__882:209413 Length = 380 Score = 431 bits (1107), Expect = e-125 Identities = 218/384 (56%), Positives = 282/384 (73%), Gaps = 12/384 (3%) Query: 33 FIEGDGIGVDISPVMIKVVDAAVEKAYKGERKIAWMEVYAGEKATQVYDQDTWLPQETLD 92 +IEGDGIG ++ V+DAAVEK+Y R I W E+ AGEKA + + +LPQ TLD Sbjct: 7 WIEGDGIGPEVWKAARPVIDAAVEKSYGDSRSIEWKELLAGEKAHR--ETGEYLPQSTLD 64 Query: 93 AVRDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCQRPVRWFEGVPSPVKKPGDVDMV 152 + ++IKGPL TPVG G RSLNV +RQ LDLY C RP+R+F+G+ SPVK+P VDMV Sbjct: 65 TLATAELAIKGPLGTPVGKGFRSLNVTMRQTLDLYACIRPIRYFDGIMSPVKRPDLVDMV 124 Query: 153 IFRENSEDIYAGVEWKAGSPEAEKVIKFLTEEMGVKKIRFTENCGIGIKPVSQEGTKRLV 212 +FREN+ED+YAG+E++AG+PEA+++I FL +E+G K +GIKP++++G+KRLV Sbjct: 125 VFRENTEDVYAGIEYRAGTPEAKRLIAFLRDELGAK---VDIEAAVGIKPMTEKGSKRLV 181 Query: 213 RKALQYAVDNDRSSVTLVHKGNIMKFTEGAFKDWGYEVARDEFGAELLDGGPWMQFKNPK 272 R+AL++A+D R ++TLVHKGNIMKFTEG F++WGYEVARDEF A+L + Sbjct: 182 RRALRFAIDQKRPNLTLVHKGNIMKFTEGGFREWGYEVARDEF-ADLTTT------ETEG 234 Query: 273 TGKNVVVKDVIADAMLQQILLRPAEYDVIATLNLNGDYLSDALAAEVGGIGIAPGANLSD 332 T +VVKD IADAM Q++L+RP +Y VIAT NLNGDY+SDALAA+VGG+G+APG N+SD Sbjct: 235 TAGRLVVKDRIADAMFQEVLIRPQQYSVIATSNLNGDYISDALAAQVGGLGLAPGVNMSD 294 Query: 333 SVAMFEATHGTAPKYAGQDKVNPGSLILSAEMMLRHMGWTEAADLIIKGTNGAIAAKTVT 392 S+A FEATHGTAP AGQDK NPGSLIL +ML HMGW EAA+ I K N AIA++ VT Sbjct: 295 SLAFFEATHGTAPTIAGQDKANPGSLILCGALMLEHMGWNEAAERIYKAVNEAIASRRVT 354 Query: 393 YDFERLMDGATLLSCSEFGDAMIA 416 D M+ AT + FGD + A Sbjct: 355 VDLATQMENATTVGTVAFGDIVTA 378 Lambda K H 0.317 0.135 0.397 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: 507 Number of extensions: 22 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: 418 Length of database: 380 Length adjustment: 31 Effective length of query: 387 Effective length of database: 349 Effective search space: 135063 Effective search space used: 135063 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 (21.6 bits) S2: 50 (23.9 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