Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate Dsui_3296 Dsui_3296 isocitrate dehydrogenase, NADP-dependent, prokaryotic type
Query= BRENDA::Q4J6C9 (411 letters) >FitnessBrowser__PS:Dsui_3296 Length = 408 Score = 373 bits (958), Expect = e-108 Identities = 199/409 (48%), Positives = 273/409 (66%), Gaps = 12/409 (2%) Query: 6 KEPQDGEPIKFEKGKWVVPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKW 65 K PQ G+ K G+ PN PII +IEGDGIG +IT I+VV+ AV+KAY ++I W Sbjct: 6 KVPQGGQ--KIIPGQ-PTPNHPIIPFIEGDGIGVDITPVMIKVVDAAVQKAYGGQKKIHW 62 Query: 66 LEVYAGEKANKITG--DRFPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLY 123 +EVYAGEK+ +I G + PKET D L +Y V +KGP+ TP+G G +S+NVA+R LDLY Sbjct: 63 MEVYAGEKSTRIYGADEWLPKETFDALKEYSVSIKGPMTTPVGGGIRSLNVALRQELDLY 122 Query: 124 ANIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL-- 181 +RPV+Y +G+ SPLK PE +M+IFRENT+D+Y GIE+ + SE KK+ KFL+EE+ Sbjct: 123 QCVRPVQYFKGVPSPLKQPELCNMVIFRENTEDIYAGIEWAHGSEACKKVIKFLQEEMGV 182 Query: 182 -KVDIEDDTGIGLKVMSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREWA 240 K+ + +GIG+K +S T+R+ R A+ YA+ N RK VT++HKGN+MK+TEG+FR+ A Sbjct: 183 KKIRFPESSGIGIKPISVEGTERLVRAAIKYAIDNGRKSVTIVHKGNIMKFTEGNFRDTA 242 Query: 241 YEVALNEYRDKIVTEEEINRGVNSEGKVILNDRIADNMLQQIIIRPDEYDIILAPNVNGD 300 Y +A E+ + + N +++ D IAD LQQI++RP EYD+I N+NGD Sbjct: 243 YALAKREFGGVDIDGGPWQKLPNG---IVIKDAIADAFLQQILLRPAEYDVIATTNLNGD 299 Query: 301 YISDAAGALIGNIGMLGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELMLYFM 360 YISDA A +G IG+ GANI D FEA HGTAPKYAGK+ NP +I S E+ML + Sbjct: 300 YISDALAAQVGGIGIAPGANISDQYACFEATHGTAPKYAGKDKVNPGSLILSAEMMLRHL 359 Query: 361 GWSEAARLIEKAINESIKQKKVTQDIARYL-GITPLGTKEYTDTLVQIM 408 GW EAA LI K++ +I K VT D AR + G T + E+ + ++ M Sbjct: 360 GWKEAADLIIKSMEAAIGDKVVTYDFARLMEGATEVSCSEFGEAMIARM 408 Lambda K H 0.317 0.137 0.394 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: 511 Number of extensions: 17 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: 411 Length of database: 408 Length adjustment: 31 Effective length of query: 380 Effective length of database: 377 Effective search space: 143260 Effective search space used: 143260 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 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