Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate 15258 b1136 isocitrate dehydrogenase (NCBI)
Query= BRENDA::Q4J6C9 (411 letters) >FitnessBrowser__Keio:15258 Length = 416 Score = 394 bits (1011), Expect = e-114 Identities = 198/409 (48%), Positives = 278/409 (67%), Gaps = 8/409 (1%) Query: 8 PQDGEPIKFEKGKWVVPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWLE 67 P G+ I + GK VP PII YIEGDGIG ++T + ++VV+ AVEKAYK R+I W+E Sbjct: 8 PAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWME 67 Query: 68 VYAGEKANKITGDR--FPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYAN 125 +Y GEK+ ++ G P ET D++ +YRV +KGPL TP+G G +S+NVA+R LDLY Sbjct: 68 IYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYIC 127 Query: 126 IRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL---K 182 +RPV+Y +G SP+KHPE DM+IFREN++D+Y GIE+ DS +A+K+ KFLREE+ K Sbjct: 128 LRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLREEMGVKK 187 Query: 183 VDIEDDTGIGLKVMSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREWAYE 242 + + GIG+K S+ T+R+ R A+ YA+ N R VT++HKGN+MK+TEG+F++W Y+ Sbjct: 188 IRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFKDWGYQ 247 Query: 243 VALNEYRDKIVTEEEINR--GVNSEGKVILNDRIADNMLQQIIIRPDEYDIILAPNVNGD 300 +A E+ +++ + N+ ++++ D IAD LQQI++RP EYD+I N+NGD Sbjct: 248 LAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACMNLNGD 307 Query: 301 YISDAAGALIGNIGMLGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELMLYFM 360 YISDA A +G IG+ GANIGD +FEA HGTAPKYAG++ NP II S E+ML M Sbjct: 308 YISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHM 367 Query: 361 GWSEAARLIEKAINESIKQKKVTQDIARYL-GITPLGTKEYTDTLVQIM 408 GW+EAA LI K + +I K VT D R + G L E+ D +++ M Sbjct: 368 GWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM 416 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: 520 Number of extensions: 18 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: 411 Length of database: 416 Length adjustment: 31 Effective length of query: 380 Effective length of database: 385 Effective search space: 146300 Effective search space used: 146300 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 Aug 03 2021. The underlying query database was built on Aug 03 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