Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate WP_011885784.1 isocitrate dehydrogenase (NADP(+))
Query= BRENDA::Q4J6C9 (411 letters) >NCBI__GCF_000016205.1:WP_011885784.1 Length = 418 Score = 370 bits (949), Expect = e-107 Identities = 193/412 (46%), Positives = 277/412 (67%), Gaps = 9/412 (2%) Query: 6 KEPQDGEPIKFEKGKWV-VPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIK 64 K P+ G+ I K + V ++PII YIEGDG G +IT I+VV+ AV YK R+I Sbjct: 7 KVPEGGDKITVNKDFSLNVSDQPIIPYIEGDGTGFDITPVMIKVVDAAVAHTYKGKRKIH 66 Query: 65 WLEVYAGEKANKITGDR--FPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDL 122 W+E++AGEKA K+ G P ET +L +Y V +KGPL TP+G G +S+NVA+R LDL Sbjct: 67 WMEIFAGEKATKVYGPDVWLPDETLQVLKEYVVSIKGPLTTPVGGGIRSLNVALRQELDL 126 Query: 123 YANIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL- 181 Y +RP++Y +G+ SP++ P+K+DM+IFREN++D+Y GIE+ SE+AKK+ KFL++E+ Sbjct: 127 YVCLRPIQYFKGVPSPVREPQKIDMVIFRENSEDIYAGIEWAAGSEQAKKVIKFLQDEMG 186 Query: 182 --KVDIEDDTGIGLKVMSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREW 239 K+ + +GIG+K +S T+R+ R A+ YA+ N RK VT++HKGN+MK+TEG FR+ Sbjct: 187 VKKIRFPETSGIGIKPVSTEGTERLVRKAIQYAIDNDRKSVTLVHKGNIMKFTEGLFRDA 246 Query: 240 AYEVALNEYRDKIVTEEEINRGVNSE--GKVILNDRIADNMLQQIIIRPDEYDIILAPNV 297 Y +A E+ +++ R N + ++++ D IAD LQQI++RP EYD+I N+ Sbjct: 247 GYALAQKEFGGELIDGGPWMRVKNPKTGAEIVIKDSIADAFLQQILLRPAEYDVIATLNL 306 Query: 298 NGDYISDAAGALIGNIGMLGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELML 357 NGDY+SDA A +G IG+ GAN+ D+ MFEA HGTAPKYAGK+ NP I S E+ML Sbjct: 307 NGDYVSDALAAQVGGIGIAPGANLSDSVAMFEATHGTAPKYAGKDYVNPGSEILSAEMML 366 Query: 358 YFMGWSEAARLIEKAINESIKQKKVTQDIARYL-GITPLGTKEYTDTLVQIM 408 +GW+EAA I A+ +SI QK+VT D AR + G T + + D L++ M Sbjct: 367 RHLGWTEAADTIIAAMEKSILQKRVTYDFARLMEGATQVSCSGFGDVLIENM 418 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: 503 Number of extensions: 23 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: 418 Length adjustment: 31 Effective length of query: 380 Effective length of database: 387 Effective search space: 147060 Effective search space used: 147060 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 10 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