Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate WP_077280246.1 B1C78_RS16450 NADP-dependent isocitrate dehydrogenase
Query= BRENDA::Q4J6C9 (411 letters) >NCBI__GCF_002000365.1:WP_077280246.1 Length = 419 Score = 357 bits (916), Expect = e-103 Identities = 190/417 (45%), Positives = 267/417 (64%), Gaps = 19/417 (4%) Query: 6 KEPQDGEPIKFEKGKWV-VPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIK 64 K P++G I + +P+ P+I YIEGDGIG +IT VV+ AVEKAY R I Sbjct: 7 KIPENGTKITANDDNSLNIPDNPVIPYIEGDGIGVDITPVMKTVVDAAVEKAYGGKRAIA 66 Query: 65 WLEVYAGEKANKITGDR--FPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDL 122 W+E+YAGEKA ++ P ET D++ Y + +KGPL TP+G G +S+NVA+R LDL Sbjct: 67 WMEIYAGEKATQVYDKDTWMPAETLDVVRDYLISIKGPLTTPVGGGIRSLNVALRQELDL 126 Query: 123 YANIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL- 181 Y +RPV+Y G SP++ PEK DM+IFREN++D+Y GIE+ S EA+K+ FL +E+ Sbjct: 127 YVCLRPVRYFAGTPSPVREPEKTDMVIFRENSEDIYAGIEWESGSAEARKVIDFLVKEMG 186 Query: 182 --KVDIEDDTGIGLKVMSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREW 239 K+ + +GIG+K +S+ T+R+ R A+ YA+ N R VT++HKGN+MK+TEG+F+ W Sbjct: 187 VQKIRFPETSGIGVKPVSRDGTRRLVRKAIQYAIDNDRDSVTLVHKGNIMKFTEGAFKSW 246 Query: 240 AYEVALNEYRDKIVTEEEINRGV-------NSEGKVILNDRIADNMLQQIIIRPDEYDII 292 YE+A E+ +EI+ G N+ ++++ D IAD LQQI++RP EY +I Sbjct: 247 GYELAREEFG-----AQEIDGGPWCSFKNPNTGTEIVIKDVIADAFLQQILLRPAEYSVI 301 Query: 293 LAPNVNGDYISDAAGALIGNIGMLGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKS 352 N+NGDYISDA A +G IG+ GAN+ DT MFEA HGTAPKYAG++ NP +I S Sbjct: 302 ATLNLNGDYISDALAAQVGGIGIAPGANLSDTVAMFEATHGTAPKYAGQDKVNPGSLILS 361 Query: 353 CELMLYFMGWSEAARLIEKAINESIKQKKVTQDIARYL-GITPLGTKEYTDTLVQIM 408 E+ML MGW+EAA + K + +I +VT D AR G T L E+ ++ M Sbjct: 362 AEMMLRHMGWTEAADRVIKGLEGAISSGRVTYDFARLKEGATELSCSEFGQNIIDHM 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: 490 Number of extensions: 16 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: 419 Length adjustment: 31 Effective length of query: 380 Effective length of database: 388 Effective search space: 147440 Effective search space used: 147440 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