Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate WP_010627814.1 BZY95_RS15605 NADP-dependent isocitrate dehydrogenase
Query= BRENDA::Q4J6C9 (411 letters) >NCBI__GCF_002151265.1:WP_010627814.1 Length = 418 Score = 357 bits (916), Expect = e-103 Identities = 186/391 (47%), Positives = 265/391 (67%), Gaps = 8/391 (2%) Query: 8 PQDGEPIKFEKGKWV-VPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWL 66 P+ GE I + VPN PII +IEGDGIG ++T + ++ AV+KAY R+I W+ Sbjct: 9 PEGGEKITVNADNTLNVPNNPIIPFIEGDGIGVDVTPAMKIAIDAAVQKAYNGERKIHWM 68 Query: 67 EVYAGEKANKI--TGDRFPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYA 124 EVYAGEKA ++ P+ET + + +Y V +KGPL TP+G G +S+NVA+R LDLY Sbjct: 69 EVYAGEKATQVYDADTWLPEETLEAVQEYVVSIKGPLTTPVGGGIRSLNVALRQKLDLYV 128 Query: 125 NIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREELKVD 184 +RPV++ EG+ SP+K P VDM+IFREN++D+Y GIE+ + EA K+ KFLREE+ V Sbjct: 129 CLRPVRWFEGVPSPVKKPADVDMVIFRENSEDIYAGIEWKAGTPEADKVIKFLREEMGVT 188 Query: 185 ---IEDDTGIGLKVMSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREWAY 241 ++ GIG+K +S+ T+R+ R AL Y + N R+ +T++HKGN+MK+TEGSF++W Y Sbjct: 189 NIRFPENCGIGVKPVSEEGTKRLVRQALQYTVDNDRESLTLVHKGNIMKFTEGSFKDWGY 248 Query: 242 EVALNEYRDKIVTEEEINRGVNSE-GK-VILNDRIADNMLQQIIIRPDEYDIILAPNVNG 299 EVA E+ +++ + N + GK +++ D IAD MLQQI++RP EYD+I N+NG Sbjct: 249 EVAKQEFGAELLDGGPWMQFKNPKTGKNIVVKDVIADAMLQQILLRPAEYDVIATLNLNG 308 Query: 300 DYISDAAGALIGNIGMLGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELMLYF 359 DY+SDA A +G IG+ GAN+ D MFEA HGTAPKYAG++ NP +I S E+ML Sbjct: 309 DYLSDALAAEVGGIGIAPGANLADAVAMFEATHGTAPKYAGQDKVNPGSVILSAEMMLRH 368 Query: 360 MGWSEAARLIEKAINESIKQKKVTQDIARYL 390 MGW EAA L+ K + ++I + +VT D R + Sbjct: 369 MGWVEAADLVLKGMEKAIAKGEVTYDFHRLM 399 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: 502 Number of extensions: 17 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: 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