Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate PP_4011 PP_4011 isocitrate dehydrogenase, NADP(+)-specific
Query= BRENDA::Q4J6C9 (411 letters) >FitnessBrowser__Putida:PP_4011 Length = 418 Score = 370 bits (951), Expect = e-107 Identities = 197/412 (47%), Positives = 275/412 (66%), Gaps = 9/412 (2%) Query: 6 KEPQDGEPIKFEKGKWV-VPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIK 64 K P DG I + VP+ PII YIEGDGIG +++ I+VV+ AV+KAY R+I Sbjct: 7 KVPTDGTKITVNADHSLNVPDHPIIPYIEGDGIGVDVSPVMIKVVDAAVQKAYGGKRKIA 66 Query: 65 WLEVYAGEKANKITGDR--FPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDL 122 W+EVYAGEKA ++ P+ET D + Y V +KGPL TP+G G +S+NVA+R LDL Sbjct: 67 WMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVALRQQLDL 126 Query: 123 YANIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL- 181 Y +RPV + +G+ SP+K P VDM+IFREN++D+Y GIE+ S EA K+ KFL+EE+ Sbjct: 127 YVCLRPVLWFQGVPSPVKKPGDVDMVIFRENSEDIYAGIEWKAGSPEANKVIKFLKEEMG 186 Query: 182 --KVDIEDDTGIGLKVMSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREW 239 K+ + D GIG+K +SK T+R+ R AL Y + N R+ +T++HKGN+MK+TEG+F++W Sbjct: 187 VTKIRFDQDCGIGVKPVSKEGTKRLVRKALQYVVDNDRESLTLVHKGNIMKFTEGAFKDW 246 Query: 240 AYEVALNEYRDKIVTEEEINRGVNSEG--KVILNDRIADNMLQQIIIRPDEYDIILAPNV 297 YEVA +E+ +++ + N + +VI+ D IAD MLQQI++RP EYD+I N+ Sbjct: 247 GYEVARDEFGAELLDGGPWMKFKNPKTGREVIVKDAIADAMLQQILLRPAEYDVIATLNL 306 Query: 298 NGDYISDAAGALIGNIGMLGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELML 357 NGDY+SDA A +G IG+ GAN+ DT MFEA HGTAPKYAG++ NP +I S E+ML Sbjct: 307 NGDYLSDALAAEVGGIGIAPGANLSDTVAMFEATHGTAPKYAGQDKVNPGSVILSAEMML 366 Query: 358 YFMGWSEAARLIEKAINESIKQKKVTQDIARYL-GITPLGTKEYTDTLVQIM 408 MGW+EAA LI K N +I K VT D R + G + + + D +++ M Sbjct: 367 RHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMEGAKLVSSSGFGDEMIKHM 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: 494 Number of extensions: 15 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 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