Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate PfGW456L13_2643 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42)
Query= BRENDA::Q4J6C9 (411 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2643 Length = 418 Score = 370 bits (950), Expect = e-107 Identities = 197/394 (50%), Positives = 267/394 (67%), Gaps = 8/394 (2%) Query: 23 VPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWLEVYAGEKANKITGDR- 81 VPN PII +IEGDGIG +I+ I+VV+ AV+KAY R+I W+EVYAGEKA ++ Sbjct: 25 VPNNPIIPFIEGDGIGVDISPVMIKVVDAAVKKAYGGERKISWMEVYAGEKATQVYDQDT 84 Query: 82 -FPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYANIRPVKYIEGLESPLK 140 P+ET D + Y V +KGPL TP+G G +S+NVA+R LDLY +RPV++ EG+ SP+K Sbjct: 85 WLPQETLDAVKDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPVRWFEGVPSPVK 144 Query: 141 HPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL---KVDIEDDTGIGLKVMS 197 P VDM IFREN++D+Y GIE+ + EA K+ KFL+EE+ K+ +++ GIG+K +S Sbjct: 145 KPGDVDMTIFRENSEDIYAGIEWKAGTPEATKVIKFLKEEMGVTKIRFDENCGIGVKPVS 204 Query: 198 KFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREWAYEVALNEYRDKIVTEEE 257 T+R+ R AL Y + N R +T++HKGN+MK+TEG+F+EWAYEVA E+ ++ Sbjct: 205 LQGTKRLARKALQYVVDNDRDSLTIVHKGNIMKFTEGAFKEWAYEVAAEEFGATLLDGGP 264 Query: 258 INRGVNSE-GK-VILNDRIADNMLQQIIIRPDEYDIILAPNVNGDYISDAAGALIGNIGM 315 + N + GK VI+ D IAD MLQQI++RP EYD+I N+NGDY+SDA A +G IG+ Sbjct: 265 WMQFKNPKTGKNVIVKDAIADAMLQQILLRPAEYDVIATLNLNGDYLSDALAAEVGGIGI 324 Query: 316 LGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELMLYFMGWSEAARLIEKAINE 375 GAN+ DT MFEA HGTAPKYAGK+ NP +I S E+ML MGW+EAA LI K N Sbjct: 325 APGANLSDTVAMFEATHGTAPKYAGKDQVNPGSLILSAEMMLRHMGWTEAADLIIKGTNG 384 Query: 376 SIKQKKVTQDIARYL-GITPLGTKEYTDTLVQIM 408 +I K VT D R + G + + + D L+ M Sbjct: 385 AISAKTVTYDFERLMEGAKLVSSSGFGDALISHM 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: 480 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: 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 09 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