Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate HSERO_RS07015 HSERO_RS07015 isocitrate dehydrogenase
Query= BRENDA::Q4J6C9 (411 letters) >FitnessBrowser__HerbieS:HSERO_RS07015 Length = 418 Score = 360 bits (924), Expect = e-104 Identities = 181/394 (45%), Positives = 262/394 (66%), Gaps = 8/394 (2%) Query: 23 VPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWLEVYAGEKANKITGDR- 81 VPN PII YI GDG+G ++T ++VVN AVEKAY +R+I W+E+YAGEKA ++ G Sbjct: 25 VPNNPIIPYIVGDGVGVDVTPVMLKVVNAAVEKAYGGARKIHWMEIYAGEKATRLYGPDV 84 Query: 82 -FPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYANIRPVKYIEGLESPLK 140 P+ET +L KY V +KGPL TP+G G +S+NVA+R LDLY +RPV+Y +G+ SPL+ Sbjct: 85 WLPEETLAVLKKYLVAIKGPLSTPVGGGIRSLNVAMRQQLDLYVCLRPVRYFKGVPSPLR 144 Query: 141 HPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL---KVDIEDDTGIGLKVMS 197 PEK DM+IFREN++D+Y GIE+ + E K+ L E+ K+ + + +G+K +S Sbjct: 145 EPEKTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDLLTREMGVKKLRFPESSALGIKPVS 204 Query: 198 KFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREWAYEVALNEYRDKIVTEEE 257 + T+R+ R A+ YA+ + + VT++HKGN+MK+TEG+FR+W Y +A E+ +++ + Sbjct: 205 REGTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTEGAFRDWGYALAAREFGAELIDDGP 264 Query: 258 INRGVNSEG--KVILNDRIADNMLQQIIIRPDEYDIILAPNVNGDYISDAAGALIGNIGM 315 R N + +I+ D I D QQ+++RP EY +I N+NGDYISDA A +G IG+ Sbjct: 265 WMRLKNPKTGRAIIIKDAITDAFFQQVLMRPAEYSVIATLNLNGDYISDAVAAQVGGIGI 324 Query: 316 LGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELMLYFMGWSEAARLIEKAINE 375 GAN+ D+ +FEA HGTAPKYAGK+ NP I S E+ML MGW EAA LI A+ + Sbjct: 325 APGANMSDSVAVFEATHGTAPKYAGKDYVNPGSSILSAEMMLRHMGWIEAADLIISAMQK 384 Query: 376 SIKQKKVTQDIARYL-GITPLGTKEYTDTLVQIM 408 S+ K+VT D AR L G T + + + +++ M Sbjct: 385 SVSSKRVTYDFARLLEGATQVSCSGFGEVMIENM 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: 473 Number of extensions: 20 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