Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate Synpcc7942_1719 Synpcc7942_1719 isocitrate dehydrogenase
Query= BRENDA::Q4J6C9 (411 letters) >FitnessBrowser__SynE:Synpcc7942_1719 Length = 475 Score = 340 bits (873), Expect = 4e-98 Identities = 188/467 (40%), Positives = 276/467 (59%), Gaps = 65/467 (13%) Query: 8 PQDGEPIKFEKGKWVVPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWLE 67 P +G I+FE GK +VP+ PII +I GDG G +I + RV++ AV KAY R+I W + Sbjct: 8 PSEGSKIRFEAGKPIVPDNPIIPFIRGDGTGVDIWPATERVLDAAVAKAYGGQRKITWFK 67 Query: 68 VYAGEKANKITG--DRFPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYAN 125 VYAG++A + G P++T + +Y V +KGPL TPIG G +S+NVA+R + DLYA Sbjct: 68 VYAGDEACDLYGTYQYLPEDTLTAIREYGVAIKGPLTTPIGGGIRSLNVALRQIFDLYAC 127 Query: 126 IRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL---- 181 +RP +Y G SP + PE++D++++RENT+D+Y GIE+ ++ K L E+ Sbjct: 128 VRPCRYYTGTPSPHRTPEQLDVVVYRENTEDIYLGIEWKQGDPTGDRLIKLLNEDFIPNS 187 Query: 182 ----KVDIEDDTGIGLKVMSKFKTQRITRLALNYA--LQNSRKKVTVMHKGNVMKYTEGS 235 K I D+GIG+K +SK +QR+ R A+ +A L+ ++ VT++HKGN+MK+TEG+ Sbjct: 188 PSLGKKQIRLDSGIGIKPISKTGSQRLIRRAIEHALRLEGRKRHVTLVHKGNIMKFTEGA 247 Query: 236 FREWAYEVALNEYRDKIVTEEE---------------------INRGVNS---------- 264 FR+W YE+A E+R VTE E I G ++ Sbjct: 248 FRDWGYELATTEFRTDCVTERESWILANQESKPDLSLEDNARLIEPGYDAMTPEKQAAVV 307 Query: 265 -------------------EGKVILNDRIADNMLQQIIIRPDEYDIILAPNVNGDYISDA 305 + KV+++DRIAD++ QQI RP EY ++ N+NGDYISDA Sbjct: 308 AEVKAVLDSIGATHGNGQWKSKVLVDDRIADSIFQQIQTRPGEYSVLATMNLNGDYISDA 367 Query: 306 AGALIGNIGMLGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELMLYFMGWSEA 365 A A++G +GM GANIGD +FEA HGTAPK+AG + NP +I S +ML ++GW EA Sbjct: 368 AAAVVGGLGMAPGANIGDEAAIFEATHGTAPKHAGLDRINPGSVILSGVMMLEYLGWQEA 427 Query: 366 ARLIEKAINESIKQKKVTQDIARYLGIT---PLGTKEYTDTLVQIMD 409 A LI K I+++I ++VT D+AR + PL E+ + +V+ D Sbjct: 428 ADLITKGISQAIANREVTYDLARLMEPAVDQPLKCSEFAEAIVKHFD 474 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: 544 Number of extensions: 26 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 411 Length of database: 475 Length adjustment: 32 Effective length of query: 379 Effective length of database: 443 Effective search space: 167897 Effective search space used: 167897 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: 51 (24.3 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