Align 3-isopropylmalate dehydrogenase; EC 1.1.1.85 (characterized)
to candidate Synpcc7942_1719 Synpcc7942_1719 isocitrate dehydrogenase
Query= SwissProt::D4GYE8 (324 letters) >FitnessBrowser__SynE:Synpcc7942_1719 Length = 475 Score = 90.5 bits (223), Expect = 7e-23 Identities = 46/119 (38%), Positives = 69/119 (57%) Query: 189 VETEEVLMDAFATRVCLDPTQFDTIVCPNLAGDVLSDLAAGLVGGLGLLPSANIGPDAAL 248 V ++ + D+ ++ P ++ + NL GD +SD AA +VGGLG+ P ANIG +AA+ Sbjct: 330 VLVDDRIADSIFQQIQTRPGEYSVLATMNLNGDYISDAAAAVVGGLGMAPGANIGDEAAI 389 Query: 249 FEPVHGSAPDIAGEGIANPAATILSAAMLLDYLDHEAEADRVRSAVEGVLADGPRTPDL 307 FE HG+AP AG NP + ILS M+L+YL + AD + + +A+ T DL Sbjct: 390 FEATHGTAPKHAGLDRINPGSVILSGVMMLEYLGWQEAADLITKGISQAIANREVTYDL 448 Score = 52.8 bits (125), Expect = 2e-11 Identities = 59/222 (26%), Positives = 89/222 (40%), Gaps = 48/222 (21%) Query: 5 IVVIPGDGIGAEVIPAAVDVL-----KAVGD---FEFVEADAGDHVKEETG--EALPQET 54 I I GDG G ++ PA VL KA G + + AGD + G + LP++T Sbjct: 29 IPFIRGDGTGVDIWPATERVLDAAVAKAYGGQRKITWFKVYAGDEACDLYGTYQYLPEDT 88 Query: 55 YDLAAEADATLFGAA----GETAADVILPLRTAVDSFVNVRPAKAYPGVDALR---PETD 107 E + G G + + LR D + VRP + Y G + + D Sbjct: 89 LTAIREYGVAIKGPLTTPIGGGIRSLNVALRQIFDLYACVRPCRYYTGTPSPHRTPEQLD 148 Query: 108 LVFLRENTEGVYSGHE--------DRLSE--------------------DLSTLTRVVTT 139 +V RENTE +Y G E DRL + D + ++ Sbjct: 149 VVVYRENTEDIYLGIEWKQGDPTGDRLIKLLNEDFIPNSPSLGKKQIRLDSGIGIKPISK 208 Query: 140 SASERLAEYACDY---VGGEGGSFQVAHKANVMRETDGRFRD 178 + S+RL A ++ + G + HK N+M+ T+G FRD Sbjct: 209 TGSQRLIRRAIEHALRLEGRKRHVTLVHKGNIMKFTEGAFRD 250 Lambda K H 0.315 0.134 0.377 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: 425 Number of extensions: 31 Number of successful extensions: 4 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: 324 Length of database: 475 Length adjustment: 31 Effective length of query: 293 Effective length of database: 444 Effective search space: 130092 Effective search space used: 130092 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: 42 (22.0 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