Align isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) (characterized)
to candidate GFF1677 HP15_1636 NADP-dependent isocitrate dehydrogenase-like protein
Query= BRENDA::A4ADB8 (580 letters) >FitnessBrowser__Marino:GFF1677 Length = 572 Score = 839 bits (2168), Expect = 0.0 Identities = 411/568 (72%), Positives = 479/568 (84%) Query: 10 PLVILHGDEMAQIAFERLLEQFVTSRLDINLLEVDLSAEKRFTTNGQVVLDAIDALIEHG 69 PLVILHGDEMAQ+AFE +L++FV SRLDI L E+DLSAE R TNGQVV+DAID+L HG Sbjct: 4 PLVILHGDEMAQVAFEHILKKFVNSRLDIQLEEIDLSAENRLLTNGQVVIDAIDSLQRHG 63 Query: 70 VGIKNAGMTVNRSQLDELLAKYPDVKESELDKLATKSPNGAIRKGIGGNITREDIEFQNL 129 VG+KNAGMTVNR QL++LL K+P V L LATKSPNGAIRKGI GNITREDI+F+NL Sbjct: 64 VGVKNAGMTVNRQQLEDLLRKHPGVDGENLHPLATKSPNGAIRKGISGNITREDIQFRNL 123 Query: 130 TSVRPDWIDRDIEVDTMDSGGLDFSYSELSNATGVAKVMFVGSSGDPVELHRRTLKKGDP 189 RP W+ RDIEVDTM+ GG+ S+++LS ATGV K+MFVGSSGDPVELHRR ++KGDP Sbjct: 124 NIRRPQWVGRDIEVDTMEFGGIKDSFNQLSLATGVVKLMFVGSSGDPVELHRREIRKGDP 183 Query: 190 WMLANNSLEEVEAWAHRFFQRALDEKRDIYLGLKDTVVPGYDGVMRAAIEAIYERDYKEK 249 W+LA N +E+V+AWAHRFFQRA+ EKRD+YLGLKDTV+PGYDG MR+ IE IY DYK++ Sbjct: 184 WLLATNDIEDVKAWAHRFFQRAIAEKRDVYLGLKDTVIPGYDGAMRSVIEDIYHSDYKKQ 243 Query: 250 VAAAGLKYHYELIDAQAARIVSNPPERALWGVPDNVSGMKLYKLVQQLKHYGLPERKANV 309 + GL Y+YELIDAQAARIVSNPPERALWGVPDN +G KL KLV QLK +G+P R A+V Sbjct: 244 IEDLGLNYYYELIDAQAARIVSNPPERALWGVPDNTTGRKLLKLVNQLKEFGIPGRGAHV 303 Query: 310 SISRMSAGGGDQYGSYNTPAPEDGIIKVVVDGVEKHARMVKANDPILFMSNDRDAIKDWV 369 SISRMSAGGGDQYGS+N A EDGI+KV+VDG EKHAR V+ DP+L MSNDR+AIKDWV Sbjct: 304 SISRMSAGGGDQYGSFNMAAKEDGILKVIVDGDEKHARRVRKGDPMLLMSNDREAIKDWV 363 Query: 370 KQVFKDASINKKEVYFGLKREFVNYDEVYSSIILEIRKELAALDTPPPSFMIMRPSRQLS 429 QVF+DAS KEVYFGLKRE++ YDEVYS +I E+R+ELA+ TPPPSFMIMRPS QL Sbjct: 364 LQVFRDASRKDKEVYFGLKREYMEYDEVYSEVITEVRRELASEHTPPPSFMIMRPSSQLK 423 Query: 430 KMICDPPRWGLYPAQNLDGDIFSDISAALGGSLATASSVIKSKDGTLLYEAPHGTAHDLY 489 KMI DPPR LYP+QNLDGDIFSDISAALGGSLATASS+I+SKDGT+L+EAPHGTAHDLY Sbjct: 424 KMITDPPRNALYPSQNLDGDIFSDISAALGGSLATASSIIESKDGTMLFEAPHGTAHDLY 483 Query: 490 LRYLETDGKEAHFNSSALIFAVANALEEMARREENEALADYAQRLKAALIDTVAQGTITG 549 L+YLE+DGK AHFN SALIFA+ NALE + RE NE L+ YA +LKAAL DTV +G +T Sbjct: 484 LKYLESDGKVAHFNPSALIFALGNALETLGEREGNEPLSQYAVQLKAALTDTVDRGIVTA 543 Query: 550 DLKGKTLDPESENVVDMYGFLDAIEANL 577 DLKGKT+DP+SE VVDM GFL+A+E L Sbjct: 544 DLKGKTVDPDSEQVVDMIGFLEAVEKAL 571 Lambda K H 0.316 0.134 0.382 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: 995 Number of extensions: 31 Number of successful extensions: 3 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: 580 Length of database: 572 Length adjustment: 36 Effective length of query: 544 Effective length of database: 536 Effective search space: 291584 Effective search space used: 291584 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: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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