Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate PfGW456L13_2641 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate dehydrogenase [NADP] (EC 1.1.1.42)
Query= SwissProt::P16100 (741 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 Length = 741 Score = 1196 bits (3093), Expect = 0.0 Identities = 601/736 (81%), Positives = 659/736 (89%), Gaps = 1/736 (0%) Query: 5 KIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKISD 64 KIIYT TDEAPALATYSLLPI++AFT S+ IAVETRDISLAGR++A+FPE L D + ++D Sbjct: 6 KIIYTFTDEAPALATYSLLPIVEAFTASADIAVETRDISLAGRILASFPEQLGD-KAVAD 64 Query: 65 DLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDVKA 124 LAELG LA TP+ANIIKLPNISASVPQL+AAIKELQ QGY LPDYPE D +K+ KA Sbjct: 65 HLAELGALAVTPEANIIKLPNISASVPQLQAAIKELQAQGYALPDYPETVTCDADKEAKA 124 Query: 125 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFYGS 184 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAW+ DSKSH+AHM GDFYGS Sbjct: 125 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAKDSKSHIAHMSTGDFYGS 184 Query: 185 EKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAK 244 EKAALI A +VKIELIA+DG++TVLK KTSVQAGEI+D +V+SKNALR+FIAAEIEDAK Sbjct: 185 EKAALIDAADAVKIELIAQDGTATVLKEKTSVQAGEILDCAVLSKNALRSFIAAEIEDAK 244 Query: 245 KQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARI 304 QGVLLSVHLKATMMKVSDPIMFGQIV+EFYKDAL KHA+VL QIGF++NNGIGDLYARI Sbjct: 245 AQGVLLSVHLKATMMKVSDPIMFGQIVAEFYKDALAKHADVLSQIGFNLNNGIGDLYARI 304 Query: 305 KTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364 K LP +Q +IEADIQAVYA RP LAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW Sbjct: 305 KALPAEQQAQIEADIQAVYAVRPSLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364 Query: 365 GPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGSHD 424 G DG+LHDTKAVIPDRCYA +YQ VIEDCK +GAFDPTTMGSVPNVGLMA+KAEEYGSHD Sbjct: 365 GTDGQLHDTKAVIPDRCYATIYQAVIEDCKANGAFDPTTMGSVPNVGLMAKKAEEYGSHD 424 Query: 425 KTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNTPA 484 KTFQI ADGVVRVTD G LL+EQ+VEAGDI+RMCQ KDAPIQDWVKLAVNRARA++TPA Sbjct: 425 KTFQIKADGVVRVTDSKGNLLMEQAVEAGDIFRMCQTKDAPIQDWVKLAVNRARASSTPA 484 Query: 485 VFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVTGN 544 +FWLDP RAHD VI KV+ YLKD+DT+GLDI+I++PV+A + +L R R GKDTISVTGN Sbjct: 485 IFWLDPMRAHDGVVIEKVQAYLKDHDTAGLDIQIMAPVDAMKSTLQRTRAGKDTISVTGN 544 Query: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWDSL 604 VLRDYLTDLFPIMELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQ LEE +LRWDSL Sbjct: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQLLEENFLRWDSL 604 Query: 605 GEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFYLA 664 GEFLALAASLEHLG Y NPKALVLA TLDQATG+ LDNNKSP+RKVG IDNRGSHFYLA Sbjct: 605 GEFLALAASLEHLGVTYNNPKALVLAKTLDQATGQFLDNNKSPSRKVGNIDNRGSHFYLA 664 Query: 665 LYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDLTS 724 LYWAQALAAQTED LQAQF +AK LT+NE IV EL A QGKPVDI GYYH + +L S Sbjct: 665 LYWAQALAAQTEDAALQAQFATLAKTLTENEATIVAELNAVQGKPVDIGGYYHADAELIS 724 Query: 725 KAIRPSATFNAALAPL 740 KA+RPSATFNAA+A L Sbjct: 725 KAMRPSATFNAAVAAL 740 Lambda K H 0.315 0.131 0.374 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: 1529 Number of extensions: 53 Number of successful extensions: 2 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: 741 Length of database: 741 Length adjustment: 40 Effective length of query: 701 Effective length of database: 701 Effective search space: 491401 Effective search space used: 491401 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 (21.5 bits) S2: 55 (25.8 bits)
Align candidate PfGW456L13_2641 (Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate dehydrogenase [NADP] (EC 1.1.1.42))
to HMM TIGR00178 (isocitrate dehydrogenase, NADP-dependent (EC 1.1.1.42))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR00178.hmm # target sequence database: /tmp/gapView.2488.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00178 [M=744] Accession: TIGR00178 Description: monomer_idh: isocitrate dehydrogenase, NADP-dependent Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1370.3 8.4 0 1370.2 8.4 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 Isocitrate dehydrogenase [NADP] Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isoc # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1370.2 8.4 0 0 5 742 .. 4 740 .. 1 741 [] 0.99 Alignments for each domain: == domain 1 score: 1370.2 bits; conditional E-value: 0 TIGR00178 5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylt 59 ++kiiyt tdeap+latysllpiv+af+asa i+vetrdislagrila+fpe+l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 4 RSKIIYTFTDEAPALATYSLLPIVEAFTASADIAVETRDISLAGRILASFPEQLG 58 59****************************************************8 PP TIGR00178 60 eeqkvddalaelGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdype 114 + + v d+laelG la tpeaniiklpnisasvpql+aaikelq++Gy+lpdype lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 59 D-KAVADHLAELGALAVTPEANIIKLPNISASVPQLQAAIKELQAQGYALPDYPE 112 6.68*************************************************** PP TIGR00178 115 epktdeekdikaryakikGsavnpvlreGnsdrraplavkeyarkhphkmGewsa 169 + d++k+ kary+kikGsavnpvlreGnsdrrapl+vk+yarkhphkmG+w++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 113 TVTCDADKEAKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAK 167 ******************************************************* PP TIGR00178 170 dskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevi 224 dsksh+ahm++gdfy+sek++l+daa+ vkielia+dG++tvlk+k+++++ge++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 168 DSKSHIAHMSTGDFYGSEKAALIDAADAVKIELIAQDGTATVLKEKTSVQAGEIL 222 ******************************************************* PP TIGR00178 225 dssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykd 279 d++vlsk+al+ f+++eiedak++gvlls+hlkatmmkvsdpi+fG++v +fykd lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 223 DCAVLSKNALRSFIAAEIEDAKAQGVLLSVHLKATMMKVSDPIMFGQIVAEFYKD 277 ******************************************************* PP TIGR00178 280 vfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamv 334 ++akha++l+q+G++ +nG++dlya+i++lpa ++ +iead+++vy+ rp lamv lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 278 ALAKHADVLSQIGFNLNNGIGDLYARIKALPAEQQAQIEADIQAVYAVRPSLAMV 332 ******************************************************* PP TIGR00178 335 dsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyq 389 +sdkGitnlhvpsdvivdasmpamir+sGkm+g+dg+l+dtkavipd++ya +yq lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 333 NSDKGITNLHVPSDVIVDASMPAMIRDSGKMWGTDGQLHDTKAVIPDRCYATIYQ 387 ******************************************************* PP TIGR00178 390 aviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssG 444 aviedck nGafdpttmG+vpnvGlma+kaeeyGshdktf+i+adGvvrv+ds+G lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 388 AVIEDCKANGAFDPTTMGSVPNVGLMAKKAEEYGSHDKTFQIKADGVVRVTDSKG 442 ******************************************************* PP TIGR00178 445 evlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdee 499 ++l+e+ veagdi+rmcq kdapiqdwvklav+rar+s+tpa+fwldp rahd lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 443 NLLMEQAVEAGDIFRMCQTKDAPIQDWVKLAVNRARASSTPAIFWLDPMRAHDGV 497 ******************************************************* PP TIGR00178 500 likkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltd 554 +i+kv+ ylkdhdt Gldiqi+ pv+a++ +l+r r G+dtisvtGnvlrdyltd lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 498 VIEKVQAYLKDHDTAGLDIQIMAPVDAMKSTLQRTRAGKDTISVTGNVLRDYLTD 552 ******************************************************* PP TIGR00178 555 lfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGef 609 lfpi+elGtsakmls+vplm+GGGlfetGaGGsapkhvqql een+lrwdslGef lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 553 LFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQLLEENFLRWDSLGEF 607 ******************************************************* PP TIGR00178 610 lalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfy 664 lalaasleh++v+++n+ka vla+tld+atg++ld++kspsrkvG++dnrgs+fy lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 608 LALAASLEHLGVTYNNPKALVLAKTLDQATGQFLDNNKSPSRKVGNIDNRGSHFY 662 ******************************************************* PP TIGR00178 665 lakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyya 719 la ywaq+laaqted+ l+a+fa++a++lt+ne++ivael+avqG++vd+gGyy+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 663 LALYWAQALAAQTEDAALQAQFATLAKTLTENEATIVAELNAVQGKPVDIGGYYH 717 ******************************************************* PP TIGR00178 720 pdtdlttkvlrpsatfnaileal 742 +d +l++k++rpsatfna+++al lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2641 718 ADAELISKAMRPSATFNAAVAAL 740 ********************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (744 nodes) Target sequences: 1 (741 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 11.26 // [ok]
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