Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate Pf6N2E2_288 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate dehydrogenase [NADP] (EC 1.1.1.42)
Query= SwissProt::P16100 (741 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 Length = 741 Score = 1210 bits (3130), Expect = 0.0 Identities = 607/736 (82%), Positives = 665/736 (90%), 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 TD EKD +A Sbjct: 65 HLAELGDLAVTPEANIIKLPNISASVPQLQAAIKELQAQGYALPDYPETVTTDAEKDARA 124 Query: 125 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFYGS 184 RYDK+KGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAW+ADSKSHVAHM GDFYGS Sbjct: 125 RYDKVKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAADSKSHVAHMSTGDFYGS 184 Query: 185 EKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAK 244 EKAALI A GSVKIELIA+DG++TVLK KT+VQAGEI+D +VMSKNALR+FIAAEIEDAK Sbjct: 185 EKAALIDAAGSVKIELIAQDGTATVLKEKTTVQAGEILDCAVMSKNALRDFIAAEIEDAK 244 Query: 245 KQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARI 304 ++GVLLSVHLKATMMKVSDPIMFGQIV+EFYKDAL KHA+VL+QIGF++NNGIGDLYARI Sbjct: 245 QKGVLLSVHLKATMMKVSDPIMFGQIVAEFYKDALAKHAQVLEQIGFNLNNGIGDLYARI 304 Query: 305 KTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364 K LP +Q +IEADIQAVYA RP LAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW Sbjct: 305 KALPAEQQAQIEADIQAVYAARPSLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364 Query: 365 GPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGSHD 424 G DG+LHDTKAVIPDRCYA +YQ VIEDCKQHGAFDPTTMGSVPNVGLMA+KAEEYGSHD Sbjct: 365 GTDGQLHDTKAVIPDRCYATIYQAVIEDCKQHGAFDPTTMGSVPNVGLMAKKAEEYGSHD 424 Query: 425 KTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNTPA 484 KTFQI DGVVRV+D +G+ LLEQSVEAGDI+RMCQ KDAPIQDWVKLAVNRARA++TPA Sbjct: 425 KTFQIKVDGVVRVSDSNGRTLLEQSVEAGDIFRMCQTKDAPIQDWVKLAVNRARASDTPA 484 Query: 485 VFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVTGN 544 +FWLDP RAHD VI KV+ YLKDYDT+GLDIRI++PV+A +F+LAR REGKDTISVTGN Sbjct: 485 IFWLDPMRAHDGVVIEKVQTYLKDYDTAGLDIRIMAPVDAMKFTLARTREGKDTISVTGN 544 Query: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWDSL 604 VLRDYLTDLFPIMELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQ LEE +LRWDSL Sbjct: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQLLEENFLRWDSL 604 Query: 605 GEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFYLA 664 GEFLALAASLEHLG Y NPKALVLA TLDQATG+ LD NKSP+RKVG IDNRGSHFYL Sbjct: 605 GEFLALAASLEHLGVTYNNPKALVLAKTLDQATGEFLDRNKSPSRKVGGIDNRGSHFYLT 664 Query: 665 LYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDLTS 724 L+WAQALAAQ +D L+AQF +AK LTDNE KIV EL A QGKPVDI GYY N +LTS Sbjct: 665 LFWAQALAAQDDDAALKAQFATLAKTLTDNEEKIVAELNAVQGKPVDIGGYYFANPELTS 724 Query: 725 KAIRPSATFNAALAPL 740 KA+RPS TFNAA+A L Sbjct: 725 KAMRPSNTFNAAIAAL 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: 1553 Number of extensions: 54 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 Pf6N2E2_288 (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.4257.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 1377.2 5.5 0 1377.1 5.5 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 Isocitrate dehydrogenase [NADP] Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate deh # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1377.1 5.5 0 0 5 742 .. 4 740 .. 1 741 [] 0.99 Alignments for each domain: == domain 1 score: 1377.1 bits; conditional E-value: 0 TIGR00178 5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddala 69 ++kiiyt tdeap+latysllpiv+af+asa i+vetrdislagrila+fpe+l + + v d+la lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 4 RSKIIYTFTDEAPALATYSLLPIVEAFTASADIAVETRDISLAGRILASFPEQLGD-KAVADHLA 67 59****************************************************86.68****** PP TIGR00178 70 elGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGs 134 elG+la tpeaniiklpnisasvpql+aaikelq++Gy+lpdype +td+ekd +ary+k+kGs lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 68 ELGDLAVTPEANIIKLPNISASVPQLQAAIKELQAQGYALPDYPETVTTDAEKDARARYDKVKGS 132 ***************************************************************** PP TIGR00178 135 avnpvlreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevk 199 avnpvlreGnsdrrapl+vk+yarkhphkmG+w+adskshvahm++gdfy+sek++l+daa +vk lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 133 AVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAADSKSHVAHMSTGDFYGSEKAALIDAAGSVK 197 ***************************************************************** PP TIGR00178 200 ieliakdGketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvs 264 ielia+dG++tvlk+k+++++ge++d++v+sk+al++f+++eiedak++gvlls+hlkatmmkvs lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 198 IELIAQDGTATVLKEKTTVQAGEILDCAVMSKNALRDFIAAEIEDAKQKGVLLSVHLKATMMKVS 262 ***************************************************************** PP TIGR00178 265 dpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerp 329 dpi+fG++v +fykd++akha++leq+G++ +nG++dlya+i++lpa ++ +iead+++vy+ rp lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 263 DPIMFGQIVAEFYKDALAKHAQVLEQIGFNLNNGIGDLYARIKALPAEQQAQIEADIQAVYAARP 327 ***************************************************************** PP TIGR00178 330 elamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqavied 394 lamv+sdkGitnlhvpsdvivdasmpamir+sGkm+g+dg+l+dtkavipd++ya +yqavied lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 328 SLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMWGTDGQLHDTKAVIPDRCYATIYQAVIED 392 ***************************************************************** PP TIGR00178 395 ckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwr 459 ck++GafdpttmG+vpnvGlma+kaeeyGshdktf+i+ dGvvrv ds+G lle++veagdi+r lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 393 CKQHGAFDPTTMGSVPNVGLMAKKAEEYGSHDKTFQIKVDGVVRVSDSNGRTLLEQSVEAGDIFR 457 ***************************************************************** PP TIGR00178 460 mcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspv 524 mcq kdapiqdwvklav+rar+s+tpa+fwldp rahd +i+kv++ylkd+dt Gldi+i+ pv lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 458 MCQTKDAPIQDWVKLAVNRARASDTPAIFWLDPMRAHDGVVIEKVQTYLKDYDTAGLDIRIMAPV 522 ***************************************************************** PP TIGR00178 525 katrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsap 589 +a++f+l+r r+G+dtisvtGnvlrdyltdlfpi+elGtsakmls+vplm+GGGlfetGaGGsap lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 523 DAMKFTLARTREGKDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAP 587 ***************************************************************** PP TIGR00178 590 khvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvG 654 khvqql een+lrwdslGeflalaasleh++v+++n+ka vla+tld+atg +ld +kspsrkvG lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 588 KHVQQLLEENFLRWDSLGEFLALAASLEHLGVTYNNPKALVLAKTLDQATGEFLDRNKSPSRKVG 652 ***************************************************************** PP TIGR00178 655 eldnrgskfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyya 719 +dnrgs+fyl+ +waq+laaq +d+ l+a+fa++a++lt+neekivael+avqG++vd+gGyy+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 653 GIDNRGSHFYLTLFWAQALAAQDDDAALKAQFATLAKTLTDNEEKIVAELNAVQGKPVDIGGYYF 717 ***************************************************************** PP TIGR00178 720 pdtdlttkvlrpsatfnaileal 742 ++ +lt+k++rps+tfna+++al lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_288 718 ANPELTSKAMRPSNTFNAAIAAL 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: 00:00:00.05 # Mc/sec: 9.42 // [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