Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate GFF3229 PS417_16530 isocitrate dehydrogenase
Query= SwissProt::P16100
(741 letters)
>FitnessBrowser__WCS417:GFF3229
Length = 741
Score = 1193 bits (3087), Expect = 0.0
Identities = 600/736 (81%), Positives = 656/736 (89%), Gaps = 1/736 (0%)
Query: 5 KIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKISD 64
KIIYT TDEAPALATYSLLPI++AFT S+ IAVETRDISLA R++A+FPE L + I D
Sbjct: 6 KIIYTFTDEAPALATYSLLPIVEAFTASADIAVETRDISLAARILASFPEQL-GAKAIPD 64
Query: 65 DLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDVKA 124
LAELG LA TP+ANIIKLPNISAS PQL+AAIKELQ QGY LPDYPE TD EK+ +A
Sbjct: 65 HLAELGDLAVTPEANIIKLPNISASTPQLQAAIKELQAQGYALPDYPETVTTDAEKETRA 124
Query: 125 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFYGS 184
RYDK+KGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAW+ADSKSH+AHM+NGDFYGS
Sbjct: 125 RYDKVKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAADSKSHIAHMNNGDFYGS 184
Query: 185 EKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAK 244
EKA I A +VKIELIA+DG++TVLK KTSVQAGEIID++V+SK ALR FIAAEIEDAK
Sbjct: 185 EKAVQIEAADAVKIELIAQDGTATVLKEKTSVQAGEIIDTAVLSKKALRAFIAAEIEDAK 244
Query: 245 KQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARI 304
KQGVLLSVHLKATMMKVSDPIMFGQIV+EFYKDALTKHA VL+QIGF++NNGIGDLYARI
Sbjct: 245 KQGVLLSVHLKATMMKVSDPIMFGQIVAEFYKDALTKHATVLEQIGFNLNNGIGDLYARI 304
Query: 305 KTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364
K LP +Q +IEADIQAVYA RP LAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW
Sbjct: 305 KALPAEQQAQIEADIQAVYAARPSLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 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+NTPA
Sbjct: 425 KTFQIKADGVVRVTDSKGSLLMEQKVEAGDIFRMCQTKDAPIQDWVKLAVNRARASNTPA 484
Query: 485 VFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVTGN 544
+FWLDP RAHD V+ KV+ YLKDY+T GLDIRI+SPV+A +F+L R R+G DTISVTGN
Sbjct: 485 IFWLDPQRAHDGVVVEKVQAYLKDYNTEGLDIRIMSPVDAMKFTLERTRKGLDTISVTGN 544
Query: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWDSL 604
VLRDYLTDLFPIMELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQ +EE +LRWDSL
Sbjct: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQLVEENFLRWDSL 604
Query: 605 GEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFYLA 664
GEFLALAASLEHLG Y NPKALVL+ TLDQATG+ LDNNKSP+RKVG IDNRGSHFYLA
Sbjct: 605 GEFLALAASLEHLGVTYNNPKALVLSKTLDQATGQFLDNNKSPSRKVGNIDNRGSHFYLA 664
Query: 665 LYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDLTS 724
LYWAQALAAQTED LQAQF +AK L++NE IV EL A QGKPVDI GYY PN +LTS
Sbjct: 665 LYWAQALAAQTEDTALQAQFGELAKTLSENEATIVAELNAVQGKPVDIGGYYAPNPELTS 724
Query: 725 KAIRPSATFNAALAPL 740
KA+RPS T NAA+A L
Sbjct: 725 KAMRPSTTLNAAIAKL 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: 1539
Number of extensions: 46
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 GFF3229 PS417_16530 (isocitrate dehydrogenase)
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.20741.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 1368.8 5.9 0 1368.6 5.9 1.0 1 lcl|FitnessBrowser__WCS417:GFF3229 PS417_16530 isocitrate dehydroge
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3229 PS417_16530 isocitrate dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1368.6 5.9 0 0 5 743 .. 4 741 .] 1 741 [] 0.99
Alignments for each domain:
== domain 1 score: 1368.6 bits; conditional E-value: 0
TIGR00178 5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelaktpe 79
++kiiyt tdeap+latysllpiv+af+asa i+vetrdisla+rila+fpe+l + ++d+laelG+la tpe
lcl|FitnessBrowser__WCS417:GFF3229 4 RSKIIYTFTDEAPALATYSLLPIVEAFTASADIAVETRDISLAARILASFPEQLGA-KAIPDHLAELGDLAVTPE 77
59****************************************************86.68**************** PP
TIGR00178 80 aniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrraplavk 154
aniiklpnisas pql+aaikelq++Gy+lpdype +td+ek+ +ary+k+kGsavnpvlreGnsdrrapl+vk
lcl|FitnessBrowser__WCS417:GFF3229 78 ANIIKLPNISASTPQLQAAIKELQAQGYALPDYPETVTTDAEKETRARYDKVKGSAVNPVLREGNSDRRAPLSVK 152
*************************************************************************** PP
TIGR00178 155 eyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevidssvl 229
+yarkhphkmG+w+adsksh+ahm++gdfy+sek+v ++aa+ vkielia+dG++tvlk+k+++++ge+id++vl
lcl|FitnessBrowser__WCS417:GFF3229 153 NYARKHPHKMGAWAADSKSHIAHMNNGDFYGSEKAVQIEAADAVKIELIAQDGTATVLKEKTSVQAGEIIDTAVL 227
*************************************************************************** PP
TIGR00178 230 skkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlya 304
skkal++f+++eiedak++gvlls+hlkatmmkvsdpi+fG++v +fykd+++kha +leq+G++ +nG++dlya
lcl|FitnessBrowser__WCS417:GFF3229 228 SKKALRAFIAAEIEDAKKQGVLLSVHLKATMMKVSDPIMFGQIVAEFYKDALTKHATVLEQIGFNLNNGIGDLYA 302
*************************************************************************** PP
TIGR00178 305 kieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavi 379
+i++lpa ++ +iead+++vy+ rp lamv+sdkGitnlhvpsdvivdasmpamir+sGkm+g+dg+l+dtkavi
lcl|FitnessBrowser__WCS417:GFF3229 303 RIKALPAEQQAQIEADIQAVYAARPSLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMWGTDGQLHDTKAVI 377
*************************************************************************** PP
TIGR00178 380 pdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeevea 454
pd++ya +yqaviedck nGafdpttmG+vpnvGlma+kaeeyGshdktf+i+adGvvrv+ds+G +l+e++vea
lcl|FitnessBrowser__WCS417:GFF3229 378 PDRCYATIYQAVIEDCKANGAFDPTTMGSVPNVGLMAKKAEEYGSHDKTFQIKADGVVRVTDSKGSLLMEQKVEA 452
*************************************************************************** PP
TIGR00178 455 gdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrf 529
gdi+rmcq kdapiqdwvklav+rar+s+tpa+fwldp+rahd +++kv+ ylkd++teGldi+i+spv+a++f
lcl|FitnessBrowser__WCS417:GFF3229 453 GDIFRMCQTKDAPIQDWVKLAVNRARASNTPAIFWLDPQRAHDGVVVEKVQAYLKDYNTEGLDIRIMSPVDAMKF 527
*************************************************************************** PP
TIGR00178 530 slerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwd 604
+ler r+G dtisvtGnvlrdyltdlfpi+elGtsakmls+vplm+GGGlfetGaGGsapkhvqql+een+lrwd
lcl|FitnessBrowser__WCS417:GFF3229 528 TLERTRKGLDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQLVEENFLRWD 602
*************************************************************************** PP
TIGR00178 605 slGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqted 679
slGeflalaasleh++v+++n+ka vl++tld+atg++ld++kspsrkvG++dnrgs+fyla ywaq+laaqted
lcl|FitnessBrowser__WCS417:GFF3229 603 SLGEFLALAASLEHLGVTYNNPKALVLSKTLDQATGQFLDNNKSPSRKVGNIDNRGSHFYLALYWAQALAAQTED 677
*************************************************************************** PP
TIGR00178 680 kelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnailealk 743
+ l+a+f +a++l++ne++ivael+avqG++vd+gGyyap+ +lt+k++rps t+na+++ lk
lcl|FitnessBrowser__WCS417:GFF3229 678 TALQAQFGELAKTLSENEATIVAELNAVQGKPVDIGGYYAPNPELTSKAMRPSTTLNAAIAKLK 741
***********************************************************99875 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 7.99
//
[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