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.12713.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: 0.04u 0.03s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 7.80
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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