Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate N515DRAFT_3517 N515DRAFT_3517 isocitrate dehydrogenase
Query= SwissProt::P16100
(741 letters)
>FitnessBrowser__Dyella79:N515DRAFT_3517
Length = 743
Score = 1186 bits (3069), Expect = 0.0
Identities = 593/740 (80%), Positives = 649/740 (87%)
Query: 2 STPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQK 61
+TPKIIYTLTDEAP LAT SLLPI+KAF G++GIAVETRDISLAGR++A FP+ L QK
Sbjct: 3 NTPKIIYTLTDEAPFLATQSLLPIVKAFAGAAGIAVETRDISLAGRILAQFPDLLKPEQK 62
Query: 62 ISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKD 121
I+DDLAELG+LATTPDANIIKLPNISASVPQLKAAIKELQQQGY LPDYP+EPK + EKD
Sbjct: 63 IADDLAELGQLATTPDANIIKLPNISASVPQLKAAIKELQQQGYALPDYPDEPKNEQEKD 122
Query: 122 VKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDF 181
KARYD+ KGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWS DS+SHVAHMD GDF
Sbjct: 123 AKARYDRTKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSKDSQSHVAHMDGGDF 182
Query: 182 YGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIE 241
YGSEK+A + SVKIE DG STVLK KT++ AGEIID++VMS+ AL F+ A++
Sbjct: 183 YGSEKSATVAQATSVKIEWTGTDGKSTVLKDKTAISAGEIIDAAVMSRKALAAFVDAQVA 242
Query: 242 DAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLY 301
DAK+QGVL S+HLKATMMKVSDPIMFG +V EFYKD L KHA+ LKQIGFD NNGIGDLY
Sbjct: 243 DAKQQGVLFSLHLKATMMKVSDPIMFGIVVGEFYKDVLAKHADTLKQIGFDPNNGIGDLY 302
Query: 302 ARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSG 361
AR+ LP KQ EI ADI+A YA+RP LAMVNSDKGITNLHVPSDVIVDASMPAMIRDSG
Sbjct: 303 ARLNALPTDKQAEITADIKAEYARRPALAMVNSDKGITNLHVPSDVIVDASMPAMIRDSG 362
Query: 362 KMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYG 421
KMW +GKL DTKAVIPDR YAGVYQVVIEDCK HGAFDP +MGSVPNVGLMAQ AEEYG
Sbjct: 363 KMWNAEGKLQDTKAVIPDRSYAGVYQVVIEDCKAHGAFDPASMGSVPNVGLMAQAAEEYG 422
Query: 422 SHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATN 481
SH+KTFQI ADGVVRV D++G +LLE +VEAGDIWRMCQ KDAPIQDWVKLAV RAR +
Sbjct: 423 SHNKTFQIAADGVVRVVDDAGNVLLEHAVEAGDIWRMCQTKDAPIQDWVKLAVTRARLSG 482
Query: 482 TPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISV 541
TPAVFWLDP RAHDAQ+I KVERYLKD+DT GLDIR++SPV+ATRFSL RIR+G+DTISV
Sbjct: 483 TPAVFWLDPKRAHDAQLIQKVERYLKDHDTGGLDIRVMSPVDATRFSLERIRKGQDTISV 542
Query: 542 TGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRW 601
TGNVLRDYLTDLFPIMELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQFLEE YLRW
Sbjct: 543 TGNVLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGLFETGAGGSAPKHVQQFLEEDYLRW 602
Query: 602 DSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHF 661
DSLGEFLALAAS EHLGN Y N KA VLA LDQA GKILDNNKSPARKVGE+DNRGSHF
Sbjct: 603 DSLGEFLALAASFEHLGNRYGNAKAGVLAKALDQANGKILDNNKSPARKVGELDNRGSHF 662
Query: 662 YLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTD 721
YLA+YWAQALA Q +D EL+A F +AKALT+NE KI+GEL AQGK VDI GYYHP+
Sbjct: 663 YLAMYWAQALAGQDDDAELKATFAPVAKALTENEEKIIGELNGAQGKAVDIHGYYHPDIA 722
Query: 722 LTSKAIRPSATFNAALAPLA 741
L SKA+RPSATFNAA+ LA
Sbjct: 723 LLSKAMRPSATFNAAVDGLA 742
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: 1641
Number of extensions: 60
Number of successful extensions: 1
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: 743
Length adjustment: 40
Effective length of query: 701
Effective length of database: 703
Effective search space: 492803
Effective search space used: 492803
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 N515DRAFT_3517 N515DRAFT_3517 (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.9606.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 1388.8 3.6 0 1388.7 3.6 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 N515DRAFT_3517 isocitrate dehydr
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 N515DRAFT_3517 isocitrate dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1388.7 3.6 0 0 4 743 .. 3 742 .. 1 743 [] 1.00
Alignments for each domain:
== domain 1 score: 1388.7 bits; conditional E-value: 0
TIGR00178 4 ekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddala 69
+++kiiytltdeap lat sllpivkafa++aGi+vetrdislagrila+fp+ l eqk+ d+la
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 3 NTPKIIYTLTDEAPFLATQSLLPIVKAFAGAAGIAVETRDISLAGRILAQFPDLLKPEQKIADDLA 68
569*************************************************************** PP
TIGR00178 70 elGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsa 135
elG+la+tp+aniiklpnisasvpqlkaaikelq++Gy+lpdyp+epk+++ekd kary++ kGsa
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 69 ELGQLATTPDANIIKLPNISASVPQLKAAIKELQQQGYALPDYPDEPKNEQEKDAKARYDRTKGSA 134
****************************************************************** PP
TIGR00178 136 vnpvlreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkie 201
vnpvlreGnsdrrapl+vk+yarkhphkmG+ws+ds+shvahmd gdfy+seks+++ +a++vkie
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 135 VNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSKDSQSHVAHMDGGDFYGSEKSATVAQATSVKIE 200
****************************************************************** PP
TIGR00178 202 liakdGketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpi 267
+ dGk+tvlk+k+ + +ge+id++v+s+kal++f++++++dak++gvl+slhlkatmmkvsdpi
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 201 WTGTDGKSTVLKDKTAISAGEIIDAAVMSRKALAAFVDAQVADAKQQGVLFSLHLKATMMKVSDPI 266
****************************************************************** PP
TIGR00178 268 vfGhvvrvfykdvfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelam 333
+fG vv +fykdv+akha++l+q+G+d +nG++dlya++++lp k+ ei+ad+++ y++rp lam
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 267 MFGIVVGEFYKDVLAKHADTLKQIGFDPNNGIGDLYARLNALPTDKQAEITADIKAEYARRPALAM 332
****************************************************************** PP
TIGR00178 334 vdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknG 399
v+sdkGitnlhvpsdvivdasmpamir+sGkm++++gkl+dtkavipd+syagvyq+viedck +G
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 333 VNSDKGITNLHVPSDVIVDASMPAMIRDSGKMWNAEGKLQDTKAVIPDRSYAGVYQVVIEDCKAHG 398
****************************************************************** PP
TIGR00178 400 afdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvkd 465
afdp++mG+vpnvGlmaq aeeyGsh+ktf+i adGvvrvvd+ G+vlle+ veagdiwrmcq kd
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 399 AFDPASMGSVPNVGLMAQAAEEYGSHNKTFQIAADGVVRVVDDAGNVLLEHAVEAGDIWRMCQTKD 464
****************************************************************** PP
TIGR00178 466 apiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfsl 531
apiqdwvklavtrarlsgtpavfwldp+rahd++li+kve+ylkdhdt Gldi+++spv+atrfsl
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 465 APIQDWVKLAVTRARLSGTPAVFWLDPKRAHDAQLIQKVERYLKDHDTGGLDIRVMSPVDATRFSL 530
****************************************************************** PP
TIGR00178 532 erirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqlee 597
erir+G+dtisvtGnvlrdyltdlfpi+elGtsakmls+vplmaGGGlfetGaGGsapkhvqq+ e
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 531 ERIRKGQDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGLFETGAGGSAPKHVQQFLE 596
****************************************************************** PP
TIGR00178 598 enhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskf 663
e++lrwdslGeflalaas+eh+++++gn+ka vla++ld+a gk+ld++ksp+rkvGeldnrgs+f
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 597 EDYLRWDSLGEFLALAASFEHLGNRYGNAKAGVLAKALDQANGKILDNNKSPARKVGELDNRGSHF 662
****************************************************************** PP
TIGR00178 664 ylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvl 729
yla+ywaq+la q +d+el+a+fa+va+alt+neeki++el+ +qG+avd+ Gyy+pd l++k++
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 663 YLAMYWAQALAGQDDDAELKATFAPVAKALTENEEKIIGELNGAQGKAVDIHGYYHPDIALLSKAM 728
****************************************************************** PP
TIGR00178 730 rpsatfnailealk 743
rpsatfna+++ l+
lcl|FitnessBrowser__Dyella79:N515DRAFT_3517 729 RPSATFNAAVDGLA 742
**********9986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (743 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.05
# Mc/sec: 10.97
//
[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