Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate WP_034212296.1 N787_RS07575 NADP-dependent isocitrate dehydrogenase
Query= SwissProt::P16100
(741 letters)
>NCBI__GCF_000747155.1:WP_034212296.1
Length = 741
Score = 1090 bits (2819), Expect = 0.0
Identities = 542/738 (73%), Positives = 620/738 (84%)
Query: 3 TPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKI 62
TPKI+YTLTDEAP LAT SLLPI++AF G++GIAVETRDISL+GR++A FPE L + Q+I
Sbjct: 4 TPKILYTLTDEAPFLATQSLLPIVQAFAGAAGIAVETRDISLSGRILAQFPERLREDQRI 63
Query: 63 SDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDV 122
D LAELG+LATTP+ANIIKLPNISAS+PQLKAAIKELQ QGY LPDYPEEP+ D EKDV
Sbjct: 64 GDHLAELGQLATTPEANIIKLPNISASLPQLKAAIKELQAQGYDLPDYPEEPRDDAEKDV 123
Query: 123 KARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFY 182
KARY K GSAVNPVLREGNSDRRAP +VK RKHPH+MG W++DSKSHVAHM DF+
Sbjct: 124 KARYGKAMGSAVNPVLREGNSDRRAPKAVKENVRKHPHRMGKWASDSKSHVAHMAGDDFF 183
Query: 183 GSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIED 242
GSEK+A + A GS+KI + DG+ VLK V+ GEI+D+SVM + +L F A +I D
Sbjct: 184 GSEKSATMAAAGSLKIAFVGADGAERVLKESVKVKEGEIVDASVMRRASLARFAAEQIAD 243
Query: 243 AKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYA 302
AK GVL S+HLKATMMKVSDPIMFG V+EFYKDAL +HA+VL ++GFD NNGIGDLYA
Sbjct: 244 AKATGVLFSLHLKATMMKVSDPIMFGVFVTEFYKDALARHAKVLDEVGFDPNNGIGDLYA 303
Query: 303 RIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGK 362
R+ LPEA Q I+ADI AVYA P LAMVNSDKGITNLHVPSDVIVDASMPAMIRDSG+
Sbjct: 304 RLGQLPEATQAAIKADIDAVYASAPGLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGR 363
Query: 363 MWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGS 422
MW G+L DTKAVIPDRCYAG+YQ VI+DCK +GAFDP TMGSVPNVGLMAQKAEEYGS
Sbjct: 364 MWNAKGELQDTKAVIPDRCYAGIYQAVIDDCKANGAFDPATMGSVPNVGLMAQKAEEYGS 423
Query: 423 HDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNT 482
HDKTFQ+ A G VRVTD SG ++ E +V+AGDIWRMCQ KDAPIQDWVKLAV+R+R ++T
Sbjct: 424 HDKTFQLDAAGTVRVTDASGAVVFEHAVQAGDIWRMCQTKDAPIQDWVKLAVDRSRLSST 483
Query: 483 PAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVT 542
PA+FWLD ARAHDAQ+IAKVERYLKD+DT GLDIRIL PVEA + SL RIR G+DTISVT
Sbjct: 484 PAIFWLDAARAHDAQLIAKVERYLKDFDTQGLDIRILPPVEAMKVSLQRIRAGQDTISVT 543
Query: 543 GNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWD 602
GNVLRDYLTDLFPIMELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQF++E YLRWD
Sbjct: 544 GNVLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGLFETGAGGSAPKHVQQFVQENYLRWD 603
Query: 603 SLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFY 662
SLGEFLALAASLEH+ + N A VLA TLD A G+ILD ++ P+RKVG +DNRGSHFY
Sbjct: 604 SLGEFLALAASLEHISERWLNSSAPVLAKTLDLANGRILDEDRGPSRKVGGLDNRGSHFY 663
Query: 663 LALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDL 722
LALYWAQALAAQ EDK L+A+F +AK L++ E+ IV EL A QG+PVDI GYY P+
Sbjct: 664 LALYWAQALAAQDEDKALKAKFAPLAKLLSEQESTIVDELLAVQGQPVDIGGYYRPDMAK 723
Query: 723 TSKAIRPSATFNAALAPL 740
T+ A+RPS TFN AL+ L
Sbjct: 724 TTAAMRPSNTFNIALSTL 741
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: 1514
Number of extensions: 63
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: 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 WP_034212296.1 N787_RS07575 (NADP-dependent 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.2983301.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 1313.5 0.5 0 1313.3 0.5 1.0 1 NCBI__GCF_000747155.1:WP_034212296.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000747155.1:WP_034212296.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1313.3 0.5 0 0 3 742 .. 2 741 .] 1 741 [] 1.00
Alignments for each domain:
== domain 1 score: 1313.3 bits; conditional E-value: 0
TIGR00178 3 tekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGela 75
++++ki+ytltdeap lat sllpiv+afa++aGi+vetrdisl+grila+fpe+l e+q+++d+laelG+la
NCBI__GCF_000747155.1:WP_034212296.1 2 ADTPKILYTLTDEAPFLATQSLLPIVQAFAGAAGIAVETRDISLSGRILAQFPERLREDQRIGDHLAELGQLA 74
6789********************************************************************* PP
TIGR00178 76 ktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrr 148
+tpeaniiklpnisas+pqlkaaikelq++Gydlpdypeep+ d+ekd+kary k +GsavnpvlreGnsdrr
NCBI__GCF_000747155.1:WP_034212296.1 75 TTPEANIIKLPNISASLPQLKAAIKELQAQGYDLPDYPEEPRDDAEKDVKARYGKAMGSAVNPVLREGNSDRR 147
************************************************************************* PP
TIGR00178 149 aplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldg 221
ap+avke +rkhph+mG+w+ dskshvahm+ +df++seks+++ aa ++ki ++ +dG e vlk+++k+++g
NCBI__GCF_000747155.1:WP_034212296.1 148 APKAVKENVRKHPHRMGKWASDSKSHVAHMAGDDFFGSEKSATMAAAGSLKIAFVGADGAERVLKESVKVKEG 220
************************************************************************* PP
TIGR00178 222 evidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGld 294
e++d+sv+ + +l+ f +e+i+dak++gvl+slhlkatmmkvsdpi+fG v +fykd++a+ha++l+++G+d
NCBI__GCF_000747155.1:WP_034212296.1 221 EIVDASVMRRASLARFAAEQIADAKATGVLFSLHLKATMMKVSDPIMFGVFVTEFYKDALARHAKVLDEVGFD 293
************************************************************************* PP
TIGR00178 295 venGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmyg 367
+nG++dlya++ +lp+a + i+ad+++vy++ p lamv+sdkGitnlhvpsdvivdasmpamir+sG+m++
NCBI__GCF_000747155.1:WP_034212296.1 294 PNNGIGDLYARLGQLPEATQAAIKADIDAVYASAPGLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGRMWN 366
************************************************************************* PP
TIGR00178 368 kdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvv 440
+ g+l+dtkavipd++yag+yqavi+dck nGafdp+tmG+vpnvGlmaqkaeeyGshdktf+++a+G+vrv+
NCBI__GCF_000747155.1:WP_034212296.1 367 AKGELQDTKAVIPDRCYAGIYQAVIDDCKANGAFDPATMGSVPNVGLMAQKAEEYGSHDKTFQLDAAGTVRVT 439
************************************************************************* PP
TIGR00178 441 dssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdt 513
d+sG v++e+ v+agdiwrmcq kdapiqdwvklav r+rls+tpa+fwld +rahd++li+kve+ylkd+dt
NCBI__GCF_000747155.1:WP_034212296.1 440 DASGAVVFEHAVQAGDIWRMCQTKDAPIQDWVKLAVDRSRLSSTPAIFWLDAARAHDAQLIAKVERYLKDFDT 512
************************************************************************* PP
TIGR00178 514 eGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGG 586
+Gldi+il pv+a++ sl+rir G+dtisvtGnvlrdyltdlfpi+elGtsakmls+vplmaGGGlfetGaGG
NCBI__GCF_000747155.1:WP_034212296.1 513 QGLDIRILPPVEAMKVSLQRIRAGQDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGLFETGAGG 585
************************************************************************* PP
TIGR00178 587 sapkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnr 659
sapkhvqq+++en+lrwdslGeflalaasleh++ + n+ a vla+tld a g++lde++ psrkvG ldnr
NCBI__GCF_000747155.1:WP_034212296.1 586 SAPKHVQQFVQENYLRWDSLGEFLALAASLEHISERWLNSSAPVLAKTLDLANGRILDEDRGPSRKVGGLDNR 658
************************************************************************* PP
TIGR00178 660 gskfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrps 732
gs+fyla ywaq+laaq edk l+a+fa++a+ l+++e++iv el avqG++vd+gGyy pd +tt+++rps
NCBI__GCF_000747155.1:WP_034212296.1 659 GSHFYLALYWAQALAAQDEDKALKAKFAPLAKLLSEQESTIVDELLAVQGQPVDIGGYYRPDMAKTTAAMRPS 731
************************************************************************* PP
TIGR00178 733 atfnaileal 742
+tfn +l++l
NCBI__GCF_000747155.1:WP_034212296.1 732 NTFNIALSTL 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 38.02
//
[ok]
This GapMind analysis is from Sep 24 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