Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate Dsui_3295 Dsui_3295 isocitrate dehydrogenase, NADP-dependent, monomeric type
Query= BRENDA::O53611
(745 letters)
>FitnessBrowser__PS:Dsui_3295
Length = 746
Score = 1163 bits (3009), Expect = 0.0
Identities = 567/742 (76%), Positives = 646/742 (87%)
Query: 1 MSAEQPTIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTE 60
MSA + IIYTLTDEAPLLAT AFLPI+R F PAG++I SDISVAAR+LAEF DYL +
Sbjct: 1 MSAGKSKIIYTLTDEAPLLATCAFLPIIRTFTGPAGVEIAESDISVAARVLAEFSDYLRD 60
Query: 61 EQRVPDNLAELGRLTQLPDTNIIKLPNISASVPQLVAAIKELQDKGYAVPDYPADPKTDQ 120
+Q+VPDNLAELGRLTQ PDTNIIKLPNISASV QLVA +KELQ KGYA+PDYP +P TD+
Sbjct: 61 DQKVPDNLAELGRLTQDPDTNIIKLPNISASVAQLVACVKELQAKGYAIPDYPENPTTDE 120
Query: 121 EKAIKERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRH 180
EKA+K RY +CLGSAVNPVLR+GNSDRRAP AVK YA+KHPHSMGEW S+THVAHM H
Sbjct: 121 EKALKTRYGKCLGSAVNPVLREGNSDRRAPAAVKNYAKKHPHSMGEWKPWSQTHVAHMDH 180
Query: 181 GDFYAGEKSMTLDRARNVRMELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEE 240
GDFY GEKS+TLD+AR+V+MEL+ KSGKTIVLKP+V L DG++IDSMFMSKKALCDFYE+
Sbjct: 181 GDFYHGEKSLTLDKARDVKMELVTKSGKTIVLKPKVALKDGEIIDSMFMSKKALCDFYEK 240
Query: 241 QMQDAFETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLS 300
+++D + G++FSLHVKATMMKVSHPIVFGH V+I+YK+AF KH +LFD+LG+NVNNG++
Sbjct: 241 ELEDCRQAGILFSLHVKATMMKVSHPIVFGHCVKIYYKEAFEKHGKLFDELGINVNNGMA 300
Query: 301 DLYSKIESLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIR 360
LY KI++LP S+RDEII DLH C EHRP LAMVDSA+GI+NFHSP+D+IVDASMPAMIR
Sbjct: 301 TLYEKIDTLPESKRDEIIRDLHACQEHRPRLAMVDSAKGITNFHSPNDIIVDASMPAMIR 360
Query: 361 AGGKMYGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQFDPTTMGTVPNVGLMAQQAE 420
GGKM+GADGK D KAV PESTF+RIYQE+INFCK +G FDP TMGTVPNVGLMAQ+AE
Sbjct: 361 GGGKMWGADGKPYDCKAVMPESTFARIYQEMINFCKWHGNFDPKTMGTVPNVGLMAQKAE 420
Query: 421 EYGSHDKTFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRA 480
EYGSHDKTFEI E G+ANIVD+ATGEVLL++NVE GDIWRMC VKD PIRDWVKLAVTRA
Sbjct: 421 EYGSHDKTFEIAEAGIANIVDLATGEVLLSQNVEEGDIWRMCQVKDEPIRDWVKLAVTRA 480
Query: 481 RISGMPVLFWLDPYRPHENELIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLD 540
R SGMP +FWLDPYRPHE ELIKKV+ YLKDHDT GL+I IMSQVR+MR+T ER+ RGLD
Sbjct: 481 RNSGMPAVFWLDPYRPHEAELIKKVEKYLKDHDTSGLEIHIMSQVRAMRFTLERVARGLD 540
Query: 541 TIAATGNILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEEN 600
TI+ TGNILRDYLTDLFPI+ELGTSAKMLS+VPLMAGGGMYETGAGGSAPKHV+QLVEEN
Sbjct: 541 TISVTGNILRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMYETGAGGSAPKHVQQLVEEN 600
Query: 601 HLRWDSLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNR 660
HLRWDSLGEFLAL E++GIKTGN +AKLL KTLD A GKLLD +KSPSR+TGELDNR
Sbjct: 601 HLRWDSLGEFLALAVSLEELGIKTGNAKAKLLAKTLDEATGKLLDENKSPSRRTGELDNR 660
Query: 661 GSQFYLAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDVIVRELTEVQGEPVDIGGYYA 720
GSQFYLA+YWAQ LAAQ++D+ LA F LA L +NE IV EL VQG+PVDIGGYY
Sbjct: 661 GSQFYLALYWAQALAAQSEDKDLATKFGPLAKSLAENEQKIVDELKAVQGKPVDIGGYYL 720
Query: 721 PDSDMTTAVMRPSKTFNAALEA 742
D TAVMRPS T N+ L+A
Sbjct: 721 ADQAKVTAVMRPSATLNSLLQA 742
Lambda K H
0.317 0.134 0.388
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: 1519
Number of extensions: 36
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: 745
Length of database: 746
Length adjustment: 40
Effective length of query: 705
Effective length of database: 706
Effective search space: 497730
Effective search space used: 497730
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 (21.7 bits)
S2: 55 (25.8 bits)
Align candidate Dsui_3295 Dsui_3295 (isocitrate dehydrogenase, NADP-dependent, monomeric type)
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.1281701.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 1345.4 0.0 0 1345.2 0.0 1.0 1 FitnessBrowser__PS:Dsui_3295
Domain annotation for each sequence (and alignments):
>> FitnessBrowser__PS:Dsui_3295
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1345.2 0.0 0 0 1 741 [. 1 742 [. 1 745 [. 1.00
Alignments for each domain:
== domain 1 score: 1345.2 bits; conditional E-value: 0
TIGR00178 1 mstekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelaktpean 81
ms+ k+kiiytltdeapllat ++lpi+++f+++aG+e+ +dis+a+r+laef +yl ++qkv+d+laelG+l++ p++n
FitnessBrowser__PS:Dsui_3295 1 MSAGKSKIIYTLTDEAPLLATCAFLPIIRTFTGPAGVEIAESDISVAARVLAEFSDYLRDDQKVPDNLAELGRLTQDPDTN 81
8999***************************************************************************** PP
TIGR00178 82 iiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrraplavkeyarkhph 162
iiklpnisasv ql+a++kelq+kGy++pdype+p+tdeek++k+ry k++GsavnpvlreGnsdrrap+avk+ya+khph
FitnessBrowser__PS:Dsui_3295 82 IIKLPNISASVAQLVACVKELQAKGYAIPDYPENPTTDEEKALKTRYGKCLGSAVNPVLREGNSDRRAPAAVKNYAKKHPH 162
********************************************************************************* PP
TIGR00178 163 kmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgevidssvlskkalvefleeeie 243
+mGew s++hvahmd+gdfy++eks++ld+a++vk+el++k+Gk++vlk+k+ l+dge+ids+++skkal++f+e+e+e
FitnessBrowser__PS:Dsui_3295 163 SMGEWKPWSQTHVAHMDHGDFYHGEKSLTLDKARDVKMELVTKSGKTIVLKPKVALKDGEIIDSMFMSKKALCDFYEKELE 243
********************************************************************************* PP
TIGR00178 244 dakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakieslpaakkeeieadlekv 324
d ++ g+l+slh+katmmkvs+pivfGh v+++yk++f kh++l+++lG++v+nG+a ly ki++lp++k++ei+ dl+++
FitnessBrowser__PS:Dsui_3295 244 DCRQAGILFSLHVKATMMKVSHPIVFGHCVKIYYKEAFEKHGKLFDELGINVNNGMATLYEKIDTLPESKRDEIIRDLHAC 324
********************************************************************************* PP
TIGR00178 325 yeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdptt 405
e+rp lamvds+kGitn+h+p d+ivdasmpamir +Gkm+g+dgk d kav+p+s++a++yq++i++ck +G+fdp t
FitnessBrowser__PS:Dsui_3295 325 QEHRPRLAMVDSAKGITNFHSPNDIIVDASMPAMIRGGGKMWGADGKPYDCKAVMPESTFARIYQEMINFCKWHGNFDPKT 405
********************************************************************************* PP
TIGR00178 406 mGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvd.ssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtp 485
mGtvpnvGlmaqkaeeyGshdktfei ++G++++vd ++Gevll ++ve+gdiwrmcqvkd pi+dwvklavtrar sg+p
FitnessBrowser__PS:Dsui_3295 406 MGTVPNVGLMAQKAEEYGSHDKTFEIAEAGIANIVDlATGEVLLSQNVEEGDIWRMCQVKDEPIRDWVKLAVTRARNSGMP 486
************************************99******************************************* PP
TIGR00178 486 avfwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsak 566
avfwldp+r+h++elikkvekylkdhdt+Gl+i+i+s+v+a+rf+ler++rG dtisvtGn+lrdyltdlfpi+elGtsak
FitnessBrowser__PS:Dsui_3295 487 AVFWLDPYRPHEAELIKKVEKYLKDHDTSGLEIHIMSQVRAMRFTLERVARGLDTISVTGNILRDYLTDLFPIMELGTSAK 567
********************************************************************************* PP
TIGR00178 567 mlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeek 647
mls+vplmaGGG++etGaGGsapkhvqql+eenhlrwdslGeflala sle++++ktgn+kak+la+tld+atgkllde+k
FitnessBrowser__PS:Dsui_3295 568 MLSIVPLMAGGGMYETGAGGSAPKHVQQLVEENHLRWDSLGEFLALAVSLEELGIKTGNAKAKLLAKTLDEATGKLLDENK 648
********************************************************************************* PP
TIGR00178 648 spsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkv 728
spsr++Geldnrgs+fyla ywaq+laaq+edk+la +f ++a++l++ne+kiv el+avqG++vd+gGyy +d+ ++t+v
FitnessBrowser__PS:Dsui_3295 649 SPSRRTGELDNRGSQFYLALYWAQALAAQSEDKDLATKFGPLAKSLAENEQKIVDELKAVQGKPVDIGGYYLADQAKVTAV 729
********************************************************************************* PP
TIGR00178 729 lrpsatfnailea 741
+rpsat+n++l+a
FitnessBrowser__PS:Dsui_3295 730 MRPSATLNSLLQA 742
**********998 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (746 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 0.02s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 16.47
//
[ok]
This GapMind analysis is from Apr 09 2024. 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