Align isocitrate dehydrogenase (EC 1.1.1.42) (characterized)
to candidate WP_013460323.1 SULKU_RS07370 NADP-dependent isocitrate dehydrogenase
Query= metacyc::MONOMER-11847
(741 letters)
>NCBI__GCF_000183725.1:WP_013460323.1
Length = 731
Score = 889 bits (2296), Expect = 0.0
Identities = 458/735 (62%), Positives = 550/735 (74%), Gaps = 7/735 (0%)
Query: 7 IIYTKIDEAPALATYSLLPIIQAFTRGTGVDVETRDISLAGRIIANFPENLTEEQRIPDY 66
II++ IDEAPALATYSLLPI+ AFT+ GV+V T DISLAGR+IA FPE +T+ QRIPD
Sbjct: 4 IIWSVIDEAPALATYSLLPIVNAFTKAAGVEVVTSDISLAGRVIATFPERMTDAQRIPDN 63
Query: 67 LAQLGELALTPEANIIKLPNISASIPQLKAAIKELQEHGYNVPNYPEAPSNDEEKAIQAR 126
LAQLG +A P+ IIKLPNISASIPQLKA I+ELQ GY++PNYPE P NDEEK IQAR
Sbjct: 64 LAQLGVVATQPDGVIIKLPNISASIPQLKACIEELQSQGYDLPNYPEEPKNDEEKEIQAR 123
Query: 127 YAKVLGSAVNPVLREGNSDRRAPLSVKAYAQKHPHRMAAWSKDSKAHVSHMNEGDFYGSE 186
Y+ LGSAVNPVLREGNSDRRA ++VK +A+K+PH++ W + SK V+HMN GDFY +E
Sbjct: 124 YSACLGSAVNPVLREGNSDRRAAVAVKNFAKKNPHKLRGWDEGSKTRVAHMNSGDFYANE 183
Query: 187 QSVTVPAATTVRIEYVNGANEVTVLKEKTALLAGEVIDTSVMNVRKLRDFYAEQIEDAKS 246
QS+ V I +NG LKE A EV+D + M+ + LR F AE +++AK
Sbjct: 184 QSIIKNGDGKVTIA-LNGKT----LKEIDAK-DKEVLDGTFMSAKALRSFLAESMDEAKE 237
Query: 247 QGVLLSLHLKATMMKISDPIMFGHAVSVFYKDVFDKHGALLAELGVNVNNGLGDLYAKIQ 306
+G+L S+HLKATMMK+SDPIMFGHAVSVF+KDV++K +GVN N GLGDL K+Q
Sbjct: 238 KGILWSIHLKATMMKVSDPIMFGHAVSVFFKDVYEKFADDFKSVGVNPNLGLGDLEKKMQ 297
Query: 307 TLPEDKRAEIEADIMAVYKTRPELAMVDSDKGITNLHVPNDIIIDASMPVVVRDGGKMWG 366
L +K+AEI A + AVY +R +AMVDSDKGITNLH NDIIIDAS+PVVVRDGGKMWG
Sbjct: 298 KLSAEKQAEINAAMQAVYASRAPMAMVDSDKGITNLHFSNDIIIDASLPVVVRDGGKMWG 357
Query: 367 PDGQLHDCKAVIPDRCYATMYGEIVDDCRKNGAFDPSTIGSVPNVGLMAQKAEEYGSHDK 426
PDG+++ C IPDRCYATMY EI++DC+ NG FD +T+GSV NVGLMAQKAEEYGSH
Sbjct: 358 PDGKVNQCIVTIPDRCYATMYSEIIEDCKINGQFDVTTMGSVSNVGLMAQKAEEYGSHPT 417
Query: 427 TFTAAGDGVIRVVDADGTVLMSQKVETGDIFRMCQAKDAPIRDWVGLAVRRAKATGAPAV 486
TF DGV+ V DA G LMS VE GDI+RM + KD P++DWV LAV R++ P V
Sbjct: 418 TFEMNEDGVVTVSDASGA-LMSFNVEKGDIWRMSRTKDIPVKDWVRLAVERSEIENVPVV 476
Query: 487 FWLDSNRAHDAQIIAKVNEYLKDLDTDGVEIKIMPPVEAMRFTLGRFRAGQDTISVTGNV 546
FWLD NRAHDA II KVN YL + + VE IM P +AM F+L R RAGQ+TIS TGNV
Sbjct: 477 FWLDENRAHDANIIKKVNAYLPEFNKSNVEYHIMAPEKAMAFSLKRVRAGQNTISATGNV 536
Query: 547 LRDYLTDLFPIIELGTSAKMLSIVPLLNGGGLFETGAGGSAPKHVQQFQKEGYLRWDSLG 606
LRDYLTDLFPI+ELGTSAKMLSIVPLL GGGLFETGAGGSAPKHV QF EG+LRWDSLG
Sbjct: 537 LRDYLTDLFPILELGTSAKMLSIVPLLAGGGLFETGAGGSAPKHVDQFVNEGHLRWDSLG 596
Query: 607 EFSALAASLEHLAQTFGNPKAQVLADTLDQAIGKFLDNQKSPARKVGQIDNRGSHFYLAL 666
EF ALA ++ H+ +T + K L LD+A +LDN K P+RK G+ DN+ SHF+LA
Sbjct: 597 EFLALAEAMRHINKTEKSNKLSALTAALDEANAAYLDNNKEPSRKAGEPDNKASHFFLAQ 656
Query: 667 YWAEALAAQDSDAEMKARFAGVASSLAAKEELINAELIAAQGSPVDMGGYYQPDDEKTAA 726
+WA+ALA Q DAE+ ARFA VA +L+ E I EL++ +G D+GGY+ PD KT
Sbjct: 657 FWAKALANQTVDAELAARFAPVAKALSENEAKIMEELLSVEGKAQDIGGYFHPDFAKTEK 716
Query: 727 AMRPSGTLNAIIDAM 741
AMRPS TLNAII A+
Sbjct: 717 AMRPSATLNAIIAAI 731
Lambda K H
0.316 0.133 0.380
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: 1374
Number of extensions: 59
Number of successful extensions: 3
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: 731
Length adjustment: 40
Effective length of query: 701
Effective length of database: 691
Effective search space: 484391
Effective search space used: 484391
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 (21.6 bits)
S2: 55 (25.8 bits)
Align candidate WP_013460323.1 SULKU_RS07370 (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.9645.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 1113.2 4.3 0 1113.0 4.3 1.0 1 lcl|NCBI__GCF_000183725.1:WP_013460323.1 SULKU_RS07370 NADP-dependent iso
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183725.1:WP_013460323.1 SULKU_RS07370 NADP-dependent isocitrate dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1113.0 4.3 0 0 5 742 .. 1 731 [] 1 731 [] 0.99
Alignments for each domain:
== domain 1 score: 1113.0 bits; conditional E-value: 0
TIGR00178 5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGe 73
+akii+++ deap+latysllpiv+af+++aG+ev t+dislagr++a+fpe++t+ q+++d+la+lG
lcl|NCBI__GCF_000183725.1:WP_013460323.1 1 MAKIIWSVIDEAPALATYSLLPIVNAFTKAAGVEVVTSDISLAGRVIATFPERMTDAQRIPDNLAQLGV 69
58******************************************************************* PP
TIGR00178 74 laktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlre 142
+a+ p+ iiklpnisas+pqlka+i elq++Gydlp+ypeepk+deek+i+ary++++Gsavnpvlre
lcl|NCBI__GCF_000183725.1:WP_013460323.1 70 VATQPDGVIIKLPNISASIPQLKACIEELQSQGYDLPNYPEEPKNDEEKEIQARYSACLGSAVNPVLRE 138
********************************************************************* PP
TIGR00178 143 GnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketv 211
Gnsdrra +avk++a+k+phk+ w sk++vahm++gdfya+e+s++ ++ +v i a +Gk+
lcl|NCBI__GCF_000183725.1:WP_013460323.1 139 GNSDRRAAVAVKNFAKKNPHKLRGWDEGSKTRVAHMNSGDFYANEQSIIKNGDGKVTI---ALNGKT-- 202
******************************************************9986...678886.. PP
TIGR00178 212 lkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdv 280
l ++++ +d+ev+d++++s+kal+ fl+e +++ake+g+l s+hlkatmmkvsdpi+fGh+v+vf+kdv
lcl|NCBI__GCF_000183725.1:WP_013460323.1 203 L-KEIDAKDKEVLDGTFMSAKALRSFLAESMDEAKEKGILWSIHLKATMMKVSDPIMFGHAVSVFFKDV 270
4.47999************************************************************** PP
TIGR00178 281 fakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdv 349
+ k+a+ ++++G++ + Gl+dl k+++l a k+ ei+a++++vy++r +amvdsdkGitnlh d+
lcl|NCBI__GCF_000183725.1:WP_013460323.1 271 YEKFADDFKSVGVNPNLGLGDLEKKMQKLSAEKQAEINAAMQAVYASRAPMAMVDSDKGITNLHFSNDI 339
********************************************************************* PP
TIGR00178 350 ivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqk 418
i+das+p ++r++Gkm+g+dgk ++ + ipd++ya +y+++iedck nG+fd ttmG+v nvGlmaqk
lcl|NCBI__GCF_000183725.1:WP_013460323.1 340 IIDASLPVVVRDGGKMWGPDGKVNQCIVTIPDRCYATMYSEIIEDCKINGQFDVTTMGSVSNVGLMAQK 408
********************************************************************* PP
TIGR00178 419 aeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpav 487
aeeyGsh tfe+++dGvv v d+sG l+ +ve+gdiwrm + kd p++dwv+lav r+ + ++p+v
lcl|NCBI__GCF_000183725.1:WP_013460323.1 409 AEEYGSHPTTFEMNEDGVVTVSDASGA-LMSFNVEKGDIWRMSRTKDIPVKDWVRLAVERSEIENVPVV 476
************************996.7899************************************* PP
TIGR00178 488 fwldperahdeelikkvekylkdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlf 556
fwld++rahd+++ikkv+ yl +++ + ++ +i+ p ka+ fsl+r+r G++tis+tGnvlrdyltdlf
lcl|NCBI__GCF_000183725.1:WP_013460323.1 477 FWLDENRAHDANIIKKVNAYLPEFNKSNVEYHIMAPEKAMAFSLKRVRAGQNTISATGNVLRDYLTDLF 545
********************************************************************* PP
TIGR00178 557 pilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehvavktgn 625
pilelGtsakmls+vpl+aGGGlfetGaGGsapkhv+q+++e+hlrwdslGeflala++++h+ +++
lcl|NCBI__GCF_000183725.1:WP_013460323.1 546 PILELGTSAKMLSIVPLLAGGGLFETGAGGSAPKHVDQFVNEGHLRWDSLGEFLALAEAMRHINKTEKS 614
********************************************************************* PP
TIGR00178 626 ekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaealt 694
+k l+ +ld+a ld++k psrk Ge dn+ s+f+la++wa++la qt d+elaa+fa+va+al+
lcl|NCBI__GCF_000183725.1:WP_013460323.1 615 NKLSALTAALDEANAAYLDNNKEPSRKAGEPDNKASHFFLAQFWAKALANQTVDAELAARFAPVAKALS 683
********************************************************************* PP
TIGR00178 695 kneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnaileal 742
+ne+ki++el +v+G+a d+gGy++pd +t+k++rpsat+nai++a+
lcl|NCBI__GCF_000183725.1:WP_013460323.1 684 ENEAKIMEELLSVEGKAQDIGGYFHPDFAKTEKAMRPSATLNAIIAAI 731
*********************************************985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (731 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 12.92
//
[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