Align isocitrate dehydrogenase (EC 1.1.1.42) (characterized)
to candidate WP_011372677.1 SUDEN_RS05495 NADP-dependent isocitrate dehydrogenase
Query= metacyc::MONOMER-11847
(741 letters)
>NCBI__GCF_000012965.1:WP_011372677.1
Length = 729
Score = 850 bits (2197), Expect = 0.0
Identities = 440/737 (59%), Positives = 545/737 (73%), Gaps = 9/737 (1%)
Query: 5 STIIYTKIDEAPALATYSLLPIIQAFTRGTGVDVETRDISLAGRIIANFPENLTEEQRIP 64
S II++KIDEAPALATYSLLPI+ AFT+ GV+V T DISLAGR+I+ F + L EQRI
Sbjct: 2 SKIIWSKIDEAPALATYSLLPIVNAFTKAAGVEVVTSDISLAGRVISKFSDRLKPEQRIN 61
Query: 65 DYLAQLGELALTPEANIIKLPNISASIPQLKAAIKELQEHGYNVPNYPEAPSNDEEKAIQ 124
D LA+LG + L P+ NIIKLPNISAS+ QL I ELQ GY+VPNYPE DEEKA++
Sbjct: 62 DELAELGNVVLQPDGNIIKLPNISASVGQLIECITELQAQGYDVPNYPEDAKTDEEKALK 121
Query: 125 ARYAKVLGSAVNPVLREGNSDRRAPLSVKAYAQKHPHRMAAWSKDSKAHVSHMNEGDFYG 184
Y+ LGSAVNPVLREGNSDRRA +VK +AQK+PH++ A+ SKA+V+HMN GDF+
Sbjct: 122 EIYSTCLGSAVNPVLREGNSDRRAAAAVKRFAQKNPHKLRAFESPSKAYVAHMNGGDFFS 181
Query: 185 SEQSVTVPAATTVRIEYVNGANEVTVLKEKTALLAGEVIDTSVMNVRKLRDFYAEQIEDA 244
+E+SV V V IE +NG VLK ++ E++D + M+ + L+ FY + ++DA
Sbjct: 182 NEKSVIVEGNAPVTIE-LNGK----VLKTLNDVVDKEIMDATFMSAKALQAFYQKTLDDA 236
Query: 245 KSQGVLLSLHLKATMMKISDPIMFGHAVSVFYKDVFDKHGALLAELGVNVNNGLGDLYAK 304
K GVL SLHLKATMMK+SDPIMFGHAV VF+KDVF K+G L +G N N GLGDLY K
Sbjct: 237 KKNGVLWSLHLKATMMKVSDPIMFGHAVKVFFKDVFAKYGDELTAIGYNANMGLGDLYKK 296
Query: 305 IQTLPEDKRAEIEADIMAVYKTRPELAMVDSDKGITNLHVPNDIIIDASMPVVVRDGGKM 364
++ K+AEI A I A Y +P +AMVDSDKGITNLH NDIIIDASMPVVVRDGGKM
Sbjct: 297 LEK--SSKKAEIIAAIEATYDIQPPMAMVDSDKGITNLHASNDIIIDASMPVVVRDGGKM 354
Query: 365 WGPDGQLHDCKAVIPDRCYATMYGEIVDDCRKNGAFDPSTIGSVPNVGLMAQKAEEYGSH 424
W DG++ +C +VIPD YA + +VDDC NG +D +T+G+V NVGLMAQKAEEYGSH
Sbjct: 355 WNRDGKVQECVSVIPDASYAFFHKAMVDDCVANGQYDVTTMGNVANVGLMAQKAEEYGSH 414
Query: 425 DKTFTAAGDGVIRVVDADGTVLMSQKVETGDIFRMCQAKDAPIRDWVGLAVRRAKATGAP 484
TF A +G + V +G VLMS VE GDI+RM + KD PI+DWV LAV RA+ TG+P
Sbjct: 415 PTTFEIAENGSVEVKQ-NGKVLMSHNVEAGDIWRMSRVKDIPIQDWVRLAVERARLTGSP 473
Query: 485 AVFWLDSNRAHDAQIIAKVNEYLKDLDTDGVEIKIMPPVEAMRFTLGRFRAGQDTISVTG 544
AVFWLD NRAHDA +I KVNEYLK+ DT G+E+ IM A ++T R R G+DTISVTG
Sbjct: 474 AVFWLDKNRAHDANMIKKVNEYLKNHDTTGLELPIMDVASAAKYTNARVRKGEDTISVTG 533
Query: 545 NVLRDYLTDLFPIIELGTSAKMLSIVPLLNGGGLFETGAGGSAPKHVQQFQKEGYLRWDS 604
NVLRD+LTD++PI+ELGTSAKMLSIVPLL GGG+FETGAGGSAPKHV QF +EG+LRWDS
Sbjct: 534 NVLRDHLTDMYPILELGTSAKMLSIVPLLAGGGVFETGAGGSAPKHVDQFLEEGHLRWDS 593
Query: 605 LGEFSALAASLEHLAQTFGNPKAQVLADTLDQAIGKFLDNQKSPARKVGQIDNRGSHFYL 664
LGEF ALA SL +AQ + K + LD A +LDN K+P+RK G+ DN+ SHF+L
Sbjct: 594 LGEFLALAESLRFIAQKNSDDKLAAVTTALDIANAAYLDNNKAPSRKAGEPDNKASHFFL 653
Query: 665 ALYWAEALAAQDSDAEMKARFAGVASSLAAKEELINAELIAAQGSPVDMGGYYQPDDEKT 724
A YWA+AL ++ +AE+ A+FA +A +L E I EL++ +G D+GGYY PDD+K
Sbjct: 654 AQYWAKAL-SEGKNAELAAKFAPIAKALTENEAKIIEELLSIEGKAQDIGGYYHPDDKKA 712
Query: 725 AAAMRPSGTLNAIIDAM 741
AAMRPS TLN I+D++
Sbjct: 713 EAAMRPSATLNKIVDSI 729
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: 1388
Number of extensions: 64
Number of successful extensions: 5
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: 729
Length adjustment: 40
Effective length of query: 701
Effective length of database: 689
Effective search space: 482989
Effective search space used: 482989
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_011372677.1 SUDEN_RS05495 (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.1226782.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 1089.9 7.7 0 1089.7 7.7 1.0 1 NCBI__GCF_000012965.1:WP_011372677.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000012965.1:WP_011372677.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1089.7 7.7 0 0 5 741 .. 1 728 [. 1 729 [] 0.99
Alignments for each domain:
== domain 1 score: 1089.7 bits; conditional E-value: 0
TIGR00178 5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelakt 77
++kii++ deap+latysllpiv+af+++aG+ev t+dislagr++++f ++l eq+++d+laelG++
NCBI__GCF_000012965.1:WP_011372677.1 1 MSKIIWSKIDEAPALATYSLLPIVNAFTKAAGVEVVTSDISLAGRVISKFSDRLKPEQRINDELAELGNVVLQ 73
58*********************************************************************** PP
TIGR00178 78 peaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrrap 150
p+ niiklpnisasv ql +i elq++Gyd+p+ype++ktdeek++k+ y+ ++GsavnpvlreGnsdrra
NCBI__GCF_000012965.1:WP_011372677.1 74 PDGNIIKLPNISASVGQLIECITELQAQGYDVPNYPEDAKTDEEKALKEIYSTCLGSAVNPVLREGNSDRRAA 146
************************************************************************* PP
TIGR00178 151 lavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgev 223
+avk++a+k+phk+ ++ sk+ vahm+ gdf+++eksv++++ v iel +G vlk+ ++ d+e+
NCBI__GCF_000012965.1:WP_011372677.1 147 AAVKRFAQKNPHKLRAFESPSKAYVAHMNGGDFFSNEKSVIVEGNAPVTIEL---NG--KVLKTLNDVVDKEI 214
**************************************************98...44..48************ PP
TIGR00178 224 idssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldve 296
+d++++s+kal++f+++ ++dak++gvl slhlkatmmkvsdpi+fGh+v+vf+kdvfak+++ l+++G +++
NCBI__GCF_000012965.1:WP_011372677.1 215 MDATFMSAKALQAFYQKTLDDAKKNGVLWSLHLKATMMKVSDPIMFGHAVKVFFKDVFAKYGDELTAIGYNAN 287
************************************************************************* PP
TIGR00178 297 nGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkd 369
Gl+dly k+e+ ++kk ei+a++e++y+ +p +amvdsdkGitnlh+ d+i+dasmp ++r++Gkm+++d
NCBI__GCF_000012965.1:WP_011372677.1 288 MGLGDLYKKLEK--SSKKAEIIAAIEATYDIQPPMAMVDSDKGITNLHASNDIIIDASMPVVVRDGGKMWNRD 358
**********97..6789******************************************************* PP
TIGR00178 370 gklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvds 442
gk ++ vipd sya ++a+++dc nG++d ttmG v nvGlmaqkaeeyGsh tfei ++G v+v ++
NCBI__GCF_000012965.1:WP_011372677.1 359 GKVQECVSVIPDASYAFFHKAMVDDCVANGQYDVTTMGNVANVGLMAQKAEEYGSHPTTFEIAENGSVEV-KQ 430
********************************************************************97.67 PP
TIGR00178 443 sGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteG 515
+G+vl+ ++veagdiwrm +vkd piqdwv+lav rarl+g pavfwld++rahd+++ikkv++ylk+hdt+G
NCBI__GCF_000012965.1:WP_011372677.1 431 NGKVLMSHNVEAGDIWRMSRVKDIPIQDWVRLAVERARLTGSPAVFWLDKNRAHDANMIKKVNEYLKNHDTTG 503
9************************************************************************ PP
TIGR00178 516 ldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsa 588
l++ i++ a++++ +r+r+GedtisvtGnvlrd+ltd++pilelGtsakmls+vpl+aGGG+fetGaGGsa
NCBI__GCF_000012965.1:WP_011372677.1 504 LELPIMDVASAAKYTNARVRKGEDTISVTGNVLRDHLTDMYPILELGTSAKMLSIVPLLAGGGVFETGAGGSA 576
************************************************************************* PP
TIGR00178 589 pkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgs 661
pkhv+q+ ee+hlrwdslGeflala+sl+ +a+k+ ++k ++ +ld a ld++k+psrk Ge dn+ s
NCBI__GCF_000012965.1:WP_011372677.1 577 PKHVDQFLEEGHLRWDSLGEFLALAESLRFIAQKNSDDKLAAVTTALDIANAAYLDNNKAPSRKAGEPDNKAS 649
************************************************************************* PP
TIGR00178 662 kfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsat 734
+f+la+ywa++l+ + +++elaa+fa++a+alt+ne+ki++el +++G+a d+gGyy+pd++++++++rpsat
NCBI__GCF_000012965.1:WP_011372677.1 650 HFFLAQYWAKALS-EGKNAELAAKFAPIAKALTENEAKIIEELLSIEGKAQDIGGYYHPDDKKAEAAMRPSAT 721
***********97.67899****************************************************** PP
TIGR00178 735 fnailea 741
+n+i+++
NCBI__GCF_000012965.1:WP_011372677.1 722 LNKIVDS 728
****997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (729 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 24.46
//
[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