Align isocitrate dehydrogenase (EC 1.1.1.42) (characterized)
to candidate WP_099019356.1 CCS90_RS09825 NADP-dependent isocitrate dehydrogenase
Query= metacyc::MONOMER-11847
(741 letters)
>NCBI__GCF_002591915.1:WP_099019356.1
Length = 740
Score = 952 bits (2462), Expect = 0.0
Identities = 486/739 (65%), Positives = 573/739 (77%)
Query: 3 SKSTIIYTKIDEAPALATYSLLPIIQAFTRGTGVDVETRDISLAGRIIANFPENLTEEQR 62
+K TIIYT DEAPALATYS LPI+Q F V+VET+DISLA RI+A FPE L Q+
Sbjct: 2 TKQTIIYTITDEAPALATYSFLPIVQKFAGQADVEVETKDISLASRILAQFPERLKAGQK 61
Query: 63 IPDYLAQLGELALTPEANIIKLPNISASIPQLKAAIKELQEHGYNVPNYPEAPSNDEEKA 122
D L QLG LA TPEANIIKLPNISAS+PQL AAIKELQ GY++P+ PE P +EEKA
Sbjct: 62 CEDALGQLGVLAKTPEANIIKLPNISASVPQLNAAIKELQAAGYDLPDCPEDPETEEEKA 121
Query: 123 IQARYAKVLGSAVNPVLREGNSDRRAPLSVKAYAQKHPHRMAAWSKDSKAHVSHMNEGDF 182
I A+YA VLGSAVNPVLREGNSDRR +VKAYA+K+PHR+ A +K+SK HV+HM+ DF
Sbjct: 122 IMAKYANVLGSAVNPVLREGNSDRRVAAAVKAYARKNPHRLGAITKNSKTHVAHMDANDF 181
Query: 183 YGSEQSVTVPAATTVRIEYVNGANEVTVLKEKTALLAGEVIDTSVMNVRKLRDFYAEQIE 242
YGSEQS +PAA VRIE+V +VTV+K AL AGEVID+S M+VR LR F+A++I+
Sbjct: 182 YGSEQSYVMPAADEVRIEHVGTDGQVTVMKSAVALQAGEVIDSSCMSVRALRQFFAKEIK 241
Query: 243 DAKSQGVLLSLHLKATMMKISDPIMFGHAVSVFYKDVFDKHGALLAELGVNVNNGLGDLY 302
DAKS GVLLSLHLKATMMK+SDPIMFGH+V V+Y +VF KH A ++GV VNNG+G +Y
Sbjct: 242 DAKSSGVLLSLHLKATMMKVSDPIMFGHSVEVYYAEVFKKHAATFEKIGVEVNNGIGSVY 301
Query: 303 AKIQTLPEDKRAEIEADIMAVYKTRPELAMVDSDKGITNLHVPNDIIIDASMPVVVRDGG 362
KI LP K+AEI+ADI A Y +P LAMVDSDKGITNLHVPND+IIDASMP ++
Sbjct: 302 NKITELPAAKQAEIKADIAACYANQPALAMVDSDKGITNLHVPNDVIIDASMPAAIKSSA 361
Query: 363 KMWGPDGQLHDCKAVIPDRCYATMYGEIVDDCRKNGAFDPSTIGSVPNVGLMAQKAEEYG 422
KMW +G+L D KA+IPDR YA +Y EI+ C+++GAFD T+G+V NVGLMAQKAEEYG
Sbjct: 362 KMWNAEGKLQDTKAMIPDRSYAGIYQEIIAYCKEHGAFDVVTMGNVCNVGLMAQKAEEYG 421
Query: 423 SHDKTFTAAGDGVIRVVDADGTVLMSQKVETGDIFRMCQAKDAPIRDWVGLAVRRAKATG 482
SHDKTF A DG++RVV++ G +LM +VE GDI+R CQ KD PIRDWV LAV RAK TG
Sbjct: 422 SHDKTFEMASDGMMRVVNSSGEILMQHEVEQGDIWRACQTKDLPIRDWVKLAVTRAKNTG 481
Query: 483 APAVFWLDSNRAHDAQIIAKVNEYLKDLDTDGVEIKIMPPVEAMRFTLGRFRAGQDTISV 542
+ AVFWLD NRAHD +I KV YL+D DT G+EIKIM P AMR+T R AG DTISV
Sbjct: 482 SAAVFWLDENRAHDRNLIEKVELYLQDHDTTGLEIKIMNPKAAMRYTCERVTAGLDTISV 541
Query: 543 TGNVLRDYLTDLFPIIELGTSAKMLSIVPLLNGGGLFETGAGGSAPKHVQQFQKEGYLRW 602
TGNVLRDYLTDLFPI+ELGTSAKMLSIVPLL GGGLFETGAGGSAPKHVQQF EG+LRW
Sbjct: 542 TGNVLRDYLTDLFPILELGTSAKMLSIVPLLAGGGLFETGAGGSAPKHVQQFVTEGHLRW 601
Query: 603 DSLGEFSALAASLEHLAQTFGNPKAQVLADTLDQAIGKFLDNQKSPARKVGQIDNRGSHF 662
DSLGEF ALA SLE +A+ N +A+VLA LD A ++L KSP+RKV ++DNRGS +
Sbjct: 602 DSLGEFLALAVSLEDIAEKTNNQQAKVLAAALDDANERYLSFNKSPSRKVNELDNRGSQY 661
Query: 663 YLALYWAEALAAQDSDAEMKARFAGVASSLAAKEELINAELIAAQGSPVDMGGYYQPDDE 722
YL YWA+AL+AQD DA +KA F V +L E I ELI AQGSPVD+GGY+QP+D
Sbjct: 662 YLTKYWAKALSAQDEDAALKATFTQVFEALKNNEAQILQELIDAQGSPVDIGGYFQPNDA 721
Query: 723 KTAAAMRPSGTLNAIIDAM 741
AAMRPS T N IID++
Sbjct: 722 LAKAAMRPSSTFNQIIDSI 740
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: 1396
Number of extensions: 53
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: 740
Length adjustment: 40
Effective length of query: 701
Effective length of database: 700
Effective search space: 490700
Effective search space used: 490700
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_099019356.1 CCS90_RS09825 (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.3347674.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 1248.2 8.2 0 1248.1 8.2 1.0 1 NCBI__GCF_002591915.1:WP_099019356.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002591915.1:WP_099019356.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1248.1 8.2 0 0 5 741 .. 3 739 .. 1 740 [] 1.00
Alignments for each domain:
== domain 1 score: 1248.1 bits; conditional E-value: 0
TIGR00178 5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelakt 77
k++iiyt+tdeap+latys+lpiv+ fa++a +evet+disla+rila+fpe+l qk +dal +lG lakt
NCBI__GCF_002591915.1:WP_099019356.1 3 KQTIIYTITDEAPALATYSFLPIVQKFAGQADVEVETKDISLASRILAQFPERLKAGQKCEDALGQLGVLAKT 75
579********************************************************************** PP
TIGR00178 78 peaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrrap 150
peaniiklpnisasvpql+aaikelq+ Gydlpd pe+p+t+eek+i a+ya+++GsavnpvlreGnsdrr
NCBI__GCF_002591915.1:WP_099019356.1 76 PEANIIKLPNISASVPQLNAAIKELQAAGYDLPDCPEDPETEEEKAIMAKYANVLGSAVNPVLREGNSDRRVA 148
************************************************************************* PP
TIGR00178 151 lavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeevkieliakdGketvlkaklklldgev 223
+avk yark+ph++G+ +++sk+hvahmda+dfy+se+s ++ aa+ev+ie++ dG++tv+k+ + l++gev
NCBI__GCF_002591915.1:WP_099019356.1 149 AAVKAYARKNPHRLGAITKNSKTHVAHMDANDFYGSEQSYVMPAADEVRIEHVGTDGQVTVMKSAVALQAGEV 221
************************************************************************* PP
TIGR00178 224 idssvlskkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldve 296
idss +s +al++f+++ei+dak gvllslhlkatmmkvsdpi+fGh v v+y++vf kha+++e++G++v+
NCBI__GCF_002591915.1:WP_099019356.1 222 IDSSCMSVRALRQFFAKEIKDAKSSGVLLSLHLKATMMKVSDPIMFGHSVEVYYAEVFKKHAATFEKIGVEVN 294
************************************************************************* PP
TIGR00178 297 nGladlyakieslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkd 369
nG++ +y ki +lpaak+ ei+ad+ ++y+++p lamvdsdkGitnlhvp dvi+dasmpa+i++s km++++
NCBI__GCF_002591915.1:WP_099019356.1 295 NGIGSVYNKITELPAAKQAEIKADIAACYANQPALAMVDSDKGITNLHVPNDVIIDASMPAAIKSSAKMWNAE 367
************************************************************************* PP
TIGR00178 370 gklkdtkavipdssyagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvds 442
gkl+dtka+ipd+syag+yq++i +ck++Gafd tmG v nvGlmaqkaeeyGshdktfe+ +dG++rvv+s
NCBI__GCF_002591915.1:WP_099019356.1 368 GKLQDTKAMIPDRSYAGIYQEIIAYCKEHGAFDVVTMGNVCNVGLMAQKAEEYGSHDKTFEMASDGMMRVVNS 440
************************************************************************* PP
TIGR00178 443 sGevlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteG 515
sGe+l+++eve+gdiwr+cq kd pi+dwvklavtra+ +g avfwld++rahd++li+kve yl+dhdt+G
NCBI__GCF_002591915.1:WP_099019356.1 441 SGEILMQHEVEQGDIWRACQTKDLPIRDWVKLAVTRAKNTGSAAVFWLDENRAHDRNLIEKVELYLQDHDTTG 513
************************************************************************* PP
TIGR00178 516 ldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsa 588
l+i+i++p a+r+++er++ G dtisvtGnvlrdyltdlfpilelGtsakmls+vpl+aGGGlfetGaGGsa
NCBI__GCF_002591915.1:WP_099019356.1 514 LEIKIMNPKAAMRYTCERVTAGLDTISVTGNVLRDYLTDLFPILELGTSAKMLSIVPLLAGGGLFETGAGGSA 586
************************************************************************* PP
TIGR00178 589 pkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgs 661
pkhvqq++ e+hlrwdslGeflala sle++a kt+n++akvla +ld+a ++ l +kspsrkv eldnrgs
NCBI__GCF_002591915.1:WP_099019356.1 587 PKHVQQFVTEGHLRWDSLGEFLALAVSLEDIAEKTNNQQAKVLAAALDDANERYLSFNKSPSRKVNELDNRGS 659
************************************************************************* PP
TIGR00178 662 kfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsat 734
++yl+kywa++l+aq ed+ l+a+f++v eal++ne++i +el ++qG++vd+gGy++p++ l+++++rps t
NCBI__GCF_002591915.1:WP_099019356.1 660 QYYLTKYWAKALSAQDEDAALKATFTQVFEALKNNEAQILQELIDAQGSPVDIGGYFQPNDALAKAAMRPSST 732
************************************************************************* PP
TIGR00178 735 fnailea 741
fn+i+++
NCBI__GCF_002591915.1:WP_099019356.1 733 FNQIIDS 739
****997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (740 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: 39.41
//
[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