Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate H281DRAFT_03806 H281DRAFT_03806 isocitrate dehydrogenase
Query= SwissProt::P16100
(741 letters)
>FitnessBrowser__Burk376:H281DRAFT_03806
Length = 742
Score = 1209 bits (3128), Expect = 0.0
Identities = 606/742 (81%), Positives = 663/742 (89%), Gaps = 1/742 (0%)
Query: 1 MSTP-KIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDT 59
MSTP KIIYTLTDEAPALATYSLLPI+KAFT SS + VETRDISLAGR+IA FP+YLT
Sbjct: 1 MSTPPKIIYTLTDEAPALATYSLLPIVKAFTRSSDVIVETRDISLAGRIIAAFPDYLTAE 60
Query: 60 QKISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTE 119
QK SDDLAELG L T P+ANIIKLPNISASVPQLKAAI EL+ QGYKLP YP+ T+TE
Sbjct: 61 QKGSDDLAELGGLTTRPEANIIKLPNISASVPQLKAAITELRDQGYKLPAYPDVATTETE 120
Query: 120 KDVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNG 179
KDVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHM G
Sbjct: 121 KDVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMSGG 180
Query: 180 DFYGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAE 239
DFYGSEK+ALI A G+VKIEL A DG+ TVLK KT VQAGEIID+SV+SKNALR+FI AE
Sbjct: 181 DFYGSEKSALIAAAGAVKIELTAADGTKTVLKEKTPVQAGEIIDASVLSKNALRSFIEAE 240
Query: 240 IEDAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGD 299
I DAK++GVL SVHLKATMMKVSDPI+FG +VS FYKD LTKHA+ L Q GF+ NNGIGD
Sbjct: 241 IADAKRKGVLFSVHLKATMMKVSDPIIFGHVVSVFYKDVLTKHADALAQAGFNPNNGIGD 300
Query: 300 LYARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRD 359
LYAR+K LP +IEADI+A Y QRPQLAMVNSDKGIT+LHVPSDVIVDASMPAMIR+
Sbjct: 301 LYARLKDLPAETAAQIEADIKAQYEQRPQLAMVNSDKGITSLHVPSDVIVDASMPAMIRE 360
Query: 360 SGKMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEE 419
SGKMWG DG LHD KAVIPDRCYAGVYQ VIEDCK++GAFDP TMG+VPNVGLMAQ AEE
Sbjct: 361 SGKMWGADGALHDAKAVIPDRCYAGVYQAVIEDCKKNGAFDPVTMGTVPNVGLMAQAAEE 420
Query: 420 YGSHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARA 479
YGSHDKTFQIPA+GVVRVTD SG +L+EQ+VEAGDIWRMCQ KDAP+QDWVKLAVNRARA
Sbjct: 421 YGSHDKTFQIPANGVVRVTDASGAVLIEQAVEAGDIWRMCQTKDAPVQDWVKLAVNRARA 480
Query: 480 TNTPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTI 539
TNTPAVFWLD ARAHDAQ+I KVE+YLKD+DT+GLDIRI++PVEAT+FS+ RIR GKDTI
Sbjct: 481 TNTPAVFWLDAARAHDAQIIKKVEQYLKDHDTNGLDIRIMTPVEATKFSVERIRAGKDTI 540
Query: 540 SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYL 599
SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLM+GGG+FETGAGGSAPKHVQQ +EEG+L
Sbjct: 541 SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMFETGAGGSAPKHVQQLVEEGFL 600
Query: 600 RWDSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGS 659
RWDSLGEFLALAASLEHL +AY NPKA VLA TLDQATGK LDN+KSPARKVG +DNRGS
Sbjct: 601 RWDSLGEFLALAASLEHLSSAYHNPKAQVLAKTLDQATGKFLDNDKSPARKVGGLDNRGS 660
Query: 660 HFYLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPN 719
HFYLA+YWA+ALAAQTED LQAQF G+AKA+ DNE KI+ EL AAQGKPVDI GYY PN
Sbjct: 661 HFYLAMYWAEALAAQTEDAALQAQFAGVAKAMADNEAKILEELRAAQGKPVDIGGYYRPN 720
Query: 720 TDLTSKAIRPSATFNAALAPLA 741
+LTSKA+RPSAT N + +A
Sbjct: 721 VELTSKAMRPSATLNEIVDSIA 742
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: 1553
Number of extensions: 47
Number of successful extensions: 2
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: 742
Length adjustment: 40
Effective length of query: 701
Effective length of database: 702
Effective search space: 492102
Effective search space used: 492102
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 H281DRAFT_03806 H281DRAFT_03806 (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.19144.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 1378.9 5.2 0 1378.8 5.2 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_03806 H281DRAFT_03806 isocitrate dehyd
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_03806 H281DRAFT_03806 isocitrate dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1378.8 5.2 0 0 1 742 [. 1 741 [. 1 742 [] 1.00
Alignments for each domain:
== domain 1 score: 1378.8 bits; conditional E-value: 0
TIGR00178 1 mstekakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvdd 66
mst+ +kiiytltdeap+latysllpivkaf+ s+ + vetrdislagri+a fp+ylt eqk +d
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 1 MSTP-PKIIYTLTDEAPALATYSLLPIVKAFTRSSDVIVETRDISLAGRIIAAFPDYLTAEQKGSD 65
7787.9************************************************************ PP
TIGR00178 67 alaelGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakik 132
+laelG l++ peaniiklpnisasvpqlkaai el+d+Gy+lp yp+ ++t++ekd+kary+kik
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 66 DLAELGGLTTRPEANIIKLPNISASVPQLKAAITELRDQGYKLPAYPDVATTETEKDVKARYDKIK 131
****************************************************************** PP
TIGR00178 133 GsavnpvlreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlldaaeev 198
GsavnpvlreGnsdrrapl+vk+yarkhphkmG+wsadskshvahm+ gdfy+seks+l+ aa v
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 132 GSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMSGGDFYGSEKSALIAAAGAV 197
****************************************************************** PP
TIGR00178 199 kieliakdGketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhlkatmmkvs 264
kiel a+dG++tvlk+k+++++ge+id+svlsk+al+ f+e+ei+dak++gvl+s+hlkatmmkvs
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 198 KIELTAADGTKTVLKEKTPVQAGEIIDASVLSKNALRSFIEAEIADAKRKGVLFSVHLKATMMKVS 263
****************************************************************** PP
TIGR00178 265 dpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakieslpaakkeeieadlekvyeerpe 330
dpi+fGhvv+vfykdv++kha+ l q+G++ +nG++dlya+++ lpa +iead+++ ye+rp+
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 264 DPIIFGHVVSVFYKDVLTKHADALAQAGFNPNNGIGDLYARLKDLPAETAAQIEADIKAQYEQRPQ 329
****************************************************************** PP
TIGR00178 331 lamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipdssyagvyqaviedck 396
lamv+sdkGit lhvpsdvivdasmpamir+sGkm+g+dg l+d+kavipd++yagvyqaviedck
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 330 LAMVNSDKGITSLHVPSDVIVDASMPAMIRESGKMWGADGALHDAKAVIPDRCYAGVYQAVIEDCK 395
****************************************************************** PP
TIGR00178 397 knGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiwrmcq 462
knGafdp tmGtvpnvGlmaq aeeyGshdktf+i+a+Gvvrv+d+sG vl+e+ veagdiwrmcq
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 396 KNGAFDPVTMGTVPNVGLMAQAAEEYGSHDKTFQIPANGVVRVTDASGAVLIEQAVEAGDIWRMCQ 461
****************************************************************** PP
TIGR00178 463 vkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatr 528
kdap+qdwvklav+rar+++tpavfwld +rahd+++ikkve+ylkdhdt+Gldi+i+ pv+at+
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 462 TKDAPVQDWVKLAVNRARATNTPAVFWLDAARAHDAQIIKKVEQYLKDHDTNGLDIRIMTPVEATK 527
****************************************************************** PP
TIGR00178 529 fslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqq 594
fs+erir G+dtisvtGnvlrdyltdlfpi+elGtsakmls+vplmaGGG+fetGaGGsapkhvqq
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 528 FSVERIRAGKDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMFETGAGGSAPKHVQQ 593
****************************************************************** PP
TIGR00178 595 leeenhlrwdslGeflalaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrg 660
l+ee++lrwdslGeflalaasleh++ ++ n+ka+vla+tld+atgk+ld++ksp+rkvG ldnrg
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 594 LVEEGFLRWDSLGEFLALAASLEHLSSAYHNPKAQVLAKTLDQATGKFLDNDKSPARKVGGLDNRG 659
****************************************************************** PP
TIGR00178 661 skfylakywaqelaaqtedkelaasfasvaealtkneekivaelaavqGeavdlgGyyapdtdltt 726
s+fyla+ywa++laaqted+ l+a+fa+va+a+++ne+ki +el a+qG++vd+gGyy p+ +lt+
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 660 SHFYLAMYWAEALAAQTEDAALQAQFAGVAKAMADNEAKILEELRAAQGKPVDIGGYYRPNVELTS 725
****************************************************************** PP
TIGR00178 727 kvlrpsatfnaileal 742
k++rpsat+n+i++++
lcl|FitnessBrowser__Burk376:H281DRAFT_03806 726 KAMRPSATLNEIVDSI 741
*************987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (742 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 10.97
//
[ok]
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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