Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate AO356_22125 AO356_22125 isocitrate dehydrogenase
Query= SwissProt::P16100
(741 letters)
>FitnessBrowser__pseudo5_N2C3_1:AO356_22125
Length = 741
Score = 1212 bits (3135), Expect = 0.0
Identities = 607/736 (82%), Positives = 666/736 (90%), Gaps = 1/736 (0%)
Query: 5 KIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKISD 64
KIIYT TDEAPALATYSLLPI++AFT S+ IAVETRDISLAGR++A+FPE L D + ++D
Sbjct: 6 KIIYTFTDEAPALATYSLLPIVEAFTASADIAVETRDISLAGRILASFPEQLGD-KAVAD 64
Query: 65 DLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDVKA 124
LAELG LA TP+ANIIKLPNISASVPQL+AAIKELQ QGY LPDYPE TD EKD +A
Sbjct: 65 HLAELGDLAVTPEANIIKLPNISASVPQLQAAIKELQAQGYALPDYPETVSTDAEKDARA 124
Query: 125 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFYGS 184
RYDK+KGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAW+ADSKSHVAHM GDFYGS
Sbjct: 125 RYDKVKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAADSKSHVAHMSTGDFYGS 184
Query: 185 EKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAK 244
EKAALI A GSVKIELIA+DG++TVLK KT+VQAGEI+D +VMSKNALR+FIAAEIEDAK
Sbjct: 185 EKAALIDAAGSVKIELIAQDGTATVLKEKTTVQAGEILDCAVMSKNALRDFIAAEIEDAK 244
Query: 245 KQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARI 304
++GVLLSVHLKATMMKVSDPIMFGQIV+EFYKDAL KHA+VL+QIGF++NNGIGDLYARI
Sbjct: 245 QKGVLLSVHLKATMMKVSDPIMFGQIVAEFYKDALAKHAQVLEQIGFNLNNGIGDLYARI 304
Query: 305 KTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364
K LP +Q +IEADIQAVYA RP LAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW
Sbjct: 305 KALPAEQQAQIEADIQAVYAARPSLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364
Query: 365 GPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGSHD 424
G DG+LHDTKAVIPDRCYA +YQ VIEDCKQHGAFDPTTMGSVPNVGLMA+KAEEYGSHD
Sbjct: 365 GTDGQLHDTKAVIPDRCYATIYQAVIEDCKQHGAFDPTTMGSVPNVGLMAKKAEEYGSHD 424
Query: 425 KTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNTPA 484
KTFQI A+GVVRV+D +G+ LLEQ+VEAGDI+RMCQ KDAPIQDWVKLAVNRARA++TPA
Sbjct: 425 KTFQIKANGVVRVSDNTGRTLLEQNVEAGDIFRMCQTKDAPIQDWVKLAVNRARASSTPA 484
Query: 485 VFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVTGN 544
+FWLDP RAHD VI KV+ YLKD+DTSGLDIRI+SPV+A +F+L R REGKDTISVTGN
Sbjct: 485 IFWLDPMRAHDGVVIEKVQTYLKDHDTSGLDIRIMSPVDAMKFTLGRTREGKDTISVTGN 544
Query: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWDSL 604
VLRDYLTDLFPIMELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQ LEE +LRWDSL
Sbjct: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQLLEENFLRWDSL 604
Query: 605 GEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFYLA 664
GEFLALAASLEHLG Y NPKALVLA TLDQATG+ LD NKSP+RKVG IDNRGSHFYL
Sbjct: 605 GEFLALAASLEHLGGTYNNPKALVLAKTLDQATGEFLDRNKSPSRKVGGIDNRGSHFYLT 664
Query: 665 LYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDLTS 724
L+WAQALAAQ +D L+AQF +AK LTDNE KIV EL A QGKPVDI GYY N +LTS
Sbjct: 665 LFWAQALAAQDDDAALKAQFASLAKTLTDNEEKIVAELNAVQGKPVDIGGYYFANPELTS 724
Query: 725 KAIRPSATFNAALAPL 740
KA+RPSATFNAA+A L
Sbjct: 725 KAMRPSATFNAAIAAL 740
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: 1578
Number of extensions: 55
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: 741
Length adjustment: 40
Effective length of query: 701
Effective length of database: 701
Effective search space: 491401
Effective search space used: 491401
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 AO356_22125 AO356_22125 (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.2949.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 1378.4 4.4 0 1378.2 4.4 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 AO356_22125 isocitrate dehydroge
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 AO356_22125 isocitrate dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1378.2 4.4 0 0 5 742 .. 4 740 .. 1 741 [] 0.99
Alignments for each domain:
== domain 1 score: 1378.2 bits; conditional E-value: 0
TIGR00178 5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvdda 67
++kiiyt tdeap+latysllpiv+af+asa i+vetrdislagrila+fpe+l + + v d+
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 4 RSKIIYTFTDEAPALATYSLLPIVEAFTASADIAVETRDISLAGRILASFPEQLGD-KAVADH 65
59****************************************************86.68**** PP
TIGR00178 68 laelGelaktpeaniiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryak 130
laelG+la tpeaniiklpnisasvpql+aaikelq++Gy+lpdype td+ekd +ary+k
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 66 LAELGDLAVTPEANIIKLPNISASVPQLQAAIKELQAQGYALPDYPETVSTDAEKDARARYDK 128
*************************************************************** PP
TIGR00178 131 ikGsavnpvlreGnsdrraplavkeyarkhphkmGewsadskshvahmdagdfyaseksvlld 193
+kGsavnpvlreGnsdrrapl+vk+yarkhphkmG+w+adskshvahm++gdfy+sek++l+d
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 129 VKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAADSKSHVAHMSTGDFYGSEKAALID 191
*************************************************************** PP
TIGR00178 194 aaeevkieliakdGketvlkaklklldgevidssvlskkalvefleeeiedakeegvllslhl 256
aa +vkielia+dG++tvlk+k+++++ge++d++v+sk+al++f+++eiedak++gvlls+hl
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 192 AAGSVKIELIAQDGTATVLKEKTTVQAGEILDCAVMSKNALRDFIAAEIEDAKQKGVLLSVHL 254
*************************************************************** PP
TIGR00178 257 katmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyakieslpaakkeeiea 319
katmmkvsdpi+fG++v +fykd++akha++leq+G++ +nG++dlya+i++lpa ++ +iea
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 255 KATMMKVSDPIMFGQIVAEFYKDALAKHAQVLEQIGFNLNNGIGDLYARIKALPAEQQAQIEA 317
*************************************************************** PP
TIGR00178 320 dlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipds 382
d+++vy+ rp lamv+sdkGitnlhvpsdvivdasmpamir+sGkm+g+dg+l+dtkavipd+
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 318 DIQAVYAARPSLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMWGTDGQLHDTKAVIPDR 380
*************************************************************** PP
TIGR00178 383 syagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGe 445
+ya +yqaviedck++GafdpttmG+vpnvGlma+kaeeyGshdktf+i+a+Gvvrv d++G
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 381 CYATIYQAVIEDCKQHGAFDPTTMGSVPNVGLMAKKAEEYGSHDKTFQIKANGVVRVSDNTGR 443
*************************************************************** PP
TIGR00178 446 vlleeeveagdiwrmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekyl 508
lle++veagdi+rmcq kdapiqdwvklav+rar+s+tpa+fwldp rahd +i+kv++yl
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 444 TLLEQNVEAGDIFRMCQTKDAPIQDWVKLAVNRARASSTPAIFWLDPMRAHDGVVIEKVQTYL 506
*************************************************************** PP
TIGR00178 509 kdhdteGldiqilspvkatrfslerirrGedtisvtGnvlrdyltdlfpilelGtsakmlsvv 571
kdhdt+Gldi+i+spv+a++f+l r r+G+dtisvtGnvlrdyltdlfpi+elGtsakmls+v
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 507 KDHDTSGLDIRIMSPVDAMKFTLGRTREGKDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIV 569
*************************************************************** PP
TIGR00178 572 plmaGGGlfetGaGGsapkhvqqleeenhlrwdslGeflalaaslehvavktgnekakvladt 634
plm+GGGlfetGaGGsapkhvqql een+lrwdslGeflalaasleh++ +++n+ka vla+t
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 570 PLMNGGGLFETGAGGSAPKHVQQLLEENFLRWDSLGEFLALAASLEHLGGTYNNPKALVLAKT 632
*************************************************************** PP
TIGR00178 635 ldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasfasvaealtkne 697
ld+atg +ld +kspsrkvG +dnrgs+fyl+ +waq+laaq +d+ l+a+fas+a++lt+ne
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 633 LDQATGEFLDRNKSPSRKVGGIDNRGSHFYLTLFWAQALAAQDDDAALKAQFASLAKTLTDNE 695
*************************************************************** PP
TIGR00178 698 ekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnaileal 742
ekivael+avqG++vd+gGyy+++ +lt+k++rpsatfna+++al
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22125 696 EKIVAELNAVQGKPVDIGGYYFANPELTSKAMRPSATFNAAIAAL 740
******************************************998 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (744 nodes)
Target sequences: 1 (741 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: 00:00:00.04
# Mc/sec: 11.17
//
[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:
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