Query psy16645
Match_columns 94
No_of_seqs 120 out of 748
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 18:21:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16645.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16645hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0452|consensus 100.0 4.8E-32 1E-36 224.2 6.0 91 2-94 6-96 (892)
2 PLN00070 aconitate hydratase 100.0 5.5E-30 1.2E-34 219.2 7.1 90 3-94 43-135 (936)
3 PTZ00092 aconitate hydratase-l 99.9 1.1E-28 2.3E-33 210.8 6.1 89 3-94 14-103 (898)
4 PRK09277 aconitate hydratase; 99.9 1.1E-28 2.3E-33 210.7 6.0 90 2-94 4-97 (888)
5 PRK12881 acnA aconitate hydrat 99.9 1.5E-28 3.2E-33 209.9 6.1 91 1-94 2-96 (889)
6 TIGR01341 aconitase_1 aconitat 99.9 5E-28 1.1E-32 206.4 4.3 75 18-94 2-79 (876)
7 TIGR02333 2met_isocit_dHY 2-me 99.9 2.8E-26 6.1E-31 195.3 4.9 75 11-94 7-86 (858)
8 COG1048 AcnA Aconitase A [Ener 99.9 6.4E-23 1.4E-27 174.3 5.2 84 5-94 3-88 (861)
9 PF00330 Aconitase: Aconitase 95.4 0.0015 3.3E-08 53.6 -2.5 36 57-94 5-40 (465)
10 TIGR01340 aconitase_mito aconi 95.4 0.0048 1E-07 53.4 0.3 21 74-94 49-69 (745)
11 PRK07229 aconitate hydratase; 93.6 0.033 7.1E-07 47.6 1.3 21 74-94 22-42 (646)
12 TIGR01342 acon_putative aconit 92.5 0.038 8.3E-07 47.4 0.1 21 74-94 19-39 (658)
13 PRK12466 isopropylmalate isome 89.4 0.12 2.6E-06 42.8 0.3 19 76-94 23-41 (471)
14 PHA01735 hypothetical protein 75.3 4.6 0.0001 25.8 3.2 29 40-68 16-44 (76)
15 TIGR00170 leuC 3-isopropylmala 70.6 1.6 3.4E-05 36.2 0.4 21 74-94 20-40 (465)
16 PF03474 DMA: DMRTA motif; In 62.8 7.3 0.00016 22.0 1.9 16 39-54 17-32 (39)
17 PRK05478 isopropylmalate isome 57.8 3.4 7.4E-05 34.3 0.0 21 74-94 20-40 (466)
18 PF05003 DUF668: Protein of un 51.1 18 0.0004 23.8 2.6 37 31-67 37-81 (89)
19 KOG0453|consensus 39.1 10 0.00022 33.2 0.1 20 74-93 82-101 (778)
20 cd08200 catalase_peroxidase_2 38.9 33 0.00072 27.1 2.9 50 33-85 73-133 (297)
21 COG5140 UFD1 Ubiquitin fusion- 37.3 20 0.00042 28.4 1.3 12 39-50 141-152 (331)
22 TIGR00198 cat_per_HPI catalase 34.1 71 0.0015 28.2 4.3 51 32-85 490-546 (716)
23 PF09336 Vps4_C: Vps4 C termin 31.6 70 0.0015 19.2 2.9 35 31-67 25-59 (62)
24 KOG1816|consensus 28.3 34 0.00074 27.3 1.4 12 39-50 133-144 (308)
25 cd00649 catalase_peroxidase_1 28.0 88 0.0019 25.9 3.7 50 33-85 111-160 (409)
26 PRK15061 catalase/hydroperoxid 27.7 55 0.0012 29.0 2.6 49 33-84 498-557 (726)
27 PRK11413 putative hydratase; P 26.4 38 0.00083 30.0 1.5 19 74-92 51-69 (751)
28 PF15127 DUF4565: Protein of u 25.7 94 0.002 20.6 2.9 33 40-80 53-86 (91)
29 PF00034 Cytochrom_C: Cytochro 25.5 61 0.0013 18.6 1.9 16 53-68 74-89 (91)
30 KOG2796|consensus 24.8 1.8E+02 0.004 23.5 4.9 48 15-62 99-148 (366)
31 cd08309 Death_IRAK Death domai 24.6 64 0.0014 20.8 2.0 15 32-46 4-18 (95)
32 PHA01513 mnt Mnt 23.8 1.4E+02 0.0031 19.3 3.4 36 32-68 10-45 (82)
33 PRK14459 ribosomal RNA large s 22.5 1.1E+02 0.0024 24.7 3.3 61 21-81 241-323 (373)
34 PF08265 YL1_C: YL1 nuclear pr 22.4 40 0.00087 17.8 0.6 7 88-94 4-10 (30)
35 PF04036 DUF372: Domain of unk 21.3 17 0.00036 20.5 -1.1 10 85-94 14-23 (38)
36 PF06881 Elongin_A: RNA polyme 20.8 1.4E+02 0.003 19.5 3.0 27 30-64 3-29 (109)
37 PF03869 Arc: Arc-like DNA bin 20.1 1.9E+02 0.0041 16.5 3.4 36 32-68 9-44 (50)
No 1
>KOG0452|consensus
Probab=99.97 E-value=4.8e-32 Score=224.18 Aligned_cols=91 Identities=64% Similarity=1.048 Sum_probs=86.7
Q ss_pred CCchhhhhcceeeCCeeEEEeeCCCcCCCCCCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhhhccCCCCccccccc
Q psy16645 2 KNPYEHLKKTLNIGEKTYNYYDLPGLGQSYDKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEENQRLEGGVEVPFKP 81 (94)
Q Consensus 2 ~~~~~~~~~~l~~~~~~~~y~~l~~l~~~~~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~~~~~~~~~eIpF~P 81 (94)
+++|....++|+..+..++||||+++..++++||||||||||+++||||++.++++||++|++|..+.+. +.||||+|
T Consensus 6 ~~~f~~~~~~l~~~~~~~kyf~l~~l~~ryd~LP~SIrvLLEsAvRnCD~f~v~k~DVe~IldW~~t~~k--~vEvpFkP 83 (892)
T KOG0452|consen 6 ENPFAQLIETLPKPGGVYKYFDLPKLNSRYDKLPYSIRVLLESAVRNCDNFHVKKKDVENILDWKNTQKK--QVEVPFKP 83 (892)
T ss_pred cccHHHHHhccCCCCCcceeeeccccccccccCchhHHHHHHHHHhcCccceeeHHHHHHHhCccccCcc--ceeecccc
Confidence 5689987889999998999999999988999999999999999999999999999999999999998887 89999999
Q ss_pred ceeecccccCccC
Q psy16645 82 ARVILQDLTGVNI 94 (94)
Q Consensus 82 aRVllQDfTGVPa 94 (94)
+||+|||||||||
T Consensus 84 ARViLQDFTGvPa 96 (892)
T KOG0452|consen 84 ARVILQDFTGVPA 96 (892)
T ss_pred ceeeeecccCCch
Confidence 9999999999997
No 2
>PLN00070 aconitate hydratase
Probab=99.96 E-value=5.5e-30 Score=219.22 Aligned_cols=90 Identities=53% Similarity=0.923 Sum_probs=81.5
Q ss_pred CchhhhhcceeeC-Cee-EEEeeCCCcCC-CCCCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhhhccCCCCccccc
Q psy16645 3 NPYEHLKKTLNIG-EKT-YNYYDLPGLGQ-SYDKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEENQRLEGGVEVPF 79 (94)
Q Consensus 3 ~~~~~~~~~l~~~-~~~-~~y~~l~~l~~-~~~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~~~~~~~~~eIpF 79 (94)
|+|+...++|+++ +++ |+||+|.+++. ++++|||||||||||+||||||+.++++||++|++|.+++.. +.||||
T Consensus 43 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~lP~s~rillE~~lR~~d~~~~~~~~~~~~~~w~~~~~~--~~ei~f 120 (936)
T PLN00070 43 NPFKGILTSLPKPGGGEFGKYYSLPALNDPRIDKLPYSIRILLESAIRNCDNFQVTKEDVEKIIDWENTSPK--QVEIPF 120 (936)
T ss_pred CchhhhhheeeecCCCceEEEEEhhhcccCChhhCCcHHHHHHHHHhhhcCCccCCHHHHHHHHhccccCCC--Cceecc
Confidence 7787644789987 777 99999998853 789999999999999999999999999999999999887766 789999
Q ss_pred ccceeecccccCccC
Q psy16645 80 KPARVILQDLTGVNI 94 (94)
Q Consensus 80 ~PaRVllQDfTGVPa 94 (94)
+|+||+|||||||||
T Consensus 121 ~P~RV~~QD~Tgvpa 135 (936)
T PLN00070 121 KPARVLLQDFTGVPA 135 (936)
T ss_pred CCceEEeecCCCCcc
Confidence 999999999999997
No 3
>PTZ00092 aconitate hydratase-like protein; Provisional
Probab=99.95 E-value=1.1e-28 Score=210.82 Aligned_cols=89 Identities=61% Similarity=1.021 Sum_probs=80.2
Q ss_pred CchhhhhcceeeCCeeEEEeeCCCcCC-CCCCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhhhccCCCCccccccc
Q psy16645 3 NPYEHLKKTLNIGEKTYNYYDLPGLGQ-SYDKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEENQRLEGGVEVPFKP 81 (94)
Q Consensus 3 ~~~~~~~~~l~~~~~~~~y~~l~~l~~-~~~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~~~~~~~~~eIpF~P 81 (94)
|+|....++|+ .++.|+||+|+++.. ++++|||||||||||+||||||..+++++|++|++|.++... +.||||+|
T Consensus 14 ~~~~~~~~~l~-~~~~~~~~~l~~~~~~~~~~lP~s~rvllE~~lr~~d~~~~~~~~~~~~~~w~~~~~~--~~ei~~~p 90 (898)
T PTZ00092 14 NPFEKVLKTLK-DGGSYKYYSLNELHDPRLKKLPYSIRVLLESAVRNCDEFDVTSKDVENILNWEENSKK--QIEIPFKP 90 (898)
T ss_pred CchhhhhccCC-CCCeEEEEEhhhcccCChhhCCchHHHHHHHHhhcCCCcCCCHHHHHHHHcCcccCCC--Cceeeecc
Confidence 56776336788 888999999998853 789999999999999999999999999999999999887766 78999999
Q ss_pred ceeecccccCccC
Q psy16645 82 ARVILQDLTGVNI 94 (94)
Q Consensus 82 aRVllQDfTGVPa 94 (94)
+||+|||||||||
T Consensus 91 ~Rvl~QD~Tgvpa 103 (898)
T PTZ00092 91 ARVLLQDFTGVPA 103 (898)
T ss_pred ceEEeecccCchH
Confidence 9999999999996
No 4
>PRK09277 aconitate hydratase; Validated
Probab=99.95 E-value=1.1e-28 Score=210.66 Aligned_cols=90 Identities=40% Similarity=0.788 Sum_probs=81.4
Q ss_pred CCchhhhhcceeeCCeeEEEeeCCCcCC----CCCCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhhhccCCCCccc
Q psy16645 2 KNPYEHLKKTLNIGEKTYNYYDLPGLGQ----SYDKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEENQRLEGGVEV 77 (94)
Q Consensus 2 ~~~~~~~~~~l~~~~~~~~y~~l~~l~~----~~~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~~~~~~~~~eI 77 (94)
.++|.. .++|++.++.|+||+|.+++. ++++|||||||||||+|||||++.+++++|++|++|.+++.. +.||
T Consensus 4 ~~~~~~-~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lP~sirillE~~lr~~d~~~~~~~~v~~~~~w~~~~~~--~~ei 80 (888)
T PRK09277 4 TDSFKA-RKTLEVGGKSYDYYSLRALEAKGLGDISRLPYSLRVLLENLLRNEDGRSVTEEDIEALAEWLPKAKP--DREI 80 (888)
T ss_pred CCcccc-cceeeeCCeeEEEEEhHHhhhcccCChhhCCcHHHHHHHHHhhcCCCccCCHHHHHHHHhchhcCCC--Ccee
Confidence 467776 578999999999999987742 789999999999999999999999999999999999887666 7899
Q ss_pred ccccceeecccccCccC
Q psy16645 78 PFKPARVILQDLTGVNI 94 (94)
Q Consensus 78 pF~PaRVllQDfTGVPa 94 (94)
||+|+||+|||||||||
T Consensus 81 ~f~p~rvl~QD~TGvpa 97 (888)
T PRK09277 81 PFRPARVVMQDFTGVPA 97 (888)
T ss_pred eeccceeeecccccchH
Confidence 99999999999999996
No 5
>PRK12881 acnA aconitate hydratase; Provisional
Probab=99.95 E-value=1.5e-28 Score=209.95 Aligned_cols=91 Identities=42% Similarity=0.761 Sum_probs=83.2
Q ss_pred CCCchhhhhcceeeCCeeEEEeeCCCcCC----CCCCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhhhccCCCCcc
Q psy16645 1 MKNPYEHLKKTLNIGEKTYNYYDLPGLGQ----SYDKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEENQRLEGGVE 76 (94)
Q Consensus 1 ~~~~~~~~~~~l~~~~~~~~y~~l~~l~~----~~~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~~~~~~~~~e 76 (94)
|.|+|.. .++|++.++.|+||+|.+++. ++++|||||||||||+||||||..|++++|+++++|.+++.. +.|
T Consensus 2 ~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lP~s~rvllE~~lr~~d~~~v~~~~~~~~~~w~~~~~~--~~e 78 (889)
T PRK12881 2 AHNLHKT-LKEFDVGGKTYKFYSLPALGKELGGDLARLPVSLRVLLENLLRNEDGKKVTEEHLEALANWLPERKS--DDE 78 (889)
T ss_pred CCCcccc-ccceeeCCeeEEEEEhHHhhccccCChhhCCchHHHHHHHHhhcCCCCCCCHHHHHHHHhchhcCCC--Cce
Confidence 5678886 578999999999999998842 789999999999999999999999999999999999887766 789
Q ss_pred cccccceeecccccCccC
Q psy16645 77 VPFKPARVILQDLTGVNI 94 (94)
Q Consensus 77 IpF~PaRVllQDfTGVPa 94 (94)
|||+|+||+||||||+||
T Consensus 79 i~~~pdRvllqD~Tg~~a 96 (889)
T PRK12881 79 IPFVPARVVMQDFTGVPA 96 (889)
T ss_pred eccccceeeeecccCccH
Confidence 999999999999999996
No 6
>TIGR01341 aconitase_1 aconitate hydratase 1. This model represents one form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It is found in bacteria, archaea, and eukaryotic cytosol. It has been shown to act also as an iron-responsive element binding protein in animals and may have the same role in other eukaryotes.
Probab=99.94 E-value=5e-28 Score=206.39 Aligned_cols=75 Identities=51% Similarity=0.894 Sum_probs=69.7
Q ss_pred eEEEeeCCCcCC---CCCCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhhhccCCCCcccccccceeecccccCccC
Q psy16645 18 TYNYYDLPGLGQ---SYDKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEENQRLEGGVEVPFKPARVILQDLTGVNI 94 (94)
Q Consensus 18 ~~~y~~l~~l~~---~~~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~~~~~~~~~eIpF~PaRVllQDfTGVPa 94 (94)
+|+||+|++|+. ++++|||||||||||+||||||+.+++++|++|++|.++... +.||||+|+||+|||||||||
T Consensus 2 ~~~~~~l~~l~~~~~~~~~lP~s~rvllE~~lr~~d~~~~~~~~~~~~~~w~~~~~~--~~ei~f~p~RvllQD~TGvpa 79 (876)
T TIGR01341 2 TYYYYSLKALEESGGKISKLPYSIRILLESVLRNLDGFSITEEDIENILKWKIGEVA--DTEIAFKPARVVMQDFTGVPA 79 (876)
T ss_pred ceEEEehHHhhcccCChhhCCcHHHHHHHHHHhcCCCCCCCHHHHHHHHcCcccCCC--CceeccCchhheeccccCchH
Confidence 599999998853 789999999999999999999999999999999999877765 789999999999999999996
No 7
>TIGR02333 2met_isocit_dHY 2-methylisocitrate dehydratase, Fe/S-dependent. Members of this family appear in an operon for the degradation of propionyl-CoA via 2-methylcitrate. This family is homologous to aconitases A and B and appears to act the part as 2-methylisocitrate dehydratase, the enzyme after PrpD and before PrpB. In Escherichia coli, which lacks a member of this family, 2-methylisocitrate dehydratase activity was traced to aconitase B (TIGR00117) (PubMed:12473114).
Probab=99.92 E-value=2.8e-26 Score=195.34 Aligned_cols=75 Identities=32% Similarity=0.643 Sum_probs=66.3
Q ss_pred ceeeCCeeEEEeeCC-CcCC----CCCCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhhhccCCCCcccccccceee
Q psy16645 11 TLNIGEKTYNYYDLP-GLGQ----SYDKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEENQRLEGGVEVPFKPARVI 85 (94)
Q Consensus 11 ~l~~~~~~~~y~~l~-~l~~----~~~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~~~~~~~~~eIpF~PaRVl 85 (94)
.+. ++.|+||+|. +++. ++++|||||||||||+||||||..++++ |+++++| .. +.||||+|+||+
T Consensus 7 ~~~--~~~~~~~~~~~~~~~~~~~~~~~lP~s~rillE~~lr~~d~~~~~~~-~~~~~~w----~~--~~ei~f~P~RV~ 77 (858)
T TIGR02333 7 PLP--GTDLDYFDTRAAVEAIKPGAYDKLPYTSRILAENLVRRCDPETLSAS-LLQIIER----KR--DLDFPWYPARVV 77 (858)
T ss_pred cCC--CCceEEEEcHHhhhhcccCChhhCCchHHHHHHHHhhcCCChhhHHH-HHHHHcC----CC--CCeeccCcceee
Confidence 445 6679999996 6642 7899999999999999999999999988 9999999 22 579999999999
Q ss_pred cccccCccC
Q psy16645 86 LQDLTGVNI 94 (94)
Q Consensus 86 lQDfTGVPa 94 (94)
|||||||||
T Consensus 78 mqD~Tgvpa 86 (858)
T TIGR02333 78 CHDILGQTA 86 (858)
T ss_pred eccccCcch
Confidence 999999997
No 8
>COG1048 AcnA Aconitase A [Energy production and conversion]
Probab=99.87 E-value=6.4e-23 Score=174.31 Aligned_cols=84 Identities=43% Similarity=0.843 Sum_probs=76.3
Q ss_pred hhhhhcceeeCCeeEEEeeCCCcCC--CCCCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhhhccCCCCcccccccc
Q psy16645 5 YEHLKKTLNIGEKTYNYYDLPGLGQ--SYDKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEENQRLEGGVEVPFKPA 82 (94)
Q Consensus 5 ~~~~~~~l~~~~~~~~y~~l~~l~~--~~~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~~~~~~~~~eIpF~Pa 82 (94)
|.. ++++.+++..|+||++++++. .+++||||+|||+||++|++|+ +++++++++.|.+++.. +.||+|+|+
T Consensus 3 ~~~-~~~~~~~~~~~~y~~l~~~~~~~~~~~Lp~s~kiL~e~l~r~~d~---~~~~i~~~~~w~~~~~~--~~ei~~~p~ 76 (861)
T COG1048 3 FKA-RKTLTVGGKTYYYYDLPKLEESGKISKLPYSLKILLENLLRGEDG---TEEHIEALARWLPSGKP--EKEIAFRPA 76 (861)
T ss_pred cch-hhhcccCCceeEEeehhhhhhccccccCChhHHHHHHHhcccccc---chhHHHHHhccccccCc--ccccccccc
Confidence 443 678999999999999999965 6899999999999999999998 89999999999987766 789999999
Q ss_pred eeecccccCccC
Q psy16645 83 RVILQDLTGVNI 94 (94)
Q Consensus 83 RVllQDfTGVPa 94 (94)
||+||||||||+
T Consensus 77 RVvmQD~tgvpa 88 (861)
T COG1048 77 RVVMQDFTGVPA 88 (861)
T ss_pred eeeeecccCCCe
Confidence 999999999995
No 9
>PF00330 Aconitase: Aconitase family (aconitate hydratase); InterPro: IPR001030 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [, ]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) []. Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway []. The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [, ]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated []. IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis []. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [, ]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. 3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family []. Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively [, ]. LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis []. Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus []. This entry represents a region containing 3 domains, each with a 3-layer alpha/beta/alpha topology. This regions represents the [4Fe-4S] cluster-binding region found at the N-terminal of eukaryotic mAcn, cAcn/IPR1 and IRP2, and bacterial AcnA, but in the C-terminal of bacterial AcnB. This domain is also found in the large subunit of isopropylmalate dehydratase (LeuC). More information about these proteins can be found at Protein of the Month: Aconitase [].; GO: 0008152 metabolic process; PDB: 1L5J_B 1B0M_A 1B0J_A 1B0K_A 7ACN_A 6ACN_A 5ACN_A 3SNP_B 3SN2_A 2B3Y_A ....
Probab=95.41 E-value=0.0015 Score=53.63 Aligned_cols=36 Identities=31% Similarity=0.326 Sum_probs=22.9
Q ss_pred HHHHHHHhhhhhccCCCCcccccccceeecccccCccC
Q psy16645 57 SHVENILKWEENQRLEGGVEVPFKPARVILQDLTGVNI 94 (94)
Q Consensus 57 ~~v~~l~~w~~~~~~~~~~eIpF~PaRVllQDfTGVPa 94 (94)
+.+.+.+.|...... +.+|.|+|.||++||+||.||
T Consensus 5 KI~~~h~~~~~~~~~--~~~v~i~~D~~l~hD~Tgp~a 40 (465)
T PF00330_consen 5 KILARHAGREVVARG--GDIVYIRPDRVLLHDITGPPA 40 (465)
T ss_dssp HHHHCCCTHCCHTTT--TSEEEE--SEEEEEHHHHHHH
T ss_pred HHHHHHhCCCccCCC--CeEEEEEeceEEeecccCccc
Confidence 334444445442233 568999999999999999764
No 10
>TIGR01340 aconitase_mito aconitate hydratase, mitochondrial. This model represents mitochondrial forms of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase.
Probab=95.37 E-value=0.0048 Score=53.44 Aligned_cols=21 Identities=24% Similarity=0.354 Sum_probs=19.1
Q ss_pred CcccccccceeecccccCccC
Q psy16645 74 GVEVPFKPARVILQDLTGVNI 94 (94)
Q Consensus 74 ~~eIpF~PaRVllQDfTGVPa 94 (94)
+.+|+|+|.||+|||+||+||
T Consensus 49 g~~v~~~~d~v~~~D~tg~~a 69 (745)
T TIGR01340 49 KSYLKLRPDRVAMQDASAQMA 69 (745)
T ss_pred CCEEEEeccEEEEeccccHHH
Confidence 468999999999999999875
No 11
>PRK07229 aconitate hydratase; Validated
Probab=93.56 E-value=0.033 Score=47.58 Aligned_cols=21 Identities=29% Similarity=0.442 Sum_probs=18.7
Q ss_pred CcccccccceeecccccCccC
Q psy16645 74 GVEVPFKPARVILQDLTGVNI 94 (94)
Q Consensus 74 ~~eIpF~PaRVllQDfTGVPa 94 (94)
+.+|.++|.||+|||+||++|
T Consensus 22 G~~v~~~vd~v~~~D~t~~~a 42 (646)
T PRK07229 22 GEEIAIRIDQTLTQDATGTMA 42 (646)
T ss_pred CCEEEEECcEEEEeccchHHH
Confidence 457999999999999999874
No 12
>TIGR01342 acon_putative aconitate hydratase, putative, Aquifex type. This model represents a small family of proteins homologous (and likely functionally equivalent to) aconitase 1. Members are found, so far in the anaerobe Clostridium acetobutylicum, in the microaerophilic, early-branching bacterium Aquifex aeolicus, and in the halophilic archaeon Halobacterium sp. NRC-1. No member is experimentally characterized.
Probab=92.47 E-value=0.038 Score=47.36 Aligned_cols=21 Identities=29% Similarity=0.401 Sum_probs=18.8
Q ss_pred CcccccccceeecccccCccC
Q psy16645 74 GVEVPFKPARVILQDLTGVNI 94 (94)
Q Consensus 74 ~~eIpF~PaRVllQDfTGVPa 94 (94)
+.+|.++|.||+|||+||++|
T Consensus 19 G~~v~~~vD~v~~hD~Tg~~a 39 (658)
T TIGR01342 19 GEEIAIEIDQTLSQDATGTMC 39 (658)
T ss_pred CCEEEEEccEEEEeccchHHH
Confidence 458999999999999999874
No 13
>PRK12466 isopropylmalate isomerase large subunit; Provisional
Probab=89.41 E-value=0.12 Score=42.81 Aligned_cols=19 Identities=21% Similarity=0.219 Sum_probs=17.7
Q ss_pred ccccccceeecccccCccC
Q psy16645 76 EVPFKPARVILQDLTGVNI 94 (94)
Q Consensus 76 eIpF~PaRVllQDfTGVPa 94 (94)
+|.++|.||+|||+||.+|
T Consensus 23 ~v~~~vD~~~~hD~t~p~a 41 (471)
T PRK12466 23 HVLLYIDRHLLNEYTSPQA 41 (471)
T ss_pred EEEEeccEEEEeccccHHH
Confidence 8999999999999999864
No 14
>PHA01735 hypothetical protein
Probab=75.31 E-value=4.6 Score=25.83 Aligned_cols=29 Identities=7% Similarity=0.207 Sum_probs=22.9
Q ss_pred HHHHHHHhhcCcccccHHHHHHHHhhhhh
Q psy16645 40 VLLESAVRNCDEFQVKKSHVENILKWEEN 68 (94)
Q Consensus 40 ILLEn~lR~~d~~~v~~~~v~~l~~w~~~ 68 (94)
.|-+.++|+.-...-|..|+.+-.+|..+
T Consensus 16 ~lt~El~~RiksgeATtaDL~AA~d~Lk~ 44 (76)
T PHA01735 16 LLTNELLSRIKSGEATTADLRAACDWLKS 44 (76)
T ss_pred HHHHHHHHHHhcCcccHHHHHHHHHHHHH
Confidence 45677788876667789999999999864
No 15
>TIGR00170 leuC 3-isopropylmalate dehydratase, large subunit. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. These homologs are now described by a separate model of subfamily (rather than equivalog) homology type, and the priors and cutoffs for this model have been changed to focus this equivalog family more narrowly.
Probab=70.62 E-value=1.6 Score=36.23 Aligned_cols=21 Identities=14% Similarity=0.200 Sum_probs=18.1
Q ss_pred CcccccccceeecccccCccC
Q psy16645 74 GVEVPFKPARVILQDLTGVNI 94 (94)
Q Consensus 74 ~~eIpF~PaRVllQDfTGVPa 94 (94)
+..+.+++.|++|||+||.+|
T Consensus 20 g~~v~~~vD~~~~hD~t~~~a 40 (465)
T TIGR00170 20 GETPLLYIDRHLIHEVTSPQA 40 (465)
T ss_pred CCEEEEEeeeeeecccchHHH
Confidence 456899999999999999764
No 16
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=62.75 E-value=7.3 Score=22.03 Aligned_cols=16 Identities=31% Similarity=0.503 Sum_probs=13.4
Q ss_pred HHHHHHHHhhcCcccc
Q psy16645 39 RVLLESAVRNCDEFQV 54 (94)
Q Consensus 39 RILLEn~lR~~d~~~v 54 (94)
|=-||.+|+.|+|+.+
T Consensus 17 r~~Le~iL~~C~GDvv 32 (39)
T PF03474_consen 17 RSVLELILQRCNGDVV 32 (39)
T ss_pred hHHHHHHHHHcCCcHH
Confidence 4568999999998876
No 17
>PRK05478 isopropylmalate isomerase large subunit; Validated
Probab=57.78 E-value=3.4 Score=34.29 Aligned_cols=21 Identities=10% Similarity=0.036 Sum_probs=18.0
Q ss_pred CcccccccceeecccccCccC
Q psy16645 74 GVEVPFKPARVILQDLTGVNI 94 (94)
Q Consensus 74 ~~eIpF~PaRVllQDfTGVPa 94 (94)
+..|-+++.|++|||.||.+|
T Consensus 20 g~~v~~~vD~~~~hD~t~~~a 40 (466)
T PRK05478 20 DGPDLLYIDRHLVHEVTSPQA 40 (466)
T ss_pred CCEEEEEeccceeecccHHHH
Confidence 457899999999999999753
No 18
>PF05003 DUF668: Protein of unknown function (DUF668); InterPro: IPR007700 This is a family of uncharacterised plant proteins of unknown function.
Probab=51.07 E-value=18 Score=23.83 Aligned_cols=37 Identities=38% Similarity=0.533 Sum_probs=27.1
Q ss_pred CCCCchHHHHHHHHHHhhcCcc----cc----cHHHHHHHHhhhh
Q psy16645 31 YDKLPFSIRVLLESAVRNCDEF----QV----KKSHVENILKWEE 67 (94)
Q Consensus 31 ~~~LP~siRILLEn~lR~~d~~----~v----~~~~v~~l~~w~~ 67 (94)
+.-||-+||.-|.+-||..... .. -++.++.++.|..
T Consensus 37 Y~mLP~~ir~aLr~kL~~~~~~~~~d~~~a~~~~~~m~kiL~WL~ 81 (89)
T PF05003_consen 37 YQMLPPSIRSALRSKLRSYWKKAIYDELLAAEWKDAMEKILEWLA 81 (89)
T ss_pred HhhCcHHHHHHHHHhccccccccccchhhHHHHHHHHHHHHHHHH
Confidence 4789999999999999976433 11 2456778888864
No 19
>KOG0453|consensus
Probab=39.08 E-value=10 Score=33.22 Aligned_cols=20 Identities=30% Similarity=0.513 Sum_probs=16.3
Q ss_pred CcccccccceeecccccCcc
Q psy16645 74 GVEVPFKPARVILQDLTGVN 93 (94)
Q Consensus 74 ~~eIpF~PaRVllQDfTGVP 93 (94)
..=+-.+|.||.|||-|--|
T Consensus 82 ~~Yl~lrPdrva~qDasaqm 101 (778)
T KOG0453|consen 82 GSYLKLRPDRVAMQDASAQM 101 (778)
T ss_pred cceEEEcccceecccchhhH
Confidence 44588999999999998544
No 20
>cd08200 catalase_peroxidase_2 C-terminal non-catalytic domain of catalase-peroxidases. This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. These enzymes are found in many archaeal and bacterial organisms where they neutralize potentially lethal hydrogen peroxide molecules generated during photosynthesis or stationary phase. Along with related intracellular fungal and plant peroxidases, catalase-peroxidases belong to plant peroxidase superfamily. Unlike the eukaryotic enzymes, they are typically comprised of two homologous domains that probably arose via a single gene duplication event. The heme binding motif is present only in the N-terminal domain; the function of the C-terminal do
Probab=38.93 E-value=33 Score=27.13 Aligned_cols=50 Identities=18% Similarity=0.276 Sum_probs=32.0
Q ss_pred CCchHHHHHHHHHHhhcC-----cccccHHHHHHHHhhhh----h--ccCCCCcccccccceee
Q psy16645 33 KLPFSIRVLLESAVRNCD-----EFQVKKSHVENILKWEE----N--QRLEGGVEVPFKPARVI 85 (94)
Q Consensus 33 ~LP~siRILLEn~lR~~d-----~~~v~~~~v~~l~~w~~----~--~~~~~~~eIpF~PaRVl 85 (94)
.|.-.++ +||-+-.... +..|+-.|+-.|+.--. . +.- ..+|||.|+|+=
T Consensus 73 ~L~~~~~-~Le~ik~~~~~~~~~~~~vS~ADLivLaG~vAiE~agg~ag~--~p~Ipf~pGR~D 133 (297)
T cd08200 73 ELAKVLA-VLEGIQKEFNESQSGGKKVSLADLIVLGGCAAVEKAAKDAGV--DIKVPFTPGRTD 133 (297)
T ss_pred HHHHHHH-HHHHHHHHhcccccCCccccHHHHHHHHhHHHHHHHHhccCC--CceeccCCCCCC
Confidence 3777776 5788888764 44788888765554311 0 111 258999999973
No 21
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=37.33 E-value=20 Score=28.35 Aligned_cols=12 Identities=33% Similarity=0.656 Sum_probs=10.5
Q ss_pred HHHHHHHHhhcC
Q psy16645 39 RVLLESAVRNCD 50 (94)
Q Consensus 39 RILLEn~lR~~d 50 (94)
|+.|||+|||..
T Consensus 141 kavLEn~LRNfs 152 (331)
T COG5140 141 KAVLENCLRNFS 152 (331)
T ss_pred HHHHHHHHhhcc
Confidence 788999999964
No 22
>TIGR00198 cat_per_HPI catalase/peroxidase HPI. Note that the translation PID:g296476 from accession X71420 from Rhodobacter capsulatus B10 contains extensive frameshift differences from the rest of the orthologous family.
Probab=34.07 E-value=71 Score=28.24 Aligned_cols=51 Identities=24% Similarity=0.238 Sum_probs=33.1
Q ss_pred CCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhh---h---ccCCCCcccccccceee
Q psy16645 32 DKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEE---N---QRLEGGVEVPFKPARVI 85 (94)
Q Consensus 32 ~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~---~---~~~~~~~eIpF~PaRVl 85 (94)
..|.-.+.+ ||-+........|+-.|+-.|+.--. . +.. .++|||.|+|+=
T Consensus 490 ~gL~~vl~~-Le~Ik~~f~~~~vS~ADLivLaG~vAVE~aa~~gG~--~~~Vpf~pGR~D 546 (716)
T TIGR00198 490 TRLAKVLAV-LEKIQAEFAKGPVSLADLIVLGGGAAVEKAALDAGI--SVNVPFLPGRVD 546 (716)
T ss_pred HHHHHHHHH-HHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHhCCC--CcccCcCCCCCc
Confidence 456666655 79988887644678777665554311 1 111 358999999974
No 23
>PF09336 Vps4_C: Vps4 C terminal oligomerisation domain; InterPro: IPR015415 This domain is found at the C-terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation []. ; PDB: 1XWI_A 3EIH_C 2QPA_C 3EIE_A 2RKO_A 2QP9_X 3MHV_C 3CF3_C 3CF1_A 3CF2_A ....
Probab=31.57 E-value=70 Score=19.20 Aligned_cols=35 Identities=14% Similarity=0.411 Sum_probs=23.6
Q ss_pred CCCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhh
Q psy16645 31 YDKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEE 67 (94)
Q Consensus 31 ~~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~ 67 (94)
+..-|.+++=+ +.+|++. ...|++++|+....|..
T Consensus 25 l~~p~it~~DF-~~Al~~~-kpSVs~~dl~~ye~w~~ 59 (62)
T PF09336_consen 25 LKEPPITMEDF-EEALKKV-KPSVSQEDLKKYEEWTK 59 (62)
T ss_dssp B-HHHBCHHHH-HHHHHTC-GGSS-HHHHHHHHHHHH
T ss_pred ccCCCCCHHHH-HHHHHHc-CCCCCHHHHHHHHHHHH
Confidence 43346666655 4556665 47899999999999974
No 24
>KOG1816|consensus
Probab=28.29 E-value=34 Score=27.27 Aligned_cols=12 Identities=42% Similarity=0.695 Sum_probs=10.2
Q ss_pred HHHHHHHHhhcC
Q psy16645 39 RVLLESAVRNCD 50 (94)
Q Consensus 39 RILLEn~lR~~d 50 (94)
|..|||+|||..
T Consensus 133 KAvLE~~LRn~a 144 (308)
T KOG1816|consen 133 KAVLENALRNYA 144 (308)
T ss_pred HHHHHHHHhhcc
Confidence 678999999963
No 25
>cd00649 catalase_peroxidase_1 N-terminal catalytic domain of catalase-peroxidases. This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. These enzymes are found in many archaeal and bacterial organisms, where they neutralize potentially lethal hydrogen peroxide molecules generated during photosynthesis or stationary phase. Along with related intracellular fungal and plant peroxidases, catalase-peroxidases belong to class I of the plant peroxidase superfamily. Unlike the eukaryotic enzymes, they are typically comprised of two homologous domains that probably arose via a single gene duplication event. The heme binding motif is present only in the N-terminal domain; the function of the C
Probab=27.98 E-value=88 Score=25.88 Aligned_cols=50 Identities=14% Similarity=0.024 Sum_probs=33.6
Q ss_pred CCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhhhccCCCCcccccccceee
Q psy16645 33 KLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEENQRLEGGVEVPFKPARVI 85 (94)
Q Consensus 33 ~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~~~~~~~~~eIpF~PaRVl 85 (94)
.|.-.++ +||-+...+. ..|+-.|+-.|+.--.-... |...|||.|+|+=
T Consensus 111 gL~~a~~-~L~pik~k~~-~~iS~ADL~~LaG~~AiE~~-Ggp~ipf~~GR~D 160 (409)
T cd00649 111 NLDKARR-LLWPIKQKYG-NKISWADLMILAGNVALESM-GFKTFGFAGGRED 160 (409)
T ss_pred hHHHHHH-HHHHHHHHcC-CCccHHHHHHHHHHHHHHHc-CCCcccccCCCCc
Confidence 5666666 5788888774 45888887777654321111 2578999999973
No 26
>PRK15061 catalase/hydroperoxidase HPI(I); Provisional
Probab=27.73 E-value=55 Score=29.00 Aligned_cols=49 Identities=22% Similarity=0.234 Sum_probs=31.7
Q ss_pred CCchHHHHHHHHHHhhc-----CcccccHHHHHHHHhhhh---h---ccCCCCccccccccee
Q psy16645 33 KLPFSIRVLLESAVRNC-----DEFQVKKSHVENILKWEE---N---QRLEGGVEVPFKPARV 84 (94)
Q Consensus 33 ~LP~siRILLEn~lR~~-----d~~~v~~~~v~~l~~w~~---~---~~~~~~~eIpF~PaRV 84 (94)
.|--.+++ ||-+.... ++..|+-.|+-.|+.--. . +.. +.+|||.|+|+
T Consensus 498 ~L~~vl~~-LE~Ik~~f~~~~~~~~~vS~ADLivLaG~vAIE~aa~~aG~--~~~VPf~pGR~ 557 (726)
T PRK15061 498 QLAKVLAV-LEGIQAEFNAAQSGGKKVSLADLIVLGGNAAVEQAAKAAGH--DVTVPFTPGRT 557 (726)
T ss_pred HHHHHHHH-HHHHHHHHhhccCCCCceeHHHHHHHHHHHHHHHHHHhCCC--CcccCcCCCCC
Confidence 57666655 68887765 345788888766554311 1 111 36899999996
No 27
>PRK11413 putative hydratase; Provisional
Probab=26.44 E-value=38 Score=29.98 Aligned_cols=19 Identities=21% Similarity=0.076 Sum_probs=16.7
Q ss_pred CcccccccceeecccccCc
Q psy16645 74 GVEVPFKPARVILQDLTGV 92 (94)
Q Consensus 74 ~~eIpF~PaRVllQDfTGV 92 (94)
..-|-.++.++++||.||+
T Consensus 51 g~~v~~~vD~~~~~D~t~~ 69 (751)
T PRK11413 51 MDKLKIKFDSLASHDITFV 69 (751)
T ss_pred CCEEEEEcceeeeehhhHH
Confidence 3469999999999999986
No 28
>PF15127 DUF4565: Protein of unknown function (DUF4565)
Probab=25.69 E-value=94 Score=20.62 Aligned_cols=33 Identities=27% Similarity=0.468 Sum_probs=22.6
Q ss_pred HHHHHHHhhcCcccccHHHHH-HHHhhhhhccCCCCcccccc
Q psy16645 40 VLLESAVRNCDEFQVKKSHVE-NILKWEENQRLEGGVEVPFK 80 (94)
Q Consensus 40 ILLEn~lR~~d~~~v~~~~v~-~l~~w~~~~~~~~~~eIpF~ 80 (94)
|+||-+-|= ++|-|. ||..|...+.. =.+|||-
T Consensus 53 vvlEyA~rL------SqEIl~dAlqQWA~~n~k--Y~DIPYI 86 (91)
T PF15127_consen 53 VVLEYAHRL------SQEILSDALQQWAENNIK--YSDIPYI 86 (91)
T ss_pred hhHHHHHHH------HHHHHHHHHHHHHHhCcc--ccCCCcc
Confidence 678887764 334343 79999887765 5678885
No 29
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=25.52 E-value=61 Score=18.55 Aligned_cols=16 Identities=0% Similarity=0.214 Sum_probs=13.7
Q ss_pred cccHHHHHHHHhhhhh
Q psy16645 53 QVKKSHVENILKWEEN 68 (94)
Q Consensus 53 ~v~~~~v~~l~~w~~~ 68 (94)
.++++++.+|++|..+
T Consensus 74 ~ls~~e~~~l~ayl~s 89 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRS 89 (91)
T ss_dssp TSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH
Confidence 4899999999999754
No 30
>KOG2796|consensus
Probab=24.76 E-value=1.8e+02 Score=23.48 Aligned_cols=48 Identities=17% Similarity=0.216 Sum_probs=27.8
Q ss_pred CCeeEEEeeCCCcCC--CCCCCchHHHHHHHHHHhhcCcccccHHHHHHH
Q psy16645 15 GEKTYNYYDLPGLGQ--SYDKLPFSIRVLLESAVRNCDEFQVKKSHVENI 62 (94)
Q Consensus 15 ~~~~~~y~~l~~l~~--~~~~LP~siRILLEn~lR~~d~~~v~~~~v~~l 62 (94)
++..+.|-..|.+-. .=+=.|||+|+|=-.+.|......-+-+.+.++
T Consensus 99 D~pdl~Yey~p~iyp~rrGSmVPFsmR~lhAe~~~~lgnpqesLdRl~~L 148 (366)
T KOG2796|consen 99 DQPDLYYEYYPHVYPGRRGSMVPFSMRILHAELQQYLGNPQESLDRLHKL 148 (366)
T ss_pred CCcceeeeeccccCCCCcCccccHHHHHHHHHHHHhcCCcHHHHHHHHHH
Confidence 344444444444422 226689999999888888875544333333333
No 31
>cd08309 Death_IRAK Death domain of Interleukin-1 Receptor-Associated Kinases. Death Domains (DDs) found in Interleukin-1 (IL-1) Receptor-Associated Kinases (IRAK1-4) and similar proteins. IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. All four types are involved in signal transduction involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein kinase pathways. IRAK1 and IRAK4 are active kinases while IRAK2 and IRAK-M (also called IRAK3) are inactive. In general, IRAKs are expressed ubiquitously, except for IRAK-M which is detected only in macrophages. The insect homologs, Pelle and Tube, are important components of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and also in the innate immune response. Most members have an N-terminal DD followed by a kinase domain. In general, DDs are protein-protein interaction domains found in a variety of domain a
Probab=24.61 E-value=64 Score=20.77 Aligned_cols=15 Identities=27% Similarity=0.487 Sum_probs=7.6
Q ss_pred CCCchHHHHHHHHHH
Q psy16645 32 DKLPFSIRVLLESAV 46 (94)
Q Consensus 32 ~~LP~siRILLEn~l 46 (94)
-+||+++|==|..+|
T Consensus 4 ~~Lp~~~~~~L~~~L 18 (95)
T cd08309 4 RQLPYSVLARLCKVL 18 (95)
T ss_pred eeCCHHHHHHHHHHh
Confidence 345555554444444
No 32
>PHA01513 mnt Mnt
Probab=23.84 E-value=1.4e+02 Score=19.32 Aligned_cols=36 Identities=11% Similarity=0.170 Sum_probs=29.8
Q ss_pred CCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhhh
Q psy16645 32 DKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEEN 68 (94)
Q Consensus 32 ~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~~ 68 (94)
=|||-.|+--|+.+.... |..++.+-+..|.+|...
T Consensus 10 LRLP~eLk~rL~~aA~~n-GRSmNaeIv~~Le~al~~ 45 (82)
T PHA01513 10 LRLPYELKEKLKQRAKAN-GRSLNAELVQIVQDALSK 45 (82)
T ss_pred eeCCHHHHHHHHHHHHHh-CCCHHHHHHHHHHHHhcC
Confidence 589999999999988764 788889988888888653
No 33
>PRK14459 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=22.49 E-value=1.1e+02 Score=24.75 Aligned_cols=61 Identities=11% Similarity=0.130 Sum_probs=36.6
Q ss_pred EeeCCCcCCCC--CCCc----hHHHHHHHHHHhhc--------------CcccccHHHHHHHHhhhhhccCC-CC-cccc
Q psy16645 21 YYDLPGLGQSY--DKLP----FSIRVLLESAVRNC--------------DEFQVKKSHVENILKWEENQRLE-GG-VEVP 78 (94)
Q Consensus 21 y~~l~~l~~~~--~~LP----~siRILLEn~lR~~--------------d~~~v~~~~v~~l~~w~~~~~~~-~~-~eIp 78 (94)
.+||++..... .-.| |++.-++|++.+-. +|..-+++++++|+++...-... -. .=||
T Consensus 241 avSLha~d~e~R~~l~p~n~~~~l~~ll~a~~~~~~~~grrv~ieyvLi~GvNDs~e~a~~L~~llk~~~~~~~~VNLIp 320 (373)
T PRK14459 241 AVSLHAPDDELRDELVPVNTRWKVDEVLDAARYYADATGRRVSIEYALIRDINDQPWRADLLGKKLHGRGGGWVHVNLIP 320 (373)
T ss_pred EEEeCCCCHHHHHHhcCcccCCCHHHHHHHHHHHHHHhCCEEEEEEEEeCCCCCCHHHHHHHHHHHhhccCCCeEEEEEc
Confidence 56676664211 3367 88999999866543 35566788888887776533100 01 1377
Q ss_pred ccc
Q psy16645 79 FKP 81 (94)
Q Consensus 79 F~P 81 (94)
|.|
T Consensus 321 yNp 323 (373)
T PRK14459 321 LNP 323 (373)
T ss_pred cCC
Confidence 777
No 34
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=22.41 E-value=40 Score=17.78 Aligned_cols=7 Identities=43% Similarity=0.795 Sum_probs=5.4
Q ss_pred cccCccC
Q psy16645 88 DLTGVNI 94 (94)
Q Consensus 88 DfTGVPa 94 (94)
|.||.||
T Consensus 4 ~iTglpA 10 (30)
T PF08265_consen 4 DITGLPA 10 (30)
T ss_pred cccCCCc
Confidence 6788876
No 35
>PF04036 DUF372: Domain of unknown function (DUF372); InterPro: IPR007179 This is a group of proteins of unknown function. It is found N-terminal to another domain of unknown function (IPR007181 from INTERPRO).; PDB: 2I52_B 2IEC_D 2OGF_C.
Probab=21.33 E-value=17 Score=20.50 Aligned_cols=10 Identities=10% Similarity=0.524 Sum_probs=6.3
Q ss_pred ecccccCccC
Q psy16645 85 ILQDLTGVNI 94 (94)
Q Consensus 85 llQDfTGVPa 94 (94)
|.|-|+|.|+
T Consensus 14 LyHQF~GtPv 23 (38)
T PF04036_consen 14 LYHQFVGTPV 23 (38)
T ss_dssp HHHHHTT-EE
T ss_pred HHHHhcCCcC
Confidence 4577888884
No 36
>PF06881 Elongin_A: RNA polymerase II transcription factor SIII (Elongin) subunit A; InterPro: IPR010684 This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0016021 integral to membrane
Probab=20.81 E-value=1.4e+02 Score=19.46 Aligned_cols=27 Identities=19% Similarity=0.518 Sum_probs=20.2
Q ss_pred CCCCCchHHHHHHHHHHhhcCcccccHHHHHHHHh
Q psy16645 30 SYDKLPFSIRVLLESAVRNCDEFQVKKSHVENILK 64 (94)
Q Consensus 30 ~~~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~ 64 (94)
+++.+||. ||+.+|.+| +.+++..|-.
T Consensus 3 dvG~~py~---ll~piL~~~-----~~~QL~~iE~ 29 (109)
T PF06881_consen 3 DVGDVPYH---LLRPILEKC-----SPEQLRRIED 29 (109)
T ss_pred ccCCCCHH---HHHHHHccC-----CHHHHHHHHH
Confidence 57889999 689999987 4566666544
No 37
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=20.07 E-value=1.9e+02 Score=16.52 Aligned_cols=36 Identities=11% Similarity=0.108 Sum_probs=28.1
Q ss_pred CCCchHHHHHHHHHHhhcCcccccHHHHHHHHhhhhh
Q psy16645 32 DKLPFSIRVLLESAVRNCDEFQVKKSHVENILKWEEN 68 (94)
Q Consensus 32 ~~LP~siRILLEn~lR~~d~~~v~~~~v~~l~~w~~~ 68 (94)
-|||--++--|+...... |..+..+-+..|..+...
T Consensus 9 lRlP~~l~~~lk~~A~~~-gRS~NsEIv~~L~~~l~~ 44 (50)
T PF03869_consen 9 LRLPEELKEKLKERAEEN-GRSMNSEIVQRLEEALKK 44 (50)
T ss_dssp EECEHHHHHHHHHHHHHT-TS-HHHHHHHHHHHHHHH
T ss_pred eECCHHHHHHHHHHHHHh-CCChHHHHHHHHHHHHhc
Confidence 368999998888887764 788889988888887654
Done!