Query 026743
Match_columns 234
No_of_seqs 20 out of 22
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 12:04:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026743.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026743hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00072 chlL photochlorophyll 71.1 16 0.00036 32.0 6.7 114 82-202 145-272 (290)
2 PF10076 DUF2313: Uncharacteri 60.4 26 0.00057 28.4 5.6 52 130-182 59-110 (179)
3 PF12007 DUF3501: Protein of u 58.2 8.3 0.00018 33.8 2.5 27 111-137 83-113 (192)
4 PF05225 HTH_psq: helix-turn-h 50.2 18 0.00038 24.4 2.5 19 141-159 1-19 (45)
5 cd08062 MPN_RPN7_8 Mpr1p, Pad1 47.4 85 0.0018 28.2 7.1 75 107-181 144-237 (280)
6 cd08064 MPN_eIF3f Mpr1p, Pad1p 45.4 38 0.00082 29.6 4.5 75 106-180 138-232 (265)
7 PRK11200 grxA glutaredoxin 1; 45.4 54 0.0012 23.1 4.5 27 91-117 12-39 (85)
8 PRK11177 phosphoenolpyruvate-p 39.7 61 0.0013 32.1 5.4 70 85-155 394-466 (575)
9 TIGR02194 GlrX_NrdH Glutaredox 39.3 51 0.0011 22.6 3.5 36 91-133 10-45 (72)
10 TIGR01588 citE citrate lyase, 37.4 71 0.0015 28.3 5.0 41 85-128 95-135 (288)
11 PF11491 DUF3213: Protein of u 36.9 14 0.0003 29.6 0.5 45 133-177 40-84 (88)
12 COG3443 Predicted periplasmic 35.5 21 0.00047 31.8 1.5 12 165-176 164-175 (193)
13 TIGR01969 minD_arch cell divis 34.1 2.2E+02 0.0047 22.9 6.9 61 128-194 182-249 (251)
14 PF06972 DUF1296: Protein of u 32.9 20 0.00044 26.9 0.8 23 186-208 20-42 (60)
15 TIGR01828 pyru_phos_dikin pyru 30.8 82 0.0018 32.8 4.9 117 85-209 704-841 (856)
16 smart00709 Zpr1 Duplicated dom 30.7 75 0.0016 26.7 3.9 33 86-124 121-153 (160)
17 TIGR01417 PTS_I_fam phosphoeno 29.2 1.1E+02 0.0024 30.1 5.3 44 86-130 394-439 (565)
18 PRK08045 cystathionine gamma-s 29.1 81 0.0017 28.7 4.1 13 143-155 374-386 (386)
19 PF03328 HpcH_HpaI: HpcH/HpaI 28.7 48 0.001 27.4 2.4 36 93-128 99-134 (221)
20 PRK10840 transcriptional regul 28.7 3E+02 0.0064 21.8 6.8 96 111-211 78-178 (216)
21 PRK10329 glutaredoxin-like pro 28.5 81 0.0018 22.9 3.3 36 91-133 12-47 (81)
22 cd04765 HTH_MlrA-like_sg2 Heli 28.2 88 0.0019 23.8 3.6 51 85-153 39-89 (99)
23 PRK11061 fused phosphoenolpyru 27.2 1.1E+02 0.0023 31.2 4.9 82 86-168 561-652 (748)
24 PLN03246 26S proteasome regula 26.1 1.2E+02 0.0025 27.9 4.5 74 108-181 151-243 (303)
25 PF13034 DUF3895: Protein of u 26.1 50 0.0011 25.7 1.9 31 130-162 7-39 (78)
26 TIGR00340 zpr1_rel ZPR1-relate 25.6 1.1E+02 0.0024 26.0 4.0 28 94-124 121-148 (163)
27 PRK01099 rpoK DNA-directed RNA 24.5 57 0.0012 23.8 1.9 20 141-160 36-55 (62)
28 PF03367 zf-ZPR1: ZPR1 zinc-fi 23.6 1.1E+02 0.0025 25.5 3.7 29 93-124 126-154 (161)
29 cd03035 ArsC_Yffb Arsenate Red 23.2 1.7E+02 0.0036 22.4 4.3 51 82-151 33-83 (105)
30 PRK06464 phosphoenolpyruvate s 22.0 1.3E+02 0.0028 30.9 4.4 41 107-149 661-706 (795)
31 cd02977 ArsC_family Arsenate R 21.9 3E+02 0.0066 20.1 5.3 21 96-117 12-32 (105)
32 PRK09279 pyruvate phosphate di 21.5 1.5E+02 0.0033 31.2 4.9 114 85-206 710-844 (879)
33 TIGR02190 GlrX-dom Glutaredoxi 21.4 1.5E+02 0.0033 20.7 3.5 22 91-116 19-40 (79)
34 cd00480 malate_synt Malate syn 21.3 1.8E+02 0.0039 28.7 5.1 40 86-128 195-234 (511)
35 smart00027 EH Eps15 homology d 21.2 63 0.0014 23.5 1.5 28 85-115 4-33 (96)
No 1
>CHL00072 chlL photochlorophyllide reductase subunit L
Probab=71.11 E-value=16 Score=32.00 Aligned_cols=114 Identities=11% Similarity=0.111 Sum_probs=67.1
Q ss_pred ccCCChHhHHHHHHHHHHHHHHHhhccccccceEEEEeecCcHHH--HHHHhhCCCCCCCCChH-HHHHHHHHhhcCCC-
Q 026743 82 EEEATPEDLENIAQVKRVLELLRKNRDMLFSEVKLTIMIEDPREV--ERRRLLGIEDSNAPTRD-DLAEALEQVNEGKV- 157 (234)
Q Consensus 82 ~~e~sPeDl~~v~eIkrvL~lLk~~RDMsF~EVKLTImIEDPR~~--Errr~lGIED~~g~srd-dla~AL~eV~eGri- 157 (234)
+-.|++.+++-+..+.++++.++++....+.-|=++ +. +.|.. +-.+.+|+.=..-+.++ .+.+| ...|+.
T Consensus 145 p~~p~~~sl~~~~~l~~~i~~~~~~~~l~~~gvv~n-~~-~~~~~~~~~~~~~~~~vl~~Ip~~~~v~~A---~~~g~pv 219 (290)
T CHL00072 145 ITDNGFDALFAANRIAASVREKARTHPLRLAGLVGN-RT-SKRDLIDKYVEACPMPVLEVLPLIEDIRVS---RVKGKTL 219 (290)
T ss_pred EecCCHHHHHHHHHHHHHHHHHhccCCCceEEEEEe-CC-CchhHHHHHHHHcCCceEEECCCChHHHHH---HhCCCce
Confidence 357888899999999988888876544322112111 22 12221 11234454322234333 34444 334432
Q ss_pred ----Cch------HHHHHHHHHHHhcCCCccccccccCCCccchhhcccCCCCHH
Q 026743 158 ----PKN------RVALRMLAEEMVQWPNLEVEATKQKPSKSLYAKVTDTGIDPE 202 (234)
Q Consensus 158 ----P~d------R~AL~~L~eEm~~WP~LE~e~~k~~p~ks~YakatdTGidp~ 202 (234)
|+. ..+.+.|++|+..++.- ..|+.-++.-+..-.-+-||+|.
T Consensus 220 ~~~~p~s~~~~~~a~~y~~La~ell~~~~~--~~~~~~~~~~~~~~~~~~~~~~~ 272 (290)
T CHL00072 220 FEMVESEPSLNYVCDYYLNIADQLLSQPEG--VVPKEVPDRELFSLLSDFYLNPI 272 (290)
T ss_pred EEeCCCCcchhHHHHHHHHHHHHHHhCCCC--cCCCCCCHHHHHHHHHHhccCCC
Confidence 443 47789999999998543 46766777777777888888884
No 2
>PF10076 DUF2313: Uncharacterized protein conserved in bacteria (DUF2313); InterPro: IPR018755 Members of this family of proteins comprise various hypothetical and putative bacteriophage tail proteins, including Gp48 from Bacteriophage Mu and other Mu-like prophages such as FluMu.
Probab=60.42 E-value=26 Score=28.38 Aligned_cols=52 Identities=23% Similarity=0.297 Sum_probs=47.4
Q ss_pred HhhCCCCCCCCChHHHHHHHHHhhcCCCCchHHHHHHHHHHHhcCCCcccccc
Q 026743 130 RLLGIEDSNAPTRDDLAEALEQVNEGKVPKNRVALRMLAEEMVQWPNLEVEAT 182 (234)
Q Consensus 130 r~lGIED~~g~srddla~AL~eV~eGriP~dR~AL~~L~eEm~~WP~LE~e~~ 182 (234)
+.|||.+..+.|-|+--.++..--.++.|-+...|+.+++.+ ++++.++...
T Consensus 59 ~~lgi~~~~~~tle~RR~~i~~k~~~~~~~T~~~l~~~a~~~-G~~~v~I~e~ 110 (179)
T PF10076_consen 59 RMLGIPPNPTDTLEERRARILAKLNSKGPYTIAYLEQLANSL-GYGNVEITEF 110 (179)
T ss_pred HHcCCCCCCCCCHHHHHHHHHHHHHccCCcCHHHHHHHHHHh-CCCCEEEEEe
Confidence 489999999999999999999988899999999999999999 9988877664
No 3
>PF12007 DUF3501: Protein of unknown function (DUF3501); InterPro: IPR021890 This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are about 200 amino acids in length. The structure of protein of unknown function (YP_111841.1) from B. pseudomallei has been solved. ; PDB: 3FJV_B.
Probab=58.23 E-value=8.3 Score=33.80 Aligned_cols=27 Identities=59% Similarity=0.730 Sum_probs=20.4
Q ss_pred ccceEEEEeecCcHHHHHHHh----hCCCCC
Q 026743 111 FSEVKLTIMIEDPREVERRRL----LGIEDS 137 (234)
Q Consensus 111 F~EVKLTImIEDPR~~Errr~----lGIED~ 137 (234)
=++.|.|+|||=|...|||+. .||||.
T Consensus 83 ~~~l~ATl~IE~~d~~~r~~~L~~L~Gie~~ 113 (192)
T PF12007_consen 83 GGNLKATLMIEIPDEDERRRELARLVGIEDS 113 (192)
T ss_dssp SSEEEEEEEE--SSHHHHHHHHHHCTTGGGC
T ss_pred CCcEEEEEEEEcCCHHHHHHHHHHhcCccce
Confidence 378999999999999999865 588764
No 4
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=50.18 E-value=18 Score=24.40 Aligned_cols=19 Identities=42% Similarity=0.679 Sum_probs=15.1
Q ss_pred ChHHHHHHHHHhhcCCCCc
Q 026743 141 TRDDLAEALEQVNEGKVPK 159 (234)
Q Consensus 141 srddla~AL~eV~eGriP~ 159 (234)
|.|+|..||..|..|+..-
T Consensus 1 tee~l~~Ai~~v~~g~~S~ 19 (45)
T PF05225_consen 1 TEEDLQKAIEAVKNGKMSI 19 (45)
T ss_dssp -HHHHHHHHHHHHTTSS-H
T ss_pred CHHHHHHHHHHHHhCCCCH
Confidence 5789999999999998543
No 5
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=47.45 E-value=85 Score=28.23 Aligned_cols=75 Identities=29% Similarity=0.385 Sum_probs=51.6
Q ss_pred ccccccceEEEEeecCcHHHHHHHhh-CCCCCCCCCh------------------HHHHHHHHHhhcCCCCchHHHHHHH
Q 026743 107 RDMLFSEVKLTIMIEDPREVERRRLL-GIEDSNAPTR------------------DDLAEALEQVNEGKVPKNRVALRML 167 (234)
Q Consensus 107 RDMsF~EVKLTImIEDPR~~Errr~l-GIED~~g~sr------------------ddla~AL~eV~eGriP~dR~AL~~L 167 (234)
.-+.|-+|..+|.-+++-.+==..++ ++.+...-+- +.+..-|+.|.+|++|-|...||.|
T Consensus 144 ~~~~F~~vp~~i~~~eaE~igve~l~r~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~IlR~l 223 (280)
T cd08062 144 TSKTFVHVPSEIGAEEAEEVGVEHLLRDIKDVTVSTLSTRVTNKLNSLKGLQSKLKEIKDYLQLVVEGKLPINHQIIYNL 223 (280)
T ss_pred ceeEEEEcceEeeccchHHHHHHHHHhhccCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH
Confidence 44789999999888775432222232 3444322211 3344567789999999999999999
Q ss_pred HHHHhcCCCccccc
Q 026743 168 AEEMVQWPNLEVEA 181 (234)
Q Consensus 168 ~eEm~~WP~LE~e~ 181 (234)
..=+..=|+++.+.
T Consensus 224 ~~~~~~lP~l~~~~ 237 (280)
T cd08062 224 QDIFNLLPNLNLPE 237 (280)
T ss_pred HHHHHhCCCCCHHH
Confidence 99999999987643
No 6
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=45.38 E-value=38 Score=29.61 Aligned_cols=75 Identities=20% Similarity=0.315 Sum_probs=48.1
Q ss_pred hccccccceEEEEeecCcHHHHHHHhh-CCCCCCCC-C----h--------------HHHHHHHHHhhcCCCCchHHHHH
Q 026743 106 NRDMLFSEVKLTIMIEDPREVERRRLL-GIEDSNAP-T----R--------------DDLAEALEQVNEGKVPKNRVALR 165 (234)
Q Consensus 106 ~RDMsF~EVKLTImIEDPR~~Errr~l-GIED~~g~-s----r--------------ddla~AL~eV~eGriP~dR~AL~ 165 (234)
...+.|.||.++|.-+++-.+==..+. .+.+...- + . +.+..-|+.|..|++|.|-.-+|
T Consensus 138 ~~~~~F~~ip~~i~~~eaE~i~v~~l~~~~~~~~~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~i~r 217 (265)
T cd08064 138 TLGSMFVPIPLELLYSEAERVALDLLAKTLASPSRSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLAGKVKADNAIGR 217 (265)
T ss_pred CcceEEEEcceeeecCcHHHHHHHHHHhhccCCcccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHH
Confidence 345778899999988765321111122 12222111 1 1 23334456788899999999999
Q ss_pred HHHHHHhcCCCcccc
Q 026743 166 MLAEEMVQWPNLEVE 180 (234)
Q Consensus 166 ~L~eEm~~WP~LE~e 180 (234)
.|.+=+...|.++.+
T Consensus 218 ~l~~~~~~lp~~~~~ 232 (265)
T cd08064 218 YLMDALTSVPKLDPE 232 (265)
T ss_pred HHHHHHhhCCCCCHH
Confidence 999999999998743
No 7
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=45.36 E-value=54 Score=23.05 Aligned_cols=27 Identities=19% Similarity=0.260 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHhh-ccccccceEEE
Q 026743 91 ENIAQVKRVLELLRKN-RDMLFSEVKLT 117 (234)
Q Consensus 91 ~~v~eIkrvL~lLk~~-RDMsF~EVKLT 117 (234)
-+|..++++|+.|+.. ++..|.++.+.
T Consensus 12 ~~C~~a~~~L~~l~~~~~~i~~~~idi~ 39 (85)
T PRK11200 12 PYCVRAKELAEKLSEERDDFDYRYVDIH 39 (85)
T ss_pred hhHHHHHHHHHhhcccccCCcEEEEECC
Confidence 4799999999999876 57777766654
No 8
>PRK11177 phosphoenolpyruvate-protein phosphotransferase; Provisional
Probab=39.69 E-value=61 Score=32.07 Aligned_cols=70 Identities=19% Similarity=0.330 Sum_probs=44.1
Q ss_pred CChHhHHHHHHHHHHHHHHHhhccccccc-eEEEEeecCcHHHHHHHhhCCCCCCCC--ChHHHHHHHHHhhcC
Q 026743 85 ATPEDLENIAQVKRVLELLRKNRDMLFSE-VKLTIMIEDPREVERRRLLGIEDSNAP--TRDDLAEALEQVNEG 155 (234)
Q Consensus 85 ~sPeDl~~v~eIkrvL~lLk~~RDMsF~E-VKLTImIEDPR~~Errr~lGIED~~g~--srddla~AL~eV~eG 155 (234)
-|+++++-+.++.+-...--+.....|++ +++-+|||.|..+..=..+- +.-|++ -.-||..-+-.+..|
T Consensus 394 ~t~eE~~~~~~~~~~~~~~l~~~~~~~~~~~~~g~mIE~p~a~~~~d~i~-~~vDf~sIGtnDL~qy~la~dr~ 466 (575)
T PRK11177 394 ISVEEVRELKAEIEILKQELRDEGKAFDESIEIGVMVETPAAAVIARHLA-KEVDFFSIGTNDLTQYTLAVDRG 466 (575)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhccccCCCcEEEEEEeCHHHHHhHHHHH-hhCCEEEECcHHHHHHHHHhccC
Confidence 35677666665544332222355677864 99999999999998644442 233443 357888877655555
No 9
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=39.34 E-value=51 Score=22.56 Aligned_cols=36 Identities=22% Similarity=0.476 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHhhccccccceEEEEeecCcHHHHHHHhhC
Q 026743 91 ENIAQVKRVLELLRKNRDMLFSEVKLTIMIEDPREVERRRLLG 133 (234)
Q Consensus 91 ~~v~eIkrvL~lLk~~RDMsF~EVKLTImIEDPR~~Errr~lG 133 (234)
-+|+.++++|+ .+++.|.++.+. +||...++-+.+|
T Consensus 10 p~C~~ak~~L~----~~~i~~~~~di~---~~~~~~~~~~~~g 45 (72)
T TIGR02194 10 VQCKMTKKALE----EHGIAFEEINID---EQPEAIDYVKAQG 45 (72)
T ss_pred HHHHHHHHHHH----HCCCceEEEECC---CCHHHHHHHHHcC
Confidence 37888888886 578999888765 5665544433344
No 10
>TIGR01588 citE citrate lyase, beta subunit. This is a model of the beta subunit of the holoenzyme citrate lyase (EC 4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC 4.1.3.34), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The beta subunit catalyzes the reaction (3S)-citryl-CoA = acetyl-CoA + oxaloacetate. The seed contains an experimentally characterized member from Leuconostoc mesenteroides. The model covers a wide range of Gram positive bacteria. For Gram negative bacteria, it appears that only gamma proteobacteria hit this model. The model is quite robust with queries scoring either quite well or quite poorly against the model. There are currently no hits in-between the noise cutoff and trusted cutoff.
Probab=37.36 E-value=71 Score=28.28 Aligned_cols=41 Identities=22% Similarity=0.251 Sum_probs=28.3
Q ss_pred CChHhHHHHHHHHHHHHHHHhhccccccceEEEEeecCcHHHHH
Q 026743 85 ATPEDLENIAQVKRVLELLRKNRDMLFSEVKLTIMIEDPREVER 128 (234)
Q Consensus 85 ~sPeDl~~v~eIkrvL~lLk~~RDMsF~EVKLTImIEDPR~~Er 128 (234)
-|++|++++.+..+ .+-......-+++++..+||.|..+++
T Consensus 95 ~s~~~v~~~~~~l~---~~~~~~~~~~~~~~i~~~IET~~gv~~ 135 (288)
T TIGR01588 95 DTAEDIHELEKLIE---RIEKEIGREVGSTKLMAAIESALGVVN 135 (288)
T ss_pred CCHHHHHHHHHHHH---HHHHhcCCCCCCeeEEEEeCCHHHHHh
Confidence 35777776665443 233334445578999999999999876
No 11
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=36.89 E-value=14 Score=29.58 Aligned_cols=45 Identities=22% Similarity=0.426 Sum_probs=16.9
Q ss_pred CCCCCCCCChHHHHHHHHHhhcCCCCchHHHHHHHHHHHhcCCCc
Q 026743 133 GIEDSNAPTRDDLAEALEQVNEGKVPKNRVALRMLAEEMVQWPNL 177 (234)
Q Consensus 133 GIED~~g~srddla~AL~eV~eGriP~dR~AL~~L~eEm~~WP~L 177 (234)
=|=|+..+++|++.++|++.+---|-...+.++.|.+.=..|-|.
T Consensus 40 VifDe~kl~~e~lL~~le~~kpEVi~ek~lTveELIE~SmSW~Ni 84 (88)
T PF11491_consen 40 VIFDESKLSKEELLEMLEEFKPEVIEEKELTVEELIESSMSWNNI 84 (88)
T ss_dssp EE--B-S-SHHHH---HHHTTT-SS-------SS-----------
T ss_pred EEECcccCCHHHHHHHHHhcChhheeeccccHHHHHHHhccHhhh
Confidence 366888999999999999998888888999999999999999885
No 12
>COG3443 Predicted periplasmic or secreted protein [General function prediction only]
Probab=35.52 E-value=21 Score=31.82 Aligned_cols=12 Identities=42% Similarity=0.949 Sum_probs=10.2
Q ss_pred HHHHHHHhcCCC
Q 026743 165 RMLAEEMVQWPN 176 (234)
Q Consensus 165 ~~L~eEm~~WP~ 176 (234)
+.|++||.|||-
T Consensus 164 eaLl~EmeNWPT 175 (193)
T COG3443 164 EALLDEMENWPT 175 (193)
T ss_pred HHHHHHHhcCCc
Confidence 568999999994
No 13
>TIGR01969 minD_arch cell division ATPase MinD, archaeal. This model represents the archaeal branch of the MinD family. MinD, a weak ATPase, works in bacteria with MinC as a generalized cell division inhibitor and, through interaction with MinE, prevents septum placement inappropriate sites. Often several members of this family are found in archaeal genomes, and the function is uncharacterized. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. The exact roles of the various archaeal MinD homologs are unknown.
Probab=34.15 E-value=2.2e+02 Score=22.90 Aligned_cols=61 Identities=20% Similarity=0.194 Sum_probs=37.1
Q ss_pred HHHhhCCCCCCCCChHHHHHHHHHhhcCCC-----Cc--hHHHHHHHHHHHhcCCCccccccccCCCccchhhc
Q 026743 128 RRRLLGIEDSNAPTRDDLAEALEQVNEGKV-----PK--NRVALRMLAEEMVQWPNLEVEATKQKPSKSLYAKV 194 (234)
Q Consensus 128 rrr~lGIED~~g~srddla~AL~eV~eGri-----P~--dR~AL~~L~eEm~~WP~LE~e~~k~~p~ks~Yaka 194 (234)
..+++|+.-...+.++.-+. +.++.|+. |. -+.+++.|++|+..||. .++.++++|+.+|.
T Consensus 182 l~~~~~~~~l~~Ip~~~~~~--~a~~~g~~v~~~~~~~~~~~~~~~la~~i~~~~~----~~~~~~~~~~~~~~ 249 (251)
T TIGR01969 182 IETILEVPVLGVVPEDPEVR--RAAAFGEPVVIYNPNSPAAQAFMELAAELAGIEY----EPKEPKKEGFIAKV 249 (251)
T ss_pred HHHhhCCcEEEEecCCHhHH--HHHHcCCceEEeCCCCHHHHHHHHHHHHHHhccc----ccccchhhhHHHHh
Confidence 33456775543444444322 34567763 33 34679999999999983 23445566777764
No 14
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=32.90 E-value=20 Score=26.91 Aligned_cols=23 Identities=30% Similarity=0.645 Sum_probs=20.2
Q ss_pred CCccchhhcccCCCCHHHHHhhh
Q 026743 186 PSKSLYAKVTDTGIDPEMAAKRL 208 (234)
Q Consensus 186 p~ks~YakatdTGidp~~AAkRl 208 (234)
+-.-+||-.-+.+.||-+|++||
T Consensus 20 se~eIya~L~ecnMDpnea~qrL 42 (60)
T PF06972_consen 20 SEEEIYAMLKECNMDPNEAVQRL 42 (60)
T ss_pred CHHHHHHHHHHhCCCHHHHHHHH
Confidence 34458999999999999999998
No 15
>TIGR01828 pyru_phos_dikin pyruvate, phosphate dikinase. This model represents pyruvate,phosphate dikinase, also called pyruvate,orthophosphate dikinase. It is similar in sequence to other PEP-utilizing enzymes.
Probab=30.82 E-value=82 Score=32.83 Aligned_cols=117 Identities=20% Similarity=0.250 Sum_probs=69.2
Q ss_pred CChHhHHHHHHHHH-HHHHHHhhccccccceEEEEeecCcHHHHHHHhh---------CCCCC----CCCChHHHHHHHH
Q 026743 85 ATPEDLENIAQVKR-VLELLRKNRDMLFSEVKLTIMIEDPREVERRRLL---------GIEDS----NAPTRDDLAEALE 150 (234)
Q Consensus 85 ~sPeDl~~v~eIkr-vL~lLk~~RDMsF~EVKLTImIEDPR~~Errr~l---------GIED~----~g~srddla~AL~ 150 (234)
-+.++++.++++.+ +.+-|++...+.|+ +++=+|||=||.+=.=..+ |-.|. =|++|++....+.
T Consensus 704 ~~~~E~~~~k~~i~~~~~~l~~~~g~~~~-~~iG~MiE~P~aal~ad~la~~~DFfSiGTNDLtQ~tlg~dR~~~~~~~~ 782 (856)
T TIGR01828 704 GEKNELKILKDVLEEVAAEVFKEYGVTVP-YEIGTMIEIPRAALTADKIAEEADFFSFGTNDLTQMTFGFSRDDAGKFLP 782 (856)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhcCCccC-CeEEEEEehHHHHHHHHHHHHhCCEEEECccHHHHHHhccCccchhhhHH
Confidence 35777777775443 55666665567787 9999999999987543222 33332 2677887754455
Q ss_pred H-hhcCCCCch------HHHHHHHHHHHhcCCCccccccccCCCccchhhcccCCCCHHHHHhhhc
Q 026743 151 Q-VNEGKVPKN------RVALRMLAEEMVQWPNLEVEATKQKPSKSLYAKVTDTGIDPEMAAKRLN 209 (234)
Q Consensus 151 e-V~eGriP~d------R~AL~~L~eEm~~WP~LE~e~~k~~p~ks~YakatdTGidp~~AAkRl~ 209 (234)
. +..|-++.| ..|+..|.+...+. +-++|+++.+.- .=..|-||..+.--++
T Consensus 783 ~y~~~~i~~~~P~~~ld~paV~~li~~~i~~------a~~~~~~~~vgv-CGE~a~dp~~i~~l~~ 841 (856)
T TIGR01828 783 KYLEKGILEKDPFESLDQTGVGQLMRMAVEK------GRQTRPNLKVGI-CGEHGGDPSSIEFCHK 841 (856)
T ss_pred HHHhcCcccCCcccccCcHHHHHHHHHHHHH------HhhcCCCCEEEe-CCCCcCCHHHHHHHHH
Confidence 4 445666665 45666666655432 223345544433 2445677776654433
No 16
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=30.74 E-value=75 Score=26.68 Aligned_cols=33 Identities=27% Similarity=0.423 Sum_probs=19.9
Q ss_pred ChHhHHHHHHHHHHHHHHHhhccccccceEEEEeecCcH
Q 026743 86 TPEDLENIAQVKRVLELLRKNRDMLFSEVKLTIMIEDPR 124 (234)
Q Consensus 86 sPeDl~~v~eIkrvL~lLk~~RDMsF~EVKLTImIEDPR 124 (234)
.|+..+.+.++.+-|+-++ =++.+.|+-|+||-
T Consensus 121 ~~e~~~k~~~~~~~L~~~~------~g~~~fTliidDP~ 153 (160)
T smart00709 121 DPETKEKIDEFLEKLKELI------EGKEPFTLILDDPA 153 (160)
T ss_pred CHHHHHHHHHHHHHHHHHH------cCCCCEEEEEECCC
Confidence 4555555554444443333 34678999999994
No 17
>TIGR01417 PTS_I_fam phosphoenolpyruvate-protein phosphotransferase. This model recognizes a distinct clade of phophoenolpyruvate (PEP)-dependent enzymes. Most members are known or deduced to function as the phosphoenolpyruvate-protein phosphotransferase (or enzyme I) of PTS sugar transport systems. However, some species with both a member of this family and a homolog of the phosphocarrier protein HPr lack a IIC component able to serve as a permease. An HPr homolog designated NPr has been implicated in the regulation of nitrogen assimilation, which demonstrates that not all phosphotransferase system components are associated directly with PTS transport.
Probab=29.25 E-value=1.1e+02 Score=30.11 Aligned_cols=44 Identities=20% Similarity=0.273 Sum_probs=26.5
Q ss_pred ChHhHHHHHHHHHHHH-HHHhhcccccc-ceEEEEeecCcHHHHHHH
Q 026743 86 TPEDLENIAQVKRVLE-LLRKNRDMLFS-EVKLTIMIEDPREVERRR 130 (234)
Q Consensus 86 sPeDl~~v~eIkrvL~-lLk~~RDMsF~-EVKLTImIEDPR~~Errr 130 (234)
|+++++.+.++.+-.. -|+ ..-..|| ++.+-+|||-|..++.=.
T Consensus 394 t~eE~~~~~~~~~~~~~~l~-~~~~~~~~~~~vg~mIEtpaav~~~d 439 (565)
T TIGR01417 394 TVEEIRAVKQELEEEKQELN-DEGKAFDENIEVGVMIEIPSAALIAD 439 (565)
T ss_pred CHHHHHHHHHHHHHHHHHHH-HhccccccCcEEEEEEcCHHHHHhHH
Confidence 4556555444433221 122 2234555 599999999999998743
No 18
>PRK08045 cystathionine gamma-synthase; Provisional
Probab=29.10 E-value=81 Score=28.75 Aligned_cols=13 Identities=31% Similarity=0.608 Sum_probs=10.1
Q ss_pred HHHHHHHHHhhcC
Q 026743 143 DDLAEALEQVNEG 155 (234)
Q Consensus 143 ddla~AL~eV~eG 155 (234)
+||.+||..++.|
T Consensus 374 ~dl~~al~~~~~~ 386 (386)
T PRK08045 374 ADLENGFRAANKG 386 (386)
T ss_pred HHHHHHHHHhhcC
Confidence 5788888887766
No 19
>PF03328 HpcH_HpaI: HpcH/HpaI aldolase/citrate lyase family; InterPro: IPR005000 This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (4.1.2 from EC) and 4-hydroxy-2-oxovalerate aldolase (4.1.2 from EC). ; GO: 0016830 carbon-carbon lyase activity, 0006725 cellular aromatic compound metabolic process; PDB: 1DXF_B 1DXE_A 3QZ6_A 3QLL_C 3QQW_F 3OYZ_A 3PUG_A 3OYX_A 1IZC_A 2V5K_B ....
Probab=28.73 E-value=48 Score=27.44 Aligned_cols=36 Identities=28% Similarity=0.250 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHhhccccccceEEEEeecCcHHHHH
Q 026743 93 IAQVKRVLELLRKNRDMLFSEVKLTIMIEDPREVER 128 (234)
Q Consensus 93 v~eIkrvL~lLk~~RDMsF~EVKLTImIEDPR~~Er 128 (234)
++++.+.++.....+-..-+.+++.+|||.|..+++
T Consensus 99 ~~~~~~~~~~~~~~~~~~~~~~~i~~~IET~~gv~~ 134 (221)
T PF03328_consen 99 ARQAVAALRYPPAGRRGANGSTKIIPMIETPEGVEN 134 (221)
T ss_dssp HHHHHHHHSHTTTCTTTHHCHSEEEEEE-SHHHHHT
T ss_pred HHHHHHHHhhcccccccccCceEEEEeeccHHHHhC
Confidence 333444444443333335678999999999999987
No 20
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=28.65 E-value=3e+02 Score=21.77 Aligned_cols=96 Identities=20% Similarity=0.231 Sum_probs=50.8
Q ss_pred ccceEEEEee--cCcHHHHHHHhhCCCC--CCCCChHHHHHHHHHhhcCCCCchHHHHHHHHHHHh-cCCCccccccccC
Q 026743 111 FSEVKLTIMI--EDPREVERRRLLGIED--SNAPTRDDLAEALEQVNEGKVPKNRVALRMLAEEMV-QWPNLEVEATKQK 185 (234)
Q Consensus 111 F~EVKLTImI--EDPR~~Errr~lGIED--~~g~srddla~AL~eV~eGriP~dR~AL~~L~eEm~-~WP~LE~e~~k~~ 185 (234)
+..+++.+.- .++...++=-..|+.+ ....+.+++.+|+..|..|+..-.....+ +..... .+.... ..+ +
T Consensus 78 ~~~~~iIvls~~~~~~~~~~a~~~Ga~~yl~K~~~~~~l~~ai~~v~~g~~~~~~~~~~-~~~~~~~~~~~~~-~Lt--~ 153 (216)
T PRK10840 78 FPSLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSR-LLEKISAGGYGDK-RLS--P 153 (216)
T ss_pred CCCCcEEEEEecCCHHHHHHHHHCCCeEEEECCCCHHHHHHHHHHHHCCCeecCHHHHH-HHHHhccCCCccc-cCC--H
Confidence 4445655554 4454444434456553 24567899999999999999765554433 222221 110000 000 0
Q ss_pred CCccchhhcccCCCCHHHHHhhhccC
Q 026743 186 PSKSLYAKVTDTGIDPEMAAKRLNID 211 (234)
Q Consensus 186 p~ks~YakatdTGidp~~AAkRl~id 211 (234)
.-+-+ ....=.|..-++-|++|+|-
T Consensus 154 rE~ev-l~~~~~G~s~~eIA~~l~iS 178 (216)
T PRK10840 154 KESEV-LRLFAEGFLVTEIAKKLNRS 178 (216)
T ss_pred HHHHH-HHHHHCCCCHHHHHHHHCCC
Confidence 00000 11122688888889998874
No 21
>PRK10329 glutaredoxin-like protein; Provisional
Probab=28.46 E-value=81 Score=22.87 Aligned_cols=36 Identities=25% Similarity=0.377 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHhhccccccceEEEEeecCcHHHHHHHhhC
Q 026743 91 ENIAQVKRVLELLRKNRDMLFSEVKLTIMIEDPREVERRRLLG 133 (234)
Q Consensus 91 ~~v~eIkrvL~lLk~~RDMsF~EVKLTImIEDPR~~Errr~lG 133 (234)
-||..++++|+ .+.+.|.++.++ +||-..++-+..|
T Consensus 12 p~C~~ak~~L~----~~gI~~~~idi~---~~~~~~~~~~~~g 47 (81)
T PRK10329 12 VQCHATKRAME----SRGFDFEMINVD---RVPEAAETLRAQG 47 (81)
T ss_pred HhHHHHHHHHH----HCCCceEEEECC---CCHHHHHHHHHcC
Confidence 47888888774 468899988776 5665555443334
No 22
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.24 E-value=88 Score=23.78 Aligned_cols=51 Identities=18% Similarity=0.277 Sum_probs=35.5
Q ss_pred CChHhHHHHHHHHHHHHHHHhhccccccceEEEEeecCcHHHHHHHhhCCCCCCCCChHHHHHHHHHhh
Q 026743 85 ATPEDLENIAQVKRVLELLRKNRDMLFSEVKLTIMIEDPREVERRRLLGIEDSNAPTRDDLAEALEQVN 153 (234)
Q Consensus 85 ~sPeDl~~v~eIkrvL~lLk~~RDMsF~EVKLTImIEDPR~~Errr~lGIED~~g~srddla~AL~eV~ 153 (234)
-|++|+..++.|+.. .+...|+.++++ ++++-++.....++++..+|.+|.
T Consensus 39 Yt~~di~~l~~I~~l----lr~~G~~l~~i~--------------~~l~~~~~~~~~~~~~~~~~~~~~ 89 (99)
T cd04765 39 YRPKDVELLLLIKHL----LYEKGYTIEGAK--------------QALKEDGAAAIREEEAEERLPSIR 89 (99)
T ss_pred eCHHHHHHHHHHHHH----HHHCCCCHHHHH--------------HHHHhccccccchhhHHHHHHHHH
Confidence 456677766666553 245678877764 567767777788899998888764
No 23
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=27.16 E-value=1.1e+02 Score=31.19 Aligned_cols=82 Identities=17% Similarity=0.164 Sum_probs=47.1
Q ss_pred ChHhHHHHHHHHH-HHHHHHhhccccccceEEEEeecCcHHHHHHHhhCCCCCCC--CChHHHHHHHHHhhcCC------
Q 026743 86 TPEDLENIAQVKR-VLELLRKNRDMLFSEVKLTIMIEDPREVERRRLLGIEDSNA--PTRDDLAEALEQVNEGK------ 156 (234)
Q Consensus 86 sPeDl~~v~eIkr-vL~lLk~~RDMsF~EVKLTImIEDPR~~Errr~lGIED~~g--~srddla~AL~eV~eGr------ 156 (234)
+.++++.++++.+ +-+-|+......|..+++=||||=|..+-.=..+ .+--|. +---||.+-+-.+-++-
T Consensus 561 ~~~E~~~~~~~~~~~~~~l~~~~~~~~~~~~~G~MiE~Paa~~~~~~~-a~~~DF~SIGtNDL~Qy~la~DR~n~~v~~~ 639 (748)
T PRK11061 561 SIDEVDEARRLIDRAGREVEEMLGYEIPKPRIGIMIEVPSMVFMLPHL-ASRVDFISVGTNDLTQYLLAVDRNNTRVASL 639 (748)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcCCCCCCceEEEEEehHHHHHHHHHH-HHhCCEEEECccHHHHHHHHhcCCChHHHhh
Confidence 4556555555443 3334555567888889999999999988654333 111222 22346666555555543
Q ss_pred -CCchHHHHHHHH
Q 026743 157 -VPKNRVALRMLA 168 (234)
Q Consensus 157 -iP~dR~AL~~L~ 168 (234)
-|-+-..|+++.
T Consensus 640 ~~~~~Pavlr~i~ 652 (748)
T PRK11061 640 YDSLHPAMLRALK 652 (748)
T ss_pred cCCCCHHHHHHHH
Confidence 344555555554
No 24
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=26.10 E-value=1.2e+02 Score=27.93 Aligned_cols=74 Identities=30% Similarity=0.424 Sum_probs=49.8
Q ss_pred cccccceEEEEeecCcHHHHHHHhh-CCCCCCCCCh------------------HHHHHHHHHhhcCCCCchHHHHHHHH
Q 026743 108 DMLFSEVKLTIMIEDPREVERRRLL-GIEDSNAPTR------------------DDLAEALEQVNEGKVPKNRVALRMLA 168 (234)
Q Consensus 108 DMsF~EVKLTImIEDPR~~Errr~l-GIED~~g~sr------------------ddla~AL~eV~eGriP~dR~AL~~L~ 168 (234)
.+.|-+|..+|.-+++-.+==..++ ++.+...-+- +.+.+-|+.|.+|++|-|...||.|.
T Consensus 151 ~~~F~~vp~~i~~~EaE~Igve~l~r~~~~~~~s~l~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~IlR~l~ 230 (303)
T PLN03246 151 QKVFVHVPSEIGAHEAEEIGVEHLLRDVKDTTVSTLATEVTGKLTALKGLDARLREIRSYLDLVVEGKLPLNHEILYHLQ 230 (303)
T ss_pred ccEEEECCeeeeecCHHHHHHHHHHhcccCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Confidence 4679999999988885322111111 2333222111 23445567789999999999999999
Q ss_pred HHHhcCCCccccc
Q 026743 169 EEMVQWPNLEVEA 181 (234)
Q Consensus 169 eEm~~WP~LE~e~ 181 (234)
.=+..=|.++.+.
T Consensus 231 ~l~~~lP~l~~~~ 243 (303)
T PLN03246 231 DVFNLLPNLNVEE 243 (303)
T ss_pred HHHhhCCCCCHHH
Confidence 9999999987543
No 25
>PF13034 DUF3895: Protein of unknown function (DUF3895)
Probab=26.06 E-value=50 Score=25.75 Aligned_cols=31 Identities=23% Similarity=0.511 Sum_probs=26.6
Q ss_pred HhhC--CCCCCCCChHHHHHHHHHhhcCCCCchHH
Q 026743 130 RLLG--IEDSNAPTRDDLAEALEQVNEGKVPKNRV 162 (234)
Q Consensus 130 r~lG--IED~~g~srddla~AL~eV~eGriP~dR~ 162 (234)
..+. |++.+++|..|+.+-| |.+|.+|+.|-
T Consensus 7 ~~i~~yi~n~~~Isa~elcE~L--I~~~~~~~~ry 39 (78)
T PF13034_consen 7 EFINWYIQNEEEISARELCEYL--IENGGSPNKRY 39 (78)
T ss_pred HHHHHHHhccccccHHHHHHHH--HHcCCCccccc
Confidence 5777 9999999999999987 67899998773
No 26
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=25.58 E-value=1.1e+02 Score=25.98 Aligned_cols=28 Identities=29% Similarity=0.514 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHhhccccccceEEEEeecCcH
Q 026743 94 AQVKRVLELLRKNRDMLFSEVKLTIMIEDPR 124 (234)
Q Consensus 94 ~eIkrvL~lLk~~RDMsF~EVKLTImIEDPR 124 (234)
..+..+|+-|++-++. +...|+-|+||-
T Consensus 121 ~k~~~~l~kL~~~~~g---~~pfTlIldDP~ 148 (163)
T TIGR00340 121 KKCEEILKRIREVIEG---KFKFTLIIEDPF 148 (163)
T ss_pred HHHHHHHHHHHHHHhC---CCCeEEEEECCC
Confidence 4445555555554443 668999999994
No 27
>PRK01099 rpoK DNA-directed RNA polymerase subunit K; Provisional
Probab=24.53 E-value=57 Score=23.82 Aligned_cols=20 Identities=30% Similarity=0.421 Sum_probs=16.6
Q ss_pred ChHHHHHHHHHhhcCCCCch
Q 026743 141 TRDDLAEALEQVNEGKVPKN 160 (234)
Q Consensus 141 srddla~AL~eV~eGriP~d 160 (234)
+.+-+.-||.||.+|+||-.
T Consensus 36 ~~kPv~iAl~Ei~~gkI~~~ 55 (62)
T PRK01099 36 STDPLDIAEEEFKRGVLPIT 55 (62)
T ss_pred CCCHHHHHHHHHHcCCCCeE
Confidence 45667899999999999854
No 28
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=23.63 E-value=1.1e+02 Score=25.47 Aligned_cols=29 Identities=21% Similarity=0.441 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHhhccccccceEEEEeecCcH
Q 026743 93 IAQVKRVLELLRKNRDMLFSEVKLTIMIEDPR 124 (234)
Q Consensus 93 v~eIkrvL~lLk~~RDMsF~EVKLTImIEDPR 124 (234)
...+..+++.|++-++ ++...|+-|+||-
T Consensus 126 ~~~~~~~i~~L~~~~~---g~~pfTlIidDP~ 154 (161)
T PF03367_consen 126 KEKIEEFIEKLDELIE---GKRPFTLIIDDPS 154 (161)
T ss_dssp HHHHHHHHHHHHHHHC---TSS-EEEEEEETT
T ss_pred HHHHHHHHHHHHHHHc---CCCCEEEEEECCC
Confidence 3444555555555555 4568999999994
No 29
>cd03035 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine.
Probab=23.20 E-value=1.7e+02 Score=22.38 Aligned_cols=51 Identities=12% Similarity=0.081 Sum_probs=32.4
Q ss_pred ccCCChHhHHHHHHHHHHHHHHHhhccccccceEEEEeecCcHHHHHHHhhCCCCCCCCChHHHHHHHHH
Q 026743 82 EEEATPEDLENIAQVKRVLELLRKNRDMLFSEVKLTIMIEDPREVERRRLLGIEDSNAPTRDDLAEALEQ 151 (234)
Q Consensus 82 ~~e~sPeDl~~v~eIkrvL~lLk~~RDMsF~EVKLTImIEDPR~~Errr~lGIED~~g~srddla~AL~e 151 (234)
+.++|.++|+.+-.-.. ++-|-.+|.+.|.+. |..+.+..|.+++.++|.+
T Consensus 33 ~~p~s~~eL~~~l~~~g-~~~li~~~~~~yk~l------------------~l~~~~~~s~~e~~~~l~~ 83 (105)
T cd03035 33 KDGLDAATLERWLAKVG-WETLLNKRGTTWRKL------------------DDAQKAALDAAKAIALMLE 83 (105)
T ss_pred cCCCCHHHHHHHHHHhC-hHHHHccCchHHHhC------------------ChhhhccCCHHHHHHHHHh
Confidence 36788888887776555 355666777777554 3332245677777766643
No 30
>PRK06464 phosphoenolpyruvate synthase; Validated
Probab=22.01 E-value=1.3e+02 Score=30.94 Aligned_cols=41 Identities=17% Similarity=0.188 Sum_probs=25.5
Q ss_pred ccccc--cceEEEEeecCcHHHHHHH-hhCCCCCCCC--ChHHHHHHH
Q 026743 107 RDMLF--SEVKLTIMIEDPREVERRR-LLGIEDSNAP--TRDDLAEAL 149 (234)
Q Consensus 107 RDMsF--~EVKLTImIEDPR~~Errr-~lGIED~~g~--srddla~AL 149 (234)
+.+.+ +++++-+|||.|..++.=. ++.. -|++ -.-||...+
T Consensus 661 ~g~~~~~~~~~vg~MIEtp~av~~~deIa~~--vDfi~IGtnDLtq~~ 706 (795)
T PRK06464 661 NGLKRGENGLKVIMMCEIPSNALLAEEFLEY--FDGFSIGSNDLTQLT 706 (795)
T ss_pred hCccccccCcEEEEEEcCHHHHHHHHHHHHh--CCEEEECchHHHHHH
Confidence 34445 3799999999999998732 2222 3332 345666643
No 31
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=21.85 E-value=3e+02 Score=20.12 Aligned_cols=21 Identities=10% Similarity=0.279 Sum_probs=12.7
Q ss_pred HHHHHHHHHhhccccccceEEE
Q 026743 96 VKRVLELLRKNRDMLFSEVKLT 117 (234)
Q Consensus 96 IkrvL~lLk~~RDMsF~EVKLT 117 (234)
-++++++|+. ++..|.++.++
T Consensus 12 c~ka~~~L~~-~~i~~~~idi~ 32 (105)
T cd02977 12 SRKALAWLEE-HGIEYEFIDYL 32 (105)
T ss_pred HHHHHHHHHH-cCCCcEEEeec
Confidence 3444444443 47888888765
No 32
>PRK09279 pyruvate phosphate dikinase; Provisional
Probab=21.52 E-value=1.5e+02 Score=31.16 Aligned_cols=114 Identities=22% Similarity=0.291 Sum_probs=66.9
Q ss_pred CChHhHHHHHH-HHHHHHHHHhhccccccceEEEEeecCcHHHHHHHh---------hCCCCC----CCCChHHHHHHHH
Q 026743 85 ATPEDLENIAQ-VKRVLELLRKNRDMLFSEVKLTIMIEDPREVERRRL---------LGIEDS----NAPTRDDLAEALE 150 (234)
Q Consensus 85 ~sPeDl~~v~e-IkrvL~lLk~~RDMsF~EVKLTImIEDPR~~Errr~---------lGIED~----~g~srddla~AL~ 150 (234)
-+.++++.+++ |.++.+-|.+...+.| .+++=+|||=||.+=.=.. .|-.|. =|+||++-...|.
T Consensus 710 ~~~~E~~~~r~~i~~~~~~~~~e~g~~~-~~~vG~MIEvP~Aal~ad~iA~~adFfSiGTNDLTQ~t~g~dRdd~~~fl~ 788 (879)
T PRK09279 710 GTVKELKLVKAIIDAVAEEVFAEKGVKL-DYKVGTMIELPRAALTADEIAEEAEFFSFGTNDLTQTTFGFSRDDAGKFLP 788 (879)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhhCCCC-CceEEEEEehHHHHHhHHHHHHhCCEEEEcccHHHHHHhccCccchhhhHH
Confidence 46778888876 4566666665555555 6899999999998643211 133333 3788999865665
Q ss_pred H-hhcCCCCch------HHHHHHHHHHHhcCCCccccccccCCCccchhhcccCCCCHHHHHh
Q 026743 151 Q-VNEGKVPKN------RVALRMLAEEMVQWPNLEVEATKQKPSKSLYAKVTDTGIDPEMAAK 206 (234)
Q Consensus 151 e-V~eGriP~d------R~AL~~L~eEm~~WP~LE~e~~k~~p~ks~YakatdTGidp~~AAk 206 (234)
. +..|-+|.| ..|+-.|.+.-.+- +-+.||++.+.- .=..|-||....-
T Consensus 789 ~y~~~~i~~~dPf~~lD~~aV~~Li~~~v~~------~r~~~~~~~vgI-CGE~ggdp~~i~~ 844 (879)
T PRK09279 789 DYLEKGILEEDPFESLDQEGVGELVEIAVER------GRATRPDLKLGI-CGEHGGDPASIEF 844 (879)
T ss_pred HHHhcCcccCCcchhcChHHHHHHHHHHHHH------HHhcCCCCEEEE-CCCCccCHHHHHH
Confidence 5 566666654 35565555544321 222334443333 2344567766554
No 33
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=21.44 E-value=1.5e+02 Score=20.71 Aligned_cols=22 Identities=27% Similarity=0.363 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHhhccccccceEE
Q 026743 91 ENIAQVKRVLELLRKNRDMLFSEVKL 116 (234)
Q Consensus 91 ~~v~eIkrvL~lLk~~RDMsF~EVKL 116 (234)
-||..+|++|+ .....|.++.+
T Consensus 19 p~C~~ak~~L~----~~gi~y~~idi 40 (79)
T TIGR02190 19 PFCAKAKATLK----EKGYDFEEIPL 40 (79)
T ss_pred HhHHHHHHHHH----HcCCCcEEEEC
Confidence 47888888886 45788888665
No 34
>cd00480 malate_synt Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their carbon requirements from two-carbon compounds, by bypassing the two carboxylation steps of the citric acid cycle.
Probab=21.32 E-value=1.8e+02 Score=28.71 Aligned_cols=40 Identities=15% Similarity=0.089 Sum_probs=28.9
Q ss_pred ChHhHHHHHHHHHHHHHHHhhccccccceEEEEeecCcHHHHH
Q 026743 86 TPEDLENIAQVKRVLELLRKNRDMLFSEVKLTIMIEDPREVER 128 (234)
Q Consensus 86 sPeDl~~v~eIkrvL~lLk~~RDMsF~EVKLTImIEDPR~~Er 128 (234)
||+|++.+.+++ ..+.....+.=+=+|+++|||-++..-+
T Consensus 195 s~~Ev~~~~~~~---~~~E~~~gl~~gtiki~vlIET~~a~~~ 234 (511)
T cd00480 195 SPLEARLWNDVF---SRAEDYLGLPRGTIKATVLIETLPAAFE 234 (511)
T ss_pred CHHHHHHHHHHH---HHHHHhcCCCCCCeeEEEEECCHHHHHH
Confidence 677777666655 4445556666677999999999997654
No 35
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=21.18 E-value=63 Score=23.48 Aligned_cols=28 Identities=36% Similarity=0.500 Sum_probs=16.1
Q ss_pred CChHhHHHHHHHHHHHHHHHhhcc--ccccceE
Q 026743 85 ATPEDLENIAQVKRVLELLRKNRD--MLFSEVK 115 (234)
Q Consensus 85 ~sPeDl~~v~eIkrvL~lLk~~RD--MsF~EVK 115 (234)
.|++++..+.+++..+. ++++ +++.|++
T Consensus 4 ls~~~~~~l~~~F~~~D---~d~~G~Is~~el~ 33 (96)
T smart00027 4 ISPEDKAKYEQIFRSLD---KNQDGTVTGAQAK 33 (96)
T ss_pred CCHHHHHHHHHHHHHhC---CCCCCeEeHHHHH
Confidence 46677777666666554 4433 4555543
Done!