Query 031998
Match_columns 149
No_of_seqs 111 out of 128
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 08:13:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031998.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031998hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05811 DUF842: Eukaryotic pr 100.0 2.4E-53 5.1E-58 322.0 14.3 129 17-145 1-131 (131)
2 KOG3377 Uncharacterized conser 100.0 1.6E-52 3.5E-57 319.3 16.5 140 7-149 2-143 (143)
3 PF02953 zf-Tim10_DDP: Tim10/D 94.5 0.14 3E-06 33.8 5.5 59 82-143 7-65 (66)
4 KOG3479 Mitochondrial import i 82.4 6.1 0.00013 28.2 5.9 44 93-143 20-63 (83)
5 PF05811 DUF842: Eukaryotic pr 78.9 5 0.00011 30.3 4.9 46 90-135 46-93 (131)
6 KOG3489 Mitochondrial import i 73.8 14 0.0003 26.5 5.7 68 75-146 12-81 (86)
7 PF02953 zf-Tim10_DDP: Tim10/D 53.8 30 0.00064 22.5 4.1 39 48-86 23-64 (66)
8 PF07445 priB_priC: Primosomal 39.5 77 0.0017 24.9 5.1 34 60-96 125-158 (173)
9 KOG1733 Mitochondrial import i 39.2 88 0.0019 22.9 4.9 45 48-95 45-91 (97)
10 KOG3377 Uncharacterized conser 37.6 86 0.0019 24.5 4.9 52 85-136 31-102 (143)
11 PRK10093 primosomal replicatio 32.7 49 0.0011 26.5 3.0 35 60-96 122-156 (171)
12 PF02320 UCR_hinge: Ubiquinol- 31.6 61 0.0013 21.8 2.9 32 98-129 26-58 (65)
13 PF03172 Sp100: Sp100 domain; 30.7 1.1E+02 0.0025 22.6 4.4 40 8-47 38-79 (103)
14 COG3923 PriC Primosomal replic 27.4 70 0.0015 25.7 3.0 21 76-96 140-160 (175)
15 PF05482 Serendipity_A: Serend 23.0 3.9E+02 0.0085 25.3 7.4 69 24-94 281-368 (552)
16 PF15546 DUF4653: Domain of un 22.9 1.1E+02 0.0024 25.5 3.5 35 12-47 198-232 (239)
17 PF10732 DUF2524: Protein of u 22.4 1.1E+02 0.0024 21.9 2.9 25 58-82 2-26 (84)
18 KOG3480 Mitochondrial import i 21.9 3.2E+02 0.0069 19.8 5.5 63 75-141 12-75 (90)
19 KOG0804 Cytoplasmic Zn-finger 20.7 4.3E+02 0.0094 24.6 7.0 31 70-100 369-399 (493)
No 1
>PF05811 DUF842: Eukaryotic protein of unknown function (DUF842); InterPro: IPR008560 This family consists of a number of conserved eukaryotic proteins of unknown function. The sequences carry three sets of CxxxC motifs, which might suggest a type of zinc-finger formation.
Probab=100.00 E-value=2.4e-53 Score=321.99 Aligned_cols=129 Identities=35% Similarity=0.626 Sum_probs=124.9
Q ss_pred HHHHHHHHHHHHHhhchhhhhhhHHhHHHhhhhhhhhhccc-cCHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 031998 17 RRKLEEVNAAAQAHLAPVQDHVNFTLQQAYFKCAYECFDRT-RKQEEISNCVEHCSVPVVRAQQHFENEMAKFQERLNRS 95 (149)
Q Consensus 17 e~~~~rvq~av~~mv~~ld~~~lR~mQk~~f~Caa~Ccd~~-~s~e~V~~CVe~C~~pl~~aq~~vq~El~~FQ~RLqRC 95 (149)
|++++||+.||++||++||++||||||++||+|+|+||||+ +|+++|++||++|+.||.+||++|++||++||+||+||
T Consensus 1 ~~~~~rvq~av~~mv~~ld~~~lr~mQ~~~f~C~a~Ccdd~~~s~e~V~~Cve~C~~pl~~aq~~vq~El~~FQ~rlqrC 80 (131)
T PF05811_consen 1 EQQQQRVQKAVEKMVDDLDRKYLRKMQKKMFKCAAKCCDDSSASMEQVQRCVERCQQPLQQAQNYVQNELEQFQNRLQRC 80 (131)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999999999999999999888 99999999999999999999999999999999999999
Q ss_pred HHHHHHhhHhhhhhhhh-HHHHHHHHhHHHHHHHhHhhCChHHHHHHHhhh
Q 031998 96 LMVCQDKYESAKLQKIG-IEAVNDLESCVNQSIDDNIKTLPPLVERLKTQF 145 (149)
Q Consensus 96 ~~~CqDk~kd~~~~~~~-~~~~~~le~Cv~~Cvd~hi~lLP~l~krmk~~l 145 (149)
+|+|+|+++|++++++. .++.++||+||++|||+||++||+|++|||++|
T Consensus 81 ~~~C~dk~~d~~~~~~~~~~~~~~~e~C~~~Cvd~hi~llP~l~~r~k~~L 131 (131)
T PF05811_consen 81 VMHCQDKAKDKMDPNPNESDAEKQLESCVNKCVDDHIKLLPSLTKRMKKSL 131 (131)
T ss_pred HHHHHHHHHhhccCCCCchHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhC
Confidence 99999999999988875 688899999999999999999999999999987
No 2
>KOG3377 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.6e-52 Score=319.27 Aligned_cols=140 Identities=41% Similarity=0.730 Sum_probs=133.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhchhhhhhhHHhHHHhhhhhhhhhccc-cCHHHHHHHHHhcCHHHHHHHHHHHHHH
Q 031998 7 MEEQIVSERMRRKLEEVNAAAQAHLAPVQDHVNFTLQQAYFKCAYECFDRT-RKQEEISNCVEHCSVPVVRAQQHFENEM 85 (149)
Q Consensus 7 ~~~~~~~~~~e~~~~rvq~av~~mv~~ld~~~lR~mQk~~f~Caa~Ccd~~-~s~e~V~~CVe~C~~pl~~aq~~vq~El 85 (149)
+|++++ +|+++.+|++|+++|+++|++.|||+||+.||+|||+||||+ ++.+.|++||++|+.||++||+||++||
T Consensus 2 ~~~~~m---~E~~r~kveeav~~m~~~L~r~hir~mQ~~mfrCaa~Ccdd~r~~~e~v~~ci~~c~~pl~~aQ~~~~~El 78 (143)
T KOG3377|consen 2 AEEQIM---LERQRRKVEEAVDEMQSDLDRDHIRKMQQAMFRCAAECCDDSRASEEAVNCCIECCVPPLTKAQQYVQSEL 78 (143)
T ss_pred cHHHHH---HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHhcchHHHHHHHHHHHHH
Confidence 577774 566777899999999999999999999999999999999999 9999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhHhhhhhhhh-HHHHHHHHhHHHHHHHhHhhCChHHHHHHHhhhccCC
Q 031998 86 AKFQERLNRSLMVCQDKYESAKLQKIG-IEAVNDLESCVNQSIDDNIKTLPPLVERLKTQFSIKD 149 (149)
Q Consensus 86 ~~FQ~RLqRC~~~CqDk~kd~~~~~~~-~~~~~~le~Cv~~Cvd~hi~lLP~l~krmk~~l~~~~ 149 (149)
++||+||+||+|+||||+++++.++++ .++..+||+||++|||+|++|||+|++|||++|+|.+
T Consensus 79 ~~FQ~RL~Rc~m~C~Dk~~~~~~~~~~~~~~~~~~e~Cvn~cvd~~v~liP~m~k~MK~al~~~~ 143 (143)
T KOG3377|consen 79 GKFQDRLNRCLMVCNDKFEASKLQGSKRLKAVQQFESCVNKCVDDHVGLIPTMVKRMKEALSIGG 143 (143)
T ss_pred HHHHHHHHHHHHHHhHHHHHhcccCCchHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhcCC
Confidence 999999999999999999999999984 7899999999999999999999999999999999864
No 3
>PF02953 zf-Tim10_DDP: Tim10/DDP family zinc finger; InterPro: IPR004217 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 a putative zinc binding domain with four conserved cysteine residues. Members of this family include subunits 8, 9, 10 and 13 of the mitochondrial inner membrane translocase complex, which are involved in mitochondrial protein import [, ]. Defects in TIM8 are the cause of 2 human syndromes: Mohr-Tranebjaerg syndrome (MTS) [MIM:304700]; also known as dystonia-deafness syndrome (DDS) or X-linked progressive deafness type 1 (DFN-1). It is a recessive neurodegenerative syndrome characterised by postlingual progressive sensorineural deafness as the first presenting symptom in early childhood, followed by progressive dystonia, spasticity, dysphagia, mental deterioration, paranoia and cortical blindness. Jensen syndrome [MIM:311150]; also known as opticoacoustic nerve atrophy with dementia. This X-linked disease is characterised by deafness, blindness and muscle weakness. The small alpha helical proteins Tim8 and Tim13 assemble into a hexameric complex which can bind Tim23 as its substrate and chaperone the hydrophobic Tim23 across the aqueous membrane space []. More information on zinc fingers can be found at Protein of the Month: Zinc Fingers [].; GO: 0006626 protein targeting to mitochondrion, 0045039 protein import into mitochondrial inner membrane, 0042719 mitochondrial intermembrane space protein transporter complex; PDB: 2BSK_B 3CJH_A 3DXR_A.
Probab=94.46 E-value=0.14 Score=33.82 Aligned_cols=59 Identities=27% Similarity=0.396 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhHhhhhhhhhHHHHHHHHhHHHHHHHhHhhCChHHHHHHHh
Q 031998 82 ENEMAKFQERLNRSLMVCQDKYESAKLQKIGIEAVNDLESCVNQSIDDNIKTLPPLVERLKT 143 (149)
Q Consensus 82 q~El~~FQ~RLqRC~~~CqDk~kd~~~~~~~~~~~~~le~Cv~~Cvd~hi~lLP~l~krmk~ 143 (149)
+.++..|++-+++-...|.||=-+.+..+ .+...=++|+..|+++|+...-.+.+++.+
T Consensus 7 ~~q~~~~~~~~~~~t~~Cf~kCv~~~~~~---~L~~~E~~Ci~~C~~ky~~~~~~v~~~~~~ 65 (66)
T PF02953_consen 7 EQQMKDFQELFNKLTERCFDKCVTKFPSS---SLSSKEESCIDNCVDKYIDTNQFVSKRFQQ 65 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHS-TTSSS---S--HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCCC---CCchhHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 34667788888777777777655442211 222344889999999999988777777653
No 4
>KOG3479 consensus Mitochondrial import inner membrane translocase, subunit TIM9 [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.38 E-value=6.1 Score=28.19 Aligned_cols=44 Identities=18% Similarity=0.388 Sum_probs=30.8
Q ss_pred HHHHHHHHHhhHhhhhhhhhHHHHHHHHhHHHHHHHhHhhCChHHHHHHHh
Q 031998 93 NRSLMVCQDKYESAKLQKIGIEAVNDLESCVNQSIDDNIKTLPPLVERLKT 143 (149)
Q Consensus 93 qRC~~~CqDk~kd~~~~~~~~~~~~~le~Cv~~Cvd~hi~lLP~l~krmk~ 143 (149)
.+|-.+|-|.+-..-.. .+=+.|+.+|++++++.=--+.+|..+
T Consensus 20 E~CF~dCV~dft~r~l~-------~~Ee~C~~~C~~Kflk~nqRv~qrf~e 63 (83)
T KOG3479|consen 20 ELCFSDCVDDFTTRDLS-------GKEETCVMRCAEKFLKMNQRVSQRFQE 63 (83)
T ss_pred HHHHHHHHhHhhccccc-------chHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67888887765443322 344889999999999876666666544
No 5
>PF05811 DUF842: Eukaryotic protein of unknown function (DUF842); InterPro: IPR008560 This family consists of a number of conserved eukaryotic proteins of unknown function. The sequences carry three sets of CxxxC motifs, which might suggest a type of zinc-finger formation.
Probab=78.94 E-value=5 Score=30.33 Aligned_cols=46 Identities=24% Similarity=0.367 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHhhHhhh--hhhhhHHHHHHHHhHHHHHHHhHhhCCh
Q 031998 90 ERLNRSLMVCQDKYESAK--LQKIGIEAVNDLESCVNQSIDDNIKTLP 135 (149)
Q Consensus 90 ~RLqRC~~~CqDk~kd~~--~~~~~~~~~~~le~Cv~~Cvd~hi~lLP 135 (149)
+.+++|+..|+..+..+- -.+....++..|..|+-.|.|+.-..+|
T Consensus 46 e~V~~Cve~C~~pl~~aq~~vq~El~~FQ~rlqrC~~~C~dk~~d~~~ 93 (131)
T PF05811_consen 46 EQVQRCVERCQQPLQQAQNYVQNELEQFQNRLQRCVMHCQDKAKDKMD 93 (131)
T ss_pred HHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 455677777765433321 1222356778999999999999886663
No 6
>KOG3489 consensus Mitochondrial import inner membrane translocase, subunit TIM8 [Intracellular trafficking, secretion, and vesicular transport]
Probab=73.82 E-value=14 Score=26.53 Aligned_cols=68 Identities=28% Similarity=0.340 Sum_probs=45.5
Q ss_pred HHHHHHHHHHH--HHHHHHHHHHHHHHHHhhHhhhhhhhhHHHHHHHHhHHHHHHHhHhhCChHHHHHHHhhhc
Q 031998 75 VRAQQHFENEM--AKFQERLNRSLMVCQDKYESAKLQKIGIEAVNDLESCVNQSIDDNIKTLPPLVERLKTQFS 146 (149)
Q Consensus 75 ~~aq~~vq~El--~~FQ~RLqRC~~~CqDk~kd~~~~~~~~~~~~~le~Cv~~Cvd~hi~lLP~l~krmk~~l~ 146 (149)
.+.+.+++.|- .+||..+..=+-.|-||--++++++ +...-|.|...||+-+|..=-.|++|+.....
T Consensus 12 ~el~~fl~~E~qk~k~~~~VHqft~~CWdKCi~~~~sk----lds~~e~ClsnCV~RfiDts~~I~~r~~~~~~ 81 (86)
T KOG3489|consen 12 PELQQFLEAETQKQKFQEQVHQFTEICWDKCIEKPGSK----LDSSEETCLSNCVNRFIDTSLFIVKRLAQMNQ 81 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccc----ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35566666654 4688887655555555544444422 12344789999999999888889999877643
No 7
>PF02953 zf-Tim10_DDP: Tim10/DDP family zinc finger; InterPro: IPR004217 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 a putative zinc binding domain with four conserved cysteine residues. Members of this family include subunits 8, 9, 10 and 13 of the mitochondrial inner membrane translocase complex, which are involved in mitochondrial protein import [, ]. Defects in TIM8 are the cause of 2 human syndromes: Mohr-Tranebjaerg syndrome (MTS) [MIM:304700]; also known as dystonia-deafness syndrome (DDS) or X-linked progressive deafness type 1 (DFN-1). It is a recessive neurodegenerative syndrome characterised by postlingual progressive sensorineural deafness as the first presenting symptom in early childhood, followed by progressive dystonia, spasticity, dysphagia, mental deterioration, paranoia and cortical blindness. Jensen syndrome [MIM:311150]; also known as opticoacoustic nerve atrophy with dementia. This X-linked disease is characterised by deafness, blindness and muscle weakness. The small alpha helical proteins Tim8 and Tim13 assemble into a hexameric complex which can bind Tim23 as its substrate and chaperone the hydrophobic Tim23 across the aqueous membrane space []. More information on zinc fingers can be found at Protein of the Month: Zinc Fingers [].; GO: 0006626 protein targeting to mitochondrion, 0045039 protein import into mitochondrial inner membrane, 0042719 mitochondrial intermembrane space protein transporter complex; PDB: 2BSK_B 3CJH_A 3DXR_A.
Probab=53.80 E-value=30 Score=22.48 Aligned_cols=39 Identities=13% Similarity=0.486 Sum_probs=27.0
Q ss_pred hhhhhhhcc-c-cCHH-HHHHHHHhcCHHHHHHHHHHHHHHH
Q 031998 48 KCAYECFDR-T-RKQE-EISNCVEHCSVPVVRAQQHFENEMA 86 (149)
Q Consensus 48 ~Caa~Ccd~-~-~s~e-~V~~CVe~C~~pl~~aq~~vq~El~ 86 (149)
.|-.+|-++ + .+.. .=..||.+|-.....+...|..-+.
T Consensus 23 ~Cf~kCv~~~~~~~L~~~E~~Ci~~C~~ky~~~~~~v~~~~~ 64 (66)
T PF02953_consen 23 RCFDKCVTKFPSSSLSSKEESCIDNCVDKYIDTNQFVSKRFQ 64 (66)
T ss_dssp HHHHHHS-TTSSSS--HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 477888887 4 3222 3378999999999999888866543
No 8
>PF07445 priB_priC: Primosomal replication protein priB and priC; InterPro: IPR010890 This family contains the bacterial primosomal replication proteins priB and priC (approximately 180 residues long). In Escherichia coli, these function in the assembly of the primosome [].
Probab=39.50 E-value=77 Score=24.93 Aligned_cols=34 Identities=24% Similarity=0.344 Sum_probs=25.4
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031998 60 QEEISNCVEHCSVPVVRAQQHFENEMAKFQERLNRSL 96 (149)
Q Consensus 60 ~e~V~~CVe~C~~pl~~aq~~vq~El~~FQ~RLqRC~ 96 (149)
+++.+...+.|+.- -+..+++|+...+.||.||-
T Consensus 125 i~~~e~~l~~~~~~---~~~~lq~ei~a~e~RL~RCr 158 (173)
T PF07445_consen 125 IQEREQQLEQAQSF---EQQQLQQEILALEQRLQRCR 158 (173)
T ss_pred HHHHHHHHHhCChH---HHHHHHHHHHHHHHHHHHHH
Confidence 34556666776654 56678889999999999983
No 9
>KOG1733 consensus Mitochondrial import inner membrane translocase, subunit TIM13 [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.21 E-value=88 Score=22.86 Aligned_cols=45 Identities=20% Similarity=0.474 Sum_probs=32.1
Q ss_pred hhhhhhhccc-cCHH-HHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 031998 48 KCAYECFDRT-RKQE-EISNCVEHCSVPVVRAQQHFENEMAKFQERLNRS 95 (149)
Q Consensus 48 ~Caa~Ccd~~-~s~e-~V~~CVe~C~~pl~~aq~~vq~El~~FQ~RLqRC 95 (149)
+|--+|--.+ .|.+ .=..||.+|-..-..|.++|-.- ++.||||=
T Consensus 45 kCf~KCit~PGssl~~~e~~Cis~CmdRyMdawniVSrt---y~sRlQre 91 (97)
T KOG1733|consen 45 KCFDKCITKPGSSLDSSEKSCISRCMDRYMDAWNIVSRT---YISRLQRE 91 (97)
T ss_pred HHHHHHhCCCCcccCcchHHHHHHHHHHHHHHHHHHHHH---HHHHHHHH
Confidence 4555666656 3332 23689999999999999999764 56788873
No 10
>KOG3377 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.59 E-value=86 Score=24.50 Aligned_cols=52 Identities=17% Similarity=0.147 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHhhHhhhh--------------------hhhhHHHHHHHHhHHHHHHHhHhhCChH
Q 031998 85 MAKFQERLNRSLMVCQDKYESAKL--------------------QKIGIEAVNDLESCVNQSIDDNIKTLPP 136 (149)
Q Consensus 85 l~~FQ~RLqRC~~~CqDk~kd~~~--------------------~~~~~~~~~~le~Cv~~Cvd~hi~lLP~ 136 (149)
|...|.-+-||.-.|-|+.+.... .+...+++..|..|+-.|-|+--.-.|.
T Consensus 31 ir~mQ~~mfrCaa~Ccdd~r~~~e~v~~ci~~c~~pl~~aQ~~~~~El~~FQ~RL~Rc~m~C~Dk~~~~~~~ 102 (143)
T KOG3377|consen 31 IRKMQQAMFRCAAECCDDSRASEEAVNCCIECCVPPLTKAQQYVQSELGKFQDRLNRCLMVCNDKFEASKLQ 102 (143)
T ss_pred HHHHHHHHHHHHHHHHccccccHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccc
Confidence 344666667777777665333211 1112567789999999999987644443
No 11
>PRK10093 primosomal replication protein N''; Provisional
Probab=32.71 E-value=49 Score=26.48 Aligned_cols=35 Identities=23% Similarity=0.280 Sum_probs=26.6
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031998 60 QEEISNCVEHCSVPVVRAQQHFENEMAKFQERLNRSL 96 (149)
Q Consensus 60 ~e~V~~CVe~C~~pl~~aq~~vq~El~~FQ~RLqRC~ 96 (149)
+.+=+..+..|+... -+..++.||.-+..||.||-
T Consensus 122 v~dre~~L~~a~~~~--~qq~lq~el~alegRL~RCr 156 (171)
T PRK10093 122 VAERRARLARATDLV--EQQTLHREVEAYEGRLARCR 156 (171)
T ss_pred HHHHHHHHHhCCCHH--HHHHHHHHHHHHHHHHHHHH
Confidence 345566777777643 45668999999999999993
No 12
>PF02320 UCR_hinge: Ubiquinol-cytochrome C reductase hinge protein; InterPro: IPR023184 The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex []. The bc1 complex contains 11 subunits; 3 respiratory subunits (cytochrome B, cytochrome C1, Rieske protein), 2 core proteins and 6 low molecular weight proteins. This family represents the 'hinge' protein of the complex which is thought to mediate formation of the cytochrome c1 and cytochrome c complex. Proteins in this entry from an alpha-helical hairpin. This entry represents the structural domain found in these proteins.; PDB: 1BCC_H 1SQP_H 1SQB_H 1BE3_H 2A06_U 1L0L_H 2BCC_H 2FYU_H 1PPJ_U 2YBB_H ....
Probab=31.56 E-value=61 Score=21.77 Aligned_cols=32 Identities=25% Similarity=0.443 Sum_probs=17.2
Q ss_pred HHHHhhHhhhhhhhh-HHHHHHHHhHHHHHHHh
Q 031998 98 VCQDKYESAKLQKIG-IEAVNDLESCVNQSIDD 129 (149)
Q Consensus 98 ~CqDk~kd~~~~~~~-~~~~~~le~Cv~~Cvd~ 129 (149)
.|.+++.+..+.... .+=--.|-.|+..||..
T Consensus 26 ~C~eRV~~~~~~~e~C~ee~fd~~hCvD~Cvap 58 (65)
T PF02320_consen 26 ECVERVNSRSETKEDCVEEYFDLVHCVDHCVAP 58 (65)
T ss_dssp HHHHHHHHCSSSSG-SHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCCCCCcHHHHHHHHHHHHHhhhH
Confidence 356766665442211 11112677888888863
No 13
>PF03172 Sp100: Sp100 domain; InterPro: IPR004865 The Sp100 and promyelocytic leukemia proteins (PML) are constituents of nuclear domains, known as nuclear dots (NDs or NBs - nuclear bodies or PML bodies), and are both covalently modified by the small ubiquitin-related protein SUMO-1. NBs play a role in autoimmunity, virus infections, and in the etiology of acute promyelocytic leukemia []. A functional nuclear localization signal and an NB-targeting region that coincides with an Sp100 homodimerization domain have been mapped. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins, which include the autoimmune regulator proteins (AIRE) and other numerous other transiently or permanently localised proteins. PML is expressed as a family of isoforms (PML I-VII) as a result of alternative splicing, most of which are found in the nucleus. Although there are many other functions of PML NBs in a wide range of cellular pathways, there is accumulating evidence that they represent preferential targets for viral infections and that PML plays a role in the mechanism of the antiviral action of interferon []. The Sp100 domain is usually found at the amino terminus of proteins that contain a SAND domain IPR000770 from INTERPRO. ; GO: 0005634 nucleus
Probab=30.66 E-value=1.1e+02 Score=22.55 Aligned_cols=40 Identities=18% Similarity=0.115 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHH--HHHHHHHhhchhhhhhhHHhHHHhh
Q 031998 8 EEQIVSERMRRKLEE--VNAAAQAHLAPVQDHVNFTLQQAYF 47 (149)
Q Consensus 8 ~~~~~~~~~e~~~~r--vq~av~~mv~~ld~~~lR~mQk~~f 47 (149)
=|++..+.++.-.+. ++.+|-++++.||+..++.+=..-|
T Consensus 38 tE~~y~e~~e~crnlvpv~rvvY~vLs~Lek~f~~~fl~~LF 79 (103)
T PF03172_consen 38 TEQMYKESQEACRNLVPVQRVVYNVLSWLEKTFIRSFLEALF 79 (103)
T ss_pred cHHHHHHHHHHHhccccHHHHHHHHHHHHHHHhhHHHHHHHh
Confidence 356666666663433 8999999999999998877655444
No 14
>COG3923 PriC Primosomal replication protein N'' [DNA replication, recombination, and repair]
Probab=27.44 E-value=70 Score=25.73 Aligned_cols=21 Identities=29% Similarity=0.539 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 031998 76 RAQQHFENEMAKFQERLNRSL 96 (149)
Q Consensus 76 ~aq~~vq~El~~FQ~RLqRC~ 96 (149)
-=|+.++.||.-.+.||.||-
T Consensus 140 vEqq~lqqel~~~e~RlarCr 160 (175)
T COG3923 140 VEQQKLQQELEAYEQRLARCR 160 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 335569999999999999994
No 15
>PF05482 Serendipity_A: Serendipity locus alpha protein (SRY-A); InterPro: IPR008837 The Drosophila serendipity alpha (sry alpha) gene is specifically transcribed at the blastoderm stage, from nuclear cycle 11 to the onset of gastrulation, in all somatic nuclei []. SRY-A is required for the cellularisation of the embryo and is involved in the localisation of the actin filaments just prior to and during plasma membrane invagination [].; GO: 0007349 cellularization, 0005737 cytoplasm, 0016020 membrane
Probab=22.95 E-value=3.9e+02 Score=25.28 Aligned_cols=69 Identities=22% Similarity=0.478 Sum_probs=53.8
Q ss_pred HHHHHHhhchhhhhhhHHhHHHhhhhhhhhhccccCHHHHHHHH------HhcCHHHHH-------------HHHHHHHH
Q 031998 24 NAAAQAHLAPVQDHVNFTLQQAYFKCAYECFDRTRKQEEISNCV------EHCSVPVVR-------------AQQHFENE 84 (149)
Q Consensus 24 q~av~~mv~~ld~~~lR~mQk~~f~Caa~Ccd~~~s~e~V~~CV------e~C~~pl~~-------------aq~~vq~E 84 (149)
.+.+++++.+.|-..=|-||-..| |..|++|-..--.|..|. +.|=.|--+ ...+...|
T Consensus 281 ~~~ld~lI~DFD~n~DRi~QIGlF--AIa~s~d~K~kt~IRSCLASlEsLDt~LIPalql~~s~~~~~hs~iLe~Hf~eE 358 (552)
T PF05482_consen 281 SNDLDELIADFDVNMDRIMQIGLF--AIAFSPDLKRKTIIRSCLASLESLDTCLIPALQLPDSKSSDHHSEILEQHFNEE 358 (552)
T ss_pred HHHHHHHHHHHHhhHHHHHHHhHH--HHHhCcchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHH
Confidence 678999999999999999999999 677888875555666664 356666655 34668899
Q ss_pred HHHHHHHHHH
Q 031998 85 MAKFQERLNR 94 (149)
Q Consensus 85 l~~FQ~RLqR 94 (149)
|.+|++-++.
T Consensus 359 ~~~fr~~I~e 368 (552)
T PF05482_consen 359 MNKFRNAIHE 368 (552)
T ss_pred HHHHHHHHHH
Confidence 9999987753
No 16
>PF15546 DUF4653: Domain of unknown function (DUF4653)
Probab=22.94 E-value=1.1e+02 Score=25.46 Aligned_cols=35 Identities=11% Similarity=0.107 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhchhhhhhhHHhHHHhh
Q 031998 12 VSERMRRKLEEVNAAAQAHLAPVQDHVNFTLQQAYF 47 (149)
Q Consensus 12 ~~~~~e~~~~rvq~av~~mv~~ld~~~lR~mQk~~f 47 (149)
+...+-.+|.|+|+.++.+|+. -++.||-||..+-
T Consensus 198 LQ~~~~dQQ~RLQeSFDtILdn-RKELiRclqq~~~ 232 (239)
T PF15546_consen 198 LQHQLVDQQNRLQESFDTILDN-RKELIRCLQQRAA 232 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh-HHHHHHHHHcccC
Confidence 3467788999999999999874 4667888886543
No 17
>PF10732 DUF2524: Protein of unknown function (DUF2524); InterPro: IPR019668 This entry represents proteins with unknown function, and appear to be restricted to the Bacillaceae.
Probab=22.45 E-value=1.1e+02 Score=21.90 Aligned_cols=25 Identities=20% Similarity=0.511 Sum_probs=21.1
Q ss_pred cCHHHHHHHHHhcCHHHHHHHHHHH
Q 031998 58 RKQEEISNCVEHCSVPVVRAQQHFE 82 (149)
Q Consensus 58 ~s~e~V~~CVe~C~~pl~~aq~~vq 82 (149)
++.++|..|+++|..-+..|+..++
T Consensus 2 atRqs~~~~lq~~e~~i~~a~eQ~~ 26 (84)
T PF10732_consen 2 ATRQSVDEFLQQCEQAIRFAQEQFE 26 (84)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999988764
No 18
>KOG3480 consensus Mitochondrial import inner membrane translocase, subunits TIM10/TIM12 [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.88 E-value=3.2e+02 Score=19.77 Aligned_cols=63 Identities=17% Similarity=0.254 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHh-hhhhhhhHHHHHHHHhHHHHHHHhHhhCChHHHHHH
Q 031998 75 VRAQQHFENEMAKFQERLNRSLMVCQDKYES-AKLQKIGIEAVNDLESCVNQSIDDNIKTLPPLVERL 141 (149)
Q Consensus 75 ~~aq~~vq~El~~FQ~RLqRC~~~CqDk~kd-~~~~~~~~~~~~~le~Cv~~Cvd~hi~lLP~l~krm 141 (149)
++|| .-+.|++---+-++|=++.|..|--+ ... ++++.+-=..|...||.+|...=-.|.++|
T Consensus 12 ~k~q-~Ae~E~emm~d~fNrl~~tC~~KCI~~~y~---EaeLtKGE~~CiDRCVaKy~~~n~~vG~~l 75 (90)
T KOG3480|consen 12 QKAQ-MAELEVEMMSDMFNRLTNTCHKKCIPPRYK---EAELTKGESVCIDRCVAKYLDVNEKVGKKL 75 (90)
T ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHHHHhCCcccc---cccccCchhhHHHHHHHHHHHHHHHHHHHH
Confidence 3444 45566665555555555555544211 111 123334335677777777765444444444
No 19
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=20.71 E-value=4.3e+02 Score=24.56 Aligned_cols=31 Identities=13% Similarity=0.184 Sum_probs=25.0
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031998 70 CSVPVVRAQQHFENEMAKFQERLNRSLMVCQ 100 (149)
Q Consensus 70 C~~pl~~aq~~vq~El~~FQ~RLqRC~~~Cq 100 (149)
=+.-+..+...+.+-|.+||+++.+|...=.
T Consensus 369 ~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~ 399 (493)
T KOG0804|consen 369 ESSDLEAEKKIVERKLQQLQTKLKKCQKELK 399 (493)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456788899999999999999999865433
Done!