Query 035061
Match_columns 74
No_of_seqs 102 out of 104
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 08:53:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035061.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035061hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10615 DUF2470: Protein of u 99.2 1.3E-11 2.8E-16 77.0 3.1 41 1-45 43-83 (83)
2 COG0748 HugZ Putative heme iro 94.1 0.046 9.9E-07 41.6 2.8 46 1-47 192-237 (245)
3 PF11799 IMS_C: impB/mucB/samB 76.2 7.4 0.00016 23.8 4.3 42 10-51 56-101 (127)
4 PF11148 DUF2922: Protein of u 75.3 14 0.00031 22.1 5.3 39 9-47 3-41 (69)
5 smart00874 B5 tRNA synthetase 63.2 11 0.00023 21.9 2.9 39 4-45 28-66 (71)
6 PF11799 IMS_C: impB/mucB/samB 50.4 20 0.00044 21.8 2.7 36 19-54 12-47 (127)
7 PF14062 DUF4253: Domain of un 49.3 29 0.00063 22.8 3.4 34 3-40 39-72 (111)
8 PF13783 DUF4177: Domain of un 48.9 12 0.00027 21.7 1.5 26 32-57 17-42 (61)
9 PF08406 CbbQ_C: CbbQ/NirQ/Nor 48.0 7.7 0.00017 24.7 0.5 26 23-48 60-85 (86)
10 cd01812 BAG1_N Ubiquitin-like 46.7 34 0.00074 19.3 3.1 37 9-49 1-37 (71)
11 cd01813 UBP_N UBP ubiquitin pr 41.6 47 0.001 20.0 3.3 40 10-53 2-41 (74)
12 PF06183 DinI: DinI-like famil 40.0 35 0.00075 20.8 2.5 14 38-51 46-59 (65)
13 PF11543 UN_NPL4: Nuclear pore 39.7 60 0.0013 20.2 3.6 36 9-48 5-40 (80)
14 COG5417 Uncharacterized small 38.4 44 0.00094 21.9 2.9 28 18-55 16-43 (81)
15 cd03586 PolY_Pol_IV_kappa DNA 37.0 82 0.0018 23.0 4.5 37 19-55 236-272 (334)
16 PTZ00044 ubiquitin; Provisiona 36.6 81 0.0018 18.2 3.7 34 10-46 2-35 (76)
17 PF10397 ADSL_C: Adenylosuccin 35.4 39 0.00085 20.5 2.2 23 33-55 19-41 (81)
18 PF08259 Periviscerokin: Periv 33.7 18 0.00038 15.9 0.3 6 24-29 5-10 (11)
19 cd01806 Nedd8 Nebb8-like ubiq 33.4 95 0.0021 17.6 4.6 33 9-44 1-33 (76)
20 PF03484 B5: tRNA synthetase B 33.0 1.1E+02 0.0023 18.1 3.8 37 4-44 28-64 (70)
21 cd01791 Ubl5 UBL5 ubiquitin-li 32.4 94 0.002 18.8 3.6 35 9-46 2-36 (73)
22 PF03703 bPH_2: Bacterial PH d 31.0 44 0.00094 18.9 1.8 29 11-40 51-79 (80)
23 TIGR00496 frr ribosome recycli 30.8 51 0.0011 23.4 2.5 26 22-47 88-114 (176)
24 PRK01810 DNA polymerase IV; Va 30.6 1.3E+02 0.0027 23.1 4.8 41 9-49 289-329 (407)
25 cd00424 PolY Y-family of DNA p 30.5 1.2E+02 0.0025 22.7 4.5 37 19-55 239-275 (343)
26 PF13889 Chromosome_seg: Chrom 30.3 43 0.00094 20.4 1.8 32 6-37 4-39 (56)
27 PRK15058 cytochrome b562; Prov 30.2 92 0.002 21.7 3.6 32 30-62 41-72 (128)
28 PF12202 OSR1_C: Oxidative-str 29.9 64 0.0014 18.3 2.3 29 9-37 3-37 (38)
29 PRK03858 DNA polymerase IV; Va 29.2 95 0.0021 23.5 3.8 36 19-54 239-274 (396)
30 PRK10597 DNA damage-inducible 29.0 52 0.0011 21.2 2.1 15 37-51 59-73 (81)
31 PRK00083 frr ribosome recyclin 28.9 58 0.0012 23.3 2.5 37 7-48 87-124 (185)
32 smart00213 UBQ Ubiquitin homol 28.8 1E+02 0.0022 16.5 4.5 33 9-45 1-33 (64)
33 PLN02150 terpene synthase/cycl 28.8 81 0.0017 20.2 3.0 19 33-51 20-38 (96)
34 PRK02794 DNA polymerase IV; Pr 27.9 1.5E+02 0.0033 22.9 4.8 42 9-50 317-358 (419)
35 cd01792 ISG15_repeat1 ISG15 ub 26.8 1.3E+02 0.0028 17.9 3.5 37 7-46 1-37 (80)
36 PRK14133 DNA polymerase IV; Pr 26.5 1.4E+02 0.003 22.3 4.3 35 19-53 238-272 (347)
37 PF10213 MRP-S28: Mitochondria 26.4 48 0.001 22.6 1.7 30 27-56 70-99 (127)
38 smart00304 HAMP HAMP (Histidin 25.9 79 0.0017 14.2 3.2 28 19-47 20-47 (53)
39 PF04327 DUF464: Protein of un 25.7 1.8E+02 0.004 18.4 5.3 47 7-55 51-97 (103)
40 cd03586 PolY_Pol_IV_kappa DNA 25.5 1.9E+02 0.0042 21.0 4.8 41 9-49 279-319 (334)
41 cd01809 Scythe_N Ubiquitin-lik 25.3 1.3E+02 0.0029 16.7 4.8 33 9-44 1-33 (72)
42 COG1199 DinG Rad3-related DNA 24.8 31 0.00067 27.8 0.6 25 8-33 541-565 (654)
43 PRK02406 DNA polymerase IV; Va 24.8 1.7E+02 0.0038 21.7 4.5 38 19-56 233-270 (343)
44 KOG2327 DNA-binding subunit of 23.8 1.6E+02 0.0035 25.5 4.6 53 7-62 418-472 (602)
45 PF01343 Peptidase_S49: Peptid 23.5 1.6E+02 0.0034 19.6 3.7 44 4-51 55-98 (154)
46 PRK03858 DNA polymerase IV; Va 23.4 2.7E+02 0.0059 21.1 5.4 42 9-50 282-323 (396)
47 cd06405 PB1_Mekk2_3 The PB1 do 22.7 37 0.00081 22.2 0.6 20 10-32 2-21 (79)
48 PF08897 DUF1841: Domain of un 22.5 1.6E+02 0.0034 20.8 3.7 30 32-61 98-128 (137)
49 PRK03609 umuC DNA polymerase V 22.5 1.9E+02 0.0041 22.4 4.5 35 19-53 245-279 (422)
50 PRK03103 DNA polymerase IV; Re 22.4 1.3E+02 0.0028 23.0 3.5 34 20-53 249-282 (409)
51 PRK01810 DNA polymerase IV; Va 21.8 1.6E+02 0.0034 22.6 3.8 32 23-54 250-281 (407)
52 PRK01216 DNA polymerase IV; Va 21.5 1.6E+02 0.0035 22.6 3.9 36 19-54 243-278 (351)
53 PRK03352 DNA polymerase IV; Va 20.6 1.6E+02 0.0035 21.9 3.7 32 22-53 247-278 (346)
54 cd01701 PolY_Rev1 DNA polymera 20.5 1.8E+02 0.004 22.5 4.0 36 19-54 290-325 (404)
55 PRK03352 DNA polymerase IV; Va 20.2 2.8E+02 0.006 20.7 4.8 40 9-48 287-326 (346)
No 1
>PF10615 DUF2470: Protein of unknown function (DUF2470); InterPro: IPR019595 This entry represents a putative haem-iron utilisation family of proteins, as many members are annotated as being pyridoxamine 5'-phosphate oxidase-related, FMN-binding; however the function of this domain is not known. ; PDB: 3GAS_D 3SWJ_A 2ARZ_B.
Probab=99.19 E-value=1.3e-11 Score=76.98 Aligned_cols=41 Identities=49% Similarity=0.747 Sum_probs=34.7
Q ss_pred CceeeeccceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHH
Q 035061 1 MIWVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMS 45 (74)
Q Consensus 1 m~~VDRlG~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~ 45 (74)
|++||++||++++ + +...+||||++|++|.++++.+|++|+
T Consensus 43 m~~id~~G~~l~~---~-~~~~~ripF~~p~~~~~e~r~~lV~ma 83 (83)
T PF10615_consen 43 MTDIDRDGFDLRV---G-GDQDVRIPFPPPVTDPEEARDALVEMA 83 (83)
T ss_dssp EEEEETTEEEEEE---T-TTEEEEEE-SS---SHCCHHHHHHHHH
T ss_pred EEEEeccccEEEE---e-CCcceEcCCCCCCCCHHHHHHHHHHhC
Confidence 6899999999999 3 789999999999999999999999996
No 2
>COG0748 HugZ Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=94.13 E-value=0.046 Score=41.56 Aligned_cols=46 Identities=9% Similarity=-0.027 Sum_probs=41.6
Q ss_pred CceeeeccceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHH
Q 035061 1 MIWVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQ 47 (74)
Q Consensus 1 m~~VDRlG~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~ 47 (74)
|..||+.|+++.++... +..-.|+.|+.|..+.++...+++.|+..
T Consensus 192 I~~Id~~gdfll~~l~~-~~gl~v~gFgqa~~~~~d~~~~lV~l~~~ 237 (245)
T COG0748 192 IKGIDAMGDFLLFQLTP-GQGLFVKGFGQAYAISGDGRIALVGLAGG 237 (245)
T ss_pred hhcccccccceeeeccC-CCceEEeccchhhccccchhHHHHHHhcC
Confidence 67899999999998765 77789999999999999999999999875
No 3
>PF11799 IMS_C: impB/mucB/samB family C-terminal domain; InterPro: IPR017961 This entry represents the little finger domain found in Y-family (lesion bypass) DNA polymerases. Y-family polymerases were originally known as UmuC/DinB/Rev1/Rad30 after each branch of the family. These enzymes are characterised by their low-fidelity synthesis on undamaged DNA templates and by their ability to traverse replication-blocking lesions. By contrast, high-fidelity polymerases (such as DNA polymerase III) are sensitive to distortions in the DNA template. As a result, Y-family polymerases can extend primer strands across DNA strand lesions that would otherwise stall replicative polymerases. To minimize mutations through their low fidelity synthesis, these enzymes are regulated, and are thought to interact with processivity factors, beta-clamp or proliferating cell nuclear antigen (PCNA), which are also essential for the function of replicative DNA polymerases []. Organisms can contain more than one Y-family polymerase, each with a unique DNA damage bypass and fidelity profile. For example, humans posses four Y-family polymerases: DNA polymerases kappa, iota, eta and Rev1. Y-family polymerases show no homology to DNA polymerases from the A-, B-, C-, D- or X-families []. The Y-family of DNA polymerases includes the following enzymes: Prokaryotic DNA polymerase IV (DinB) []. Archaeal DinB homologue DNA polymerase IV []. Eukaryotic DinB homologue DNA polymerase kappa []. Prokarytoic DNA repair proteins UmuC and UmuD []. Eukaryotic Rad30 homologues DNA polymerase eta and iota [, ]. Eukaryotic DNA repair protein Rev1 []. Human DNA polymerase kappa is a right-handed shaped molecule with palm, fingers, thumb, little finger and wrist subdomains []. This entry represents the little finger domain.; GO: 0003684 damaged DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006281 DNA repair; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 3GV8_B 3G6V_A 4EBC_A 3GV5_B ....
Probab=76.23 E-value=7.4 Score=23.82 Aligned_cols=42 Identities=10% Similarity=0.132 Sum_probs=30.7
Q ss_pred eEEEEcCCCC---ceeeeecCCCccCCHHHHHHHHHHHH-HHHHHH
Q 035061 10 DVRISCPQKG---LFDVRIPFPTEVTDEKGAKSSFNCMS-QQAWEV 51 (74)
Q Consensus 10 ~lRve~~~~g---~~dvRLPFprPV~D~~~lk~~i~~M~-q~Awe~ 51 (74)
.|.+.+++++ ...-..+|+.|..|...+..++..|. +..|..
T Consensus 56 ~l~l~~~~~~~~~~~~~~~~l~~p~~~~~~l~~~~~~l~~~~~~~~ 101 (127)
T PF11799_consen 56 TLKLRYSDFGRCSSRSRSIRLPFPTNDADELLKAARELLERLLYDP 101 (127)
T ss_dssp EEEEEETTSCSCEEEEEEEEECCCEHCHHHHHHHHHHHHHHHHHHT
T ss_pred EEEEEecCCcccceeeEEEeccCCcCCHHHHHHHHHHHHHHHhcCC
Confidence 3444555534 45567788889999999999999998 666765
No 4
>PF11148 DUF2922: Protein of unknown function (DUF2922); InterPro: IPR021321 This bacterial family of proteins has no known function.
Probab=75.35 E-value=14 Score=22.05 Aligned_cols=39 Identities=18% Similarity=0.345 Sum_probs=32.5
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQ 47 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~ 47 (74)
+.|.....+|..+.++|+.|.+--+..+++.+...|...
T Consensus 3 L~l~F~~~~gk~~ti~i~~pk~~lt~~~V~~~m~~ii~~ 41 (69)
T PF11148_consen 3 LELVFKTEDGKTFTISIPNPKEDLTEAEVKAAMQAIIAK 41 (69)
T ss_pred EEEEEEcCCCCEEEEEcCCCCCCCCHHHHHHHHHHHHHh
Confidence 345666666789999999999999999999999988643
No 5
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=63.23 E-value=11 Score=21.91 Aligned_cols=39 Identities=23% Similarity=0.318 Sum_probs=25.4
Q ss_pred eeeccceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHH
Q 035061 4 VDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMS 45 (74)
Q Consensus 4 VDRlG~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~ 45 (74)
+-|+||.+.....+ +...|.+|..|+ |...-...+.+++
T Consensus 28 L~~lg~~~~~~~~~-~~~~v~~P~~R~--Di~~~~DliEei~ 66 (71)
T smart00874 28 LKRLGFEVEVSGDD-DTLEVTVPSYRF--DILIEADLIEEVA 66 (71)
T ss_pred HHHCCCeEEecCCC-CeEEEECCCCcc--ccCcccHHHHHHH
Confidence 46889888543223 668899999996 6555555555444
No 6
>PF11799 IMS_C: impB/mucB/samB family C-terminal domain; InterPro: IPR017961 This entry represents the little finger domain found in Y-family (lesion bypass) DNA polymerases. Y-family polymerases were originally known as UmuC/DinB/Rev1/Rad30 after each branch of the family. These enzymes are characterised by their low-fidelity synthesis on undamaged DNA templates and by their ability to traverse replication-blocking lesions. By contrast, high-fidelity polymerases (such as DNA polymerase III) are sensitive to distortions in the DNA template. As a result, Y-family polymerases can extend primer strands across DNA strand lesions that would otherwise stall replicative polymerases. To minimize mutations through their low fidelity synthesis, these enzymes are regulated, and are thought to interact with processivity factors, beta-clamp or proliferating cell nuclear antigen (PCNA), which are also essential for the function of replicative DNA polymerases []. Organisms can contain more than one Y-family polymerase, each with a unique DNA damage bypass and fidelity profile. For example, humans posses four Y-family polymerases: DNA polymerases kappa, iota, eta and Rev1. Y-family polymerases show no homology to DNA polymerases from the A-, B-, C-, D- or X-families []. The Y-family of DNA polymerases includes the following enzymes: Prokaryotic DNA polymerase IV (DinB) []. Archaeal DinB homologue DNA polymerase IV []. Eukaryotic DinB homologue DNA polymerase kappa []. Prokarytoic DNA repair proteins UmuC and UmuD []. Eukaryotic Rad30 homologues DNA polymerase eta and iota [, ]. Eukaryotic DNA repair protein Rev1 []. Human DNA polymerase kappa is a right-handed shaped molecule with palm, fingers, thumb, little finger and wrist subdomains []. This entry represents the little finger domain.; GO: 0003684 damaged DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006281 DNA repair; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 3GV8_B 3G6V_A 4EBC_A 3GV5_B ....
Probab=50.36 E-value=20 Score=21.83 Aligned_cols=36 Identities=11% Similarity=0.193 Sum_probs=30.2
Q ss_pred CceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhhc
Q 035061 19 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 54 (74)
Q Consensus 19 g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er~ 54 (74)
.....-..|+.|..|..++...|..|+..+.+.-+.
T Consensus 12 ksi~~~~t~~~~~~~~~~i~~~l~~l~~~l~~rL~~ 47 (127)
T PF11799_consen 12 KSIGSERTFPEPISDREEIEEWLRELAEELAERLRE 47 (127)
T ss_dssp SEEEEEEEECEEESSHHHHHHHHHHHHHHHHHHHHH
T ss_pred CEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 344566778899999999999999999999988763
No 7
>PF14062 DUF4253: Domain of unknown function (DUF4253)
Probab=49.26 E-value=29 Score=22.80 Aligned_cols=34 Identities=12% Similarity=0.221 Sum_probs=26.6
Q ss_pred eeeeccceEEEEcCCCCceeeeecCCCccCCHHHHHHH
Q 035061 3 WVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSS 40 (74)
Q Consensus 3 ~VDRlG~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~ 40 (74)
|=||||+.+-.-+.+ .+=+-|++|.++.+++...
T Consensus 39 W~er~ga~i~~i~~d----~le~~v~~pP~~~~ea~~l 72 (111)
T PF14062_consen 39 WEERYGAEIVGIGFD----TLELSVARPPQTPEEAEAL 72 (111)
T ss_pred HHHHhCEEEEEEECC----EEEEEECCCCCCHHHHHHH
Confidence 568999998887755 6778889999888776544
No 8
>PF13783 DUF4177: Domain of unknown function (DUF4177)
Probab=48.90 E-value=12 Score=21.66 Aligned_cols=26 Identities=15% Similarity=0.316 Sum_probs=21.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHhhcCCC
Q 035061 32 TDEKGAKSSFNCMSQQAWEVEKNYQS 57 (74)
Q Consensus 32 ~D~~~lk~~i~~M~q~Awe~er~~~~ 57 (74)
.+..++...|+.+.+..||.=.-..+
T Consensus 17 ~~~~~~~~~Ln~~g~eGWeLV~~~~~ 42 (61)
T PF13783_consen 17 IDPEDLEEILNEYGKEGWELVSIIPP 42 (61)
T ss_pred CCHHHHHHHHHHHHhCCcEEEEEEcC
Confidence 58899999999999999997654433
No 9
>PF08406 CbbQ_C: CbbQ/NirQ/NorQ C-terminal ; InterPro: IPR013615 This domain is found at the C terminus of proteins of the CbbQ/NirQ/NorQ family of proteins which play a role in the post-translational activation of Rubisco []. It is also found in the Thauera aromaticaTutH protein which is similar to the CbbQ/NirQ/NorQ family [], as well as in putative chaperones. The ATPase domain associated with various cellular activities (AAA) IPR011704 from INTERPRO is found in the same bacterial and archaeal proteins as the domain described here.
Probab=47.97 E-value=7.7 Score=24.75 Aligned_cols=26 Identities=12% Similarity=0.248 Sum_probs=23.3
Q ss_pred eeecCCCccCCHHHHHHHHHHHHHHH
Q 035061 23 VRIPFPTEVTDEKGAKSSFNCMSQQA 48 (74)
Q Consensus 23 vRLPFprPV~D~~~lk~~i~~M~q~A 48 (74)
++..+-+|.+|-+++..+|++|.+.-
T Consensus 60 ~~~ai~~~Ltdd~~~~~al~~~i~~~ 85 (86)
T PF08406_consen 60 CRAAIVEPLTDDPDVREALRELIDAV 85 (86)
T ss_pred HHHHHhccCCCCHHHHHHHHHHHHHh
Confidence 67789999999999999999998763
No 10
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=46.71 E-value=34 Score=19.34 Aligned_cols=37 Identities=14% Similarity=0.048 Sum_probs=25.9
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAW 49 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~Aw 49 (74)
+.+.|...+ ..+.++++ |-.+..++|+.|..++....
T Consensus 1 i~i~vk~~g-~~~~i~v~---~~~tv~~lK~~i~~~~gi~~ 37 (71)
T cd01812 1 IRVRVKHGG-ESHDLSIS---SQATFGDLKKMLAPVTGVEP 37 (71)
T ss_pred CEEEEEECC-EEEEEEEC---CCCcHHHHHHHHHHhhCCCh
Confidence 356777764 78888876 55678888888877654433
No 11
>cd01813 UBP_N UBP ubiquitin processing protease. The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=41.60 E-value=47 Score=20.01 Aligned_cols=40 Identities=13% Similarity=-0.004 Sum_probs=28.3
Q ss_pred eEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhh
Q 035061 10 DVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEK 53 (74)
Q Consensus 10 ~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er 53 (74)
.+-|.-.+ ..+++.++ |-++..++|+.|..++..-++..|
T Consensus 2 ~i~vk~~g-~~~~v~v~---~~~Tv~~lK~~i~~~tgvp~~~QK 41 (74)
T cd01813 2 PVIVKWGG-QEYSVTTL---SEDTVLDLKQFIKTLTGVLPERQK 41 (74)
T ss_pred EEEEEECC-EEEEEEEC---CCCCHHHHHHHHHHHHCCCHHHEE
Confidence 34555544 78888877 558888999999888765555444
No 12
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=39.96 E-value=35 Score=20.83 Aligned_cols=14 Identities=29% Similarity=0.503 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHH
Q 035061 38 KSSFNCMSQQAWEV 51 (74)
Q Consensus 38 k~~i~~M~q~Awe~ 51 (74)
|..|.+|+|..||-
T Consensus 46 k~~i~~iLqe~we~ 59 (65)
T PF06183_consen 46 KERIEEILQEMWED 59 (65)
T ss_dssp HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhc
Confidence 99999999999996
No 13
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=39.72 E-value=60 Score=20.16 Aligned_cols=36 Identities=8% Similarity=0.136 Sum_probs=25.1
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQA 48 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~A 48 (74)
+-+||.+++ |.+.|=++ |-++..+|+..|.+-++.+
T Consensus 5 milRvrS~d-G~~Rie~~---~~~t~~~L~~kI~~~l~~~ 40 (80)
T PF11543_consen 5 MILRVRSKD-GMKRIEVS---PSSTLSDLKEKISEQLSIP 40 (80)
T ss_dssp -EEEEE-SS-EEEEEEE----TTSBHHHHHHHHHHHS---
T ss_pred EEEEEECCC-CCEEEEcC---CcccHHHHHHHHHHHcCCC
Confidence 458999998 98866654 7888999999988877654
No 14
>COG5417 Uncharacterized small protein [Function unknown]
Probab=38.39 E-value=44 Score=21.94 Aligned_cols=28 Identities=25% Similarity=0.420 Sum_probs=22.4
Q ss_pred CCceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhhcC
Q 035061 18 KGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNY 55 (74)
Q Consensus 18 ~g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er~~ 55 (74)
++.+|+|||=.-|+ ..+.-.+||.++==
T Consensus 16 g~~yDLrl~d~~pi----------kklIdivwe~~kis 43 (81)
T COG5417 16 GGTYDLRLPDYLPI----------KKLIDIVWESLKIS 43 (81)
T ss_pred CceEEEeccccchH----------HHHHHHHHHHhhcc
Confidence 59999999988875 46677899998743
No 15
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=36.97 E-value=82 Score=22.98 Aligned_cols=37 Identities=14% Similarity=0.132 Sum_probs=33.2
Q ss_pred CceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhhcC
Q 035061 19 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNY 55 (74)
Q Consensus 19 g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er~~ 55 (74)
..+..+..|+.|+++..++...|..|+.......+.-
T Consensus 236 ks~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~rL~~~ 272 (334)
T cd03586 236 KSIGVERTFSEDLTDPEELLEELLELAEELAERLRKR 272 (334)
T ss_pred CeeeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHhC
Confidence 6788999999999999999999999999998876654
No 16
>PTZ00044 ubiquitin; Provisional
Probab=36.56 E-value=81 Score=18.16 Aligned_cols=34 Identities=6% Similarity=-0.058 Sum_probs=24.0
Q ss_pred eEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHH
Q 035061 10 DVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQ 46 (74)
Q Consensus 10 ~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q 46 (74)
.+-|....|..+.+++. |-++..++|..|.....
T Consensus 2 ~i~vk~~~G~~~~l~v~---~~~tv~~lK~~i~~~~g 35 (76)
T PTZ00044 2 QILIKTLTGKKQSFNFE---PDNTVQQVKMALQEKEG 35 (76)
T ss_pred EEEEEeCCCCEEEEEEC---CCCcHHHHHHHHHHHHC
Confidence 45566555566677666 77889999998877653
No 17
>PF10397 ADSL_C: Adenylosuccinate lyase C-terminus; InterPro: IPR019468 Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide (the fifth step of de novo IMP biosynthesis); the formation of adenosine monophosphate (AMP) from adenylosuccinate (the final step in the synthesis of AMP from IMP) []. This entry represents the C-terminal, seven alpha-helical, domain of adenylosuccinate lyase [].; PDB: 1YIS_A 1C3U_B 1C3C_A 3C8T_A 2PFM_B 1RE5_D 1Q5N_A 2VD6_D 2J91_B 2X75_A.
Probab=35.43 E-value=39 Score=20.53 Aligned_cols=23 Identities=17% Similarity=0.339 Sum_probs=18.3
Q ss_pred CHHHHHHHHHHHHHHHHHHhhcC
Q 035061 33 DEKGAKSSFNCMSQQAWEVEKNY 55 (74)
Q Consensus 33 D~~~lk~~i~~M~q~Awe~er~~ 55 (74)
+++++-..+..++..||+..+++
T Consensus 19 gR~~Ah~lv~~~a~~a~~~~~~l 41 (81)
T PF10397_consen 19 GRQEAHELVQEAAMEAWENGRDL 41 (81)
T ss_dssp -HHHHHHHHHHHHHHHHHTTS-H
T ss_pred CHHHHHHHHHHHHHHHHHHCCCH
Confidence 57888999999999999976554
No 18
>PF08259 Periviscerokin: Periviscerokinin family; InterPro: IPR013231 Perviscerokinin neuropeptides are found in the abdominal perisympathetic organs of insects. They mediate visceral muscle contractile activity (myotropic activity). CAPA, which are in the periviscerokinin and pyrokinin peptide families, has potential medical importance. This is due to its myotropic effects on, for example, heart muscles and due to its occurrence in the Ixodoidea (ticks), which are important vectors in the transmission of many animal diseases []. These peptides also have a strong diuretic or anti-diuretic effect, suggesting they have significant medical implications [].
Probab=33.67 E-value=18 Score=15.85 Aligned_cols=6 Identities=67% Similarity=1.320 Sum_probs=4.5
Q ss_pred eecCCC
Q 035061 24 RIPFPT 29 (74)
Q Consensus 24 RLPFpr 29 (74)
=|||||
T Consensus 5 lI~fpR 10 (11)
T PF08259_consen 5 LIPFPR 10 (11)
T ss_pred ccccCC
Confidence 378887
No 19
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=33.45 E-value=95 Score=17.57 Aligned_cols=33 Identities=6% Similarity=0.064 Sum_probs=22.3
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCM 44 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M 44 (74)
|.+.|...+|....++++ |-.+..++|..|...
T Consensus 1 m~i~v~~~~g~~~~~~v~---~~~tv~~lK~~i~~~ 33 (76)
T cd01806 1 MLIKVKTLTGKEIEIDIE---PTDKVERIKERVEEK 33 (76)
T ss_pred CEEEEEeCCCCEEEEEEC---CCCCHHHHHHHHhHh
Confidence 456777766455666554 667888888887653
No 20
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=33.04 E-value=1.1e+02 Score=18.11 Aligned_cols=37 Identities=22% Similarity=0.295 Sum_probs=22.9
Q ss_pred eeeccceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHH
Q 035061 4 VDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCM 44 (74)
Q Consensus 4 VDRlG~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M 44 (74)
+-|+||.+.... ++...|.+|.-| .|...-...+.+.
T Consensus 28 L~~lg~~~~~~~--~~~~~v~vP~~R--~Di~~~~DliEEi 64 (70)
T PF03484_consen 28 LKRLGFKVEKID--GDTLEVTVPSYR--FDIEHEEDLIEEI 64 (70)
T ss_dssp HHHTT-EEEE-C--TTEEEEEEETTS--TT-SSHHHHHHHH
T ss_pred HHHCCCEEEECC--CCEEEEEcCCCc--CCcCcccHHHHHH
Confidence 457888888763 378999999999 4444444444433
No 21
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=32.37 E-value=94 Score=18.75 Aligned_cols=35 Identities=9% Similarity=-0.056 Sum_probs=23.4
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQ 46 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q 46 (74)
+.+.|.+..|..+.+.+ .|-.++.+||..|.....
T Consensus 2 ~~i~vkt~~Gk~~~~~v---~~~~TV~~LK~~I~~~~~ 36 (73)
T cd01791 2 IEVVCNDRLGKKVRVKC---NPDDTIGDLKKLIAAQTG 36 (73)
T ss_pred EEEEEECCCCCEEEEEe---CCCCcHHHHHHHHHHHhC
Confidence 45667665445665555 378899999988865543
No 22
>PF03703 bPH_2: Bacterial PH domain; InterPro: IPR005182 A domain that is found in uncharacterised family of membrane proteins. 1-3 copies found in each protein, with each copy flanked by transmembrane helices.
Probab=31.03 E-value=44 Score=18.95 Aligned_cols=29 Identities=17% Similarity=0.277 Sum_probs=19.3
Q ss_pred EEEEcCCCCceeeeecCCCccCCHHHHHHH
Q 035061 11 VRISCPQKGLFDVRIPFPTEVTDEKGAKSS 40 (74)
Q Consensus 11 lRve~~~~g~~dvRLPFprPV~D~~~lk~~ 40 (74)
+.+..+++...++.||| .+.+++.++.+.
T Consensus 51 i~i~~~~~~~~~~~i~~-~~~~~a~~i~~~ 79 (80)
T PF03703_consen 51 IKIDTAGGSGEKIEIPF-LSIEDAEEIYDW 79 (80)
T ss_pred EEEEECCCCCceeEEec-CCHHHHHHHHhh
Confidence 66666653434478888 777777777654
No 23
>TIGR00496 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily.
Probab=30.83 E-value=51 Score=23.41 Aligned_cols=26 Identities=15% Similarity=0.317 Sum_probs=16.8
Q ss_pred eeeecCCCccCCHH-HHHHHHHHHHHH
Q 035061 22 DVRIPFPTEVTDEK-GAKSSFNCMSQQ 47 (74)
Q Consensus 22 dvRLPFprPV~D~~-~lk~~i~~M~q~ 47 (74)
-+|||||.+=+++. ++...+..++..
T Consensus 88 ~Iri~iP~lT~E~RkelvK~~k~~~E~ 114 (176)
T TIGR00496 88 VIRVNFPPLTEERRKELVKHAKKIAEQ 114 (176)
T ss_pred EEEecCCCCCHHHHHHHHHHHHHHHHH
Confidence 69999999877654 444444444333
No 24
>PRK01810 DNA polymerase IV; Validated
Probab=30.56 E-value=1.3e+02 Score=23.07 Aligned_cols=41 Identities=7% Similarity=0.178 Sum_probs=31.7
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAW 49 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~Aw 49 (74)
+.|.+...+.+.....+.++.|.+|...+-.+...+.+..|
T Consensus 289 l~l~lr~~~~~~~~~~~~l~~pt~~~~~l~~~~~~ll~~~~ 329 (407)
T PRK01810 289 VQIMIRYHDRRTITRSKTLKNPIWEKRDIFQAASRLFKQHW 329 (407)
T ss_pred eEEEEEECCCCceEEEEECCCCCCCHHHHHHHHHHHHHhcc
Confidence 44555555445667888899999999999999998887766
No 25
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=30.46 E-value=1.2e+02 Score=22.70 Aligned_cols=37 Identities=8% Similarity=0.110 Sum_probs=33.0
Q ss_pred CceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhhcC
Q 035061 19 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNY 55 (74)
Q Consensus 19 g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er~~ 55 (74)
.......-|+.+++|..++...+..|++...+..+.-
T Consensus 239 ksi~~~~tf~~~~~~~~~l~~~l~~l~~~l~~rL~~~ 275 (343)
T cd00424 239 KSFSHERVLPRDSRNAEDARPLLRLLLEKLARRLRRD 275 (343)
T ss_pred CceeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence 5677899999999999999999999999999877643
No 26
>PF13889 Chromosome_seg: Chromosome segregation during meiosis
Probab=30.30 E-value=43 Score=20.38 Aligned_cols=32 Identities=28% Similarity=0.602 Sum_probs=25.1
Q ss_pred eccceEEEEcCCCCc----eeeeecCCCccCCHHHH
Q 035061 6 RLGFDVRISCPQKGL----FDVRIPFPTEVTDEKGA 37 (74)
Q Consensus 6 RlG~~lRve~~~~g~----~dvRLPFprPV~D~~~l 37 (74)
||-+.||..++..|. .|+||=|++-+.|.++.
T Consensus 4 RYliHLrf~~~~~gr~YLh~dIRvvF~~r~~d~de~ 39 (56)
T PF13889_consen 4 RYLIHLRFCCPRSGRFYLHTDIRVVFARRSPDSDEG 39 (56)
T ss_pred EEEEEEEEecCCCCcEEEECCeEEEEeccCCCCCcc
Confidence 788999998876443 47999999999776653
No 27
>PRK15058 cytochrome b562; Provisional
Probab=30.20 E-value=92 Score=21.65 Aligned_cols=32 Identities=16% Similarity=0.316 Sum_probs=27.2
Q ss_pred ccCCHHHHHHHHHHHHHHHHHHhhcCCCCcchh
Q 035061 30 EVTDEKGAKSSFNCMSQQAWEVEKNYQSPNFKK 62 (74)
Q Consensus 30 PV~D~~~lk~~i~~M~q~Awe~er~~~~~~~~k 62 (74)
.++|..+++.++..|-.+|=.--+++ ||..+.
T Consensus 41 ~A~~a~~~k~al~~mr~aa~~Ak~~~-P~kl~~ 72 (128)
T PRK15058 41 KTDNAAEVKDALTKMRAAALDAQKAT-PPKLED 72 (128)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHhccC-Cchhhc
Confidence 46899999999999999998888885 887654
No 28
>PF12202 OSR1_C: Oxidative-stress-responsive kinase 1 C terminal; InterPro: IPR024678 Oxidative-stress-responsive kinase 1 (OSR1) is involved in the signalling cascade which activates Na/K/2Cl co-transporter during osmotic stress. This entry represents the CCT domain found in OSR1, STE20/SPS1-related kinase and in WNK activators []. This domain is found in eukaryotes, and is approximately 40 amino acids in length. There is a single completely conserved residue F that may be functionally important. ; PDB: 2V3S_A 2LRU_A.
Probab=29.88 E-value=64 Score=18.33 Aligned_cols=29 Identities=14% Similarity=0.222 Sum_probs=20.3
Q ss_pred ceEEEEcCCC------CceeeeecCCCccCCHHHH
Q 035061 9 FDVRISCPQK------GLFDVRIPFPTEVTDEKGA 37 (74)
Q Consensus 9 ~~lRve~~~~------g~~dvRLPFprPV~D~~~l 37 (74)
|.|||+.+.. ...+++..|.-..+++.++
T Consensus 3 l~Lrv~d~kK~~~k~ken~aI~F~F~~~~D~~e~V 37 (38)
T PF12202_consen 3 LRLRVRDPKKRKGKHKENEAIEFEFDLGKDTAEEV 37 (38)
T ss_dssp EEEEEC-TTSSSSS--TCEEEEEEEETTT--HHHH
T ss_pred EEEEEeccccccCccccCccEEEEEecCCCccccc
Confidence 6788887664 5677999999888887775
No 29
>PRK03858 DNA polymerase IV; Validated
Probab=29.17 E-value=95 Score=23.53 Aligned_cols=36 Identities=0% Similarity=-0.070 Sum_probs=31.5
Q ss_pred CceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhhc
Q 035061 19 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 54 (74)
Q Consensus 19 g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er~ 54 (74)
........|..|.+|..++...|..|++...+..+.
T Consensus 239 ksi~~~~t~~~~~~~~~~l~~~l~~L~~~l~~rLr~ 274 (396)
T PRK03858 239 RSVGAQRALGRGPNSPAEVDAVVVALVDRVARRMRA 274 (396)
T ss_pred ccccceeEcCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 455678899999999999999999999999987754
No 30
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=28.98 E-value=52 Score=21.16 Aligned_cols=15 Identities=27% Similarity=0.541 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHH
Q 035061 37 AKSSFNCMSQQAWEV 51 (74)
Q Consensus 37 lk~~i~~M~q~Awe~ 51 (74)
=|..|.+++|..||-
T Consensus 59 dK~~i~eiLqE~we~ 73 (81)
T PRK10597 59 DKDRISEILQETWES 73 (81)
T ss_pred hHHHHHHHHHHHHhC
Confidence 388899999999996
No 31
>PRK00083 frr ribosome recycling factor; Reviewed
Probab=28.91 E-value=58 Score=23.32 Aligned_cols=37 Identities=19% Similarity=0.378 Sum_probs=21.5
Q ss_pred ccceEEEEcCCCCceeeeecCCCccCCHH-HHHHHHHHHHHHH
Q 035061 7 LGFDVRISCPQKGLFDVRIPFPTEVTDEK-GAKSSFNCMSQQA 48 (74)
Q Consensus 7 lG~~lRve~~~~g~~dvRLPFprPV~D~~-~lk~~i~~M~q~A 48 (74)
||++-.. + | .-+|||||.+=+.+. ++...+..++..|
T Consensus 87 lgl~P~~---d-g-~~Iri~iP~lT~E~R~elvK~~k~~~E~a 124 (185)
T PRK00083 87 LGLNPSN---D-G-TVIRLPIPPLTEERRKELVKQVKKEAEEA 124 (185)
T ss_pred CCCCccc---C-C-CEEEecCCCCCHHHHHHHHHHHHHHHHHH
Confidence 5555543 2 2 369999997665543 5555555554444
No 32
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=28.84 E-value=1e+02 Score=16.50 Aligned_cols=33 Identities=6% Similarity=0.182 Sum_probs=23.0
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMS 45 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~ 45 (74)
|.++|...+ +.+.++++ |-++..+|+..|...+
T Consensus 1 ~~i~vk~~~-~~~~~~v~---~~~tv~~lk~~i~~~~ 33 (64)
T smart00213 1 IELTVKTLD-GTITLEVK---PSDTVSELKEKIAELT 33 (64)
T ss_pred CEEEEEECC-ceEEEEEC---CCCcHHHHHHHHHHHH
Confidence 456777766 67777765 5568888888886654
No 33
>PLN02150 terpene synthase/cyclase family protein
Probab=28.84 E-value=81 Score=20.23 Aligned_cols=19 Identities=16% Similarity=0.312 Sum_probs=17.1
Q ss_pred CHHHHHHHHHHHHHHHHHH
Q 035061 33 DEKGAKSSFNCMSQQAWEV 51 (74)
Q Consensus 33 D~~~lk~~i~~M~q~Awe~ 51 (74)
+.+++...|..|...||+.
T Consensus 20 seeeA~~~i~~li~~~WK~ 38 (96)
T PLN02150 20 TKEEAVSELKKMIRDNYKI 38 (96)
T ss_pred CHHHHHHHHHHHHHHHHHH
Confidence 5678999999999999995
No 34
>PRK02794 DNA polymerase IV; Provisional
Probab=27.93 E-value=1.5e+02 Score=22.90 Aligned_cols=42 Identities=5% Similarity=-0.022 Sum_probs=30.1
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWE 50 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe 50 (74)
+.+.+...+.......+.++.|..|...+-.++..+....|.
T Consensus 317 l~l~l~~~~~~~~~~~~~l~~pt~~~~~l~~~~~~ll~~~~~ 358 (419)
T PRK02794 317 VTLKLKTADFRLRTRRRTLEDPTQLADRIFRTARELLEKETD 358 (419)
T ss_pred EEEEEEECCCCceEEEEECCCCcCCHHHHHHHHHHHHHhccc
Confidence 445555544344556678888999999999998888877653
No 35
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=26.78 E-value=1.3e+02 Score=17.94 Aligned_cols=37 Identities=14% Similarity=0.189 Sum_probs=25.0
Q ss_pred ccceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHH
Q 035061 7 LGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQ 46 (74)
Q Consensus 7 lG~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q 46 (74)
.||.+.|....|..+.+.++ |-.++.++|..|.....
T Consensus 1 ~~~~i~Vk~~~G~~~~~~v~---~~~TV~~lK~~I~~~~~ 37 (80)
T cd01792 1 MGWDLKVKMLGGNEFLVSLR---DSMTVSELKQQIAQKIG 37 (80)
T ss_pred CceEEEEEeCCCCEEEEEcC---CCCcHHHHHHHHHHHhC
Confidence 36788888766455555443 55788899988876543
No 36
>PRK14133 DNA polymerase IV; Provisional
Probab=26.53 E-value=1.4e+02 Score=22.31 Aligned_cols=35 Identities=14% Similarity=0.070 Sum_probs=30.5
Q ss_pred CceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhh
Q 035061 19 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEK 53 (74)
Q Consensus 19 g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er 53 (74)
..+..+..|+.|+++..++...+..|++..-...+
T Consensus 238 ksi~~~~~~~~~~~~~~~l~~~l~~L~~~l~~rL~ 272 (347)
T PRK14133 238 KSIGKETTLKKDTKDKEELKKYLKDFSNIISEELK 272 (347)
T ss_pred cceEeeEEcCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 67889999999999999999999999988766443
No 37
>PF10213 MRP-S28: Mitochondrial ribosomal subunit protein ; InterPro: IPR019349 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae (Baker's yeast) it is mitochondrial ribosomal protein S24 whereas in humans it is S35.
Probab=26.39 E-value=48 Score=22.56 Aligned_cols=30 Identities=17% Similarity=0.385 Sum_probs=26.6
Q ss_pred CCCccCCHHHHHHHHHHHHHHHHHHhhcCC
Q 035061 27 FPTEVTDEKGAKSSFNCMSQQAWEVEKNYQ 56 (74)
Q Consensus 27 FprPV~D~~~lk~~i~~M~q~Awe~er~~~ 56 (74)
|+.+..+.+-+...|..|.++||.....|.
T Consensus 70 ~~~~~qN~~~l~~~l~~L~~EA~~~~~~f~ 99 (127)
T PF10213_consen 70 FPTRAQNKKYLSDLLTRLIHEAKDLTDDFE 99 (127)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhhccCChh
Confidence 899999999999999999999999755553
No 38
>smart00304 HAMP HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain.
Probab=25.86 E-value=79 Score=14.24 Aligned_cols=28 Identities=25% Similarity=0.415 Sum_probs=18.9
Q ss_pred CceeeeecCCCccCCHHHHHHHHHHHHHH
Q 035061 19 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQ 47 (74)
Q Consensus 19 g~~dvRLPFprPV~D~~~lk~~i~~M~q~ 47 (74)
|+....+++..+ .+...+...++.|.+.
T Consensus 20 ~~~~~~~~~~~~-~e~~~l~~~~~~~~~~ 47 (53)
T smart00304 20 GDLTVRLPVDGR-DEIGELARAFNEMADR 47 (53)
T ss_pred CCCceeCCCCCC-cHHHHHHHHHHHHHHH
Confidence 566677777654 4567777788777654
No 39
>PF04327 DUF464: Protein of unknown function (DUF464); InterPro: IPR007422 This entry is represented by Bacteriophage Cp-1, Orf13. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2IDL_A 2G0J_D 2G0I_B 2P92_B 1S12_C.
Probab=25.74 E-value=1.8e+02 Score=18.40 Aligned_cols=47 Identities=23% Similarity=0.421 Sum_probs=36.9
Q ss_pred ccceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhhcC
Q 035061 7 LGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNY 55 (74)
Q Consensus 7 lG~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er~~ 55 (74)
++.+..++..+ |...+++|..-.- +.+.+...+..|.-.--..+++|
T Consensus 51 ~~~~~~~~~~~-G~l~~~i~~~~~~-~~~~~q~ll~~~~~gL~~i~~~Y 97 (103)
T PF04327_consen 51 LGLDVDIEIED-GYLKIEIPNDLDE-KDEKAQLLLETLLLGLKSIEEQY 97 (103)
T ss_dssp TSSSEEEEETT-TEEEEEETTTTTC-TCHHHHHHHHHHHHHHHHHHHHT
T ss_pred hCCCceEEecC-CEEEEEEcCCCcc-ccHHHHHHHHHHHHHHHHHHHHh
Confidence 46677777765 9999999986333 77888888888888888888888
No 40
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=25.54 E-value=1.9e+02 Score=21.02 Aligned_cols=41 Identities=7% Similarity=0.019 Sum_probs=30.4
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAW 49 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~Aw 49 (74)
+.+.+...++......++++.|..|...+-.++..+....|
T Consensus 279 l~l~l~~~~~~~~~~~~~l~~~t~~~~~l~~~~~~~l~~~~ 319 (334)
T cd03586 279 VTVKLKYADFSTRTRSRTLPEPTDDAEDIYELALELLEELL 319 (334)
T ss_pred EEEEEEECCCCeEEEEEECCCCCCCHHHHHHHHHHHHHhcc
Confidence 34445444435667888999999999999998888886654
No 41
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=25.28 E-value=1.3e+02 Score=16.72 Aligned_cols=33 Identities=3% Similarity=0.004 Sum_probs=22.3
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCM 44 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M 44 (74)
|.+.|....|..+.++++-. .+..++|..|...
T Consensus 1 i~i~vk~~~g~~~~~~v~~~---~tv~~lK~~i~~~ 33 (72)
T cd01809 1 IEIKVKTLDSQTHTFTVEEE---ITVLDLKEKIAEE 33 (72)
T ss_pred CEEEEEeCCCCEEEEEECCC---CcHHHHHHHHHHH
Confidence 46777777656777777643 6677888777553
No 42
>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]
Probab=24.80 E-value=31 Score=27.85 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=15.8
Q ss_pred cceEEEEcCCCCceeeeecCCCccCC
Q 035061 8 GFDVRISCPQKGLFDVRIPFPTEVTD 33 (74)
Q Consensus 8 G~~lRve~~~~g~~dvRLPFprPV~D 33 (74)
|+|+.-+... +..=++||||.|=+=
T Consensus 541 GVD~~g~~l~-~vvI~~lPfp~p~dp 565 (654)
T COG1199 541 GVDFPGDALR-LVVIVGLPFPNPDDP 565 (654)
T ss_pred cccCCCCCee-EEEEEecCCCCCCCH
Confidence 4555444433 556699999998543
No 43
>PRK02406 DNA polymerase IV; Validated
Probab=24.80 E-value=1.7e+02 Score=21.70 Aligned_cols=38 Identities=8% Similarity=0.077 Sum_probs=33.8
Q ss_pred CceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhhcCC
Q 035061 19 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNYQ 56 (74)
Q Consensus 19 g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er~~~ 56 (74)
..+.....|+.|++|..++...+..|+...-...+.-+
T Consensus 233 ksi~~~~~~~~~~~~~~~l~~~l~~l~~~l~~rL~~~~ 270 (343)
T PRK02406 233 KSVGVERTFAEDLYDLEACLAELPRLAEKLERRLERAK 270 (343)
T ss_pred cceeeeeeCCCCCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 67889999999999999999999999999888776554
No 44
>KOG2327 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku70 autoantigen) [Replication, recombination and repair]
Probab=23.84 E-value=1.6e+02 Score=25.46 Aligned_cols=53 Identities=15% Similarity=0.222 Sum_probs=44.0
Q ss_pred ccceEE--EEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhhcCCCCcchh
Q 035061 7 LGFDVR--ISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNYQSPNFKK 62 (74)
Q Consensus 7 lG~~lR--ve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er~~~~~~~~k 62 (74)
+||.|- +.. .|..=++||+.++......-..+..|.|--=-.-|++.||.|+-
T Consensus 418 ~GF~LV~flp~---aDdirk~p~~~~v~~~p~~~eqmk~i~Qki~f~~rsd~~p~feN 472 (602)
T KOG2327|consen 418 CGFQLVGFLPF---ADDIRKFPLQDKVSTEPEQEEQMKAIVQKIRFKLRSDYPPFFEN 472 (602)
T ss_pred cceEEEEeecc---cchhccCCCcccccCCcchHHHHHHHHHHHHHHhhcCCcccccC
Confidence 488865 434 45556899999999999999999999999889999999987764
No 45
>PF01343 Peptidase_S49: Peptidase family S49 peptidase classification.; InterPro: IPR002142 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. The domain defines sequences in viruses, archaea, bacteria and plants. These sequences are variously annotated in the different taxonomic groups, examples are: Viruses: capsid protein Archaea: proteinase IV homolog Bacteria: proteinase IV, sohB, SppA, pfaP, putative protease Plants: SppA, protease IV This group also contains proteins classified as non-peptidase homologues that either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases. Related proteins, non-peptidase homologs and unclassified S49 members are also to be found in IPR002810 from INTERPRO.; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3RST_B 3BEZ_D 3BF0_A.
Probab=23.51 E-value=1.6e+02 Score=19.65 Aligned_cols=44 Identities=16% Similarity=0.431 Sum_probs=27.4
Q ss_pred eeeccceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHHHHHH
Q 035061 4 VDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEV 51 (74)
Q Consensus 4 VDRlG~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~ 51 (74)
+|++|+...+... |.++--. |++.--++. .+..+..++...|+.
T Consensus 55 l~k~GV~~~~~~~--g~~K~~~-~~~~~~s~~-~r~~~~~~l~~~~~~ 98 (154)
T PF01343_consen 55 LEKLGVKVEVVRS--GEYKSAG-FPRDPMSEE-ERENLQELLDELYDQ 98 (154)
T ss_dssp HHHTT-EEEEEES--STTCCCC-CTTSS--HH-HHHHHHHHHHHHHHH
T ss_pred HHHCCCeEEEEec--Ccccccc-CcCCCCCHH-HHHHHHHHHHHHHHH
Confidence 6889999999885 4555444 665555553 456677777777754
No 46
>PRK03858 DNA polymerase IV; Validated
Probab=23.40 E-value=2.7e+02 Score=21.08 Aligned_cols=42 Identities=7% Similarity=-0.043 Sum_probs=31.5
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWE 50 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe 50 (74)
+.+.+...+.......+.++.|..|...+-.+...+++..|.
T Consensus 282 l~l~l~~~~~~~~~~~~~l~~~t~~~~~l~~l~~~ll~~~~~ 323 (396)
T PRK03858 282 VVLRLRFDDFTRATRSHTLPRPTASTATLLAAARDLVAAAAP 323 (396)
T ss_pred EEEEEEeCCCCEEEEEEECCCCcCCHHHHHHHHHHHHHhhhh
Confidence 344444444345566788889999999999999999988764
No 47
>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, f
Probab=22.68 E-value=37 Score=22.16 Aligned_cols=20 Identities=20% Similarity=0.283 Sum_probs=12.1
Q ss_pred eEEEEcCCCCceeeeecCCCccC
Q 035061 10 DVRISCPQKGLFDVRIPFPTEVT 32 (74)
Q Consensus 10 ~lRve~~~~g~~dvRLPFprPV~ 32 (74)
++..|..+ .+-=|+|+|||.
T Consensus 2 RiKfE~~g---EKRIi~f~RPvk 21 (79)
T cd06405 2 RIKFEHNG---EKRIIQFPRPVK 21 (79)
T ss_pred eEEEEecC---ceEEEecCCCcc
Confidence 44555533 223489999995
No 48
>PF08897 DUF1841: Domain of unknown function (DUF1841); InterPro: IPR014993 This group of proteins are functionally uncharacterised.
Probab=22.53 E-value=1.6e+02 Score=20.77 Aligned_cols=30 Identities=23% Similarity=0.584 Sum_probs=22.9
Q ss_pred CCHHHHHHHHH-HHHHHHHHHhhcCCCCcch
Q 035061 32 TDEKGAKSSFN-CMSQQAWEVEKNYQSPNFK 61 (74)
Q Consensus 32 ~D~~~lk~~i~-~M~q~Awe~er~~~~~~~~ 61 (74)
.|+.++-..+. +|.+..|+..|+=.|||-+
T Consensus 98 ~~~h~A~H~~mecL~e~iW~aQR~g~~pD~~ 128 (137)
T PF08897_consen 98 GDRHEAEHAMMECLAEMIWEAQRNGRPPDEA 128 (137)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHcCCCCCHH
Confidence 45666666554 5899999999999998754
No 49
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=22.52 E-value=1.9e+02 Score=22.39 Aligned_cols=35 Identities=14% Similarity=0.120 Sum_probs=29.9
Q ss_pred CceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhh
Q 035061 19 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEK 53 (74)
Q Consensus 19 g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er 53 (74)
........|+.|++|..++...|..|+..+=+..+
T Consensus 245 ksi~~~~tf~~~~~~~~~l~~~l~~l~~~l~~rLr 279 (422)
T PRK03609 245 QEIVCSRSFGERITDYESMRQAICSYAARAAEKLR 279 (422)
T ss_pred ceEEEeeECCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 36778999999999999999999999987655544
No 50
>PRK03103 DNA polymerase IV; Reviewed
Probab=22.40 E-value=1.3e+02 Score=23.02 Aligned_cols=34 Identities=6% Similarity=0.123 Sum_probs=29.7
Q ss_pred ceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhh
Q 035061 20 LFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEK 53 (74)
Q Consensus 20 ~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er 53 (74)
.+...+.|+.|.+|..++...|..|++..-+..+
T Consensus 249 si~~~~t~~~~~~~~~~l~~~l~~L~~~l~~rLr 282 (409)
T PRK03103 249 AIGHQMTLPRDYRGFEEIKVVLLELCEEVCRRAR 282 (409)
T ss_pred ccCCCeECCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5668899999999999999999999999776653
No 51
>PRK01810 DNA polymerase IV; Validated
Probab=21.77 E-value=1.6e+02 Score=22.57 Aligned_cols=32 Identities=9% Similarity=0.114 Sum_probs=28.8
Q ss_pred eeecCCCccCCHHHHHHHHHHHHHHHHHHhhc
Q 035061 23 VRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 54 (74)
Q Consensus 23 vRLPFprPV~D~~~lk~~i~~M~q~Awe~er~ 54 (74)
....|+.|++|..++...|..|+....+..+.
T Consensus 250 ~~~~~~~~~~~~~~l~~~l~~L~~~l~~rLr~ 281 (407)
T PRK01810 250 NSTTLSHDMDEEKELLDVLRRLSKSVSKRLQK 281 (407)
T ss_pred ceEECCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 58899999999999999999999998887664
No 52
>PRK01216 DNA polymerase IV; Validated
Probab=21.50 E-value=1.6e+02 Score=22.64 Aligned_cols=36 Identities=11% Similarity=0.116 Sum_probs=32.0
Q ss_pred CceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhhc
Q 035061 19 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 54 (74)
Q Consensus 19 g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er~ 54 (74)
..+...+.|+.+.+|..++...|..|+.......+.
T Consensus 243 ksi~~~~tl~~di~~~~~l~~~l~~L~~~~~~rl~~ 278 (351)
T PRK01216 243 KSIGRYVTLPRNTRDLEEIKPYLKRAIEEAYYKLDG 278 (351)
T ss_pred CCCcCeEECCCccCCHHHHHHHHHHHHHHHHHHHHh
Confidence 467789999999999999999999999988887665
No 53
>PRK03352 DNA polymerase IV; Validated
Probab=20.58 E-value=1.6e+02 Score=21.88 Aligned_cols=32 Identities=16% Similarity=0.346 Sum_probs=27.8
Q ss_pred eeeecCCCccCCHHHHHHHHHHHHHHHHHHhh
Q 035061 22 DVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEK 53 (74)
Q Consensus 22 dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er 53 (74)
....-|+++++|..++...+..|++......+
T Consensus 247 ~~~~tf~~~~~~~~~l~~~l~~L~~~l~~rLr 278 (346)
T PRK03352 247 SREVTFPQDLTDRAEVESAVRELARRVLDEVV 278 (346)
T ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45568999999999999999999999887664
No 54
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=20.50 E-value=1.8e+02 Score=22.48 Aligned_cols=36 Identities=8% Similarity=0.089 Sum_probs=31.4
Q ss_pred CceeeeecCCCccCCHHHHHHHHHHHHHHHHHHhhc
Q 035061 19 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 54 (74)
Q Consensus 19 g~~dvRLPFprPV~D~~~lk~~i~~M~q~Awe~er~ 54 (74)
........|+.|.+|..++...|..|++...+..+.
T Consensus 290 ksi~~~~tf~~~~~~~~~l~~~l~~L~~~l~~rLr~ 325 (404)
T cd01701 290 KSVSAEINYGIRFTNVDDVEQFLQRLSEELSKRLEE 325 (404)
T ss_pred ccccceeeCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 456688999999999999999999999999886654
No 55
>PRK03352 DNA polymerase IV; Validated
Probab=20.22 E-value=2.8e+02 Score=20.65 Aligned_cols=40 Identities=10% Similarity=-0.028 Sum_probs=28.3
Q ss_pred ceEEEEcCCCCceeeeecCCCccCCHHHHHHHHHHHHHHH
Q 035061 9 FDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQA 48 (74)
Q Consensus 9 ~~lRve~~~~g~~dvRLPFprPV~D~~~lk~~i~~M~q~A 48 (74)
+.+.+...++..+...+.++.|..|...+-.+...+.+.-
T Consensus 287 l~l~l~~~~~~~~~~~~~l~~pt~d~~~l~~~~~~ll~~~ 326 (346)
T PRK03352 287 VAVKVRTATFYTRTKIRKLPEPTTDPDVIEAAALDVLDRF 326 (346)
T ss_pred EEEEEEeCCCceeEEEEECCCCcCCHHHHHHHHHHHHHhc
Confidence 4455555543455667788889999999888888887643
Done!