Query 034496
Match_columns 93
No_of_seqs 105 out of 182
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 03:29:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034496.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034496hhsearch_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 99.5 1.7E-14 3.7E-19 93.5 5.3 57 4-64 26-83 (83)
2 COG0748 HugZ Putative heme iro 97.7 2.4E-05 5.1E-10 61.0 2.0 64 6-70 177-241 (245)
3 PF14062 DUF4253: Domain of un 53.5 37 0.0008 23.1 4.6 57 22-82 39-96 (111)
4 PF11799 IMS_C: impB/mucB/samB 53.1 30 0.00066 22.0 4.0 36 38-73 12-47 (127)
5 TIGR00496 frr ribosome recycli 50.1 7.1 0.00015 28.7 0.6 47 40-86 87-134 (176)
6 COG4472 Uncharacterized protei 46.5 35 0.00077 23.1 3.5 37 38-78 4-40 (88)
7 smart00491 HELICc2 helicase su 44.7 34 0.00074 23.8 3.4 41 17-58 48-92 (142)
8 PRK03609 umuC DNA polymerase V 43.2 45 0.00097 26.9 4.3 37 38-74 245-281 (422)
9 cd00520 RRF Ribosome recycling 42.8 8.9 0.00019 28.1 0.2 48 40-87 92-140 (179)
10 PRK00083 frr ribosome recyclin 42.6 8.8 0.00019 28.5 0.2 46 40-85 96-142 (185)
11 PRK03103 DNA polymerase IV; Re 42.6 28 0.0006 27.8 3.0 54 19-73 230-283 (409)
12 PF01765 RRF: Ribosome recycli 42.1 31 0.00068 24.6 3.0 43 40-82 78-121 (165)
13 PF11799 IMS_C: impB/mucB/samB 39.2 97 0.0021 19.6 4.7 32 39-70 69-101 (127)
14 PF08406 CbbQ_C: CbbQ/NirQ/Nor 39.1 12 0.00025 24.7 0.3 27 40-66 58-84 (86)
15 cd00424 PolY Y-family of DNA p 38.6 40 0.00087 26.2 3.3 53 19-74 223-275 (343)
16 PRK01810 DNA polymerase IV; Va 38.1 46 0.00099 26.6 3.6 33 41-73 249-281 (407)
17 KOG1794 N-Acetylglucosamine ki 32.6 96 0.0021 25.6 4.6 59 6-72 1-61 (336)
18 PF02575 YbaB_DNA_bd: YbaB/Ebf 31.0 1.4E+02 0.003 18.8 4.9 53 18-72 21-76 (93)
19 PRK02406 DNA polymerase IV; Va 30.8 98 0.0021 24.0 4.3 38 38-75 233-270 (343)
20 PRK14133 DNA polymerase IV; Pr 30.6 99 0.0022 24.1 4.3 51 20-73 223-273 (347)
21 cd03586 PolY_Pol_IV_kappa DNA 29.7 1.1E+02 0.0024 23.3 4.4 37 38-74 236-272 (334)
22 PF10397 ADSL_C: Adenylosuccin 29.2 52 0.0011 20.7 2.1 23 52-74 19-41 (81)
23 COG0748 HugZ Putative heme iro 27.8 51 0.0011 26.0 2.2 46 13-63 25-70 (245)
24 cd01701 PolY_Rev1 DNA polymera 27.4 1E+02 0.0022 24.8 4.0 37 38-74 290-326 (404)
25 PLN02590 probable tyrosine dec 26.4 1.4E+02 0.0031 25.5 4.9 36 38-73 501-536 (539)
26 PRK15058 cytochrome b562; Prov 26.0 1.1E+02 0.0024 21.9 3.5 32 49-81 41-72 (128)
27 cd01734 YlxS_C YxlS is a Bacil 24.8 1.4E+02 0.003 18.8 3.6 31 17-48 43-73 (83)
28 PF07637 PSD5: Protein of unkn 24.6 64 0.0014 19.7 1.9 28 45-74 14-41 (64)
29 PF10406 TAF8_C: Transcription 24.6 1.3E+02 0.0027 17.8 3.1 29 46-74 22-50 (51)
30 PRK03858 DNA polymerase IV; Va 23.7 1.2E+02 0.0026 23.9 3.7 36 38-73 239-274 (396)
31 PF02576 DUF150: Uncharacteris 23.5 2E+02 0.0043 19.8 4.4 31 17-48 105-135 (141)
32 PF13778 DUF4174: Domain of un 23.1 1.3E+02 0.0027 20.4 3.3 39 21-63 73-111 (118)
33 PRK03348 DNA polymerase IV; Pr 22.6 1.7E+02 0.0038 24.1 4.6 36 38-73 246-281 (454)
34 KOG2327 DNA-binding subunit of 21.6 1.7E+02 0.0038 26.0 4.5 56 25-81 417-472 (602)
35 cd01702 PolY_Pol_eta DNA Polym 21.5 1.1E+02 0.0025 24.4 3.2 52 19-73 235-287 (359)
36 cd00823 TopoIIB_Trans TopoIIB_ 20.9 1.3E+02 0.0029 22.1 3.2 35 40-74 100-138 (151)
37 cd01700 PolY_Pol_V_umuC umuC s 20.7 2E+02 0.0044 22.3 4.4 36 38-73 242-277 (344)
38 PF04175 DUF406: Protein of un 20.6 1.1E+02 0.0025 20.6 2.6 28 44-71 29-56 (94)
39 PRK05473 hypothetical protein; 20.4 1.2E+02 0.0027 20.4 2.7 34 41-78 7-40 (86)
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=99.52 E-value=1.7e-14 Score=93.47 Aligned_cols=57 Identities=37% Similarity=0.547 Sum_probs=46.8
Q ss_pred hhhhhhhcCc-ccceeEEeeeecCccEEEEEcCCCCeeeEEecCCcccCChHHHHHHHHHHH
Q 034496 4 TILMKFQWSK-QVLEAKMIWVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMS 64 (93)
Q Consensus 4 ~~~~~~~~~~-~at~ArMlgIDr~GmdLrV~~~g~~~~~vRIpF~~pvtD~~dar~aLV~M~ 64 (93)
.+|++++.|+ .++.|+|++||++||++++ + +...+||||++|++|.+++|.+||+|+
T Consensus 26 ~~~~~~~~~~~~~~~a~m~~id~~G~~l~~---~-~~~~~ripF~~p~~~~~e~r~~lV~ma 83 (83)
T PF10615_consen 26 LLYARHYGGVPDAASARMTDIDRDGFDLRV---G-GDQDVRIPFPPPVTDPEEARDALVEMA 83 (83)
T ss_dssp HHHHHHHHT-SSSSS-EEEEEETTEEEEEE---T-TTEEEEEE-SS---SHCCHHHHHHHHH
T ss_pred HHHHHhcCCCCCCCCEEEEEEeccccEEEE---e-CCcceEcCCCCCCCCHHHHHHHHHHhC
Confidence 4688999999 4789999999999999999 4 679999999999999999999999996
No 2
>COG0748 HugZ Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=97.66 E-value=2.4e-05 Score=61.01 Aligned_cols=64 Identities=6% Similarity=-0.052 Sum_probs=53.5
Q ss_pred hhhhhcCcc-cceeEEeeeecCccEEEEEcCCCCeeeEEecCCcccCChHHHHHHHHHHHHHHHHh
Q 034496 6 LMKFQWSKQ-VLEAKMIWVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEV 70 (93)
Q Consensus 6 ~~~~~~~~~-at~ArMlgIDr~GmdLrV~~~g~~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~ 70 (93)
++..+-++. ++..+|.+||+.|+++.++..+ +....|++|.+|+.+.+|.+.+++.|++.+...
T Consensus 177 yaqv~~~~~e~~~~~I~~Id~~gdfll~~l~~-~~gl~v~gFgqa~~~~~d~~~~lV~l~~~~h~~ 241 (245)
T COG0748 177 YAQVLAQLAEATGGRIKGIDAMGDFLLFQLTP-GQGLFVKGFGQAYAISGDGRIALVGLAGGPHGF 241 (245)
T ss_pred HHHHHHHHhhhhcchhhcccccccceeeeccC-CCceEEeccchhhccccchhHHHHHHhcCcccc
Confidence 444455553 5567799999999999999877 889999999999999999999999999875543
No 3
>PF14062 DUF4253: Domain of unknown function (DUF4253)
Probab=53.48 E-value=37 Score=23.07 Aligned_cols=57 Identities=11% Similarity=0.132 Sum_probs=39.8
Q ss_pred eeecCccEEEEEcCCCCeeeEEecCCcccCChHHHHHHHHHHHHHHHH-hhcCCCCCCcccc
Q 034496 22 WVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWE-VEKNYQSPNFKKV 82 (93)
Q Consensus 22 gIDr~GmdLrV~~~g~~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e-~~r~~~p~~~~~~ 82 (93)
|=|++|..+-.-+. ..+-+-|++|.++.+++...-.+.+.-+.- ..+++.+.++++.
T Consensus 39 W~er~ga~i~~i~~----d~le~~v~~pP~~~~ea~~lA~E~y~fCpD~v~qg~~~~~l~~l 96 (111)
T PF14062_consen 39 WEERYGAEIVGIGF----DTLELSVARPPQTPEEAEALAAEHYAFCPDIVDQGYGNFTLEEL 96 (111)
T ss_pred HHHHhCEEEEEEEC----CEEEEEECCCCCCHHHHHHHHHHHHHhCccHHhcCCCCCCHHHH
Confidence 44777877766543 367777888999999998888888776665 4455555555544
No 4
>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=53.08 E-value=30 Score=21.98 Aligned_cols=36 Identities=11% Similarity=0.193 Sum_probs=31.0
Q ss_pred CeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcC
Q 034496 38 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 73 (93)
Q Consensus 38 ~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~ 73 (93)
........|+.|+.|.+++...|..|+..+.++-+.
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 455667788999999999999999999999888763
No 5
>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=50.06 E-value=7.1 Score=28.75 Aligned_cols=47 Identities=21% Similarity=0.255 Sum_probs=34.1
Q ss_pred eeEEecCCcccCChH-HHHHHHHHHHHHHHHhhcCCCCCCcccccccc
Q 034496 40 FDVRIPFPTEVTDEK-GAKSSFNCMSQQAWEVEKNYQSPNFKKVKHLK 86 (93)
Q Consensus 40 ~~vRIpF~~pvtD~~-dar~aLV~M~r~A~e~~r~~~p~~~~~~~~~~ 86 (93)
..+|||||.+=+++. ++-..+..++..|...-|+.+=-..++++.++
T Consensus 87 ~~Iri~iP~lT~E~RkelvK~~k~~~E~aKv~iRniRr~~~~~iKk~~ 134 (176)
T TIGR00496 87 SVIRVNFPPLTEERRKELVKHAKKIAEQAKVAVRNVRRDANDKVKKLE 134 (176)
T ss_pred CEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 579999998766644 77777777777777777777666666666553
No 6
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.45 E-value=35 Score=23.07 Aligned_cols=37 Identities=24% Similarity=0.265 Sum_probs=30.2
Q ss_pred CeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcCCCCCC
Q 034496 38 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNYQSPN 78 (93)
Q Consensus 38 ~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~~~p~~ 78 (93)
.+.++|+.|.. .+.++++..|...+..- .|++|+|.+
T Consensus 4 ~D~T~~f~~~d--~~~~~v~e~L~~VY~sL--~ekGYNpiN 40 (88)
T COG4472 4 TDETMRFDVGD--SDKKDVKETLNDVYNSL--EEKGYNPIN 40 (88)
T ss_pred ccceeeeecCC--ChHHHHHHHHHHHHHHH--HHcCCChHH
Confidence 35688999998 78899999999998775 567888864
No 7
>smart00491 HELICc2 helicase superfamily c-terminal domain.
Probab=44.69 E-value=34 Score=23.84 Aligned_cols=41 Identities=27% Similarity=0.297 Sum_probs=26.9
Q ss_pred eeEEeeeec----CccEEEEEcCCCCeeeEEecCCcccCChHHHHH
Q 034496 17 EAKMIWVDR----LGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKS 58 (93)
Q Consensus 17 ~ArMlgIDr----~GmdLrV~~~g~~~~~vRIpF~~pvtD~~dar~ 58 (93)
.+-++++.+ +|+|+.=..-. ...-+.|||+.|-...-+++.
T Consensus 48 g~iL~~v~~G~~~EGiD~~g~~~r-~vii~glPfp~~~d~~~~~~~ 92 (142)
T smart00491 48 GALLLAVARGKVSEGIDFPDDLGR-AVIIVGIPFPNPDSPILRARL 92 (142)
T ss_pred CEEEEEEeCCeeecceecCCCccE-EEEEEecCCCCCCCHHHHHHH
Confidence 377888874 88888543323 345569999988755544443
No 8
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=43.24 E-value=45 Score=26.91 Aligned_cols=37 Identities=14% Similarity=0.093 Sum_probs=33.1
Q ss_pred CeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcCC
Q 034496 38 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNY 74 (93)
Q Consensus 38 ~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~~ 74 (93)
.....+..|+++++|.++++..+..|+..+.+.-|.-
T Consensus 245 ksi~~~~tf~~~~~~~~~l~~~l~~l~~~l~~rLr~~ 281 (422)
T PRK03609 245 QEIVCSRSFGERITDYESMRQAICSYAARAAEKLRGE 281 (422)
T ss_pred ceEEEeeECCCCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence 3677899999999999999999999999999987754
No 9
>cd00520 RRF Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another round of protein synthesis. RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear. RRF is essential for bacterial growth. It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species.
Probab=42.82 E-value=8.9 Score=28.12 Aligned_cols=48 Identities=17% Similarity=0.225 Sum_probs=35.4
Q ss_pred eeEEecCCcccCCh-HHHHHHHHHHHHHHHHhhcCCCCCCccccccccc
Q 034496 40 FDVRIPFPTEVTDE-KGAKSSFNCMSQQAWEVEKNYQSPNFKKVKHLKQ 87 (93)
Q Consensus 40 ~~vRIpF~~pvtD~-~dar~aLV~M~r~A~e~~r~~~p~~~~~~~~~~~ 87 (93)
..+|||||.+=.++ +++-..+-.++..|...-|+.+=.-..++++++.
T Consensus 92 ~~iri~iP~lT~E~R~~lvK~~k~~~E~~Kv~iRniR~~~~~~lKk~~k 140 (179)
T cd00520 92 AVIRVNLPPLTEERRKELVKDAKKIAEEAKVAIRNIRRDANDKIKKLEK 140 (179)
T ss_pred CEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 49999999876654 4777777778888888878776666666666543
No 10
>PRK00083 frr ribosome recycling factor; Reviewed
Probab=42.63 E-value=8.8 Score=28.46 Aligned_cols=46 Identities=20% Similarity=0.242 Sum_probs=32.5
Q ss_pred eeEEecCCcccCC-hHHHHHHHHHHHHHHHHhhcCCCCCCccccccc
Q 034496 40 FDVRIPFPTEVTD-EKGAKSSFNCMSQQAWEVEKNYQSPNFKKVKHL 85 (93)
Q Consensus 40 ~~vRIpF~~pvtD-~~dar~aLV~M~r~A~e~~r~~~p~~~~~~~~~ 85 (93)
..+|||||.+=++ ++++-..+..++..|...-|+-+=.-.++++++
T Consensus 96 ~~Iri~iP~lT~E~R~elvK~~k~~~E~aKv~iRniRr~~~~~iKk~ 142 (185)
T PRK00083 96 TVIRLPIPPLTEERRKELVKQVKKEAEEAKVAIRNIRRDANDKLKKL 142 (185)
T ss_pred CEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5799999965444 447777777777777777777766666666655
No 11
>PRK03103 DNA polymerase IV; Reviewed
Probab=42.56 E-value=28 Score=27.81 Aligned_cols=54 Identities=7% Similarity=-0.001 Sum_probs=38.2
Q ss_pred EEeeeecCccEEEEEcCCCCeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcC
Q 034496 19 KMIWVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 73 (93)
Q Consensus 19 rMlgIDr~GmdLrV~~~g~~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~ 73 (93)
...|+|..-....-.... ......+.|+.|++|.++++..|..|++...++.|+
T Consensus 230 ~a~G~d~~~v~~~~~~~~-ksi~~~~t~~~~~~~~~~l~~~l~~L~~~l~~rLr~ 283 (409)
T PRK03103 230 TANGIDYSPVTPHSLDRQ-KAIGHQMTLPRDYRGFEEIKVVLLELCEEVCRRARA 283 (409)
T ss_pred HhcCCCCCcCCcccCCCC-CccCCCeECCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 345555554433221112 356678999999999999999999999998887643
No 12
>PF01765 RRF: Ribosome recycling factor; InterPro: IPR023584 The ribosome recycling factor or ribosome release factor (RRF) dissociates ribosomes from mRNA after termination of translation, and is essential for bacterial growth []. Thus ribosomes are 'recycled' and ready for another round of protein synthesis. This entry represents a domain found in ribosome recycling factors.; PDB: 3R8N_Y 1Y69_8 1ISE_A 1EK8_A 1DD5_A 1WIH_A 2Z4L_6 2QBE_6 2V46_Y 1EH1_A ....
Probab=42.07 E-value=31 Score=24.62 Aligned_cols=43 Identities=19% Similarity=0.299 Sum_probs=20.3
Q ss_pred eeEEecCCcccCC-hHHHHHHHHHHHHHHHHhhcCCCCCCcccc
Q 034496 40 FDVRIPFPTEVTD-EKGAKSSFNCMSQQAWEVEKNYQSPNFKKV 82 (93)
Q Consensus 40 ~~vRIpF~~pvtD-~~dar~aLV~M~r~A~e~~r~~~p~~~~~~ 82 (93)
..+|||+|.|=.+ ++++-..+-.++..|...-|+.+-...++.
T Consensus 78 ~~i~v~iP~~T~E~R~~l~k~~k~~~E~~k~~iR~iR~~~~~~l 121 (165)
T PF01765_consen 78 NTIRVPIPPPTEERRKELVKQAKKIAEEAKVSIRNIRRDAMKKL 121 (165)
T ss_dssp TEEEEE--SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7899999987332 333333344444444444444433333333
No 13
>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=39.23 E-value=97 Score=19.58 Aligned_cols=32 Identities=9% Similarity=0.056 Sum_probs=25.1
Q ss_pred eeeEEecCCcccCChHHHHHHHHHHH-HHHHHh
Q 034496 39 LFDVRIPFPTEVTDEKGAKSSFNCMS-QQAWEV 70 (93)
Q Consensus 39 ~~~vRIpF~~pvtD~~dar~aLV~M~-r~A~e~ 70 (93)
......+|+.|..|.+.+...+..|. +..+..
T Consensus 69 ~~~~~~~l~~p~~~~~~l~~~~~~l~~~~~~~~ 101 (127)
T PF11799_consen 69 SRSRSIRLPFPTNDADELLKAARELLERLLYDP 101 (127)
T ss_dssp EEEEEEEECCCEHCHHHHHHHHHHHHHHHHHHT
T ss_pred eeeEEEeccCCcCCHHHHHHHHHHHHHHHhcCC
Confidence 56668888889999999999999988 444443
No 14
>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=39.14 E-value=12 Score=24.68 Aligned_cols=27 Identities=11% Similarity=0.202 Sum_probs=23.7
Q ss_pred eeEEecCCcccCChHHHHHHHHHHHHH
Q 034496 40 FDVRIPFPTEVTDEKGAKSSFNCMSQQ 66 (93)
Q Consensus 40 ~~vRIpF~~pvtD~~dar~aLV~M~r~ 66 (93)
..++..+.+|++|..|++.+|..|.+.
T Consensus 58 ~A~~~ai~~~Ltdd~~~~~al~~~i~~ 84 (86)
T PF08406_consen 58 QACRAAIVEPLTDDPDVREALRELIDA 84 (86)
T ss_pred HHHHHHHhccCCCCHHHHHHHHHHHHH
Confidence 446778999999999999999999876
No 15
>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=38.58 E-value=40 Score=26.23 Aligned_cols=53 Identities=9% Similarity=0.114 Sum_probs=40.2
Q ss_pred EEeeeecCccEEEEEcCCCCeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcCC
Q 034496 19 KMIWVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNY 74 (93)
Q Consensus 19 rMlgIDr~GmdLrV~~~g~~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~~ 74 (93)
...|+|..-+... .+. ........|+.+++|.+++...|..|++...+.-|..
T Consensus 223 ~a~G~d~~~v~~~--~~~-ksi~~~~tf~~~~~~~~~l~~~l~~l~~~l~~rL~~~ 275 (343)
T cd00424 223 ALRGIDDEPLSPP--RPR-KSFSHERVLPRDSRNAEDARPLLRLLLEKLARRLRRD 275 (343)
T ss_pred HhCCcCCCCCCCC--CCC-CceeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence 3455565555332 222 6788899999999999999999999999999887654
No 16
>PRK01810 DNA polymerase IV; Validated
Probab=38.08 E-value=46 Score=26.55 Aligned_cols=33 Identities=9% Similarity=0.111 Sum_probs=29.6
Q ss_pred eEEecCCcccCChHHHHHHHHHHHHHHHHhhcC
Q 034496 41 DVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 73 (93)
Q Consensus 41 ~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~ 73 (93)
.....|+.|++|.+++...|..|++...+.-|.
T Consensus 249 ~~~~~~~~~~~~~~~l~~~l~~L~~~l~~rLr~ 281 (407)
T PRK01810 249 GNSTTLSHDMDEEKELLDVLRRLSKSVSKRLQK 281 (407)
T ss_pred cceEECCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 358899999999999999999999999987764
No 17
>KOG1794 consensus N-Acetylglucosamine kinase [Carbohydrate transport and metabolism]
Probab=32.62 E-value=96 Score=25.62 Aligned_cols=59 Identities=17% Similarity=0.090 Sum_probs=44.2
Q ss_pred hhhhhcCcc--cceeEEeeeecCccEEEEEcCCCCeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhc
Q 034496 6 LMKFQWSKQ--VLEAKMIWVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEK 72 (93)
Q Consensus 6 ~~~~~~~~~--at~ArMlgIDr~GmdLrV~~~g~~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r 72 (93)
+++.+.|++ +|.-+++-||..|=.+--.+.+ ++-. =..+...+.+.|..|.+.|.|++.
T Consensus 1 ~~~~y~GvEGgaT~s~~Vivd~~~~~~~~a~~~-~Tnh-------~~ig~~~~~~rie~~i~~A~~k~g 61 (336)
T KOG1794|consen 1 LKDFYGGVEGGATCSRLVIVDEDGTILGRAVGG-GTNH-------WLIGSTTCASRIEDMIREAKEKAG 61 (336)
T ss_pred CCceeEeecCCcceeEEEEECCCCCEeeEeecc-cccc-------ccCCchHHHHHHHHHHHHHHhhcC
Confidence 356778887 7889999999988776665544 3322 233478899999999999999874
No 18
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=31.05 E-value=1.4e+02 Score=18.79 Aligned_cols=53 Identities=11% Similarity=-0.015 Sum_probs=32.6
Q ss_pred eEEeeeecCccEEEEEcCCCCeeeEEecCCccc---CChHHHHHHHHHHHHHHHHhhc
Q 034496 18 AKMIWVDRLGFDVRISCPQKGLFDVRIPFPTEV---TDEKGAKSSFNCMSQQAWEVEK 72 (93)
Q Consensus 18 ArMlgIDr~GmdLrV~~~g~~~~~vRIpF~~pv---tD~~dar~aLV~M~r~A~e~~r 72 (93)
.+..+-+..| .++|+.++ ...-+.|-|+..+ .|++++...|+.-+..|.+.-+
T Consensus 21 ~~~~~~s~~g-~V~V~v~g-~g~v~~i~i~~~~~~~~~~~~L~~~I~~A~n~A~~~a~ 76 (93)
T PF02575_consen 21 IEVTGTSGDG-LVTVTVNG-NGEVVDIEIDPSALRPLDPEELEDLIVEAVNDAQKKAR 76 (93)
T ss_dssp SEEEEEETCC-TEEEEEET-TS-EEEEEE-GGGGCTS-HHHHHHHHHHHHHHHHHHHH
T ss_pred CEEEEEECCC-EEEEEEec-CceEEEEEEehHhhccCCHHHHHHHHHHHHHHHHHHHH
Confidence 4555555555 45555555 3444555555333 6889999999999988887654
No 19
>PRK02406 DNA polymerase IV; Validated
Probab=30.84 E-value=98 Score=24.01 Aligned_cols=38 Identities=8% Similarity=0.077 Sum_probs=34.1
Q ss_pred CeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcCCC
Q 034496 38 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNYQ 75 (93)
Q Consensus 38 ~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~~~ 75 (93)
.....+..|+.+++|.++++..|..|+......-+.-.
T Consensus 233 ksi~~~~~~~~~~~~~~~l~~~l~~l~~~l~~rL~~~~ 270 (343)
T PRK02406 233 KSVGVERTFAEDLYDLEACLAELPRLAEKLERRLERAK 270 (343)
T ss_pred cceeeeeeCCCCCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 57888999999999999999999999999998877654
No 20
>PRK14133 DNA polymerase IV; Provisional
Probab=30.61 E-value=99 Score=24.07 Aligned_cols=51 Identities=14% Similarity=0.078 Sum_probs=38.7
Q ss_pred EeeeecCccEEEEEcCCCCeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcC
Q 034496 20 MIWVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 73 (93)
Q Consensus 20 MlgIDr~GmdLrV~~~g~~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~ 73 (93)
..|+|..-+...- +. .....+..|+.|+++.+++...+..|++.....-|.
T Consensus 223 a~G~d~~~v~~~~--~~-ksi~~~~~~~~~~~~~~~l~~~l~~L~~~l~~rL~~ 273 (347)
T PRK14133 223 IRGIDYREVEVSR--ER-KSIGKETTLKKDTKDKEELKKYLKDFSNIISEELKK 273 (347)
T ss_pred hCCCCCCCCCCCC--CC-cceEeeEEcCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 3466665554322 23 678899999999999999999999999998876543
No 21
>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=29.75 E-value=1.1e+02 Score=23.29 Aligned_cols=37 Identities=14% Similarity=0.132 Sum_probs=33.2
Q ss_pred CeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcCC
Q 034496 38 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNY 74 (93)
Q Consensus 38 ~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~~ 74 (93)
.....+..|+.|+++.+++...|..|+...+..-+.-
T Consensus 236 ks~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~rL~~~ 272 (334)
T cd03586 236 KSIGVERTFSEDLTDPEELLEELLELAEELAERLRKR 272 (334)
T ss_pred CeeeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHhC
Confidence 6788999999999999999999999999988876654
No 22
>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=29.20 E-value=52 Score=20.68 Aligned_cols=23 Identities=17% Similarity=0.339 Sum_probs=18.6
Q ss_pred ChHHHHHHHHHHHHHHHHhhcCC
Q 034496 52 DEKGAKSSFNCMSQQAWEVEKNY 74 (93)
Q Consensus 52 D~~dar~aLV~M~r~A~e~~r~~ 74 (93)
++++++..+..++..||+..+++
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 57899999999999999976554
No 23
>COG0748 HugZ Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=27.82 E-value=51 Score=26.00 Aligned_cols=46 Identities=22% Similarity=0.240 Sum_probs=37.2
Q ss_pred cccceeEEeeeecCccEEEEEcCCCCeeeEEecCCcccCChHHHHHHHHHH
Q 034496 13 KQVLEAKMIWVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCM 63 (93)
Q Consensus 13 ~~at~ArMlgIDr~GmdLrV~~~g~~~~~vRIpF~~pvtD~~dar~aLV~M 63 (93)
...+..-..++|..|+|+.- ..-..+|+-|++.. |..|.|..|..+
T Consensus 25 ~~~~g~p~~sv~~~gid~~g----~p~~~~~~~~~h~~-~~~d~r~sil~~ 70 (245)
T COG0748 25 EPVTGVPFVSVVPVGIDIDG----NPLILLSRLFPHTA-DEADPRCSILLG 70 (245)
T ss_pred CCCCCCceeeeccceeccCC----CcceeEeeeccccc-cccChhhhheec
Confidence 33566788889999988743 24578999999999 999999998776
No 24
>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=27.35 E-value=1e+02 Score=24.82 Aligned_cols=37 Identities=8% Similarity=0.070 Sum_probs=32.4
Q ss_pred CeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcCC
Q 034496 38 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNY 74 (93)
Q Consensus 38 ~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~~ 74 (93)
........|+.|++|.+++...|..|++.....-|.-
T Consensus 290 ksi~~~~tf~~~~~~~~~l~~~l~~L~~~l~~rLr~~ 326 (404)
T cd01701 290 KSVSAEINYGIRFTNVDDVEQFLQRLSEELSKRLEES 326 (404)
T ss_pred ccccceeeCCCCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence 5567889999999999999999999999999876653
No 25
>PLN02590 probable tyrosine decarboxylase
Probab=26.36 E-value=1.4e+02 Score=25.51 Aligned_cols=36 Identities=22% Similarity=0.411 Sum_probs=32.2
Q ss_pred CeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcC
Q 034496 38 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 73 (93)
Q Consensus 38 ~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~ 73 (93)
+..-+|+-+-.|.|+.+|+...+-.|.+.|.+.-|+
T Consensus 501 g~~~lR~~i~n~~T~~~dv~~~~~~i~~~a~~~~~~ 536 (539)
T PLN02590 501 GKFVLRFAVGAPLTEEKHVTEAWQIIQKHASKFTRN 536 (539)
T ss_pred CEEEEEEEecCCCCCHHHHHHHHHHHHHHHHHhccc
Confidence 567899999999999999999999999988887665
No 26
>PRK15058 cytochrome b562; Provisional
Probab=26.00 E-value=1.1e+02 Score=21.87 Aligned_cols=32 Identities=16% Similarity=0.316 Sum_probs=26.6
Q ss_pred ccCChHHHHHHHHHHHHHHHHhhcCCCCCCccc
Q 034496 49 EVTDEKGAKSSFNCMSQQAWEVEKNYQSPNFKK 81 (93)
Q Consensus 49 pvtD~~dar~aLV~M~r~A~e~~r~~~p~~~~~ 81 (93)
-.+|.++++.+|..|-.+|-..-+++ |+..+.
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 35789999999999999998888885 877654
No 27
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=24.79 E-value=1.4e+02 Score=18.84 Aligned_cols=31 Identities=19% Similarity=0.225 Sum_probs=23.1
Q ss_pred eeEEeeeecCccEEEEEcCCCCeeeEEecCCc
Q 034496 17 EAKMIWVDRLGFDVRISCPQKGLFDVRIPFPT 48 (93)
Q Consensus 17 ~ArMlgIDr~GmdLrV~~~g~~~~~vRIpF~~ 48 (93)
...+.++|..++.+.+...+ ....+.|||+.
T Consensus 43 ~G~L~~~~~~~v~l~~~~~~-~~~~~~i~~~~ 73 (83)
T cd01734 43 EGTLLGVDDDTVTLEVDIKT-RGKTVEIPLDK 73 (83)
T ss_pred EEEEEeEeCCEEEEEEecCC-CCeEEEEEhHH
Confidence 47889999999988875433 35688888863
No 28
>PF07637 PSD5: Protein of unknown function (DUF1595); InterPro: IPR013043 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013042 from INTERPRO.
Probab=24.61 E-value=64 Score=19.66 Aligned_cols=28 Identities=18% Similarity=0.355 Sum_probs=20.4
Q ss_pred cCCcccCChHHHHHHHHHHHHHHHHhhcCC
Q 034496 45 PFPTEVTDEKGAKSSFNCMSQQAWEVEKNY 74 (93)
Q Consensus 45 pF~~pvtD~~dar~aLV~M~r~A~e~~r~~ 74 (93)
.|-+|+++.+ -..++.+++.+.+...+|
T Consensus 14 AfRRp~~~~e--~~~~~~~~~~~~~~g~~~ 41 (64)
T PF07637_consen 14 AFRRPLTDEE--VDRYLALYDSARAQGEDF 41 (64)
T ss_pred HhCCCCCHHH--HHHHHHHHHHHHHcCCCH
Confidence 5778888887 677888888877754443
No 29
>PF10406 TAF8_C: Transcription factor TFIID complex subunit 8 C-term ; InterPro: IPR019473 This entry represents the C-terminal region of subunit 8 (also known as TAF8) of the transcription factor TFIID []. The adjacent N-terminal region generally contains a histone fold domain (IPR006565 from INTERPRO). This subunit is one of the key subunits of TFIID, being one of several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery [].
Probab=24.60 E-value=1.3e+02 Score=17.83 Aligned_cols=29 Identities=17% Similarity=0.108 Sum_probs=22.2
Q ss_pred CCcccCChHHHHHHHHHHHHHHHHhhcCC
Q 034496 46 FPTEVTDEKGAKSSFNCMSQQAWEVEKNY 74 (93)
Q Consensus 46 F~~pvtD~~dar~aLV~M~r~A~e~~r~~ 74 (93)
|..+.+|...+|..+++-.+.+.+..+++
T Consensus 22 ~~~~~~d~~~~r~~~~~~~r~~e~aL~~l 50 (51)
T PF10406_consen 22 YNERETDPKKIREKAAEQSRLAEKALRKL 50 (51)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 56789999999988877777776666543
No 30
>PRK03858 DNA polymerase IV; Validated
Probab=23.68 E-value=1.2e+02 Score=23.93 Aligned_cols=36 Identities=0% Similarity=-0.070 Sum_probs=31.6
Q ss_pred CeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcC
Q 034496 38 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 73 (93)
Q Consensus 38 ~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~ 73 (93)
........|..|++|.+++...|..|++...++-|.
T Consensus 239 ksi~~~~t~~~~~~~~~~l~~~l~~L~~~l~~rLr~ 274 (396)
T PRK03858 239 RSVGAQRALGRGPNSPAEVDAVVVALVDRVARRMRA 274 (396)
T ss_pred ccccceeEcCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 456678899999999999999999999999987754
No 31
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=23.54 E-value=2e+02 Score=19.76 Aligned_cols=31 Identities=26% Similarity=0.369 Sum_probs=23.8
Q ss_pred eeEEeeeecCccEEEEEcCCCCeeeEEecCCc
Q 034496 17 EAKMIWVDRLGFDVRISCPQKGLFDVRIPFPT 48 (93)
Q Consensus 17 ~ArMlgIDr~GmdLrV~~~g~~~~~vRIpF~~ 48 (93)
...++++|..++.+.+...+ ....+.|||+.
T Consensus 105 ~G~L~~~~~~~i~l~~~~~~-~~~~~~I~~~~ 135 (141)
T PF02576_consen 105 EGKLLEVDEDEITLEVEGKG-KKKEVEIPFSD 135 (141)
T ss_dssp EEEEEEEETTEEEEEEE-SS--EEEEEE-SS-
T ss_pred EEEEEEEeCCEEEEEECCcc-ceEEEEEEHHH
Confidence 57899999999999988766 66899999975
No 32
>PF13778 DUF4174: Domain of unknown function (DUF4174)
Probab=23.13 E-value=1.3e+02 Score=20.38 Aligned_cols=39 Identities=21% Similarity=0.392 Sum_probs=26.6
Q ss_pred eeeecCccEEEEEcCCCCeeeEEecCCcccCChHHHHHHHHHH
Q 034496 21 IWVDRLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCM 63 (93)
Q Consensus 21 lgIDr~GmdLrV~~~g~~~~~vRIpF~~pvtD~~dar~aLV~M 63 (93)
+.++..||.+-+..-+ |...+| |+.|+ |.+++-..|=.|
T Consensus 73 l~~~~~~f~~vLiGKD-G~vK~r--~~~p~-~~~~lf~~ID~M 111 (118)
T PF13778_consen 73 LRIPPGGFTVVLIGKD-GGVKLR--WPEPI-DPEELFDTIDAM 111 (118)
T ss_pred hCCCCCceEEEEEeCC-CcEEEe--cCCCC-CHHHHHHHHhCC
Confidence 3455677776666555 556666 88888 888887777665
No 33
>PRK03348 DNA polymerase IV; Provisional
Probab=22.55 E-value=1.7e+02 Score=24.09 Aligned_cols=36 Identities=8% Similarity=0.148 Sum_probs=32.2
Q ss_pred CeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcC
Q 034496 38 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 73 (93)
Q Consensus 38 ~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~ 73 (93)
........|+.+++|.+++...|..|+..+....+.
T Consensus 246 ksis~e~tf~~~i~~~~~l~~~L~~L~~~l~~rL~~ 281 (454)
T PRK03348 246 KQISAESTFAVDLTTRAQLREAIERIAEHAHRRLLK 281 (454)
T ss_pred ceEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 567889999999999999999999999999887653
No 34
>KOG2327 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku70 autoantigen) [Replication, recombination and repair]
Probab=21.64 E-value=1.7e+02 Score=25.97 Aligned_cols=56 Identities=16% Similarity=0.168 Sum_probs=45.4
Q ss_pred cCccEEEEEcCCCCeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcCCCCCCccc
Q 034496 25 RLGFDVRISCPQKGLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNYQSPNFKK 81 (93)
Q Consensus 25 r~GmdLrV~~~g~~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~~~p~~~~~ 81 (93)
.+||-|---.+- .+.-=++||..++......-..+.+|.|.-.-.-|++-||.|+-
T Consensus 417 ~~GF~LV~flp~-aDdirk~p~~~~v~~~p~~~eqmk~i~Qki~f~~rsd~~p~feN 472 (602)
T KOG2327|consen 417 PCGFQLVGFLPF-ADDIRKFPLQDKVSTEPEQEEQMKAIVQKIRFKLRSDYPPFFEN 472 (602)
T ss_pred ccceEEEEeecc-cchhccCCCcccccCCcchHHHHHHHHHHHHHHhhcCCcccccC
Confidence 348877521233 45677899999999999999999999999999999999887764
No 35
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, 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. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=21.52 E-value=1.1e+02 Score=24.40 Aligned_cols=52 Identities=8% Similarity=0.004 Sum_probs=39.3
Q ss_pred EEeeeecCccEEEEEcCCCCeeeEEecCCcccCCh-HHHHHHHHHHHHHHHHhhcC
Q 034496 19 KMIWVDRLGFDVRISCPQKGLFDVRIPFPTEVTDE-KGAKSSFNCMSQQAWEVEKN 73 (93)
Q Consensus 19 rMlgIDr~GmdLrV~~~g~~~~~vRIpF~~pvtD~-~dar~aLV~M~r~A~e~~r~ 73 (93)
...|+|..-+..+ .+. ........|+.++++. +++...|..|++...++-|.
T Consensus 235 ~a~G~d~~~v~~~--~~~-ksi~~~~tf~~~~~~~~~~l~~~l~~L~~~l~~rL~~ 287 (359)
T cd01702 235 LLRGIDHEPVKPR--PLP-KSMGSSKNFPGKTALSTEDVQHWLLVLASELNSRLED 287 (359)
T ss_pred HhCCCCCCCCCCC--CCC-ceeeeeeecCCCCCChHHHHHHHHHHHHHHHHHHHHh
Confidence 4456666554422 223 6778899999999999 99999999999998887654
No 36
>cd00823 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Probab=20.89 E-value=1.3e+02 Score=22.13 Aligned_cols=35 Identities=20% Similarity=0.330 Sum_probs=29.6
Q ss_pred eeEEecCCcc----cCChHHHHHHHHHHHHHHHHhhcCC
Q 034496 40 FDVRIPFPTE----VTDEKGAKSSFNCMSQQAWEVEKNY 74 (93)
Q Consensus 40 ~~vRIpF~~p----vtD~~dar~aLV~M~r~A~e~~r~~ 74 (93)
..+.|||..+ +.|..++..+|.--+|.|..+.++|
T Consensus 100 ~St~VPfts~~KeaIadvpEI~~EIrlAl~~~~R~L~~~ 138 (151)
T cd00823 100 ASTKVPFTSEGKEAIADIPEIEEEIKLALQEVARKLKRY 138 (151)
T ss_pred eecCCCcCCcchhhhcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4568999965 7788999999999999998888877
No 37
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. 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. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=20.66 E-value=2e+02 Score=22.25 Aligned_cols=36 Identities=19% Similarity=0.160 Sum_probs=31.8
Q ss_pred CeeeEEecCCcccCChHHHHHHHHHHHHHHHHhhcC
Q 034496 38 GLFDVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKN 73 (93)
Q Consensus 38 ~~~~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~ 73 (93)
.+......|+.+++|.+++...|..|++.....-|.
T Consensus 242 ks~~~~~~~~~~~~~~~~l~~~l~~L~~~l~~~L~~ 277 (344)
T cd01700 242 KSIGSSRSFGRDVTDLDELKQALAEYAERAAEKLRR 277 (344)
T ss_pred cEEEEeeEcCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999999999999998886643
No 38
>PF04175 DUF406: Protein of unknown function (DUF406) ; InterPro: IPR005272 These small proteins are approximately 100 amino acids in length and appear to be found only in gamma proteobacteria. The function of this protein family is unknown. ; PDB: 2JZ5_A 2KHD_A 2K3I_A.
Probab=20.60 E-value=1.1e+02 Score=20.58 Aligned_cols=28 Identities=18% Similarity=0.241 Sum_probs=23.6
Q ss_pred ecCCcccCChHHHHHHHHHHHHHHHHhh
Q 034496 44 IPFPTEVTDEKGAKSSFNCMSQQAWEVE 71 (93)
Q Consensus 44 IpF~~pvtD~~dar~aLV~M~r~A~e~~ 71 (93)
+.|+.--.+..++...+..|++.|+.++
T Consensus 29 ~~~~~~~~~~~~Ae~~l~~l~~kAk~v~ 56 (94)
T PF04175_consen 29 AEVSIVFASEAEAEAALAKLTEKAKQVE 56 (94)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHHHHS
T ss_pred EEEEEEeCCHHHHHHHHHHHHHHHHhhc
Confidence 3445556789999999999999999998
No 39
>PRK05473 hypothetical protein; Provisional
Probab=20.37 E-value=1.2e+02 Score=20.43 Aligned_cols=34 Identities=21% Similarity=0.299 Sum_probs=23.0
Q ss_pred eEEecCCcccCChHHHHHHHHHHHHHHHHhhcCCCCCC
Q 034496 41 DVRIPFPTEVTDEKGAKSSFNCMSQQAWEVEKNYQSPN 78 (93)
Q Consensus 41 ~vRIpF~~pvtD~~dar~aLV~M~r~A~e~~r~~~p~~ 78 (93)
+.++.|. -.+..+++..|..-+.+-. ||+|.|.+
T Consensus 7 Tm~F~~~--~~~~~~v~eiL~~Vy~AL~--EKGYNPin 40 (86)
T PRK05473 7 TMRFDFD--DEKKKDVREILTTVYDALE--EKGYNPIN 40 (86)
T ss_pred ceeeeCC--cccHHHHHHHHHHHHHHHH--HcCCChHH
Confidence 4444443 3456688888888887764 58999864
Done!