Query 006448
Match_columns 644
No_of_seqs 123 out of 140
Neff 3.4
Searched_HMMs 46136
Date Thu Mar 28 23:25:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006448.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006448hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12014 DUF3506: Domain of un 100.0 8.3E-49 1.8E-53 361.7 13.5 129 478-610 1-134 (134)
2 PF02151 UVR: UvrB/uvrC motif; 97.5 0.00019 4E-09 53.6 4.4 35 110-144 1-35 (36)
3 COG3880 Modulator of heat shoc 95.4 0.019 4E-07 56.8 4.3 38 109-146 134-171 (176)
4 PF02151 UVR: UvrB/uvrC motif; 93.5 0.059 1.3E-06 40.3 2.4 26 148-173 4-29 (36)
5 PRK14668 uvrC excinuclease ABC 92.5 0.31 6.8E-06 55.8 7.3 48 96-143 179-231 (577)
6 PRK14671 uvrC excinuclease ABC 92.2 0.32 6.9E-06 56.1 7.1 49 95-143 194-247 (621)
7 COG0322 UvrC Nuclease subunit 91.6 0.42 9.1E-06 54.9 7.0 47 97-143 180-234 (581)
8 TIGR00194 uvrC excinuclease AB 91.4 0.51 1.1E-05 54.1 7.5 48 96-143 174-226 (574)
9 PRK14666 uvrC excinuclease ABC 90.9 0.52 1.1E-05 55.2 7.0 50 94-143 179-233 (694)
10 PRK14670 uvrC excinuclease ABC 90.7 0.62 1.3E-05 53.5 7.3 49 95-143 156-209 (574)
11 PRK07883 hypothetical protein; 90.6 0.33 7.1E-06 55.1 5.0 47 97-143 387-438 (557)
12 TIGR00631 uvrb excinuclease AB 90.0 0.36 7.9E-06 55.8 4.8 36 107-142 619-654 (655)
13 PRK05298 excinuclease ABC subu 89.8 0.45 9.8E-06 54.8 5.3 37 108-144 610-646 (652)
14 PRK12306 uvrC excinuclease ABC 89.4 0.46 1E-05 53.8 4.9 47 97-143 173-224 (519)
15 PRK00558 uvrC excinuclease ABC 88.8 0.53 1.2E-05 54.0 4.9 34 110-143 201-234 (598)
16 PRK14667 uvrC excinuclease ABC 88.4 0.57 1.2E-05 53.6 4.8 48 96-143 179-231 (567)
17 COG0556 UvrB Helicase subunit 88.3 0.65 1.4E-05 53.3 5.1 40 106-145 619-658 (663)
18 PRK14672 uvrC excinuclease ABC 87.4 0.74 1.6E-05 53.9 5.0 49 95-143 184-237 (691)
19 PRK14669 uvrC excinuclease ABC 86.9 0.83 1.8E-05 52.9 5.0 47 97-143 184-235 (624)
20 KOG4825 Component of synaptic 79.2 3.9 8.5E-05 46.4 6.1 61 110-173 170-234 (666)
21 PRK14666 uvrC excinuclease ABC 72.5 2.7 5.9E-05 49.5 2.9 50 124-173 179-228 (694)
22 KOG1538 Uncharacterized conser 71.8 2.6 5.6E-05 49.7 2.5 72 97-170 787-859 (1081)
23 PRK07883 hypothetical protein; 71.8 2.9 6.3E-05 47.7 2.8 49 123-173 383-433 (557)
24 PRK12306 uvrC excinuclease ABC 70.7 3.2 6.9E-05 47.3 2.9 48 124-173 170-219 (519)
25 PRK14669 uvrC excinuclease ABC 70.4 3.1 6.8E-05 48.4 2.7 51 123-173 180-230 (624)
26 PRK14667 uvrC excinuclease ABC 70.0 3.3 7.2E-05 47.7 2.8 49 124-174 177-227 (567)
27 PRK14670 uvrC excinuclease ABC 69.9 3.2 6.9E-05 47.9 2.6 50 124-173 155-204 (574)
28 PRK00558 uvrC excinuclease ABC 69.6 3.3 7.1E-05 47.8 2.7 48 124-173 180-229 (598)
29 PRK14671 uvrC excinuclease ABC 68.5 3.8 8.2E-05 47.6 2.9 50 124-173 193-242 (621)
30 TIGR00194 uvrC excinuclease AB 68.3 3.6 7.8E-05 47.4 2.7 48 124-173 172-221 (574)
31 KOG1832 HIV-1 Vpr-binding prot 67.0 2.5 5.5E-05 51.1 1.1 13 190-202 1274-1286(1516)
32 PRK14668 uvrC excinuclease ABC 65.7 4.5 9.7E-05 46.7 2.7 48 124-173 177-226 (577)
33 PRK14672 uvrC excinuclease ABC 65.4 4.5 9.6E-05 47.8 2.7 50 124-173 183-232 (691)
34 COG3880 Modulator of heat shoc 60.2 6.7 0.00014 39.4 2.5 25 149-173 139-163 (176)
35 COG2602 Beta-lactamase class D 59.6 7.4 0.00016 41.1 2.8 51 149-200 173-228 (254)
36 PF09059 TyeA: TyeA; InterPro 55.0 12 0.00026 33.7 3.0 28 101-128 58-85 (87)
37 COG0322 UvrC Nuclease subunit 52.3 9.4 0.0002 44.3 2.4 50 122-173 178-229 (581)
38 PF04931 DNA_pol_phi: DNA poly 48.9 13 0.00029 43.9 3.0 11 302-312 623-633 (784)
39 PF07743 HSCB_C: HSCB C-termin 44.3 77 0.0017 26.7 6.1 50 116-170 13-62 (78)
40 KOG3483 Uncharacterized conser 40.6 13 0.00028 33.4 0.9 13 2-14 59-71 (94)
41 PRK05298 excinuclease ABC subu 38.2 59 0.0013 38.0 5.9 31 143-173 610-640 (652)
42 cd01766 Ufm1 Urm1-like ubiquit 35.5 16 0.00035 32.6 0.7 13 2-14 48-60 (82)
43 PF14559 TPR_19: Tetratricopep 35.4 1.2E+02 0.0026 23.6 5.6 50 123-173 1-50 (68)
44 PF07304 SRA1: Steroid recepto 31.7 47 0.001 32.4 3.2 45 118-163 95-139 (157)
45 KOG0316 Conserved WD40 repeat- 31.3 29 0.00062 37.2 1.8 24 497-520 45-68 (307)
46 KOG2387 CTP synthase (UTP-ammo 30.0 32 0.00069 39.5 2.0 53 496-556 39-93 (585)
47 PF13838 Clathrin_H_link: Clat 27.4 71 0.0015 27.6 3.2 24 114-137 7-30 (66)
48 PF08336 P4Ha_N: Prolyl 4-Hydr 26.8 54 0.0012 30.5 2.7 42 93-135 70-111 (134)
49 PF03671 Ufm1: Ubiquitin fold 25.5 32 0.00069 30.6 0.8 12 2-13 48-59 (76)
50 TIGR00631 uvrb excinuclease AB 25.2 38 0.00082 39.8 1.6 29 145-173 622-650 (655)
51 PF15469 Sec5: Exocyst complex 24.7 2.5E+02 0.0054 27.1 6.8 45 126-170 64-108 (182)
52 COG0556 UvrB Helicase subunit 24.6 57 0.0012 38.4 2.8 27 147-173 625-651 (663)
53 PF03863 Phage_mat-A: Phage ma 24.4 1.5E+02 0.0033 33.5 5.9 83 106-212 142-242 (400)
54 KOG0553 TPR repeat-containing 23.8 2E+02 0.0043 31.6 6.4 64 108-172 76-139 (304)
55 PF04931 DNA_pol_phi: DNA poly 23.3 44 0.00095 39.8 1.7 9 439-447 729-737 (784)
56 KOG2376 Signal recognition par 23.3 1.3E+02 0.0027 35.9 5.1 62 114-176 13-74 (652)
57 KOG1832 HIV-1 Vpr-binding prot 23.2 41 0.00089 41.5 1.4 21 205-227 1344-1364(1516)
58 PF07064 RIC1: RIC1; InterPro 23.1 2E+02 0.0044 30.3 6.2 73 93-172 166-244 (258)
59 COG5406 Nucleosome binding fac 23.1 48 0.001 39.6 1.9 13 301-313 874-886 (1001)
60 PRK01773 hscB co-chaperone Hsc 21.0 2.4E+02 0.0052 28.1 6.0 18 57-74 57-75 (173)
61 PF09617 Cas_GSU0053: CRISPR-a 20.3 1.1E+02 0.0024 30.6 3.5 56 128-183 84-140 (169)
62 PF07352 Phage_Mu_Gam: Bacteri 20.1 4.9E+02 0.011 24.8 7.7 77 96-181 2-81 (149)
No 1
>PF12014 DUF3506: Domain of unknown function (DUF3506); InterPro: IPR021894 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 131 to 148 amino acids in length. This domain has a conserved KLTGD sequence motif.
Probab=100.00 E-value=8.3e-49 Score=361.67 Aligned_cols=129 Identities=43% Similarity=0.763 Sum_probs=115.7
Q ss_pred ccccceeeee-eeeCCCCCCCCCCceEeeccCCCccEEEEEEEecCCCCCCCC--CCCccccceEEEEEEEcCCCCccCe
Q 006448 478 SRLSEYTTFS-RINTSEGDLDPFDGLYVGAFGPYGTEVVQLRRKYGQWSGEGE--KSSDMEFFEYVEAVKLTGDLNVPAG 554 (644)
Q Consensus 478 ~~l~~~ttf~-rIytPt~~~dP~~GLwVGdYG~HG~EfL~L~~~~g~~~~~d~--~~sd~~~~~~LEAVKLTGDpNVPRG 554 (644)
+.++||+|++ ++||||+ .|||+|||||+||+||||||+|+|++++|++++. ++++.+|+++|||||||||||||||
T Consensus 1 ~~~ttfstl~p~lytpt~-~~P~~GiwVGdyg~hG~Efl~l~q~~~~~~~~~~~~~~~~~~~~~~leAiKLTGDpNVPrG 79 (134)
T PF12014_consen 1 EGVTTFSTLDPELYTPTP-EKPFRGIWVGDYGPHGCEFLLLHQPDGQWDEDDGSKEPSDREFRGRLEAIKLTGDPNVPRG 79 (134)
T ss_pred CCceEEEecChhccCCCC-CCCccceEEcccCCCCeEEEEEEccCCCccccccccccccccccceEEEEEecCCCCCcCc
Confidence 3567777777 8889999 9999999999999999999999999999988776 3578999999999999999999999
Q ss_pred eEEEEEE-cCCCcCCCCCCCCCCCCCceeE-EEeeeeecCCCCCCCceeeeEEEEEcC
Q 006448 555 EVTFRAK-IGKGSRLPNRGKFPDELGVVAS-YSGQGRIADFGFRNPKWVDGELLQLNG 610 (644)
Q Consensus 555 eVTF~A~-ig~~~~lp~~G~~peElg~gAR-vkG~G~VA~~GF~np~wI~gqLIlis~ 610 (644)
||||+|+ ||+.++| +++.++++.|+| |||+||||++||+|++||+|||||||+
T Consensus 80 evtF~A~DiG~~~~i---~~a~~~~f~G~r~vk~~G~vA~~GF~~~~~id~eLilis~ 134 (134)
T PF12014_consen 80 EVTFRADDIGPGGRI---RVAHEGPFPGARRVKGQGHVAEPGFRNDKWIDGELILISG 134 (134)
T ss_pred cEEEEecccCCCccc---ccccCCCCCceEEEecCCeEcCcCcCCCcceeeEEEEecC
Confidence 9999999 9999998 444555555555 999999999999999999999999986
No 2
>PF02151 UVR: UvrB/uvrC motif; InterPro: IPR001943 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand [].; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3PXG_D 3PXI_C 1E52_B 1QOJ_B 2D7D_B 2NMV_B.
Probab=97.46 E-value=0.00019 Score=53.59 Aligned_cols=35 Identities=37% Similarity=0.548 Sum_probs=30.7
Q ss_pred hhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHhc
Q 006448 110 ESYASLLKFQLEDAIEREDFEEAANLKNAIAEAAS 144 (644)
Q Consensus 110 e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~~ 144 (644)
+.++..|+.+|+.||+.+||+.||+||+.|..+..
T Consensus 1 ~~~i~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l~~ 35 (36)
T PF02151_consen 1 EKLIKELEEKMEEAVENEDFEKAARLRDQIKALKK 35 (36)
T ss_dssp HHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHc
Confidence 35788999999999999999999999999998863
No 3
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=95.37 E-value=0.019 Score=56.78 Aligned_cols=38 Identities=39% Similarity=0.517 Sum_probs=33.4
Q ss_pred HhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHhcCC
Q 006448 109 AESYASLLKFQLEDAIEREDFEEAANLKNAIAEAASKD 146 (644)
Q Consensus 109 ~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~~~D 146 (644)
..+=+.+|+.-|+++|++||||+||-+||.|+++..++
T Consensus 134 ~~~~I~~L~e~Lq~~i~~EefEeAA~iRDqIr~Lk~k~ 171 (176)
T COG3880 134 PKRKIIALKEALQDLIEREEFEEAAVIRDQIRALKAKN 171 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34456889999999999999999999999999998654
No 4
>PF02151 UVR: UvrB/uvrC motif; InterPro: IPR001943 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand [].; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3PXG_D 3PXI_C 1E52_B 1QOJ_B 2D7D_B 2NMV_B.
Probab=93.52 E-value=0.059 Score=40.30 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 148 VAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 148 V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
+..+...|..|+++++|+.|++|||.
T Consensus 4 i~~l~~~m~~a~~~~dfE~Aa~~Rd~ 29 (36)
T PF02151_consen 4 IKELEEKMEEAVENEDFEKAARLRDQ 29 (36)
T ss_dssp HHHHHHHHHHHHHTT-CHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCHHHHHHHHHH
Confidence 45678899999999999999999996
No 5
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=92.45 E-value=0.31 Score=55.75 Aligned_cols=48 Identities=23% Similarity=0.383 Sum_probs=38.7
Q ss_pred hhHHHhhhhhHHH-----HhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 96 WNRWTRHFSEIEQ-----AESYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 96 W~rW~rhF~~ve~-----~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
=+.|+....++-. ...++..|+.+|+.|.++.+||+||+||+.|.++.
T Consensus 179 ~e~Y~~~v~~~~~fL~G~~~~~~~~l~~~m~~aa~~l~FE~Aa~~Rd~i~~l~ 231 (577)
T PRK14668 179 EEAYAEDVESAERFFEGETGVLADPLRREMEAAAQAQEFERAANLRDRLEAVE 231 (577)
T ss_pred HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 3456655555554 34578999999999999999999999999998865
No 6
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=92.22 E-value=0.32 Score=56.11 Aligned_cols=49 Identities=24% Similarity=0.297 Sum_probs=39.1
Q ss_pred ChhHHHhhhhhHH-----HHhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 95 DWNRWTRHFSEIE-----QAESYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 95 dW~rW~rhF~~ve-----~~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
+=+.|+....++. .-..++..|+.+|+.|.++.+||.||++|+.|.++.
T Consensus 194 s~e~Y~~~v~~~~~fL~G~~~~l~~~L~~~M~~as~~l~FE~Aa~~RD~i~~l~ 247 (621)
T PRK14671 194 SEEDYLEMIEEIVRLLKGKTSALIRSLTEEMQRAAAELKFEEAAELKDQIESLK 247 (621)
T ss_pred CHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHH
Confidence 3455775555554 235677999999999999999999999999998875
No 7
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=91.56 E-value=0.42 Score=54.90 Aligned_cols=47 Identities=26% Similarity=0.261 Sum_probs=37.5
Q ss_pred hHHHhhhhhHHHHh--------hHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 97 NRWTRHFSEIEQAE--------SYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 97 ~rW~rhF~~ve~~e--------~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
..+..|+..|+++. .++..|+.+|+.|.+..|||.||+||+.|.++.
T Consensus 180 is~e~Y~e~v~~~~~fL~G~~~~v~~~L~~~M~~As~~l~FE~Aa~~RD~i~al~ 234 (581)
T COG0322 180 ISEEEYREIVEEVKGFLKGKDDAVLQELEEKMEEASENLDFERAARLRDQIKALE 234 (581)
T ss_pred CCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHH
Confidence 33444555555554 455889999999999999999999999999886
No 8
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=91.41 E-value=0.51 Score=54.07 Aligned_cols=48 Identities=27% Similarity=0.356 Sum_probs=37.2
Q ss_pred hhHHHhhhhhHHHH-----hhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 96 WNRWTRHFSEIEQA-----ESYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 96 W~rW~rhF~~ve~~-----e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
=+.|+....++-+. ..++..|+.+|+.|+++.+||.||++|+.|.++.
T Consensus 174 ~e~Y~~~v~~~~~fL~g~~~~~~~~L~~~M~~aa~~l~FE~Aa~~Rd~i~~l~ 226 (574)
T TIGR00194 174 EEEYQQIVEKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAVR 226 (574)
T ss_pred HHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 34555444444332 4567889999999999999999999999998875
No 9
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=90.90 E-value=0.52 Score=55.21 Aligned_cols=50 Identities=22% Similarity=0.310 Sum_probs=39.4
Q ss_pred CChhHHHhhhhhHHH-----HhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 94 WDWNRWTRHFSEIEQ-----AESYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 94 ~dW~rW~rhF~~ve~-----~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
.+-+.|+....++.. ...++..|+.+|+.|+++.+||+||+||+.|.++.
T Consensus 179 is~e~Y~~~V~~v~~fL~G~~~~l~~~L~~~M~~AAe~l~FE~AA~lRD~i~aL~ 233 (694)
T PRK14666 179 VPRETYAALVRKVEMLLSGRSGELVDALRTEMEAASEALEFERAAVLRDQIRAVE 233 (694)
T ss_pred CCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHH
Confidence 344667755555543 24577899999999999999999999999998876
No 10
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=90.75 E-value=0.62 Score=53.46 Aligned_cols=49 Identities=22% Similarity=0.387 Sum_probs=39.0
Q ss_pred ChhHHHhhhhhHHH-----HhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 95 DWNRWTRHFSEIEQ-----AESYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 95 dW~rW~rhF~~ve~-----~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
+=+.|+..+..+.. -..++..|+.+|+.|.++.+||.||++|+.|.++.
T Consensus 156 ~~e~Y~~~v~~~~~fL~G~~~~~~~~L~~~M~~aa~~l~FE~Aa~~RD~i~al~ 209 (574)
T PRK14670 156 LEKEYQKEVDKIKHILNGNISKLLSQIEIKMKEAIQKEDFEAAIKLKETKRSLI 209 (574)
T ss_pred CHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 34567755555543 24677899999999999999999999999998876
No 11
>PRK07883 hypothetical protein; Validated
Probab=90.57 E-value=0.33 Score=55.11 Aligned_cols=47 Identities=19% Similarity=0.347 Sum_probs=36.8
Q ss_pred hHHHhhhhhHHH-----HhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 97 NRWTRHFSEIEQ-----AESYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 97 ~rW~rhF~~ve~-----~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
+.++.+..++.. -..++..|+.+|+.|+++.+||.||++|+.|.+++
T Consensus 387 ~~Y~~~v~~~~~fL~G~~~~~~~~l~~~M~~aa~~l~FE~Aa~~Rd~i~~l~ 438 (557)
T PRK07883 387 AEYAEAVARARAALTGDDDAVLAALRARIDRLAAAERFEEAARLRDRLAALL 438 (557)
T ss_pred HHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 445544444432 23577999999999999999999999999998775
No 12
>TIGR00631 uvrb excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)
Probab=90.04 E-value=0.36 Score=55.84 Aligned_cols=36 Identities=28% Similarity=0.416 Sum_probs=33.0
Q ss_pred HHHhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHH
Q 006448 107 EQAESYASLLKFQLEDAIEREDFEEAANLKNAIAEA 142 (644)
Q Consensus 107 e~~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~ 142 (644)
++.+.++..|+.+|..|+++.+||+||+||+.|.++
T Consensus 619 ~~~~~~i~~l~~~M~~aa~~l~FE~Aa~~RD~i~~L 654 (655)
T TIGR00631 619 KELKKLIKQLEKEMKQAARNLEFEEAARLRDEILEL 654 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence 567789999999999999999999999999999876
No 13
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=89.76 E-value=0.45 Score=54.80 Aligned_cols=37 Identities=32% Similarity=0.443 Sum_probs=33.1
Q ss_pred HHhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHhc
Q 006448 108 QAESYASLLKFQLEDAIEREDFEEAANLKNAIAEAAS 144 (644)
Q Consensus 108 ~~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~~ 144 (644)
..+.++..|+.+|..|+++.+||+||++|+.|.+++.
T Consensus 610 ~~~~~~~~l~~~M~~aa~~l~fE~Aa~~Rd~i~~l~~ 646 (652)
T PRK05298 610 ELEKLIKELEKQMKEAAKNLEFEEAARLRDEIKELKE 646 (652)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 4457889999999999999999999999999999874
No 14
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=89.40 E-value=0.46 Score=53.84 Aligned_cols=47 Identities=13% Similarity=0.316 Sum_probs=36.4
Q ss_pred hHHHhhhhhHHH-----HhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 97 NRWTRHFSEIEQ-----AESYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 97 ~rW~rhF~~ve~-----~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
+.++.....+.. ...++..|+.+|+.|.++.+||+||++|+.|.++.
T Consensus 173 e~Y~~~v~~~~~fL~G~~~~~~~~L~~~M~~aa~~l~FE~Aa~~RD~l~~l~ 224 (519)
T PRK12306 173 DEYLEQVKKAEEVLKGKIDELIEKLEEEMAEKAKNQQFERALVIRDEINAIE 224 (519)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 455544444332 24567889999999999999999999999998876
No 15
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=88.79 E-value=0.53 Score=54.00 Aligned_cols=34 Identities=26% Similarity=0.364 Sum_probs=30.7
Q ss_pred hhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 110 ESYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 110 e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
..++..|+.+|+.|+++.+||+||+||+.|.++.
T Consensus 201 ~~~i~~L~~~M~~aa~~l~FE~Aa~~RD~i~aL~ 234 (598)
T PRK00558 201 DEVLKELEEKMEEASENLEFERAARYRDQIQALR 234 (598)
T ss_pred HHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHH
Confidence 3466889999999999999999999999998876
No 16
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=88.36 E-value=0.57 Score=53.64 Aligned_cols=48 Identities=15% Similarity=0.156 Sum_probs=37.7
Q ss_pred hhHHHhhhhhHHH-----HhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 96 WNRWTRHFSEIEQ-----AESYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 96 W~rW~rhF~~ve~-----~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
=+.|+.....+-. ...++..|+.+|+.|+++.+||+||++|+.|.+++
T Consensus 179 ~e~Y~~~v~~~~~fL~G~~~~l~~~L~~~M~~aa~~l~FE~Aa~~RD~i~~l~ 231 (567)
T PRK14667 179 KEDYELSVKSAKAFLSGNVKEVLPELYDKIEEYSQKLMFEKAAVIRDQILALE 231 (567)
T ss_pred HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 3556655444432 24577899999999999999999999999998875
No 17
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=88.31 E-value=0.65 Score=53.35 Aligned_cols=40 Identities=28% Similarity=0.410 Sum_probs=35.5
Q ss_pred HHHHhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHhcC
Q 006448 106 IEQAESYASLLKFQLEDAIEREDFEEAANLKNAIAEAASK 145 (644)
Q Consensus 106 ve~~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~~~ 145 (644)
-.+.+.++..|+.||.+|++.-+||.||+||+.|.+++..
T Consensus 619 ~~e~~~~I~~Le~~M~~aA~~l~FE~Aa~lRD~i~~L~~~ 658 (663)
T COG0556 619 KKELEKLIKKLEKEMKEAAKNLEFEEAARLRDEIKELKEE 658 (663)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 3566778899999999999999999999999999998753
No 18
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=87.42 E-value=0.74 Score=53.94 Aligned_cols=49 Identities=20% Similarity=0.361 Sum_probs=38.4
Q ss_pred ChhHHHhhhhhHHH-----HhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 95 DWNRWTRHFSEIEQ-----AESYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 95 dW~rW~rhF~~ve~-----~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
+=+.|+....++.. -..++..|+.+|+.|+++.+||.||++|+.|.+++
T Consensus 184 s~e~Y~~~V~~v~~fL~G~~~~ll~~L~~~M~~AA~~l~FE~AA~lRD~i~aL~ 237 (691)
T PRK14672 184 SPRTYQKDIHEITLLLEGNIDATVARLEKRMKRAVRQEAFEAAARIRDDIQAIR 237 (691)
T ss_pred CHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 34567755555443 23567899999999999999999999999998876
No 19
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=86.86 E-value=0.83 Score=52.94 Aligned_cols=47 Identities=19% Similarity=0.292 Sum_probs=37.5
Q ss_pred hHHHhhhhhHHH-----HhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHh
Q 006448 97 NRWTRHFSEIEQ-----AESYASLLKFQLEDAIEREDFEEAANLKNAIAEAA 143 (644)
Q Consensus 97 ~rW~rhF~~ve~-----~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~ 143 (644)
+.++.....+.. ...++..|+.+|+.|+++.+||+||++|+.|.+++
T Consensus 184 e~Y~~~v~~v~~fL~G~~~~l~~~L~~~M~~aa~~l~FE~Aa~~RD~i~~l~ 235 (624)
T PRK14669 184 EAYAEAVRDVRLFLEGRHSDLARSLRARMEAAALEMQFELAAKYRDLITTVE 235 (624)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 556655454443 24677899999999999999999999999998865
No 20
>KOG4825 consensus Component of synaptic membrane glycine-, glutamate- and thienylcyclohexylpiperidine-binding glycoprotein (43kDa) [Signal transduction mechanisms]
Probab=79.18 E-value=3.9 Score=46.42 Aligned_cols=61 Identities=23% Similarity=0.284 Sum_probs=49.3
Q ss_pred hhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHH----HHHhhhhhhhhhhhhcc
Q 006448 110 ESYASLLKFQLEDAIEREDFEEAANLKNAIAEAASKDTVAEIMAQLK----NAIDEERYHDASRLCRY 173 (644)
Q Consensus 110 e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk----~AI~EERY~DAA~lRD~ 173 (644)
..+.-.|...-++||.+|||.-|-++|.||+.+.. +++-|..|+ .||+.|.|+-|--+.|+
T Consensus 170 aaiIgaidenKqeAVakEdfdlAKkaklAiaDLkK---sgeeleelEndKgcAVadEDfdlAkdkkde 234 (666)
T KOG4825|consen 170 AAIIGAIDENKQEAVAKEDFDLAKKAKLAIADLKK---SGEELEELENDKGCAVADEDFDLAKDKKDE 234 (666)
T ss_pred HHHHHHHHhhHHHHHhhhhhhHHHHHHHHHHHHHH---HHHHHHHHhhcccccccchhhhHHHHHHHH
Confidence 34455667777899999999999999999999984 566666665 49999999998877665
No 21
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=72.48 E-value=2.7 Score=49.49 Aligned_cols=50 Identities=14% Similarity=0.225 Sum_probs=40.1
Q ss_pred HhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 124 IEREDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 124 v~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
+..|+|.+..+--.++-+-..++.+..+...|++|.++.+|+.||+|||.
T Consensus 179 is~e~Y~~~V~~v~~fL~G~~~~l~~~L~~~M~~AAe~l~FE~AA~lRD~ 228 (694)
T PRK14666 179 VPRETYAALVRKVEMLLSGRSGELVDALRTEMEAASEALEFERAAVLRDQ 228 (694)
T ss_pred CCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccHHHHHHHHHH
Confidence 56688877665544444445567899999999999999999999999996
No 22
>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]
Probab=71.79 E-value=2.6 Score=49.66 Aligned_cols=72 Identities=22% Similarity=0.387 Sum_probs=52.1
Q ss_pred hHHHhhhhhHHHHhhHHHHHHHHHHH-HHhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhh
Q 006448 97 NRWTRHFSEIEQAESYASLLKFQLED-AIEREDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRL 170 (644)
Q Consensus 97 ~rW~rhF~~ve~~e~~~~~Lk~QLe~-Av~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~l 170 (644)
-+|..-|+-.|.--.|+.....|-.. -+++..|+||.+ .-+++=+..+.+..+..+-++||.|+||.||+++
T Consensus 787 ~~W~eAFalAe~hPe~~~dVy~pyaqwLAE~DrFeEAqk--AfhkAGr~~EA~~vLeQLtnnav~E~Rf~DA~y~ 859 (1081)
T KOG1538|consen 787 QRWDEAFALAEKHPEFKDDVYMPYAQWLAENDRFEEAQK--AFHKAGRQREAVQVLEQLTNNAVAESRFNDAAYY 859 (1081)
T ss_pred ccchHhHhhhhhCccccccccchHHHHhhhhhhHHHHHH--HHHHhcchHHHHHHHHHhhhhhhhhhhhccchhH
Confidence 46888898888777777665544432 357788999975 3455556666666666666899999999999973
No 23
>PRK07883 hypothetical protein; Validated
Probab=71.76 E-value=2.9 Score=47.70 Aligned_cols=49 Identities=18% Similarity=0.293 Sum_probs=39.0
Q ss_pred HHhhhcHHHHHHHHHHHHHHhc--CChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 123 AIEREDFEEAANLKNAIAEAAS--KDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 123 Av~~EDy~eAArLK~ai~~~~~--~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
.+..|+|. ..++.++.-+++ ++.+..+..+|++|-++.+|+.||+|||.
T Consensus 383 ~~~~~~Y~--~~v~~~~~fL~G~~~~~~~~l~~~M~~aa~~l~FE~Aa~~Rd~ 433 (557)
T PRK07883 383 RESAAEYA--EAVARARAALTGDDDAVLAALRARIDRLAAAERFEEAARLRDR 433 (557)
T ss_pred CCCHHHHH--HHHHHHHHHHCCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence 45667885 455666666644 45788999999999999999999999996
No 24
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=70.71 E-value=3.2 Score=47.30 Aligned_cols=48 Identities=8% Similarity=0.219 Sum_probs=38.7
Q ss_pred HhhhcHHHHHHHHHHHHHHhc--CChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 124 IEREDFEEAANLKNAIAEAAS--KDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 124 v~~EDy~eAArLK~ai~~~~~--~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
+..|+|. ++++.++.-+++ ++.+..+...|++|-++.+|+.||+|||.
T Consensus 170 ~s~e~Y~--~~v~~~~~fL~G~~~~~~~~L~~~M~~aa~~l~FE~Aa~~RD~ 219 (519)
T PRK12306 170 ISSDEYL--EQVKKAEEVLKGKIDELIEKLEEEMAEKAKNQQFERALVIRDE 219 (519)
T ss_pred CCHHHHH--HHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 4568886 455566666655 57888999999999999999999999996
No 25
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=70.40 E-value=3.1 Score=48.39 Aligned_cols=51 Identities=18% Similarity=0.178 Sum_probs=40.0
Q ss_pred HHhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 123 AIEREDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 123 Av~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
.+..|+|.+..+--..+-.-..++.+..+...|++|-++.+|+.||+|||.
T Consensus 180 ~i~~e~Y~~~v~~v~~fL~G~~~~l~~~L~~~M~~aa~~l~FE~Aa~~RD~ 230 (624)
T PRK14669 180 LTTDEAYAEAVRDVRLFLEGRHSDLARSLRARMEAAALEMQFELAAKYRDL 230 (624)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence 345688877655444444445567889999999999999999999999996
No 26
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=70.03 E-value=3.3 Score=47.67 Aligned_cols=49 Identities=20% Similarity=0.317 Sum_probs=38.7
Q ss_pred HhhhcHHHHHHHHHHHHHHhc--CChHHHHHHHHHHHHhhhhhhhhhhhhccc
Q 006448 124 IEREDFEEAANLKNAIAEAAS--KDTVAEIMAQLKNAIDEERYHDASRLCRYT 174 (644)
Q Consensus 124 v~~EDy~eAArLK~ai~~~~~--~D~V~~~~~~Lk~AI~EERY~DAA~lRD~a 174 (644)
+..|+|.+ +++.++.-+++ ++.+..+...|++|-++.+|+.||+|||.-
T Consensus 177 ~s~e~Y~~--~v~~~~~fL~G~~~~l~~~L~~~M~~aa~~l~FE~Aa~~RD~i 227 (567)
T PRK14667 177 ISKEDYEL--SVKSAKAFLSGNVKEVLPELYDKIEEYSQKLMFEKAAVIRDQI 227 (567)
T ss_pred CCHHHHHH--HHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 45677854 45555555654 567889999999999999999999999973
No 27
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=69.90 E-value=3.2 Score=47.89 Aligned_cols=50 Identities=16% Similarity=0.264 Sum_probs=38.7
Q ss_pred HhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 124 IEREDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 124 v~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
+..|+|.+..+--..+-.-..++.+..+...|++|-++.+|+.||+|||.
T Consensus 155 ~~~e~Y~~~v~~~~~fL~G~~~~~~~~L~~~M~~aa~~l~FE~Aa~~RD~ 204 (574)
T PRK14670 155 DLEKEYQKEVDKIKHILNGNISKLLSQIEIKMKEAIQKEDFEAAIKLKET 204 (574)
T ss_pred CCHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence 45688876554433333334567899999999999999999999999995
No 28
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=69.61 E-value=3.3 Score=47.77 Aligned_cols=48 Identities=17% Similarity=0.307 Sum_probs=38.0
Q ss_pred HhhhcHHHHHHHHHHHHHHhc--CChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 124 IEREDFEEAANLKNAIAEAAS--KDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 124 v~~EDy~eAArLK~ai~~~~~--~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
+..|+|.+ +++.+++-+.+ .+.+..+...|+.|.++.+|+.||+|||.
T Consensus 180 ~~~e~Y~~--~v~~~~~fL~G~~~~~i~~L~~~M~~aa~~l~FE~Aa~~RD~ 229 (598)
T PRK00558 180 ISKEEYAE--LVDEAKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQ 229 (598)
T ss_pred CCHHHHHH--HHHHHHHHhcCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHH
Confidence 45677754 55566666654 46788899999999999999999999996
No 29
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=68.49 E-value=3.8 Score=47.58 Aligned_cols=50 Identities=14% Similarity=0.234 Sum_probs=38.8
Q ss_pred HhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 124 IEREDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 124 v~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
+..|+|.+..+--..+-+-..++.+..+..+|++|-++.+|+.||+|||.
T Consensus 193 ~s~e~Y~~~v~~~~~fL~G~~~~l~~~L~~~M~~as~~l~FE~Aa~~RD~ 242 (621)
T PRK14671 193 QSEEDYLEMIEEIVRLLKGKTSALIRSLTEEMQRAAAELKFEEAAELKDQ 242 (621)
T ss_pred CCHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhccHHHHHHHHHH
Confidence 45688866554444444444567899999999999999999999999996
No 30
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=68.32 E-value=3.6 Score=47.37 Aligned_cols=48 Identities=13% Similarity=0.304 Sum_probs=38.1
Q ss_pred HhhhcHHHHHHHHHHHHHHhc--CChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 124 IEREDFEEAANLKNAIAEAAS--KDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 124 v~~EDy~eAArLK~ai~~~~~--~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
+..|+|.+ +++.++.-+++ ++.+.++...|++|-++.+|+.||+|||.
T Consensus 172 ~s~e~Y~~--~v~~~~~fL~g~~~~~~~~L~~~M~~aa~~l~FE~Aa~~Rd~ 221 (574)
T TIGR00194 172 ITEEEYQQ--IVEKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQ 221 (574)
T ss_pred CCHHHHHH--HHHHHHHHHCCCcHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 45678854 45555555554 57888999999999999999999999995
No 31
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=67.02 E-value=2.5 Score=51.13 Aligned_cols=13 Identities=23% Similarity=0.268 Sum_probs=6.8
Q ss_pred CCCcceEEEeecC
Q 006448 190 DDPFGRLIQIKPG 202 (644)
Q Consensus 190 ~DP~GrIirIsp~ 202 (644)
=+|.|.=|-|-.+
T Consensus 1274 FHP~g~eVIINSE 1286 (1516)
T KOG1832|consen 1274 FHPSGNEVIINSE 1286 (1516)
T ss_pred ccCCCceEEeech
Confidence 4566655555444
No 32
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=65.74 E-value=4.5 Score=46.68 Aligned_cols=48 Identities=15% Similarity=0.193 Sum_probs=36.9
Q ss_pred HhhhcHHHHHHHHHHHHHHhc--CChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 124 IEREDFEEAANLKNAIAEAAS--KDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 124 v~~EDy~eAArLK~ai~~~~~--~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
+..|+|.+.. +.++.-+++ .+.+..+...+++|-++.+|+.||+|||.
T Consensus 177 ~s~e~Y~~~v--~~~~~fL~G~~~~~~~~l~~~m~~aa~~l~FE~Aa~~Rd~ 226 (577)
T PRK14668 177 IDEEAYAEDV--ESAERFFEGETGVLADPLRREMEAAAQAQEFERAANLRDR 226 (577)
T ss_pred CCHHHHHHHH--HHHHHHHcCCcHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 4567776544 444444555 45677899999999999999999999996
No 33
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=65.39 E-value=4.5 Score=47.75 Aligned_cols=50 Identities=18% Similarity=0.314 Sum_probs=38.2
Q ss_pred HhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 124 IEREDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 124 v~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
+..|+|.+..+--..+-+-..++.+..+...|++|-++.+|+.||+|||.
T Consensus 183 is~e~Y~~~V~~v~~fL~G~~~~ll~~L~~~M~~AA~~l~FE~AA~lRD~ 232 (691)
T PRK14672 183 VSPRTYQKDIHEITLLLEGNIDATVARLEKRMKRAVRQEAFEAAARIRDD 232 (691)
T ss_pred CCHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence 45577776554433444444567788999999999999999999999996
No 34
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=60.22 E-value=6.7 Score=39.37 Aligned_cols=25 Identities=16% Similarity=0.352 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 149 AEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 149 ~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
-++...|+.+|+.|.|+.||-+||.
T Consensus 139 ~~L~e~Lq~~i~~EefEeAA~iRDq 163 (176)
T COG3880 139 IALKEALQDLIEREEFEEAAVIRDQ 163 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456789999999999999999996
No 35
>COG2602 Beta-lactamase class D [Defense mechanisms]
Probab=59.58 E-value=7.4 Score=41.08 Aligned_cols=51 Identities=25% Similarity=0.458 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHhhhhhhhhhhhhcccCCcee-----eeeeeccCCCCCCcceEEEee
Q 006448 149 AEIMAQLKNAIDEERYHDASRLCRYTGSGLV-----GWWVGYSKDSDDPFGRLIQIK 200 (644)
Q Consensus 149 ~~~~~~Lk~AI~EERY~DAA~lRD~aGaGLv-----GWW~G~s~d~~DP~GrIirIs 200 (644)
.++|...++-+-=||=+- =.|+-+||+|.+ |||||+-+..+++|.--.+|.
T Consensus 173 ~~a~~~v~~~m~~~~~~~-~~l~GKTG~~~~~~~~~GWfVG~v~~~~~~y~FA~nld 228 (254)
T COG2602 173 AKAQDLVKAIMILERGPN-WELHGKTGTGIVNTKNLGWFVGWVETNENKYVFATNLD 228 (254)
T ss_pred HHHHHHHHHHHhhhcCCC-eEEEecccccccCCCCceeEEEEEEeCCcEEEEEEeec
Confidence 456777777777777666 778999999985 899999998888876544443
No 36
>PF09059 TyeA: TyeA; InterPro: IPR015144 This domain is composed of two pairs of parallel alpha-helices, and interacts with the bacterial protein YopN via hydrophobic residues located on the helices. Association of TyeA with the C terminus of YopN is accompanied by conformational changes in both polypeptides that create order out of disorder: the resulting structure then serves as an impediment to type III secretion of YopN []. ; PDB: 1XL3_D.
Probab=55.03 E-value=12 Score=33.70 Aligned_cols=28 Identities=32% Similarity=0.462 Sum_probs=25.3
Q ss_pred hhhhhHHHHhhHHHHHHHHHHHHHhhhc
Q 006448 101 RHFSEIEQAESYASLLKFQLEDAIERED 128 (644)
Q Consensus 101 rhF~~ve~~e~~~~~Lk~QLe~Av~~ED 128 (644)
..|++.|+.++++...+.-|..||++||
T Consensus 58 ~vF~D~EqR~~vL~a~Q~alD~aI~~E~ 85 (87)
T PF09059_consen 58 DVFNDEEQRQNVLDAVQEALDQAIEREE 85 (87)
T ss_dssp GGSS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhcCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3689999999999999999999999997
No 37
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=52.29 E-value=9.4 Score=44.29 Aligned_cols=50 Identities=18% Similarity=0.288 Sum_probs=38.2
Q ss_pred HHHhhhcHHHHHHHHHHHHHHhcC--ChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 122 DAIEREDFEEAANLKNAIAEAASK--DTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 122 ~Av~~EDy~eAArLK~ai~~~~~~--D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
..|..|+|+++.+ .+..-+.++ ..+..+...++.|-++.+|+.||+|||.
T Consensus 178 ~~is~e~Y~e~v~--~~~~fL~G~~~~v~~~L~~~M~~As~~l~FE~Aa~~RD~ 229 (581)
T COG0322 178 GLISEEEYREIVE--EVKGFLKGKDDAVLQELEEKMEEASENLDFERAARLRDQ 229 (581)
T ss_pred ccCCHHHHHHHHH--HHHHHHcCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHH
Confidence 3577888888754 333444454 4677888899999999999999999994
No 38
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=48.90 E-value=13 Score=43.89 Aligned_cols=11 Identities=18% Similarity=0.619 Sum_probs=4.8
Q ss_pred hhhHHHHHhhh
Q 006448 302 EGIKSVINFLK 312 (644)
Q Consensus 302 EGi~~v~nflk 312 (644)
+|+..+++.|.
T Consensus 623 ~~l~~ll~vl~ 633 (784)
T PF04931_consen 623 SGLQLLLDVLD 633 (784)
T ss_pred HHHHHHHHHhc
Confidence 44444444443
No 39
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=44.27 E-value=77 Score=26.68 Aligned_cols=50 Identities=30% Similarity=0.462 Sum_probs=32.7
Q ss_pred HHHHHHHHHhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhh
Q 006448 116 LKFQLEDAIEREDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRL 170 (644)
Q Consensus 116 Lk~QLe~Av~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~l 170 (644)
++.+|++|...++..+...|+..+.... ..+...|..+++...|..|+.+
T Consensus 13 ~rE~le~~~~~~~~~~L~~l~~~~~~~~-----~~~~~~l~~~f~~~d~~~A~~~ 62 (78)
T PF07743_consen 13 LREELEEAQNSDDEAELEELKKEIEERI-----KELIKELAEAFDAKDWEEAKEA 62 (78)
T ss_dssp HHHHHHHHCCCTSHHHHHHHHHHHHHHH-----HHHHHHHHHHHHTT-HHHHHHH
T ss_pred HHHHHHHhhcCCCHHHHHHHHHHHHHHH-----HHHHHHHHHHHccCcHHHHHHH
Confidence 3445555555455566666666666554 6778888888888888888764
No 40
>KOG3483 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.57 E-value=13 Score=33.43 Aligned_cols=13 Identities=69% Similarity=1.086 Sum_probs=11.9
Q ss_pred eeecCCccccccc
Q 006448 2 IITNNGWGITPAT 14 (644)
Q Consensus 2 ~~~~~~~~~~~~~ 14 (644)
||||.|.||.|+.
T Consensus 59 iitndgiginpaq 71 (94)
T KOG3483|consen 59 IITNDGIGINPAQ 71 (94)
T ss_pred EEecCccccCccc
Confidence 8999999999974
No 41
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=38.18 E-value=59 Score=38.02 Aligned_cols=31 Identities=23% Similarity=0.328 Sum_probs=26.9
Q ss_pred hcCChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 143 ASKDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 143 ~~~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
..++.+..+..+|++|.++.+|+.||+|||.
T Consensus 610 ~~~~~~~~l~~~M~~aa~~l~fE~Aa~~Rd~ 640 (652)
T PRK05298 610 ELEKLIKELEKQMKEAAKNLEFEEAARLRDE 640 (652)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 3445677888999999999999999999996
No 42
>cd01766 Ufm1 Urm1-like ubiquitin domain. Ufm1 (ubiquitin-fold modifier 1) is a post-translational UBL (ubiquitin-like) modifier with a tertiary structure similar to that of ubiquitin. Ufm1 is initially expressed as a precursor which undergoes C-terminal cleavage to expose a conserved glycine residue that is required for the conjugation reactions involving Ufm1.
Probab=35.54 E-value=16 Score=32.61 Aligned_cols=13 Identities=69% Similarity=1.086 Sum_probs=11.8
Q ss_pred eeecCCccccccc
Q 006448 2 IITNNGWGITPAT 14 (644)
Q Consensus 2 ~~~~~~~~~~~~~ 14 (644)
||||.|.||.|+.
T Consensus 48 iiTndGvGINP~q 60 (82)
T cd01766 48 IITNDGIGINPAQ 60 (82)
T ss_pred EEecCccccChhh
Confidence 8999999999973
No 43
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=35.40 E-value=1.2e+02 Score=23.57 Aligned_cols=50 Identities=16% Similarity=0.298 Sum_probs=35.5
Q ss_pred HHhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 123 AIEREDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 123 Av~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
+++.++|++|.++=..+-....+++-..+ ..-+-.++..+|.+|..+-..
T Consensus 1 ll~~~~~~~A~~~~~~~l~~~p~~~~~~~-~la~~~~~~g~~~~A~~~l~~ 50 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQRNPDNPEARL-LLAQCYLKQGQYDEAEELLER 50 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHHHTTTSHHHHH-HHHHHHHHTT-HHHHHHHHHC
T ss_pred ChhccCHHHHHHHHHHHHHHCCCCHHHHH-HHHHHHHHcCCHHHHHHHHHH
Confidence 46788999998887777777666655554 455666788888888876553
No 44
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=31.67 E-value=47 Score=32.38 Aligned_cols=45 Identities=22% Similarity=0.361 Sum_probs=32.8
Q ss_pred HHHHHHHhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhh
Q 006448 118 FQLEDAIEREDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEER 163 (644)
Q Consensus 118 ~QLe~Av~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EER 163 (644)
.+|-.|++..||++|..|-..|.. ..-|-++.-|..+|+-|.+=|
T Consensus 95 ~~L~~aL~~~d~~~A~~Ih~~L~t-~h~~E~~~WmvGVKRLI~~~r 139 (157)
T PF07304_consen 95 HQLAQALQARDYDAADEIHVDLMT-DHVDECGNWMVGVKRLIAMAR 139 (157)
T ss_dssp HHHHHHHHHT-HHHHHHHHHHHHH-SSHHHHTTTHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHh-ccHHHhhhHHHHHHHHHHHHH
Confidence 456678888888888888888874 555677777788888777654
No 45
>KOG0316 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=31.27 E-value=29 Score=37.17 Aligned_cols=24 Identities=21% Similarity=0.463 Sum_probs=20.4
Q ss_pred CCCCceEeeccCCCccEEEEEEEe
Q 006448 497 DPFDGLYVGAFGPYGTEVVQLRRK 520 (644)
Q Consensus 497 dP~~GLwVGdYG~HG~EfL~L~~~ 520 (644)
+|++|.-+-+|++||-|+|-+.-.
T Consensus 45 Np~rg~liktYsghG~EVlD~~~s 68 (307)
T KOG0316|consen 45 NPLRGALIKTYSGHGHEVLDAALS 68 (307)
T ss_pred cccccceeeeecCCCceeeecccc
Confidence 588999999999999999965433
No 46
>KOG2387 consensus CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism]
Probab=29.95 E-value=32 Score=39.48 Aligned_cols=53 Identities=30% Similarity=0.538 Sum_probs=38.8
Q ss_pred CCCCCceEeeccCC--CccEEEEEEEecCCCCCCCCCCCccccceEEEEEEEcCCCCccCeeE
Q 006448 496 LDPFDGLYVGAFGP--YGTEVVQLRRKYGQWSGEGEKSSDMEFFEYVEAVKLTGDLNVPAGEV 556 (644)
Q Consensus 496 ~dP~~GLwVGdYG~--HG~EfL~L~~~~g~~~~~d~~~sd~~~~~~LEAVKLTGDpNVPRGeV 556 (644)
-|||=-+=-|++++ ||--|++ ++| .+-.-|+--++|.-.|+||+|.|++-|.+
T Consensus 39 IDPYlN~DAGTmSPyEHGEVfVL---DDG-----gEvDLDLGNYERfldi~Lt~dNNITtGKi 93 (585)
T KOG2387|consen 39 IDPYLNIDAGTMSPYEHGEVFVL---DDG-----GEVDLDLGNYERFLDITLTRDNNITTGKI 93 (585)
T ss_pred eccceeccCcccCccccceEEEe---cCC-----ceecccccchhhhccceeeccCCcccchH
Confidence 47888888899998 8876665 112 11123455567888999999999999986
No 47
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=27.45 E-value=71 Score=27.64 Aligned_cols=24 Identities=25% Similarity=0.405 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHhhhcHHHHHHHHH
Q 006448 114 SLLKFQLEDAIEREDFEEAANLKN 137 (644)
Q Consensus 114 ~~Lk~QLe~Av~~EDy~eAArLK~ 137 (644)
++...|.+.-+...||++||++-.
T Consensus 7 ~l~~~~F~~l~~~g~y~eAA~~AA 30 (66)
T PF13838_consen 7 DLYVQQFNELFSQGQYEEAAKVAA 30 (66)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHH
Confidence 457788899999999999999743
No 48
>PF08336 P4Ha_N: Prolyl 4-Hydroxylase alpha-subunit, N-terminal region; InterPro: IPR013547 The members found in this entry are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme (1.14.11.2 from EC) is important in the post-translational modification of collagen, as it catalyses the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase [, , , ]. The function of the N-terminal region featured in this family does not seem to be known. ; GO: 0004656 procollagen-proline 4-dioxygenase activity, 0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen, 0055114 oxidation-reduction process, 0005783 endoplasmic reticulum
Probab=26.83 E-value=54 Score=30.51 Aligned_cols=42 Identities=24% Similarity=0.306 Sum_probs=29.1
Q ss_pred CCChhHHHhhhhhHHHHhhHHHHHHHHHHHHHhhhcHHHHHHH
Q 006448 93 DWDWNRWTRHFSEIEQAESYASLLKFQLEDAIEREDFEEAANL 135 (644)
Q Consensus 93 ~~dW~rW~rhF~~ve~~e~~~~~Lk~QLe~Av~~EDy~eAArL 135 (644)
-.||..|.++....-..+ ++..++.-....=..||+++||+=
T Consensus 70 ~~dW~~~~~~~~~~~~~~-~~~~~~~~~~~~Pt~~Dl~gA~~~ 111 (134)
T PF08336_consen 70 HQDWPKWEKLMEQPVGQE-QLQNLQELRSKLPTEEDLEGAAEG 111 (134)
T ss_pred HHhhhhHHHHHHHhhhHH-HHHHHHHHHhcCCCHHHHHHHHHH
Confidence 478999987766553333 666666655556678999999863
No 49
>PF03671 Ufm1: Ubiquitin fold modifier 1 protein; InterPro: IPR005375 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin-like molecules (UBLs) can be divided into two subclasses: type-1 UBLs, which ligate to target proteins in a manner similar, but not identical, to the ubiquitylation pathway, such as SUMO, NEDD8, and UCRP/ISG15, and type-2 UBLs (also called UDPs, ubiquitin-domain proteins), which contain ubiquitin-like structure embedded in a variety of different classes of large proteins with apparently distinct functions, such as Rad23, Elongin B, Scythe, Parkin, and HOIL-1. This entry represents Ufm1 (ubiquitin-fold modifier), which is a ubiquitin-like protein with structural similarities to ubiquitin [, ]. Ufm1 is one of a number of ubiquitin-like modifiers that conjugate to target proteins in cells through Uba5 (E1) and Ufc1 (E2). The Ufm1-system is conserved in metazoa and plants, suggesting it has a potential role in multicellular organisms []. Human Ufm1 is synthesized as a precursor consisting of 85 amino-acid residues. Prior to activation by Uba5, the extra amino acids at the C-terminal region of Ufm1 are removed to expose Gly, which is necessary for conjugation to target molecule(s). C-terminal processing of Ufm1 requires two specific cysteine peptidases (IPR012462 from INTERPRO): UfSP1 and UfSP2; both peptidases are also able to release Ufm1 from Ufm1-conjugated cellular proteins. UfSP2 is present in most, if not all, of multi-cellular organisms including plant, nematode, fly, and mammal, whereas UfSP1 is not present in plants and nematodes []. For further information on ubiquitin, please see Protein of the Month [].; PDB: 1J0G_A 1WXS_A 1L7Y_A.
Probab=25.53 E-value=32 Score=30.60 Aligned_cols=12 Identities=67% Similarity=1.082 Sum_probs=9.4
Q ss_pred eeecCCcccccc
Q 006448 2 IITNNGWGITPA 13 (644)
Q Consensus 2 ~~~~~~~~~~~~ 13 (644)
||||.|-||.|.
T Consensus 48 iItndG~GInP~ 59 (76)
T PF03671_consen 48 IITNDGVGINPQ 59 (76)
T ss_dssp EEESSS-EE-TT
T ss_pred EEecCCcccccc
Confidence 899999999996
No 50
>TIGR00631 uvrb excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)
Probab=25.18 E-value=38 Score=39.79 Aligned_cols=29 Identities=21% Similarity=0.353 Sum_probs=25.2
Q ss_pred CChHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 145 KDTVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 145 ~D~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
++.+..+..+|++|.++.+|+.||+|||.
T Consensus 622 ~~~i~~l~~~M~~aa~~l~FE~Aa~~RD~ 650 (655)
T TIGR00631 622 KKLIKQLEKEMKQAARNLEFEEAARLRDE 650 (655)
T ss_pred HHHHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence 34566788899999999999999999996
No 51
>PF15469 Sec5: Exocyst complex component Sec5
Probab=24.71 E-value=2.5e+02 Score=27.14 Aligned_cols=45 Identities=22% Similarity=0.264 Sum_probs=39.0
Q ss_pred hhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhh
Q 006448 126 REDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRL 170 (644)
Q Consensus 126 ~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~l 170 (644)
.+.-+.|.+|+.++.-++..-.+..+=+.|+++|+..+|..|.+.
T Consensus 64 l~~~~k~~~l~~~l~~l~r~~flF~LP~~L~~~i~~~dy~~~i~d 108 (182)
T PF15469_consen 64 LERREKADKLRNALEFLQRNRFLFNLPSNLRECIKKGDYDQAIND 108 (182)
T ss_pred HccHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHcCcHHHHHHH
Confidence 456678899999999999999999999999999999999888754
No 52
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=24.65 E-value=57 Score=38.41 Aligned_cols=27 Identities=19% Similarity=0.340 Sum_probs=23.8
Q ss_pred hHHHHHHHHHHHHhhhhhhhhhhhhcc
Q 006448 147 TVAEIMAQLKNAIDEERYHDASRLCRY 173 (644)
Q Consensus 147 ~V~~~~~~Lk~AI~EERY~DAA~lRD~ 173 (644)
.+-.+..+|++|-++-+|+.||+|||+
T Consensus 625 ~I~~Le~~M~~aA~~l~FE~Aa~lRD~ 651 (663)
T COG0556 625 LIKKLEKEMKEAAKNLEFEEAARLRDE 651 (663)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 456677889999999999999999996
No 53
>PF03863 Phage_mat-A: Phage maturation protein; InterPro: IPR005563 This entry is represented by Bacteriophage MS2, Orf: MS2g1, the assembly/maturation protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The single-stranded RNA genome of bacteriophage MS2 is 3,569 nt long and contains 4 genes. Their products are necessary for phage maturation, encapsidation, lysis of the host, and phage RNA replication, respectively. The maturation protein is required for the typical attachment of the phage to the side of the bacterial pili. It accompanies the viral DNA into the cell.; GO: 0046718 entry of virus into host cell
Probab=24.35 E-value=1.5e+02 Score=33.49 Aligned_cols=83 Identities=22% Similarity=0.347 Sum_probs=55.5
Q ss_pred HHHHhhHHHHHHHHHHH------HHhhhcHHHHHHHHHHH--HHHhcCCh----------HHHHHHHHHHHHhhhhhhhh
Q 006448 106 IEQAESYASLLKFQLED------AIEREDFEEAANLKNAI--AEAASKDT----------VAEIMAQLKNAIDEERYHDA 167 (644)
Q Consensus 106 ve~~e~~~~~Lk~QLe~------Av~~EDy~eAArLK~ai--~~~~~~D~----------V~~~~~~Lk~AI~EERY~DA 167 (644)
+-|.-+-++.|..|+.. ||++.|++++.|+.+.- .....++. ..=+|.+++.|++
T Consensus 142 iaE~ReT~s~L~~~~~~l~kay~AvrrGd~rr~~~~i~~~~~~~~~~~~~a~~WLE~~yG~mPL~~Diq~~~e------- 214 (400)
T PF03863_consen 142 IAEARETASYLALQLRRLVKAYRAVRRGDLRRLRRYIRSFHDRKWKSKSAANLWLEFRYGWMPLFYDIQGAYE------- 214 (400)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHhhcCCccCcccccceeeeeechhHhHHHHHHHHH-------
Confidence 34555556667766654 78888888777766644 22222232 2346777777777
Q ss_pred hhhhcccCCceeeeeeeccCCCCCCcceEEEeecCCceeeeecCC
Q 006448 168 SRLCRYTGSGLVGWWVGYSKDSDDPFGRLIQIKPGVGRFVARNYS 212 (644)
Q Consensus 168 A~lRD~aGaGLvGWW~G~s~d~~DP~GrIirIsp~~GRyVaksYs 212 (644)
| |. ...++...++|++++||--+-.+|.
T Consensus 215 ----d---------~~----r~h~~~~~~~r~s~~~g~~~~~~~~ 242 (400)
T PF03863_consen 215 ----D---------FM----RVHDKIAKPLRFSRGHGKNVKLSYR 242 (400)
T ss_pred ----H---------HH----HhcchhheeEEeecCCCCceeeecc
Confidence 1 22 3578899999999999999988874
No 54
>KOG0553 consensus TPR repeat-containing protein [General function prediction only]
Probab=23.80 E-value=2e+02 Score=31.56 Aligned_cols=64 Identities=19% Similarity=0.225 Sum_probs=47.2
Q ss_pred HHhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhhhc
Q 006448 108 QAESYASLLKFQLEDAIEREDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRLCR 172 (644)
Q Consensus 108 ~~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~lRD 172 (644)
+.-.++.-||.|=..+.+.+||++|.-+-.+..++.-+|+|.--++. ..-..=..|.+|..=|.
T Consensus 76 e~~~~AE~LK~eGN~~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRA-AAy~~Lg~~~~AVkDce 139 (304)
T KOG0553|consen 76 EDKALAESLKNEGNKLMKNKDYQEAVDKYTEAIELDPTNAVYYCNRA-AAYSKLGEYEDAVKDCE 139 (304)
T ss_pred hHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcchHHHHHH-HHHHHhcchHHHHHHHH
Confidence 45678899999999999999999999999999999999999654332 11122234556655444
No 55
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=23.30 E-value=44 Score=39.76 Aligned_cols=9 Identities=33% Similarity=0.420 Sum_probs=3.4
Q ss_pred hhHHHHHHH
Q 006448 439 MSKLKVAAL 447 (644)
Q Consensus 439 ~~~~kv~~~ 447 (644)
++.+.+-+|
T Consensus 729 mdDe~m~~l 737 (784)
T PF04931_consen 729 MDDEQMMAL 737 (784)
T ss_pred cCHHHHHHH
Confidence 333344333
No 56
>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.28 E-value=1.3e+02 Score=35.86 Aligned_cols=62 Identities=24% Similarity=0.334 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHhhhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhhhcccCC
Q 006448 114 SLLKFQLEDAIEREDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRLCRYTGS 176 (644)
Q Consensus 114 ~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~lRD~aGa 176 (644)
..|=.+|..+...++|++|++--..|-..- .|+...+..-+=.-|..++|+||-++-...|+
T Consensus 13 ~~l~t~ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~ 74 (652)
T KOG2376|consen 13 EALLTDLNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGA 74 (652)
T ss_pred HHHHHHHHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcch
Confidence 456678888889999999999888877766 68888889999999999999999988776554
No 57
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=23.18 E-value=41 Score=41.55 Aligned_cols=21 Identities=29% Similarity=0.384 Sum_probs=10.2
Q ss_pred eeeeecCChhhhcccCCCCceEE
Q 006448 205 RFVARNYSPRQLVTASPGTPLFE 227 (644)
Q Consensus 205 RyVaksYspRQLata~~G~PlFE 227 (644)
-|=|+-||| |+|-..--|||-
T Consensus 1344 Tf~a~dYs~--iaTi~v~R~~~D 1364 (1516)
T KOG1832|consen 1344 TFDAIDYSD--IATIPVDRCLLD 1364 (1516)
T ss_pred ccccccccc--ceeeecccchhh
Confidence 344555553 445444445544
No 58
>PF07064 RIC1: RIC1; InterPro: IPR009771 This entry represents RIC1 (Ribosomal control protein1) and has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network. It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor [] which activates YPT6 by exchanging bound GDP for free GTP. RIC1 is thereby required for efficient fusion of endosome-derived vesicles with the Golgi. The RIC1-RGP1 complex participates in the recycling of SNC1, presumably by mediating fusion of endosomal vesicles with the Golgi compartment and may also be indirectly involved in the transcription of both ribosomal protein genes and ribosomal RNA [, , ].
Probab=23.15 E-value=2e+02 Score=30.26 Aligned_cols=73 Identities=14% Similarity=0.211 Sum_probs=57.4
Q ss_pred CCChhHHHhhhhhHHHHhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHHHhcCCh------HHHHHHHHHHHHhhhhhhh
Q 006448 93 DWDWNRWTRHFSEIEQAESYASLLKFQLEDAIEREDFEEAANLKNAIAEAASKDT------VAEIMAQLKNAIDEERYHD 166 (644)
Q Consensus 93 ~~dW~rW~rhF~~ve~~e~~~~~Lk~QLe~Av~~EDy~eAArLK~ai~~~~~~D~------V~~~~~~Lk~AI~EERY~D 166 (644)
+-+=.+|..-|+.+-.-. + =++.+++..+++.||.+=.-+......+. ...+.+.|+.|+++++|+=
T Consensus 166 KtE~~~W~~LF~~lg~P~---d----Lf~~cl~~~~l~tAa~yLlVl~~~e~~~~~~~~~~~~~al~LL~~a~~~~~w~L 238 (258)
T PF07064_consen 166 KTEVRYWPYLFDYLGSPR---D----LFEECLENGNLKTAASYLLVLQNLEGSSVVKDEESRQCALRLLVMALESGDWDL 238 (258)
T ss_pred hhHHHHHHHHHHhcCCHH---H----HHHHHHHcCcHHHHHHHHHHHHhcCCcchhhhHHHHHHHHHHHHHHHhcccHHH
Confidence 456678888888775333 2 25678899999999999999988887775 6778899999999999988
Q ss_pred hhhhhc
Q 006448 167 ASRLCR 172 (644)
Q Consensus 167 AA~lRD 172 (644)
|..|.+
T Consensus 239 c~eL~R 244 (258)
T PF07064_consen 239 CFELVR 244 (258)
T ss_pred HHHHHH
Confidence 776643
No 59
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=23.10 E-value=48 Score=39.57 Aligned_cols=13 Identities=15% Similarity=0.371 Sum_probs=7.1
Q ss_pred hhhhHHHHHhhhc
Q 006448 301 EEGIKSVINFLKE 313 (644)
Q Consensus 301 ~EGi~~v~nflkd 313 (644)
-|-|..++++|-+
T Consensus 874 vesld~lKewLds 886 (1001)
T COG5406 874 VESLDKLKEWLDS 886 (1001)
T ss_pred HHHHHHHHHHhhh
Confidence 3455555666555
No 60
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=20.96 E-value=2.4e+02 Score=28.09 Aligned_cols=18 Identities=11% Similarity=0.143 Sum_probs=11.6
Q ss_pred cccccccCCC-CCCceeec
Q 006448 57 SKYKKVKHPL-PQPLCCLC 74 (644)
Q Consensus 57 ~~~~~~~~~~-~~~~~~~c 74 (644)
.-|+-.|.|. |..+-|..
T Consensus 57 ~AY~tLkdPl~RA~YLL~L 75 (173)
T PRK01773 57 DALQILKDPILRAEAIIAL 75 (173)
T ss_pred HHHHHHCChHHHHHHHHHh
Confidence 4588888886 44455544
No 61
>PF09617 Cas_GSU0053: CRISPR-associated protein GSU0053 (Cas_GSU0053); InterPro: IPR013403 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry is found in CRISPR-associated (cas) proteins in the genomes of Geobacter sulfurreducens PCA and Desulfotalea psychrophila LSv54 (both Desulfobacterales from the Deltaproteobacteria), Gemmata obscuriglobus (a Planctomycete), and Actinomyces naeslundii MG1 (Actinobacteria).
Probab=20.30 E-value=1.1e+02 Score=30.63 Aligned_cols=56 Identities=20% Similarity=0.202 Sum_probs=34.8
Q ss_pred cHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhhhcc-cCCceeeeee
Q 006448 128 DFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRLCRY-TGSGLVGWWV 183 (644)
Q Consensus 128 Dy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~lRD~-aGaGLvGWW~ 183 (644)
++++++|+-+++--...-|-..-....+++|+....=.+|.-|=.. -.+=|-|||-
T Consensus 84 sl~~pHR~~Da~ir~s~~~g~~~~~~~~~~~l~~~~~~~~~all~~~P~sLlfG~wd 140 (169)
T PF09617_consen 84 SLEAPHRIADAYIRDSELDGKPFRDSELGRALRNATPGNARALLELDPTSLLFGVWD 140 (169)
T ss_pred hhhchhhhhhhhhhhcccCCCchhhhHHHHHHHhccccChHHHHhhCcceeeeeEEe
Confidence 6889999999987433222222345566777776666666554433 3455679997
No 62
>PF07352 Phage_Mu_Gam: Bacteriophage Mu Gam like protein; InterPro: IPR009951 The Gam protein, originally characterised in Bacteriophage Mu, protects linear double stranded DNA from exonuclease degradation in vitro and in vivo []. This protein is also found in many bacterial species as part of a suspected prophage. Further studies have shown that Gam is a functional counterpart of the eukaryotic Ku protein, which has key roles in DNA repair and in certain transposition events. Gam displays DNA binding characteristics remarkably similar to those of human Ku []. In addition, Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae (Baker's yeast). These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved [].; GO: 0003690 double-stranded DNA binding, 0042262 DNA protection; PDB: 2P2U_B.
Probab=20.09 E-value=4.9e+02 Score=24.83 Aligned_cols=77 Identities=17% Similarity=0.126 Sum_probs=38.1
Q ss_pred hhHHHhhhhhHHHHhhHHHHHHHHHHHHHh---hhcHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhhhhhhhhhhhhc
Q 006448 96 WNRWTRHFSEIEQAESYASLLKFQLEDAIE---REDFEEAANLKNAIAEAASKDTVAEIMAQLKNAIDEERYHDASRLCR 172 (644)
Q Consensus 96 W~rW~rhF~~ve~~e~~~~~Lk~QLe~Av~---~EDy~eAArLK~ai~~~~~~D~V~~~~~~Lk~AI~EERY~DAA~lRD 172 (644)
|+.=...|.+|-+..+-+..++.+|++.|. ..-=++++.|+..|..++ .++..+-.+-.+|-. -+-.-
T Consensus 2 ~~~a~~al~ki~~l~~~~~~i~~~~~~~I~~i~~~~~~~~~~l~~~i~~l~------~~l~~y~e~~r~e~~---k~Ks~ 72 (149)
T PF07352_consen 2 REEADWALRKIAELQREIARIEAEANDEIARIKEWYEAEIAPLQNRIEYLE------GLLQAYAEANRDELT---KKKSL 72 (149)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH------HHHHHHHHCTHHHH--------E
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHCHHhcc---cceEE
Confidence 444445677888888877778877776553 233344566777766654 233333333333333 22233
Q ss_pred ccCCceeee
Q 006448 173 YTGSGLVGW 181 (644)
Q Consensus 173 ~aGaGLvGW 181 (644)
....|-|||
T Consensus 73 ~l~~G~v~~ 81 (149)
T PF07352_consen 73 KLPFGTVGF 81 (149)
T ss_dssp E-SS-EE--
T ss_pred EcCCeeEEE
Confidence 355666666
Done!