Query 019342
Match_columns 342
No_of_seqs 184 out of 739
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 08:41:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019342.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019342hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4434 Molecular chaperone SE 100.0 3.4E-41 7.4E-46 324.1 19.3 237 14-314 129-519 (520)
2 smart00611 SEC63 Domain of unk 100.0 3.2E-34 6.9E-39 275.4 23.2 192 5-263 120-312 (312)
3 PF02889 Sec63: Sec63 Brl doma 100.0 6.7E-34 1.5E-38 272.9 20.3 195 5-262 117-314 (314)
4 COG5407 SEC63 Preprotein trans 99.9 3.7E-22 8E-27 197.2 13.2 214 5-268 303-551 (610)
5 KOG0951 RNA helicase BRR2, DEA 99.7 6.5E-20 1.4E-24 197.5 -4.1 334 1-340 118-476 (1674)
6 KOG0951 RNA helicase BRR2, DEA 99.7 1.5E-16 3.3E-21 171.9 16.5 217 6-309 922-1144(1674)
7 PRK01172 ski2-like helicase; P 98.4 3.4E-07 7.4E-12 97.4 6.2 86 7-107 570-668 (674)
8 KOG0952 DNA/RNA helicase MER3/ 98.4 9.3E-07 2E-11 96.1 9.0 206 7-292 713-920 (1230)
9 PRK02362 ski2-like helicase; P 98.0 6.5E-06 1.4E-10 88.7 6.5 84 6-107 623-706 (737)
10 PRK00254 ski2-like helicase; P 97.7 5.5E-05 1.2E-09 81.4 6.6 79 11-107 623-701 (720)
11 PF14520 HHH_5: Helix-hairpin- 93.3 0.14 3E-06 37.8 4.2 54 48-105 6-59 (60)
12 KOG1824 TATA-binding protein-i 88.5 0.22 4.8E-06 55.0 1.6 18 295-312 327-344 (1233)
13 PRK04301 radA DNA repair and r 83.0 2.7 5.9E-05 40.8 6.0 57 46-106 5-61 (317)
14 PF04931 DNA_pol_phi: DNA poly 81.1 0.72 1.6E-05 50.6 1.3 6 23-28 311-316 (784)
15 KOG1832 HIV-1 Vpr-binding prot 80.8 1.4 3.1E-05 48.8 3.3 6 249-254 1371-1376(1516)
16 PF15243 ANAPC15: Anaphase-pro 80.7 1.1 2.4E-05 36.5 2.0 39 277-315 52-90 (92)
17 PF06524 NOA36: NOA36 protein; 80.2 1.1 2.5E-05 42.9 2.1 9 101-109 57-65 (314)
18 PF09026 CENP-B_dimeris: Centr 79.0 0.63 1.4E-05 38.2 0.0 8 285-292 13-20 (101)
19 PTZ00035 Rad51 protein; Provis 78.1 5 0.00011 39.7 6.1 58 48-109 22-81 (337)
20 PF03118 RNA_pol_A_CTD: Bacter 77.9 4.3 9.3E-05 30.8 4.3 55 46-105 11-65 (66)
21 TIGR02236 recomb_radA DNA repa 76.8 6.3 0.00014 38.0 6.3 53 49-105 1-53 (310)
22 PRK07758 hypothetical protein; 76.1 8.4 0.00018 31.6 5.7 51 52-106 39-89 (95)
23 PRK14133 DNA polymerase IV; Pr 74.4 9.8 0.00021 37.4 7.0 50 25-87 164-213 (347)
24 PF11731 Cdd1: Pathogenicity l 73.4 11 0.00025 30.7 5.9 48 45-92 10-57 (93)
25 PF13543 KSR1-SAM: SAM like do 72.3 14 0.00029 32.0 6.4 60 46-107 60-128 (129)
26 TIGR02239 recomb_RAD51 DNA rep 71.6 10 0.00022 37.3 6.2 54 50-107 4-57 (316)
27 cd03586 PolY_Pol_IV_kappa DNA 70.9 13 0.00029 35.9 6.9 55 47-108 171-225 (334)
28 PRK02406 DNA polymerase IV; Va 70.1 14 0.0003 36.2 7.0 54 47-107 168-221 (343)
29 TIGR02238 recomb_DMC1 meiotic 69.9 11 0.00023 37.1 6.0 54 52-109 6-59 (313)
30 TIGR01954 nusA_Cterm_rpt trans 69.9 14 0.0003 25.5 5.1 47 55-105 1-47 (50)
31 PF10446 DUF2457: Protein of u 69.6 2.5 5.4E-05 43.4 1.5 16 249-264 13-28 (458)
32 PF01835 A2M_N: MG2 domain; I 69.1 54 0.0012 25.8 11.4 42 123-175 10-51 (99)
33 PRK01216 DNA polymerase IV; Va 69.0 9.4 0.0002 38.0 5.5 62 25-105 169-230 (351)
34 PLN03187 meiotic recombination 68.0 12 0.00025 37.4 5.9 54 51-108 35-88 (344)
35 KOG1832 HIV-1 Vpr-binding prot 67.5 4.3 9.2E-05 45.3 2.8 7 47-53 1000-1006(1516)
36 PRK12766 50S ribosomal protein 65.3 20 0.00044 33.9 6.6 55 47-105 3-57 (232)
37 PRK02794 DNA polymerase IV; Pr 64.0 19 0.00042 36.4 6.7 56 47-109 209-264 (419)
38 PF14229 DUF4332: Domain of un 62.7 19 0.00041 30.4 5.4 57 53-110 1-61 (122)
39 PRK03352 DNA polymerase IV; Va 62.7 12 0.00027 36.6 4.9 41 47-87 177-217 (346)
40 PRK03348 DNA polymerase IV; Pr 62.4 24 0.00052 36.3 7.1 56 47-108 180-235 (454)
41 PF04281 Tom22: Mitochondrial 61.9 4.8 0.0001 35.1 1.6 19 295-313 30-48 (137)
42 PRK03609 umuC DNA polymerase V 59.9 29 0.00062 35.2 7.1 55 47-108 179-233 (422)
43 PLN03186 DNA repair protein RA 59.9 25 0.00053 35.1 6.5 77 23-106 5-83 (342)
44 PRK03103 DNA polymerase IV; Re 59.8 25 0.00055 35.3 6.7 41 47-87 181-221 (409)
45 KOG1834 Calsyntenin [Extracell 58.9 9.1 0.0002 41.3 3.3 10 243-252 831-840 (952)
46 COG5407 SEC63 Preprotein trans 58.3 3.7 8E-05 42.5 0.4 42 228-269 525-567 (610)
47 cd01700 PolY_Pol_V_umuC umuC s 58.2 34 0.00074 33.5 7.2 42 46-87 175-216 (344)
48 PRK01810 DNA polymerase IV; Va 58.2 28 0.00061 34.9 6.7 53 47-106 179-231 (407)
49 cd00424 PolY Y-family of DNA p 57.4 33 0.00073 33.6 6.9 54 47-107 173-227 (343)
50 PF12826 HHH_2: Helix-hairpin- 55.9 21 0.00045 26.6 4.1 51 50-105 6-56 (64)
51 TIGR00596 rad1 DNA repair prot 55.6 20 0.00043 39.9 5.5 53 48-106 758-810 (814)
52 PF03066 Nucleoplasmin: Nucleo 55.1 4 8.6E-05 36.0 0.0 11 172-182 29-39 (149)
53 PRK03858 DNA polymerase IV; Va 54.8 20 0.00044 35.7 5.0 54 47-106 173-226 (396)
54 PF07495 Y_Y_Y: Y_Y_Y domain; 54.8 35 0.00076 24.6 5.1 35 230-265 31-66 (66)
55 cd01701 PolY_Rev1 DNA polymera 53.3 39 0.00084 34.1 6.8 57 47-109 222-280 (404)
56 KOG3540 Beta amyloid precursor 53.1 12 0.00025 39.1 2.9 22 162-183 117-138 (615)
57 KOG1189 Global transcriptional 51.3 12 0.00026 41.1 2.7 10 173-182 787-796 (960)
58 COG2251 Predicted nuclease (Re 49.5 28 0.00061 36.1 5.0 88 11-111 201-289 (474)
59 PF00868 Transglut_N: Transglu 45.2 66 0.0014 27.0 5.9 21 228-248 95-118 (118)
60 PF13897 GOLD_2: Golgi-dynamic 45.1 1.1E+02 0.0023 26.9 7.1 35 230-268 7-43 (136)
61 KOG3064 RNA-binding nuclear pr 40.1 15 0.00033 35.4 1.4 7 245-251 169-175 (303)
62 KOG1189 Global transcriptional 38.0 19 0.0004 39.7 1.8 15 241-255 760-774 (960)
63 COG2231 Uncharacterized protei 37.9 67 0.0015 30.1 5.2 53 58-111 50-106 (215)
64 KOG3540 Beta amyloid precursor 36.7 19 0.00041 37.6 1.5 16 240-255 170-185 (615)
65 PF04994 TfoX_C: TfoX C-termin 35.6 31 0.00068 27.1 2.3 35 47-81 3-37 (81)
66 PRK05182 DNA-directed RNA poly 34.5 56 0.0012 32.1 4.4 50 54-107 255-304 (310)
67 PF04147 Nop14: Nop14-like fam 33.5 36 0.00077 38.1 3.1 7 246-252 316-322 (840)
68 cd01703 PolY_Pol_iota DNA Poly 32.6 1.4E+02 0.0031 30.0 7.0 57 47-109 172-243 (379)
69 PRK14973 DNA topoisomerase I; 32.3 64 0.0014 36.6 4.9 67 23-104 789-856 (936)
70 PF12482 DUF3701: Phage integr 32.3 61 0.0013 26.6 3.6 57 55-111 21-77 (96)
71 KOG1834 Calsyntenin [Extracell 32.3 22 0.00047 38.6 1.2 9 25-33 484-492 (952)
72 PF06051 DUF928: Domain of Unk 32.1 1.5E+02 0.0033 26.9 6.5 33 236-268 88-122 (189)
73 TIGR02027 rpoA DNA-directed RN 31.5 68 0.0015 31.3 4.4 49 55-107 242-290 (297)
74 KOG2393 Transcription initiati 31.2 24 0.00051 37.2 1.2 30 284-313 280-310 (555)
75 PF03985 Paf1: Paf1 ; InterPr 30.9 32 0.00069 35.3 2.1 16 254-269 337-352 (436)
76 PTZ00415 transmission-blocking 30.5 35 0.00075 41.0 2.4 7 309-315 184-190 (2849)
77 PRK13901 ruvA Holliday junctio 30.5 1.3E+02 0.0029 27.7 5.9 74 15-104 83-168 (196)
78 PTZ00007 (NAP-L) nucleosome as 29.7 45 0.00097 33.4 2.8 18 295-312 294-311 (337)
79 KOG3064 RNA-binding nuclear pr 29.0 35 0.00075 33.0 1.8 10 99-108 92-101 (303)
80 PRK02515 psbU photosystem II c 27.6 1.2E+02 0.0026 26.4 4.7 49 46-106 60-109 (132)
81 KOG2141 Protein involved in hi 27.6 28 0.0006 38.1 1.0 13 283-295 208-220 (822)
82 PF00386 C1q: C1q domain; Int 27.3 1E+02 0.0022 25.4 4.2 18 230-247 37-54 (127)
83 KOG2841 Structure-specific end 27.0 90 0.0019 29.9 4.1 55 47-106 195-249 (254)
84 cd03468 PolY_like DNA Polymera 24.9 1.2E+02 0.0025 29.3 4.8 40 47-87 171-210 (335)
85 PF11705 RNA_pol_3_Rpc31: DNA- 24.3 37 0.0008 31.7 1.1 33 283-315 174-206 (233)
86 PRK13482 DNA integrity scannin 24.3 1.4E+02 0.003 30.1 5.2 57 46-107 286-342 (352)
87 cd00146 PKD polycystic kidney 24.1 1.9E+02 0.0041 21.5 4.9 32 231-264 50-81 (81)
88 COG1470 Predicted membrane pro 23.6 1.7E+02 0.0037 30.7 5.7 42 225-269 443-487 (513)
89 PF04151 PPC: Bacterial pre-pe 23.5 68 0.0015 23.7 2.2 17 229-245 53-69 (70)
90 KOG1991 Nuclear transport rece 23.3 33 0.00072 38.7 0.6 13 20-32 583-595 (1010)
91 cd01702 PolY_Pol_eta DNA Polym 23.2 2.5E+02 0.0054 28.0 6.8 57 47-109 182-241 (359)
92 PF05764 YL1: YL1 nuclear prot 23.2 62 0.0013 30.6 2.4 9 303-311 57-65 (240)
93 PRK13913 3-methyladenine DNA g 22.6 1.7E+02 0.0038 27.3 5.2 37 70-107 68-104 (218)
94 COG1948 MUS81 ERCC4-type nucle 22.1 1.7E+02 0.0038 28.1 5.1 56 49-109 184-239 (254)
95 PF14524 Wzt_C: Wzt C-terminal 21.7 1.3E+02 0.0029 24.4 3.9 41 226-266 86-130 (142)
96 KOG0772 Uncharacterized conser 21.2 75 0.0016 33.7 2.7 20 312-331 147-166 (641)
97 PHA02608 67 prohead core prote 21.0 50 0.0011 26.2 1.0 6 277-282 43-48 (80)
98 PF14686 fn3_3: Polysaccharide 20.8 1.5E+02 0.0033 23.9 3.9 34 230-265 50-85 (95)
99 PF06991 Prp19_bind: Splicing 20.7 48 0.001 32.2 1.1 7 306-312 26-32 (276)
100 KOG0442 Structure-specific end 20.6 1.5E+02 0.0033 33.2 4.9 53 48-106 822-874 (892)
101 KOG3130 Uncharacterized conser 20.5 62 0.0013 33.2 1.9 37 94-133 96-133 (514)
102 KOG2051 Nonsense-mediated mRNA 20.5 82 0.0018 36.0 2.9 14 301-314 909-922 (1128)
No 1
>KOG4434 consensus Molecular chaperone SEC63, endoplasmic reticulum translocon component [Intracellular trafficking, secretion, and vesicular transport; Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.4e-41 Score=324.08 Aligned_cols=237 Identities=32% Similarity=0.537 Sum_probs=201.8
Q ss_pred HHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhc-CCCCHHHHHcCCHHHHHHHHhhccCC
Q 019342 14 LRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARK-KVRTFQELRDMSLQDRAELLSQVGGF 92 (342)
Q Consensus 14 L~~al~~m~L~Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~-~v~tl~~L~~m~~~er~~lL~~~~~l 92 (342)
+.+.-+||.|++|+|||+|. ..||||||||++++.+.++.++ +|+++++|..|..+.|+.||+. |
T Consensus 129 iet~eNcmKlspM~vQgLwq-----------fkSPLLQLPHitednL~~~~KKr~vks~qdla~lk~e~rr~lL~~---L 194 (520)
T KOG4434|consen 129 IETFENCMKLSPMFVQGLWQ-----------FKSPLLQLPHITEDNLQHLRKKRKVKSCQDLAVLKAETRRSLLRS---L 194 (520)
T ss_pred HHHHHHHHhccHHHHHHHHH-----------hcChhhcCCccchHHHHHHhhhcccccHHHHhhcCHHHHHHHHHh---c
Confidence 67888999999999999998 8999999999999999999755 4999999999999999999997 8
Q ss_pred ChHHHHHHHHHHhcCCceeEEEEEEecCCc---cccCCCeEEEEEeeeeecc----------------------------
Q 019342 93 SSTEVQDVEMVLQMMPSLTVEVTCETEGEE---GIQEGDIVTIQAWVTLKRG---------------------------- 141 (342)
Q Consensus 93 ~~~~~~~v~~v~~~iP~I~i~a~~~v~gee---~It~g~~vtl~~~V~L~R~---------------------------- 141 (342)
++..+.+++.||.+||.|.|++.+.|.|++ .||+|++||+. |+|+|.
T Consensus 195 sdeeYe~vM~VLg~mP~~~~~ik~~V~dded~n~~TaG~vVTv~--Vtl~R~~l~d~~e~~~~d~~k~paedG~~de~n~ 272 (520)
T KOG4434|consen 195 SDEEYEDVMVVLGMMPRLQIEIKTVVEDDEDKNELTAGCVVTVK--VTLRRSRLIDPQEAGLADQYKKPAEDGGDDENNL 272 (520)
T ss_pred chHHHHHHHHHHccCcceEEEeeEEEecCCcccceeeeeEEEEE--EEEEeccccChHhhhhhhhhhCchhhCCCcccch
Confidence 999999999999999999999999998875 59999999999 888873
Q ss_pred --------------------------------------------------------------------------C-----
Q 019342 142 --------------------------------------------------------------------------N----- 142 (342)
Q Consensus 142 --------------------------------------------------------------------------n----- 142 (342)
|
T Consensus 273 ea~g~~~eaaa~~~~~~vKK~kpw~K~Kpk~~kkpaq~Q~~qK~v~~~aas~at~ka~eeea~~~~sD~E~e~~n~Ds~d 352 (520)
T KOG4434|consen 273 EASGAPEEAAATVEEEEVKKRKPWEKNKPKQKKKPAQGQGQQKFVKKNAASPATEKALEEEAKDKGSDSEEEETNRDSQD 352 (520)
T ss_pred hccCChhhhccccchhhhhhcCchhhcCCCcccCccccchhhhhcccccCChhhhhhhHHHhhhcCcchhhhhhcccccc
Confidence 0
Q ss_pred ------------------------------------------CCCCCCccCCCCCCCCcccEEEEEEECCCCeEEEEeee
Q 019342 143 ------------------------------------------GLIGALPHAPYYPFHKEENFWFLLADSVSNNVWFSQKV 180 (342)
Q Consensus 143 ------------------------------------------~~~~~~~~aP~FP~~K~E~WwvllgD~~~n~Ll~~krv 180 (342)
......+||||||..|.|.||++|.|.++..|+.+...
T Consensus 353 ees~asd~~~D~e~~~~~ddddd~EWe~lqa~~~kr~~lEtKs~~tHtVh~pyFPeEKqEwWW~Yi~drKsrtLlt~Pyh 432 (520)
T KOG4434|consen 353 EESDASDRDSDREQDEKQDDDDDAEWEELQASIQKRALLETKSKITHTVHSPYFPEEKQEWWWLYIADRKSRTLLTMPYH 432 (520)
T ss_pred cccccCccccchhhccccccccHHHHHHHHHHHHHHHhhhcccccceeeccCCCcchhhheeeeeeecccccceecchhh
Confidence 01234599999999999999999999999999875322
Q ss_pred ecccchhHHhhhhhhhhhhhcCCCCccchhhHHHHHHHhhhhcCceeEEEEEEcCC-CCceeEEEEEEcCCCcccceEEE
Q 019342 181 SFMDEPAAITAASKAIEDTMEGSGATVKETSAAVREAAEKVRSGSRLVMGKIQAPA-EGNYNLTCYCLCDSWLGCDKRTN 259 (342)
Q Consensus 181 ~~~~~~~~~~~~~k~i~~~~~~~g~~~~~~~~~~~~~~~~~k~~s~~v~l~F~aP~-~G~~~l~l~viSDsYlG~D~~~~ 259 (342)
+.. +. .+..|.|+|++|. ||.|+|+|++.||||+|+||..+
T Consensus 433 -V~t-----------L~--------------------------d~eei~lkF~AP~~pG~Ytytv~lrSDSYmg~dq~~~ 474 (520)
T KOG4434|consen 433 -VCT-----------LK--------------------------DTEEIELKFPAPGKPGNYTYTVFLRSDSYMGLDQIKP 474 (520)
T ss_pred -hhc-----------cc--------------------------ccceeEEeccCCCCCCceEEEEEEecccccChhhccc
Confidence 111 10 1246889999994 99999999999999999999999
Q ss_pred EEEEeeecCcCCCCCccccCCCCCccCCCCCcccccccccCCcCCccccchhhhh
Q 019342 260 LKVKILKRTRAGTRGGIVSEEGPIVEDGAEEEEEDEEEEYDDYESEYSEDEEDER 314 (342)
Q Consensus 260 i~l~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~ 314 (342)
++|.|.+++. |++..|.+++.++++|+-++ ++.=++|++|++++.
T Consensus 475 lKldV~eAk~-------vp~~Hpqwd~~~~e~e~~~~---~e~~~Dyted~~~eE 519 (520)
T KOG4434|consen 475 LKLDVHEAKP-------VPENHPQWDTAIEEDEDQED---SEGFEDYTEDEEEEE 519 (520)
T ss_pred eeeeeccCCC-------CCCCCccccccccccccccc---ccccccccccccccc
Confidence 9999998876 88899999999988886653 334467777766653
No 2
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=100.00 E-value=3.2e-34 Score=275.43 Aligned_cols=192 Identities=34% Similarity=0.533 Sum_probs=164.1
Q ss_pred cchhhccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHH
Q 019342 5 PRTAQGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAE 84 (342)
Q Consensus 5 ~~~a~~~GwL~~al~~m~L~Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~ 84 (342)
-.+|+.+||+++++++|+|+|||+||+|+ ..+||+|||||+.+.++++.++++.++.+|.+++.++++.
T Consensus 120 ~di~~~~~~~~~~~~~l~L~q~i~q~~w~-----------~~~~L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~~~~~~~~ 188 (312)
T smart00611 120 VDIALERGWLSTALNALNLSQMIIQALWP-----------TDSPLLQLPHLPEEILKRLEKKKVLSLEDLLELEDEERGE 188 (312)
T ss_pred HHHHHhcchHHHHHHHHHHHHHHHHhhCC-----------CCCccccCCCCCHHHHHHHHhCCCCCHHHHHhcCHHHHHH
Confidence 35788999999999999999999999999 7899999999999999999988899999999999999999
Q ss_pred HHhhccCCChHHHHHHHHHHhcCCceeEEEEEEecCCccccCCCeEEEEEeeeeeccCCCCCCCccCCCCCCCCcccEEE
Q 019342 85 LLSQVGGFSSTEVQDVEMVLQMMPSLTVEVTCETEGEEGIQEGDIVTIQAWVTLKRGNGLIGALPHAPYYPFHKEENFWF 164 (342)
Q Consensus 85 lL~~~~~l~~~~~~~v~~v~~~iP~I~i~a~~~v~gee~It~g~~vtl~~~V~L~R~n~~~~~~~~aP~FP~~K~E~Wwv 164 (342)
+++ +.+.+++++.++|++||+|+|++++. +.+.++.+..++|+ +.+++.+ ..| +|.|+||+
T Consensus 189 ll~----~~~~~~~~i~~~~~~~P~l~v~~~~~--~~~~~~~~~~~~i~--~~~~~~~-----~~~------~k~e~~~l 249 (312)
T smart00611 189 LLG----LLDAEGERVYKVLSRLPKLNIEISLE--PITRTVLGVEVTLT--VDLTWDD-----EIH------GKQEGWWL 249 (312)
T ss_pred HHc----CCHHHHHHHHHHHHhCCcceeEEEEc--CCcccccCceEEEE--EEEEEcc-----ccc------CCcccEEE
Confidence 986 67789999999999999999876544 43345556667777 8777642 122 68999999
Q ss_pred EEEECCCCeEEEEeeeecccchhHHhhhhhhhhhhhcCCCCccchhhHHHHHHHhhhhcCceeEEEEEEcCC-CCceeEE
Q 019342 165 LLADSVSNNVWFSQKVSFMDEPAAITAASKAIEDTMEGSGATVKETSAAVREAAEKVRSGSRLVMGKIQAPA-EGNYNLT 243 (342)
Q Consensus 165 llgD~~~n~Ll~~krv~~~~~~~~~~~~~k~i~~~~~~~g~~~~~~~~~~~~~~~~~k~~s~~v~l~F~aP~-~G~~~l~ 243 (342)
+|+|+++|+|++++|++++... ..+.+.+.|.+|. +|.|+|+
T Consensus 250 ~v~d~~~~~il~~~~~~~~~~~-------------------------------------~~~~~~l~f~~P~~~~~~~~~ 292 (312)
T smart00611 250 VIGDSDGNELLHIERFSLNKKN-------------------------------------VSEEVKLDFTAPATEGNYQYT 292 (312)
T ss_pred EEEeCCCCEEEEEEEEEEEeec-------------------------------------CCCcEEEEEEecCCCCcceEE
Confidence 9999999999999999986611 0024668999995 7899999
Q ss_pred EEEEcCCCcccceEEEEEEE
Q 019342 244 CYCLCDSWLGCDKRTNLKVK 263 (342)
Q Consensus 244 l~viSDsYlG~D~~~~i~l~ 263 (342)
|+++||+|+|||++++++|+
T Consensus 293 v~v~SD~y~g~d~~~~i~~~ 312 (312)
T smart00611 293 LRLVSDSYLGCDQEYPLSFD 312 (312)
T ss_pred EEEEecccCCcceEEEEeeC
Confidence 99999999999999999874
No 3
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=100.00 E-value=6.7e-34 Score=272.87 Aligned_cols=195 Identities=30% Similarity=0.530 Sum_probs=145.8
Q ss_pred cchhhccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHH
Q 019342 5 PRTAQGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAE 84 (342)
Q Consensus 5 ~~~a~~~GwL~~al~~m~L~Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~ 84 (342)
...|+.+||+++++++|+|+|||+||+|+ ..+||+|||||+++.++++.++++.++++|.++++.++..
T Consensus 117 ~ei~~~~~~~~~~~~~l~l~q~i~q~~w~-----------~~~~L~Qlp~i~~~~~~~l~~~~i~~l~~l~~~~~~e~~~ 185 (314)
T PF02889_consen 117 IEIALEKGWLSTALNALELSQCIVQALWD-----------SDSPLLQLPHIGEESLKKLEKRGIKTLQDLRDLSPEELEE 185 (314)
T ss_dssp HHHHHHTTBCCHHHHHHHHHHHHHHTS-T-----------TS-GGGGSTT--HHHHHHHHHTT--SHHHHHHS-HHHHHH
T ss_pred HHHHHhcccHHHHHHHHHHHHHHHhhcCC-----------CCChhhcCCCCCHHHHHHHhccCCCcHHHHhhCCHHHHHH
Confidence 35688999999999999999999999997 6899999999999999999999999999999999999999
Q ss_pred HHhhccCCChHHHHHHHHHHhcCCceeEEEEEEecCCccccCCCeEEEEEeeeeeccCCCCCCCccCCCCCCCCcccEEE
Q 019342 85 LLSQVGGFSSTEVQDVEMVLQMMPSLTVEVTCETEGEEGIQEGDIVTIQAWVTLKRGNGLIGALPHAPYYPFHKEENFWF 164 (342)
Q Consensus 85 lL~~~~~l~~~~~~~v~~v~~~iP~I~i~a~~~v~gee~It~g~~vtl~~~V~L~R~n~~~~~~~~aP~FP~~K~E~Wwv 164 (342)
+|+ ..+.+++++.+++++||.++|++++++.+++.+ ..++|. |.++|.+ .+.++||+.|.++||+
T Consensus 186 ll~----~~~~~~~~i~~~~~~~P~~~i~~~~~~~~~~~~---~~~~v~--v~i~~~~------~~~~~~~~~k~~~~~~ 250 (314)
T PF02889_consen 186 LLN----RNPPFGKEILEVASRIPRLEIKASVQVIDEEIV---PILTVQ--VSITRKF------SWSDRFPKKKKESWWL 250 (314)
T ss_dssp HH-----S-HHHHHHHHHHHCCS--EEEEEEETTCCGEEC---SEEEEE--EEEEESS------S-SST-SS--B--EEE
T ss_pred HHh----hhhhhHHHHHHHHHHCCCEEEEEEEeccccccC---CcEEEE--EEEEccc------ccccCCCCCCcccEEE
Confidence 987 456899999999999999999888877665422 456777 8888753 4456999999999999
Q ss_pred EEEECCCCeEEEEeeeecccchhHHhhhhhhhhhhhcCCCCccchhhHHHHHHHhhhhcCceeEEEEEEcCC-CCc--ee
Q 019342 165 LLADSVSNNVWFSQKVSFMDEPAAITAASKAIEDTMEGSGATVKETSAAVREAAEKVRSGSRLVMGKIQAPA-EGN--YN 241 (342)
Q Consensus 165 llgD~~~n~Ll~~krv~~~~~~~~~~~~~k~i~~~~~~~g~~~~~~~~~~~~~~~~~k~~s~~v~l~F~aP~-~G~--~~ 241 (342)
+|+|.++|+|++++|+.+..+. ......++|++|. +|+ ++
T Consensus 251 ~v~~~~~~~l~~~~~~~~~~~~-------------------------------------~~~~~~~~f~vp~~~~~~~~~ 293 (314)
T PF02889_consen 251 FVGDSKNNELLHFERITISKKK-------------------------------------SKDTVKISFQVPIPVGPRPYQ 293 (314)
T ss_dssp EEEECCCTEEEEEEEE---SS---------------------------------------EEEEEEEEE--SS-EE--EE
T ss_pred EEEECCCCeEEEEeeeehhhhc-------------------------------------cCCcEEEEEEecCCCCCCCce
Confidence 9999999999999999883200 0124668999995 476 99
Q ss_pred EEEEEEcCCCcccceEEEEEE
Q 019342 242 LTCYCLCDSWLGCDKRTNLKV 262 (342)
Q Consensus 242 l~l~viSDsYlG~D~~~~i~l 262 (342)
|+++++||+|+|+|++++|+|
T Consensus 294 ~~v~v~sd~y~G~d~~~~i~~ 314 (314)
T PF02889_consen 294 YTVYVISDSYLGLDQEVPINF 314 (314)
T ss_dssp EEEEEEESS-SS--EEEEEEE
T ss_pred EEEEEEECCccccceEEEeeC
Confidence 999999999999999999986
No 4
>COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion]
Probab=99.88 E-value=3.7e-22 Score=197.16 Aligned_cols=214 Identities=12% Similarity=0.074 Sum_probs=170.0
Q ss_pred cchhhccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHH
Q 019342 5 PRTAQGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAE 84 (342)
Q Consensus 5 ~~~a~~~GwL~~al~~m~L~Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~ 84 (342)
-|+|++||++..+.+.+.+.|||+||++.+ ..-+++||||++.+.++.+.-+.|.++.+|+.+..+..+.
T Consensus 303 L~ia~~F~f~~~~~g~~n~~q~iVqAiPld----------~~f~ilQlp~~d~E~~~~~s~r~I~~~~~~~sL~~~~~g~ 372 (610)
T COG5407 303 LRIASNFAFPLKECGKENKGQYIVQAIPLD----------HLFRILQLPRSDVEYAQRVSLRLIEGMKAIGSLIAKRYGN 372 (610)
T ss_pred HHHHhhccCCchhhccchhhheeeEeccCC----------CCchhhcccchhHHHHHHhhhhhhhhhhhHhhHHHHHHhh
Confidence 489999999999999999999999999993 6889999999999999988777899999999999999999
Q ss_pred HHhhccCCChHHHHHHHHHHhcCCcee-EEEEEEecCCccccCCCeEEEEEeeeeecc-------------C--------
Q 019342 85 LLSQVGGFSSTEVQDVEMVLQMMPSLT-VEVTCETEGEEGIQEGDIVTIQAWVTLKRG-------------N-------- 142 (342)
Q Consensus 85 lL~~~~~l~~~~~~~v~~v~~~iP~I~-i~a~~~v~gee~It~g~~vtl~~~V~L~R~-------------n-------- 142 (342)
.|.+ ++..++.++.+++++||++. |.|.|.|.++..||++++..+.|++.+... |
T Consensus 373 vl~n---~~~~~l~e~~~va~gIPr~~~~~a~flv~~d~~it~~s~~~vslk~~~g~~~~pe~~ts~~~~~n~~e~~dfe 449 (610)
T COG5407 373 VLKN---LVVLELMEIQAVADGIPRYFLLQAPFLVFEDLFITEKSKERVSLKGYLGAIPGPEHRTSALNVYNQVEISDFE 449 (610)
T ss_pred hhhh---HHHHHHHHHHHHhcCCCceEEEecceeecccceecccceeeEEEEEEeccccCCcccccccccccccChHHHh
Confidence 9987 78889999999999999999 789999999999999999998877766431 1
Q ss_pred ----------C--CCCCCccCCCCCCCCcccEEEEEEECCCCeEEEEeeeecccchhHHhhhhhhhhhhhcCCCCccchh
Q 019342 143 ----------G--LIGALPHAPYYPFHKEENFWFLLADSVSNNVWFSQKVSFMDEPAAITAASKAIEDTMEGSGATVKET 210 (342)
Q Consensus 143 ----------~--~~~~~~~aP~FP~~K~E~WwvllgD~~~n~Ll~~krv~~~~~~~~~~~~~k~i~~~~~~~g~~~~~~ 210 (342)
+ ...++++||+||..+.-.|||.+.+++.+.++ +..+++.+-+. +.+
T Consensus 450 ~~~~~~~ai~~d~~~~pys~Ap~f~t~~~~~w~~~v~~~~Qt~~I-ip~~Si~~v~K--~~~------------------ 508 (610)
T COG5407 450 ASVIETGAIKNDSSDSPYSEAPDFATRNDSEWAVRVAKCEQTVYI-IPGGSIATVSK--VTL------------------ 508 (610)
T ss_pred hhccCccccccCCCCCCcccCcccccccCcceEEEeeccccceEE-eCCccccccch--hhh------------------
Confidence 1 22368999999999999999999999987776 45666654110 011
Q ss_pred hHHHHHHHhhhhcCceeEEEEEEcCC-CCceeEEEEEEcCCCcccceEEEEEEEeeecC
Q 019342 211 SAAVREAAEKVRSGSRLVMGKIQAPA-EGNYNLTCYCLCDSWLGCDKRTNLKVKILKRT 268 (342)
Q Consensus 211 ~~~~~~~~~~~k~~s~~v~l~F~aP~-~G~~~l~l~viSDsYlG~D~~~~i~l~V~~~~ 268 (342)
...++|++|+ .++..+.+.+++..|+|.+....|.|-+.+.+
T Consensus 509 ----------------d~Ri~~dv~pvd~T~~~ql~~~ap~~vg~f~~~~ivm~t~d~~ 551 (610)
T COG5407 509 ----------------DRRIQGDVAPVDKTGGKQLIVHAPFMVGAFSVKWIVMLTVDNV 551 (610)
T ss_pred ----------------hcccccccCccccccceeeeecCchhhccceeeeEEEEeechh
Confidence 1124455543 45566666667777777666666665555544
No 5
>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]
Probab=99.74 E-value=6.5e-20 Score=197.53 Aligned_cols=334 Identities=26% Similarity=0.240 Sum_probs=261.5
Q ss_pred CCcccchhhccCCHHHHHHHHHHHHHHHH---------------hcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhh
Q 019342 1 MAVIPRTAQGHGWLRPAVGVVELSQSIIQ---------------AVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR 65 (342)
Q Consensus 1 ~~~~~~~a~~~GwL~~al~~m~L~Q~IvQ---------------A~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~ 65 (342)
|++++|+++.+||+.+.+..|...||+.| ++..++|++..-+.+...+.+| |||++.+.+.+.+
T Consensus 118 ~~~ilr~~~~~~~lE~~L~~ll~~e~~slV~~l~kNr~~i~~~t~L~~aaresE~~siEe~m~~lg-p~l~d~V~~~~a~ 196 (1674)
T KOG0951|consen 118 AAEILRTASDDGDLEPKLVVLLQFEKISLVEFLRKNRLGIVWCTRLARAARESERLSIEEIMRFLG-PELNDIVAKYIAT 196 (1674)
T ss_pred HHHhHhhccCchhhhHHHHHhhhhhhhHHHHHHHhhcchhhHHHHhhhhhccchhccHHHHHhhcC-hhhHHHHHHHHhh
Confidence 57889999999999999999999999999 6666666665556678889999 9999988888887
Q ss_pred cCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCceeEEEEEEecCCccccCCCeEEEEEeeeeeccCCCC
Q 019342 66 KKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPSLTVEVTCETEGEEGIQEGDIVTIQAWVTLKRGNGLI 145 (342)
Q Consensus 66 ~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~iP~I~i~a~~~v~gee~It~g~~vtl~~~V~L~R~n~~~ 145 (342)
....+.+++-.+....+..++....+++ ..++..+..+.|.|+++..+..+|+..++.|+......|+.++++++..
T Consensus 197 ~~~~~~qeek~~~l~~~e~~~~~~~~ls---~td~~~v~~~~~~iDLekt~ftEGe~lm~e~~c~lP~GS~rl~kk~yee 273 (1674)
T KOG0951|consen 197 RQTKSEQEEKEKKLEKREELLVSVIALS---KTDVLGVLEMRPVIDLEKTCFTEGEELMQEGKCKLPQGSFRLKKKGYEE 273 (1674)
T ss_pred hcccccchhhhhhhhccchhhhhhhhhc---ccccccccccCcccchhhhhhhhhhhhhccCceecCCccEEEecCCceE
Confidence 7778888888777655555554322232 2344558899999999988999999999999988888899999998877
Q ss_pred CCCccCCCCCCCCcccEEEEEEECCCCeEEEEeeeecccchhHHhhhhhhhhhhhcCCC-CccchhhHHHHHHHhhhhcC
Q 019342 146 GALPHAPYYPFHKEENFWFLLADSVSNNVWFSQKVSFMDEPAAITAASKAIEDTMEGSG-ATVKETSAAVREAAEKVRSG 224 (342)
Q Consensus 146 ~~~~~aP~FP~~K~E~WwvllgD~~~n~Ll~~krv~~~~~~~~~~~~~k~i~~~~~~~g-~~~~~~~~~~~~~~~~~k~~ 224 (342)
...+|.||||+.+.|.+|.+..+++-|+.++....+|++...++..+.+...+.+.--| .+.+.|..++....+.++.+
T Consensus 274 vhVPa~~~~pf~~~Ekl~~iselP~Wnq~aF~g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h 353 (1674)
T KOG0951|consen 274 VHVPAPSYFPFHKEEKLVKISELPKWNQPAFFGKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNH 353 (1674)
T ss_pred EeCCCCCCCCCCccceeEeecCCcchhhhhcccchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcc
Confidence 77888999999999999999999999999998888888866566666677777665444 45678999999999999888
Q ss_pred ceeEEEEEE-cCCCCceeEEEEEEcCCCcc--cceEEEEEEEeeecCcCCCCCccccCCCCCccCCCCCcc-cccccccC
Q 019342 225 SRLVMGKIQ-APAEGNYNLTCYCLCDSWLG--CDKRTNLKVKILKRTRAGTRGGIVSEEGPIVEDGAEEEE-EDEEEEYD 300 (342)
Q Consensus 225 s~~v~l~F~-aP~~G~~~l~l~viSDsYlG--~D~~~~i~l~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ 300 (342)
.+.. +.|. .|-.+.|...++++++-|+| |++..++.++|.+.+.++++|. ...++....-+-.|.- ..+.+.+|
T Consensus 354 ~r~d-gs~nl~~fKIVYIAPmKaLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~-~qieeTqVIV~TPEK~DiITRk~gd 431 (1674)
T KOG0951|consen 354 LRED-GSVNLAPFKIVYIAPMKALVQEMVGSFSKRLAPLGITVLELTGDSQLGK-EQIEETQVIVTTPEKWDIITRKSGD 431 (1674)
T ss_pred cccc-cceecccceEEEEeeHHHHHHHHHHHHHhhccccCcEEEEecccccchh-hhhhcceeEEeccchhhhhhcccCc
Confidence 7755 4444 45588999999999999999 9999999999999999888766 3444444444443333 33445555
Q ss_pred -CcCCccccchhhhh---hhcccCCCCCCccccCCC-CCCCCCCC
Q 019342 301 -DYESEYSEDEEDER---DTKKKVPAANGTVSKKGT-NSELSGSD 340 (342)
Q Consensus 301 -~~~s~~~~~~~~~~---~~~~~~~~~~~~~~~~~~-~~~~~~~~ 340 (342)
+|++.|+.+..||. ..++.....++++..... +++.+|+.
T Consensus 432 raY~qlvrLlIIDEIHLLhDdRGpvLESIVaRt~r~ses~~e~~R 476 (1674)
T KOG0951|consen 432 RAYEQLVRLLIIDEIHLLHDDRGPVLESIVARTFRRSESTEEGSR 476 (1674)
T ss_pred hhHHHHHHHHhhhhhhhcccccchHHHHHHHHHHHHhhhcccCce
Confidence 99999999999998 344555556777665544 44666664
No 6
>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]
Probab=99.71 E-value=1.5e-16 Score=171.91 Aligned_cols=217 Identities=13% Similarity=0.260 Sum_probs=180.8
Q ss_pred chhhccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHH
Q 019342 6 RTAQGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAEL 85 (342)
Q Consensus 6 ~~a~~~GwL~~al~~m~L~Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~l 85 (342)
.+.+.+||+..+..++.+|+|+.+.+|+ ...||+|+|.++.+++++++.+. ..++.+.++++.+...+
T Consensus 922 ei~l~rgw~~~~~~~l~~ck~v~~r~w~-----------~~~plrqf~~~~~ev~~~lE~k~-~~~~r~~~l~~~elg~l 989 (1674)
T KOG0951|consen 922 EIVLKRGWAGLAQMALNLCKMVEKRMWP-----------TQTPLRQFKGCPKEVLRRLEKKE-LPWGRYYDLDPAELGEL 989 (1674)
T ss_pred HHHhhcCcchHHHHHHHhHhHhhhhccc-----------ccCchhhcCCCCHHHHHHHHhcc-CcchhhhccCHHHHHHH
Confidence 4678999999999999999999999999 78999999999999999998776 47999999999999988
Q ss_pred HhhccCCChHHHHHHHHHHhcCCceeEEEEEEecCCccccCCCeEEEEEeeeeeccCCCCCCCccCCCCCC-----CCcc
Q 019342 86 LSQVGGFSSTEVQDVEMVLQMMPSLTVEVTCETEGEEGIQEGDIVTIQAWVTLKRGNGLIGALPHAPYYPF-----HKEE 160 (342)
Q Consensus 86 L~~~~~l~~~~~~~v~~v~~~iP~I~i~a~~~v~gee~It~g~~vtl~~~V~L~R~n~~~~~~~~aP~FP~-----~K~E 160 (342)
++ .++..+.+..++.+||++.+.+.+++ |+.+ .+.+. +. +.|.|-| +-.|
T Consensus 990 I~-----~~k~G~~l~~~~~~fpk~s~~~~vqp-----itr~-~~~~~--l~------------i~~~f~wd~~vh~~~e 1044 (1674)
T KOG0951|consen 990 IG-----VPKMGKPLHLFIRQFPKLSVSAHVQP-----ITRS-VYRVE--LT------------ITPDFDWDDKVHGSVE 1044 (1674)
T ss_pred hc-----CcccChhHHHHHHhcccceeeeeeee-----eeee-EEEEE--EE------------Eeecccchhhhccccc
Confidence 87 24556778889999999998766553 6643 55555 43 3455554 2468
Q ss_pred cEEEEEEECCCCeEEEEeeeecccchhHHhhhhhhhhhhhcCCCCccchhhHHHHHHHhhhhcCceeEEEEEEcC-CCCc
Q 019342 161 NFWFLLADSVSNNVWFSQKVSFMDEPAAITAASKAIEDTMEGSGATVKETSAAVREAAEKVRSGSRLVMGKIQAP-AEGN 239 (342)
Q Consensus 161 ~WwvllgD~~~n~Ll~~krv~~~~~~~~~~~~~k~i~~~~~~~g~~~~~~~~~~~~~~~~~k~~s~~v~l~F~aP-~~G~ 239 (342)
.||++|.|....+|++..-+-+.+ ....+.|++| -.++
T Consensus 1045 ~F~i~ved~dge~il~~e~~~~~k-----------------------------------------~~~~v~ft~~~~~~p 1083 (1674)
T KOG0951|consen 1045 PFWIIVEDTDGEKILHHEFFLLKK-----------------------------------------KEHTVNFTVPLFEPP 1083 (1674)
T ss_pred ceEEEEEccCccceeeeeeEEecc-----------------------------------------CceEEEEEeecCCCC
Confidence 899999999999999988877654 1245799999 3348
Q ss_pred eeEEEEEEcCCCcccceEEEEEEEeeecCcCCCCCccccCCCCCccCCCCCcccccccccCCcCCccccc
Q 019342 240 YNLTCYCLCDSWLGCDKRTNLKVKILKRTRAGTRGGIVSEEGPIVEDGAEEEEEDEEEEYDDYESEYSED 309 (342)
Q Consensus 240 ~~l~l~viSDsYlG~D~~~~i~l~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 309 (342)
++|.|.++||.|+|....+|+.|+.+..|++-.+.+++.+.-|+.-.+...++ ++.-|-|+
T Consensus 1084 P~~fi~lvSd~wl~s~~~~Pvsfr~l~lpek~p~pt~lld~~~~~~~~l~N~~---------~~~lf~~~ 1144 (1674)
T KOG0951|consen 1084 PQYFIRLVSDRWLHSETVLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNPS---------FETLFQDF 1144 (1674)
T ss_pred CceEEEEeeccccCCCcccccchhhccCcccCCCCchhhhccccchhccCCcc---------hhhhcccc
Confidence 99999999999999999999999999999999999999999999888887664 66677666
No 7
>PRK01172 ski2-like helicase; Provisional
Probab=98.40 E-value=3.4e-07 Score=97.41 Aligned_cols=86 Identities=12% Similarity=0.220 Sum_probs=76.7
Q ss_pred hhhccCCHHHHHHH------HHHHHH-------HHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHH
Q 019342 7 TAQGHGWLRPAVGV------VELSQS-------IIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQE 73 (342)
Q Consensus 7 ~a~~~GwL~~al~~------m~L~Q~-------IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~ 73 (342)
.....+|+..++.. |+|+|| |+||+|. ...||+|||||+...+++|.+.+++|+.+
T Consensus 570 ~~~~~~~~~~a~~~~~~~~~~~~~~~l~~~~~rl~~gv~~-----------~~~~L~~ip~~~~~~a~~l~~~g~~~~~d 638 (674)
T PRK01172 570 RASSADWISYSLARLSSIYKPEMRRKLEILNIRIKEGIRE-----------DLIDLVLIPKVGRVRARRLYDAGFKTVDD 638 (674)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHcCCCH-----------HHHhhcCCCCCCHHHHHHHHHcCCCCHHH
Confidence 35678999878777 999999 9999998 79999999999999999999999999999
Q ss_pred HHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019342 74 LRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 107 (342)
Q Consensus 74 L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~i 107 (342)
+.++++++|.++++ +++++++.+...++++
T Consensus 639 i~~~~~~~~~~i~~----~~~~~~~~i~~~~~~~ 668 (674)
T PRK01172 639 IARSSPERIKKIYG----FSDTLANAIVNRAMKI 668 (674)
T ss_pred HHhCCHHHHHHHhc----cCHHHHHHHHHHHHHH
Confidence 99999999999876 8888888887776654
No 8
>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]
Probab=98.39 E-value=9.3e-07 Score=96.15 Aligned_cols=206 Identities=15% Similarity=0.115 Sum_probs=147.9
Q ss_pred hhhccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHH
Q 019342 7 TAQGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELL 86 (342)
Q Consensus 7 ~a~~~GwL~~al~~m~L~Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL 86 (342)
++...||-..+.+++.||+||...||- ...|+.|++.... .+ .+++ . .|+.|...+.++++
T Consensus 713 i~~~~~~~~~~~~~l~l~k~ier~mw~-----------~~~~l~qf~~~~~---~~-~~~~-~---~l~~L~~~~~g~~w 773 (1230)
T KOG0952|consen 713 IVLRQNWHLLSNRMLNLCKRIERRMWD-----------FFIPLKQFTLLLN---RK-ERKK-L---TLLLLRKDELGELW 773 (1230)
T ss_pred HHHHhCchHHHHHHHHHHHHHHHHHHh-----------hhhhhhcCCcccc---hh-hhhc-c---hHHhhhhhhhcccc
Confidence 456789999999999999999999997 7899999987654 23 2222 2 67888877888887
Q ss_pred hhccCCChHHHHHHHHHHhcCCceeEEEEEEecCCccccCCCeEEEEEeeeeeccCCCCCCCccCCCCCCCCcccEEEEE
Q 019342 87 SQVGGFSSTEVQDVEMVLQMMPSLTVEVTCETEGEEGIQEGDIVTIQAWVTLKRGNGLIGALPHAPYYPFHKEENFWFLL 166 (342)
Q Consensus 87 ~~~~~l~~~~~~~v~~v~~~iP~I~i~a~~~v~gee~It~g~~vtl~~~V~L~R~n~~~~~~~~aP~FP~~K~E~Wwvll 166 (342)
.+ . ...++.+..+|.+++++.+.. ++. +++.|. +.+.+ .+.|.-.... ..|-.+++
T Consensus 774 ~~----~----~~~~k~l~~ip~v~v~a~~~p-----~t~-~vlri~--~~~~~------~f~w~~~~hg--~~g~~i~~ 829 (1230)
T KOG0952|consen 774 HN----V----PYGLKQLSGIPLVNVEALIQP-----ITR-NVLRIE--VAITP------DFEWNDGIHG--KAGQPIFK 829 (1230)
T ss_pred cc----C----chhhhhhccCCceehhhhhcc-----chh-hhheee--eccCC------ceEEeccccc--ccCceeEe
Confidence 63 1 223888999999998877653 222 345555 44332 1233222222 22333999
Q ss_pred EECCCCeEEEEeeeecccchhHHhhhhhhhhhhhcCCCCccchhhHHHHHHHhhhhcCceeEEEEEEcC--CCCceeEEE
Q 019342 167 ADSVSNNVWFSQKVSFMDEPAAITAASKAIEDTMEGSGATVKETSAAVREAAEKVRSGSRLVMGKIQAP--AEGNYNLTC 244 (342)
Q Consensus 167 gD~~~n~Ll~~krv~~~~~~~~~~~~~k~i~~~~~~~g~~~~~~~~~~~~~~~~~k~~s~~v~l~F~aP--~~G~~~l~l 244 (342)
.|...+.+++++..-+..... +.++ -+.|.+| +|-+.++.+
T Consensus 830 ed~~~~~i~h~e~~~~~~~~~-----------------------------------~~s~--~lvf~ipis~pLps~~~~ 872 (1230)
T KOG0952|consen 830 EDSSLLPILHIEVFLVNCKKV-----------------------------------NESQ--LLVFTIPISDPLPSQIRH 872 (1230)
T ss_pred ecCCCCcceeeeeehhhhhhh-----------------------------------hhhh--heeEEeecccCCccceEE
Confidence 999999999988776544110 0112 2678888 688899999
Q ss_pred EEEcCCCcccceEEEEEEEeeecCcCCCCCccccCCCCCccCCCCCcc
Q 019342 245 YCLCDSWLGCDKRTNLKVKILKRTRAGTRGGIVSEEGPIVEDGAEEEE 292 (342)
Q Consensus 245 ~viSDsYlG~D~~~~i~l~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 292 (342)
++.||.|+|++..+++.+.....+......+.+.+.+|....-...+.
T Consensus 873 ~~~s~~~l~~e~~~~~s~~~~il~~~~~~~t~ll~l~plp~~~L~~~~ 920 (1230)
T KOG0952|consen 873 RAVSDNWLGAETVYPLSFQHLILPDNEPPLTELLDLRPLPSSALKNVV 920 (1230)
T ss_pred eeecccccCCceeccccccceeccccccccccccccCCCcchhhcccc
Confidence 999999999999999999999998888888888888887766555443
No 9
>PRK02362 ski2-like helicase; Provisional
Probab=98.05 E-value=6.5e-06 Score=88.73 Aligned_cols=84 Identities=12% Similarity=0.039 Sum_probs=72.4
Q ss_pred chhhccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHH
Q 019342 6 RTAQGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAEL 85 (342)
Q Consensus 6 ~~a~~~GwL~~al~~m~L~Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~l 85 (342)
+. ++.+|+..+..+|+|+|||.||+|. +..||+|||||....+++|.+.++.++.+|..+.++++..+
T Consensus 623 ~i-~~~~~~~~~~~~~~l~~~l~~gv~~-----------~~~~L~~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~ 690 (737)
T PRK02362 623 RL-ASELDLDLARAARELEKRVEYGVRE-----------ELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI 690 (737)
T ss_pred HH-HHHhCccHHHHHHHHHHHHHhCCCH-----------HHHHHhCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH
Confidence 44 3457788899999999999999998 78999999999999999998899999999999999998888
Q ss_pred HhhccCCChHHHHHHHHHHhcC
Q 019342 86 LSQVGGFSSTEVQDVEMVLQMM 107 (342)
Q Consensus 86 L~~~~~l~~~~~~~v~~v~~~i 107 (342)
++ ++..+.+.+.+...
T Consensus 691 ~g------~~~~~~i~~~~~~~ 706 (737)
T PRK02362 691 LG------EKIAENILEQAGRR 706 (737)
T ss_pred HC------HHHHHHHHHHhCcc
Confidence 65 46677777777743
No 10
>PRK00254 ski2-like helicase; Provisional
Probab=97.71 E-value=5.5e-05 Score=81.44 Aligned_cols=79 Identities=11% Similarity=0.170 Sum_probs=67.1
Q ss_pred cCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhcc
Q 019342 11 HGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVG 90 (342)
Q Consensus 11 ~GwL~~al~~m~L~Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~ 90 (342)
.+|++ ++. +|+|||+||+|. ..+||.|+|||....+++|-+.++.++.++..++.+++.++ .
T Consensus 623 ~~~~~-~l~--~l~~rl~~g~~~-----------~~~~L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~----~ 684 (720)
T PRK00254 623 QEVLD-YLE--TLHLRVKHGVRE-----------ELLELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKV----E 684 (720)
T ss_pred hhHHH-HHH--HHHHHHHcCCCH-----------HHhhhhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcC----C
Confidence 45554 333 899999999998 79999999999999999998888999999999999988665 3
Q ss_pred CCChHHHHHHHHHHhcC
Q 019342 91 GFSSTEVQDVEMVLQMM 107 (342)
Q Consensus 91 ~l~~~~~~~v~~v~~~i 107 (342)
|+..+.++.|.+.++..
T Consensus 685 gi~~~~a~~i~~~~~~~ 701 (720)
T PRK00254 685 GIGAKIVEGIFKHLGVE 701 (720)
T ss_pred CCCHHHHHHHHHHhccc
Confidence 57888889998887743
No 11
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=93.34 E-value=0.14 Score=37.76 Aligned_cols=54 Identities=15% Similarity=0.317 Sum_probs=45.7
Q ss_pred CccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019342 48 PFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 105 (342)
Q Consensus 48 pLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~ 105 (342)
.|+++|++.+..+.+|...++.|+.+|.+.+.+++..+ .|++++..+.+...++
T Consensus 6 ~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i----~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 6 DLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEI----PGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTS----TTSSHHHHHHHHHHHH
T ss_pred hhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcC----CCCCHHHHHHHHHHHh
Confidence 57889999999999998888999999999987765543 6799999998887765
No 12
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=88.54 E-value=0.22 Score=55.04 Aligned_cols=18 Identities=50% Similarity=0.813 Sum_probs=12.3
Q ss_pred cccccCCcCCccccchhh
Q 019342 295 EEEEYDDYESEYSEDEED 312 (342)
Q Consensus 295 ~~~~~~~~~s~~~~~~~~ 312 (342)
||+++|++++|||||||-
T Consensus 327 ed~eDde~~deYsDDeD~ 344 (1233)
T KOG1824|consen 327 EDEEDDEQDDEYSDDEDM 344 (1233)
T ss_pred hccccchhccccccccch
Confidence 444444556999999764
No 13
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=83.02 E-value=2.7 Score=40.85 Aligned_cols=57 Identities=12% Similarity=0.125 Sum_probs=48.1
Q ss_pred CCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019342 46 TAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 106 (342)
Q Consensus 46 ~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~ 106 (342)
.-||..+|.+.+..+++|.+.++.|+.+|..+++.++.++++ ++.+....+.+.++.
T Consensus 5 ~~~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g----~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 5 EKDLEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAG----IGESTAAKIIEAARE 61 (317)
T ss_pred cccHhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcC----CCHHHHHHHHHHHHH
Confidence 468899999999999999999999999999999988877754 677777777766654
No 14
>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=81.08 E-value=0.72 Score=50.63 Aligned_cols=6 Identities=17% Similarity=-0.103 Sum_probs=2.2
Q ss_pred HHHHHH
Q 019342 23 LSQSII 28 (342)
Q Consensus 23 L~Q~Iv 28 (342)
+.+.+.
T Consensus 311 ~l~~~~ 316 (784)
T PF04931_consen 311 FLQFFE 316 (784)
T ss_pred HHHHHh
Confidence 333333
No 15
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=80.77 E-value=1.4 Score=48.75 Aligned_cols=6 Identities=67% Similarity=1.171 Sum_probs=3.1
Q ss_pred CCCccc
Q 019342 249 DSWLGC 254 (342)
Q Consensus 249 DsYlG~ 254 (342)
|+|+|+
T Consensus 1371 D~~l~v 1376 (1516)
T KOG1832|consen 1371 DSFLGV 1376 (1516)
T ss_pred cceEEE
Confidence 555553
No 16
>PF15243 ANAPC15: Anaphase-promoting complex subunit 15
Probab=80.72 E-value=1.1 Score=36.48 Aligned_cols=39 Identities=41% Similarity=0.533 Sum_probs=18.5
Q ss_pred ccCCCCCccCCCCCcccccccccCCcCCccccchhhhhh
Q 019342 277 VSEEGPIVEDGAEEEEEDEEEEYDDYESEYSEDEEDERD 315 (342)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~ 315 (342)
|+..+|..+.-.++++++|++++++.++|.++.++|+.+
T Consensus 52 vPIGK~~se~~~~~e~d~e~~~dd~d~~e~~~~d~de~~ 90 (92)
T PF15243_consen 52 VPIGKPASEPEEEEEEDDEDEDDDSDDSEESMQDDDEMN 90 (92)
T ss_pred CccCCCCCcccccccccccccccccccccchhccchhcc
Confidence 444555555222233333334444555666666666553
No 17
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=80.20 E-value=1.1 Score=42.92 Aligned_cols=9 Identities=22% Similarity=0.254 Sum_probs=4.6
Q ss_pred HHHHhcCCc
Q 019342 101 EMVLQMMPS 109 (342)
Q Consensus 101 ~~v~~~iP~ 109 (342)
.+.++++|.
T Consensus 57 C~s~qrlp~ 65 (314)
T PF06524_consen 57 CQSVQRLPM 65 (314)
T ss_pred hhhhhcCch
Confidence 344555554
No 18
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=78.99 E-value=0.63 Score=38.16 Aligned_cols=8 Identities=38% Similarity=0.746 Sum_probs=0.0
Q ss_pred cCCCCCcc
Q 019342 285 EDGAEEEE 292 (342)
Q Consensus 285 ~~~~~~~~ 292 (342)
+.+.++++
T Consensus 13 e~dsdEde 20 (101)
T PF09026_consen 13 ESDSDEDE 20 (101)
T ss_dssp --------
T ss_pred ccccccch
Confidence 33333333
No 19
>PTZ00035 Rad51 protein; Provisional
Probab=78.13 E-value=5 Score=39.75 Aligned_cols=58 Identities=17% Similarity=0.250 Sum_probs=48.3
Q ss_pred CccCC--CCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019342 48 PFLQL--PHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 109 (342)
Q Consensus 48 pLlQL--Ph~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~iP~ 109 (342)
.|-.| |.+++..+++|+..++.|+.+|+..++.++.++ .|++...+.++.+.++.+..
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~----~gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAYATKKDLCNI----KGISEAKVEKIKEAASKLVP 81 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHh----hCCCHHHHHHHHHHHHHhcc
Confidence 34444 789999999999999999999999999888776 45999988888888877644
No 20
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=77.95 E-value=4.3 Score=30.78 Aligned_cols=55 Identities=16% Similarity=0.305 Sum_probs=41.2
Q ss_pred CCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019342 46 TAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 105 (342)
Q Consensus 46 ~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~ 105 (342)
+.|+-.| +++......|.+.+|.|+.+|+.++.+++..+ .+|...-+.+|...++
T Consensus 11 ~~~I~~L-~LS~Ra~n~L~~~~I~tv~dL~~~s~~~L~~i----~n~G~ksl~EI~~~L~ 65 (66)
T PF03118_consen 11 DTPIEDL-GLSVRAYNCLKRAGIHTVGDLVKYSEEDLLKI----KNFGKKSLEEIKEKLK 65 (66)
T ss_dssp CSBGGGS-TSBHHHHHHHHCTT--BHHHHHCS-HHHHHTS----TTSHHHHHHHHHHHHH
T ss_pred cCcHHHh-CCCHHHHHHHHHhCCcCHHHHHhCCHHHHHhC----CCCCHhHHHHHHHHHc
Confidence 4677777 58899999999999999999999998775544 4577777888877764
No 21
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=76.84 E-value=6.3 Score=38.01 Aligned_cols=53 Identities=17% Similarity=0.224 Sum_probs=43.7
Q ss_pred ccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019342 49 FLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 105 (342)
Q Consensus 49 LlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~ 105 (342)
|.++|++.+..+++|.+.++.|+.+|...+.+++..+++ ++.+....+.+.+.
T Consensus 1 l~~i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g----~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREAGYDTFEAIAVASPKELSEIAG----ISEGTAAKIIQAAR 53 (310)
T ss_pred CcccCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHhccC----CCHHHHHHHHHHHH
Confidence 457999999999999999999999999999998877754 66666666666654
No 22
>PRK07758 hypothetical protein; Provisional
Probab=76.05 E-value=8.4 Score=31.58 Aligned_cols=51 Identities=16% Similarity=0.297 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019342 52 LPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 106 (342)
Q Consensus 52 LPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~ 106 (342)
||.++.....-|.+.+|.++.+|..++++++.++ -+|.++-+++|...+..
T Consensus 39 ~~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~i----knlGkKSL~EIkekL~E 89 (95)
T PRK07758 39 LSLLSAPARRALEHHGIHTVEELSKYSEKEILKL----HGMGPASLPKLRKALEE 89 (95)
T ss_pred CccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHc----cCCCHHHHHHHHHHHHH
Confidence 5678888888888889999999999999987765 34888888888877765
No 23
>PRK14133 DNA polymerase IV; Provisional
Probab=74.38 E-value=9.8 Score=37.39 Aligned_cols=50 Identities=14% Similarity=0.184 Sum_probs=43.1
Q ss_pred HHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHh
Q 019342 25 QSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLS 87 (342)
Q Consensus 25 Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~ 87 (342)
+.+.|.+|. -|+..||++...+.++|.+.+++|+.+|..++...+...++
T Consensus 164 ~~~~~~L~~-------------lpv~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~rfG 213 (347)
T PRK14133 164 DMIPDILKP-------------LPISKVHGIGKKSVEKLNNIGIYTIEDLLKLSREFLIEYFG 213 (347)
T ss_pred HHHHHHHHh-------------CCccccCCCCHHHHHHHHHcCCccHHHHhhCCHHHHHHHHh
Confidence 456667765 59999999999999999999999999999999888777765
No 24
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=73.35 E-value=11 Score=30.69 Aligned_cols=48 Identities=17% Similarity=0.289 Sum_probs=39.2
Q ss_pred CCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCC
Q 019342 45 GTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGF 92 (342)
Q Consensus 45 ~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l 92 (342)
..+.|.+||+|.+.+++-|...+|.++.+|...++.++-.-|..+.|.
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~Ly~~lc~~~G~ 57 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRLLGIRSPADLKGRDPEELYERLCALTGQ 57 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHHcCCCCHHHHhCCCHHHHHHHHHHHcCC
Confidence 357899999999999999999999999999999998876555433333
No 25
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=72.25 E-value=14 Score=32.03 Aligned_cols=60 Identities=25% Similarity=0.325 Sum_probs=46.6
Q ss_pred CCCccCCCC---------CCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019342 46 TAPFLQLPH---------FTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 107 (342)
Q Consensus 46 ~spLlQLPh---------~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~i 107 (342)
...|.+.|. +.++.++.+-. ++.||..|++|++.+.+.+|.. .|..+++...+.+++.++
T Consensus 60 ~~~l~~yP~l~~WL~vVgl~~~~i~~i~~-~~~tLe~Llemsd~el~~~l~~-~g~~~EE~rRL~~Al~~L 128 (129)
T PF13543_consen 60 AAELNSYPSLRQWLRVVGLRPESIQAILS-KVLTLEALLEMSDEELKEILNR-CGAREEECRRLCRALSNL 128 (129)
T ss_pred chhcccCCcHHHHhhhcCCCHHHHHHHHH-hhcCHHHHHhCCHHHHHHHHHH-hCCCHHHHHHHHHHHHhc
Confidence 456667774 56788887743 3679999999999999999997 677788888888777654
No 26
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=71.55 E-value=10 Score=37.27 Aligned_cols=54 Identities=17% Similarity=0.156 Sum_probs=44.7
Q ss_pred cCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019342 50 LQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 107 (342)
Q Consensus 50 lQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~i 107 (342)
+|-+.+++..+++|++.++.|+.+|+..++.++.++.. ++.....++...++.+
T Consensus 4 ~~~~~~~~~~~~~l~~~g~~t~~~~~~~~~~~L~~i~~----ls~~~~~~~~~~~~~~ 57 (316)
T TIGR02239 4 LEGNGITAADIKKLQEAGLHTVESVAYAPKKQLLEIKG----ISEAKADKILAEAAKL 57 (316)
T ss_pred hhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhC----CCHHHHHHHHHHHHHh
Confidence 45556999999999999999999999999999888754 8888887777766644
No 27
>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=70.89 E-value=13 Score=35.90 Aligned_cols=55 Identities=11% Similarity=0.224 Sum_probs=43.7
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCC
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMP 108 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~iP 108 (342)
-|+..||++...+.++|.+.++.|+.+|..++...+...++ .....+...+.-+-
T Consensus 171 lpl~~l~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g-------~~~~~l~~~~~G~~ 225 (334)
T cd03586 171 LPVRKIPGVGKVTAEKLKELGIKTIGDLAKLDVELLKKLFG-------KSGRRLYELARGID 225 (334)
T ss_pred CCchhhCCcCHHHHHHHHHcCCcCHHHHHcCCHHHHHHHHh-------HHHHHHHHHhCCCC
Confidence 58999999999999999999999999999999888776654 24555555555443
No 28
>PRK02406 DNA polymerase IV; Validated
Probab=70.06 E-value=14 Score=36.16 Aligned_cols=54 Identities=11% Similarity=0.140 Sum_probs=43.9
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 107 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~i 107 (342)
-|+..||++...+.++|.+.++.|+.+|..++...+...++. ....+...+.-+
T Consensus 168 lpi~~l~giG~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~fG~-------~~~~l~~~a~G~ 221 (343)
T PRK02406 168 LPVEKIPGVGKVTAEKLHALGIYTCADLQKYDLAELIRHFGK-------FGRRLYERARGI 221 (343)
T ss_pred CCcchhcCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHHhH-------HHHHHHHHhCCC
Confidence 599999999999999999999999999999998888777652 345555555554
No 29
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=69.90 E-value=11 Score=37.07 Aligned_cols=54 Identities=15% Similarity=0.173 Sum_probs=45.6
Q ss_pred CCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019342 52 LPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 109 (342)
Q Consensus 52 LPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~iP~ 109 (342)
-+.+++..+++|++.++.|+.+++..++.++.++ .|++...+.++.+.+..+-.
T Consensus 6 ~~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~----~gls~~~~~~i~~~~~~~~~ 59 (313)
T TIGR02238 6 AHGINAADIKKLKSAGICTVNGVIMTTRRALCKI----KGLSEAKVDKIKEAASKIIN 59 (313)
T ss_pred cCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHh----cCCCHHHHHHHHHHHHhhhc
Confidence 3569999999999999999999999998887766 45899988888888777643
No 30
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=69.86 E-value=14 Score=25.48 Aligned_cols=47 Identities=11% Similarity=0.271 Sum_probs=38.3
Q ss_pred CCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019342 55 FTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 105 (342)
Q Consensus 55 ~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~ 105 (342)
+++..+.++...++.|+.+|...+++++..+ .|+++.....+...++
T Consensus 1 i~~~~~~~L~~~G~~s~e~la~~~~~eL~~i----~g~~~e~a~~ii~~a~ 47 (50)
T TIGR01954 1 IDEEIAQLLVEEGFTTVEDLAYVPIDELLSI----EGFDEETAKELINRAR 47 (50)
T ss_pred CCHHHHHHHHHcCCCCHHHHHccCHHHHhcC----CCCCHHHHHHHHHHHH
Confidence 4677888888889999999999999988765 4588888888777665
No 31
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=69.63 E-value=2.5 Score=43.38 Aligned_cols=16 Identities=31% Similarity=0.607 Sum_probs=6.6
Q ss_pred CCCcccceEEEEEEEe
Q 019342 249 DSWLGCDKRTNLKVKI 264 (342)
Q Consensus 249 DsYlG~D~~~~i~l~V 264 (342)
|.||--+..+.-+|+|
T Consensus 13 ddWi~~~~~~~~KlTi 28 (458)
T PF10446_consen 13 DDWIRQDTDYKRKLTI 28 (458)
T ss_pred hhhhhccccccccccH
Confidence 3444444444433333
No 32
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=69.15 E-value=54 Score=25.75 Aligned_cols=42 Identities=12% Similarity=0.181 Sum_probs=25.3
Q ss_pred cccCCCeEEEEEeeeeeccCCCCCCCccCCCCCCCCcccEEEEEEECCCCeEE
Q 019342 123 GIQEGDIVTIQAWVTLKRGNGLIGALPHAPYYPFHKEENFWFLLADSVSNNVW 175 (342)
Q Consensus 123 ~It~g~~vtl~~~V~L~R~n~~~~~~~~aP~FP~~K~E~WwvllgD~~~n~Ll 175 (342)
-..||+.|++. +.+...++ .++......-.|.|.|+..+.+.
T Consensus 10 iYrPGetV~~~--~~~~~~~~---------~~~~~~~~~~~v~i~dp~g~~v~ 51 (99)
T PF01835_consen 10 IYRPGETVHFR--AIVRDLDN---------DFKPPANSPVTVTIKDPSGNEVF 51 (99)
T ss_dssp EE-TTSEEEEE--EEEEEECT---------TCSCESSEEEEEEEEETTSEEEE
T ss_pred CcCCCCEEEEE--EEEecccc---------ccccccCCceEEEEECCCCCEEE
Confidence 46889999988 76654321 13333445566899999555543
No 33
>PRK01216 DNA polymerase IV; Validated
Probab=69.05 E-value=9.4 Score=38.03 Aligned_cols=62 Identities=5% Similarity=0.164 Sum_probs=48.1
Q ss_pred HHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHH
Q 019342 25 QSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVL 104 (342)
Q Consensus 25 Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~ 104 (342)
+.+.|.+|+ -|+..||.+.....++|.+.++.|+.+|..++...+...++ ......+.+.+
T Consensus 169 ~~~~~~L~~-------------LPi~~l~giG~~~~~~L~~~Gi~TigdL~~~~~~~L~~rfG------~~~~~~L~~~a 229 (351)
T PRK01216 169 EEVKRFINE-------------LDIADIPGIGDITAEKLKKLGVNKLVDTLRIEFDELKGIIG------EAKAKYLFSLA 229 (351)
T ss_pred HHHHHHHhc-------------CCcccccCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHC------HHHHHHHHHHh
Confidence 456667775 59999999999999999999999999999999888777665 23344555544
Q ss_pred h
Q 019342 105 Q 105 (342)
Q Consensus 105 ~ 105 (342)
.
T Consensus 230 ~ 230 (351)
T PRK01216 230 R 230 (351)
T ss_pred C
Confidence 3
No 34
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=68.01 E-value=12 Score=37.44 Aligned_cols=54 Identities=13% Similarity=0.141 Sum_probs=45.3
Q ss_pred CCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCC
Q 019342 51 QLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMP 108 (342)
Q Consensus 51 QLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~iP 108 (342)
|-+.+++..+++|+..++.|+.+|+..++.++.++ .|+++..+.++++.++.+-
T Consensus 35 ~~~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~----~g~s~~~~~ki~~~a~~~~ 88 (344)
T PLN03187 35 ISQGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGI----KGLSEAKVDKICEAAEKLL 88 (344)
T ss_pred hhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHh----cCCCHHHHHHHHHHHHHhh
Confidence 33679999999999999999999999998887765 5699988888887777763
No 35
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=67.54 E-value=4.3 Score=45.26 Aligned_cols=7 Identities=14% Similarity=0.164 Sum_probs=3.0
Q ss_pred CCccCCC
Q 019342 47 APFLQLP 53 (342)
Q Consensus 47 spLlQLP 53 (342)
+.+-|+|
T Consensus 1000 s~~gq~~ 1006 (1516)
T KOG1832|consen 1000 SRLGQMT 1006 (1516)
T ss_pred cccccCC
Confidence 3444443
No 36
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=65.31 E-value=20 Score=33.92 Aligned_cols=55 Identities=7% Similarity=0.170 Sum_probs=47.5
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 105 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~ 105 (342)
..|.++|++.+..+++|-..++.|+..|...+.+++.++ .|++...++.|...+.
T Consensus 3 ~~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V----~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 3 EELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEV----DGIGNALAARIKADVG 57 (232)
T ss_pred cccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHc----cCCCHHHHHHHHHHhc
Confidence 578999999999999998888999999999998887655 4688888888888877
No 37
>PRK02794 DNA polymerase IV; Provisional
Probab=63.96 E-value=19 Score=36.40 Aligned_cols=56 Identities=14% Similarity=0.099 Sum_probs=45.3
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 109 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~iP~ 109 (342)
-||..||++...+.++|.+.+|.|+.+|..++...+...++. ....++..+.-+..
T Consensus 209 lPl~~L~GiG~~~~~~L~~~GI~tigdL~~l~~~~L~~rfG~-------~g~~l~~~a~G~d~ 264 (419)
T PRK02794 209 KPVGIIWGVGPATAARLARDGIRTIGDLQRADEADLMRRFGS-------MGLRLWRLARGIDD 264 (419)
T ss_pred CChhhhCCCCHHHHHHHHHhccchHHHHhhCCHHHHHHHHhH-------HHHHHHHHhCCCCC
Confidence 599999999999999999999999999999998888777652 35556666655543
No 38
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=62.65 E-value=19 Score=30.42 Aligned_cols=57 Identities=16% Similarity=0.214 Sum_probs=43.3
Q ss_pred CCCCHHHHHHHhhcCCCCHHHHHcCCHHH--HHHHHhhccCCChHHHHHHHHHHhc--CCce
Q 019342 53 PHFTEAVIKKIARKKVRTFQELRDMSLQD--RAELLSQVGGFSSTEVQDVEMVLQM--MPSL 110 (342)
Q Consensus 53 Ph~~~~~v~~l~~~~v~tl~~L~~m~~~e--r~~lL~~~~~l~~~~~~~v~~v~~~--iP~I 110 (342)
|.+.+....+|.+.+|.|..+|++..... |+.|... .|++.+.+....+.+.- +|-|
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~-~~i~~~~l~~w~~~AdL~ri~gi 61 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAGDTPLGRKALAKK-LGISERNLLKWVNQADLMRIPGI 61 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHh-cCCCHHHHHHHHhHHHhhhcCCC
Confidence 77888999999999999999999887544 4447665 67888888877766554 4444
No 39
>PRK03352 DNA polymerase IV; Validated
Probab=62.65 E-value=12 Score=36.63 Aligned_cols=41 Identities=17% Similarity=0.126 Sum_probs=37.3
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHh
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLS 87 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~ 87 (342)
-|+..||++...+.++|.+.+|.|+.+|..++...+...++
T Consensus 177 lpl~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~fG 217 (346)
T PRK03352 177 RPTDALWGVGPKTAKRLAALGITTVADLAAADPAELAATFG 217 (346)
T ss_pred CCHHHcCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHHhC
Confidence 69999999999999999999999999999999888777665
No 40
>PRK03348 DNA polymerase IV; Provisional
Probab=62.38 E-value=24 Score=36.35 Aligned_cols=56 Identities=20% Similarity=0.191 Sum_probs=45.3
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCC
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMP 108 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~iP 108 (342)
-|+..||++.....++|.+.+|+|+.+|..++..++...|+. .....+.+.+.-+.
T Consensus 180 LPv~~L~GIG~~t~~~L~~lGI~TigDLa~l~~~~L~~~fG~------~~g~~L~~~a~G~d 235 (454)
T PRK03348 180 LPVRRLWGIGPVTEEKLHRLGIETIGDLAALSEAEVANLLGA------TVGPALHRLARGID 235 (454)
T ss_pred CCccccCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHHHCH------HHHHHHHHHHcCCC
Confidence 599999999999999999999999999999998888877652 34555656655553
No 41
>PF04281 Tom22: Mitochondrial import receptor subunit Tom22 ; InterPro: IPR005683 The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family represents the Tom22 proteins []. The N-terminal region of Tom22 has been shown to have chaperone-like activity, and the C-terminal region faces the intermembrane face []. ; GO: 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane
Probab=61.86 E-value=4.8 Score=35.15 Aligned_cols=19 Identities=37% Similarity=0.692 Sum_probs=12.1
Q ss_pred cccccCCcCCccccchhhh
Q 019342 295 EEEEYDDYESEYSEDEEDE 313 (342)
Q Consensus 295 ~~~~~~~~~s~~~~~~~~~ 313 (342)
++++++|++|+++||++++
T Consensus 30 ~~~~~~d~~sd~~dd~d~e 48 (137)
T PF04281_consen 30 DDEDDTDTDSDISDDSDDE 48 (137)
T ss_pred cccccccccccccccccCC
Confidence 3445557777777766654
No 42
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=59.92 E-value=29 Score=35.19 Aligned_cols=55 Identities=15% Similarity=0.148 Sum_probs=43.9
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCC
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMP 108 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~iP 108 (342)
-|+..||++...+.++|.+.+|.|+.+|..++...+.+.++. ....+...+.-+.
T Consensus 179 lPv~~l~GiG~~~~~~L~~lGi~TigdL~~~~~~~L~~~fG~-------~~~~l~~~a~G~~ 233 (422)
T PRK03609 179 QPVEEVWGVGRRISKKLNAMGIKTALDLADTNIRFIRKHFNV-------VLERTVRELRGEP 233 (422)
T ss_pred CChhhcCCccHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHCH-------HHHHHHHHhCCCC
Confidence 699999999999999999999999999999998887766652 3445555555543
No 43
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=59.89 E-value=25 Score=35.08 Aligned_cols=77 Identities=19% Similarity=0.255 Sum_probs=53.2
Q ss_pred HHHHHHHhcCCCccCCCCCCCCCCCCccCC--CCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHH
Q 019342 23 LSQSIIQAVPLSSRKATGGSTEGTAPFLQL--PHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDV 100 (342)
Q Consensus 23 L~Q~IvQA~W~~~~~~~~~~~~~~spLlQL--Ph~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v 100 (342)
..||.-|+|...... +......+|-.| +.+++..+++|++.++.|+.+++..++.++.++. +++.....++
T Consensus 5 ~~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~~i~----~is~~~~~~~ 77 (342)
T PLN03186 5 VAAAAAQAMQEEEEE---EAAHGPFPIEQLQASGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIK----GISEAKVEKI 77 (342)
T ss_pred HHHHHHhhccchhhc---ccccCCccHHHHHhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhc----CCCHHHHHHH
Confidence 356677777543211 111112245445 5699999999999999999999999988887774 4888888777
Q ss_pred HHHHhc
Q 019342 101 EMVLQM 106 (342)
Q Consensus 101 ~~v~~~ 106 (342)
...++.
T Consensus 78 ~~~~~~ 83 (342)
T PLN03186 78 LEAASK 83 (342)
T ss_pred HHHHHH
Confidence 766644
No 44
>PRK03103 DNA polymerase IV; Reviewed
Probab=59.81 E-value=25 Score=35.29 Aligned_cols=41 Identities=20% Similarity=0.239 Sum_probs=37.1
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHh
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLS 87 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~ 87 (342)
-|+..||++.....++|.+.+|.|+.+|..++...+...++
T Consensus 181 lpi~~l~gig~~~~~~L~~~Gi~tigdl~~~~~~~L~~~fG 221 (409)
T PRK03103 181 LPVRKLFGVGSRMEKHLRRMGIRTIGQLANTPLERLKKRWG 221 (409)
T ss_pred CCHhhcCCccHHHHHHHHHcCCCCHHHHhcCCHHHHHHHHC
Confidence 59999999999999999999999999999999887776665
No 45
>KOG1834 consensus Calsyntenin [Extracellular structures]
Probab=58.86 E-value=9.1 Score=41.32 Aligned_cols=10 Identities=20% Similarity=0.590 Sum_probs=6.6
Q ss_pred EEEEEcCCCc
Q 019342 243 TCYCLCDSWL 252 (342)
Q Consensus 243 ~l~viSDsYl 252 (342)
.|.|+|=+|+
T Consensus 831 vViVVcVgfL 840 (952)
T KOG1834|consen 831 VVIVVCVGFL 840 (952)
T ss_pred EEEEeehhHH
Confidence 4667777764
No 46
>COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion]
Probab=58.35 E-value=3.7 Score=42.47 Aligned_cols=42 Identities=7% Similarity=-0.107 Sum_probs=31.2
Q ss_pred EEEEEEcCC-CCceeEEEEEEcCCCcccceEEEEEEEeeecCc
Q 019342 228 VMGKIQAPA-EGNYNLTCYCLCDSWLGCDKRTNLKVKILKRTR 269 (342)
Q Consensus 228 v~l~F~aP~-~G~~~l~l~viSDsYlG~D~~~~i~l~V~~~~~ 269 (342)
++|...+|. .|.+.++..+|+-.|.-.++++...+.|.+.+.
T Consensus 525 ~ql~~~ap~~vg~f~~~~ivm~t~d~~~~~eql~~~~V~D~e~ 567 (610)
T COG5407 525 KQLIVHAPFMVGAFSVKWIVMLTVDNVIYGEQLKIQVVDDFEK 567 (610)
T ss_pred eeeeecCchhhccceeeeEEEEeechhhhHHHHHHHhhccchh
Confidence 345566663 788888888888888888887777777777664
No 47
>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=58.24 E-value=34 Score=33.46 Aligned_cols=42 Identities=12% Similarity=0.046 Sum_probs=37.5
Q ss_pred CCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHh
Q 019342 46 TAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLS 87 (342)
Q Consensus 46 ~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~ 87 (342)
.-|+..||++...+.++|.+.++.|+.+|..++.+.+...++
T Consensus 175 ~lpl~~l~gig~~~~~~L~~~Gi~ti~dL~~~~~~~L~~rfG 216 (344)
T cd01700 175 ILPVGDVWGIGRRTAKKLNAMGIHTAGDLAQADPDLLRKKFG 216 (344)
T ss_pred cCChhhcCccCHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHH
Confidence 369999999999999999999999999999999888776655
No 48
>PRK01810 DNA polymerase IV; Validated
Probab=58.20 E-value=28 Score=34.92 Aligned_cols=53 Identities=11% Similarity=0.046 Sum_probs=42.8
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 106 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~ 106 (342)
-|+..||++.+.+.++|.+.+++|+.+|..++...+...++. ....++..+.-
T Consensus 179 lpv~~l~giG~~~~~~L~~~Gi~tigdL~~~~~~~L~~rfG~-------~g~~l~~~a~G 231 (407)
T PRK01810 179 LPVGEMHGIGEKTAEKLKDIGIQTIGDLAKADEHILRAKLGI-------NGVRLQRRANG 231 (407)
T ss_pred CCHhhcCCcCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHHhH-------HHHHHHHHhcC
Confidence 588899999999999999999999999999998887776652 34555555554
No 49
>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=57.40 E-value=33 Score=33.56 Aligned_cols=54 Identities=15% Similarity=0.105 Sum_probs=41.4
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCC-HHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMS-LQDRAELLSQVGGFSSTEVQDVEMVLQMM 107 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~-~~er~~lL~~~~~l~~~~~~~v~~v~~~i 107 (342)
-|+..||++.....++|.+.++.|+.+|..++ ...+...++ .....+.+.++-+
T Consensus 173 lpi~~l~giG~~~~~~L~~~Gi~ti~dl~~~~~~~~l~~~fg-------~~~~~l~~~a~G~ 227 (343)
T cd00424 173 LPLTDLPGIGAVTAKRLEAVGINPIGDLLAASPDALLALWGG-------VSGERLWYALRGI 227 (343)
T ss_pred CChhhcCCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHhh-------HHHHHHHHHhCCc
Confidence 68999999999999999999999999999999 666555544 2344555555444
No 50
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=55.87 E-value=21 Score=26.60 Aligned_cols=51 Identities=20% Similarity=0.343 Sum_probs=33.5
Q ss_pred cCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019342 50 LQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 105 (342)
Q Consensus 50 lQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~ 105 (342)
|.+||+.+...+.|.+. ..++..|...+.+++.. +.|+.+.-.+.+.++.+
T Consensus 6 LGI~~VG~~~ak~L~~~-f~sl~~l~~a~~e~L~~----i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAKH-FGSLEALMNASVEELSA----IPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp CTSTT--HHHHHHHHHC-CSCHHHHCC--HHHHCT----STT--HHHHHHHHHHHH
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHHcCHHHHhc----cCCcCHHHHHHHHHHHC
Confidence 56899999999998754 67999999888776543 35677777777777654
No 51
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=55.63 E-value=20 Score=39.89 Aligned_cols=53 Identities=23% Similarity=0.389 Sum_probs=44.3
Q ss_pred CccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019342 48 PFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 106 (342)
Q Consensus 48 pLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~ 106 (342)
-|+.||++++..+.+|-.+ +.++.+|++++.+++..+++ +++.++.+.++++.
T Consensus 758 ~L~~lPgI~~~~a~~ll~~-f~si~~l~~as~eeL~~~iG-----~~~~A~~i~~fl~~ 810 (814)
T TIGR00596 758 FLLKLPGVTKKNYRNLRKK-VKSIRELAKLSQNELNELIG-----DEEAAKRLYDFLRT 810 (814)
T ss_pred HHHHCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHHHhC-----CHHHHHHHHHHhcc
Confidence 4788999999999888654 88999999999999888754 36778888888865
No 52
>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins. They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.
Probab=55.15 E-value=4 Score=35.98 Aligned_cols=11 Identities=9% Similarity=0.108 Sum_probs=5.3
Q ss_pred CeEEEEeeeec
Q 019342 172 NNVWFSQKVSF 182 (342)
Q Consensus 172 n~Ll~~krv~~ 182 (342)
.+.|+++.+.+
T Consensus 29 ~h~L~L~~v~L 39 (149)
T PF03066_consen 29 EHQLSLRQVCL 39 (149)
T ss_dssp CEEEEEEEEEE
T ss_pred ccEEEEEEeec
Confidence 34445555554
No 53
>PRK03858 DNA polymerase IV; Validated
Probab=54.85 E-value=20 Score=35.74 Aligned_cols=54 Identities=11% Similarity=0.145 Sum_probs=42.8
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 106 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~ 106 (342)
-|+..||++...+.++|.+.+|+|+.+|..++...+...++. .....+...+.-
T Consensus 173 lpl~~l~Gig~~~~~~L~~~Gi~t~~dl~~l~~~~L~~~fG~------~~~~~l~~~a~G 226 (396)
T PRK03858 173 LPVRRLWGVGPVTAAKLRAHGITTVGDVAELPESALVSLLGP------AAGRHLHALAHN 226 (396)
T ss_pred CChhhcCCCCHHHHHHHHHhCCCcHHHHhcCCHHHHHHHhCc------HHHHHHHHHhCC
Confidence 589999999999999999999999999999998887776652 234455554543
No 54
>PF07495 Y_Y_Y: Y_Y_Y domain; InterPro: IPR011123 This region is mostly found at the end of the beta propellers (IPR011110 from INTERPRO) in a family of two component regulators. However they are also found tandemly repeated in Q891H4 from SWISSPROT without other signal conduction domains being present. It is named after the conserved tyrosines found in the alignment. The exact function is not known.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=54.77 E-value=35 Score=24.62 Aligned_cols=35 Identities=20% Similarity=0.238 Sum_probs=21.5
Q ss_pred EEEEcCCCCceeEEEEEEcCCCc-ccceEEEEEEEee
Q 019342 230 GKIQAPAEGNYNLTCYCLCDSWL-GCDKRTNLKVKIL 265 (342)
Q Consensus 230 l~F~aP~~G~~~l~l~viSDsYl-G~D~~~~i~l~V~ 265 (342)
+.|.-=+||.|.|.|+++...-. ..+. ..|.|.|+
T Consensus 31 ~~~~~L~~G~Y~l~V~a~~~~~~~~~~~-~~l~i~I~ 66 (66)
T PF07495_consen 31 ISYTNLPPGKYTLEVRAKDNNGKWSSDE-KSLTITIL 66 (66)
T ss_dssp EEEES--SEEEEEEEEEEETTS-B-SS--EEEEEEEE
T ss_pred EEEEeCCCEEEEEEEEEECCCCCcCccc-EEEEEEEC
Confidence 56665579999999999884432 3332 66666663
No 55
>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=53.25 E-value=39 Score=34.15 Aligned_cols=57 Identities=12% Similarity=0.039 Sum_probs=45.3
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCC--HHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMS--LQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 109 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~--~~er~~lL~~~~~l~~~~~~~v~~v~~~iP~ 109 (342)
-|+..||++.....++|.+.++.|+.+|..++ ...+...++ ......+...+.-+..
T Consensus 222 lPv~~l~GIG~~~~~~L~~~Gi~t~~dl~~~~~~~~~L~~~fG------~~~g~~L~~~a~G~d~ 280 (404)
T cd01701 222 LKVGDLPGVGSSLAEKLVKLFGDTCGGLELRSKTKEKLQKVLG------PKTGEKLYDYCRGIDD 280 (404)
T ss_pred CCHhHhCCCCHHHHHHHHHcCCcchHHHHhCcccHHHHHHHHC------HHHHHHHHHHhCCcCC
Confidence 59999999999999999999999999999998 777776654 2345666666666554
No 56
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=53.13 E-value=12 Score=39.11 Aligned_cols=22 Identities=23% Similarity=0.416 Sum_probs=14.3
Q ss_pred EEEEEEECCCCeEEEEeeeecc
Q 019342 162 FWFLLADSVSNNVWFSQKVSFM 183 (342)
Q Consensus 162 WwvllgD~~~n~Ll~~krv~~~ 183 (342)
+-|+.|-....-++..+++.|.
T Consensus 117 ~~Cl~gefvseallvp~kC~ff 138 (615)
T KOG3540|consen 117 YRCLAGEFVSEALLVPEKCQFF 138 (615)
T ss_pred ceeecCcchhhhccCcccchhh
Confidence 5577777767766666666553
No 57
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=51.35 E-value=12 Score=41.11 Aligned_cols=10 Identities=20% Similarity=0.375 Sum_probs=4.4
Q ss_pred eEEEEeeeec
Q 019342 173 NVWFSQKVSF 182 (342)
Q Consensus 173 ~Ll~~krv~~ 182 (342)
+|++++||.|
T Consensus 787 Eiv~~ERV~f 796 (960)
T KOG1189|consen 787 EIVNLERVQF 796 (960)
T ss_pred eeeeeeeeee
Confidence 4444444444
No 58
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=49.50 E-value=28 Score=36.08 Aligned_cols=88 Identities=15% Similarity=0.171 Sum_probs=62.5
Q ss_pred cCCHH-HHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhc
Q 019342 11 HGWLR-PAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQV 89 (342)
Q Consensus 11 ~GwL~-~al~~m~L~Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~ 89 (342)
-.|.+ -|-.|.-.-||--++.= ...|+-||++++...+.+...+|.|+.+|.+.+......+.+..
T Consensus 201 vr~~r~rC~~C~f~p~C~~~a~e-------------~~~L~Lv~Gi~~~r~~~l~~~GI~Ti~~LA~~~~~~~~~~~ga~ 267 (474)
T COG2251 201 VRWIRARCTTCQFEPQCESEALE-------------EDDLSLVPGITPSRYDVLEEVGITTIEDLADASLPILELVAGAL 267 (474)
T ss_pred chhhhhhhhHhhcchhhhHHHhh-------------ccceeccCCCCHHHHHHHHHcCcchHHHHHhccccchhhhhhhH
Confidence 34555 56777777788888863 35777899999999999999999999999998877666554421
Q ss_pred cCCChHHHHHHHHHHhcCCcee
Q 019342 90 GGFSSTEVQDVEMVLQMMPSLT 111 (342)
Q Consensus 90 ~~l~~~~~~~v~~v~~~iP~I~ 111 (342)
..+.++-..++..++...|.+.
T Consensus 268 ~~~~~~l~~qa~~~~e~~~~~~ 289 (474)
T COG2251 268 TALAAQLVLQARARVEGRPLME 289 (474)
T ss_pred HHHHHHHHHHHHhhccCCceec
Confidence 1123334456666666667665
No 59
>PF00868 Transglut_N: Transglutaminase family; InterPro: IPR001102 Synonym(s): Protein-glutamine gamma-glutamyltransferase, Fibrinoligase, TGase Protein-glutamine gamma-glutamyltransferases (2.3.2.13 from EC) (TGase) are calcium-dependent enzymes that catalyse the cross-linking of proteins by promoting the formation of isopeptide bonds between the gamma-carboxyl group of a glutamine in one polypeptide chain and the epsilon-amino group of a lysine in a second polypeptide chain. TGases also catalyse the conjugation of polyamines to proteins [, ]. Transglutaminases are widely distributed in various organs, tissues and body fluids. The best known transglutaminase is blood coagulation factor XIII, a plasma tetrameric protein composed of two catalytic A subunits and two non-catalytic B subunits. Factor XIII is responsible for cross-linking fibrin chains, thus stabilising the fibrin clot. There are commonly three domains: N-terminal, middle (IPR013808 from INTERPRO) and C-terminal (IPR013807 from INTERPRO). This entry represents the N-terminal domain found in transglutaminases.; GO: 0018149 peptide cross-linking; PDB: 1L9N_B 1NUF_A 1NUD_A 1NUG_B 1L9M_A 1KV3_C 3S3S_A 2Q3Z_A 3LY6_A 3S3P_A ....
Probab=45.17 E-value=66 Score=26.96 Aligned_cols=21 Identities=29% Similarity=0.441 Sum_probs=13.4
Q ss_pred EEEEEEcCC---CCceeEEEEEEc
Q 019342 228 VMGKIQAPA---EGNYNLTCYCLC 248 (342)
Q Consensus 228 v~l~F~aP~---~G~~~l~l~viS 248 (342)
+++.+..|. .|.|.+.|.+.|
T Consensus 95 ~tv~V~spa~A~VG~y~l~v~~~s 118 (118)
T PF00868_consen 95 VTVSVTSPANAPVGRYKLSVETKS 118 (118)
T ss_dssp EEEEEE--TTS--EEEEEEEEEEE
T ss_pred EEEEEECCCCCceEEEEEEEEEeC
Confidence 556777772 799999988764
No 60
>PF13897 GOLD_2: Golgi-dynamics membrane-trafficking
Probab=45.08 E-value=1.1e+02 Score=26.87 Aligned_cols=35 Identities=23% Similarity=0.229 Sum_probs=23.2
Q ss_pred EEEEcC--CCCceeEEEEEEcCCCcccceEEEEEEEeeecC
Q 019342 230 GKIQAP--AEGNYNLTCYCLCDSWLGCDKRTNLKVKILKRT 268 (342)
Q Consensus 230 l~F~aP--~~G~~~l~l~viSDsYlG~D~~~~i~l~V~~~~ 268 (342)
+.+.+| +.|+ .+.=-+.+|.| |.-+-+-|...+++
T Consensus 7 ~tvrVpt~~~G~-~l~WeFaTd~y---DIgFG~~few~~~~ 43 (136)
T PF13897_consen 7 VTVRVPTHPEGK-CLFWEFATDSY---DIGFGVYFEWTPPT 43 (136)
T ss_pred EEEEcccCCCCC-EEEEEEeeCCC---CceEEEEEEecCCC
Confidence 455566 5675 67777889998 55556666666655
No 61
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=40.08 E-value=15 Score=35.36 Aligned_cols=7 Identities=0% Similarity=0.021 Sum_probs=3.0
Q ss_pred EEEcCCC
Q 019342 245 YCLCDSW 251 (342)
Q Consensus 245 ~viSDsY 251 (342)
.+.|..|
T Consensus 169 RLk~G~Y 175 (303)
T KOG3064|consen 169 RLKSGTY 175 (303)
T ss_pred HHhcCCc
Confidence 3444444
No 62
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=38.04 E-value=19 Score=39.66 Aligned_cols=15 Identities=0% Similarity=-0.131 Sum_probs=6.6
Q ss_pred eEEEEEEcCCCcccc
Q 019342 241 NLTCYCLCDSWLGCD 255 (342)
Q Consensus 241 ~l~l~viSDsYlG~D 255 (342)
..+|.--|+|.+-++
T Consensus 760 sv~i~pTs~cLV~Lt 774 (960)
T KOG1189|consen 760 SVFIQPTSSCLVNLT 774 (960)
T ss_pred eeeeecchhhhhccc
Confidence 333444455554443
No 63
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=37.85 E-value=67 Score=30.08 Aligned_cols=53 Identities=11% Similarity=0.337 Sum_probs=43.7
Q ss_pred HHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHH----HHHHhcCCcee
Q 019342 58 AVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDV----EMVLQMMPSLT 111 (342)
Q Consensus 58 ~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v----~~v~~~iP~I~ 111 (342)
..+..++...+.++.++..++.+++.++++. +||-.+..+.+ ..++.++..++
T Consensus 50 kAlenLk~~~~~~l~~I~~~~~~~L~elIrp-sGFYnqKa~rLk~l~k~l~~~~~~~~ 106 (215)
T COG2231 50 KALENLKNEGILNLKKILKLDEEELAELIRP-SGFYNQKAKRLKALSKNLAKFFINLE 106 (215)
T ss_pred HHHHHHHHcccCCHHHHhcCCHHHHHHHHhc-cchHHHHHHHHHHHHHHHHHHhhhhh
Confidence 3455566777889999999999999999997 89977777777 77888888886
No 64
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=36.73 E-value=19 Score=37.64 Aligned_cols=16 Identities=25% Similarity=0.515 Sum_probs=8.5
Q ss_pred eeEEEEEEcCCCcccc
Q 019342 240 YNLTCYCLCDSWLGCD 255 (342)
Q Consensus 240 ~~l~l~viSDsYlG~D 255 (342)
|-.-+=|-+|-|-|..
T Consensus 170 ~gmLlPCg~D~F~GvE 185 (615)
T KOG3540|consen 170 YGMLLPCGLDMFRGVE 185 (615)
T ss_pred ccceeccccccccCce
Confidence 3444555556666644
No 65
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=35.60 E-value=31 Score=27.13 Aligned_cols=35 Identities=17% Similarity=0.377 Sum_probs=25.7
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHH
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQD 81 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~e 81 (342)
..|..||++.....+.|.+-+|.|..+|..+...+
T Consensus 3 ~~l~~LpNig~~~e~~L~~vGI~t~~~L~~~Ga~~ 37 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKVGIHTVEDLRELGAVE 37 (81)
T ss_dssp --GCGSTT--HHHHHHHHHTT--SHHHHHHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHHcCCCCHHHHHHhCHHH
Confidence 47889999999999999999999999999887544
No 66
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=34.48 E-value=56 Score=32.13 Aligned_cols=50 Identities=8% Similarity=0.177 Sum_probs=39.7
Q ss_pred CCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019342 54 HFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 107 (342)
Q Consensus 54 h~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~i 107 (342)
.++.....-|++.+|.|+.+|+.++.+++.++ .+|..+-++++.+.+..+
T Consensus 255 ~LS~R~~n~Lk~~~I~ti~dL~~~~~~~l~~~----~n~G~ksl~ei~~~L~~~ 304 (310)
T PRK05182 255 ELSVRSYNCLKRAGINTIGDLVQRTEEELLKT----RNLGKKSLEEIKEKLAEL 304 (310)
T ss_pred ccchHHHHHHHHcCCcCHHHHHhCCHHHHhcC----CCCChhhHHHHHHHHHHc
Confidence 35666677777889999999999999886654 347888889988888765
No 67
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=33.47 E-value=36 Score=38.05 Aligned_cols=7 Identities=29% Similarity=0.173 Sum_probs=3.1
Q ss_pred EEcCCCc
Q 019342 246 CLCDSWL 252 (342)
Q Consensus 246 viSDsYl 252 (342)
-+-|.|.
T Consensus 316 dldD~~~ 322 (840)
T PF04147_consen 316 DLDDDFE 322 (840)
T ss_pred ccccccc
Confidence 3444444
No 68
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, 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. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=32.58 E-value=1.4e+02 Score=30.03 Aligned_cols=57 Identities=12% Similarity=0.115 Sum_probs=43.9
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCC---------------HHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMS---------------LQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 109 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~---------------~~er~~lL~~~~~l~~~~~~~v~~v~~~iP~ 109 (342)
-|+.-||++.....++|.+.++.|+.+|..++ ...+...++ ......+...++-+..
T Consensus 172 lpv~~l~GiG~~~~~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG------~~~g~~l~~~a~G~d~ 243 (379)
T cd01703 172 HDLRKIPGIGYKTAAKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFG------EGIGQRIWKLLFGRDT 243 (379)
T ss_pred CCccccCCcCHHHHHHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHC------HHHHHHHHHHHCCCCC
Confidence 68999999999999999999999999999988 555555444 3345666666666554
No 69
>PRK14973 DNA topoisomerase I; Provisional
Probab=32.31 E-value=64 Score=36.59 Aligned_cols=67 Identities=15% Similarity=0.075 Sum_probs=52.7
Q ss_pred HHHHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHH-H
Q 019342 23 LSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDV-E 101 (342)
Q Consensus 23 L~Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v-~ 101 (342)
..+++.+|.-. ....|++.|++++..++++-+.+++++.+|....++++..+ .|++...+... .
T Consensus 789 ~~~~~~~a~~~-----------~~~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~p~~La~~----~g~~~~~~~~~~~ 853 (936)
T PRK14973 789 AASLLAEAKSL-----------CNISRLKEIGVPAVSLKKYQEAGFDTPEDFCSVHPAYLALK----TGISPETICRHAK 853 (936)
T ss_pred HHHHHHHHHHH-----------HHHHhhcccCCCHHHHHHHHHhcCCCHHHHHhcCHHHHhcC----CCCChhhHHHHHH
Confidence 45677777544 35679999999999999999899999999999999887755 45887776665 4
Q ss_pred HHH
Q 019342 102 MVL 104 (342)
Q Consensus 102 ~v~ 104 (342)
.++
T Consensus 854 ~~~ 856 (936)
T PRK14973 854 LVC 856 (936)
T ss_pred HHH
Confidence 444
No 70
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=32.28 E-value=61 Score=26.59 Aligned_cols=57 Identities=23% Similarity=0.358 Sum_probs=46.4
Q ss_pred CCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCcee
Q 019342 55 FTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPSLT 111 (342)
Q Consensus 55 ~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~iP~I~ 111 (342)
|.+.++..|...+|.||.+|.+.-...+..--+.+-++.......|..++...|...
T Consensus 21 f~p~va~~L~aaGi~TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~awLa~h~~~~ 77 (96)
T PF12482_consen 21 FPPRVARRLAAAGIRTLADLVDRINRRGGRWWRAVPGLGAAGARRIEAWLAAHPALL 77 (96)
T ss_pred cCHHHHHHHHHcCCchHHHHHHHHHHccchHHHhCcccchHHHHHHHHHHHHhHHHH
Confidence 678999999999999999999876655545555556788888999999999988764
No 71
>KOG1834 consensus Calsyntenin [Extracellular structures]
Probab=32.25 E-value=22 Score=38.58 Aligned_cols=9 Identities=22% Similarity=0.062 Sum_probs=5.4
Q ss_pred HHHHHhcCC
Q 019342 25 QSIIQAVPL 33 (342)
Q Consensus 25 Q~IvQA~W~ 33 (342)
|.++=|.|.
T Consensus 484 qLvVGACW~ 492 (952)
T KOG1834|consen 484 QLVVGACWQ 492 (952)
T ss_pred eeEEeeecc
Confidence 445567776
No 72
>PF06051 DUF928: Domain of Unknown Function (DUF928); InterPro: IPR010328 This is a family of uncharacterised bacterial proteins.
Probab=32.15 E-value=1.5e+02 Score=26.91 Aligned_cols=33 Identities=15% Similarity=0.136 Sum_probs=20.0
Q ss_pred CCC-ceeEEEEEEcCCCc-ccceEEEEEEEeeecC
Q 019342 236 AEG-NYNLTCYCLCDSWL-GCDKRTNLKVKILKRT 268 (342)
Q Consensus 236 ~~G-~~~l~l~viSDsYl-G~D~~~~i~l~V~~~~ 268 (342)
++| .|+..+.++||.-- --|..+.-.++...++
T Consensus 88 e~gk~Y~W~~~l~Cd~~~~s~~~~v~G~I~Rv~~~ 122 (189)
T PF06051_consen 88 EVGKTYRWYFSLICDPQDRSDDIFVEGWIQRVELS 122 (189)
T ss_pred CCCCeEEEEEEEEECCCCCCCCceEEEEEEEeCCC
Confidence 366 59999999998642 2334444445554443
No 73
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=31.47 E-value=68 Score=31.34 Aligned_cols=49 Identities=14% Similarity=0.247 Sum_probs=38.4
Q ss_pred CCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019342 55 FTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 107 (342)
Q Consensus 55 ~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~i 107 (342)
++-....-|++.+|.|+.+|+.++.+++.++ .+|..+-++++.+.+..+
T Consensus 242 LSvR~~n~Lk~~~I~ti~dL~~~~~~~l~~~----~n~G~ksl~ei~~~l~~~ 290 (297)
T TIGR02027 242 LSVRSYNCLKRAGIHTLGELVSKSEEELLKI----KNFGKKSLTEIKEKLAEL 290 (297)
T ss_pred ccHHHHhHHHHcCCcCHHHHHhCCHHHHhhC----CCCChhhHHHHHHHHHHc
Confidence 5556666677889999999999999886654 347788888888888774
No 74
>KOG2393 consensus Transcription initiation factor IIF, large subunit (RAP74) [Transcription]
Probab=31.20 E-value=24 Score=37.24 Aligned_cols=30 Identities=30% Similarity=0.588 Sum_probs=17.3
Q ss_pred ccCCCCCcccccccccC-CcCCccccchhhh
Q 019342 284 VEDGAEEEEEDEEEEYD-DYESEYSEDEEDE 313 (342)
Q Consensus 284 ~~~~~~~~~~~~~~~~~-~~~s~~~~~~~~~ 313 (342)
+.+.+++..+.+.|+.. ||+++++||||..
T Consensus 280 Dd~a~eesdd~d~e~~E~DYdee~addEE~P 310 (555)
T KOG2393|consen 280 DDEAFEESDDGDNEGRELDYDEESADDEEAP 310 (555)
T ss_pred cccccccCCCccccccccccccccCCccccc
Confidence 34444444434434333 7888899998753
No 75
>PF03985 Paf1: Paf1 ; InterPro: IPR007133 Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i [, ].
Probab=30.93 E-value=32 Score=35.29 Aligned_cols=16 Identities=19% Similarity=0.169 Sum_probs=8.5
Q ss_pred cceEEEEEEEeeecCc
Q 019342 254 CDKRTNLKVKILKRTR 269 (342)
Q Consensus 254 ~D~~~~i~l~V~~~~~ 269 (342)
...--.|.+++.+++.
T Consensus 337 ~~~~d~i~V~~R~p~e 352 (436)
T PF03985_consen 337 EQRPDQITVKHRDPTE 352 (436)
T ss_pred cCCCceEEEEeCCCCH
Confidence 3333446666666653
No 76
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=30.49 E-value=35 Score=41.03 Aligned_cols=7 Identities=71% Similarity=1.161 Sum_probs=3.0
Q ss_pred chhhhhh
Q 019342 309 DEEDERD 315 (342)
Q Consensus 309 ~~~~~~~ 315 (342)
|+||+++
T Consensus 184 ~de~~~~ 190 (2849)
T PTZ00415 184 DDEDEED 190 (2849)
T ss_pred CchhccC
Confidence 4444443
No 77
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.47 E-value=1.3e+02 Score=27.72 Aligned_cols=74 Identities=19% Similarity=0.215 Sum_probs=42.5
Q ss_pred HHHHHHH------HHHHHHHHhcCCCccCCCCCCCCCCCCccCCCCCCHHHHHHHh---hcCCCCHHHHHcC--C-HHHH
Q 019342 15 RPAVGVV------ELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIA---RKKVRTFQELRDM--S-LQDR 82 (342)
Q Consensus 15 ~~al~~m------~L~Q~IvQA~W~~~~~~~~~~~~~~spLlQLPh~~~~~v~~l~---~~~v~tl~~L~~m--~-~~er 82 (342)
.+|+++| +|.++|..+ +...|.++|++.+..+++|- +.++......... . .+..
T Consensus 83 K~ALaILs~~~~~el~~aI~~~--------------D~~~L~~vpGIGkKtAeRIIlELkdKl~~~~~~~~~~~~~~ea~ 148 (196)
T PRK13901 83 RAALRVLSGIKYNEFRDAIDRE--------------DIELISKVKGIGNKMAGKIFLKLRGKLVKNDELESSLFKFKELE 148 (196)
T ss_pred HHHHHHHcCCCHHHHHHHHHhC--------------CHHHHhhCCCCCHHHHHHHHHHHHHhhccccccccCcccHHHHH
Confidence 4566666 566666554 66889999999998888773 2223111000000 1 2334
Q ss_pred HHHHhhccCCChHHHHHHHHHH
Q 019342 83 AELLSQVGGFSSTEVQDVEMVL 104 (342)
Q Consensus 83 ~~lL~~~~~l~~~~~~~v~~v~ 104 (342)
..|+. .|+++.++..+.+.+
T Consensus 149 ~AL~~--LGy~~~ea~~al~~v 168 (196)
T PRK13901 149 QSIVN--MGFDRKLVNSAIKEI 168 (196)
T ss_pred HHHHH--cCCCHHHHHHHHHHH
Confidence 44444 789887776665543
No 78
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=29.72 E-value=45 Score=33.36 Aligned_cols=18 Identities=28% Similarity=0.523 Sum_probs=10.2
Q ss_pred cccccCCcCCccccchhh
Q 019342 295 EEEEYDDYESEYSEDEED 312 (342)
Q Consensus 295 ~~~~~~~~~s~~~~~~~~ 312 (342)
+.++||+++|-|||+.+|
T Consensus 294 ~~~~~~~~~~~~~~~~~~ 311 (337)
T PTZ00007 294 DYDSYDSSDSASSDSNSD 311 (337)
T ss_pred Cccccccccccccccccc
Confidence 444566666666665444
No 79
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=29.04 E-value=35 Score=33.01 Aligned_cols=10 Identities=20% Similarity=0.401 Sum_probs=3.7
Q ss_pred HHHHHHhcCC
Q 019342 99 DVEMVLQMMP 108 (342)
Q Consensus 99 ~v~~v~~~iP 108 (342)
+|-.-|-.||
T Consensus 92 QIde~Ll~Wp 101 (303)
T KOG3064|consen 92 QIDEQLLYWP 101 (303)
T ss_pred HHHHHHhcch
Confidence 3333333333
No 80
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=27.64 E-value=1.2e+02 Score=26.39 Aligned_cols=49 Identities=18% Similarity=0.318 Sum_probs=29.6
Q ss_pred CCCccCCCCCCHHHHHHHhhc-CCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019342 46 TAPFLQLPHFTEAVIKKIARK-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 106 (342)
Q Consensus 46 ~spLlQLPh~~~~~v~~l~~~-~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~ 106 (342)
...|.|||++-+..+++|-.+ +..++.+|..+ .|+++++.+.+.+....
T Consensus 60 ~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V------------~GIgekqk~~l~k~~~~ 109 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNL------------PGLSERQKELLEANLDN 109 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcC------------CCCCHHHHHHHHHhhcc
Confidence 346788888888877777533 35566555544 34555555555554444
No 81
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=27.59 E-value=28 Score=38.12 Aligned_cols=13 Identities=54% Similarity=0.664 Sum_probs=5.4
Q ss_pred CccCCCCCccccc
Q 019342 283 IVEDGAEEEEEDE 295 (342)
Q Consensus 283 ~~~~~~~~~~~~~ 295 (342)
.+++|.+.+||.|
T Consensus 208 ~dd~~m~~~Ee~e 220 (822)
T KOG2141|consen 208 LDDDGMEGEEEFE 220 (822)
T ss_pred hhccCCccccccc
Confidence 3344444444333
No 82
>PF00386 C1q: C1q domain; InterPro: IPR001073 This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain []. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [, ]. This domain is also found in multimerin and EMILIN proteins.; PDB: 1O91_C 2JG8_D 2JG9_A 2WNV_A 2WNU_A 1PK6_A 4DOU_A 1C3H_C 1C28_C 2OII_A ....
Probab=27.26 E-value=1e+02 Score=25.43 Aligned_cols=18 Identities=28% Similarity=0.495 Sum_probs=14.7
Q ss_pred EEEEcCCCCceeEEEEEE
Q 019342 230 GKIQAPAEGNYNLTCYCL 247 (342)
Q Consensus 230 l~F~aP~~G~~~l~l~vi 247 (342)
..|++|.+|.|.|.+.++
T Consensus 37 G~Ftap~~G~Y~F~~~~~ 54 (127)
T PF00386_consen 37 GIFTAPVPGVYFFSFTIM 54 (127)
T ss_dssp TEEE-SS-EEEEEEEEEE
T ss_pred CEEecCCCCEEEEEEEEe
Confidence 479999999999999999
No 83
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=26.97 E-value=90 Score=29.88 Aligned_cols=55 Identities=11% Similarity=0.226 Sum_probs=42.8
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 106 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~ 106 (342)
.-|.++|+++...+..|-. +..+|++|++.+.+++..+ -|+.+..++++.++++.
T Consensus 195 ~~Lt~i~~VnKtda~~LL~-~FgsLq~~~~AS~~ele~~----~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 195 GFLTTIPGVNKTDAQLLLQ-KFGSLQQISNASEGELEQC----PGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred HHHHhCCCCCcccHHHHHH-hcccHHHHHhcCHhHHHhC----cCcCHHHHHHHHHHHhc
Confidence 4677899999766665542 3579999999998887755 45888999999998875
No 84
>cd03468 PolY_like DNA Polymerase Y-family. 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. 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 order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Probab=24.85 E-value=1.2e+02 Score=29.26 Aligned_cols=40 Identities=18% Similarity=0.285 Sum_probs=33.9
Q ss_pred CCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHh
Q 019342 47 APFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLS 87 (342)
Q Consensus 47 spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~ 87 (342)
-|+ .+|++.+....+|.+.+|.|+.+|.+++...+...++
T Consensus 171 lp~-~~~gig~~~~~~L~~~Gi~t~~dl~~~~~~~l~~rfG 210 (335)
T cd03468 171 LPV-AALRLPPETVELLARLGLRTLGDLAALPRAELARRFG 210 (335)
T ss_pred CCh-hHhCCCHHHHHHHHHhCcccHHHHHhCChHHHHhhcC
Confidence 455 4788999999999999999999999999887776654
No 85
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=24.31 E-value=37 Score=31.73 Aligned_cols=33 Identities=33% Similarity=0.672 Sum_probs=0.0
Q ss_pred CccCCCCCcccccccccCCcCCccccchhhhhh
Q 019342 283 IVEDGAEEEEEDEEEEYDDYESEYSEDEEDERD 315 (342)
Q Consensus 283 ~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~ 315 (342)
..+++-++.++++++++++.+.+|.|||+++.+
T Consensus 174 ~d~~~~~e~~~eeee~eee~dee~~dee~e~~~ 206 (233)
T PF11705_consen 174 EDEEEEDEEEEEEEEDEEEEDEEFEDEEDEDDD 206 (233)
T ss_pred ccccccccccccccccccccccccchhhhccCC
No 86
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=24.26 E-value=1.4e+02 Score=30.12 Aligned_cols=57 Identities=19% Similarity=0.339 Sum_probs=44.2
Q ss_pred CCCccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019342 46 TAPFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 107 (342)
Q Consensus 46 ~spLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~i 107 (342)
+--|..+|.++..+++.|-.+ ..+|+.+++.+.+++.++ .|+.+..+..+.+.+.++
T Consensus 286 yRiLs~IPrl~k~iAk~Ll~~-FGSL~~Il~As~eeL~~V----eGIGe~rA~~I~e~l~Rl 342 (352)
T PRK13482 286 YRLLSKIPRLPSAVIENLVEH-FGSLQGLLAASIEDLDEV----EGIGEVRARAIREGLSRL 342 (352)
T ss_pred HHHHhcCCCCCHHHHHHHHHH-cCCHHHHHcCCHHHHhhC----CCcCHHHHHHHHHHHHHH
Confidence 344778999999999888643 579999999999887654 568787777777777665
No 87
>cd00146 PKD polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases.
Probab=24.08 E-value=1.9e+02 Score=21.49 Aligned_cols=32 Identities=16% Similarity=0.190 Sum_probs=22.8
Q ss_pred EEEcCCCCceeEEEEEEcCCCcccceEEEEEEEe
Q 019342 231 KIQAPAEGNYNLTCYCLCDSWLGCDKRTNLKVKI 264 (342)
Q Consensus 231 ~F~aP~~G~~~l~l~viSDsYlG~D~~~~i~l~V 264 (342)
...-+.+|.|.++|.+..+. |+.....+.+.|
T Consensus 50 ~~~y~~~G~y~v~l~v~d~~--g~~~~~~~~V~V 81 (81)
T cd00146 50 THTYTKPGTYTVTLTVTNAV--GSSSTKTTTVVV 81 (81)
T ss_pred EEEcCCCcEEEEEEEEEeCC--CCEEEEEEEEEC
Confidence 45556789999999988776 776655555443
No 88
>COG1470 Predicted membrane protein [Function unknown]
Probab=23.57 E-value=1.7e+02 Score=30.73 Aligned_cols=42 Identities=24% Similarity=0.367 Sum_probs=34.3
Q ss_pred ceeEEEEEEcCC---CCceeEEEEEEcCCCcccceEEEEEEEeeecCc
Q 019342 225 SRLVMGKIQAPA---EGNYNLTCYCLCDSWLGCDKRTNLKVKILKRTR 269 (342)
Q Consensus 225 s~~v~l~F~aP~---~G~~~l~l~viSDsYlG~D~~~~i~l~V~~~~~ 269 (342)
+..|.+.+.+|+ +|.|..++...|| -...+-.|++.|...+.
T Consensus 443 ~~tV~ltI~vP~~a~aGdY~i~i~~ksD---q~s~e~tlrV~V~~sS~ 487 (513)
T COG1470 443 SKTVSLTITVPEDAGAGDYRITITAKSD---QASSEDTLRVVVGQSST 487 (513)
T ss_pred cceEEEEEEcCCCCCCCcEEEEEEEeec---cccccceEEEEEecccc
Confidence 357889999993 8999999999999 46667778888877764
No 89
>PF04151 PPC: Bacterial pre-peptidase C-terminal domain; InterPro: IPR007280 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. This domain is normally found at the C terminus of secreted archaeal and bacterial peptidases, the majority of which belong to MEROPS peptidase families M4 (vibriolysin, IPR001570 from INTERPRO), M9A amd M9B (microbial collangenase, IPR002169 from INTERPRO), M28 (aminopeptidase Ap1, IPR007484 from INTERPRO) and S8 (subtilisin family peptidases, IPR000209 from INTERPRO).; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 4DY5_B 4DXZ_A 4DY3_B 3JQW_A 3JQX_C 1NQJ_B 1NQD_A 2O8O_A 1WMF_A 1WME_A ....
Probab=23.54 E-value=68 Score=23.74 Aligned_cols=17 Identities=35% Similarity=0.618 Sum_probs=14.4
Q ss_pred EEEEEcCCCCceeEEEE
Q 019342 229 MGKIQAPAEGNYNLTCY 245 (342)
Q Consensus 229 ~l~F~aP~~G~~~l~l~ 245 (342)
.+.|.+|++|+|.+.|+
T Consensus 53 ~i~~~~~~~GtYyi~V~ 69 (70)
T PF04151_consen 53 SITFTAPAAGTYYIRVY 69 (70)
T ss_dssp EEEEEESSSEEEEEEEE
T ss_pred EEEEEcCCCEEEEEEEE
Confidence 47899999999988875
No 90
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=23.27 E-value=33 Score=38.67 Aligned_cols=13 Identities=31% Similarity=0.434 Sum_probs=6.3
Q ss_pred HHHHHHHHHHhcC
Q 019342 20 VVELSQSIIQAVP 32 (342)
Q Consensus 20 ~m~L~Q~IvQA~W 32 (342)
+.+|||.+.++-|
T Consensus 583 A~eL~q~La~~F~ 595 (1010)
T KOG1991|consen 583 AVELCQNLAETFL 595 (1010)
T ss_pred HHHHHHHHHHHHH
Confidence 3445555555444
No 91
>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=23.24 E-value=2.5e+02 Score=27.98 Aligned_cols=57 Identities=12% Similarity=0.056 Sum_probs=41.6
Q ss_pred CCccCCCCCCHHHHHH-HhhcCCCCHHHHHcC--CHHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019342 47 APFLQLPHFTEAVIKK-IARKKVRTFQELRDM--SLQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 109 (342)
Q Consensus 47 spLlQLPh~~~~~v~~-l~~~~v~tl~~L~~m--~~~er~~lL~~~~~l~~~~~~~v~~v~~~iP~ 109 (342)
-|+.-||++......+ +.+.++.|+.+|..+ +...+.+.++. .....+...+.-+..
T Consensus 182 lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~~fG~------~~g~~l~~~a~G~d~ 241 (359)
T cd01702 182 LPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQEHFGE------KLGEWLYNLLRGIDH 241 (359)
T ss_pred CcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHHHHHH------HHHHHHHHHhCCCCC
Confidence 5888999999877665 477899999999999 88777666541 335556566665544
No 92
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=23.19 E-value=62 Score=30.57 Aligned_cols=9 Identities=22% Similarity=0.841 Sum_probs=5.2
Q ss_pred CCccccchh
Q 019342 303 ESEYSEDEE 311 (342)
Q Consensus 303 ~s~~~~~~~ 311 (342)
+|+|+++|+
T Consensus 57 Dsdf~~se~ 65 (240)
T PF05764_consen 57 DSDFDDSED 65 (240)
T ss_pred ccccCcccc
Confidence 566665554
No 93
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=22.57 E-value=1.7e+02 Score=27.31 Aligned_cols=37 Identities=11% Similarity=0.245 Sum_probs=30.0
Q ss_pred CHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019342 70 TFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 107 (342)
Q Consensus 70 tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~i 107 (342)
++..|..++.+++.++++. .|+.....+.+.+++..+
T Consensus 68 t~e~L~~a~~eeL~~~Irp-~Gf~~~KA~~Lk~la~~i 104 (218)
T PRK13913 68 NLKKIAYIEFSKLAECVRP-SGFYNQKAKRLIDLSENI 104 (218)
T ss_pred CHHHHHcCCHHHHHHHHHh-cCCHHHHHHHHHHHHHHH
Confidence 8999999999999999987 889776666666665554
No 94
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=22.10 E-value=1.7e+02 Score=28.14 Aligned_cols=56 Identities=9% Similarity=0.229 Sum_probs=43.2
Q ss_pred ccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019342 49 FLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 109 (342)
Q Consensus 49 LlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~iP~ 109 (342)
|..||++......++-.. ..++.++++.+..++..+. |+.++...++..++...-.
T Consensus 184 l~s~pgig~~~a~~ll~~-fgS~~~~~tas~~eL~~v~----gig~k~A~~I~~~~~t~~~ 239 (254)
T COG1948 184 LESIPGIGPKLAERLLKK-FGSVEDVLTASEEELMKVK----GIGEKKAREIYRFLRTEYK 239 (254)
T ss_pred HHcCCCccHHHHHHHHHH-hcCHHHHhhcCHHHHHHhc----CccHHHHHHHHHHHhchhh
Confidence 556899998888877543 6799999999998877664 5788888888888766433
No 95
>PF14524 Wzt_C: Wzt C-terminal domain; PDB: 2R5O_B.
Probab=21.71 E-value=1.3e+02 Score=24.42 Aligned_cols=41 Identities=17% Similarity=0.090 Sum_probs=23.7
Q ss_pred eeEEEEEEcC-CCCceeEEEEE--EcCCCcccceEEE-EEEEeee
Q 019342 226 RLVMGKIQAP-AEGNYNLTCYC--LCDSWLGCDKRTN-LKVKILK 266 (342)
Q Consensus 226 ~~v~l~F~aP-~~G~~~l~l~v--iSDsYlG~D~~~~-i~l~V~~ 266 (342)
..+.+.|+.+ .+|.|.+.+.+ -....-=+|+... +.|+|..
T Consensus 86 ~~~~~~i~~~L~~G~Y~i~v~l~~~~~~~~~~d~~~~~~~f~V~~ 130 (142)
T PF14524_consen 86 YEVTFTIPKPLNPGEYSISVGLGDDSSGGEVLDWIEDALSFEVED 130 (142)
T ss_dssp EEEEEEEE--B-SEEEEEEEEEEETTTEEEEEEEEEEEEEEEEE-
T ss_pred EEEEEEEcCccCCCeEEEEEEEEecCCCCEEEEEECCEEEEEEEC
Confidence 4555555555 69999999999 2233333455444 5788877
No 96
>KOG0772 consensus Uncharacterized conserved protein, contains WD40 repeat [Function unknown]
Probab=21.23 E-value=75 Score=33.70 Aligned_cols=20 Identities=25% Similarity=0.410 Sum_probs=8.5
Q ss_pred hhhhhcccCCCCCCccccCC
Q 019342 312 DERDTKKKVPAANGTVSKKG 331 (342)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~ 331 (342)
++.+--++-+.++-..-+++
T Consensus 147 ~e~~~~~~IP~shEi~l~hg 166 (641)
T KOG0772|consen 147 EEESIIKLIPGSHEIQLKHG 166 (641)
T ss_pred chhchhhcCCccceEeccCC
Confidence 34433344455444333333
No 97
>PHA02608 67 prohead core protein; Provisional
Probab=21.05 E-value=50 Score=26.17 Aligned_cols=6 Identities=50% Similarity=0.501 Sum_probs=2.5
Q ss_pred ccCCCC
Q 019342 277 VSEEGP 282 (342)
Q Consensus 277 ~~~~~~ 282 (342)
|..+|.
T Consensus 43 v~iEGE 48 (80)
T PHA02608 43 VMIEGE 48 (80)
T ss_pred HhhcCC
Confidence 344443
No 98
>PF14686 fn3_3: Polysaccharide lyase family 4, domain II; PDB: 1NKG_A 2XHN_B 3NJX_A 3NJV_A.
Probab=20.76 E-value=1.5e+02 Score=23.89 Aligned_cols=34 Identities=26% Similarity=0.482 Sum_probs=17.0
Q ss_pred EEEEcC--CCCceeEEEEEEcCCCcccceEEEEEEEee
Q 019342 230 GKIQAP--AEGNYNLTCYCLCDSWLGCDKRTNLKVKIL 265 (342)
Q Consensus 230 l~F~aP--~~G~~~l~l~viSDsYlG~D~~~~i~l~V~ 265 (342)
..|.+| .||+|.+++|. +..+|-=....-.+.|.
T Consensus 50 G~Fti~~V~pGtY~L~ay~--~g~~g~~~~~~~~ItV~ 85 (95)
T PF14686_consen 50 GNFTIPNVRPGTYRLYAYA--DGIFGDYKVASDSITVS 85 (95)
T ss_dssp SEEE---B-SEEEEEEEEE------TTEEEEEEEEEE-
T ss_pred CcEEeCCeeCcEeEEEEEE--ecccCceEEecceEEEc
Confidence 369999 59999999998 65554333323344444
No 99
>PF06991 Prp19_bind: Splicing factor, Prp19-binding domain; InterPro: IPR009730 This entry represents the C terminus (approximately 300 residues) of eukaryotic micro-fibrillar-associated protein 1, which is a component of elastin-associated microfibrils in the extracellular matrix [].
Probab=20.72 E-value=48 Score=32.24 Aligned_cols=7 Identities=29% Similarity=0.596 Sum_probs=2.7
Q ss_pred cccchhh
Q 019342 306 YSEDEED 312 (342)
Q Consensus 306 ~~~~~~~ 312 (342)
+||.|++
T Consensus 26 ~SdSEde 32 (276)
T PF06991_consen 26 SSDSEDE 32 (276)
T ss_pred ccccccc
Confidence 3443333
No 100
>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair]
Probab=20.59 E-value=1.5e+02 Score=33.25 Aligned_cols=53 Identities=19% Similarity=0.295 Sum_probs=42.6
Q ss_pred CccCCCCCCHHHHHHHhhcCCCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019342 48 PFLQLPHFTEAVIKKIARKKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 106 (342)
Q Consensus 48 pLlQLPh~~~~~v~~l~~~~v~tl~~L~~m~~~er~~lL~~~~~l~~~~~~~v~~v~~~ 106 (342)
-|+-+|+++......+..+ ++++.+|...+-+++..|++ . .+..+.++.++..
T Consensus 822 fll~lPgVs~~n~~~l~~k-~ks~~~La~sS~~el~el~~----~-~~~a~~LYdFi~~ 874 (892)
T KOG0442|consen 822 FLLSLPGVSYINYRNLRHK-FKSLKELANSSQEELSELLG----V-HENAKLLYDFIHT 874 (892)
T ss_pred HHhcCCCccHHHHHHHHHH-hhHHHHHHhCcHHHHHHHhc----c-hHHHHHHHHHHHH
Confidence 3788999999888877655 89999999999999999987 2 4566777777653
No 101
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.53 E-value=62 Score=33.22 Aligned_cols=37 Identities=22% Similarity=0.347 Sum_probs=20.3
Q ss_pred hHHHHHHHHHHhcCCc-eeEEEEEEecCCccccCCCeEEEE
Q 019342 94 STEVQDVEMVLQMMPS-LTVEVTCETEGEEGIQEGDIVTIQ 133 (342)
Q Consensus 94 ~~~~~~v~~v~~~iP~-I~i~a~~~v~gee~It~g~~vtl~ 133 (342)
.+|++++.+++.++-. +++.-.|. +-.+..|++|.|.
T Consensus 96 r~q~~~l~~~~~n~~~~vkf~~df~---~~s~~~Gd~VeIv 133 (514)
T KOG3130|consen 96 RKQIDDLKKVMKNFESRVKFTEDFQ---KMSDAAGDIVEIV 133 (514)
T ss_pred HHHHHHHHHHHHhhHHHhhhcccHh---hccCCCCCeehhH
Confidence 3677788777777643 33211111 1135667777766
No 102
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=20.48 E-value=82 Score=36.03 Aligned_cols=14 Identities=43% Similarity=0.530 Sum_probs=6.2
Q ss_pred CcCCccccchhhhh
Q 019342 301 DYESEYSEDEEDER 314 (342)
Q Consensus 301 ~~~s~~~~~~~~~~ 314 (342)
|..|+.+|+|+.+.
T Consensus 909 d~~sd~~e~e~ee~ 922 (1128)
T KOG2051|consen 909 DDGSDEDENEEEEP 922 (1128)
T ss_pred cccccccccccCCC
Confidence 44444444444443
Done!