Query 019396
Match_columns 341
No_of_seqs 181 out of 708
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 09:08:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019396.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019396hhsearch_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 1.1E-42 2.4E-47 334.7 19.1 236 14-313 129-519 (520)
2 smart00611 SEC63 Domain of unk 100.0 1.2E-33 2.6E-38 271.3 23.3 190 6-262 121-312 (312)
3 PF02889 Sec63: Sec63 Brl doma 100.0 1.3E-33 2.9E-38 270.6 20.5 193 6-261 118-314 (314)
4 COG5407 SEC63 Preprotein trans 99.9 5E-22 1.1E-26 196.4 10.4 165 5-183 303-502 (610)
5 KOG0951 RNA helicase BRR2, DEA 99.7 9.6E-20 2.1E-24 196.4 -4.0 335 1-339 118-476 (1674)
6 KOG0951 RNA helicase BRR2, DEA 99.7 5.9E-16 1.3E-20 167.5 16.5 216 7-308 923-1144(1674)
7 KOG0952 DNA/RNA helicase MER3/ 98.4 9.4E-07 2E-11 96.2 8.9 187 7-272 713-901 (1230)
8 PRK01172 ski2-like helicase; P 98.3 6.5E-07 1.4E-11 95.2 5.9 85 7-106 570-668 (674)
9 PRK02362 ski2-like helicase; P 98.0 8.9E-06 1.9E-10 87.6 6.3 81 9-106 625-706 (737)
10 PRK00254 ski2-like helicase; P 97.6 6.9E-05 1.5E-09 80.6 5.7 78 11-106 623-701 (720)
11 PF14520 HHH_5: Helix-hairpin- 90.7 0.35 7.6E-06 35.6 3.7 53 48-104 6-59 (60)
12 KOG1824 TATA-binding protein-i 86.8 0.31 6.7E-06 54.0 1.5 18 294-311 327-344 (1233)
13 PF06524 NOA36: NOA36 protein; 82.5 0.94 2E-05 43.5 2.5 8 101-108 58-65 (314)
14 PF13543 KSR1-SAM: SAM like do 81.5 4.9 0.00011 34.7 6.3 59 47-106 61-128 (129)
15 PF06524 NOA36: NOA36 protein; 81.2 1.1 2.4E-05 43.1 2.4 6 170-175 139-144 (314)
16 PRK04301 radA DNA repair and r 79.1 4.3 9.2E-05 39.5 5.8 56 46-105 5-61 (317)
17 PF10446 DUF2457: Protein of u 78.3 0.57 1.2E-05 47.9 -0.5 17 248-264 13-29 (458)
18 PTZ00035 Rad51 protein; Provis 73.8 7.2 0.00016 38.7 5.9 57 48-108 22-81 (337)
19 TIGR02236 recomb_radA DNA repa 71.5 9.4 0.0002 36.8 6.0 52 49-104 1-53 (310)
20 PRK14133 DNA polymerase IV; Pr 71.3 12 0.00025 36.8 6.7 49 25-86 164-213 (347)
21 PF01835 A2M_N: MG2 domain; I 71.2 48 0.001 26.0 11.2 45 123-179 11-55 (99)
22 PF03118 RNA_pol_A_CTD: Bacter 70.4 8.9 0.00019 29.1 4.4 54 46-104 11-65 (66)
23 PRK07758 hypothetical protein; 69.8 13 0.00029 30.5 5.5 50 52-105 39-89 (95)
24 PF12826 HHH_2: Helix-hairpin- 67.8 8.7 0.00019 28.7 3.9 51 50-104 6-56 (64)
25 cd03586 PolY_Pol_IV_kappa DNA 67.2 16 0.00036 35.2 6.7 54 47-107 171-225 (334)
26 PRK01216 DNA polymerase IV; Va 67.0 10 0.00022 37.8 5.3 60 25-103 169-229 (351)
27 PF11731 Cdd1: Pathogenicity l 66.7 13 0.00028 30.4 4.9 58 45-102 10-69 (93)
28 PRK02406 DNA polymerase IV; Va 66.4 16 0.00035 35.7 6.6 53 47-106 168-221 (343)
29 TIGR02239 recomb_RAD51 DNA rep 64.8 16 0.00034 35.9 6.0 53 50-106 4-57 (316)
30 TIGR00596 rad1 DNA repair prot 64.5 11 0.00024 41.9 5.4 53 48-105 758-810 (814)
31 KOG1834 Calsyntenin [Extracell 64.2 6.6 0.00014 42.4 3.4 10 242-251 831-840 (952)
32 TIGR02238 recomb_DMC1 meiotic 64.0 15 0.00033 36.0 5.8 54 51-108 5-59 (313)
33 PF15243 ANAPC15: Anaphase-pro 63.6 5.1 0.00011 32.7 2.0 18 297-314 73-90 (92)
34 PLN03187 meiotic recombination 63.1 15 0.00033 36.6 5.7 52 52-107 36-88 (344)
35 TIGR01954 nusA_Cterm_rpt trans 62.7 21 0.00046 24.6 4.8 46 55-104 1-47 (50)
36 KOG3540 Beta amyloid precursor 62.4 5.9 0.00013 41.2 2.6 21 161-181 117-137 (615)
37 PRK02794 DNA polymerase IV; Pr 60.9 22 0.00047 36.0 6.4 55 47-108 209-264 (419)
38 KOG1189 Global transcriptional 60.7 6.3 0.00014 43.1 2.6 12 171-182 786-797 (960)
39 PF03066 Nucleoplasmin: Nucleo 59.2 3.1 6.7E-05 36.7 0.0 10 172-181 30-39 (149)
40 PLN03186 DNA repair protein RA 59.1 25 0.00054 35.1 6.3 76 23-105 5-83 (342)
41 PRK03352 DNA polymerase IV; Va 58.9 15 0.00032 36.0 4.7 40 47-86 177-217 (346)
42 PRK03348 DNA polymerase IV; Pr 58.5 28 0.00061 35.9 6.8 56 47-108 180-236 (454)
43 PF14229 DUF4332: Domain of un 58.1 25 0.00055 29.7 5.4 53 53-106 1-56 (122)
44 PRK03103 DNA polymerase IV; Re 57.1 27 0.00058 35.1 6.3 53 47-106 181-234 (409)
45 PF04281 Tom22: Mitochondrial 55.2 7.2 0.00016 34.1 1.6 18 295-312 31-48 (137)
46 PRK03609 umuC DNA polymerase V 55.2 36 0.00078 34.5 6.9 54 47-107 179-233 (422)
47 PRK01810 DNA polymerase IV; Va 54.8 31 0.00067 34.6 6.3 52 47-105 179-231 (407)
48 PF13897 GOLD_2: Golgi-dynamic 54.2 67 0.0014 28.1 7.3 35 229-267 7-43 (136)
49 cd01700 PolY_Pol_V_umuC umuC s 53.3 26 0.00057 34.3 5.4 41 46-86 175-216 (344)
50 cd00424 PolY Y-family of DNA p 53.2 40 0.00088 33.0 6.7 53 47-106 173-227 (343)
51 PF07495 Y_Y_Y: Y_Y_Y domain; 52.7 39 0.00085 24.4 5.1 36 229-264 31-66 (66)
52 PRK03858 DNA polymerase IV; Va 51.5 22 0.00047 35.5 4.6 40 47-86 173-213 (396)
53 PRK12766 50S ribosomal protein 51.3 40 0.00086 32.0 6.0 54 47-104 3-57 (232)
54 KOG1189 Global transcriptional 50.7 8.9 0.00019 42.1 1.7 6 229-234 741-746 (960)
55 cd01701 PolY_Rev1 DNA polymera 47.2 50 0.0011 33.3 6.5 56 47-108 222-280 (404)
56 PF04147 Nop14: Nop14-like fam 44.1 19 0.00042 40.1 3.1 12 243-254 314-325 (840)
57 KOG2841 Structure-specific end 43.4 32 0.0007 32.8 4.0 55 47-105 195-249 (254)
58 KOG3064 RNA-binding nuclear pr 42.8 15 0.00032 35.5 1.7 21 241-264 166-186 (303)
59 PF06514 PsbU: Photosystem II 42.5 15 0.00032 30.1 1.4 49 46-106 22-72 (93)
60 PF00868 Transglut_N: Transglu 42.0 76 0.0016 26.6 5.8 21 227-247 95-118 (118)
61 KOG1834 Calsyntenin [Extracell 41.3 20 0.00044 38.8 2.6 9 25-33 484-492 (952)
62 PF05764 YL1: YL1 nuclear prot 41.3 20 0.00043 33.9 2.4 10 276-285 35-44 (240)
63 PRK02515 psbU photosystem II c 40.8 52 0.0011 28.6 4.6 48 47-106 61-110 (132)
64 PF04994 TfoX_C: TfoX C-termin 38.8 25 0.00053 27.8 2.2 34 47-80 3-37 (81)
65 COG2251 Predicted nuclease (Re 38.1 49 0.0011 34.4 4.7 86 12-110 202-289 (474)
66 COG5406 Nucleosome binding fac 37.6 27 0.00058 37.9 2.8 16 240-255 812-827 (1001)
67 PF05764 YL1: YL1 nuclear prot 37.1 20 0.00043 33.9 1.7 7 302-308 57-63 (240)
68 COG5407 SEC63 Preprotein trans 35.7 31 0.00067 36.0 2.8 39 229-267 512-551 (610)
69 PF04147 Nop14: Nop14-like fam 35.7 26 0.00056 39.1 2.5 6 59-64 88-93 (840)
70 PF06051 DUF928: Domain of Unk 35.5 1.2E+02 0.0027 27.5 6.5 32 236-267 89-122 (189)
71 PTZ00415 transmission-blocking 32.6 30 0.00065 41.5 2.4 6 170-175 71-76 (2849)
72 COG1470 Predicted membrane pro 32.0 1E+02 0.0022 32.4 5.8 43 223-268 442-487 (513)
73 PF00386 C1q: C1q domain; Int 30.6 80 0.0017 26.0 4.2 18 229-246 37-54 (127)
74 PRK13482 DNA integrity scannin 30.2 91 0.002 31.5 5.1 57 46-106 286-342 (352)
75 COG1470 Predicted membrane pro 30.0 1.2E+02 0.0025 32.0 5.8 41 224-266 334-377 (513)
76 COG1948 MUS81 ERCC4-type nucle 29.0 1E+02 0.0023 29.7 5.1 55 49-107 184-238 (254)
77 PRK13901 ruvA Holliday junctio 28.8 1.7E+02 0.0036 27.1 6.2 73 15-103 83-168 (196)
78 KOG2393 Transcription initiati 28.7 28 0.0006 36.8 1.2 29 284-312 281-310 (555)
79 KOG3130 Uncharacterized conser 28.5 35 0.00075 35.0 1.8 36 94-132 97-133 (514)
80 PTZ00415 transmission-blocking 28.2 32 0.00069 41.3 1.7 6 308-313 184-189 (2849)
81 PRK05182 DNA-directed RNA poly 28.2 79 0.0017 31.1 4.3 49 54-106 255-304 (310)
82 KOG3241 Uncharacterized conser 27.9 37 0.00081 31.1 1.7 24 285-308 194-217 (227)
83 KOG2051 Nonsense-mediated mRNA 27.2 50 0.0011 37.6 2.9 14 300-313 909-922 (1128)
84 PF12482 DUF3701: Phage integr 27.0 79 0.0017 26.0 3.4 57 54-110 20-77 (96)
85 cd01703 PolY_Pol_iota DNA Poly 26.9 1.9E+02 0.0041 29.2 6.8 57 47-109 172-244 (379)
86 cd00146 PKD polycystic kidney 26.7 1.6E+02 0.0034 21.9 4.9 32 230-263 50-81 (81)
87 KOG2141 Protein involved in hi 25.9 29 0.00063 38.0 0.8 8 284-291 210-217 (822)
88 PF03985 Paf1: Paf1 ; InterPr 25.4 1.1E+02 0.0023 31.5 4.8 17 252-268 336-352 (436)
89 TIGR02027 rpoA DNA-directed RN 25.3 97 0.0021 30.3 4.3 48 55-106 242-290 (297)
90 PF04151 PPC: Bacterial pre-pe 25.1 60 0.0013 24.0 2.2 17 228-244 53-69 (70)
91 PRK14666 uvrC excinuclease ABC 24.4 1.2E+02 0.0026 33.3 5.1 57 46-106 636-692 (694)
92 PRK14973 DNA topoisomerase I; 23.3 1.1E+02 0.0024 34.7 4.8 66 23-103 789-856 (936)
93 PF11705 RNA_pol_3_Rpc31: DNA- 23.1 43 0.00092 31.3 1.3 37 278-314 170-206 (233)
94 KOG3540 Beta amyloid precursor 22.3 47 0.001 34.9 1.5 15 97-111 69-84 (615)
95 KOG0442 Structure-specific end 22.2 1.3E+02 0.0028 33.8 4.8 53 48-105 822-874 (892)
96 PF14686 fn3_3: Polysaccharide 21.6 1.4E+02 0.0031 24.1 3.9 34 229-264 50-85 (95)
97 PRK14667 uvrC excinuclease ABC 21.6 1.8E+02 0.0038 31.2 5.6 54 46-104 513-566 (567)
98 PHA02608 67 prohead core prote 21.5 48 0.001 26.3 1.1 10 276-285 43-52 (80)
99 KOG0699 Serine/threonine prote 21.3 51 0.0011 33.6 1.4 39 279-317 259-300 (542)
100 cd03468 PolY_like DNA Polymera 21.3 1.5E+02 0.0032 28.6 4.6 39 47-86 171-210 (335)
101 KOG0943 Predicted ubiquitin-pr 21.2 51 0.0011 38.5 1.6 37 279-315 1727-1763(3015)
102 PTZ00007 (NAP-L) nucleosome as 20.7 87 0.0019 31.4 2.9 17 294-310 294-310 (337)
103 PF07705 CARDB: CARDB; InterP 20.2 1.4E+02 0.003 22.8 3.5 26 225-250 63-88 (101)
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=1.1e-42 Score=334.71 Aligned_cols=236 Identities=33% Similarity=0.536 Sum_probs=203.1
Q ss_pred HHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc--ccCCHHHHHcCCHHHHHHHHhhccCC
Q 019396 14 LRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR--KVRTFQELRDMSLQDRAELLSQVGGF 91 (341)
Q Consensus 14 L~~al~~m~L~QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~--~v~tl~~L~~m~~~er~~lL~~~~~l 91 (341)
+.+.-+||.|++|+|||+|. ..||||||||++++.+.++.+ +|+++++|.-|..+.|+.||+. |
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 67788999999999999998 899999999999999999876 7999999999999999999997 8
Q ss_pred ChHHHHHHHHHHhcCCceeEEEEEEecCCc---cccCCCeEEEEEeeeeecc----------------------------
Q 019396 92 SSTEVQDVEMVLQMMPSLTVEVTCETEGEE---GIQEGDIVTIQAWVTLKRG---------------------------- 140 (341)
Q Consensus 92 s~~~~~~v~~v~~~~P~I~I~~~~~v~gE~---~It~g~~vtl~~~V~L~R~---------------------------- 140 (341)
++.++.+++.||.+||.|.|++.+.|.|++ .||+|++||+. |+|+|.
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 888773
Q ss_pred --------------------------------------------------------------------------C-----
Q 019396 141 --------------------------------------------------------------------------N----- 141 (341)
Q Consensus 141 --------------------------------------------------------------------------n----- 141 (341)
|
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 019396 142 ------------------------------------------GLIGALPHAPYYPFHKEENFWFLLADSVSNNVWFSQKV 179 (341)
Q Consensus 142 ------------------------------------------~~~~~~~~aP~FP~~K~E~WwvvlgD~~~n~Il~~krv 179 (341)
......+||||||-.|.|.||++|+|.++..|+.+...
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 01235699999999999999999999999998875322
Q ss_pred eeccchhHHhhhhhhhhhhhcCCCCccchhhHHHHHHHHhhhcCceeEEEEEEcCC-CCceeEEEEEEcCCCcccceEEE
Q 019396 180 SFMDEPAAITAASKAIEDTMEGSGATVKETSAAVREAAEKVRSGSRLVMGKIQAPA-EGNYNLTCYCLCDSWLGCDKRTN 258 (341)
Q Consensus 180 s~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~k~~~~~v~l~F~aP~-~G~~~l~l~v~SDsYlG~D~~~~ 258 (341)
+. +++ ..+.|.|+|++|. ||.|+|+|++.||||+|+||..+
T Consensus 433 -V~------------------------------------tL~-d~eei~lkF~AP~~pG~Ytytv~lrSDSYmg~dq~~~ 474 (520)
T KOG4434|consen 433 -VC------------------------------------TLK-DTEEIELKFPAPGKPGNYTYTVFLRSDSYMGLDQIKP 474 (520)
T ss_pred -hh------------------------------------ccc-ccceeEEeccCCCCCCceEEEEEEecccccChhhccc
Confidence 11 111 2346889999994 99999999999999999999999
Q ss_pred EEEEeeccCccCCCCccccCCCCCccCCCCCcccccccccCCcCCcccccchhhh
Q 019396 259 LKVKILKRTRAGTRGGIVSEEGPIVEDGAEEEEEDEEEEYDDYESEYSEDEEDER 313 (341)
Q Consensus 259 i~l~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~ 313 (341)
+++.|.+++. |++++|.+++.|+++|+-++.| .=++|++|++++.
T Consensus 475 lKldV~eAk~-------vp~~Hpqwd~~~~e~e~~~~~e---~~~Dyted~~~eE 519 (520)
T KOG4434|consen 475 LKLDVHEAKP-------VPENHPQWDTAIEEDEDQEDSE---GFEDYTEDEEEEE 519 (520)
T ss_pred eeeeeccCCC-------CCCCCccccccccccccccccc---ccccccccccccc
Confidence 9999999887 9999999999999988776443 3456777666553
No 2
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=100.00 E-value=1.2e-33 Score=271.29 Aligned_cols=190 Identities=34% Similarity=0.540 Sum_probs=162.8
Q ss_pred chhhccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHH
Q 019396 6 RTAQGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAEL 84 (341)
Q Consensus 6 ~~a~~~gwL~~al~~m~L~QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~l 84 (341)
..++.+||+++++++|+|+|||+||+|+ ..+||+|||||+.+.++++.+ ++.++++|.+++.++++.+
T Consensus 121 di~~~~~~~~~~~~~l~L~q~i~q~~w~-----------~~~~L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~~~~~~~~l 189 (312)
T smart00611 121 DIALERGWLSTALNALNLSQMIIQALWP-----------TDSPLLQLPHLPEEILKRLEKKKVLSLEDLLELEDEERGEL 189 (312)
T ss_pred HHHHhcchHHHHHHHHHHHHHHHHhhCC-----------CCCccccCCCCCHHHHHHHHhCCCCCHHHHHhcCHHHHHHH
Confidence 4678899999999999999999999999 789999999999999999988 8999999999999999999
Q ss_pred HhhccCCChHHHHHHHHHHhcCCceeEEEEEEecCCccccCCCeEEEEEeeeeeccCCCCCCCccCCCCCCCCcccEEEE
Q 019396 85 LSQVGGFSSTEVQDVEMVLQMMPSLTVEVTCETEGEEGIQEGDIVTIQAWVTLKRGNGLIGALPHAPYYPFHKEENFWFL 164 (341)
Q Consensus 85 L~~~~~ls~~~~~~v~~v~~~~P~I~I~~~~~v~gE~~It~g~~vtl~~~V~L~R~n~~~~~~~~aP~FP~~K~E~Wwvv 164 (341)
++ +.+.+++++.++|++||+|+|+++++ +...++.+..++|+ +.+++.+. .| .|.|+||++
T Consensus 190 l~----~~~~~~~~i~~~~~~~P~l~v~~~~~--~~~~~~~~~~~~i~--~~~~~~~~-----~~------~k~e~~~l~ 250 (312)
T smart00611 190 LG----LLDAEGERVYKVLSRLPKLNIEISLE--PITRTVLGVEVTLT--VDLTWDDE-----IH------GKQEGWWLV 250 (312)
T ss_pred Hc----CCHHHHHHHHHHHHhCCcceeEEEEc--CCcccccCceEEEE--EEEEEccc-----cc------CCcccEEEE
Confidence 87 67799999999999999999876654 33345556667777 77777421 22 689999999
Q ss_pred EEECCCCeEEEEeeeeeccchhHHhhhhhhhhhhhcCCCCccchhhHHHHHHHHhhhcCceeEEEEEEcCC-CCceeEEE
Q 019396 165 LADSVSNNVWFSQKVSFMDEPAAITAASKAIEDTMEGSGATVKETSAAVREAAEKVRSGSRLVMGKIQAPA-EGNYNLTC 243 (341)
Q Consensus 165 lgD~~~n~Il~~krvs~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~k~~~~~v~l~F~aP~-~G~~~l~l 243 (341)
|+|+++|+|++++|+++.... ..+.+++.|.+|. +|.|+|+|
T Consensus 251 v~d~~~~~il~~~~~~~~~~~-------------------------------------~~~~~~l~f~~P~~~~~~~~~v 293 (312)
T smart00611 251 IGDSDGNELLHIERFSLNKKN-------------------------------------VSEEVKLDFTAPATEGNYQYTL 293 (312)
T ss_pred EEeCCCCEEEEEEEEEEEeec-------------------------------------CCCcEEEEEEecCCCCcceEEE
Confidence 999999999999999986521 0123678999995 78999999
Q ss_pred EEEcCCCcccceEEEEEEE
Q 019396 244 YCLCDSWLGCDKRTNLKVK 262 (341)
Q Consensus 244 ~v~SDsYlG~D~~~~i~l~ 262 (341)
+++||+|+|||++++++|+
T Consensus 294 ~v~SD~y~g~d~~~~i~~~ 312 (312)
T smart00611 294 RLVSDSYLGCDQEYPLSFD 312 (312)
T ss_pred EEEecccCCcceEEEEeeC
Confidence 9999999999999999874
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=1.3e-33 Score=270.57 Aligned_cols=193 Identities=31% Similarity=0.536 Sum_probs=144.5
Q ss_pred chhhccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHH
Q 019396 6 RTAQGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAEL 84 (341)
Q Consensus 6 ~~a~~~gwL~~al~~m~L~QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~l 84 (341)
..|+.+||+++++++|+|+|||+||+|+ ..+||+|||||+++.++++.+ ++.++++|.++++.++..+
T Consensus 118 ei~~~~~~~~~~~~~l~l~q~i~q~~w~-----------~~~~L~Qlp~i~~~~~~~l~~~~i~~l~~l~~~~~~e~~~l 186 (314)
T PF02889_consen 118 EIALEKGWLSTALNALELSQCIVQALWD-----------SDSPLLQLPHIGEESLKKLEKRGIKTLQDLRDLSPEELEEL 186 (314)
T ss_dssp HHHHHTTBCCHHHHHHHHHHHHHHTS-T-----------TS-GGGGSTT--HHHHHHHHHTT--SHHHHHHS-HHHHHHH
T ss_pred HHHHhcccHHHHHHHHHHHHHHHhhcCC-----------CCChhhcCCCCCHHHHHHHhccCCCcHHHHhhCCHHHHHHH
Confidence 4578999999999999999999999997 689999999999999999998 8899999999999999999
Q ss_pred HhhccCCChHHHHHHHHHHhcCCceeEEEEEEecCCccccCCCeEEEEEeeeeeccCCCCCCCccCCCCCCCCcccEEEE
Q 019396 85 LSQVGGFSSTEVQDVEMVLQMMPSLTVEVTCETEGEEGIQEGDIVTIQAWVTLKRGNGLIGALPHAPYYPFHKEENFWFL 164 (341)
Q Consensus 85 L~~~~~ls~~~~~~v~~v~~~~P~I~I~~~~~v~gE~~It~g~~vtl~~~V~L~R~n~~~~~~~~aP~FP~~K~E~Wwvv 164 (341)
|+ ..+.+++++.+++++||.++|++++++.+++.+ ..++|. |.++|.+ .+.++||+.|.++||++
T Consensus 187 l~----~~~~~~~~i~~~~~~~P~~~i~~~~~~~~~~~~---~~~~v~--v~i~~~~------~~~~~~~~~k~~~~~~~ 251 (314)
T PF02889_consen 187 LN----RNPPFGKEILEVASRIPRLEIKASVQVIDEEIV---PILTVQ--VSITRKF------SWSDRFPKKKKESWWLF 251 (314)
T ss_dssp H-----S-HHHHHHHHHHHCCS--EEEEEEETTCCGEEC---SEEEEE--EEEEESS------S-SST-SS--B--EEEE
T ss_pred Hh----hhhhhHHHHHHHHHHCCCEEEEEEEeccccccC---CcEEEE--EEEEccc------ccccCCCCCCcccEEEE
Confidence 87 457899999999999999999988887665432 346666 8888753 45669999999999999
Q ss_pred EEECCCCeEEEEeeeeeccchhHHhhhhhhhhhhhcCCCCccchhhHHHHHHHHhhhcCceeEEEEEEcCC-CCc--eeE
Q 019396 165 LADSVSNNVWFSQKVSFMDEPAAITAASKAIEDTMEGSGATVKETSAAVREAAEKVRSGSRLVMGKIQAPA-EGN--YNL 241 (341)
Q Consensus 165 lgD~~~n~Il~~krvs~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~k~~~~~v~l~F~aP~-~G~--~~l 241 (341)
|+|.++|+|++++|+++..+. ......++|++|. +|+ ++|
T Consensus 252 v~~~~~~~l~~~~~~~~~~~~-------------------------------------~~~~~~~~f~vp~~~~~~~~~~ 294 (314)
T PF02889_consen 252 VGDSKNNELLHFERITISKKK-------------------------------------SKDTVKISFQVPIPVGPRPYQY 294 (314)
T ss_dssp EEECCCTEEEEEEEE---SS---------------------------------------EEEEEEEEE--SS-EE--EEE
T ss_pred EEECCCCeEEEEeeeehhhhc-------------------------------------cCCcEEEEEEecCCCCCCCceE
Confidence 999999999999999883200 0124668999995 476 999
Q ss_pred EEEEEcCCCcccceEEEEEE
Q 019396 242 TCYCLCDSWLGCDKRTNLKV 261 (341)
Q Consensus 242 ~l~v~SDsYlG~D~~~~i~l 261 (341)
+++++||+|+|+|+.++|+|
T Consensus 295 ~v~v~sd~y~G~d~~~~i~~ 314 (314)
T PF02889_consen 295 TVYVISDSYLGLDQEVPINF 314 (314)
T ss_dssp EEEEEESS-SS--EEEEEEE
T ss_pred EEEEEECCccccceEEEeeC
Confidence 99999999999999999986
No 4
>COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion]
Probab=99.86 E-value=5e-22 Score=196.38 Aligned_cols=165 Identities=15% Similarity=0.149 Sum_probs=144.1
Q ss_pred cchhhccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHH
Q 019396 5 PRTAQGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAE 83 (341)
Q Consensus 5 ~~~a~~~gwL~~al~~m~L~QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~ 83 (341)
-|+|+++|++.++.+.+.+.||||||++.. ...+++||||++.+.++.+.- .|.++++|+.+..+..+.
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 688999999999988877654 789999999999999999
Q ss_pred HHhhccCCChHHHHHHHHHHhcCCcee-EEEEEEecCCccccCCCeEEEEEeeeeecc-------------C--------
Q 019396 84 LLSQVGGFSSTEVQDVEMVLQMMPSLT-VEVTCETEGEEGIQEGDIVTIQAWVTLKRG-------------N-------- 141 (341)
Q Consensus 84 lL~~~~~ls~~~~~~v~~v~~~~P~I~-I~~~~~v~gE~~It~g~~vtl~~~V~L~R~-------------n-------- 141 (341)
.|.+ ++..++.++.++++++|++. |.+.|.|.++..||++++..|.|++.+... |
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 9986 78899999999999999999 689999999999999999999988776431 1
Q ss_pred ----------C--CCCCCccCCCCCCCCcccEEEEEEECCCCeEEEEeeeeecc
Q 019396 142 ----------G--LIGALPHAPYYPFHKEENFWFLLADSVSNNVWFSQKVSFMD 183 (341)
Q Consensus 142 ----------~--~~~~~~~aP~FP~~K~E~WwvvlgD~~~n~Il~~krvs~~~ 183 (341)
+ ...++++||+||..+.-.|||.+.+++.+.++. ..+++.+
T Consensus 450 ~~~~~~~ai~~d~~~~pys~Ap~f~t~~~~~w~~~v~~~~Qt~~Ii-p~~Si~~ 502 (610)
T COG5407 450 ASVIETGAIKNDSSDSPYSEAPDFATRNDSEWAVRVAKCEQTVYII-PGGSIAT 502 (610)
T ss_pred hhccCccccccCCCCCCcccCcccccccCcceEEEeeccccceEEe-CCccccc
Confidence 1 123689999999999999999999999887775 5777765
No 5
>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]
Probab=99.73 E-value=9.6e-20 Score=196.38 Aligned_cols=335 Identities=26% Similarity=0.230 Sum_probs=257.2
Q ss_pred CccccchhhccCCHHHHHHHHHHHHHHHH---------------hcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc
Q 019396 1 MAVIPRTAQGHGWLRPAVGVVELSQSIIQ---------------AVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR 65 (341)
Q Consensus 1 ~~~~~~~a~~~gwL~~al~~m~L~QmIvQ---------------A~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~ 65 (341)
|+.++|+++++||+.+.+..|..++|+.| ++..++|+...-+.+...+.+| |||++.+.+.+.+
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 56789999999999999999999999999 6666666655556677889999 9999988888776
Q ss_pred -ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCceeEEEEEEecCCccccCCCeEEEEEeeeeeccCCCC
Q 019396 66 -KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPSLTVEVTCETEGEEGIQEGDIVTIQAWVTLKRGNGLI 144 (341)
Q Consensus 66 -~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~P~I~I~~~~~v~gE~~It~g~~vtl~~~V~L~R~n~~~ 144 (341)
...+.+++-.+....+..++....+++ ..++..+..+.|.|+++..+..+|+..++.|+..+...++++++++...
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 777777777766655555544322222 2344448889999999888999999989999988888889999998877
Q ss_pred CCCccCCCCCCCCcccEEEEEEECCCCeEEEEeeeeeccchhHHhhhhhhhhhhhcCCC-CccchhhHHHHHHHHhhhcC
Q 019396 145 GALPHAPYYPFHKEENFWFLLADSVSNNVWFSQKVSFMDEPAAITAASKAIEDTMEGSG-ATVKETSAAVREAAEKVRSG 223 (341)
Q Consensus 145 ~~~~~aP~FP~~K~E~WwvvlgD~~~n~Il~~krvs~~~~~~~~~~~~~~i~~~~~~~g-~~~~~~~~~~~~~~~~~k~~ 223 (341)
...+|.||||+.+.|.+|.+..+++-|..+.....+|++...++..+.+...+.+.--+ .+.+.|..++..+++.++++
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 78889999999999999999999999999998888888755556666666666555333 44577999999999999988
Q ss_pred ceeEEEEEEcCCCCceeEEEEEEcCCCcc--cceEEEEEEEeeccCccCCCCccccCCCCCccCCCCCcccccccccC-C
Q 019396 224 SRLVMGKIQAPAEGNYNLTCYCLCDSWLG--CDKRTNLKVKILKRTRAGTRGGIVSEEGPIVEDGAEEEEEDEEEEYD-D 300 (341)
Q Consensus 224 ~~~v~l~F~aP~~G~~~l~l~v~SDsYlG--~D~~~~i~l~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 300 (341)
.+...-.-..|-.+.|...+.++++-|+| |++..++.++|.+.+.+.++|.+=-|++-+-+.--|..+..+.+.+| +
T Consensus 354 ~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~~qieeTqVIV~TPEK~DiITRk~gdra 433 (1674)
T KOG0951|consen 354 LREDGSVNLAPFKIVYIAPMKALVQEMVGSFSKRLAPLGITVLELTGDSQLGKEQIEETQVIVTTPEKWDIITRKSGDRA 433 (1674)
T ss_pred cccccceecccceEEEEeeHHHHHHHHHHHHHhhccccCcEEEEecccccchhhhhhcceeEEeccchhhhhhcccCchh
Confidence 88654333456689999999999999999 99999999999999998887764333332223223333344555555 9
Q ss_pred cCCcccccchhhh---hhcccCCCCCCccccCCC-CCCCCCCC
Q 019396 301 YESEYSEDEEDER---DTKKKVPAANGTVSKKGT-NSELSGSD 339 (341)
Q Consensus 301 ~~s~~~~~~~~~~---~~~~~~~~~~~~~~~~~~-~~~~~~~~ 339 (341)
|++.|..+..||. ..++.....++++..... +++.+|+.
T Consensus 434 Y~qlvrLlIIDEIHLLhDdRGpvLESIVaRt~r~ses~~e~~R 476 (1674)
T KOG0951|consen 434 YEQLVRLLIIDEIHLLHDDRGPVLESIVARTFRRSESTEEGSR 476 (1674)
T ss_pred HHHHHHHHhhhhhhhcccccchHHHHHHHHHHHHhhhcccCce
Confidence 9999999999998 344555556777665544 44666664
No 6
>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]
Probab=99.68 E-value=5.9e-16 Score=167.52 Aligned_cols=216 Identities=13% Similarity=0.250 Sum_probs=176.7
Q ss_pred hhhccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhcccCCHHHHHcCCHHHHHHHHh
Q 019396 7 TAQGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKVRTFQELRDMSLQDRAELLS 86 (341)
Q Consensus 7 ~a~~~gwL~~al~~m~L~QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~~v~tl~~L~~m~~~er~~lL~ 86 (341)
+.+.+||...+..++.+|+|+.+.+|+ ...||+|+|.++.+++.+++.+-..++.++++.+.+.+.+++
T Consensus 923 i~l~rgw~~~~~~~l~~ck~v~~r~w~-----------~~~plrqf~~~~~ev~~~lE~k~~~~~r~~~l~~~elg~lI~ 991 (1674)
T KOG0951|consen 923 IVLKRGWAGLAQMALNLCKMVEKRMWP-----------TQTPLRQFKGCPKEVLRRLEKKELPWGRYYDLDPAELGELIG 991 (1674)
T ss_pred HHhhcCcchHHHHHHHhHhHhhhhccc-----------ccCchhhcCCCCHHHHHHHHhccCcchhhhccCHHHHHHHhc
Confidence 567899999999999999999999999 789999999999999999998888899999999999999887
Q ss_pred hccCCChHHHHHHHHHHhcCCceeEEEEEEecCCccccCCCeEEEEEeeeeeccCCCCCCCccCCCCCCC-----CcccE
Q 019396 87 QVGGFSSTEVQDVEMVLQMMPSLTVEVTCETEGEEGIQEGDIVTIQAWVTLKRGNGLIGALPHAPYYPFH-----KEENF 161 (341)
Q Consensus 87 ~~~~ls~~~~~~v~~v~~~~P~I~I~~~~~v~gE~~It~g~~vtl~~~V~L~R~n~~~~~~~~aP~FP~~-----K~E~W 161 (341)
..+..+-+..++.+||++.+.+.++ +|+.+ .+.+. ++ +.|.|-|. -.|+|
T Consensus 992 -----~~k~G~~l~~~~~~fpk~s~~~~vq-----pitr~-~~~~~--l~------------i~~~f~wd~~vh~~~e~F 1046 (1674)
T KOG0951|consen 992 -----VPKMGKPLHLFIRQFPKLSVSAHVQ-----PITRS-VYRVE--LT------------ITPDFDWDDKVHGSVEPF 1046 (1674)
T ss_pred -----CcccChhHHHHHHhcccceeeeeee-----eeeee-EEEEE--EE------------Eeecccchhhhcccccce
Confidence 3566788888999999999877666 36643 56666 44 34666652 46889
Q ss_pred EEEEEECCCCeEEEEeeeeeccchhHHhhhhhhhhhhhcCCCCccchhhHHHHHHHHhhhcCceeEEEEEEcC-CCCcee
Q 019396 162 WFLLADSVSNNVWFSQKVSFMDEPAAITAASKAIEDTMEGSGATVKETSAAVREAAEKVRSGSRLVMGKIQAP-AEGNYN 240 (341)
Q Consensus 162 wvvlgD~~~n~Il~~krvs~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~k~~~~~v~l~F~aP-~~G~~~ 240 (341)
|++|.|....+|++...+-+.+ + ...+.|+.| -.++.+
T Consensus 1047 ~i~ved~dge~il~~e~~~~~k---------------------------------------~--~~~v~ft~~~~~~pP~ 1085 (1674)
T KOG0951|consen 1047 WIIVEDTDGEKILHHEFFLLKK---------------------------------------K--EHTVNFTVPLFEPPPQ 1085 (1674)
T ss_pred EEEEEccCccceeeeeeEEecc---------------------------------------C--ceEEEEEeecCCCCCc
Confidence 9999999999999998887654 0 244799999 334899
Q ss_pred EEEEEEcCCCcccceEEEEEEEeeccCccCCCCccccCCCCCccCCCCCcccccccccCCcCCccccc
Q 019396 241 LTCYCLCDSWLGCDKRTNLKVKILKRTRAGTRGGIVSEEGPIVEDGAEEEEEDEEEEYDDYESEYSED 308 (341)
Q Consensus 241 l~l~v~SDsYlG~D~~~~i~l~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 308 (341)
|.|.++||.|+|....+|+.|+....|++-.+.+.+-+.-|.--.+...+ +++.-|-|+
T Consensus 1086 ~fi~lvSd~wl~s~~~~Pvsfr~l~lpek~p~pt~lld~~~~~~~~l~N~---------~~~~lf~~~ 1144 (1674)
T KOG0951|consen 1086 YFIRLVSDRWLHSETVLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNP---------SFETLFQDF 1144 (1674)
T ss_pred eEEEEeeccccCCCcccccchhhccCcccCCCCchhhhccccchhccCCc---------chhhhcccc
Confidence 99999999999999999999999999987666666666666655555544 366666655
No 7
>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]
Probab=98.38 E-value=9.4e-07 Score=96.16 Aligned_cols=187 Identities=16% Similarity=0.124 Sum_probs=132.9
Q ss_pred hhhccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhcccCCHHHHHcCCHHHHHHHHh
Q 019396 7 TAQGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIARKVRTFQELRDMSLQDRAELLS 86 (341)
Q Consensus 7 ~a~~~gwL~~al~~m~L~QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~~v~tl~~L~~m~~~er~~lL~ 86 (341)
++...||-..+.+++.||+||...||. ...|+.|++.... .+ +++.. .|+.|...+.++++.
T Consensus 713 i~~~~~~~~~~~~~l~l~k~ier~mw~-----------~~~~l~qf~~~~~---~~-~~~~~---~l~~L~~~~~g~~w~ 774 (1230)
T KOG0952|consen 713 IVLRQNWHLLSNRMLNLCKRIERRMWD-----------FFIPLKQFTLLLN---RK-ERKKL---TLLLLRKDELGELWH 774 (1230)
T ss_pred HHHHhCchHHHHHHHHHHHHHHHHHHh-----------hhhhhhcCCcccc---hh-hhhcc---hHHhhhhhhhccccc
Confidence 456789999999999999999999998 8899999986644 23 22222 778888888888876
Q ss_pred hccCCChHHHHHHHHHHhcCCceeEEEEEEecCCccccCCCeEEEEEeeeeeccCCCCCCCccCCCCCCCCcccEEEEEE
Q 019396 87 QVGGFSSTEVQDVEMVLQMMPSLTVEVTCETEGEEGIQEGDIVTIQAWVTLKRGNGLIGALPHAPYYPFHKEENFWFLLA 166 (341)
Q Consensus 87 ~~~~ls~~~~~~v~~v~~~~P~I~I~~~~~v~gE~~It~g~~vtl~~~V~L~R~n~~~~~~~~aP~FP~~K~E~Wwvvlg 166 (341)
+ . ...++.+..+|.+++++.+.. ++. ++++|. +.+.+ .+.|.-.... ..|-.+++.
T Consensus 775 ~----~----~~~~k~l~~ip~v~v~a~~~p-----~t~-~vlri~--~~~~~------~f~w~~~~hg--~~g~~i~~e 830 (1230)
T KOG0952|consen 775 N----V----PYGLKQLSGIPLVNVEALIQP-----ITR-NVLRIE--VAITP------DFEWNDGIHG--KAGQPIFKE 830 (1230)
T ss_pred c----C----chhhhhhccCCceehhhhhcc-----chh-hhheee--eccCC------ceEEeccccc--ccCceeEee
Confidence 3 1 223889999999998877653 332 355655 44332 1233222222 233349999
Q ss_pred ECCCCeEEEEeeeeeccchhHHhhhhhhhhhhhcCCCCccchhhHHHHHHHHhhhcCceeEEEEEEcC--CCCceeEEEE
Q 019396 167 DSVSNNVWFSQKVSFMDEPAAITAASKAIEDTMEGSGATVKETSAAVREAAEKVRSGSRLVMGKIQAP--AEGNYNLTCY 244 (341)
Q Consensus 167 D~~~n~Il~~krvs~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~k~~~~~v~l~F~aP--~~G~~~l~l~ 244 (341)
|...+.+++++.+-+..+.. +.++. +.|.+| .|-+.++.++
T Consensus 831 d~~~~~i~h~e~~~~~~~~~-----------------------------------~~s~~--lvf~ipis~pLps~~~~~ 873 (1230)
T KOG0952|consen 831 DSSLLPILHIEVFLVNCKKV-----------------------------------NESQL--LVFTIPISDPLPSQIRHR 873 (1230)
T ss_pred cCCCCcceeeeeehhhhhhh-----------------------------------hhhhh--eeEEeecccCCccceEEe
Confidence 99999999998776644110 01222 688888 6888999999
Q ss_pred EEcCCCcccceEEEEEEEeeccCccCCC
Q 019396 245 CLCDSWLGCDKRTNLKVKILKRTRAGTR 272 (341)
Q Consensus 245 v~SDsYlG~D~~~~i~l~V~~~~~~~~~ 272 (341)
..||.|+|++..+++.+.....+.....
T Consensus 874 ~~s~~~l~~e~~~~~s~~~~il~~~~~~ 901 (1230)
T KOG0952|consen 874 AVSDNWLGAETVYPLSFQHLILPDNEPP 901 (1230)
T ss_pred eecccccCCceeccccccceeccccccc
Confidence 9999999999999999888777654433
No 8
>PRK01172 ski2-like helicase; Provisional
Probab=98.32 E-value=6.5e-07 Score=95.24 Aligned_cols=85 Identities=12% Similarity=0.224 Sum_probs=75.3
Q ss_pred hhhccCCHHHHHHH------HHHHHH-------HHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc-ccCCHHH
Q 019396 7 TAQGHGWLRPAVGV------VELSQS-------IIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR-KVRTFQE 72 (341)
Q Consensus 7 ~a~~~gwL~~al~~------m~L~Qm-------IvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~-~v~tl~~ 72 (341)
.....+|+..++.. |+|+|| |+||+|. ...||+|||||+...+++|.+ +++|+.+
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 789999999999999999988 9999999
Q ss_pred HHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 73 LRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 73 L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
|.++++++|.++++ +++++++.+...++++
T Consensus 639 i~~~~~~~~~~i~~----~~~~~~~~i~~~~~~~ 668 (674)
T PRK01172 639 IARSSPERIKKIYG----FSDTLANAIVNRAMKI 668 (674)
T ss_pred HHhCCHHHHHHHhc----cCHHHHHHHHHHHHHH
Confidence 99999999999876 8888888888776654
No 9
>PRK02362 ski2-like helicase; Provisional
Probab=97.99 E-value=8.9e-06 Score=87.65 Aligned_cols=81 Identities=11% Similarity=0.028 Sum_probs=70.5
Q ss_pred hccCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhh
Q 019396 9 QGHGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQ 87 (341)
Q Consensus 9 ~~~gwL~~al~~m~L~QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~ 87 (341)
++.+|+..+..+|+|+|||.||+|. ...||+|||||+...+++|.+ ++.|+.+|..+.+.++..+++
T Consensus 625 ~~~~~~~~~~~~~~l~~~l~~gv~~-----------~~~~L~~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~~g- 692 (737)
T PRK02362 625 ASELDLDLARAARELEKRVEYGVRE-----------ELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAILG- 692 (737)
T ss_pred HHHhCccHHHHHHHHHHHHHhCCCH-----------HHHHHhCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHHC-
Confidence 3457788899999999999999998 789999999999999999877 999999999999999888865
Q ss_pred ccCCChHHHHHHHHHHhcC
Q 019396 88 VGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 88 ~~~ls~~~~~~v~~v~~~~ 106 (341)
.+..+.|.+.+...
T Consensus 693 -----~~~~~~i~~~~~~~ 706 (737)
T PRK02362 693 -----EKIAENILEQAGRR 706 (737)
T ss_pred -----HHHHHHHHHHhCcc
Confidence 46677787777643
No 10
>PRK00254 ski2-like helicase; Provisional
Probab=97.62 E-value=6.9e-05 Score=80.63 Aligned_cols=78 Identities=12% Similarity=0.174 Sum_probs=66.1
Q ss_pred cCCHHHHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhcc
Q 019396 11 HGWLRPAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVG 89 (341)
Q Consensus 11 ~gwL~~al~~m~L~QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~ 89 (341)
.+|++ ++. +|+|||+||+|. ..+||.|+|||....+++|-+ ++.|+.++..++.+++.++ .
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 45664 333 899999999998 789999999999999999888 6999999999999988665 3
Q ss_pred CCChHHHHHHHHHHhcC
Q 019396 90 GFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 90 ~ls~~~~~~v~~v~~~~ 106 (341)
|+..+.++.|.+.++..
T Consensus 685 gi~~~~a~~i~~~~~~~ 701 (720)
T PRK00254 685 GIGAKIVEGIFKHLGVE 701 (720)
T ss_pred CCCHHHHHHHHHHhccc
Confidence 47888899999988743
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=90.69 E-value=0.35 Score=35.61 Aligned_cols=53 Identities=15% Similarity=0.327 Sum_probs=44.5
Q ss_pred CcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019396 48 PFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 104 (341)
Q Consensus 48 pLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~ 104 (341)
.|+++|++.+..+.+|.. ++.|+.+|.+.+.+++.. +.|++++.++.+...++
T Consensus 6 ~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~----i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 6 DLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAE----IPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHT----STTSSHHHHHHHHHHHH
T ss_pred hhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhc----CCCCCHHHHHHHHHHHh
Confidence 478899999999999988 799999999998776544 36799999998888765
No 12
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=86.82 E-value=0.31 Score=53.97 Aligned_cols=18 Identities=50% Similarity=0.813 Sum_probs=12.3
Q ss_pred cccccCCcCCcccccchh
Q 019396 294 EEEEYDDYESEYSEDEED 311 (341)
Q Consensus 294 ~~~~~~~~~s~~~~~~~~ 311 (341)
||+|+|++++||||||+-
T Consensus 327 ed~eDde~~deYsDDeD~ 344 (1233)
T KOG1824|consen 327 EDEEDDEQDDEYSDDEDM 344 (1233)
T ss_pred hccccchhccccccccch
Confidence 444555666999999763
No 13
>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=82.53 E-value=0.94 Score=43.51 Aligned_cols=8 Identities=25% Similarity=0.410 Sum_probs=3.7
Q ss_pred HHHhcCCc
Q 019396 101 MVLQMMPS 108 (341)
Q Consensus 101 ~v~~~~P~ 108 (341)
..++++|.
T Consensus 58 ~s~qrlp~ 65 (314)
T PF06524_consen 58 QSVQRLPM 65 (314)
T ss_pred hhhhcCch
Confidence 34445554
No 14
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=81.55 E-value=4.9 Score=34.74 Aligned_cols=59 Identities=25% Similarity=0.327 Sum_probs=47.1
Q ss_pred CCcccCCC---------CCHHHHHHHhcccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 47 APFLQLPH---------FTEAVIKKIARKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 47 spLlQLPh---------~~~~~v~kl~~~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
..|.+.|. +.++.+..+-.++.||..|++|++.+.+.+|.. .|..+++...+.++++++
T Consensus 61 ~~l~~yP~l~~WL~vVgl~~~~i~~i~~~~~tLe~Llemsd~el~~~l~~-~g~~~EE~rRL~~Al~~L 128 (129)
T PF13543_consen 61 AELNSYPSLRQWLRVVGLRPESIQAILSKVLTLEALLEMSDEELKEILNR-CGAREEECRRLCRALSNL 128 (129)
T ss_pred hhcccCCcHHHHhhhcCCCHHHHHHHHHhhcCHHHHHhCCHHHHHHHHHH-hCCCHHHHHHHHHHHHhc
Confidence 45666674 467888877557899999999999999999987 677788888888877654
No 15
>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=81.21 E-value=1.1 Score=43.06 Aligned_cols=6 Identities=0% Similarity=0.252 Sum_probs=2.9
Q ss_pred CCeEEE
Q 019396 170 SNNVWF 175 (341)
Q Consensus 170 ~n~Il~ 175 (341)
.++|+.
T Consensus 139 GGrif~ 144 (314)
T PF06524_consen 139 GGRIFK 144 (314)
T ss_pred CCeEEE
Confidence 455553
No 16
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=79.09 E-value=4.3 Score=39.50 Aligned_cols=56 Identities=13% Similarity=0.130 Sum_probs=47.0
Q ss_pred CCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019396 46 TAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 105 (341)
Q Consensus 46 ~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~ 105 (341)
.-||..+|.+.+..+++|.+ ++.|+.+|.++++.++.++++ ++.+.+..+.+.+..
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 46899999999999999998 899999999999988877755 777777777776654
No 17
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=78.35 E-value=0.57 Score=47.92 Aligned_cols=17 Identities=29% Similarity=0.513 Sum_probs=8.9
Q ss_pred CCCcccceEEEEEEEee
Q 019396 248 DSWLGCDKRTNLKVKIL 264 (341)
Q Consensus 248 DsYlG~D~~~~i~l~V~ 264 (341)
|.||--+..+.-+|+|-
T Consensus 13 ddWi~~~~~~~~KlTi~ 29 (458)
T PF10446_consen 13 DDWIRQDTDYKRKLTIN 29 (458)
T ss_pred hhhhhccccccccccHH
Confidence 45665555555445443
No 18
>PTZ00035 Rad51 protein; Provisional
Probab=73.78 E-value=7.2 Score=38.65 Aligned_cols=57 Identities=18% Similarity=0.251 Sum_probs=47.3
Q ss_pred CcccC--CCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019396 48 PFLQL--PHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 108 (341)
Q Consensus 48 pLlQL--Ph~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~P~ 108 (341)
.|-.| |.+++..+++|+. ++.|+.+|...++.++.++. |++...+.++++.++.+..
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~----gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAYATKKDLCNIK----GISEAKVEKIKEAASKLVP 81 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhh----CCCHHHHHHHHHHHHHhcc
Confidence 34444 7899999999998 99999999999998887664 5999999888888887754
No 19
>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=71.49 E-value=9.4 Score=36.78 Aligned_cols=52 Identities=17% Similarity=0.231 Sum_probs=42.7
Q ss_pred cccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019396 49 FLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 104 (341)
Q Consensus 49 LlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~ 104 (341)
|.++|++.+..+++|.+ ++.|+.+|..++.+++..+++ ++.+....+.+.+.
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 45799999999999988 899999999999988877654 67666666666665
No 20
>PRK14133 DNA polymerase IV; Provisional
Probab=71.35 E-value=12 Score=36.82 Aligned_cols=49 Identities=14% Similarity=0.202 Sum_probs=41.8
Q ss_pred HHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHh
Q 019396 25 QSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLS 86 (341)
Q Consensus 25 QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~ 86 (341)
+.+.+.+|. -|+..||++...+.++|.+ +++|+.+|..++...+...++
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 455667765 5899999999999999988 999999999999888777665
No 21
>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=71.22 E-value=48 Score=26.04 Aligned_cols=45 Identities=13% Similarity=0.167 Sum_probs=26.8
Q ss_pred ccCCCeEEEEEeeeeeccCCCCCCCccCCCCCCCCcccEEEEEEECCCCeEEEEeee
Q 019396 123 IQEGDIVTIQAWVTLKRGNGLIGALPHAPYYPFHKEENFWFLLADSVSNNVWFSQKV 179 (341)
Q Consensus 123 It~g~~vtl~~~V~L~R~n~~~~~~~~aP~FP~~K~E~WwvvlgD~~~n~Il~~krv 179 (341)
..||+.|++. +.+...++ .++......-.|.|.|+. ++++.....
T Consensus 11 YrPGetV~~~--~~~~~~~~---------~~~~~~~~~~~v~i~dp~-g~~v~~~~~ 55 (99)
T PF01835_consen 11 YRPGETVHFR--AIVRDLDN---------DFKPPANSPVTVTIKDPS-GNEVFRWSV 55 (99)
T ss_dssp E-TTSEEEEE--EEEEEECT---------TCSCESSEEEEEEEEETT-SEEEEEEEE
T ss_pred cCCCCEEEEE--EEEecccc---------ccccccCCceEEEEECCC-CCEEEEEEe
Confidence 6899999988 66554321 133344456779999995 444443333
No 22
>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=70.38 E-value=8.9 Score=29.06 Aligned_cols=54 Identities=17% Similarity=0.313 Sum_probs=39.5
Q ss_pred CCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019396 46 TAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 104 (341)
Q Consensus 46 ~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~ 104 (341)
+.|+-.| .++......|.+ +|.|+++|+.++.+++..+ .++..+-+.+|...+.
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 4577777 588888888888 9999999999998775543 4577777888877764
No 23
>PRK07758 hypothetical protein; Provisional
Probab=69.77 E-value=13 Score=30.49 Aligned_cols=50 Identities=16% Similarity=0.296 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019396 52 LPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 105 (341)
Q Consensus 52 LPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~ 105 (341)
+|.++.....-|.+ +|.++++|..++.+++.++- +|.++-+.+|...+..
T Consensus 39 ~~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~ik----nlGkKSL~EIkekL~E 89 (95)
T PRK07758 39 LSLLSAPARRALEHHGIHTVEELSKYSEKEILKLH----GMGPASLPKLRKALEE 89 (95)
T ss_pred CccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHcc----CCCHHHHHHHHHHHHH
Confidence 56788777777777 99999999999999877653 4888888888877765
No 24
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=67.83 E-value=8.7 Score=28.71 Aligned_cols=51 Identities=20% Similarity=0.343 Sum_probs=35.3
Q ss_pred ccCCCCCHHHHHHHhcccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019396 50 LQLPHFTEAVIKKIARKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 104 (341)
Q Consensus 50 lQLPh~~~~~v~kl~~~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~ 104 (341)
|.+||+.+...+.|.+...++..|+..+.+++.. +.|+.+.-.+.+..+.+
T Consensus 6 LGI~~VG~~~ak~L~~~f~sl~~l~~a~~e~L~~----i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAKHFGSLEALMNASVEELSA----IPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp CTSTT--HHHHHHHHHCCSCHHHHCC--HHHHCT----STT--HHHHHHHHHHHH
T ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHcCHHHHhc----cCCcCHHHHHHHHHHHC
Confidence 5689999999999998888999999888776543 35677777777777664
No 25
>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=67.23 E-value=16 Score=35.24 Aligned_cols=54 Identities=11% Similarity=0.241 Sum_probs=42.4
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCC
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMP 107 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~P 107 (341)
-|+..||.+...+..+|.+ ++.|+.+|..++...+.+.++ .....+...+.-+-
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 5899999999999999988 999999999999888776554 24555555555443
No 26
>PRK01216 DNA polymerase IV; Validated
Probab=67.00 E-value=10 Score=37.78 Aligned_cols=60 Identities=5% Similarity=0.173 Sum_probs=46.5
Q ss_pred HHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHH
Q 019396 25 QSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVL 103 (341)
Q Consensus 25 QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~ 103 (341)
+.+.|.+|+ -|+..||.+......+|.+ ++.|+++|..++...+...++ ......+.+.+
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 456667776 5999999999999999988 999999999999888776665 23344555544
No 27
>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=66.66 E-value=13 Score=30.41 Aligned_cols=58 Identities=19% Similarity=0.261 Sum_probs=41.0
Q ss_pred CCCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCC-ChHHHHHHHHH
Q 019396 45 GTAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGF-SSTEVQDVEMV 102 (341)
Q Consensus 45 ~~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~l-s~~~~~~v~~v 102 (341)
..+.|.+||+|.+.+.+-|.. ++.++.+|...++.++=.-|....|. .+.-+-++...
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~Ly~~lc~~~G~~~DpCvldvfr~ 69 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRLLGIRSPADLKGRDPEELYERLCALTGQRHDPCVLDVFRC 69 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHHcCCCCHHHHhCCCHHHHHHHHHHHcCCcCCcHHHHHHHH
Confidence 356899999999999998888 99999999999988764333322333 33334444433
No 28
>PRK02406 DNA polymerase IV; Validated
Probab=66.44 E-value=16 Score=35.71 Aligned_cols=53 Identities=11% Similarity=0.156 Sum_probs=42.6
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
-|+..||++...+.++|.+ ++.|+++|..++...+...++. ....+...+.-+
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 5899999999999999988 9999999999998887777652 345555555554
No 29
>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=64.81 E-value=16 Score=35.94 Aligned_cols=53 Identities=17% Similarity=0.161 Sum_probs=43.9
Q ss_pred ccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 50 LQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 50 lQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
+|-+.+++.++++|++ ++.|+.+|+..++.++.++.. ++.....++...+..+
T Consensus 4 ~~~~~~~~~~~~~l~~~g~~t~~~~~~~~~~~L~~i~~----ls~~~~~~~~~~~~~~ 57 (316)
T TIGR02239 4 LEGNGITAADIKKLQEAGLHTVESVAYAPKKQLLEIKG----ISEAKADKILAEAAKL 57 (316)
T ss_pred hhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhC----CCHHHHHHHHHHHHHh
Confidence 4556699999999998 999999999999999887754 8888888777766644
No 30
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=64.47 E-value=11 Score=41.88 Aligned_cols=53 Identities=23% Similarity=0.389 Sum_probs=45.6
Q ss_pred CcccCCCCCHHHHHHHhcccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019396 48 PFLQLPHFTEAVIKKIARKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 105 (341)
Q Consensus 48 pLlQLPh~~~~~v~kl~~~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~ 105 (341)
-|+.||++++..+.+|-.++.++.+|++++.+++..+++ +++.++.+.++++.
T Consensus 758 ~L~~lPgI~~~~a~~ll~~f~si~~l~~as~eeL~~~iG-----~~~~A~~i~~fl~~ 810 (814)
T TIGR00596 758 FLLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNELIG-----DEEAAKRLYDFLRT 810 (814)
T ss_pred HHHHCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHHhC-----CHHHHHHHHHHhcc
Confidence 377899999999998888899999999999999888755 46788999988865
No 31
>KOG1834 consensus Calsyntenin [Extracellular structures]
Probab=64.18 E-value=6.6 Score=42.39 Aligned_cols=10 Identities=20% Similarity=0.590 Sum_probs=6.2
Q ss_pred EEEEEcCCCc
Q 019396 242 TCYCLCDSWL 251 (341)
Q Consensus 242 ~l~v~SDsYl 251 (341)
.|.|+|=+|+
T Consensus 831 vViVVcVgfL 840 (952)
T KOG1834|consen 831 VVIVVCVGFL 840 (952)
T ss_pred EEEEeehhHH
Confidence 4566776664
No 32
>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=63.98 E-value=15 Score=35.99 Aligned_cols=54 Identities=17% Similarity=0.186 Sum_probs=45.0
Q ss_pred cCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019396 51 QLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 108 (341)
Q Consensus 51 QLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~P~ 108 (341)
|-+.+++..+++|+. ++.|+.++...++.++.++. |++...+.++.+.+..+-.
T Consensus 5 ~~~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~----gls~~~~~~i~~~~~~~~~ 59 (313)
T TIGR02238 5 QAHGINAADIKKLKSAGICTVNGVIMTTRRALCKIK----GLSEAKVDKIKEAASKIIN 59 (313)
T ss_pred hcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhc----CCCHHHHHHHHHHHHhhhc
Confidence 335699999999998 99999999999988877664 5999999999888877643
No 33
>PF15243 ANAPC15: Anaphase-promoting complex subunit 15
Probab=63.58 E-value=5.1 Score=32.71 Aligned_cols=18 Identities=33% Similarity=0.435 Sum_probs=8.8
Q ss_pred ccCCcCCcccccchhhhh
Q 019396 297 EYDDYESEYSEDEEDERD 314 (341)
Q Consensus 297 ~~~~~~s~~~~~~~~~~~ 314 (341)
++++.++|.+++++++.+
T Consensus 73 ~dd~d~~e~~~~d~de~~ 90 (92)
T PF15243_consen 73 DDDSDDSEESMQDDDEMN 90 (92)
T ss_pred ccccccccchhccchhcc
Confidence 333455555555555543
No 34
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=63.12 E-value=15 Score=36.60 Aligned_cols=52 Identities=13% Similarity=0.161 Sum_probs=43.9
Q ss_pred CCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCC
Q 019396 52 LPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMP 107 (341)
Q Consensus 52 LPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~P 107 (341)
-+.+++..++||+. ++.|+.+|...++.++.++ .|++...+.++++.++.+-
T Consensus 36 ~~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~----~g~s~~~~~ki~~~a~~~~ 88 (344)
T PLN03187 36 SQGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGI----KGLSEAKVDKICEAAEKLL 88 (344)
T ss_pred hCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHh----cCCCHHHHHHHHHHHHHhh
Confidence 36799999999998 9999999999998887665 4599999988888777763
No 35
>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=62.71 E-value=21 Score=24.58 Aligned_cols=46 Identities=11% Similarity=0.268 Sum_probs=36.5
Q ss_pred CCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019396 55 FTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 104 (341)
Q Consensus 55 ~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~ 104 (341)
+++..+.++.. ++.|+.+|...+++++..+ .|+++.....+...++
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 35677777777 9999999999999887765 4588888888877665
No 36
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=62.44 E-value=5.9 Score=41.24 Aligned_cols=21 Identities=24% Similarity=0.411 Sum_probs=13.6
Q ss_pred EEEEEEECCCCeEEEEeeeee
Q 019396 161 FWFLLADSVSNNVWFSQKVSF 181 (341)
Q Consensus 161 WwvvlgD~~~n~Il~~krvs~ 181 (341)
+-|+.|...+.-++..++..|
T Consensus 117 ~~Cl~gefvseallvp~kC~f 137 (615)
T KOG3540|consen 117 YRCLAGEFVSEALLVPEKCQF 137 (615)
T ss_pred ceeecCcchhhhccCcccchh
Confidence 567777776776666555554
No 37
>PRK02794 DNA polymerase IV; Provisional
Probab=60.88 E-value=22 Score=36.02 Aligned_cols=55 Identities=15% Similarity=0.097 Sum_probs=44.0
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 108 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~P~ 108 (341)
-||..||.+...+.++|.+ ++.|+++|..++...+...++. ....++..+.-+..
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 5899999999999999988 9999999999998887777652 35556666655543
No 38
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=60.72 E-value=6.3 Score=43.14 Aligned_cols=12 Identities=17% Similarity=0.155 Sum_probs=6.6
Q ss_pred CeEEEEeeeeec
Q 019396 171 NNVWFSQKVSFM 182 (341)
Q Consensus 171 n~Il~~krvs~~ 182 (341)
=+|++++||.|.
T Consensus 786 VEiv~~ERV~f~ 797 (960)
T KOG1189|consen 786 VEIVNLERVQFG 797 (960)
T ss_pred eeeeeeeeeeec
Confidence 455555555554
No 39
>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=59.19 E-value=3.1 Score=36.69 Aligned_cols=10 Identities=10% Similarity=0.089 Sum_probs=4.3
Q ss_pred eEEEEeeeee
Q 019396 172 NVWFSQKVSF 181 (341)
Q Consensus 172 ~Il~~krvs~ 181 (341)
+.|+++.+.|
T Consensus 30 h~L~L~~v~L 39 (149)
T PF03066_consen 30 HQLSLRQVCL 39 (149)
T ss_dssp EEEEEEEEEE
T ss_pred cEEEEEEeec
Confidence 3444444444
No 40
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=59.13 E-value=25 Score=35.08 Aligned_cols=76 Identities=18% Similarity=0.234 Sum_probs=53.3
Q ss_pred HHHHHHHhcCCCccCCCCCCCCCCCCcccC--CCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHH
Q 019396 23 LSQSIIQAVPLSSRKATGGSTEGTAPFLQL--PHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDV 99 (341)
Q Consensus 23 L~QmIvQA~W~~~~~~~~~~~d~~spLlQL--Ph~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v 99 (341)
..||.-|+|......-.. ....+|-.| +.+++..+++|+. ++.|+.++...++.++.++.. ++.....++
T Consensus 5 ~~~~~~~~~~~~~~~~~~---~~~~~~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~~i~~----is~~~~~~~ 77 (342)
T PLN03186 5 VAAAAAQAMQEEEEEEAA---HGPFPIEQLQASGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKG----ISEAKVEKI 77 (342)
T ss_pred HHHHHHhhccchhhcccc---cCCccHHHHHhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcC----CCHHHHHHH
Confidence 356777777654322111 112245555 5699999999988 999999999999888877654 888888777
Q ss_pred HHHHhc
Q 019396 100 EMVLQM 105 (341)
Q Consensus 100 ~~v~~~ 105 (341)
...+..
T Consensus 78 ~~~~~~ 83 (342)
T PLN03186 78 LEAASK 83 (342)
T ss_pred HHHHHH
Confidence 776644
No 41
>PRK03352 DNA polymerase IV; Validated
Probab=58.90 E-value=15 Score=36.05 Aligned_cols=40 Identities=18% Similarity=0.146 Sum_probs=36.1
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHh
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLS 86 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~ 86 (341)
-|+..||++...+.++|.+ ++.|+.+|..++...+.+.++
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 6899999999999999998 999999999999888776665
No 42
>PRK03348 DNA polymerase IV; Provisional
Probab=58.54 E-value=28 Score=35.87 Aligned_cols=56 Identities=20% Similarity=0.214 Sum_probs=44.6
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 108 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~P~ 108 (341)
-|+..||++.....++|.+ +|+|+.+|..++..++...|+ ......+.+.+.-+..
T Consensus 180 LPv~~L~GIG~~t~~~L~~lGI~TigDLa~l~~~~L~~~fG------~~~g~~L~~~a~G~d~ 236 (454)
T PRK03348 180 LPVRRLWGIGPVTEEKLHRLGIETIGDLAALSEAEVANLLG------ATVGPALHRLARGIDD 236 (454)
T ss_pred CCccccCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHHHC------HHHHHHHHHHHcCCCC
Confidence 5899999999999999988 999999999999888877765 2345556666655533
No 43
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=58.07 E-value=25 Score=29.70 Aligned_cols=53 Identities=17% Similarity=0.176 Sum_probs=40.7
Q ss_pred CCCCHHHHHHHhc-ccCCHHHHHcCCHHH--HHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 53 PHFTEAVIKKIAR-KVRTFQELRDMSLQD--RAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 53 Ph~~~~~v~kl~~-~v~tl~~L~~m~~~e--r~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
|.+.+....+|.+ +|.|..+|++..... |..|... .+++.+.+......+.-+
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~-~~i~~~~l~~w~~~AdL~ 56 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAGDTPLGRKALAKK-LGISERNLLKWVNQADLM 56 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHh-cCCCHHHHHHHHhHHHhh
Confidence 7788888999988 999999999887544 4446664 678888888777666544
No 44
>PRK03103 DNA polymerase IV; Reviewed
Probab=57.15 E-value=27 Score=35.13 Aligned_cols=53 Identities=15% Similarity=0.124 Sum_probs=41.6
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
-|+..||.+...+.++|.+ +++|+++|..++...+...++. ....++..+.-+
T Consensus 181 lpi~~l~gig~~~~~~L~~~Gi~tigdl~~~~~~~L~~~fG~-------~~~~l~~~a~G~ 234 (409)
T PRK03103 181 LPVRKLFGVGSRMEKHLRRMGIRTIGQLANTPLERLKKRWGI-------NGEVLWRTANGI 234 (409)
T ss_pred CCHhhcCCccHHHHHHHHHcCCCCHHHHhcCCHHHHHHHHCH-------HHHHHHHHhcCC
Confidence 5899999999999999988 9999999999998877766652 344555555443
No 45
>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=55.24 E-value=7.2 Score=34.07 Aligned_cols=18 Identities=39% Similarity=0.680 Sum_probs=10.3
Q ss_pred ccccCCcCCcccccchhh
Q 019396 295 EEEYDDYESEYSEDEEDE 312 (341)
Q Consensus 295 ~~~~~~~~s~~~~~~~~~ 312 (341)
+++++|.+|+++||++++
T Consensus 31 ~~~~~d~~sd~~dd~d~e 48 (137)
T PF04281_consen 31 DEDDTDTDSDISDDSDDE 48 (137)
T ss_pred ccccccccccccccccCC
Confidence 344556667766665543
No 46
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=55.16 E-value=36 Score=34.47 Aligned_cols=54 Identities=15% Similarity=0.159 Sum_probs=42.5
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCC
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMP 107 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~P 107 (341)
-|+..||++...+.++|.+ +++|+++|..++...+.+.++. ....+...+.-+.
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 6899999999999999998 9999999999998877766652 3445555555543
No 47
>PRK01810 DNA polymerase IV; Validated
Probab=54.76 E-value=31 Score=34.63 Aligned_cols=52 Identities=12% Similarity=0.061 Sum_probs=41.5
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 105 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~ 105 (341)
-|+..||++...+.++|.+ +++|+++|..++...+...++. ....++..+.-
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 4888899999999999988 9999999999998887766652 34555555553
No 48
>PF13897 GOLD_2: Golgi-dynamics membrane-trafficking
Probab=54.21 E-value=67 Score=28.11 Aligned_cols=35 Identities=23% Similarity=0.229 Sum_probs=23.5
Q ss_pred EEEEcC--CCCceeEEEEEEcCCCcccceEEEEEEEeeccC
Q 019396 229 GKIQAP--AEGNYNLTCYCLCDSWLGCDKRTNLKVKILKRT 267 (341)
Q Consensus 229 l~F~aP--~~G~~~l~l~v~SDsYlG~D~~~~i~l~V~~~~ 267 (341)
+.+.+| +.|+ .++=-+.+|.| |.-+-+-|...+++
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 344555 5675 67778889998 55566667776655
No 49
>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=53.28 E-value=26 Score=34.26 Aligned_cols=41 Identities=12% Similarity=0.058 Sum_probs=36.2
Q ss_pred CCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHh
Q 019396 46 TAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLS 86 (341)
Q Consensus 46 ~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~ 86 (341)
.-|+..||++...+.++|.+ ++.|+++|..++.+.+...++
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 36899999999999999998 999999999999888776655
No 50
>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=53.15 E-value=40 Score=32.97 Aligned_cols=53 Identities=15% Similarity=0.117 Sum_probs=40.0
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCC-HHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMS-LQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~-~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
-|+..||++.....++|.+ ++.|+.+|..++ ...+...++ .....++..+.-+
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 6899999999999999998 999999999999 665554443 2344555555444
No 51
>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=52.66 E-value=39 Score=24.37 Aligned_cols=36 Identities=17% Similarity=0.149 Sum_probs=21.5
Q ss_pred EEEEcCCCCceeEEEEEEcCCCcccceEEEEEEEee
Q 019396 229 GKIQAPAEGNYNLTCYCLCDSWLGCDKRTNLKVKIL 264 (341)
Q Consensus 229 l~F~aP~~G~~~l~l~v~SDsYlG~D~~~~i~l~V~ 264 (341)
+.|+-=+||.|.|.|+++...-.-......|.|.|+
T Consensus 31 ~~~~~L~~G~Y~l~V~a~~~~~~~~~~~~~l~i~I~ 66 (66)
T PF07495_consen 31 ISYTNLPPGKYTLEVRAKDNNGKWSSDEKSLTITIL 66 (66)
T ss_dssp EEEES--SEEEEEEEEEEETTS-B-SS-EEEEEEEE
T ss_pred EEEEeCCCEEEEEEEEEECCCCCcCcccEEEEEEEC
Confidence 566555799999999998844322222266666663
No 52
>PRK03858 DNA polymerase IV; Validated
Probab=51.46 E-value=22 Score=35.50 Aligned_cols=40 Identities=15% Similarity=0.189 Sum_probs=35.8
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHh
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLS 86 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~ 86 (341)
-|+..||++...+.++|.+ +++|+.+|..++...+...++
T Consensus 173 lpl~~l~Gig~~~~~~L~~~Gi~t~~dl~~l~~~~L~~~fG 213 (396)
T PRK03858 173 LPVRRLWGVGPVTAAKLRAHGITTVGDVAELPESALVSLLG 213 (396)
T ss_pred CChhhcCCCCHHHHHHHHHhCCCcHHHHhcCCHHHHHHHhC
Confidence 5899999999999999988 999999999999888777665
No 53
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=51.27 E-value=40 Score=32.03 Aligned_cols=54 Identities=7% Similarity=0.175 Sum_probs=46.3
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 104 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~ 104 (341)
..|.++|++.+..+++|-. +..|+.+|...+.+++.++ .|++...++.|...+.
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 4789999999999998887 5999999999998887655 4588888888988887
No 54
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=50.67 E-value=8.9 Score=42.05 Aligned_cols=6 Identities=17% Similarity=0.357 Sum_probs=3.4
Q ss_pred EEEEcC
Q 019396 229 GKIQAP 234 (341)
Q Consensus 229 l~F~aP 234 (341)
+.|..|
T Consensus 741 ~efd~p 746 (960)
T KOG1189|consen 741 LEFDVP 746 (960)
T ss_pred eeeccc
Confidence 455555
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=47.24 E-value=50 Score=33.33 Aligned_cols=56 Identities=13% Similarity=0.052 Sum_probs=43.9
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCC--HHHHHHHHhhccCCChHHHHHHHHHHhcCCc
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMS--LQDRAELLSQVGGFSSTEVQDVEMVLQMMPS 108 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~--~~er~~lL~~~~~ls~~~~~~v~~v~~~~P~ 108 (341)
-|+..||++.....++|.+ ++.|+.+|..++ ...+...++ ...+..+...+.-+..
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 5899999999999999998 999999999998 777766654 2345666666665554
No 56
>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=44.13 E-value=19 Score=40.12 Aligned_cols=12 Identities=25% Similarity=0.088 Sum_probs=5.2
Q ss_pred EEEEcCCCcccc
Q 019396 243 CYCLCDSWLGCD 254 (341)
Q Consensus 243 l~v~SDsYlG~D 254 (341)
.--+-|.|.+-|
T Consensus 314 ~ddldD~~~~~d 325 (840)
T PF04147_consen 314 ADDLDDDFEDED 325 (840)
T ss_pred cccccccccccc
Confidence 334445554333
No 57
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=43.35 E-value=32 Score=32.83 Aligned_cols=55 Identities=11% Similarity=0.226 Sum_probs=44.9
Q ss_pred CCcccCCCCCHHHHHHHhcccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019396 47 APFLQLPHFTEAVIKKIARKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 105 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~ 105 (341)
.-|.++|+|++..+..|-.+..||+++.+.+.+++..+ -|+.+..++.+.+++++
T Consensus 195 ~~Lt~i~~VnKtda~~LL~~FgsLq~~~~AS~~ele~~----~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 195 GFLTTIPGVNKTDAQLLLQKFGSLQQISNASEGELEQC----PGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred HHHHhCCCCCcccHHHHHHhcccHHHHHhcCHhHHHhC----cCcCHHHHHHHHHHHhc
Confidence 45778999998777766667889999999998887755 45888999999999875
No 58
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=42.83 E-value=15 Score=35.52 Aligned_cols=21 Identities=14% Similarity=0.140 Sum_probs=9.9
Q ss_pred EEEEEEcCCCcccceEEEEEEEee
Q 019396 241 LTCYCLCDSWLGCDKRTNLKVKIL 264 (341)
Q Consensus 241 l~l~v~SDsYlG~D~~~~i~l~V~ 264 (341)
|...+.|..| |- .+++.+.+.
T Consensus 166 Lm~RLk~G~Y-gd--~yn~~~~~f 186 (303)
T KOG3064|consen 166 LMERLKSGTY-GD--IYNFRQHAF 186 (303)
T ss_pred HHHHHhcCCc-CC--cccchHHHH
Confidence 3445556666 32 444444443
No 59
>PF06514 PsbU: Photosystem II 12 kDa extrinsic protein (PsbU); InterPro: IPR010527 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII extrinsic protein PsbU, which forms part of the OEC in cyanobacteria and red algae. PsbU acts to stabilise the oxygen-evolving machinery of PSII against heat-induced inactivation, which is crucial for cellular thermo-tolerance [].; GO: 0015979 photosynthesis, 0042549 photosystem II stabilization, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 3BZ1_U 3KZI_U 3PRQ_U 2AXT_u 3BZ2_U 4FBY_U 3PRR_U 1S5L_U 3A0H_U 3ARC_U ....
Probab=42.51 E-value=15 Score=30.11 Aligned_cols=49 Identities=14% Similarity=0.264 Sum_probs=31.5
Q ss_pred CCCcccCCCCCHHHHHHHhc--ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 46 TAPFLQLPHFTEAVIKKIAR--KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 46 ~spLlQLPh~~~~~v~kl~~--~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
...++|||+|-+..+.+|.. .-.++.++++++ ||+++|.+-+.+....|
T Consensus 22 vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ip------------gLse~qK~~lk~~~~~F 72 (93)
T PF06514_consen 22 VRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIP------------GLSERQKALLKKYEDNF 72 (93)
T ss_dssp GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCST------------T--HHHHHHHHHHGGGE
T ss_pred HHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhcc------------CCCHHHHHHHHHHhccc
Confidence 45789999999999998876 666777766553 35555555555555544
No 60
>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=42.03 E-value=76 Score=26.61 Aligned_cols=21 Identities=29% Similarity=0.441 Sum_probs=13.4
Q ss_pred EEEEEEcCC---CCceeEEEEEEc
Q 019396 227 VMGKIQAPA---EGNYNLTCYCLC 247 (341)
Q Consensus 227 v~l~F~aP~---~G~~~l~l~v~S 247 (341)
+++.+..|. .|.|.+.|.+.|
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 61
>KOG1834 consensus Calsyntenin [Extracellular structures]
Probab=41.33 E-value=20 Score=38.83 Aligned_cols=9 Identities=22% Similarity=0.062 Sum_probs=5.5
Q ss_pred HHHHHhcCC
Q 019396 25 QSIIQAVPL 33 (341)
Q Consensus 25 QmIvQA~W~ 33 (341)
|.++=|.|.
T Consensus 484 qLvVGACW~ 492 (952)
T KOG1834|consen 484 QLVVGACWQ 492 (952)
T ss_pred eeEEeeecc
Confidence 445567776
No 62
>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=41.31 E-value=20 Score=33.91 Aligned_cols=10 Identities=30% Similarity=-0.017 Sum_probs=3.8
Q ss_pred ccCCCCCccC
Q 019396 276 VSEEGPIVED 285 (341)
Q Consensus 276 ~~~~~~~~~~ 285 (341)
+.|+..+.+.
T Consensus 35 f~Eee~D~ef 44 (240)
T PF05764_consen 35 FQEEEDDEEF 44 (240)
T ss_pred ccccCCCccc
Confidence 3444333333
No 63
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=40.81 E-value=52 Score=28.62 Aligned_cols=48 Identities=19% Similarity=0.331 Sum_probs=32.2
Q ss_pred CCcccCCCCCHHHHHHHhc--ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 47 APFLQLPHFTEAVIKKIAR--KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~--~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
..|.|||++-+..+++|-. ...++.+|..+ .|+++++.+.+.+....|
T Consensus 61 ~el~~lpGigP~~A~~IV~nGpf~sveDL~~V------------~GIgekqk~~l~k~~~~f 110 (132)
T PRK02515 61 RAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNL------------PGLSERQKELLEANLDNF 110 (132)
T ss_pred HHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcC------------CCCCHHHHHHHHHhhcce
Confidence 4578899998888887765 56677766554 356666666666655553
No 64
>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=38.84 E-value=25 Score=27.77 Aligned_cols=34 Identities=18% Similarity=0.404 Sum_probs=24.3
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHH
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQD 80 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~e 80 (341)
..|..||++.....+.+.+ +|.|+.+|..+-..+
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 4689999999999999988 999999998876544
No 65
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=38.11 E-value=49 Score=34.44 Aligned_cols=86 Identities=15% Similarity=0.179 Sum_probs=60.9
Q ss_pred CCHH-HHHHHHHHHHHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhcc
Q 019396 12 GWLR-PAVGVVELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVG 89 (341)
Q Consensus 12 gwL~-~al~~m~L~QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~ 89 (341)
.|.+ -|-.|.-.-||--++.=- ..|+-||++++...+.+.. +|.|+.+|.+.+......+.+...
T Consensus 202 r~~r~rC~~C~f~p~C~~~a~e~-------------~~L~Lv~Gi~~~r~~~l~~~GI~Ti~~LA~~~~~~~~~~~ga~~ 268 (474)
T COG2251 202 RWIRARCTTCQFEPQCESEALEE-------------DDLSLVPGITPSRYDVLEEVGITTIEDLADASLPILELVAGALT 268 (474)
T ss_pred hhhhhhhhHhhcchhhhHHHhhc-------------cceeccCCCCHHHHHHHHHcCcchHHHHHhccccchhhhhhhHH
Confidence 4555 577777778888888632 4588899999998888887 999999999988777665544211
Q ss_pred CCChHHHHHHHHHHhcCCcee
Q 019396 90 GFSSTEVQDVEMVLQMMPSLT 110 (341)
Q Consensus 90 ~ls~~~~~~v~~v~~~~P~I~ 110 (341)
.+..+-..++...+...|.+.
T Consensus 269 ~~~~~l~~qa~~~~e~~~~~~ 289 (474)
T COG2251 269 ALAAQLVLQARARVEGRPLME 289 (474)
T ss_pred HHHHHHHHHHHhhccCCceec
Confidence 123344456666666667665
No 66
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=37.61 E-value=27 Score=37.91 Aligned_cols=16 Identities=13% Similarity=0.071 Sum_probs=8.6
Q ss_pred eEEEEEEcCCCcccce
Q 019396 240 NLTCYCLCDSWLGCDK 255 (341)
Q Consensus 240 ~l~l~v~SDsYlG~D~ 255 (341)
...|.--.||.+.+|-
T Consensus 812 ~V~~~pTtdCLVqL~e 827 (1001)
T COG5406 812 SVMIKPTTDCLVQLDE 827 (1001)
T ss_pred ceeeecchhheeeccC
Confidence 3444444567666653
No 67
>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=37.14 E-value=20 Score=33.91 Aligned_cols=7 Identities=14% Similarity=0.781 Sum_probs=2.6
Q ss_pred CCccccc
Q 019396 302 ESEYSED 308 (341)
Q Consensus 302 ~s~~~~~ 308 (341)
+|+|+++
T Consensus 57 Dsdf~~s 63 (240)
T PF05764_consen 57 DSDFDDS 63 (240)
T ss_pred ccccCcc
Confidence 3333333
No 68
>COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion]
Probab=35.73 E-value=31 Score=36.02 Aligned_cols=39 Identities=3% Similarity=-0.134 Sum_probs=27.9
Q ss_pred EEEEcCC-CCceeEEEEEEcCCCcccceEEEEEEEeeccC
Q 019396 229 GKIQAPA-EGNYNLTCYCLCDSWLGCDKRTNLKVKILKRT 267 (341)
Q Consensus 229 l~F~aP~-~G~~~l~l~v~SDsYlG~D~~~~i~l~V~~~~ 267 (341)
++|++|+ .++..+.+.+++-.|+|.+....|.+-+.+-+
T Consensus 512 i~~dv~pvd~T~~~ql~~~ap~~vg~f~~~~ivm~t~d~~ 551 (610)
T COG5407 512 IQGDVAPVDKTGGKQLIVHAPFMVGAFSVKWIVMLTVDNV 551 (610)
T ss_pred cccccCccccccceeeeecCchhhccceeeeEEEEeechh
Confidence 3444443 56677888888888888888877777666655
No 69
>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=35.65 E-value=26 Score=39.15 Aligned_cols=6 Identities=0% Similarity=0.551 Sum_probs=2.5
Q ss_pred HHHHHh
Q 019396 59 VIKKIA 64 (341)
Q Consensus 59 ~v~kl~ 64 (341)
.+.++.
T Consensus 88 ml~Rf~ 93 (840)
T PF04147_consen 88 MLERFT 93 (840)
T ss_pred HHHHHH
Confidence 444443
No 70
>PF06051 DUF928: Domain of Unknown Function (DUF928); InterPro: IPR010328 This is a family of uncharacterised bacterial proteins.
Probab=35.49 E-value=1.2e+02 Score=27.53 Aligned_cols=32 Identities=16% Similarity=0.141 Sum_probs=20.2
Q ss_pred CC-ceeEEEEEEcCCCc-ccceEEEEEEEeeccC
Q 019396 236 EG-NYNLTCYCLCDSWL-GCDKRTNLKVKILKRT 267 (341)
Q Consensus 236 ~G-~~~l~l~v~SDsYl-G~D~~~~i~l~V~~~~ 267 (341)
+| .|++.+.++||.-- --|..+.-.++...++
T Consensus 89 ~gk~Y~W~~~l~Cd~~~~s~~~~v~G~I~Rv~~~ 122 (189)
T PF06051_consen 89 VGKTYRWYFSLICDPQDRSDDIFVEGWIQRVELS 122 (189)
T ss_pred CCCeEEEEEEEEECCCCCCCCceEEEEEEEeCCC
Confidence 67 49999999998642 2334444455555544
No 71
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=32.57 E-value=30 Score=41.52 Aligned_cols=6 Identities=0% Similarity=0.324 Sum_probs=2.6
Q ss_pred CCeEEE
Q 019396 170 SNNVWF 175 (341)
Q Consensus 170 ~n~Il~ 175 (341)
+|.++.
T Consensus 71 ~g~~y~ 76 (2849)
T PTZ00415 71 NGGIYN 76 (2849)
T ss_pred CCCEEe
Confidence 344443
No 72
>COG1470 Predicted membrane protein [Function unknown]
Probab=31.98 E-value=1e+02 Score=32.38 Aligned_cols=43 Identities=23% Similarity=0.353 Sum_probs=34.4
Q ss_pred CceeEEEEEEcCC---CCceeEEEEEEcCCCcccceEEEEEEEeeccCc
Q 019396 223 GSRLVMGKIQAPA---EGNYNLTCYCLCDSWLGCDKRTNLKVKILKRTR 268 (341)
Q Consensus 223 ~~~~v~l~F~aP~---~G~~~l~l~v~SDsYlG~D~~~~i~l~V~~~~~ 268 (341)
++..|.+.+++|+ +|.|..++..+|| -...+-.+++.|...+.
T Consensus 442 e~~tV~ltI~vP~~a~aGdY~i~i~~ksD---q~s~e~tlrV~V~~sS~ 487 (513)
T COG1470 442 ESKTVSLTITVPEDAGAGDYRITITAKSD---QASSEDTLRVVVGQSST 487 (513)
T ss_pred CcceEEEEEEcCCCCCCCcEEEEEEEeec---cccccceEEEEEecccc
Confidence 4567999999993 8999999999999 45666677777877664
No 73
>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=30.65 E-value=80 Score=26.02 Aligned_cols=18 Identities=28% Similarity=0.495 Sum_probs=14.9
Q ss_pred EEEEcCCCCceeEEEEEE
Q 019396 229 GKIQAPAEGNYNLTCYCL 246 (341)
Q Consensus 229 l~F~aP~~G~~~l~l~v~ 246 (341)
..|++|.+|.|.|.+.++
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 589999999999999999
No 74
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=30.22 E-value=91 Score=31.45 Aligned_cols=57 Identities=19% Similarity=0.339 Sum_probs=45.6
Q ss_pred CCCcccCCCCCHHHHHHHhcccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 46 TAPFLQLPHFTEAVIKKIARKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 46 ~spLlQLPh~~~~~v~kl~~~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
+--|..+|.++..+++.|-....+|+.+++.+.+++.++ .|+.+..+..+.+.+.++
T Consensus 286 yRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~V----eGIGe~rA~~I~e~l~Rl 342 (352)
T PRK13482 286 YRLLSKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEV----EGIGEVRARAIREGLSRL 342 (352)
T ss_pred HHHHhcCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhC----CCcCHHHHHHHHHHHHHH
Confidence 344677999999999988888889999999998887654 468787777787777665
No 75
>COG1470 Predicted membrane protein [Function unknown]
Probab=29.96 E-value=1.2e+02 Score=31.99 Aligned_cols=41 Identities=24% Similarity=0.306 Sum_probs=33.2
Q ss_pred ceeEEEEEEcC---CCCceeEEEEEEcCCCcccceEEEEEEEeecc
Q 019396 224 SRLVMGKIQAP---AEGNYNLTCYCLCDSWLGCDKRTNLKVKILKR 266 (341)
Q Consensus 224 ~~~v~l~F~aP---~~G~~~l~l~v~SDsYlG~D~~~~i~l~V~~~ 266 (341)
++.++++...| .||.|++.+.+.|-+ |.-.+.+|++++.-.
T Consensus 334 ~kdvtleV~ps~na~pG~Ynv~I~A~s~s--~v~~e~~lki~~~g~ 377 (513)
T COG1470 334 EKDVTLEVYPSLNATPGTYNVTITASSSS--GVTRELPLKIKNTGS 377 (513)
T ss_pred ceEEEEEEecCCCCCCCceeEEEEEeccc--cceeeeeEEEEeccc
Confidence 45788888888 399999999999988 777888777776543
No 76
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=29.02 E-value=1e+02 Score=29.65 Aligned_cols=55 Identities=9% Similarity=0.232 Sum_probs=44.3
Q ss_pred cccCCCCCHHHHHHHhcccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCC
Q 019396 49 FLQLPHFTEAVIKKIARKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMP 107 (341)
Q Consensus 49 LlQLPh~~~~~v~kl~~~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~P 107 (341)
|.-||++......++-+...++.++++.+..++.++. |+.++.+.+|.+++...-
T Consensus 184 l~s~pgig~~~a~~ll~~fgS~~~~~tas~~eL~~v~----gig~k~A~~I~~~~~t~~ 238 (254)
T COG1948 184 LESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVK----GIGEKKAREIYRFLRTEY 238 (254)
T ss_pred HHcCCCccHHHHHHHHHHhcCHHHHhhcCHHHHHHhc----CccHHHHHHHHHHHhchh
Confidence 4558999998888877788899999999998877664 478888888888876543
No 77
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.77 E-value=1.7e+02 Score=27.12 Aligned_cols=73 Identities=18% Similarity=0.191 Sum_probs=41.5
Q ss_pred HHHHHHH------HHHHHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc----ccCCHHHHHcC--C-HHHH
Q 019396 15 RPAVGVV------ELSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR----KVRTFQELRDM--S-LQDR 81 (341)
Q Consensus 15 ~~al~~m------~L~QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~----~v~tl~~L~~m--~-~~er 81 (341)
.+|+++| +|.++|..+ +...|.++|++.+.++++|-- ++......... . .+..
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 4567777 555555543 567899999999988887632 33211000000 1 1233
Q ss_pred HHHHhhccCCChHHHHHHHHHH
Q 019396 82 AELLSQVGGFSSTEVQDVEMVL 103 (341)
Q Consensus 82 ~~lL~~~~~ls~~~~~~v~~v~ 103 (341)
..|+. .|+++.++..+.+.+
T Consensus 149 ~AL~~--LGy~~~ea~~al~~v 168 (196)
T PRK13901 149 QSIVN--MGFDRKLVNSAIKEI 168 (196)
T ss_pred HHHHH--cCCCHHHHHHHHHHH
Confidence 34444 788887777665543
No 78
>KOG2393 consensus Transcription initiation factor IIF, large subunit (RAP74) [Transcription]
Probab=28.70 E-value=28 Score=36.78 Aligned_cols=29 Identities=31% Similarity=0.642 Sum_probs=16.8
Q ss_pred cCCCCCcccccccccC-CcCCcccccchhh
Q 019396 284 EDGAEEEEEDEEEEYD-DYESEYSEDEEDE 312 (341)
Q Consensus 284 ~~~~~~~~~~~~~~~~-~~~s~~~~~~~~~ 312 (341)
++.+++..+.+.|+.. ||+++++||||..
T Consensus 281 d~a~eesdd~d~e~~E~DYdee~addEE~P 310 (555)
T KOG2393|consen 281 DEAFEESDDGDNEGRELDYDEESADDEEAP 310 (555)
T ss_pred ccccccCCCccccccccccccccCCccccc
Confidence 3444444444444333 7888888888753
No 79
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.46 E-value=35 Score=35.02 Aligned_cols=36 Identities=22% Similarity=0.358 Sum_probs=20.4
Q ss_pred HHHHHHHHHHhcCCc-eeEEEEEEecCCccccCCCeEEEE
Q 019396 94 TEVQDVEMVLQMMPS-LTVEVTCETEGEEGIQEGDIVTIQ 132 (341)
Q Consensus 94 ~~~~~v~~v~~~~P~-I~I~~~~~v~gE~~It~g~~vtl~ 132 (341)
+|++++++++.++-. +++.-.|. +-.+..|++|.|+
T Consensus 97 ~q~~~l~~~~~n~~~~vkf~~df~---~~s~~~Gd~VeIv 133 (514)
T KOG3130|consen 97 KQIDDLKKVMKNFESRVKFTEDFQ---KMSDAAGDIVEIV 133 (514)
T ss_pred HHHHHHHHHHHhhHHHhhhcccHh---hccCCCCCeehhH
Confidence 677788777777643 33221111 1136778887776
No 80
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=28.24 E-value=32 Score=41.32 Aligned_cols=6 Identities=67% Similarity=1.094 Sum_probs=2.3
Q ss_pred cchhhh
Q 019396 308 DEEDER 313 (341)
Q Consensus 308 ~~~~~~ 313 (341)
|+||++
T Consensus 184 ~de~~~ 189 (2849)
T PTZ00415 184 DDEDEE 189 (2849)
T ss_pred Cchhcc
Confidence 333433
No 81
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=28.20 E-value=79 Score=31.12 Aligned_cols=49 Identities=8% Similarity=0.184 Sum_probs=37.8
Q ss_pred CCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 54 HFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 54 h~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
.++.....-|++ ++.|+++|+.++.+++.++ .++..+-++++.+.+..+
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 355566666666 8999999999999886554 347788888888888765
No 82
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.89 E-value=37 Score=31.14 Aligned_cols=24 Identities=25% Similarity=0.497 Sum_probs=11.2
Q ss_pred CCCCCcccccccccCCcCCccccc
Q 019396 285 DGAEEEEEDEEEEYDDYESEYSED 308 (341)
Q Consensus 285 ~~~~~~~~~~~~~~~~~~s~~~~~ 308 (341)
||..++++++++...|+|-+..|-
T Consensus 194 DDd~d~d~D~eD~~gD~e~~~eds 217 (227)
T KOG3241|consen 194 DDDSDPDSDEEDNVGDDEHDLEDS 217 (227)
T ss_pred ccccCCccccccccCccccccccc
Confidence 334444444444444555555333
No 83
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=27.20 E-value=50 Score=37.63 Aligned_cols=14 Identities=43% Similarity=0.530 Sum_probs=6.5
Q ss_pred CcCCcccccchhhh
Q 019396 300 DYESEYSEDEEDER 313 (341)
Q Consensus 300 ~~~s~~~~~~~~~~ 313 (341)
|+.|+.+|.++++.
T Consensus 909 d~~sd~~e~e~ee~ 922 (1128)
T KOG2051|consen 909 DDGSDEDENEEEEP 922 (1128)
T ss_pred cccccccccccCCC
Confidence 44444444444443
No 84
>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=26.98 E-value=79 Score=25.97 Aligned_cols=57 Identities=23% Similarity=0.356 Sum_probs=45.0
Q ss_pred CCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcCCcee
Q 019396 54 HFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMMPSLT 110 (341)
Q Consensus 54 h~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~P~I~ 110 (341)
-|.+.++.+|.. +|.||.+|.+.-..-+..--+.+.++.......|..++...|...
T Consensus 20 Wf~p~va~~L~aaGi~TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~awLa~h~~~~ 77 (96)
T PF12482_consen 20 WFPPRVARRLAAAGIRTLADLVDRINRRGGRWWRAVPGLGAAGARRIEAWLAAHPALL 77 (96)
T ss_pred hcCHHHHHHHHHcCCchHHHHHHHHHHccchHHHhCcccchHHHHHHHHHHHHhHHHH
Confidence 366889999988 999999999876555435555556788888999999999988764
No 85
>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=26.89 E-value=1.9e+02 Score=29.17 Aligned_cols=57 Identities=12% Similarity=0.099 Sum_probs=42.8
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCC---------------HHHHHHHHhhccCCChHHHHHHHHHHhcCCce
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMS---------------LQDRAELLSQVGGFSSTEVQDVEMVLQMMPSL 109 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~---------------~~er~~lL~~~~~ls~~~~~~v~~v~~~~P~I 109 (341)
.|+.-||++.....++|.+ ++.|+++|..++ ...+...++ ......+...+.-+..-
T Consensus 172 lpv~~l~GiG~~~~~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG------~~~g~~l~~~a~G~d~~ 244 (379)
T cd01703 172 HDLRKIPGIGYKTAAKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFG------EGIGQRIWKLLFGRDTS 244 (379)
T ss_pred CCccccCCcCHHHHHHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHC------HHHHHHHHHHHCCCCCC
Confidence 5899999999999999998 999999999988 555544443 33456666666665543
No 86
>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=26.72 E-value=1.6e+02 Score=21.94 Aligned_cols=32 Identities=16% Similarity=0.190 Sum_probs=23.1
Q ss_pred EEEcCCCCceeEEEEEEcCCCcccceEEEEEEEe
Q 019396 230 KIQAPAEGNYNLTCYCLCDSWLGCDKRTNLKVKI 263 (341)
Q Consensus 230 ~F~aP~~G~~~l~l~v~SDsYlG~D~~~~i~l~V 263 (341)
....+.+|.|.++|.+..+. |+.....+.+.|
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 45566799999999988766 776665555543
No 87
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=25.89 E-value=29 Score=37.99 Aligned_cols=8 Identities=63% Similarity=0.970 Sum_probs=2.9
Q ss_pred cCCCCCcc
Q 019396 284 EDGAEEEE 291 (341)
Q Consensus 284 ~~~~~~~~ 291 (341)
++|.+.+|
T Consensus 210 d~~m~~~E 217 (822)
T KOG2141|consen 210 DDGMEGEE 217 (822)
T ss_pred ccCCcccc
Confidence 33333333
No 88
>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=25.40 E-value=1.1e+02 Score=31.49 Aligned_cols=17 Identities=18% Similarity=0.139 Sum_probs=9.5
Q ss_pred ccceEEEEEEEeeccCc
Q 019396 252 GCDKRTNLKVKILKRTR 268 (341)
Q Consensus 252 G~D~~~~i~l~V~~~~~ 268 (341)
....--.|.+++.+++.
T Consensus 336 ~~~~~d~i~V~~R~p~e 352 (436)
T PF03985_consen 336 REQRPDQITVKHRDPTE 352 (436)
T ss_pred ccCCCceEEEEeCCCCH
Confidence 33434446677766663
No 89
>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=25.34 E-value=97 Score=30.29 Aligned_cols=48 Identities=15% Similarity=0.254 Sum_probs=36.5
Q ss_pred CCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 55 FTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 55 ~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
++-....-|++ ++.|+.+|+.++.+++.++ .+|..+-+++|.+.+..+
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 44555556666 8999999999999886554 347788888888888774
No 90
>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=25.06 E-value=60 Score=24.03 Aligned_cols=17 Identities=35% Similarity=0.618 Sum_probs=14.4
Q ss_pred EEEEEcCCCCceeEEEE
Q 019396 228 MGKIQAPAEGNYNLTCY 244 (341)
Q Consensus 228 ~l~F~aP~~G~~~l~l~ 244 (341)
.+.|.+|.+|+|.+.|+
T Consensus 53 ~i~~~~~~~GtYyi~V~ 69 (70)
T PF04151_consen 53 SITFTAPAAGTYYIRVY 69 (70)
T ss_dssp EEEEEESSSEEEEEEEE
T ss_pred EEEEEcCCCEEEEEEEE
Confidence 37899999999988875
No 91
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=24.40 E-value=1.2e+02 Score=33.33 Aligned_cols=57 Identities=11% Similarity=0.174 Sum_probs=46.0
Q ss_pred CCCcccCCCCCHHHHHHHhcccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhcC
Q 019396 46 TAPFLQLPHFTEAVIKKIARKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQMM 106 (341)
Q Consensus 46 ~spLlQLPh~~~~~v~kl~~~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~~ 106 (341)
.|.|..+|++.+..+++|-+...|+..+...+.+++.++ .|+..+.++.|.+.++++
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~FGSle~I~~AS~eELa~V----~Gig~k~Ae~I~~~L~~~ 692 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAV----PGIGPARAAALHEHLKTL 692 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhc----CCcCHHHHHHHHHHHHHh
Confidence 478899999999888887776779999999888886654 468888888888887654
No 92
>PRK14973 DNA topoisomerase I; Provisional
Probab=23.34 E-value=1.1e+02 Score=34.69 Aligned_cols=66 Identities=15% Similarity=0.079 Sum_probs=50.6
Q ss_pred HHHHHHHhcCCCccCCCCCCCCCCCCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHH-H
Q 019396 23 LSQSIIQAVPLSSRKATGGSTEGTAPFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDV-E 100 (341)
Q Consensus 23 L~QmIvQA~W~~~~~~~~~~~d~~spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v-~ 100 (341)
..+++.+|.-. ....|++.|+|++..++++-+ ++.++++|....++++..+ .|++..-+... .
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 45677777543 245799999999999999877 9999999999999887655 45887766655 3
Q ss_pred HHH
Q 019396 101 MVL 103 (341)
Q Consensus 101 ~v~ 103 (341)
.++
T Consensus 854 ~~~ 856 (936)
T PRK14973 854 LVC 856 (936)
T ss_pred HHH
Confidence 344
No 93
>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=23.13 E-value=43 Score=31.32 Aligned_cols=37 Identities=32% Similarity=0.619 Sum_probs=0.0
Q ss_pred CCCCCccCCCCCcccccccccCCcCCcccccchhhhh
Q 019396 278 EEGPIVEDGAEEEEEDEEEEYDDYESEYSEDEEDERD 314 (341)
Q Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~ 314 (341)
+....++++-++.++++++++++.+.+|.|||+++.+
T Consensus 170 ~~~~~d~~~~~e~~~eeee~eee~dee~~dee~e~~~ 206 (233)
T PF11705_consen 170 EAEDEDEEEEDEEEEEEEEDEEEEDEEFEDEEDEDDD 206 (233)
T ss_pred hcccccccccccccccccccccccccccchhhhccCC
No 94
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=22.34 E-value=47 Score=34.87 Aligned_cols=15 Identities=13% Similarity=0.231 Sum_probs=7.8
Q ss_pred HHHHHHH-hcCCceeE
Q 019396 97 QDVEMVL-QMMPSLTV 111 (341)
Q Consensus 97 ~~v~~v~-~~~P~I~I 111 (341)
..|+..| ..||.+.|
T Consensus 69 l~il~ycreaYPelqi 84 (615)
T KOG3540|consen 69 LLILIYCREAYPELQI 84 (615)
T ss_pred HHHHHHHHHhChHHHH
Confidence 3444455 34676654
No 95
>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair]
Probab=22.16 E-value=1.3e+02 Score=33.76 Aligned_cols=53 Identities=19% Similarity=0.288 Sum_probs=43.5
Q ss_pred CcccCCCCCHHHHHHHhcccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHhc
Q 019396 48 PFLQLPHFTEAVIKKIARKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQM 105 (341)
Q Consensus 48 pLlQLPh~~~~~v~kl~~~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~~ 105 (341)
-|+-+|+|+.-....+..+++++.+|...+-+++..|++ ..+.++.++.+++.
T Consensus 822 fll~lPgVs~~n~~~l~~k~ks~~~La~sS~~el~el~~-----~~~~a~~LYdFi~~ 874 (892)
T KOG0442|consen 822 FLLSLPGVSYINYRNLRHKFKSLKELANSSQEELSELLG-----VHENAKLLYDFIHT 874 (892)
T ss_pred HHhcCCCccHHHHHHHHHHhhHHHHHHhCcHHHHHHHhc-----chHHHHHHHHHHHH
Confidence 367899999888877777899999999999999999987 25667777777753
No 96
>PF14686 fn3_3: Polysaccharide lyase family 4, domain II; PDB: 1NKG_A 2XHN_B 3NJX_A 3NJV_A.
Probab=21.57 E-value=1.4e+02 Score=24.13 Aligned_cols=34 Identities=26% Similarity=0.482 Sum_probs=17.0
Q ss_pred EEEEcC--CCCceeEEEEEEcCCCcccceEEEEEEEee
Q 019396 229 GKIQAP--AEGNYNLTCYCLCDSWLGCDKRTNLKVKIL 264 (341)
Q Consensus 229 l~F~aP--~~G~~~l~l~v~SDsYlG~D~~~~i~l~V~ 264 (341)
..|.+| .||+|.+.+|. +..+|-=....-.+.|.
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 489999 59999999988 55554333323444454
No 97
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=21.56 E-value=1.8e+02 Score=31.23 Aligned_cols=54 Identities=15% Similarity=0.168 Sum_probs=44.6
Q ss_pred CCCcccCCCCCHHHHHHHhcccCCHHHHHcCCHHHHHHHHhhccCCChHHHHHHHHHHh
Q 019396 46 TAPFLQLPHFTEAVIKKIARKVRTFQELRDMSLQDRAELLSQVGGFSSTEVQDVEMVLQ 104 (341)
Q Consensus 46 ~spLlQLPh~~~~~v~kl~~~v~tl~~L~~m~~~er~~lL~~~~~ls~~~~~~v~~v~~ 104 (341)
.|.|.++|++.+...++|=+.-.|+..+...+.+++.++ + ++.+.++.|.+.++
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~As~eeL~~v-g----i~~~~A~~I~~~l~ 566 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIYRNFKTLYDFLKADDEELKKL-G----IPPSVKQEVKKYLS 566 (567)
T ss_pred cCccccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHHc-C----CCHHHHHHHHHHhc
Confidence 589999999999888777667789999999999998765 3 78888888877663
No 98
>PHA02608 67 prohead core protein; Provisional
Probab=21.54 E-value=48 Score=26.29 Aligned_cols=10 Identities=50% Similarity=0.428 Sum_probs=4.4
Q ss_pred ccCCCCCccC
Q 019396 276 VSEEGPIVED 285 (341)
Q Consensus 276 ~~~~~~~~~~ 285 (341)
|-.+|+..++
T Consensus 43 v~iEGEe~ed 52 (80)
T PHA02608 43 VMIEGEEPED 52 (80)
T ss_pred HhhcCCCCcc
Confidence 4445544433
No 99
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=21.35 E-value=51 Score=33.63 Aligned_cols=39 Identities=38% Similarity=0.540 Sum_probs=0.0
Q ss_pred CCCCccCCCCCccccc---ccccCCcCCcccccchhhhhhcc
Q 019396 279 EGPIVEDGAEEEEEDE---EEEYDDYESEYSEDEEDERDTKK 317 (341)
Q Consensus 279 ~~~~~~~~~~~~~~~~---~~~~~~~~s~~~~~~~~~~~~~~ 317 (341)
+..+..|+.+.+||++ .++.|-|.||+.++|||+.+..+
T Consensus 259 sS~d~~D~a~~EEeD~~k~~d~sd~~sse~~eneed~Ded~e 300 (542)
T KOG0699|consen 259 SSSDGVDGAATEEEDEVKSPDDSDAESSEFVENEEDDDEDAE 300 (542)
T ss_pred CcccccccccccccccccCCcccccccchhcccccccccccc
No 100
>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=21.25 E-value=1.5e+02 Score=28.58 Aligned_cols=39 Identities=18% Similarity=0.310 Sum_probs=32.5
Q ss_pred CCcccCCCCCHHHHHHHhc-ccCCHHHHHcCCHHHHHHHHh
Q 019396 47 APFLQLPHFTEAVIKKIAR-KVRTFQELRDMSLQDRAELLS 86 (341)
Q Consensus 47 spLlQLPh~~~~~v~kl~~-~v~tl~~L~~m~~~er~~lL~ 86 (341)
.|+ .+|++...+..+|.+ ++.|+.+|.+++...+...++
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 478899999999988 999999999999887766654
No 101
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=21.19 E-value=51 Score=38.54 Aligned_cols=37 Identities=24% Similarity=0.617 Sum_probs=0.0
Q ss_pred CCCCccCCCCCcccccccccCCcCCcccccchhhhhh
Q 019396 279 EGPIVEDGAEEEEEDEEEEYDDYESEYSEDEEDERDT 315 (341)
Q Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~ 315 (341)
+|+.+-+...-|+++||.++||.|-|..+|++|+.++
T Consensus 1727 ~~ef~GEed~~Dddnddddddd~EaEdddDddDdDde 1763 (3015)
T KOG0943|consen 1727 EGEFAGEEDHHDDDNDDDDDDDAEAEDDDDDDDDDDE 1763 (3015)
T ss_pred cccccCcccccccccccccccchhhcccccccccccc
No 102
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=20.66 E-value=87 Score=31.37 Aligned_cols=17 Identities=24% Similarity=0.462 Sum_probs=8.3
Q ss_pred cccccCCcCCcccccch
Q 019396 294 EEEEYDDYESEYSEDEE 310 (341)
Q Consensus 294 ~~~~~~~~~s~~~~~~~ 310 (341)
+.++||+++|-|+|+.+
T Consensus 294 ~~~~~~~~~~~~~~~~~ 310 (337)
T PTZ00007 294 DYDSYDSSDSASSDSNS 310 (337)
T ss_pred Ccccccccccccccccc
Confidence 33445555555555433
No 103
>PF07705 CARDB: CARDB; InterPro: IPR011635 The APHP (acidic peptide-dependent hydrolases/peptidase) domain is found in a variety of different proteins.; PDB: 2KUT_A 2L0D_A 3IDU_A 2KL6_A.
Probab=20.20 E-value=1.4e+02 Score=22.80 Aligned_cols=26 Identities=19% Similarity=0.169 Sum_probs=16.7
Q ss_pred eeEEEEEEcCCCCceeEEEEEEcCCC
Q 019396 225 RLVMGKIQAPAEGNYNLTCYCLCDSW 250 (341)
Q Consensus 225 ~~v~l~F~aP~~G~~~l~l~v~SDsY 250 (341)
..+.+.+.+|.+|.|.+++.+=.+..
T Consensus 63 ~~v~~~~~~~~~G~~~i~~~iD~~n~ 88 (101)
T PF07705_consen 63 ETVTFTWTPPSPGSYTIRVVIDPDND 88 (101)
T ss_dssp EEEEEEEE-SS-CEEEEEEEESTTTS
T ss_pred EEEEEEEEeCCCCeEEEEEEEeeCCc
Confidence 45677777778998887777754443
Done!