Query 033358
Match_columns 121
No_of_seqs 64 out of 66
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 12:55:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033358.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033358hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11347 DUF3148: Protein of u 100.0 1.6E-43 3.4E-48 239.5 7.0 63 51-114 1-63 (63)
2 PF04319 NifZ: NifZ domain; I 85.6 1.5 3.3E-05 30.6 3.9 53 47-102 2-58 (75)
3 TIGR02768 TraA_Ti Ti-type conj 70.5 10 0.00023 34.8 5.6 58 47-119 605-663 (744)
4 COG2139 RPL21A Ribosomal prote 66.5 7.9 0.00017 28.7 3.2 53 43-105 26-78 (98)
5 TIGR01448 recD_rel helicase, p 61.1 16 0.00034 33.6 4.8 58 47-118 584-646 (720)
6 PRK13826 Dtr system oriT relax 60.0 19 0.00042 35.4 5.4 56 48-118 632-691 (1102)
7 PF11910 NdhO: Cyanobacterial 59.7 10 0.00022 26.5 2.6 52 50-105 1-53 (67)
8 PRK02749 photosystem I reactio 57.4 25 0.00054 24.9 4.2 43 49-108 2-47 (71)
9 PF13473 Cupredoxin_1: Cupredo 57.3 20 0.00044 24.2 3.8 57 45-112 34-93 (104)
10 PF02211 NHase_beta: Nitrile h 55.5 19 0.00041 29.2 3.9 40 45-93 130-169 (222)
11 PRK13889 conjugal transfer rel 52.1 31 0.00068 33.5 5.4 55 48-118 599-655 (988)
12 PRK12281 rplX 50S ribosomal pr 49.1 40 0.00086 23.1 4.2 34 47-99 4-37 (76)
13 PF07653 SH3_2: Variant SH3 do 48.4 55 0.0012 19.8 4.4 35 82-116 19-54 (55)
14 PRK00004 rplX 50S ribosomal pr 46.0 46 0.00099 23.9 4.3 35 46-99 1-35 (105)
15 CHL00141 rpl24 ribosomal prote 44.6 52 0.0011 22.9 4.2 36 45-99 4-39 (83)
16 PF12634 Inp1: Inheritance of 43.8 22 0.00048 27.2 2.5 42 62-104 75-121 (145)
17 PRK04306 50S ribosomal protein 42.5 68 0.0015 23.4 4.7 52 43-104 28-79 (98)
18 PRK10691 hypothetical protein; 39.1 26 0.00057 27.5 2.3 30 73-103 181-210 (219)
19 cd08988 GH43_ABN Glycosyl hydr 38.0 35 0.00076 26.8 2.9 39 70-109 20-71 (279)
20 COG0186 RpsQ Ribosomal protein 37.9 24 0.00051 25.4 1.8 21 48-68 54-74 (87)
21 PRK08572 rps17p 30S ribosomal 37.8 24 0.00053 26.1 1.9 20 49-68 77-96 (108)
22 KOG3172 Small nuclear ribonucl 37.5 18 0.00039 27.6 1.2 28 45-75 57-84 (119)
23 PRK05610 rpsQ 30S ribosomal pr 37.4 25 0.00055 24.6 1.8 19 49-67 53-71 (84)
24 TIGR01079 rplX_bact ribosomal 37.1 75 0.0016 22.9 4.2 33 48-99 2-34 (104)
25 PF08605 Rad9_Rad53_bind: Fung 36.6 46 0.001 25.1 3.2 33 87-119 27-60 (131)
26 TIGR03635 S17_bact 30S ribosom 36.4 28 0.0006 23.7 1.8 19 49-67 48-66 (71)
27 PF02427 PSI_PsaE: Photosystem 36.2 93 0.002 21.4 4.3 32 74-107 10-44 (61)
28 CHL00142 rps17 ribosomal prote 35.8 28 0.00061 24.5 1.8 19 49-67 50-68 (84)
29 TIGR02303 HpaG-C-term 4-hydrox 34.6 32 0.0007 27.6 2.2 30 73-103 204-233 (245)
30 smart00739 KOW KOW (Kyprides, 34.0 34 0.00075 17.7 1.6 12 50-61 2-13 (28)
31 TIGR03630 arch_S17P archaeal r 32.2 34 0.00074 25.2 1.9 21 48-68 74-94 (102)
32 smart00326 SH3 Src homology 3 31.7 97 0.0021 17.2 3.8 23 94-116 34-57 (58)
33 TIGR03220 catechol_dmpE 2-oxop 30.2 45 0.00097 26.6 2.4 30 73-103 217-246 (255)
34 PRK00409 recombination and DNA 28.5 1.1E+02 0.0025 28.6 5.0 47 48-116 635-681 (782)
35 cd00174 SH3 Src homology 3 dom 26.5 1.2E+02 0.0026 16.6 4.3 22 94-115 31-53 (54)
36 PRK02654 putative inner membra 25.0 37 0.0008 30.2 1.1 53 45-97 168-232 (375)
37 TIGR03096 nitroso_cyanin nitro 25.0 2E+02 0.0044 21.9 5.0 61 43-114 58-121 (135)
38 TIGR02305 HpaG-N-term 4-hydrox 24.9 62 0.0013 24.8 2.2 31 71-103 166-196 (205)
39 COG1018 Hmp Flavodoxin reducta 24.2 91 0.002 25.3 3.2 30 27-58 67-96 (266)
40 PF00366 Ribosomal_S17: Riboso 24.0 44 0.00096 22.3 1.1 18 50-67 44-61 (69)
41 TIGR01447 recD exodeoxyribonuc 23.1 1.7E+02 0.0037 26.6 4.9 55 48-118 463-519 (586)
42 PF10006 DUF2249: Uncharacteri 23.1 96 0.0021 19.8 2.6 50 45-104 18-69 (69)
43 COG0806 RimM RimM protein, req 22.9 88 0.0019 24.5 2.8 35 85-119 121-159 (174)
44 PRK11342 mhpD 2-keto-4-penteno 22.3 75 0.0016 25.4 2.3 30 73-103 221-250 (262)
45 cd09002 GH43_XYL_3 Glycosyl hy 22.3 88 0.0019 24.7 2.7 40 69-109 38-79 (280)
46 TIGR02227 sigpep_I_bact signal 21.8 3.3E+02 0.0072 20.0 5.5 27 86-115 71-97 (163)
47 cd06529 S24_LexA-like Peptidas 21.7 1.2E+02 0.0026 18.7 2.7 13 47-59 11-23 (81)
48 PRK10875 recD exonuclease V su 21.7 2.1E+02 0.0046 26.3 5.3 42 47-103 478-519 (615)
49 cd04508 TUDOR Tudor domains ar 21.5 1.3E+02 0.0029 17.2 2.7 19 86-104 16-34 (48)
50 PF04596 Pox_F15: Poxvirus pro 21.2 59 0.0013 25.4 1.5 19 86-104 117-135 (136)
51 PF12139 APS-reductase_C: Aden 21.2 1.1E+02 0.0023 22.2 2.7 32 75-106 2-33 (83)
52 KOG2904 Predicted methyltransf 20.9 60 0.0013 28.5 1.6 26 50-76 218-243 (328)
53 PRK13618 psbV cytochrome c-550 20.9 43 0.00093 26.2 0.7 17 59-75 115-131 (163)
54 KOG0439 VAMP-associated protei 20.7 75 0.0016 24.0 1.9 26 67-92 48-73 (218)
55 PF00845 Gemini_BL1: Geminivir 20.7 51 0.0011 28.3 1.1 16 90-105 189-204 (276)
56 COG3650 Predicted membrane pro 20.3 66 0.0014 25.5 1.6 16 95-110 55-70 (149)
57 PRK01191 rpl24p 50S ribosomal 20.1 95 0.0021 23.4 2.3 36 43-97 39-74 (120)
58 PF01176 eIF-1a: Translation i 20.1 2.4E+02 0.0052 18.1 4.0 24 85-108 5-28 (65)
No 1
>PF11347 DUF3148: Protein of unknown function (DUF3148); InterPro: IPR021495 This family of proteins has no known function.
Probab=100.00 E-value=1.6e-43 Score=239.53 Aligned_cols=63 Identities=52% Similarity=0.936 Sum_probs=61.6
Q ss_pred ccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEEEEEcceeEEeeCCcc
Q 033358 51 AIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWAVRLSIGTYLLEGKYF 114 (121)
Q Consensus 51 ~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~rGtFLid~~yl 114 (121)
+|||+|+|+++|||||||||||||||| |||++||+|+|++|||+|||+|||++||||||+|||
T Consensus 1 ~iG~~V~l~~~ppylKTAdpMPmLRp~-dlv~~ge~G~i~~rrp~~~w~VRf~~GtfLid~~yl 63 (63)
T PF11347_consen 1 SIGDKVRLIEAPPYLKTADPMPMLRPP-DLVKIGEVGRIVDRRPGDYWAVRFRRGTFLIDSKYL 63 (63)
T ss_pred CCCCeEEEeecCCceeccCCccccCCc-CccccCCcEEEEEecCCCEEEEEEeceeEeeccccC
Confidence 589999999999999999999999995 999999999999999999999999999999999997
No 2
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=85.59 E-value=1.5 Score=30.63 Aligned_cols=53 Identities=23% Similarity=0.353 Sum_probs=40.6
Q ss_pred ccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeec----CCCEEEEEE
Q 033358 47 RSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRK----PKDVWAVRL 102 (121)
Q Consensus 47 ~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rr----P~d~waVRF 102 (121)
..+|..|++|+.... |+---.+|-..+-.=|++.|++|.|+++- -.-.++|+|
T Consensus 2 ~p~f~~G~~V~a~~~---irNDGt~Pg~~~g~lLv~~G~~G~V~~iG~flq~~~IY~V~F 58 (75)
T PF04319_consen 2 PPRFEWGDKVRARKD---IRNDGTFPGKEIGELLVRKGDVGYVVSIGTFLQDFYIYLVHF 58 (75)
T ss_pred CCccCCCCEEEEEEE---eEcCCCCCCCCCCCEEEcCCCcEEEEEeeEEcceeEEEEEEE
Confidence 457999999998764 56666999988877789999999999752 111467777
No 3
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Probab=70.54 E-value=10 Score=34.85 Aligned_cols=58 Identities=21% Similarity=0.312 Sum_probs=41.6
Q ss_pred ccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEEEEEccee-EEeeCCccccCCC
Q 033358 47 RSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWAVRLSIGT-YLLEGKYFKPLEL 119 (121)
Q Consensus 47 ~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~rGt-FLid~~yl~~~~~ 119 (121)
...|.+||+|+...--+= .=|.-||.|+|++... +...|+|..|. ..++.+.+..++.
T Consensus 605 ~~~~~~GDrV~~~~N~~~--------------~gv~NGd~g~V~~i~~-~~i~v~~~~G~~v~~~~~~~~~l~l 663 (744)
T TIGR02768 605 ERKFAAGDRIVFLENNRD--------------LGVKNGMLGTVEEIED-GRLVVQLDSGELVIIPQAEYDALDH 663 (744)
T ss_pred CceecCCCEEEEEecccc--------------cCCcCCCEEEEEEecC-CeEEEEECCCCEEEECHHHhCccCc
Confidence 358999999998765321 1267899999999974 67889998764 4566555655543
No 4
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=66.50 E-value=7.9 Score=28.69 Aligned_cols=53 Identities=19% Similarity=0.276 Sum_probs=41.2
Q ss_pred ccccccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEEEEEcce
Q 033358 43 SDIRRSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWAVRLSIG 105 (121)
Q Consensus 43 ~~~~~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~rG 105 (121)
.+..-.+|++||.|-|.--|.+-|. ||-=|= -|-.|+|++.+..-| .|...-|
T Consensus 26 lsr~l~ey~~Gd~V~I~IdpSv~kG---mPh~rf------~G~TG~Vvg~~g~ay-~V~v~~G 78 (98)
T COG2139 26 LSRYLQEYKVGDKVHIDIDPSVHKG---MPHPRF------QGKTGTVVGVRGRAY-KVEVYDG 78 (98)
T ss_pred hhhHHhhccCCCEEEEEeCcccccC---CCCccc------cCcceEEEeccCCEE-EEEEecC
Confidence 4577799999999999999999998 776444 488999999886544 4444444
No 5
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=61.06 E-value=16 Score=33.61 Aligned_cols=58 Identities=17% Similarity=0.137 Sum_probs=41.4
Q ss_pred ccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCC-----CEEEEEEcceeEEeeCCccccCC
Q 033358 47 RSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPK-----DVWAVRLSIGTYLLEGKYFKPLE 118 (121)
Q Consensus 47 ~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~-----d~waVRF~rGtFLid~~yl~~~~ 118 (121)
...|.+||+|..+.--+= .=|.-||.|+|++..+. +...|+|.-...-++.+.+..++
T Consensus 584 ~~~~~~GDkVm~~~N~~~--------------~~v~NGdiG~I~~i~~~~~~~~~~i~v~f~g~~v~~~~~~~~~l~ 646 (720)
T TIGR01448 584 EGEYRKGDRVMQTKNDYN--------------NEIFNGDLGMIVKIEGAKQGKKDQVVVDFDGNEVELTRAELFNLT 646 (720)
T ss_pred CceecCCCEEEEeeecch--------------hccccCCeeEEEeccccccCCCceEEEEECCeEEEEcHHHhhhhh
Confidence 467999999998765421 13678999999998764 35779997666666666655544
No 6
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=59.97 E-value=19 Score=35.41 Aligned_cols=56 Identities=18% Similarity=0.453 Sum_probs=40.5
Q ss_pred cccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEEEEEcce----eEEeeCCccccCC
Q 033358 48 SKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWAVRLSIG----TYLLEGKYFKPLE 118 (121)
Q Consensus 48 ~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~rG----tFLid~~yl~~~~ 118 (121)
..|.+||+|++..--. - -=|.-||.|+|++..+ +...|+|..| ...++.+++..++
T Consensus 632 r~f~vGDrV~f~rNd~------------~--lgV~NGd~GtV~~i~~-~~i~v~~d~g~~~r~V~~~~~~~~~ld 691 (1102)
T PRK13826 632 RRFAAGDQIVFLKNEG------------S--LGVKNGMIGKVVEAAP-NRIVAEIGEGEHRRQVTVEQRFYNNLD 691 (1102)
T ss_pred ccccCCCEEEEeeecC------------c--cCccCCCeEEEEEecC-CeEEEEEcCCCCceEEEechhhccchh
Confidence 5799999999865421 0 1278899999999976 5568899776 5667766665544
No 7
>PF11910 NdhO: Cyanobacterial and plant NDH-1 subunit O; InterPro: IPR020905 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit O. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0005886 plasma membrane
Probab=59.65 E-value=10 Score=26.55 Aligned_cols=52 Identities=23% Similarity=0.202 Sum_probs=33.6
Q ss_pred cccCCcEEEEecCCceecCCcc-ccccCCCCccCCCCeeeEeeecCCCEEEEEEcce
Q 033358 50 LAIGSPVIVIEAPKMIKTAASV-PCLRANSGLVKPGDVGRIISRKPKDVWAVRLSIG 105 (121)
Q Consensus 50 ~~IG~~Vrli~~ppYLKTAdpM-PMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~rG 105 (121)
++.|+-||++.. .|..+-+.- -==||| +-+ -+.-|+|++.+ +||--|||++=
T Consensus 1 lKKG~lVrv~re-~~~nSlEa~ASD~~~P-~Yi-fe~~GEvl~ik-gdYa~vr~~~P 53 (67)
T PF11910_consen 1 LKKGSLVRVNRE-KYENSLEAKASDPRPP-SYI-FEGPGEVLDIK-GDYAQVRFRVP 53 (67)
T ss_pred CCcceEEEeehH-hhcCchhhhhcCCCCC-cce-ecCCCeEEEec-CCEEEEEecCC
Confidence 356777777643 455544322 122564 333 35679999999 99999999764
No 8
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=57.43 E-value=25 Score=24.86 Aligned_cols=43 Identities=23% Similarity=0.279 Sum_probs=31.5
Q ss_pred ccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCE---EEEEEcceeEE
Q 033358 49 KLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDV---WAVRLSIGTYL 108 (121)
Q Consensus 49 ~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~---waVRF~rGtFL 108 (121)
-++-||+||| ||| .-.=-.|+|+|++..-.+. ..|||.+=.|-
T Consensus 2 ~i~rGskVrI---------------lR~--ESYWyn~vGtV~svD~sgi~YPV~VRF~kvNY~ 47 (71)
T PRK02749 2 AISRGDKVRI---------------LRP--ESYWYNEVGTVASVDKSGIKYPVIVRFDKVNYN 47 (71)
T ss_pred ccccCCEEEE---------------ccc--cceeecCcceEEEEccCCCeeeEEEEeeeeecc
Confidence 3567888887 555 3445679999999887763 57999987775
No 9
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=57.26 E-value=20 Score=24.19 Aligned_cols=57 Identities=19% Similarity=0.200 Sum_probs=35.9
Q ss_pred ccccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEEEEE---cceeEEeeCC
Q 033358 45 IRRSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWAVRL---SIGTYLLEGK 112 (121)
Q Consensus 45 ~~~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF---~rGtFLid~~ 112 (121)
+..-+++.|++|+|. ++-.|..+ .-+.+.+.+.-..+.|++.+.+.| ..|+|-+--.
T Consensus 34 P~~i~v~~G~~v~l~-----~~N~~~~~------h~~~i~~~~~~~~l~~g~~~~~~f~~~~~G~y~~~C~ 93 (104)
T PF13473_consen 34 PSTITVKAGQPVTLT-----FTNNDSRP------HEFVIPDLGISKVLPPGETATVTFTPLKPGEYEFYCT 93 (104)
T ss_dssp S-EEEEETTCEEEEE-----EEE-SSS-------EEEEEGGGTEEEEE-TT-EEEEEEEE-S-EEEEEB-S
T ss_pred cCEEEEcCCCeEEEE-----EEECCCCc------EEEEECCCceEEEECCCCEEEEEEcCCCCEEEEEEcC
Confidence 456778999987765 33344443 223455577778999999999999 8899976443
No 10
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=55.53 E-value=19 Score=29.19 Aligned_cols=40 Identities=23% Similarity=0.189 Sum_probs=19.3
Q ss_pred ccccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeec
Q 033358 45 IRRSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRK 93 (121)
Q Consensus 45 ~~~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rr 93 (121)
....+|++||+|++...+|---|--|. .--|-.|+|+..+
T Consensus 130 ~~~~~F~vGd~Vrv~~~~~~~HtR~P~---------Y~rg~~G~I~~~~ 169 (222)
T PF02211_consen 130 DAPPRFAVGDRVRVRNLPPPGHTRLPR---------YVRGKTGTIERVH 169 (222)
T ss_dssp SSS-SS-TT-EEEE-----SS--SS-G---------GGTT-EEEEEEEE
T ss_pred CCCCCCCCCCEEEECCCCCCCcccccH---------hhCCCeeEEEEEe
Confidence 457899999999999888764333222 3357789988543
No 11
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=52.12 E-value=31 Score=33.51 Aligned_cols=55 Identities=27% Similarity=0.461 Sum_probs=38.8
Q ss_pred cccccCCcEEEEecCCceecCCccccccCCCCc-cCCCCeeeEeeecCCCEEEEEEccee-EEeeCCccccCC
Q 033358 48 SKLAIGSPVIVIEAPKMIKTAASVPCLRANSGL-VKPGDVGRIISRKPKDVWAVRLSIGT-YLLEGKYFKPLE 118 (121)
Q Consensus 48 ~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dL-V~~gE~G~Iv~rrP~d~waVRF~rGt-FLid~~yl~~~~ 118 (121)
..|.+||+|+...--+ ++ |.-||.|+|+++.+ +...|+|..|. .-++.+.+..++
T Consensus 599 r~~~vGDrVm~~rNd~---------------~lgV~NGd~GtV~~I~~-~~i~V~~d~gr~V~~~~~~~~~ld 655 (988)
T PRK13889 599 RSFASGDRVMFLQNER---------------GLGVKNGTLGTIEQVSA-QSMSVRLDDGRSVAFDLKDYDRID 655 (988)
T ss_pred ccccCCCEEEEeecCC---------------cCCEeCCCeEEEEEecC-CeEEEEECCCeEEEecHHHcCccc
Confidence 4689999999866421 22 78899999999987 46789997653 445555454444
No 12
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=49.06 E-value=40 Score=23.13 Aligned_cols=34 Identities=26% Similarity=0.424 Sum_probs=27.0
Q ss_pred ccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEE
Q 033358 47 RSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWA 99 (121)
Q Consensus 47 ~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~wa 99 (121)
++.+..||.|.+++-+ .-|-+|+|+..-+...|.
T Consensus 4 ~~~I~kGD~V~Vi~G~-------------------dKGK~G~V~~V~~~~~~V 37 (76)
T PRK12281 4 KLKVKKGDMVKVIAGD-------------------DKGKTGKVLAVLPKKNRV 37 (76)
T ss_pred cccccCCCEEEEeEcC-------------------CCCcEEEEEEEEcCCCEE
Confidence 4678899999998764 348899999998887764
No 13
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=48.41 E-value=55 Score=19.81 Aligned_cols=35 Identities=17% Similarity=0.268 Sum_probs=22.6
Q ss_pred CCCCeeeEe-eecCCCEEEEEEcceeEEeeCCcccc
Q 033358 82 KPGDVGRII-SRKPKDVWAVRLSIGTYLLEGKYFKP 116 (121)
Q Consensus 82 ~~gE~G~Iv-~rrP~d~waVRF~rGtFLid~~yl~~ 116 (121)
+.||+=.|+ +..+.+.|-++...=.=+++.+|+++
T Consensus 19 ~~Gd~i~v~~~~~~~~ww~~~~~g~~G~~P~~~v~~ 54 (55)
T PF07653_consen 19 KKGDVIEVLGEKDDDGWWLGENNGRRGWFPSSYVEE 54 (55)
T ss_dssp -TTEEEEEEEEECSTSEEEEEETTEEEEEEGGGEEE
T ss_pred ecCCEEEEEEeecCCCEEEEEECCcEEEEcHHHEEE
Confidence 345555555 66778999998843344777777765
No 14
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=46.01 E-value=46 Score=23.90 Aligned_cols=35 Identities=29% Similarity=0.406 Sum_probs=27.2
Q ss_pred cccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEE
Q 033358 46 RRSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWA 99 (121)
Q Consensus 46 ~~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~wa 99 (121)
+++.+..||.|.++.-+ .-|-.|+|+..-+...|.
T Consensus 1 ~~~~i~kGD~V~Vi~G~-------------------dKGk~G~V~~V~~~~~~V 35 (105)
T PRK00004 1 MMMKIKKGDTVIVIAGK-------------------DKGKRGKVLKVLPKKNKV 35 (105)
T ss_pred CCCcccCCCEEEEeEcC-------------------CCCcEEEEEEEEcCCCEE
Confidence 35678899999998765 248889999988877764
No 15
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=44.58 E-value=52 Score=22.86 Aligned_cols=36 Identities=19% Similarity=0.378 Sum_probs=28.7
Q ss_pred ccccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEE
Q 033358 45 IRRSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWA 99 (121)
Q Consensus 45 ~~~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~wa 99 (121)
.+++.+..||.|.+++-+ .-|-.|.|+..-+...|.
T Consensus 4 ~~~~~I~~GD~V~Vi~G~-------------------dKGK~G~V~~V~~~~~~V 39 (83)
T CHL00141 4 KKKMHVKIGDTVKIISGS-------------------DKGKIGEVLKIIKKSNKV 39 (83)
T ss_pred ceeCcccCCCEEEEeEcC-------------------CCCcEEEEEEEEcCCCEE
Confidence 567789999999998764 238899999998877664
No 16
>PF12634 Inp1: Inheritance of peroxisomes protein 1; InterPro: IPR024758 Inp1 is a peroxisomal membrane protein that binds Pex25p, Pex30p, and Vps1p, all of which are involved in controlling peroxisome division. The levels of Inp1p vary with the cell cycle, and Inp1 acts as a factor that retains peroxisomes in cells and controls peroxisome division []. Inp1p promotes the retention of peroxisomes in mother cells and buds of budding yeast by attaching peroxisomes to as-yet-unidentified cortical structures [].; GO: 0045033 peroxisome inheritance, 0005780 extrinsic to intraperoxisomal membrane
Probab=43.77 E-value=22 Score=27.17 Aligned_cols=42 Identities=7% Similarity=0.209 Sum_probs=30.4
Q ss_pred CCceecC-C-ccccccCCCCccCCCCeee--EeeecCCC-EEEEEEcc
Q 033358 62 PKMIKTA-A-SVPCLRANSGLVKPGDVGR--IISRKPKD-VWAVRLSI 104 (121)
Q Consensus 62 ppYLKTA-d-pMPMLRPp~dLV~~gE~G~--Iv~rrP~d-~waVRF~r 104 (121)
-.||+-- . ==|+| |..-+..+|+.+. |+..+... ||.|.|--
T Consensus 75 v~fLs~G~~~v~PiL-PK~q~~~vd~~~~kFvl~~~nPerYwrIe~~~ 121 (145)
T PF12634_consen 75 VAFLSCGGSIVHPIL-PKLQCWRVDGESSKFVLPIRNPERYWRIEFLS 121 (145)
T ss_pred eeeeecCchheeccc-ccccEEEEcCCCcEEEEEcCCCCcEEEEEecC
Confidence 4688887 3 34777 7778888988775 66655555 99999854
No 17
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=42.47 E-value=68 Score=23.42 Aligned_cols=52 Identities=17% Similarity=0.340 Sum_probs=40.9
Q ss_pred ccccccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEEEEEcc
Q 033358 43 SDIRRSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWAVRLSI 104 (121)
Q Consensus 43 ~~~~~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~r 104 (121)
.+....+|++||.|-|.--|.+-|. ||-=|= =|-.|+|...++. -|+|....
T Consensus 28 ls~~l~~y~~Gd~V~I~~d~sv~kG---mPh~~y------hGkTG~V~~v~~~-A~~V~v~v 79 (98)
T PRK04306 28 LSRALQEFEEGDKVHIVIDPSVHKG---MPHPRF------HGKTGTVVGKRGR-AYIVEVKD 79 (98)
T ss_pred HHHHHHhccCCCEEEEEecCceecC---Cccccc------cCCCEEEEeecCe-EEEEEEEE
Confidence 4466788999999999999999996 765333 4889999999887 56666543
No 18
>PRK10691 hypothetical protein; Provisional
Probab=39.12 E-value=26 Score=27.47 Aligned_cols=30 Identities=23% Similarity=0.265 Sum_probs=27.4
Q ss_pred cccCCCCccCCCCeeeEeeecCCCEEEEEEc
Q 033358 73 CLRANSGLVKPGDVGRIISRKPKDVWAVRLS 103 (121)
Q Consensus 73 MLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~ 103 (121)
-|+|. |+|-.|=.+.+...+|||.+.++|.
T Consensus 181 tL~aG-DvI~TGTp~g~~~l~~GD~v~~~i~ 210 (219)
T PRK10691 181 TLRAG-DVVLTGTPEGVGPLQSGDELTVTFN 210 (219)
T ss_pred ccCCC-CEEEcCCCCCCEECCCCCEEEEEEe
Confidence 68896 9999999999999999999999984
No 19
>cd08988 GH43_ABN Glycosyl hydrolase family 43. This glycosyl hydrolase family 43 (GH43) includes mostly enzymes with alpha-L-arabinofuranosidase (AFN; EC 3.2.1.55) and endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages while the ABF enzymes cleave arabinose side chains so that the combined actions of these two enzymes reduce arabinan to L-arabinose and/or arabinooligosaccharides. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bla
Probab=37.96 E-value=35 Score=26.76 Aligned_cols=39 Identities=23% Similarity=0.455 Sum_probs=32.2
Q ss_pred ccccccCCCCccCCCCeeeEeeecC-----------CCEEE--EEEcceeEEe
Q 033358 70 SVPCLRANSGLVKPGDVGRIISRKP-----------KDVWA--VRLSIGTYLL 109 (121)
Q Consensus 70 pMPMLRPp~dLV~~gE~G~Iv~rrP-----------~d~wa--VRF~rGtFLi 109 (121)
-+|+++-. ||+.=..+|.++...| ++.|| |+...|.|.|
T Consensus 20 g~~v~~S~-DL~~W~~~g~~~~~~~~~~~~~~~~~~~~~WAP~v~~~~G~yyl 71 (279)
T cd08988 20 GITILSSK-DLVNWTYSGSAFATEPTWKKRVPPSFDGHLWAPDIYQHNGKFYL 71 (279)
T ss_pred CEEEEECC-CcCCccccCccccCCCccccccCCCCCCCEecceEEEECCEEEE
Confidence 58999994 9999999999987433 47898 8888899887
No 20
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=37.93 E-value=24 Score=25.45 Aligned_cols=21 Identities=24% Similarity=0.325 Sum_probs=18.0
Q ss_pred cccccCCcEEEEecCCceecC
Q 033358 48 SKLAIGSPVIVIEAPKMIKTA 68 (121)
Q Consensus 48 ~~~~IG~~Vrli~~ppYLKTA 68 (121)
.+..+||.|++.|--|-=||-
T Consensus 54 ~~~k~GD~V~I~EtRPLSKtK 74 (87)
T COG0186 54 NEAKVGDIVRIAETRPLSKTK 74 (87)
T ss_pred ccCCCCCEEEEEEccccCCcc
Confidence 347899999999999988874
No 21
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=37.84 E-value=24 Score=26.13 Aligned_cols=20 Identities=25% Similarity=0.351 Sum_probs=17.6
Q ss_pred ccccCCcEEEEecCCceecC
Q 033358 49 KLAIGSPVIVIEAPKMIKTA 68 (121)
Q Consensus 49 ~~~IG~~Vrli~~ppYLKTA 68 (121)
+..+||.|++.+-.|.=||-
T Consensus 77 ~~kvGD~V~I~E~RPiSKtK 96 (108)
T PRK08572 77 DAKVGDKVKIAECRPLSKTK 96 (108)
T ss_pred CCCCCCEEEEEEcCCCCCce
Confidence 47899999999999988873
No 22
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=37.49 E-value=18 Score=27.62 Aligned_cols=28 Identities=25% Similarity=0.418 Sum_probs=22.4
Q ss_pred ccccccccCCcEEEEecCCceecCCcccccc
Q 033358 45 IRRSKLAIGSPVIVIEAPKMIKTAASVPCLR 75 (121)
Q Consensus 45 ~~~~~~~IG~~Vrli~~ppYLKTAdpMPMLR 75 (121)
....-|--|++||..-.|++||-| ||+.
T Consensus 57 ~le~V~IRGS~IRFlvlPdmLKnA---PmFk 84 (119)
T KOG3172|consen 57 QLEQVFIRGSKIRFLVLPDMLKNA---PMFK 84 (119)
T ss_pred eeeeEEEecCeEEEEECchHhhcC---cccc
Confidence 445567789999999999999987 5544
No 23
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=37.45 E-value=25 Score=24.62 Aligned_cols=19 Identities=32% Similarity=0.438 Sum_probs=17.2
Q ss_pred ccccCCcEEEEecCCceec
Q 033358 49 KLAIGSPVIVIEAPKMIKT 67 (121)
Q Consensus 49 ~~~IG~~Vrli~~ppYLKT 67 (121)
.+.+||.|.|.+-.|.=||
T Consensus 53 ~~k~GD~V~I~e~rPlSK~ 71 (84)
T PRK05610 53 EAKIGDVVRIMETRPLSKT 71 (84)
T ss_pred CCCCCCEEEEEEcccCCCC
Confidence 5899999999999998777
No 24
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=37.10 E-value=75 Score=22.92 Aligned_cols=33 Identities=27% Similarity=0.400 Sum_probs=25.6
Q ss_pred cccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEE
Q 033358 48 SKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWA 99 (121)
Q Consensus 48 ~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~wa 99 (121)
+.+..||+|.++.-+ .-|-.|+|+..-+...|.
T Consensus 2 ~~ikkGD~V~Vi~G~-------------------dKGK~G~V~~V~~~~~~V 34 (104)
T TIGR01079 2 MKIKKGDTVKVISGK-------------------DKGKRGKVLKVLPKTNKV 34 (104)
T ss_pred CcccCCCEEEEeEcC-------------------CCCcEEEEEEEEcCCCEE
Confidence 478899999998875 348889998887776654
No 25
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=36.64 E-value=46 Score=25.07 Aligned_cols=33 Identities=24% Similarity=0.280 Sum_probs=24.1
Q ss_pred eeEeeecCCC-EEEEEEcceeEEeeCCccccCCC
Q 033358 87 GRIISRKPKD-VWAVRLSIGTYLLEGKYFKPLEL 119 (121)
Q Consensus 87 G~Iv~rrP~d-~waVRF~rGtFLid~~yl~~~~~ 119 (121)
|++++..... ..-|+|.-|++.|+...+..+|+
T Consensus 27 a~~~~~~~~~~~~~V~Fedg~~~i~~~dv~~LDl 60 (131)
T PF08605_consen 27 ATCVGSGVDRDRSLVRFEDGTYEIKNEDVKYLDL 60 (131)
T ss_pred EEEEeecCCCCeEEEEEecCceEeCcccEeeeee
Confidence 6777775544 56788888888888877777664
No 26
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=36.42 E-value=28 Score=23.66 Aligned_cols=19 Identities=32% Similarity=0.443 Sum_probs=17.0
Q ss_pred ccccCCcEEEEecCCceec
Q 033358 49 KLAIGSPVIVIEAPKMIKT 67 (121)
Q Consensus 49 ~~~IG~~Vrli~~ppYLKT 67 (121)
.+.+||.|.|.+-.|.=||
T Consensus 48 ~~k~GD~V~I~ecrPlSK~ 66 (71)
T TIGR03635 48 ECKVGDVVRIIETRPLSKT 66 (71)
T ss_pred CCCCCCEEEEEEcCCcCCc
Confidence 4789999999999998776
No 27
>PF02427 PSI_PsaE: Photosystem I reaction centre subunit IV / PsaE; InterPro: IPR003375 PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains []. This subunit may form complexes with ferredoxin and ferredoxin-oxidoreductase in the photosystem I reaction centre.; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009538 photosystem I reaction center; PDB: 1PSF_A 1PSE_A 2WSF_E 2WSC_E 2O01_E 2WSE_E 1GXI_E 1JB0_E 3PCQ_E 1QP2_A ....
Probab=36.20 E-value=93 Score=21.43 Aligned_cols=32 Identities=25% Similarity=0.290 Sum_probs=21.7
Q ss_pred ccCCCCccCCCCeeeEeeecCCCE---EEEEEcceeE
Q 033358 74 LRANSGLVKPGDVGRIISRKPKDV---WAVRLSIGTY 107 (121)
Q Consensus 74 LRPp~dLV~~gE~G~Iv~rrP~d~---waVRF~rGtF 107 (121)
||| .-.=-.|+|+|++....+. ..|||.+=.|
T Consensus 10 lR~--ESYWyn~vGtV~svdqs~i~YPV~VRF~kvNY 44 (61)
T PF02427_consen 10 LRK--ESYWYNEVGTVASVDQSGIRYPVVVRFDKVNY 44 (61)
T ss_dssp -SS--SSTTTTSEEEEEEETTSSSSSSEEEE-SSS-S
T ss_pred ccc--cceeecccceEEEEccCCccccEEEEEEEecc
Confidence 566 3455679999999888773 6899987555
No 28
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=35.75 E-value=28 Score=24.52 Aligned_cols=19 Identities=32% Similarity=0.462 Sum_probs=17.0
Q ss_pred ccccCCcEEEEecCCceec
Q 033358 49 KLAIGSPVIVIEAPKMIKT 67 (121)
Q Consensus 49 ~~~IG~~Vrli~~ppYLKT 67 (121)
+..+||.|+|.+-.|.=||
T Consensus 50 ~~~~GD~V~I~e~RPlSKt 68 (84)
T CHL00142 50 ECNIGDQVLIEETRPLSKT 68 (84)
T ss_pred CCCCCCEEEEEEcCCCCCc
Confidence 5789999999999998776
No 29
>TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit. This model represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation. In E. coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (TIGR02305). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Probab=34.59 E-value=32 Score=27.56 Aligned_cols=30 Identities=20% Similarity=0.330 Sum_probs=27.2
Q ss_pred cccCCCCccCCCCeeeEeeecCCCEEEEEEc
Q 033358 73 CLRANSGLVKPGDVGRIISRKPKDVWAVRLS 103 (121)
Q Consensus 73 MLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~ 103 (121)
-|+|. |+|-.|=.+-+..++|||.|.+++.
T Consensus 204 tL~pG-DvIlTGTp~g~~~l~~GD~v~~~i~ 233 (245)
T TIGR02303 204 TLEPG-DVILTGTPKGLSDVKPGDVVRLEIE 233 (245)
T ss_pred CcCCC-CEEEcCCCCCCeEcCCCCEEEEEEc
Confidence 57896 9999999988899999999999996
No 30
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=33.98 E-value=34 Score=17.71 Aligned_cols=12 Identities=33% Similarity=0.589 Sum_probs=9.3
Q ss_pred cccCCcEEEEec
Q 033358 50 LAIGSPVIVIEA 61 (121)
Q Consensus 50 ~~IG~~Vrli~~ 61 (121)
|.+|+.|+++.-
T Consensus 2 ~~~G~~V~I~~G 13 (28)
T smart00739 2 FEVGDTVRVIAG 13 (28)
T ss_pred CCCCCEEEEeEC
Confidence 678888888764
No 31
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=32.23 E-value=34 Score=25.16 Aligned_cols=21 Identities=29% Similarity=0.270 Sum_probs=17.9
Q ss_pred cccccCCcEEEEecCCceecC
Q 033358 48 SKLAIGSPVIVIEAPKMIKTA 68 (121)
Q Consensus 48 ~~~~IG~~Vrli~~ppYLKTA 68 (121)
.+..+||.|++.|-.|.=||-
T Consensus 74 n~~kvGD~V~I~E~RPlSKtK 94 (102)
T TIGR03630 74 IDVKEGDIVIIGETRPLSKTK 94 (102)
T ss_pred CCCCCCCEEEEEEcCCCCCce
Confidence 357899999999999988873
No 32
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=31.73 E-value=97 Score=17.15 Aligned_cols=23 Identities=22% Similarity=0.328 Sum_probs=11.3
Q ss_pred CCCEEEEEEc-ceeEEeeCCcccc
Q 033358 94 PKDVWAVRLS-IGTYLLEGKYFKP 116 (121)
Q Consensus 94 P~d~waVRF~-rGtFLid~~yl~~ 116 (121)
..+.|-++-. .-.=+++..|++.
T Consensus 34 ~~~w~~~~~~~~~~G~vP~~~v~~ 57 (58)
T smart00326 34 DDGWWKGRLGRGKEGLFPSNYVEE 57 (58)
T ss_pred CCCeEEEEeCCCCEEEEchHHEEE
Confidence 4456666654 2233455555543
No 33
>TIGR03220 catechol_dmpE 2-oxopent-4-enoate hydratase. Members of this protein family are 2-oxopent-4-enoate hydratase, which is also called 2-hydroxypent-2,4-dienoate hydratase. It is closely related to another gene found in the same operon, 4-oxalocrotonate decarboxylase, with which it interacts closely.
Probab=30.19 E-value=45 Score=26.59 Aligned_cols=30 Identities=20% Similarity=0.356 Sum_probs=27.4
Q ss_pred cccCCCCccCCCCeeeEeeecCCCEEEEEEc
Q 033358 73 CLRANSGLVKPGDVGRIISRKPKDVWAVRLS 103 (121)
Q Consensus 73 MLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~ 103 (121)
-|+|- |+|..|=.+-++..+|||.+.++|.
T Consensus 217 ~L~aG-diV~TGt~~g~~~v~~Gd~v~~~~~ 246 (255)
T TIGR03220 217 PLKAG-EVILSGSLAALVPVKAGDNLRVSIG 246 (255)
T ss_pred CCCCC-CEEECCCCCCCeeCCCCCEEEEEEc
Confidence 57885 9999999999999999999999997
No 34
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=28.49 E-value=1.1e+02 Score=28.60 Aligned_cols=47 Identities=17% Similarity=0.191 Sum_probs=32.2
Q ss_pred cccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEEEEEcceeEEeeCCcccc
Q 033358 48 SKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWAVRLSIGTYLLEGKYFKP 116 (121)
Q Consensus 48 ~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~rGtFLid~~yl~~ 116 (121)
.+|.+||+|++. +.|..|+|++...++.|.|.+-.=..-++.+-|++
T Consensus 635 ~~~~~Gd~V~v~----------------------~~~~~g~v~~i~~~~~~~V~~g~~k~~v~~~~l~~ 681 (782)
T PRK00409 635 EELKVGDEVKYL----------------------SLGQKGEVLSIPDDKEAIVQAGIMKMKVPLSDLEK 681 (782)
T ss_pred cCCCCCCEEEEc----------------------cCCceEEEEEEcCCCeEEEEECCEEEEEeHHHcee
Confidence 458888888763 25778999999767899998754344444444443
No 35
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=26.51 E-value=1.2e+02 Score=16.62 Aligned_cols=22 Identities=23% Similarity=0.317 Sum_probs=12.3
Q ss_pred CCCEEEEEEcc-eeEEeeCCccc
Q 033358 94 PKDVWAVRLSI-GTYLLEGKYFK 115 (121)
Q Consensus 94 P~d~waVRF~r-GtFLid~~yl~ 115 (121)
-.|.|-+|-.. -+=+++..|++
T Consensus 31 ~~~w~~~~~~~~~~G~vP~~~v~ 53 (54)
T cd00174 31 DDGWWEGRLLGGKRGLFPSNYVE 53 (54)
T ss_pred CCCeEEEEECCCCEEEEccccCc
Confidence 44666666655 34455666654
No 36
>PRK02654 putative inner membrane protein translocase component YidC; Provisional
Probab=25.02 E-value=37 Score=30.24 Aligned_cols=53 Identities=23% Similarity=0.192 Sum_probs=34.2
Q ss_pred ccccccccCCcEEEEecCCceecCC------ccccccC------CCCccCCCCeeeEeeecCCCE
Q 033358 45 IRRSKLAIGSPVIVIEAPKMIKTAA------SVPCLRA------NSGLVKPGDVGRIISRKPKDV 97 (121)
Q Consensus 45 ~~~~~~~IG~~Vrli~~ppYLKTAd------pMPMLRP------p~dLV~~gE~G~Iv~rrP~d~ 97 (121)
+.-.++.+|+++.+.-.-+==|.-+ +=.-|-| ..|.|+++|.|+|.++.|||.
T Consensus 168 p~g~k~~vg~~~~~~~q~~~g~~~~~~~~~~~~~~~~p~~~v~kg~~~~~~~~~g~~~al~pgd~ 232 (375)
T PRK02654 168 PGGTKLGVGESVKIQLQTTEGKPFSQLLAEYPNSKLSPTWKVTKGEERVKVSEDGTIEALAPGDA 232 (375)
T ss_pred CCCCcccccceeEEEEecCCCCcHHHHHhcCCccccCceeEEecCceeEEECCCCcEEEecCCce
Confidence 4556889999988764322111110 0012222 358999999999999999995
No 37
>TIGR03096 nitroso_cyanin nitrosocyanin. Nitrosocyanin, as described from the obligate chemolithoautotroph Nitrosomonas europaea, is a red copper protein of unknown function with sequence similarity to a number of blue copper redox proteins.
Probab=24.97 E-value=2e+02 Score=21.89 Aligned_cols=61 Identities=11% Similarity=0.133 Sum_probs=42.3
Q ss_pred ccccccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEEEEE---cceeEEeeCCcc
Q 033358 43 SDIRRSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWAVRL---SIGTYLLEGKYF 114 (121)
Q Consensus 43 ~~~~~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF---~rGtFLid~~yl 114 (121)
-++..-.++.||+|.|.- +=.|+. | .=+.+++-|+-..+.|++.+.++| .-|+|-.--++.
T Consensus 58 ~~P~~I~VkaGD~Vtl~v-----tN~d~~----~--H~f~i~~~gis~~I~pGet~TitF~adKpG~Y~y~C~~H 121 (135)
T TIGR03096 58 NEPEALVVKKGTPVKVTV-----ENKSPI----S--EGFSIDAYGISEVIKAGETKTISFKADKAGAFTIWCQLH 121 (135)
T ss_pred EcCCEEEECCCCEEEEEE-----EeCCCC----c--cceEECCCCcceEECCCCeEEEEEECCCCEEEEEeCCCC
Confidence 346778899999998753 122333 2 335556677777899999999998 578887655543
No 38
>TIGR02305 HpaG-N-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, N-terminal subunit. This model represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation. In E. coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related C-terminal domain (TIGR02303). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Probab=24.92 E-value=62 Score=24.84 Aligned_cols=31 Identities=16% Similarity=0.174 Sum_probs=27.8
Q ss_pred cccccCCCCccCCCCeeeEeeecCCCEEEEEEc
Q 033358 71 VPCLRANSGLVKPGDVGRIISRKPKDVWAVRLS 103 (121)
Q Consensus 71 MPMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~ 103 (121)
|+ |+|. |+|..|=.+-+...+|||.+.++|.
T Consensus 166 ~~-L~aG-dvI~TGT~~g~~~l~~Gd~v~~~i~ 196 (205)
T TIGR02305 166 MT-LNPG-DVLLLGTPEARVEVGPGDRVRVEAE 196 (205)
T ss_pred CC-cCCC-CEEEeCCCCCCeecCCCCEEEEEEc
Confidence 44 8896 9999999988999999999999996
No 39
>COG1018 Hmp Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]
Probab=24.19 E-value=91 Score=25.29 Aligned_cols=30 Identities=23% Similarity=0.368 Sum_probs=23.6
Q ss_pred CceEEEEeeeCCCCCcccccccccccCCcEEE
Q 033358 27 KLNLQIKCESKESSGESDIRRSKLAIGSPVIV 58 (121)
Q Consensus 27 ~~~~~~~c~~~~~~~~~~~~~~~~~IG~~Vrl 58 (121)
...+.|+.... +..+.-.+..+++||.|.|
T Consensus 67 ~~~isVk~~~~--G~~S~~Lh~~lk~Gd~l~v 96 (266)
T COG1018 67 LYRISVKREDG--GGGSNWLHDHLKVGDTLEV 96 (266)
T ss_pred eEEEEEEEeCC--CcccHHHHhcCCCCCEEEE
Confidence 45677888765 3346788889999999999
No 40
>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....
Probab=24.01 E-value=44 Score=22.34 Aligned_cols=18 Identities=28% Similarity=0.342 Sum_probs=14.7
Q ss_pred cccCCcEEEEecCCceec
Q 033358 50 LAIGSPVIVIEAPKMIKT 67 (121)
Q Consensus 50 ~~IG~~Vrli~~ppYLKT 67 (121)
..+||.|+|.+-.|.=||
T Consensus 44 ~~vGD~V~I~e~rPiSk~ 61 (69)
T PF00366_consen 44 CKVGDKVRIRECRPISKT 61 (69)
T ss_dssp STTTSEEEEEEEEEEETT
T ss_pred CCCCCEEEEEeeeccCCc
Confidence 467999999998887665
No 41
>TIGR01447 recD exodeoxyribonuclease V, alpha subunit. This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.
Probab=23.14 E-value=1.7e+02 Score=26.59 Aligned_cols=55 Identities=20% Similarity=0.242 Sum_probs=34.6
Q ss_pred cccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEEEEEc--ceeEEeeCCccccCC
Q 033358 48 SKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWAVRLS--IGTYLLEGKYFKPLE 118 (121)
Q Consensus 48 ~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~--rGtFLid~~yl~~~~ 118 (121)
..|.+||+|.+..--+= -=|.-||.|+|+... .+ ..|.|. .|...++.+.+..++
T Consensus 463 ~~~~~Gd~Vm~t~Nd~~--------------~gl~NGdiG~i~~~~-~~-~~v~f~~~~g~~~~~~~~l~~~~ 519 (586)
T TIGR01447 463 EGWYIGRPIMVTENDYT--------------LGLFNGDIGVLLRDP-DG-LTVWFHFADGSKAVLPSRLPNYE 519 (586)
T ss_pred ceeecCCeEEEeecCcc--------------cCcCCCCeEEEEEeC-Cc-EEEEEEcCCCeEEechHHcCccc
Confidence 46778999887654221 136779999999753 33 567774 355555655555544
No 42
>PF10006 DUF2249: Uncharacterized conserved protein (DUF2249); InterPro: IPR018720 This domain is found in a number of hypothetical bacterial and archaeal proteins with no known function. It is also found in proteins described as cupin 2 and hemerythrin. It represents a conserved region that shows distant similarity to the SirA protein (see IPR001455 from INTERPRO).
Probab=23.07 E-value=96 Score=19.76 Aligned_cols=50 Identities=16% Similarity=0.202 Sum_probs=31.8
Q ss_pred ccccccccCCcEEEEecCCceecCCccccccCCCCccCC-CC-eeeEeeecCCCEEEEEEcc
Q 033358 45 IRRSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKP-GD-VGRIISRKPKDVWAVRLSI 104 (121)
Q Consensus 45 ~~~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~-gE-~G~Iv~rrP~d~waVRF~r 104 (121)
+.-..+..|+.+.|+.. -+|.|.+.- |-.- |- .-++.... .|.|.|+|.|
T Consensus 18 ~~~~~L~~Ge~l~lv~d------~~P~pL~~~---l~~~~g~~~~~~~~~~-~~~w~v~i~r 69 (69)
T PF10006_consen 18 EALDELPPGETLELVND------HDPRPLYPQ---LEERRGFFSWEYEEQG-PGEWRVRITR 69 (69)
T ss_pred HHHHcCCCCCEEEEEeC------CCCHHHHHH---HHHhCCCceEEEEEcC-CCEEEEEEEC
Confidence 34467889999988864 478887654 2222 55 33344444 4459999875
No 43
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=22.86 E-value=88 Score=24.47 Aligned_cols=35 Identities=26% Similarity=0.321 Sum_probs=23.0
Q ss_pred CeeeEeeecCCCEEEEEEcce--eEEeeC--CccccCCC
Q 033358 85 DVGRIISRKPKDVWAVRLSIG--TYLLEG--KYFKPLEL 119 (121)
Q Consensus 85 E~G~Iv~rrP~d~waVRF~rG--tFLid~--~yl~~~~~ 119 (121)
.+=.|++--.+|.|.|+.+.| .+||+- ++++.+|+
T Consensus 121 ~V~~i~~~Ga~Dvl~V~~~~~~k~~LIPf~~~~V~~Vd~ 159 (174)
T COG0806 121 KVTEILETGANDVLVVKAKGGKKERLIPFVDAVVKEVDL 159 (174)
T ss_pred EEEEEeeCCCccEEEEEecCCCcEEEecchHheeeEEec
Confidence 333445557889999998666 888862 44444444
No 44
>PRK11342 mhpD 2-keto-4-pentenoate hydratase; Provisional
Probab=22.31 E-value=75 Score=25.41 Aligned_cols=30 Identities=20% Similarity=0.455 Sum_probs=27.7
Q ss_pred cccCCCCccCCCCeeeEeeecCCCEEEEEEc
Q 033358 73 CLRANSGLVKPGDVGRIISRKPKDVWAVRLS 103 (121)
Q Consensus 73 MLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~ 103 (121)
-|+|. |+|-.|=.+-+.-.+|||.|.++|.
T Consensus 221 ~L~aG-dvV~TGt~~~~~~l~~Gd~v~~~i~ 250 (262)
T PRK11342 221 PLRAG-DIILTGALGPMVAVNAGDRFEAHIE 250 (262)
T ss_pred CcCCC-CEEEcCCCCCCeeCCCCCEEEEEEC
Confidence 58995 9999999999999999999999996
No 45
>cd09002 GH43_XYL_3 Glycosyl hydrolase family 43, beta-D-xylosidase. This glycosyl hydrolase family 43 (GH43) includes enzymes that have been characterized to have beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37) activity. They are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds between two xylose units in short xylooligosaccharides. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended subs
Probab=22.30 E-value=88 Score=24.75 Aligned_cols=40 Identities=25% Similarity=0.365 Sum_probs=32.9
Q ss_pred CccccccCCCCccCCCCeeeEeeecCCCEEE--EEEcceeEEe
Q 033358 69 ASVPCLRANSGLVKPGDVGRIISRKPKDVWA--VRLSIGTYLL 109 (121)
Q Consensus 69 dpMPMLRPp~dLV~~gE~G~Iv~rrP~d~wa--VRF~rGtFLi 109 (121)
.-+++++- .||+.=..+|.++....++.|| |+...|.|.|
T Consensus 38 ~gi~i~~S-~DL~~W~~~g~~~~~~~~~~WAP~i~~~~gkyy~ 79 (280)
T cd09002 38 PGLVIWHS-RDLVNWTPVGPALPEYEGDVWAPDLCKYDGRYYI 79 (280)
T ss_pred CCEEEEEC-CCcCCceEccccccCCCCCEEcCeeEEECCEEEE
Confidence 35788888 4999999999999888899997 6667788766
No 46
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=21.78 E-value=3.3e+02 Score=19.99 Aligned_cols=27 Identities=30% Similarity=0.432 Sum_probs=16.9
Q ss_pred eeeEeeecCCCEEEEEEcceeEEeeCCccc
Q 033358 86 VGRIISRKPKDVWAVRLSIGTYLLEGKYFK 115 (121)
Q Consensus 86 ~G~Iv~rrP~d~waVRF~rGtFLid~~yl~ 115 (121)
+.+|+++ |||+..+ ..|...|+++.+.
T Consensus 71 iKRVig~-pGd~v~i--~~~~l~vNg~~~~ 97 (163)
T TIGR02227 71 VKRVIGL-PGDKVEF--RDGKLYINGKKID 97 (163)
T ss_pred EEEEEec-CCCEEEE--ECCEEEECCEECc
Confidence 4566666 7777544 4577777766543
No 47
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=21.73 E-value=1.2e+02 Score=18.68 Aligned_cols=13 Identities=23% Similarity=0.279 Sum_probs=7.6
Q ss_pred ccccccCCcEEEE
Q 033358 47 RSKLAIGSPVIVI 59 (121)
Q Consensus 47 ~~~~~IG~~Vrli 59 (121)
...+..||.|.+-
T Consensus 11 ~p~i~~gd~lii~ 23 (81)
T cd06529 11 EPTIPDGDLVLVD 23 (81)
T ss_pred CCccCCCCEEEEc
Confidence 3347777776543
No 48
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=21.72 E-value=2.1e+02 Score=26.29 Aligned_cols=42 Identities=21% Similarity=0.290 Sum_probs=29.8
Q ss_pred ccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCEEEEEEc
Q 033358 47 RSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDVWAVRLS 103 (121)
Q Consensus 47 ~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~waVRF~ 103 (121)
...|.+||+|.+..--+= -=|.-||.|+|+.. +++.+.|.|.
T Consensus 478 ~~~~~~Gd~Vm~t~Nd~~--------------~gl~NGdiG~v~~~-~~~~l~v~f~ 519 (615)
T PRK10875 478 HSRWYEGRPVMIARNDSA--------------LGLFNGDIGIALDR-GQGELRVWFQ 519 (615)
T ss_pred CccccCCCEEEEeecCcc--------------cCcccCceEEEeec-CCCeEEEEEE
Confidence 357889999988765321 12567999999954 4667788875
No 49
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=21.45 E-value=1.3e+02 Score=17.17 Aligned_cols=19 Identities=16% Similarity=-0.060 Sum_probs=15.2
Q ss_pred eeeEeeecCCCEEEEEEcc
Q 033358 86 VGRIISRKPKDVWAVRLSI 104 (121)
Q Consensus 86 ~G~Iv~rrP~d~waVRF~r 104 (121)
-++|+...+.+.+.|+|-=
T Consensus 16 ra~V~~~~~~~~~~V~f~D 34 (48)
T cd04508 16 RAKITSILSDGKVEVFFVD 34 (48)
T ss_pred EEEEEEECCCCcEEEEEEc
Confidence 3788999888889998743
No 50
>PF04596 Pox_F15: Poxvirus protein F15; InterPro: IPR007675 Protein F15 is found in a number of Poxviruses.
Probab=21.23 E-value=59 Score=25.41 Aligned_cols=19 Identities=32% Similarity=0.601 Sum_probs=16.4
Q ss_pred eeeEeeecCCCEEEEEEcc
Q 033358 86 VGRIISRKPKDVWAVRLSI 104 (121)
Q Consensus 86 ~G~Iv~rrP~d~waVRF~r 104 (121)
.=.|+++|=+++|.+.|..
T Consensus 117 ~YiIIGLRIK~fWs~~F~i 135 (136)
T PF04596_consen 117 IYIIIGLRIKDFWSSKFEI 135 (136)
T ss_pred EEEEEEEchhhccceeEee
Confidence 4579999999999999863
No 51
>PF12139 APS-reductase_C: Adenosine-5'-phosphosulfate reductase beta subunit; InterPro: IPR022738 This domain is found in bacteria and archaea and is typically between 112 to 142 amino acids in length. It is found in association with PF00037 from PFAM, and has a conserved FPIRTT sequence motif. The whole beta subunit has the enzymic properties of 1.8.99.2 from EC. ; PDB: 1JNZ_B 2FJE_D 2FJD_B 1JNR_D 2FJB_B 2FJA_B 3GYX_J.
Probab=21.19 E-value=1.1e+02 Score=22.22 Aligned_cols=32 Identities=22% Similarity=0.416 Sum_probs=14.1
Q ss_pred cCCCCccCCCCeeeEeeecCCCEEEEEEccee
Q 033358 75 RANSGLVKPGDVGRIISRKPKDVWAVRLSIGT 106 (121)
Q Consensus 75 RPp~dLV~~gE~G~Iv~rrP~d~waVRF~rGt 106 (121)
|+=+|+|-.|-.=+++--.-.=.|.|+||.|+
T Consensus 2 RgYADFvPlG~sv~plR~~~~ImWtikFRnG~ 33 (83)
T PF12139_consen 2 RGYADFVPLGGSVRPLRGTESIMWTIKFRNGT 33 (83)
T ss_dssp ---TTTS-TT-EEEEEE-SSEEEEEEE-TTS-
T ss_pred ccccceecCCCeeEeecCCCeEEEEEEecCCc
Confidence 33355665653322222222237999999996
No 52
>KOG2904 consensus Predicted methyltransferase [General function prediction only]
Probab=20.91 E-value=60 Score=28.50 Aligned_cols=26 Identities=19% Similarity=0.302 Sum_probs=22.9
Q ss_pred cccCCcEEEEecCCceecCCccccccC
Q 033358 50 LAIGSPVIVIEAPKMIKTAASVPCLRA 76 (121)
Q Consensus 50 ~~IG~~Vrli~~ppYLKTAdpMPMLRP 76 (121)
+.-|--..|+.-|||+++-| |+-|-|
T Consensus 218 l~~~~~dllvsNPPYI~~dD-~~~l~~ 243 (328)
T KOG2904|consen 218 LLEGKIDLLVSNPPYIRKDD-NRQLKP 243 (328)
T ss_pred cccCceeEEecCCCcccccc-hhhcCc
Confidence 55677788999999999999 999987
No 53
>PRK13618 psbV cytochrome c-550; Provisional
Probab=20.89 E-value=43 Score=26.20 Aligned_cols=17 Identities=29% Similarity=0.298 Sum_probs=13.7
Q ss_pred EecCCceecCCcccccc
Q 033358 59 IEAPKMIKTAASVPCLR 75 (121)
Q Consensus 59 i~~ppYLKTAdpMPMLR 75 (121)
.+..||+|-+++||-+|
T Consensus 115 ~~~h~~ik~~~~mP~~~ 131 (163)
T PRK13618 115 SEIHPSIKSADIFTAMR 131 (163)
T ss_pred cccccccCccccCCCCC
Confidence 46668889999999766
No 54
>KOG0439 consensus VAMP-associated protein involved in inositol metabolism [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.75 E-value=75 Score=23.98 Aligned_cols=26 Identities=35% Similarity=0.647 Sum_probs=21.5
Q ss_pred cCCccccccCCCCccCCCCeeeEeee
Q 033358 67 TAASVPCLRANSGLVKPGDVGRIISR 92 (121)
Q Consensus 67 TAdpMPMLRPp~dLV~~gE~G~Iv~r 92 (121)
||--+-+.|||.++|..|+-+.|.-.
T Consensus 48 T~p~~y~VrP~~G~i~p~~t~~i~v~ 73 (218)
T KOG0439|consen 48 TAPKLYCVRPNGGVIDPGSTVEIEVT 73 (218)
T ss_pred CCCCeEEEcCCcceECCCCcEEEEEE
Confidence 34467789999999999999998754
No 55
>PF00845 Gemini_BL1: Geminivirus BL1 movement protein; InterPro: IPR000211 The movement of bipartite Geminiviruses such as squash leaf curl virus (SqLCV) requires the cooperative interaction of two essential virus-encoded movement proteins, BR1 and BL1. Recent studies of SqLCV and bean dwarf mosaic virus have shown that BR1 and BL1 act in a cooperative manner to move the viral genome intracellularly from the nucleus to the cytoplasm and across the wall cell to cell. BR1 is a nuclear shuttle protein, and it has been proposed to bind newly replicated viral ssDNA genomes and move these between the nucleus and cytoplasm. These BR1-genome complexes are then directed to the cell periphery through interactions between BR1 and BL1, where, as the result of BL1 action, the complexes are moved to adjacent uninfected cells. The precise mechanism by which BL1 acts to transport these genome complexes across the cell wall, and whether this may differ in different cell types, remains at issue [].; GO: 0003677 DNA binding, 0046740 spread of virus in host, cell to cell, 0033644 host cell membrane
Probab=20.70 E-value=51 Score=28.35 Aligned_cols=16 Identities=44% Similarity=0.871 Sum_probs=15.0
Q ss_pred eeecCCCEEEEEEcce
Q 033358 90 ISRKPKDVWAVRLSIG 105 (121)
Q Consensus 90 v~rrP~d~waVRF~rG 105 (121)
+.++||..||.|=..|
T Consensus 189 i~i~PGEsWAsrStIg 204 (276)
T PF00845_consen 189 IEIQPGESWASRSTIG 204 (276)
T ss_pred cccCCCCccccccccc
Confidence 6789999999999999
No 56
>COG3650 Predicted membrane protein [Function unknown]
Probab=20.30 E-value=66 Score=25.49 Aligned_cols=16 Identities=31% Similarity=0.634 Sum_probs=13.8
Q ss_pred CCEEEEEEcceeEEee
Q 033358 95 KDVWAVRLSIGTYLLE 110 (121)
Q Consensus 95 ~d~waVRF~rGtFLid 110 (121)
.-.|+|||+++.|.++
T Consensus 55 EPFWSvrv~~~gl~l~ 70 (149)
T COG3650 55 EPFWSVRVSRKGLILS 70 (149)
T ss_pred CcceEEEEecCceEEC
Confidence 4589999999999875
No 57
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=20.09 E-value=95 Score=23.42 Aligned_cols=36 Identities=22% Similarity=0.304 Sum_probs=28.1
Q ss_pred ccccccccccCCcEEEEecCCceecCCccccccCCCCccCCCCeeeEeeecCCCE
Q 033358 43 SDIRRSKLAIGSPVIVIEAPKMIKTAASVPCLRANSGLVKPGDVGRIISRKPKDV 97 (121)
Q Consensus 43 ~~~~~~~~~IG~~Vrli~~ppYLKTAdpMPMLRPp~dLV~~gE~G~Iv~rrP~d~ 97 (121)
-+..+..+..||.|.|+.-+ .-|..|+|+...+...
T Consensus 39 y~ir~~~IkkGD~V~VisG~-------------------~KGk~GkV~~V~~~~~ 74 (120)
T PRK01191 39 YGIRSLPVRKGDTVKVMRGD-------------------FKGEEGKVVEVDLKRG 74 (120)
T ss_pred hCCccceEeCCCEEEEeecC-------------------CCCceEEEEEEEcCCC
Confidence 44667899999999999765 2388899998876654
No 58
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=20.07 E-value=2.4e+02 Score=18.14 Aligned_cols=24 Identities=17% Similarity=0.245 Sum_probs=20.6
Q ss_pred CeeeEeeecCCCEEEEEEcceeEE
Q 033358 85 DVGRIISRKPKDVWAVRLSIGTYL 108 (121)
Q Consensus 85 E~G~Iv~rrP~d~waVRF~rGtFL 108 (121)
-.|+|+..++++...|++..|.=+
T Consensus 5 ~~~~V~~~lG~~~~~V~~~dg~~~ 28 (65)
T PF01176_consen 5 VIGRVTEMLGNNLFEVECEDGEER 28 (65)
T ss_dssp EEEEEEEEESSSEEEEEETTSEEE
T ss_pred EEEEEEEECCCCEEEEEeCCCCEE
Confidence 468999999999999999988644
Done!