Query 032316
Match_columns 143
No_of_seqs 89 out of 105
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 12:29:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032316.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032316hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00045 photosystem I reactio 100.0 8.3E-51 1.8E-55 301.4 7.6 72 72-143 30-101 (101)
2 CHL00125 psaE photosystem I su 100.0 1.2E-44 2.7E-49 251.3 5.1 62 81-143 1-62 (64)
3 PF02427 PSI_PsaE: Photosystem 100.0 4.4E-44 9.5E-49 246.6 4.4 61 82-143 1-61 (61)
4 PRK02749 photosystem I reactio 100.0 6.1E-43 1.3E-47 246.7 5.0 62 81-143 2-70 (71)
5 smart00739 KOW KOW (Kyprides, 85.6 1.6 3.4E-05 23.5 3.2 26 82-109 2-27 (28)
6 smart00326 SH3 Src homology 3 76.8 3.6 7.7E-05 23.5 2.8 24 76-99 15-39 (58)
7 PRK05609 nusG transcription an 71.8 12 0.00025 27.9 5.1 32 77-110 122-153 (181)
8 smart00743 Agenet Tudor-like d 71.5 11 0.00025 23.6 4.4 36 81-123 2-39 (61)
9 TIGR01080 rplX_A_E ribosomal p 70.4 8.4 0.00018 29.1 4.1 40 79-125 39-78 (114)
10 PRK09570 rpoH DNA-directed RNA 70.1 3.4 7.4E-05 29.7 1.9 15 79-93 49-63 (79)
11 PRK00004 rplX 50S ribosomal pr 69.9 8.3 0.00018 28.2 3.9 39 81-126 4-42 (105)
12 PRK12281 rplX 50S ribosomal pr 69.8 8.4 0.00018 27.0 3.8 29 81-111 6-34 (76)
13 PF01191 RNA_pol_Rpb5_C: RNA p 69.2 3.5 7.6E-05 29.2 1.8 15 79-93 46-60 (74)
14 PF11623 DUF3252: Protein of u 69.1 11 0.00023 26.1 4.0 52 82-140 2-53 (53)
15 CHL00141 rpl24 ribosomal prote 65.3 12 0.00026 26.5 3.9 39 81-126 8-46 (83)
16 COG0250 NusG Transcription ant 64.3 16 0.00035 28.9 4.8 34 75-110 117-150 (178)
17 TIGR00922 nusG transcription t 63.1 20 0.00044 26.6 4.9 40 78-122 116-155 (172)
18 TIGR01843 type_I_hlyD type I s 63.0 12 0.00027 30.2 4.0 43 81-124 323-376 (423)
19 PTZ00194 60S ribosomal protein 62.4 11 0.00023 29.9 3.5 35 80-119 45-79 (143)
20 cd00174 SH3 Src homology 3 dom 62.2 12 0.00026 21.1 2.9 21 78-98 14-35 (54)
21 TIGR02768 TraA_Ti Ti-type conj 61.2 12 0.00025 35.1 4.0 39 80-123 606-647 (744)
22 smart00333 TUDOR Tudor domain. 60.5 33 0.00071 20.8 4.8 37 81-123 2-38 (57)
23 COG2012 RPB5 DNA-directed RNA 56.7 8 0.00017 28.5 1.8 15 79-93 52-66 (80)
24 TIGR01079 rplX_bact ribosomal 56.7 20 0.00043 26.4 3.9 34 81-119 3-36 (104)
25 PF07653 SH3_2: Variant SH3 do 54.2 9.4 0.0002 23.7 1.6 26 76-101 12-40 (55)
26 PF11910 NdhO: Cyanobacterial 51.8 19 0.00041 25.9 3.0 35 82-121 1-50 (67)
27 PRK13889 conjugal transfer rel 50.1 23 0.00051 34.9 4.3 38 81-123 600-640 (988)
28 PTZ00061 DNA-directed RNA poly 49.6 12 0.00025 31.2 1.9 16 79-94 177-192 (205)
29 PRK01191 rpl24p 50S ribosomal 49.2 28 0.00061 26.8 3.8 29 80-110 44-72 (120)
30 PLN03111 DNA-directed RNA poly 48.5 12 0.00027 31.0 1.9 15 79-93 178-192 (206)
31 PF13437 HlyD_3: HlyD family s 47.3 40 0.00087 22.5 3.9 44 82-125 50-97 (105)
32 PF11061 DUF2862: Protein of u 47.2 21 0.00045 25.1 2.6 36 101-141 29-64 (64)
33 KOG3218 RNA polymerase, 25-kDa 47.0 12 0.00025 31.6 1.5 14 80-93 181-194 (208)
34 PF14085 DUF4265: Domain of un 45.5 18 0.00038 26.5 2.1 22 80-101 24-46 (117)
35 PF14604 SH3_9: Variant SH3 do 42.4 19 0.00042 22.3 1.7 21 79-99 12-33 (49)
36 cd03692 mtIF2_IVc mtIF2_IVc: t 41.5 27 0.00059 23.6 2.4 27 82-110 27-53 (84)
37 PRK00409 recombination and DNA 40.6 51 0.0011 31.3 4.8 25 80-109 635-659 (782)
38 PF01382 Avidin: Avidin family 40.6 17 0.00037 26.8 1.4 15 94-108 4-18 (114)
39 PF02470 MCE: mce related prot 40.2 66 0.0014 21.0 4.1 37 80-123 13-51 (81)
40 PF05641 Agenet: Agenet domain 39.7 62 0.0013 21.3 3.9 37 82-124 1-41 (68)
41 PF00199 Catalase: Catalase; 39.2 21 0.00044 30.8 1.9 14 111-124 76-89 (384)
42 PF00467 KOW: KOW motif; Inte 37.7 40 0.00087 19.5 2.4 25 84-110 1-25 (32)
43 COG1463 Ttg2C ABC-type transpo 35.7 53 0.0011 27.8 3.7 37 79-122 50-86 (359)
44 PF14743 DNA_ligase_OB_2: DNA 34.8 15 0.00032 24.9 0.3 31 89-121 30-65 (66)
45 TIGR00998 8a0101 efflux pump m 34.7 76 0.0016 25.3 4.3 42 82-124 255-317 (334)
46 TIGR00156 conserved hypothetic 34.4 18 0.00039 27.9 0.7 27 83-109 62-90 (126)
47 PF14334 DUF4390: Domain of un 34.1 31 0.00068 26.1 2.0 51 86-138 48-100 (165)
48 PRK15208 long polar fimbrial c 33.2 29 0.00063 27.9 1.8 20 80-99 78-106 (228)
49 PLN00104 MYST -like histone ac 33.1 1.7E+02 0.0037 27.0 6.8 35 73-109 45-80 (450)
50 PRK15249 fimbrial chaperone pr 32.6 30 0.00064 28.4 1.7 21 80-100 90-120 (253)
51 PRK09752 adhesin; Provisional 31.8 58 0.0013 33.7 3.9 6 89-94 952-957 (1250)
52 PRK13826 Dtr system oriT relax 31.7 56 0.0012 32.9 3.7 38 81-123 633-673 (1102)
53 PF08169 RBB1NT: RBB1NT (NUC16 30.3 40 0.00087 25.2 2.0 21 101-121 8-30 (96)
54 smart00561 MBT Present in Dros 29.9 1.4E+02 0.003 21.4 4.6 45 74-123 20-64 (96)
55 PRK08559 nusG transcription an 27.9 1.4E+02 0.0031 22.5 4.6 39 79-122 92-130 (153)
56 TIGR03177 pilus_cpaB Flp pilus 27.0 1.3E+02 0.0027 24.2 4.4 51 43-94 206-256 (261)
57 cd02788 MopB_CT_NDH-1_NuoG2-N7 26.4 1.7E+02 0.0037 19.9 4.4 47 79-132 40-87 (96)
58 PF00018 SH3_1: SH3 domain; I 26.2 55 0.0012 19.6 1.8 22 77-98 11-33 (48)
59 PF01957 NfeD: NfeD-like C-ter 25.7 43 0.00094 23.2 1.4 14 82-95 122-135 (144)
60 PRK10476 multidrug resistance 24.9 1.4E+02 0.003 24.5 4.3 42 82-124 259-325 (346)
61 PF07051 OCIA: Ovarian carcino 24.6 19 0.00042 27.5 -0.6 18 84-101 27-47 (111)
62 COG3111 Periplasmic protein wi 24.5 36 0.00078 26.9 0.9 56 83-139 62-119 (128)
63 PF11347 DUF3148: Protein of u 24.5 2.2E+02 0.0047 20.2 4.7 24 99-126 33-56 (63)
64 PF02820 MBT: mbt repeat; Int 24.3 88 0.0019 20.7 2.6 24 92-123 10-33 (73)
65 cd08150 catalase_like Catalase 23.8 46 0.001 27.1 1.4 14 112-125 34-47 (283)
66 TIGR03794 NHPM_micro_HlyD NHPM 23.5 1.6E+02 0.0035 24.9 4.6 47 82-129 308-382 (421)
67 PF04076 BOF: Bacterial OB fol 22.8 48 0.001 24.4 1.2 27 83-109 39-67 (103)
68 PF13856 Gifsy-2: ATP-binding 22.8 44 0.00095 23.2 1.0 18 82-100 66-83 (95)
69 PF07497 Rho_RNA_bind: Rho ter 22.1 89 0.0019 22.3 2.4 34 79-126 40-73 (78)
70 TIGR01000 bacteriocin_acc bact 21.7 1.7E+02 0.0037 25.3 4.5 42 81-122 371-419 (457)
71 PHA02123 hypothetical protein 21.7 94 0.002 24.9 2.7 31 82-112 110-140 (146)
72 PF11302 DUF3104: Protein of u 21.6 1.5E+02 0.0032 21.5 3.4 29 79-110 3-39 (75)
73 PF04023 FeoA: FeoA domain; I 21.6 61 0.0013 20.6 1.4 18 79-96 30-47 (74)
74 cd08152 y4iL_like Catalase-lik 21.5 53 0.0012 27.2 1.4 15 112-126 37-51 (305)
75 cd08151 AOS Allene oxide synth 21.3 55 0.0012 27.6 1.4 14 112-125 58-71 (328)
76 TIGR02971 heterocyst_DevB ABC 21.2 1.8E+02 0.0039 23.3 4.3 41 82-123 254-309 (327)
77 PF15252 DUF4589: Domain of un 21.1 43 0.00093 28.5 0.7 13 118-130 133-146 (221)
78 PRK09014 rfaH transcriptional 20.7 2.3E+02 0.005 20.9 4.5 37 80-122 108-144 (162)
79 PF09867 DUF2094: Uncharacteri 20.7 54 0.0012 24.6 1.1 19 101-120 69-88 (138)
No 1
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=100.00 E-value=8.3e-51 Score=301.41 Aligned_cols=72 Identities=85% Similarity=1.348 Sum_probs=70.5
Q ss_pred CCCCCCCCCCCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEeeeeeecccccCccccccceecC
Q 032316 72 APKPKPPPIGPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNKVNYANVSTNNYALDEIEEVK 143 (143)
Q Consensus 72 ~~~~kpp~igp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~kVNY~gvsTNNfa~~El~ev~ 143 (143)
++++|||||||+|||||||||||||||||||||++|||++||||||+||||||||+|+|||||+||||++|+
T Consensus 30 ~~~~kpp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~~girYPVvVRF~kvNY~gvnTNnfa~~El~~v~ 101 (101)
T PLN00045 30 AAKPKPPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQDPGVRYPVVVRFEKVNYAGVSTNNYALDEIEEVK 101 (101)
T ss_pred cccCCCCCcccCCCCEEEEccccceeecCcceEEEEeCCCCcccceEEEeeeeeccccccccccHhhhhccC
Confidence 689999999999999999999999999999999999999999999999999999999999999999999985
No 2
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=100.00 E-value=1.2e-44 Score=251.25 Aligned_cols=62 Identities=63% Similarity=1.062 Sum_probs=60.2
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEeeeeeecccccCccccccceecC
Q 032316 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNKVNYANVSTNNYALDEIEEVK 143 (143)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~kVNY~gvsTNNfa~~El~ev~ 143 (143)
+++|||||||||||||||||+|||++|||+ ||||||+||||||||+|+||||||+|||++++
T Consensus 1 mi~rGskVrIlR~ESYWyn~vGtV~svd~~-gi~YPV~VRF~kvNY~g~nTNnfa~~El~~v~ 62 (64)
T CHL00125 1 MVKRGSKVRILRKESYWYNEIGTVATVDQS-GIRYPVLVRFEKVNYSGTNTNNFSLDELVEVE 62 (64)
T ss_pred CcccCCEEEEccccceeecCcceEEEEcCC-CCCccEEEEEeeeeccccccccccHHHHhhhc
Confidence 589999999999999999999999999997 99999999999999999999999999999874
No 3
>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=100.00 E-value=4.4e-44 Score=246.56 Aligned_cols=61 Identities=70% Similarity=1.171 Sum_probs=53.1
Q ss_pred CCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEeeeeeecccccCccccccceecC
Q 032316 82 PKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNKVNYANVSTNNYALDEIEEVK 143 (143)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~kVNY~gvsTNNfa~~El~ev~ 143 (143)
++|||||||||||||||||+|||++|||+ ||||||+||||||||+|+|||||++|||++++
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs-~i~YPV~VRF~kvNY~g~nTnnfa~~El~~ve 61 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQS-GIRYPVVVRFDKVNYAGVNTNNFALDELEEVE 61 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTS-SSSSSEEEE-SSS-SSSSSEEEE-GGGEEE--
T ss_pred CCCCCEEEEccccceeecccceEEEEccC-CccccEEEEEEEecccCccccccchhhheecC
Confidence 68999999999999999999999999998 89999999999999999999999999999985
No 4
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=100.00 E-value=6.1e-43 Score=246.66 Aligned_cols=62 Identities=56% Similarity=1.017 Sum_probs=60.0
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEeeeeeec-------ccccCccccccceecC
Q 032316 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNKVNYA-------NVSTNNYALDEIEEVK 143 (143)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~kVNY~-------gvsTNNfa~~El~ev~ 143 (143)
+++|||||||||||||||||+|||++|||+ ||||||+||||||||+ |+||||||++||++++
T Consensus 2 ~i~rGskVrIlR~ESYWyn~vGtV~svD~s-gi~YPV~VRF~kvNY~g~sG~~gG~nTNnfa~~El~~v~ 70 (71)
T PRK02749 2 AISRGDKVRILRPESYWYNEVGTVASVDKS-GIKYPVIVRFDKVNYNGFSGVDGGINTNNFAESELEEVE 70 (71)
T ss_pred ccccCCEEEEccccceeecCcceEEEEccC-CCeeeEEEEeeeeeccccccccCccccccccHHHHhhhc
Confidence 589999999999999999999999999998 9999999999999999 8999999999999875
No 5
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=85.64 E-value=1.6 Score=23.48 Aligned_cols=26 Identities=23% Similarity=0.445 Sum_probs=22.1
Q ss_pred CCCCCeeEEeeccceeccccceEEEEcC
Q 032316 82 PKRGAKVKILRRESYWYNGIGSVVAVDQ 109 (143)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDq 109 (143)
++.|++|+|+.-. |-..+|.|.++|.
T Consensus 2 ~~~G~~V~I~~G~--~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGP--FKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECC--CCCcEEEEEEEcC
Confidence 5789999999855 7778899999986
No 6
>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=76.77 E-value=3.6 Score=23.53 Aligned_cols=24 Identities=21% Similarity=0.668 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCeeEEeec-cceecc
Q 032316 76 KPPPIGPKRGAKVKILRR-ESYWYN 99 (143)
Q Consensus 76 kpp~igp~RGskVrIlR~-ESYWyn 99 (143)
.+..+.+++|++|.|+.. +..|+.
T Consensus 15 ~~~~l~~~~Gd~v~v~~~~~~~w~~ 39 (58)
T smart00326 15 DPDELSFKKGDIITVLEKSDDGWWK 39 (58)
T ss_pred CCCCCCCCCCCEEEEEEcCCCCeEE
Confidence 445788999999999988 777874
No 7
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=71.83 E-value=12 Score=27.95 Aligned_cols=32 Identities=22% Similarity=0.381 Sum_probs=27.0
Q ss_pred CCCCCCCCCCeeEEeeccceeccccceEEEEcCC
Q 032316 77 PPPIGPKRGAKVKILRRESYWYNGIGSVVAVDQD 110 (143)
Q Consensus 77 pp~igp~RGskVrIlR~ESYWyn~vGtVvsVDqs 110 (143)
++..+++.|++|||. +--|-.-.|.|+.+|.+
T Consensus 122 ~~~~~~~~Gd~VrI~--~GPf~G~~g~v~~i~~~ 153 (181)
T PRK05609 122 KPKVDFEVGEMVRVI--DGPFADFNGTVEEVDYE 153 (181)
T ss_pred ccccCCCCCCEEEEe--ccCCCCCEEEEEEEeCC
Confidence 345789999999998 55688889999999975
No 8
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=71.46 E-value=11 Score=23.58 Aligned_cols=36 Identities=31% Similarity=0.650 Sum_probs=27.2
Q ss_pred CCCCCCeeEEee--ccceeccccceEEEEcCCCCCcccEEEEeee
Q 032316 81 GPKRGAKVKILR--RESYWYNGIGSVVAVDQDPKSRYPVVVRFNK 123 (143)
Q Consensus 81 gp~RGskVrIlR--~ESYWyn~vGtVvsVDqs~girYPVvVRF~k 123 (143)
..+.|++|-++. .-+|| -|+|..++.. -+| .|+|..
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~---~a~V~~~~~~--~~~--~V~~~~ 39 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWW---EAVVTKVLGD--GKY--LVRYLT 39 (61)
T ss_pred CcCCCCEEEEEECCCCEEE---EEEEEEECCC--CEE--EEEECC
Confidence 357899999998 55555 4899999883 355 788876
No 9
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=70.39 E-value=8.4 Score=29.14 Aligned_cols=40 Identities=28% Similarity=0.426 Sum_probs=29.5
Q ss_pred CCCCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEeeeee
Q 032316 79 PIGPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNKVN 125 (143)
Q Consensus 79 ~igp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~kVN 125 (143)
.+-+++||+|+|++-.- =...|+|..||... . .|-.|.||
T Consensus 39 ~~~IkkGD~V~Vi~Gk~--KGk~GkV~~V~~~~---~--~V~Vegvn 78 (114)
T TIGR01080 39 ALPVRKGDKVRIMRGDF--KGHEGKVSKVDLKR---Y--RIYVEGVT 78 (114)
T ss_pred cceeecCCEEEEecCCC--CCCEEEEEEEEcCC---C--EEEEcCeE
Confidence 45689999999999872 24569999999762 2 45556666
No 10
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=70.13 E-value=3.4 Score=29.74 Aligned_cols=15 Identities=47% Similarity=0.835 Sum_probs=14.1
Q ss_pred CCCCCCCCeeEEeec
Q 032316 79 PIGPKRGAKVKILRR 93 (143)
Q Consensus 79 ~igp~RGskVrIlR~ 93 (143)
..|.++|+.|||.|+
T Consensus 49 ~~g~k~GdVvkI~R~ 63 (79)
T PRK09570 49 AIGAKPGDVIKIVRK 63 (79)
T ss_pred hcCCCCCCEEEEEEC
Confidence 679999999999998
No 11
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=69.93 E-value=8.3 Score=28.23 Aligned_cols=39 Identities=26% Similarity=0.333 Sum_probs=29.3
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEeeeeee
Q 032316 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNKVNY 126 (143)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~kVNY 126 (143)
-+++||.|.|++--. -..+|+|.+||+. ++=|+| +.+|.
T Consensus 4 ~i~kGD~V~Vi~G~d--KGk~G~V~~V~~~---~~~V~V--egvn~ 42 (105)
T PRK00004 4 KIKKGDTVIVIAGKD--KGKRGKVLKVLPK---KNKVIV--EGVNI 42 (105)
T ss_pred cccCCCEEEEeEcCC--CCcEEEEEEEEcC---CCEEEE--cCcEE
Confidence 478999999999754 5788999999997 444555 44444
No 12
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=69.76 E-value=8.4 Score=27.00 Aligned_cols=29 Identities=28% Similarity=0.304 Sum_probs=24.4
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEcCCC
Q 032316 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQDP 111 (143)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDqs~ 111 (143)
-+++||+|.|++-. .-..+|+|..||...
T Consensus 6 ~I~kGD~V~Vi~G~--dKGK~G~V~~V~~~~ 34 (76)
T PRK12281 6 KVKKGDMVKVIAGD--DKGKTGKVLAVLPKK 34 (76)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 58999999999965 347789999999873
No 13
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=69.22 E-value=3.5 Score=29.20 Aligned_cols=15 Identities=47% Similarity=0.762 Sum_probs=11.8
Q ss_pred CCCCCCCCeeEEeec
Q 032316 79 PIGPKRGAKVKILRR 93 (143)
Q Consensus 79 ~igp~RGskVrIlR~ 93 (143)
..|.++|+.|||.|+
T Consensus 46 ~~g~k~GdVvkI~R~ 60 (74)
T PF01191_consen 46 YLGAKPGDVVKIIRK 60 (74)
T ss_dssp HTT--TTSEEEEEEE
T ss_pred hcCCCCCCEEEEEec
Confidence 469999999999998
No 14
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=69.09 E-value=11 Score=26.07 Aligned_cols=52 Identities=25% Similarity=0.386 Sum_probs=36.2
Q ss_pred CCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEeeeeeecccccCccccccce
Q 032316 82 PKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNKVNYANVSTNNYALDEIE 140 (143)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~kVNY~gvsTNNfa~~El~ 140 (143)
+-.|+.||+.-+.|-.|.-.|.|-.|-.. -+-|-||.=|+.-+-| |-++|||
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvsdg-----kaaVLFEGGnWdKlvT--f~l~eLe 53 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVSDG-----KAAVLFEGGNWDKLVT--FRLSELE 53 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEETT-----EEEEEEEETTEEEEEE--EEGGGEE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEeeCC-----eEEEEecCCCceEEEE--EEhhhCC
Confidence 45799999999999999999999999765 2567788877766555 6666664
No 15
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=65.27 E-value=12 Score=26.53 Aligned_cols=39 Identities=28% Similarity=0.382 Sum_probs=29.4
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEeeeeee
Q 032316 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNKVNY 126 (143)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~kVNY 126 (143)
-+.+||.|.|++-.. -...|+|..||.. ++=|+| |.+|.
T Consensus 8 ~I~~GD~V~Vi~G~d--KGK~G~V~~V~~~---~~~V~V--egvn~ 46 (83)
T CHL00141 8 HVKIGDTVKIISGSD--KGKIGEVLKIIKK---SNKVIV--KGINI 46 (83)
T ss_pred cccCCCEEEEeEcCC--CCcEEEEEEEEcC---CCEEEE--cCcEE
Confidence 688999999999753 4788999999997 333444 55554
No 16
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=64.32 E-value=16 Score=28.92 Aligned_cols=34 Identities=26% Similarity=0.398 Sum_probs=28.5
Q ss_pred CCCCCCCCCCCCeeEEeeccceeccccceEEEEcCC
Q 032316 75 PKPPPIGPKRGAKVKILRRESYWYNGIGSVVAVDQD 110 (143)
Q Consensus 75 ~kpp~igp~RGskVrIlR~ESYWyn~vGtVvsVDqs 110 (143)
++++-+.++.|++|||.. .=.-+..|+|..||.+
T Consensus 117 ~~~~~~~~e~Gd~VrI~~--GpFa~f~g~V~evd~e 150 (178)
T COG0250 117 PKKPKVDFEPGDVVRIID--GPFAGFKAKVEEVDEE 150 (178)
T ss_pred CCcccccCCCCCEEEEec--cCCCCccEEEEEEcCc
Confidence 566779999999999985 4566778999999997
No 17
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=63.08 E-value=20 Score=26.61 Aligned_cols=40 Identities=25% Similarity=0.363 Sum_probs=29.6
Q ss_pred CCCCCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEee
Q 032316 78 PPIGPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFN 122 (143)
Q Consensus 78 p~igp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~ 122 (143)
+...++.|++|+|. +--|-.-.|.|..+|.+ +.-++|+++
T Consensus 116 ~~~~~~~G~~V~I~--~Gpf~G~~g~v~~~~~~---~~r~~V~v~ 155 (172)
T TIGR00922 116 PKIDFEVGEQVRVN--DGPFANFTGTVEEVDYE---KSKLKVSVS 155 (172)
T ss_pred cccCCCCCCEEEEe--ecCCCCcEEEEEEEcCC---CCEEEEEEE
Confidence 34668999999998 45677888999999975 334555554
No 18
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.
Probab=62.97 E-value=12 Score=30.16 Aligned_cols=43 Identities=19% Similarity=0.287 Sum_probs=30.8
Q ss_pred CCCCCCeeEEeeccceeccc----cceEEEEcCCC-------CCcccEEEEeeee
Q 032316 81 GPKRGAKVKILRRESYWYNG----IGSVVAVDQDP-------KSRYPVVVRFNKV 124 (143)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~----vGtVvsVDqs~-------girYPVvVRF~kV 124 (143)
.++.|++|+| +-++|=+.. -|+|..|+..+ +..|+|.|++++-
T Consensus 323 ~i~~G~~v~v-~~~~~~~~~~~~~~g~V~~i~~~~~~~~~~~~~~~~v~i~l~~~ 376 (423)
T TIGR01843 323 FVHVGQPAEI-KFSAFPYRRYGILNGKVKSISPDTFTDERGGGPYYRVRISIDQN 376 (423)
T ss_pred hhCCCCceEE-EEecCCCcccCCccEEEEEECCCcccCccCCcceEEEEEEECHH
Confidence 4678999998 556653332 69999997642 2359999999864
No 19
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=62.40 E-value=11 Score=29.89 Aligned_cols=35 Identities=17% Similarity=0.337 Sum_probs=27.2
Q ss_pred CCCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEE
Q 032316 80 IGPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVV 119 (143)
Q Consensus 80 igp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvV 119 (143)
.-+++||+|.|++-.. =...|+|..||.. .+=|+|
T Consensus 45 ~~IkkGD~V~Vi~Gk~--KGk~GkV~~V~~k---~~~ViV 79 (143)
T PTZ00194 45 MPVRKDDEVMVVRGHH--KGREGKVTAVYRK---KWVIHI 79 (143)
T ss_pred ceeecCCEEEEecCCC--CCCceEEEEEEcC---CCEEEE
Confidence 3589999999999772 3567999999987 345555
No 20
>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=62.21 E-value=12 Score=21.12 Aligned_cols=21 Identities=19% Similarity=0.640 Sum_probs=17.2
Q ss_pred CCCCCCCCCeeEEeec-cceec
Q 032316 78 PPIGPKRGAKVKILRR-ESYWY 98 (143)
Q Consensus 78 p~igp~RGskVrIlR~-ESYWy 98 (143)
-.+.+++|+.|.|+.. +..|+
T Consensus 14 ~~l~~~~Gd~v~v~~~~~~~w~ 35 (54)
T cd00174 14 DELSFKKGDIIEVLEKSDDGWW 35 (54)
T ss_pred CCCCCCCCCEEEEEEcCCCCeE
Confidence 4678999999999988 56665
No 21
>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=61.25 E-value=12 Score=35.11 Aligned_cols=39 Identities=18% Similarity=0.312 Sum_probs=30.4
Q ss_pred CCCCCCCeeEEeec--cceecc-ccceEEEEcCCCCCcccEEEEeee
Q 032316 80 IGPKRGAKVKILRR--ESYWYN-GIGSVVAVDQDPKSRYPVVVRFNK 123 (143)
Q Consensus 80 igp~RGskVrIlR~--ESYWyn-~vGtVvsVDqs~girYPVvVRF~k 123 (143)
..+..||+|.++|. +.-||| ++|+|+.|+.+ . ++|+|+.
T Consensus 606 ~~~~~GDrV~~~~N~~~~gv~NGd~g~V~~i~~~-~----i~v~~~~ 647 (744)
T TIGR02768 606 RKFAAGDRIVFLENNRDLGVKNGMLGTVEEIEDG-R----LVVQLDS 647 (744)
T ss_pred ceecCCCEEEEEecccccCCcCCCEEEEEEecCC-e----EEEEECC
Confidence 45789999999976 334676 79999999864 2 6889974
No 22
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=60.52 E-value=33 Score=20.79 Aligned_cols=37 Identities=27% Similarity=0.401 Sum_probs=28.6
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEeee
Q 032316 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNK 123 (143)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~k 123 (143)
.++.|++|...-.+.-||. |+|..++.+ + . +.|+|.+
T Consensus 2 ~~~~G~~~~a~~~d~~wyr--a~I~~~~~~-~-~--~~V~f~D 38 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYR--ARIIKVDGE-Q-L--YEVFFID 38 (57)
T ss_pred CCCCCCEEEEEeCCCCEEE--EEEEEECCC-C-E--EEEEEEC
Confidence 4678999888777899997 599999985 2 2 4677766
No 23
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=56.73 E-value=8 Score=28.47 Aligned_cols=15 Identities=47% Similarity=0.815 Sum_probs=13.9
Q ss_pred CCCCCCCCeeEEeec
Q 032316 79 PIGPKRGAKVKILRR 93 (143)
Q Consensus 79 ~igp~RGskVrIlR~ 93 (143)
.+|-++|+.|||.|+
T Consensus 52 ~lgak~GdvVkIvRk 66 (80)
T COG2012 52 ALGAKPGDVVKIVRK 66 (80)
T ss_pred HccCCCCcEEEEEec
Confidence 689999999999997
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=56.66 E-value=20 Score=26.39 Aligned_cols=34 Identities=26% Similarity=0.347 Sum_probs=26.2
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEE
Q 032316 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVV 119 (143)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvV 119 (143)
-+++||+|.|++-.. -...|+|..||.. ++=|+|
T Consensus 3 ~ikkGD~V~Vi~G~d--KGK~G~V~~V~~~---~~~V~V 36 (104)
T TIGR01079 3 KIKKGDTVKVISGKD--KGKRGKVLKVLPK---TNKVIV 36 (104)
T ss_pred cccCCCEEEEeEcCC--CCcEEEEEEEEcC---CCEEEE
Confidence 378999999999763 3678999999987 344554
No 25
>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=54.16 E-value=9.4 Score=23.67 Aligned_cols=26 Identities=19% Similarity=0.588 Sum_probs=17.0
Q ss_pred CCCCCCCCCCCeeEEe---eccceecccc
Q 032316 76 KPPPIGPKRGAKVKIL---RRESYWYNGI 101 (143)
Q Consensus 76 kpp~igp~RGskVrIl---R~ESYWyn~v 101 (143)
.|.++..++|+.|+|+ ..+.+|+-..
T Consensus 12 ~~~~Ls~~~Gd~i~v~~~~~~~~ww~~~~ 40 (55)
T PF07653_consen 12 DPDELSFKKGDVIEVLGEKDDDGWWLGEN 40 (55)
T ss_dssp STTB-EB-TTEEEEEEEEECSTSEEEEEE
T ss_pred CCCceEEecCCEEEEEEeecCCCEEEEEE
Confidence 4456999999999999 2345676443
No 26
>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=51.77 E-value=19 Score=25.86 Aligned_cols=35 Identities=40% Similarity=0.737 Sum_probs=27.6
Q ss_pred CCCCCeeEEee---------------ccceeccccceEEEEcCCCCCcccEEEEe
Q 032316 82 PKRGAKVKILR---------------RESYWYNGIGSVVAVDQDPKSRYPVVVRF 121 (143)
Q Consensus 82 p~RGskVrIlR---------------~ESYWyn~vGtVvsVDqs~girYPVvVRF 121 (143)
+|+|+.||+.| +-+|-|..-|.|..|..+ | -.|||
T Consensus 1 lKKG~lVrv~re~~~nSlEa~ASD~~~P~Yife~~GEvl~ikgd----Y-a~vr~ 50 (67)
T PF11910_consen 1 LKKGSLVRVNREKYENSLEAKASDPRPPSYIFEGPGEVLDIKGD----Y-AQVRF 50 (67)
T ss_pred CCcceEEEeehHhhcCchhhhhcCCCCCcceecCCCeEEEecCC----E-EEEEe
Confidence 47889998875 458999999999999765 4 35677
No 27
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=50.13 E-value=23 Score=34.91 Aligned_cols=38 Identities=24% Similarity=0.346 Sum_probs=29.9
Q ss_pred CCCCCCeeEEeecc--ceecc-ccceEEEEcCCCCCcccEEEEeee
Q 032316 81 GPKRGAKVKILRRE--SYWYN-GIGSVVAVDQDPKSRYPVVVRFNK 123 (143)
Q Consensus 81 gp~RGskVrIlR~E--SYWyn-~vGtVvsVDqs~girYPVvVRF~k 123 (143)
.+..||+|.++|.. --+|| ++|+|..||.. . ++|+|++
T Consensus 600 ~~~vGDrVm~~rNd~~lgV~NGd~GtV~~I~~~-~----i~V~~d~ 640 (988)
T PRK13889 600 SFASGDRVMFLQNERGLGVKNGTLGTIEQVSAQ-S----MSVRLDD 640 (988)
T ss_pred cccCCCEEEEeecCCcCCEeCCCeEEEEEecCC-e----EEEEECC
Confidence 47899999999964 34677 79999999985 3 6788864
No 28
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=49.59 E-value=12 Score=31.22 Aligned_cols=16 Identities=38% Similarity=0.565 Sum_probs=14.2
Q ss_pred CCCCCCCCeeEEeecc
Q 032316 79 PIGPKRGAKVKILRRE 94 (143)
Q Consensus 79 ~igp~RGskVrIlR~E 94 (143)
..|.++|+.|||.|+-
T Consensus 177 y~g~k~G~vvkI~R~S 192 (205)
T PTZ00061 177 YFGLSKGQVVKIIRPS 192 (205)
T ss_pred hcCCCCCCEEEEEECC
Confidence 5799999999999973
No 29
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=49.25 E-value=28 Score=26.77 Aligned_cols=29 Identities=31% Similarity=0.491 Sum_probs=23.7
Q ss_pred CCCCCCCeeEEeeccceeccccceEEEEcCC
Q 032316 80 IGPKRGAKVKILRRESYWYNGIGSVVAVDQD 110 (143)
Q Consensus 80 igp~RGskVrIlR~ESYWyn~vGtVvsVDqs 110 (143)
.-+++||+|.|++-.. =...|+|..||..
T Consensus 44 ~~IkkGD~V~VisG~~--KGk~GkV~~V~~~ 72 (120)
T PRK01191 44 LPVRKGDTVKVMRGDF--KGEEGKVVEVDLK 72 (120)
T ss_pred ceEeCCCEEEEeecCC--CCceEEEEEEEcC
Confidence 4589999999999772 2467999999987
No 30
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=48.51 E-value=12 Score=31.03 Aligned_cols=15 Identities=53% Similarity=0.674 Sum_probs=14.0
Q ss_pred CCCCCCCCeeEEeec
Q 032316 79 PIGPKRGAKVKILRR 93 (143)
Q Consensus 79 ~igp~RGskVrIlR~ 93 (143)
..|.+||+.|||.|+
T Consensus 178 y~g~k~G~vvkI~R~ 192 (206)
T PLN03111 178 YYGLKRGQVVKIIRP 192 (206)
T ss_pred hcCCCCCCEEEEEEC
Confidence 579999999999998
No 31
>PF13437 HlyD_3: HlyD family secretion protein
Probab=47.28 E-value=40 Score=22.46 Aligned_cols=44 Identities=20% Similarity=0.229 Sum_probs=32.0
Q ss_pred CC-CCCeeEEeeccceeccccceEEEEcCCC---CCcccEEEEeeeee
Q 032316 82 PK-RGAKVKILRRESYWYNGIGSVVAVDQDP---KSRYPVVVRFNKVN 125 (143)
Q Consensus 82 p~-RGskVrIlR~ESYWyn~vGtVvsVDqs~---girYPVvVRF~kVN 125 (143)
++ .|+.|+|.=.-.=.+.--|+|..|+... +-.|+|.+++++-.
T Consensus 50 i~~~g~~v~v~~~~~~~~~~~g~V~~I~~~~~~~~~~~~v~~~i~~~~ 97 (105)
T PF13437_consen 50 IKDPGQKVTVRLDPGPEKTIEGKVSSISPSPDPQGGTYRVEISIDNPK 97 (105)
T ss_pred eEeCCCEEEEEECCCCCcEEEEEEEEEeCcccCCCcEEEEEEEECCCC
Confidence 54 8999998865221346679999998742 45899999998754
No 32
>PF11061 DUF2862: Protein of unknown function (DUF2862); InterPro: IPR021291 This family of proteins has no known function.
Probab=47.23 E-value=21 Score=25.12 Aligned_cols=36 Identities=36% Similarity=0.419 Sum_probs=26.8
Q ss_pred cceEEEEcCCCCCcccEEEEeeeeeecccccCcccccccee
Q 032316 101 IGSVVAVDQDPKSRYPVVVRFNKVNYANVSTNNYALDEIEE 141 (143)
Q Consensus 101 vGtVvsVDqs~girYPVvVRF~kVNY~gvsTNNfa~~El~e 141 (143)
+|+|..--..+|.-.-++|.|++ =+++-|=+|||+|
T Consensus 29 ~g~I~~fKmtDG~giG~vv~~~n-----g~~~WFFedEi~~ 64 (64)
T PF11061_consen 29 IGTIKGFKMTDGSGIGVVVEFSN-----GSRTWFFEDEIEE 64 (64)
T ss_pred cEEEEEEEEecCCcEEEEEEecC-----CceeEEchhhccC
Confidence 78888766666777789999974 2466778888875
No 33
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=47.02 E-value=12 Score=31.64 Aligned_cols=14 Identities=64% Similarity=0.928 Sum_probs=12.9
Q ss_pred CCCCCCCeeEEeec
Q 032316 80 IGPKRGAKVKILRR 93 (143)
Q Consensus 80 igp~RGskVrIlR~ 93 (143)
-|.|||+.|||.|+
T Consensus 181 yGLKrGqVVKI~r~ 194 (208)
T KOG3218|consen 181 YGLKRGQVVKIIRR 194 (208)
T ss_pred hccccCcEEEEEec
Confidence 49999999999997
No 34
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=45.54 E-value=18 Score=26.45 Aligned_cols=22 Identities=18% Similarity=0.430 Sum_probs=19.5
Q ss_pred CCCCCCCeeEEeec-cceecccc
Q 032316 80 IGPKRGAKVKILRR-ESYWYNGI 101 (143)
Q Consensus 80 igp~RGskVrIlR~-ESYWyn~v 101 (143)
-|+.+||.|++.+. +.|||+++
T Consensus 24 ~glA~gDvV~~~~~~g~~~~~~~ 46 (117)
T PF14085_consen 24 YGLALGDVVRAEPDDGELWFQKV 46 (117)
T ss_pred CCCCCCCEEEEEeCCCeEEEEEE
Confidence 58899999999998 58999887
No 35
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=42.42 E-value=19 Score=22.33 Aligned_cols=21 Identities=19% Similarity=0.618 Sum_probs=16.5
Q ss_pred CCCCCCCCeeEEeec-cceecc
Q 032316 79 PIGPKRGAKVKILRR-ESYWYN 99 (143)
Q Consensus 79 ~igp~RGskVrIlR~-ESYWyn 99 (143)
.+..++|+.|.|+++ ++.|+.
T Consensus 12 ELs~~~Gd~i~v~~~~~~~W~~ 33 (49)
T PF14604_consen 12 ELSFKKGDVITVLEKSDDGWWY 33 (49)
T ss_dssp B-EB-TTEEEEEEEESSTSEEE
T ss_pred EeeEcCCCEEEEEEeCCCCEEE
Confidence 578999999999998 788875
No 36
>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=41.52 E-value=27 Score=23.64 Aligned_cols=27 Identities=33% Similarity=0.498 Sum_probs=19.8
Q ss_pred CCCCCeeEEeeccceeccccceEEEEcCC
Q 032316 82 PKRGAKVKILRRESYWYNGIGSVVAVDQD 110 (143)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDqs 110 (143)
+++|++||+||...-=| .|+|.|+...
T Consensus 27 l~~g~~v~vlr~~~~~~--~g~i~sl~~~ 53 (84)
T cd03692 27 IKRNAKVRVLRNGEVIY--EGKISSLKRF 53 (84)
T ss_pred EeCCCEEEEEcCCCEEE--EEEEEEEEEc
Confidence 67899999999864222 4888888743
No 37
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=40.63 E-value=51 Score=31.34 Aligned_cols=25 Identities=28% Similarity=0.352 Sum_probs=21.8
Q ss_pred CCCCCCCeeEEeeccceeccccceEEEEcC
Q 032316 80 IGPKRGAKVKILRRESYWYNGIGSVVAVDQ 109 (143)
Q Consensus 80 igp~RGskVrIlR~ESYWyn~vGtVvsVDq 109 (143)
--++.||+|+|.. ++..|+|++|+.
T Consensus 635 ~~~~~Gd~V~v~~-----~~~~g~v~~i~~ 659 (782)
T PRK00409 635 EELKVGDEVKYLS-----LGQKGEVLSIPD 659 (782)
T ss_pred cCCCCCCEEEEcc-----CCceEEEEEEcC
Confidence 4488999999976 889999999975
No 38
>PF01382 Avidin: Avidin family; InterPro: IPR005468 Avidin [] is a minor constituent of egg white in several groups of oviparous vertebrates. Avidin, which was discovered in the 1920's, takes its name from the avidity with which it binds biotin. These two molecules bind so strongly that is extremely difficult to separate them. Streptavidin is a protein produced by Streptomyces avidinii which also binds biotin and whose sequence is evolutionary related to that of avidin. Avidin and streptavidin both form homotetrameric complexes of noncovalently associated chains. Each chain forms a very strong and specific non-covalent complex with one molecule of biotin. The three-dimensional structures of both streptavidin [, ] and avidin [] have been determined and revealed them to share a common fold: an eight stranded anti-parallel beta-barrel with a repeated +1 topology enclosing an internal ligand binding site. Fibropellins I and III [] are proteins that form the apical lamina of the sea urchin embryo, a component of the extracellular matrix. These two proteins have a modular structure composed of a CUB domain (seePDOC00908 from PROSITEDOC), followed by a variable number of EGF repeats and a C-terminal avidin-like domain.; PDB: 2OF9_B 2FHL_B 3MM0_G 1Y55_Y 1Y52_Y 1Y53_X 2OF8_A 2FHN_X 2OFA_A 2OFB_B ....
Probab=40.57 E-value=17 Score=26.78 Aligned_cols=15 Identities=33% Similarity=0.902 Sum_probs=13.3
Q ss_pred cceeccccceEEEEc
Q 032316 94 ESYWYNGIGSVVAVD 108 (143)
Q Consensus 94 ESYWyn~vGtVvsVD 108 (143)
+..||||.|+...|.
T Consensus 4 ~G~W~Ne~GS~m~I~ 18 (114)
T PF01382_consen 4 SGTWYNELGSTMTIT 18 (114)
T ss_dssp CEEEEETTSEEEEEE
T ss_pred ceEEEeCCCCEEEEE
Confidence 468999999999987
No 39
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=40.22 E-value=66 Score=21.01 Aligned_cols=37 Identities=27% Similarity=0.414 Sum_probs=25.4
Q ss_pred CCCCCCCeeEEeeccceeccccceEEEE--cCCCCCcccEEEEeee
Q 032316 80 IGPKRGAKVKILRRESYWYNGIGSVVAV--DQDPKSRYPVVVRFNK 123 (143)
Q Consensus 80 igp~RGskVrIlR~ESYWyn~vGtVvsV--Dqs~girYPVvVRF~k 123 (143)
-|++.|+.|++.= -+||+|.+| +.+ +-+--|.++.++
T Consensus 13 ~GL~~gs~V~~~G------v~VG~V~~i~l~~~-~~~v~v~~~i~~ 51 (81)
T PF02470_consen 13 GGLSVGSPVRYRG------VEVGKVTSIELDPD-GNRVRVTLRIDP 51 (81)
T ss_pred CCCCCcCEEEECC------EEEEEEEEEEEcCC-CCEEEEEEEEcC
Confidence 5889999998764 369999999 554 445444444443
No 40
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=39.68 E-value=62 Score=21.25 Aligned_cols=37 Identities=22% Similarity=0.539 Sum_probs=23.5
Q ss_pred CCCCCeeEEeecc----ceeccccceEEEEcCCCCCcccEEEEeeee
Q 032316 82 PKRGAKVKILRRE----SYWYNGIGSVVAVDQDPKSRYPVVVRFNKV 124 (143)
Q Consensus 82 p~RGskVrIlR~E----SYWyn~vGtVvsVDqs~girYPVvVRF~kV 124 (143)
.++|++|-|++.| .=||. ++|.+.... + =++|+|++.
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~--a~V~~~~~~-~---~~~V~Y~~~ 41 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFP--ATVLKENGD-D---KYLVEYDDL 41 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEE--EEEEEEETT-----EEEEEETT-
T ss_pred CCCCCEEEEEEcCCCCCcEEEE--EEEEEeCCC-c---EEEEEECCc
Confidence 3689999999977 35885 789999887 3 446666543
No 41
>PF00199 Catalase: Catalase; InterPro: IPR011614 Catalases (1.11.1.6 from EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects []. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (IPR000763 from INTERPRO) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (IPR007760 from INTERPRO) that are found in bacteria []. Based on a phylogenetic analysis, catalases can be classified into clade 1, 2 and 3. Clade 1 contains small subunit catalases from plants and a subset of bacteria; clade 2 contains large subunit catalases from fungi and a second subset of bacteria; and clade 3 contains small subunit catalases from bacteria, fungi, protists, animals, and plants [, ]. This entry represent the core-forming domain of mono-functional, haem-containing catalases. It does not cover the region that carries an immune-responsive amphipathic octa-peptide that is found in the C-terminal of some catalases (IPR010582 from INTERPRO).; GO: 0004096 catalase activity, 0020037 heme binding, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 7CAT_A 3NWL_D 4BLC_D 1TH3_D 1TH4_A 1TGU_B 1TH2_D 3RGS_D 3RE8_D 3RGP_C ....
Probab=39.24 E-value=21 Score=30.77 Aligned_cols=14 Identities=50% Similarity=1.075 Sum_probs=11.2
Q ss_pred CCCcccEEEEeeee
Q 032316 111 PKSRYPVVVRFNKV 124 (143)
Q Consensus 111 ~girYPVvVRF~kV 124 (143)
+|..|||+|||..+
T Consensus 76 ~Gk~~pv~vRFS~~ 89 (384)
T PF00199_consen 76 PGKTYPVIVRFSNA 89 (384)
T ss_dssp TT-EEEEEEEEEES
T ss_pred CCcccceeeeeccc
Confidence 47799999999876
No 42
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=37.67 E-value=40 Score=19.46 Aligned_cols=25 Identities=28% Similarity=0.574 Sum_probs=19.6
Q ss_pred CCCeeEEeeccceeccccceEEEEcCC
Q 032316 84 RGAKVKILRRESYWYNGIGSVVAVDQD 110 (143)
Q Consensus 84 RGskVrIlR~ESYWyn~vGtVvsVDqs 110 (143)
+|+.|+|++-- .-.+.|+|..||++
T Consensus 1 ~Gd~V~V~~G~--~~G~~G~I~~i~~~ 25 (32)
T PF00467_consen 1 VGDTVKVISGP--FKGKIGKIVEIDRS 25 (32)
T ss_dssp TTSEEEESSST--TTTEEEEEEEEETT
T ss_pred CCCEEEEeEcC--CCCceEEEEEEECC
Confidence 58888888643 24678999999997
No 43
>COG1463 Ttg2C ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=35.74 E-value=53 Score=27.78 Aligned_cols=37 Identities=22% Similarity=0.282 Sum_probs=28.3
Q ss_pred CCCCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEee
Q 032316 79 PIGPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFN 122 (143)
Q Consensus 79 ~igp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~ 122 (143)
--|+..|++|||.= =+||+|..|.-++ -.|-+.|+|+
T Consensus 50 ~~GL~~gs~V~~~G------V~VG~V~~I~~~~-~~~~~~v~~~ 86 (359)
T COG1463 50 AGGLYVGSPVRYRG------VKVGKVASISLDP-KPNGARVTLE 86 (359)
T ss_pred cccCCCCCceEEcC------EEeEEEEEEEecC-CCCceEEEEE
Confidence 35889999999753 2589999988764 4677888775
No 44
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=34.75 E-value=15 Score=24.94 Aligned_cols=31 Identities=35% Similarity=0.494 Sum_probs=20.1
Q ss_pred EEeeccceeccccceEEEEc-----CCCCCcccEEEEe
Q 032316 89 KILRRESYWYNGIGSVVAVD-----QDPKSRYPVVVRF 121 (143)
Q Consensus 89 rIlR~ESYWyn~vGtVvsVD-----qs~girYPVvVRF 121 (143)
.....+.+| -||++++|- .+-.-|+|+.+||
T Consensus 30 td~~R~~~~--~iG~iit~ky~~~t~~g~pRfP~f~~~ 65 (66)
T PF14743_consen 30 TDEEREEPP--YIGKIITVKYQGLTKDGSPRFPVFVRV 65 (66)
T ss_dssp -HHHHHHHH--HTT-EEEEEEE-TTSSSS-EEEEEEEE
T ss_pred CHHHHhcCC--CCCCEEEEEEEccCCCCccccCEEEEe
Confidence 334567788 799999883 2224799999987
No 45
>TIGR00998 8a0101 efflux pump membrane protein (multidrug resistance protein A).
Probab=34.73 E-value=76 Score=25.27 Aligned_cols=42 Identities=21% Similarity=0.335 Sum_probs=28.2
Q ss_pred CCCCCeeEEeeccceeccc--cceEEEEcCCC-------------C------CcccEEEEeeee
Q 032316 82 PKRGAKVKILRRESYWYNG--IGSVVAVDQDP-------------K------SRYPVVVRFNKV 124 (143)
Q Consensus 82 p~RGskVrIlR~ESYWyn~--vGtVvsVDqs~-------------g------irYPVvVRF~kV 124 (143)
++.|++|+|.- ..|-++. -|+|.+|+... | .+|||.|++++-
T Consensus 255 i~~G~~v~v~~-~~~~~~~~~~G~V~~Is~~~~~~~~~~p~~~~~~~~~~~~~~~~v~i~l~~~ 317 (334)
T TIGR00998 255 VRIGQPVTIRS-DLYGSDVVFEGKVTGISMGTGSAFSLLPAQNATGNWIKVVQRLPVRIKLDPK 317 (334)
T ss_pred CCCCCEEEEEE-ecCCCCCEEEEEEEEECCCcccccccCCCCCCCcCeEEEEEEEeEEEEEcCC
Confidence 57799999862 3333222 59999998752 1 158888888764
No 46
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=34.40 E-value=18 Score=27.86 Aligned_cols=27 Identities=19% Similarity=0.384 Sum_probs=20.8
Q ss_pred CCCCeeEEeeccceeccc-cce-EEEEcC
Q 032316 83 KRGAKVKILRRESYWYNG-IGS-VVAVDQ 109 (143)
Q Consensus 83 ~RGskVrIlR~ESYWyn~-vGt-VvsVDq 109 (143)
=+|..|+-++.|.|+|.| .|+ .+.||.
T Consensus 62 L~G~Iv~~l~~d~Y~F~D~TG~I~VeId~ 90 (126)
T TIGR00156 62 LRGNIISHIGDDRYVFRDKSGEINVVIPA 90 (126)
T ss_pred EEEEEEEEeCCceEEEECCCCCEEEEECH
Confidence 479999999999999987 454 344554
No 47
>PF14334 DUF4390: Domain of unknown function (DUF4390)
Probab=34.10 E-value=31 Score=26.05 Aligned_cols=51 Identities=20% Similarity=0.402 Sum_probs=30.1
Q ss_pred CeeEEeeccceeccccceEEEEcCCCCCcccEEEEeeeeeecc--cccCcccccc
Q 032316 86 AKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNKVNYAN--VSTNNYALDE 138 (143)
Q Consensus 86 skVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~kVNY~g--vsTNNfa~~E 138 (143)
-.++|.|+..||+++ +|+++...-.++|=-+=|==-|+..| ...+.-.++|
T Consensus 48 ~~~~l~r~R~~w~d~--~v~~~~~~~~L~Y~~Ltr~Y~v~~~~~~~~~~~~sL~~ 100 (165)
T PF14334_consen 48 FEIELYRPRWYWWDE--TVASATRRYRLSYDPLTREYRVTDGGSGLQQSFASLDE 100 (165)
T ss_pred EEEEEEeecccccCC--eeEEEEEEEEEEEeccCeeEEEEeCCCccceecCCHHH
Confidence 357899999999986 56666655456664433322344444 4444444444
No 48
>PRK15208 long polar fimbrial chaperone LpfB; Provisional
Probab=33.17 E-value=29 Score=27.91 Aligned_cols=20 Identities=40% Similarity=0.964 Sum_probs=15.6
Q ss_pred CCCCCCCeeEEee--------ccc-eecc
Q 032316 80 IGPKRGAKVKILR--------RES-YWYN 99 (143)
Q Consensus 80 igp~RGskVrIlR--------~ES-YWyn 99 (143)
+.|..+..|||++ +|| ||+|
T Consensus 78 l~p~~~q~lRIi~~~~~lP~DrESlf~ln 106 (228)
T PRK15208 78 LDPTKNNVLRIVNITNTLPQDRESVYWIN 106 (228)
T ss_pred ECCCCccEEEEEECCCCCCCCeeEEEEEE
Confidence 5677788999987 366 9987
No 49
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=33.12 E-value=1.7e+02 Score=27.05 Aligned_cols=35 Identities=14% Similarity=0.094 Sum_probs=26.7
Q ss_pred CCCCCCCCCCCCCCeeEEeec-cceeccccceEEEEcC
Q 032316 73 PKPKPPPIGPKRGAKVKILRR-ESYWYNGIGSVVAVDQ 109 (143)
Q Consensus 73 ~~~kpp~igp~RGskVrIlR~-ESYWyn~vGtVvsVDq 109 (143)
...++...-.+.|++|...+. +.=||. ++|+.+..
T Consensus 45 ~~~~~~~~~~~VGekVla~~~~Dg~~~~--A~VI~~R~ 80 (450)
T PLN00104 45 KKRPGVMLPLEVGTRVMCRWRFDGKYHP--VKVIERRR 80 (450)
T ss_pred ccCCCccceeccCCEEEEEECCCCCEEE--EEEEEEec
Confidence 334445556789999999998 677884 88988886
No 50
>PRK15249 fimbrial chaperone protein StbB; Provisional
Probab=32.61 E-value=30 Score=28.43 Aligned_cols=21 Identities=43% Similarity=0.937 Sum_probs=15.9
Q ss_pred CCCCCCCeeEEeec---------cc-eeccc
Q 032316 80 IGPKRGAKVKILRR---------ES-YWYNG 100 (143)
Q Consensus 80 igp~RGskVrIlR~---------ES-YWyn~ 100 (143)
+.|..+..|||++. || ||+|=
T Consensus 90 l~p~~~q~lRI~~~~~~~lP~DRESlf~lnv 120 (253)
T PRK15249 90 IQPKAGQVVRVIYNNTKKLPQDRESVFWFNV 120 (253)
T ss_pred ecCCCceEEEEEEcCCCCCCCCceEEEEEEe
Confidence 56777889999875 55 99863
No 51
>PRK09752 adhesin; Provisional
Probab=31.75 E-value=58 Score=33.65 Aligned_cols=6 Identities=17% Similarity=0.412 Sum_probs=4.3
Q ss_pred EEeecc
Q 032316 89 KILRRE 94 (143)
Q Consensus 89 rIlR~E 94 (143)
-++|||
T Consensus 952 PvlRPE 957 (1250)
T PRK09752 952 PVLNAK 957 (1250)
T ss_pred cccccc
Confidence 477777
No 52
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=31.68 E-value=56 Score=32.93 Aligned_cols=38 Identities=24% Similarity=0.340 Sum_probs=29.0
Q ss_pred CCCCCCeeEEeeccc--eecc-ccceEEEEcCCCCCcccEEEEeee
Q 032316 81 GPKRGAKVKILRRES--YWYN-GIGSVVAVDQDPKSRYPVVVRFNK 123 (143)
Q Consensus 81 gp~RGskVrIlR~ES--YWyn-~vGtVvsVDqs~girYPVvVRF~k 123 (143)
....||+|.++|.+- .++| ++|+|+.++.+ . ++|+|+.
T Consensus 633 ~f~vGDrV~f~rNd~~lgV~NGd~GtV~~i~~~-~----i~v~~d~ 673 (1102)
T PRK13826 633 RFAAGDQIVFLKNEGSLGVKNGMIGKVVEAAPN-R----IVAEIGE 673 (1102)
T ss_pred cccCCCEEEEeeecCccCccCCCeEEEEEecCC-e----EEEEEcC
Confidence 478999999998753 5677 69999999864 2 4777753
No 53
>PF08169 RBB1NT: RBB1NT (NUC162) domain; InterPro: IPR012603 This domain is found N-terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family [].; PDB: 2YRV_A.
Probab=30.26 E-value=40 Score=25.19 Aligned_cols=21 Identities=33% Similarity=0.578 Sum_probs=14.4
Q ss_pred cceEEEEcCCC--CCcccEEEEe
Q 032316 101 IGSVVAVDQDP--KSRYPVVVRF 121 (143)
Q Consensus 101 vGtVvsVDqs~--girYPVvVRF 121 (143)
+|+||+|+.+. +.=||.+|-=
T Consensus 8 lGkVV~V~~~~~k~~W~PALVVs 30 (96)
T PF08169_consen 8 LGKVVCVESTKKKTSWFPALVVS 30 (96)
T ss_dssp TTSEEEEE-SS-SS-EEEEEEE-
T ss_pred cCcEEEEEcCCCCCceeeEEEEc
Confidence 89999998763 3569988853
No 54
>smart00561 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
Probab=29.87 E-value=1.4e+02 Score=21.36 Aligned_cols=45 Identities=24% Similarity=0.391 Sum_probs=30.6
Q ss_pred CCCCCCCCCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEeee
Q 032316 74 KPKPPPIGPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNK 123 (143)
Q Consensus 74 ~~kpp~igp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~k 123 (143)
...++..+.+.|.|+...-+-.=..--+.||+.|. | +=+.|+||.
T Consensus 20 ~~~~~~~~F~vGmkLEavD~~~~~~i~vAtV~~v~---g--~~l~v~~dg 64 (96)
T smart00561 20 PVDSPPNGFKVGMKLEAVDPRNPSLICVATVVEVK---G--YRLLLHFDG 64 (96)
T ss_pred CCCCccCcccCCCEEEEECCCCCceEEEEEEEEEE---C--CEEEEEEcc
Confidence 45677889999999998765432222356666665 2 358889984
No 55
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=27.88 E-value=1.4e+02 Score=22.48 Aligned_cols=39 Identities=28% Similarity=0.331 Sum_probs=28.1
Q ss_pred CCCCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEee
Q 032316 79 PIGPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFN 122 (143)
Q Consensus 79 ~igp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~ 122 (143)
..+.+.|++|||.+- =|=+..|.|..+|.. .-+ ++|.+=
T Consensus 92 ~~~~~~G~~V~I~~G--pf~g~~g~V~~vd~~-k~~--v~v~ll 130 (153)
T PRK08559 92 VEGIKEGDIVELIAG--PFKGEKARVVRVDES-KEE--VTVELL 130 (153)
T ss_pred ccCCCCCCEEEEecc--CCCCceEEEEEEcCC-CCE--EEEEEE
Confidence 467999999999873 355667999999976 322 555543
No 56
>TIGR03177 pilus_cpaB Flp pilus assembly protein CpaB. Members of this protein family are the CpaB protein of Flp-type pilus assembly. Similar proteins include the FlgA protein of bacterial flagellum biosynthesis.
Probab=27.01 E-value=1.3e+02 Score=24.24 Aligned_cols=51 Identities=22% Similarity=0.264 Sum_probs=25.0
Q ss_pred ceeeEEeeccccCCCCCccccCCCcCCCCCCCCCCCCCCCCCCCeeEEeecc
Q 032316 43 SFRLVVRASEEAAAPPAAATTAAPAEGEAAPKPKPPPIGPKRGAKVKILRRE 94 (143)
Q Consensus 43 ~~rlvvra~e~~a~~~~~a~~~~~~~~~~~~~~kpp~igp~RGskVrIlR~E 94 (143)
.-+|++|...+...+.++.......... ....+.......|...|+|.|-.
T Consensus 206 ~l~lvLr~~~d~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~V~~~~g~ 256 (261)
T TIGR03177 206 TLSLALRNAADTDEAAATAVLAATLSLA-PALAKAVDAAAPRRAAVEVIRGG 256 (261)
T ss_pred eEEEEeeCcccccccccccccccccccc-ccccccccCCCCCCceEEEEeCc
Confidence 4788998876654322111111111111 12223334444567788888753
No 57
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=26.38 E-value=1.7e+02 Score=19.85 Aligned_cols=47 Identities=17% Similarity=0.119 Sum_probs=26.8
Q ss_pred CCCCCCCCeeEEeeccceeccccceEE-EEcCCCCCcccEEEEeeeeeecccccC
Q 032316 79 PIGPKRGAKVKILRRESYWYNGIGSVV-AVDQDPKSRYPVVVRFNKVNYANVSTN 132 (143)
Q Consensus 79 ~igp~RGskVrIlR~ESYWyn~vGtVv-sVDqs~girYPVvVRF~kVNY~gvsTN 132 (143)
..|++-||+|+|. ++.|+|. .+--+++++--+|.-...-+|.|...|
T Consensus 40 ~lGi~~Gd~V~v~-------s~~G~i~~~v~v~~~v~~g~V~~p~g~~~~~~~~~ 87 (96)
T cd02788 40 RLGLADGDLVEFS-------LGDGTLTLPVQISKYLPAGVVGLPLGAGFPGAPVA 87 (96)
T ss_pred HcCCCCCCEEEEE-------ECCeEEEEEEEECCCCCCCEEEEecCCCCcccccc
Confidence 4799999999995 5567653 333333465444433222356555443
No 58
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 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 []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=26.17 E-value=55 Score=19.62 Aligned_cols=22 Identities=23% Similarity=0.726 Sum_probs=16.2
Q ss_pred CCCCCCCCCCeeEEeec-cceec
Q 032316 77 PPPIGPKRGAKVKILRR-ESYWY 98 (143)
Q Consensus 77 pp~igp~RGskVrIlR~-ESYWy 98 (143)
+-.+..++|+++.|+.+ ++-|+
T Consensus 11 ~~eLs~~~Gd~i~v~~~~~~~Ww 33 (48)
T PF00018_consen 11 PDELSFKKGDIIEVLEKSDDGWW 33 (48)
T ss_dssp TTBSEB-TTEEEEEEEESSSSEE
T ss_pred CCEEeEECCCEEEEEEecCCCEE
Confidence 44688999999999985 44476
No 59
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=25.71 E-value=43 Score=23.22 Aligned_cols=14 Identities=21% Similarity=0.489 Sum_probs=10.6
Q ss_pred CCCCCeeEEeeccc
Q 032316 82 PKRGAKVKILRRES 95 (143)
Q Consensus 82 p~RGskVrIlR~ES 95 (143)
+++|++|+|.+-|.
T Consensus 122 i~~G~~V~Vv~v~g 135 (144)
T PF01957_consen 122 IPKGDRVRVVGVEG 135 (144)
T ss_dssp B-TT-EEEEEEEES
T ss_pred CCCCCEEEEEEEEC
Confidence 99999999998774
No 60
>PRK10476 multidrug resistance protein MdtN; Provisional
Probab=24.88 E-value=1.4e+02 Score=24.48 Aligned_cols=42 Identities=17% Similarity=0.128 Sum_probs=28.6
Q ss_pred CCCCCeeEEeeccceecc-ccceEEEEcCCCC------------------------CcccEEEEeeee
Q 032316 82 PKRGAKVKILRRESYWYN-GIGSVVAVDQDPK------------------------SRYPVVVRFNKV 124 (143)
Q Consensus 82 p~RGskVrIlR~ESYWyn-~vGtVvsVDqs~g------------------------irYPVvVRF~kV 124 (143)
++.|+.|+|.= ..|.+. --|+|..|..+.+ .+|||.+++++-
T Consensus 259 v~~Gq~v~i~~-~~~~~~~~~G~V~~Is~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~V~i~l~~~ 325 (346)
T PRK10476 259 IRVGDCATVYS-MIDRGRPFEGKVDSIGWGVLPDDGGNVPRGLPYVPRSINWVRVAQRFPVRIMLDKP 325 (346)
T ss_pred CCCCCEEEEEE-ecCCCceEEEEEEEECCcccccccccccccCCCCCCCCceEeEEEeeeEEEEeCCC
Confidence 56799999842 333322 2499999987421 359999999864
No 61
>PF07051 OCIA: Ovarian carcinoma immunoreactive antigen (OCIA); InterPro: IPR009764 This family consists of several ovarian carcinoma immunoreactive antigen (OCIA) and related eukaryotic sequences. The function of this family is unknown [,].
Probab=24.56 E-value=19 Score=27.50 Aligned_cols=18 Identities=39% Similarity=0.925 Sum_probs=12.4
Q ss_pred CCCeeEEee---ccceecccc
Q 032316 84 RGAKVKILR---RESYWYNGI 101 (143)
Q Consensus 84 RGskVrIlR---~ESYWyn~v 101 (143)
+-+-.||+| +|||||.-+
T Consensus 27 T~EE~kvlrEC~~ESFwyRsl 47 (111)
T PF07051_consen 27 TEEERKVLRECNEESFWYRSL 47 (111)
T ss_pred CHHHHHHHHHHHHhhhHhccC
Confidence 344556664 799999864
No 62
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=24.53 E-value=36 Score=26.93 Aligned_cols=56 Identities=23% Similarity=0.308 Sum_probs=31.5
Q ss_pred CCCCeeEEeeccceecccc-ceEEEEcCCCCCcccEEEE-eeeeeecccccCccccccc
Q 032316 83 KRGAKVKILRRESYWYNGI-GSVVAVDQDPKSRYPVVVR-FNKVNYANVSTNNYALDEI 139 (143)
Q Consensus 83 ~RGskVrIlR~ESYWyn~v-GtVvsVDqs~girYPVvVR-F~kVNY~gvsTNNfa~~El 139 (143)
=+|..||=++.+-|||.|. |++ .||-+..+--+..|. =+||+-.|==-|-+..-||
T Consensus 62 l~GnIv~qi~~D~y~FrD~sGeI-~VeIdd~~w~g~tv~P~dkV~I~GevDk~~~~~eI 119 (128)
T COG3111 62 LEGNIVRQIGDDRYVFRDASGEI-NVDIDDKVWNGQTVTPKDKVRIQGEVDKDWNSVEI 119 (128)
T ss_pred EEeeEEEeeCCceEEEEcCCccE-EEEecccccCCcccCcccEEEEEeEEcCCCcccee
Confidence 4899999999999999985 544 344432222222222 1345555543444444443
No 63
>PF11347 DUF3148: Protein of unknown function (DUF3148); InterPro: IPR021495 This family of proteins has no known function.
Probab=24.52 E-value=2.2e+02 Score=20.18 Aligned_cols=24 Identities=21% Similarity=0.410 Sum_probs=17.0
Q ss_pred cccceEEEEcCCCCCcccEEEEeeeeee
Q 032316 99 NGIGSVVAVDQDPKSRYPVVVRFNKVNY 126 (143)
Q Consensus 99 n~vGtVvsVDqs~girYPVvVRF~kVNY 126 (143)
.|+|+|++.-.. +. .-|||.+=.|
T Consensus 33 ge~G~i~~rrp~-~~---w~VRf~~Gtf 56 (63)
T PF11347_consen 33 GEVGRIVDRRPG-DY---WAVRFRRGTF 56 (63)
T ss_pred CCcEEEEEecCC-CE---EEEEEeceeE
Confidence 688888887765 32 4688887655
No 64
>PF02820 MBT: mbt repeat; InterPro: IPR004092 The function of the malignant brain tumor (MBT) repeat is unknown, but is found in a number of nuclear proteins involved in transcriptional repression. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function. The crystal structure of the two MBT repeats of human SCM-like 2 protein has been reported. Each repeat consists of an extended "arm" and a globular core. The arm of the first repeat packs against the core of the second repeat and vice versa. The structure of the core-interacting part of each arm consists of an N-terminal alpha-helix and a turn of 310 helix connected by a short beta-strand. The core consists of an Src homology 3-like five-stranded beta-barrel followed by a C-terminal alpha-helix and another short beta-strand. Each arm interacts with its partner core in a similar way, with the orientation of the N-terminal helix relative to the barrel varying slightly. There are also extensive interactions between the two barrels [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P0K_A 3F70_B 3CEY_A 2VYT_A 2BIV_A 1OI1_A 3OQ5_A 2RJE_B 2RJD_A 2RI3_A ....
Probab=24.32 E-value=88 Score=20.73 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=17.1
Q ss_pred eccceeccccceEEEEcCCCCCcccEEEEeee
Q 032316 92 RRESYWYNGIGSVVAVDQDPKSRYPVVVRFNK 123 (143)
Q Consensus 92 R~ESYWyn~vGtVvsVDqs~girYPVvVRF~k 123 (143)
.++.+| +.||+.|... + +.||||.
T Consensus 10 ~~~~~~---vAtV~~v~g~---~--l~v~~dg 33 (73)
T PF02820_consen 10 NPSLIC---VATVVKVCGG---R--LLVRYDG 33 (73)
T ss_dssp ECCEEE---EEEEEEEETT---E--EEEEETT
T ss_pred CCCeEE---EEEEEEEeCC---E--EEEEEcC
Confidence 456677 6777777643 4 9999986
No 65
>cd08150 catalase_like Catalase-like heme-binding proteins and protein domains. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity.
Probab=23.77 E-value=46 Score=27.11 Aligned_cols=14 Identities=29% Similarity=0.579 Sum_probs=11.8
Q ss_pred CCcccEEEEeeeee
Q 032316 112 KSRYPVVVRFNKVN 125 (143)
Q Consensus 112 girYPVvVRF~kVN 125 (143)
|-.|||+|||.+..
T Consensus 34 ~~~~pv~~RfS~~~ 47 (283)
T cd08150 34 GKVYPAYIRFSNGA 47 (283)
T ss_pred CCeeEEEEEeCCCC
Confidence 56899999998864
No 66
>TIGR03794 NHPM_micro_HlyD NHPM bacteriocin system secretion protein. Members of this protein family are homologs of the HlyD membrane fusion protein of type I secretion systems. Their occurrence in prokaryotic genomes is associated with the occurrence of a novel class of microcin (small bacteriocins) with a propeptide region related to nitrile hydratase. We designate the class of bacteriocin as Nitrile Hydratase Propeptide Microcin, or NHPM. This family, therefore, is designated as NHPM bacteriocin system secretion protein. Some but not all NHPM-class putative microcins belong to the TOMM (thiazole/oxazole modified microcin) class as assessed by the presence of the scaffolding protein and/or cyclodehydratase in the same gene clusters.
Probab=23.51 E-value=1.6e+02 Score=24.93 Aligned_cols=47 Identities=19% Similarity=0.233 Sum_probs=32.6
Q ss_pred CCCCCeeEEeeccceecc----ccceEEEEcCCC----------------------CCcccEEEEe--eeeeeccc
Q 032316 82 PKRGAKVKILRRESYWYN----GIGSVVAVDQDP----------------------KSRYPVVVRF--NKVNYANV 129 (143)
Q Consensus 82 p~RGskVrIlR~ESYWyn----~vGtVvsVDqs~----------------------girYPVvVRF--~kVNY~gv 129 (143)
++.|++|+|. ..+|=|. -.|+|.+|+.++ |..|-|.|++ +..+..|+
T Consensus 308 v~~G~~v~v~-~~~~~~~~~~~~~g~V~~Is~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~v~v~l~~~~~~~~~~ 382 (421)
T TIGR03794 308 IRPGMSVQIT-PSTVKAERDGYIRGTVTSVSEYPATKEAMDRTLGNEAFVQYLLAQGPPIEVFVALERDRSSPSGF 382 (421)
T ss_pred CCCCCEEEEE-EcccccceeeeEEEEEEEecCCCCCHHHHHHHhCCHHHHHHHHhcCCcEEEEEEEecCCCCCCCC
Confidence 5789999986 4443232 258999998664 3458899999 55666655
No 67
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=22.84 E-value=48 Score=24.36 Aligned_cols=27 Identities=30% Similarity=0.575 Sum_probs=19.3
Q ss_pred CCCCeeEEeeccceecccc-ceE-EEEcC
Q 032316 83 KRGAKVKILRRESYWYNGI-GSV-VAVDQ 109 (143)
Q Consensus 83 ~RGskVrIlR~ESYWyn~v-GtV-vsVDq 109 (143)
=+|-.||-++.|.|.|.|- |+| +.||.
T Consensus 39 L~G~Iv~~l~~d~Y~F~D~TG~I~VeId~ 67 (103)
T PF04076_consen 39 LEGNIVKQLGDDKYLFRDATGEIEVEIDD 67 (103)
T ss_dssp EEEEEEEEEETTEEEEEETTEEEEEE--G
T ss_pred EEEEEEEEecCCEEEEECCCCcEEEEECh
Confidence 3688999999999999974 543 33444
No 68
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=22.82 E-value=44 Score=23.19 Aligned_cols=18 Identities=39% Similarity=0.750 Sum_probs=11.4
Q ss_pred CCCCCeeEEeeccceeccc
Q 032316 82 PKRGAKVKILRRESYWYNG 100 (143)
Q Consensus 82 p~RGskVrIlR~ESYWyn~ 100 (143)
|++|+.| ++..++||-++
T Consensus 66 P~~gd~v-~~dG~~y~V~~ 83 (95)
T PF13856_consen 66 PRRGDRV-VIDGESYTVTR 83 (95)
T ss_dssp --TT-EE-EETTEEEEEEE
T ss_pred CCCCCEE-EECCeEEEEeE
Confidence 6789999 55688998544
No 69
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=22.14 E-value=89 Score=22.27 Aligned_cols=34 Identities=26% Similarity=0.412 Sum_probs=21.9
Q ss_pred CCCCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEeeeeee
Q 032316 79 PIGPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFNKVNY 126 (143)
Q Consensus 79 ~igp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~kVNY 126 (143)
--++++|+.|. |.|-.= + .+-||+-++|-+.||-
T Consensus 40 rf~LR~GD~V~------------G~vr~p-~-~~ek~~aL~~V~~VNg 73 (78)
T PF07497_consen 40 RFGLRTGDLVE------------GQVRPP-R-EGEKYFALLRVESVNG 73 (78)
T ss_dssp CTT--TTEEEE------------EEEE---S-TTSSSEEECEECEETT
T ss_pred HcCCCCCCEEE------------EEEeCC-C-CCCcceeeEEEEeECC
Confidence 45888999886 222211 3 3679999999999984
No 70
>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein. This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.
Probab=21.74 E-value=1.7e+02 Score=25.25 Aligned_cols=42 Identities=21% Similarity=0.304 Sum_probs=29.2
Q ss_pred CCCCCCeeEEeeccceecc--ccceEEEEcCCC-----CCcccEEEEee
Q 032316 81 GPKRGAKVKILRRESYWYN--GIGSVVAVDQDP-----KSRYPVVVRFN 122 (143)
Q Consensus 81 gp~RGskVrIlR~ESYWyn--~vGtVvsVDqs~-----girYPVvVRF~ 122 (143)
.++.|+.|+|.=.-.|... =-|+|..|..++ +.-|.|.|+++
T Consensus 371 ~v~~Gq~V~v~~~a~~~~~~~~~G~V~~Is~~~~~~~~~~~y~v~v~l~ 419 (457)
T TIGR01000 371 GIKVGQKVRFKLTQNVPKPIILDGTITSISSAPTATKKGNFYKVIATIK 419 (457)
T ss_pred hcCCCCeEEEEEecCCCCceEEEEEEEEEcCCCccCCCCCEEEEEEEec
Confidence 3577999998644333332 369999997542 45799999986
No 71
>PHA02123 hypothetical protein
Probab=21.72 E-value=94 Score=24.88 Aligned_cols=31 Identities=23% Similarity=0.410 Sum_probs=26.7
Q ss_pred CCCCCeeEEeeccceeccccceEEEEcCCCC
Q 032316 82 PKRGAKVKILRRESYWYNGIGSVVAVDQDPK 112 (143)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDqs~g 112 (143)
+.-||-+-|.|+..==||-+|.|.+|..+.|
T Consensus 110 irsgsaivi~r~dnp~fnp~g~v~sitt~~g 140 (146)
T PHA02123 110 IRSGSAIVIRRMDNPTFNPIGDVLSITTSSG 140 (146)
T ss_pred EecCcEEEEEecCCCCCCcccceEEEecCCC
Confidence 4568889999999999999999999988654
No 72
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=21.63 E-value=1.5e+02 Score=21.51 Aligned_cols=29 Identities=21% Similarity=0.535 Sum_probs=21.9
Q ss_pred CCCCCCCCeeEEeecc--------ceeccccceEEEEcCC
Q 032316 79 PIGPKRGAKVKILRRE--------SYWYNGIGSVVAVDQD 110 (143)
Q Consensus 79 ~igp~RGskVrIlR~E--------SYWyn~vGtVvsVDqs 110 (143)
-...|.|+.|-|...+ +|| +|.|..++-+
T Consensus 3 FL~Vk~Gd~ViV~~~~~~~~~~~~dWW---mg~Vi~~~gg 39 (75)
T PF11302_consen 3 FLSVKPGDTVIVQDEQEVGQKQDKDWW---MGQVIHCEGG 39 (75)
T ss_pred ccccCCCCEEEEecCccccccCCCCcE---EEEEEEEecc
Confidence 3567899999888776 888 5777777763
No 73
>PF04023 FeoA: FeoA domain; InterPro: IPR007167 This entry represents the core domain of the ferrous iron (Fe2+) transport protein FeoA found in bacteria. This domain also occurs at the C terminus in related proteins. The transporter Feo is composed of three proteins: FeoA a small, soluble SH3-domain protein probably located in the cytosol; FeoB, a large protein with a cytosolic N-terminal G-protein domain and a C-terminal integral inner-membrane domain containing two 'Gate' motifs which likely functions as the Fe2+ permease; and FeoC, a small protein apparently functioning as an [Fe-S]-dependent transcriptional repressor [, ]. Feo allows the bacterial cell to acquire iron from its environment. ; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 1G3T_A 1C0W_B 1BI3_A 1QVP_A 1BI1_A 1BYM_A 2QQB_A ....
Probab=21.56 E-value=61 Score=20.59 Aligned_cols=18 Identities=17% Similarity=0.693 Sum_probs=13.6
Q ss_pred CCCCCCCCeeEEeeccce
Q 032316 79 PIGPKRGAKVKILRRESY 96 (143)
Q Consensus 79 ~igp~RGskVrIlR~ESY 96 (143)
..|+..|++|+|+++..+
T Consensus 30 ~lGl~~G~~i~v~~~~~~ 47 (74)
T PF04023_consen 30 DLGLTPGSEITVIRKNPF 47 (74)
T ss_dssp HCT-STTEEEEEEEEETT
T ss_pred HCCCCCCCEEEEEEeCCC
Confidence 368999999999987543
No 74
>cd08152 y4iL_like Catalase-like heme-binding proteins similar to the uncharacterized y4iL. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity. This family contains uncharacterized proteins similar to Rhizobium sp. NGR234 y4iL, of mostly bacterial origin.
Probab=21.50 E-value=53 Score=27.19 Aligned_cols=15 Identities=33% Similarity=0.671 Sum_probs=12.5
Q ss_pred CCcccEEEEeeeeee
Q 032316 112 KSRYPVVVRFNKVNY 126 (143)
Q Consensus 112 girYPVvVRF~kVNY 126 (143)
|-.|||+|||.+..-
T Consensus 37 ~~~~pv~vRfS~~~~ 51 (305)
T cd08152 37 PGTYPAVIRFSNAPG 51 (305)
T ss_pred CCeEEEEEEecCCCC
Confidence 558999999998754
No 75
>cd08151 AOS Allene oxide synthase. Allene oxide synthase converts a fatty acid hydroperoxide to an allene oxide, which is an unstable epoxide. In corals, the enzyme is part of a eiconaosid synthesis pathway that is initiated by a lipoxygenase, which generates the fatty acid hydroperoxides in the first step. The structure of allene oxide synthase closely resembles that of catalase, but allene oxide synthase does not have catalase activity.
Probab=21.30 E-value=55 Score=27.58 Aligned_cols=14 Identities=29% Similarity=0.731 Sum_probs=12.0
Q ss_pred CCcccEEEEeeeee
Q 032316 112 KSRYPVVVRFNKVN 125 (143)
Q Consensus 112 girYPVvVRF~kVN 125 (143)
|..|||+|||.++.
T Consensus 58 g~~~pv~~RfS~~~ 71 (328)
T cd08151 58 GKRFPVILRHANIV 71 (328)
T ss_pred CCeEEEEEEecCCC
Confidence 66899999998873
No 76
>TIGR02971 heterocyst_DevB ABC exporter membrane fusion protein, DevB family. Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. DevB from Anabaena sp. strain PCC 7120 is partially characterized as a membrane fusion protein of the DevBCA ABC exporter, probably a glycolipid exporter, required for heterocyst formation. Most Cyanobacteria have one member only, but Nostoc sp. PCC 7120 has seven members.
Probab=21.22 E-value=1.8e+02 Score=23.30 Aligned_cols=41 Identities=17% Similarity=0.187 Sum_probs=26.6
Q ss_pred CCCCCeeEEeeccceeccccceEEEEcC--------------CC-CCcccEEEEeee
Q 032316 82 PKRGAKVKILRRESYWYNGIGSVVAVDQ--------------DP-KSRYPVVVRFNK 123 (143)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDq--------------s~-girYPVvVRF~k 123 (143)
++.|++|+|.-. +|=..--|+|..|.. ++ .-.|||.|+|+.
T Consensus 254 i~~G~~v~i~~~-~~~~~~~g~V~~Is~~~~~~~~~~~~~~~~~~~~~~~v~i~l~~ 309 (327)
T TIGR02971 254 VRVGQRATITST-ALSGPLRGTVRRIGSLIAKNDVLSTDPAADADARVVEVKIRLDP 309 (327)
T ss_pred CCCCCEEEEEEc-CCCCcEEEEEEEeccccccccccCCCCcccCCcceEEEEEEECC
Confidence 567999998543 332223688988842 11 224999999984
No 77
>PF15252 DUF4589: Domain of unknown function (DUF4589)
Probab=21.05 E-value=43 Score=28.55 Aligned_cols=13 Identities=46% Similarity=0.705 Sum_probs=10.7
Q ss_pred EEEe-eeeeecccc
Q 032316 118 VVRF-NKVNYANVS 130 (143)
Q Consensus 118 vVRF-~kVNY~gvs 130 (143)
=||| |||-|.|+=
T Consensus 133 RVRFSdKVlYHalC 146 (221)
T PF15252_consen 133 RVRFSDKVLYHALC 146 (221)
T ss_pred eeeccccceeeeee
Confidence 3789 799999975
No 78
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=20.72 E-value=2.3e+02 Score=20.92 Aligned_cols=37 Identities=24% Similarity=0.267 Sum_probs=25.6
Q ss_pred CCCCCCCeeEEeeccceeccccceEEEEcCCCCCcccEEEEee
Q 032316 80 IGPKRGAKVKILRRESYWYNGIGSVVAVDQDPKSRYPVVVRFN 122 (143)
Q Consensus 80 igp~RGskVrIlR~ESYWyn~vGtVvsVDqs~girYPVvVRF~ 122 (143)
...+.|++|||..-- +=+-.|.|..+|-. .| ++|.++
T Consensus 108 ~~~~~G~~V~I~~Gp--~~g~eg~v~~~~~~--~r--~~v~v~ 144 (162)
T PRK09014 108 ETPKPGDKVIITEGA--FEGLQAIYTEPDGE--AR--SILLLN 144 (162)
T ss_pred cCCCCCCEEEEecCC--CCCcEEEEEEeCCC--eE--EEEeeh
Confidence 358899999998743 55566999999843 23 445544
No 79
>PF09867 DUF2094: Uncharacterized protein conserved in bacteria (DUF2094); InterPro: IPR017748 These proteins are found exclusively, although not universally, in bacterial species that possess a type VI secretion system and are encoded in type VI secretion-associated gene clusters. Their specific function is not yet known. Occasionally a domain is found C-terminal to this entry, but it shows little if any conservation between sequences.; PDB: 2QNU_B.
Probab=20.67 E-value=54 Score=24.62 Aligned_cols=19 Identities=26% Similarity=0.557 Sum_probs=9.1
Q ss_pred cceE-EEEcCCCCCcccEEEE
Q 032316 101 IGSV-VAVDQDPKSRYPVVVR 120 (143)
Q Consensus 101 vGtV-vsVDqs~girYPVvVR 120 (143)
+|.+ -|+|.. |-+||.+|-
T Consensus 69 ~G~l~pS~D~v-GR~fPl~~~ 88 (138)
T PF09867_consen 69 AGVLMPSVDRV-GRRFPLTLA 88 (138)
T ss_dssp EEEEE--B-TT-S-B--EEEE
T ss_pred EEEEeeccccc-CCcCceeee
Confidence 3443 589997 999999873
Done!