Query 033136
Match_columns 126
No_of_seqs 92 out of 94
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 10:15:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033136.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033136hhsearch_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 1.4E-36 2.9E-41 222.1 6.7 54 72-126 30-83 (101)
2 CHL00125 psaE photosystem I su 100.0 1.6E-30 3.5E-35 177.9 4.7 44 81-126 1-44 (64)
3 PRK02749 photosystem I reactio 100.0 4.1E-30 8.8E-35 178.8 5.0 44 81-126 2-45 (71)
4 PF02427 PSI_PsaE: Photosystem 100.0 2.4E-30 5.1E-35 175.7 3.5 43 82-126 1-43 (61)
5 smart00739 KOW KOW (Kyprides, 86.2 1.5 3.2E-05 23.1 3.2 27 82-110 2-28 (28)
6 COG3758 Uncharacterized protei 81.6 1.1 2.5E-05 36.3 2.2 36 86-121 2-62 (193)
7 smart00333 TUDOR Tudor domain. 76.3 10 0.00022 22.6 4.8 37 81-124 2-38 (57)
8 smart00743 Agenet Tudor-like d 75.3 9.5 0.00021 23.5 4.6 35 82-124 3-39 (61)
9 smart00326 SH3 Src homology 3 75.1 4.3 9.4E-05 22.7 2.8 24 76-99 15-39 (58)
10 PRK05609 nusG transcription an 72.8 14 0.00031 26.9 5.7 33 78-112 123-155 (181)
11 PF14743 DNA_ligase_OB_2: DNA 72.7 1.9 4.2E-05 28.7 1.1 32 88-122 29-65 (66)
12 PF11910 NdhO: Cyanobacterial 69.2 6.7 0.00014 27.6 3.1 31 82-112 1-46 (67)
13 PRK09570 rpoH DNA-directed RNA 66.4 4.6 9.9E-05 28.6 1.9 15 79-93 49-63 (79)
14 PF01191 RNA_pol_Rpb5_C: RNA p 65.6 4.7 0.0001 28.0 1.8 16 79-94 46-61 (74)
15 TIGR01080 rplX_A_E ribosomal p 65.3 9.9 0.00021 28.2 3.6 31 79-111 39-69 (114)
16 PRK00409 recombination and DNA 64.2 11 0.00024 34.9 4.5 27 80-111 635-661 (782)
17 PRK00004 rplX 50S ribosomal pr 63.7 13 0.00029 26.6 3.9 30 81-112 4-33 (105)
18 PRK12281 rplX 50S ribosomal pr 63.5 14 0.00031 25.3 3.9 30 81-112 6-35 (76)
19 COG0250 NusG Transcription ant 63.5 19 0.00041 28.0 5.0 35 75-111 117-151 (178)
20 TIGR02768 TraA_Ti Ti-type conj 60.8 12 0.00026 34.3 4.0 38 80-123 606-646 (744)
21 cd00174 SH3 Src homology 3 dom 60.6 14 0.0003 20.5 2.9 21 78-98 14-35 (54)
22 CHL00141 rpl24 ribosomal prote 57.4 21 0.00045 24.9 3.9 30 81-112 8-37 (83)
23 TIGR00922 nusG transcription t 55.7 43 0.00093 24.4 5.5 31 79-111 117-147 (172)
24 COG1596 Wza Periplasmic protei 54.9 22 0.00048 28.2 4.1 44 74-119 40-85 (239)
25 PTZ00194 60S ribosomal protein 54.4 18 0.00039 28.1 3.5 29 81-111 46-74 (143)
26 COG2012 RPB5 DNA-directed RNA 54.1 9.5 0.00021 27.6 1.8 15 79-93 52-66 (80)
27 PF05641 Agenet: Agenet domain 50.1 34 0.00073 22.1 3.8 35 83-124 2-40 (68)
28 TIGR01843 type_I_hlyD type I s 49.7 31 0.00068 27.3 4.2 42 82-124 324-375 (423)
29 TIGR01079 rplX_bact ribosomal 49.0 32 0.0007 24.8 3.9 29 81-111 3-31 (104)
30 PF07576 BRAP2: BRCA1-associat 48.9 20 0.00044 26.0 2.9 15 108-124 49-63 (110)
31 PRK13889 conjugal transfer rel 47.5 32 0.00068 33.4 4.6 32 81-112 600-634 (988)
32 PF14334 DUF4390: Domain of un 47.3 17 0.00038 26.9 2.3 28 86-116 48-75 (165)
33 PF07653 SH3_2: Variant SH3 do 47.3 14 0.0003 22.4 1.6 26 76-101 12-40 (55)
34 KOG3218 RNA polymerase, 25-kDa 45.9 13 0.00027 30.9 1.5 15 80-94 181-195 (208)
35 PTZ00061 DNA-directed RNA poly 45.3 15 0.00033 30.0 1.9 16 79-94 177-192 (205)
36 PLN03111 DNA-directed RNA poly 44.3 16 0.00035 29.8 1.9 15 79-93 178-192 (206)
37 PLN00104 MYST -like histone ac 43.9 1E+02 0.0022 27.9 6.9 49 75-125 47-98 (450)
38 PF02470 MCE: mce related prot 43.5 75 0.0016 20.3 4.6 27 80-112 13-41 (81)
39 PF11347 DUF3148: Protein of u 43.3 63 0.0014 22.4 4.4 21 99-124 33-53 (63)
40 PF14604 SH3_9: Variant SH3 do 42.3 18 0.00039 22.1 1.5 21 79-99 12-33 (49)
41 PRK15208 long polar fimbrial c 42.0 18 0.00038 28.6 1.8 20 80-99 78-106 (228)
42 cd04508 TUDOR Tudor domains ar 41.1 70 0.0015 18.3 4.5 33 85-124 1-34 (48)
43 PRK01191 rpl24p 50S ribosomal 41.0 48 0.001 25.1 3.9 31 80-112 44-74 (120)
44 TIGR01069 mutS2 MutS2 family p 40.7 34 0.00075 31.8 3.7 23 83-110 626-648 (771)
45 PF00467 KOW: KOW motif; Inte 39.4 37 0.00079 19.3 2.4 27 84-112 1-27 (32)
46 PRK15249 fimbrial chaperone pr 38.4 21 0.00046 28.7 1.7 21 80-100 90-120 (253)
47 PF14085 DUF4265: Domain of un 38.3 27 0.00059 25.0 2.1 22 80-101 24-46 (117)
48 cd03692 mtIF2_IVc mtIF2_IVc: t 37.7 35 0.00076 22.7 2.4 27 82-110 27-53 (84)
49 PRK13826 Dtr system oriT relax 37.1 48 0.001 32.8 4.2 31 81-111 633-666 (1102)
50 PF02237 BPL_C: Biotin protein 36.7 81 0.0018 19.2 3.8 24 85-112 3-27 (48)
51 PRK15195 fimbrial chaperone pr 34.9 25 0.00055 27.9 1.7 21 80-100 82-111 (229)
52 TIGR00156 conserved hypothetic 34.7 17 0.00038 27.4 0.7 27 83-109 62-90 (126)
53 TIGR02971 heterocyst_DevB ABC 34.1 96 0.0021 24.4 4.7 42 82-124 254-309 (327)
54 PRK15136 multidrug efflux syst 33.4 1.1E+02 0.0024 25.5 5.2 43 81-124 265-327 (390)
55 PF13437 HlyD_3: HlyD family s 32.5 1.2E+02 0.0026 19.7 4.4 42 84-125 53-96 (105)
56 PF07051 OCIA: Ovarian carcino 31.7 12 0.00026 28.1 -0.6 17 85-101 28-47 (111)
57 TIGR03177 pilus_cpaB Flp pilus 31.3 1E+02 0.0022 24.3 4.4 51 43-94 206-256 (261)
58 TIGR00998 8a0101 efflux pump m 30.4 1.6E+02 0.0035 23.0 5.4 42 82-124 255-316 (334)
59 TIGR03027 pepcterm_export puta 30.1 73 0.0016 23.4 3.3 35 82-120 3-37 (165)
60 COG1463 Ttg2C ABC-type transpo 29.7 71 0.0015 26.5 3.5 36 80-123 51-86 (359)
61 PRK13828 rimM 16S rRNA-process 26.7 1E+02 0.0023 23.0 3.7 29 84-112 61-109 (161)
62 PF08169 RBB1NT: RBB1NT (NUC16 26.5 66 0.0014 23.6 2.5 22 100-121 7-29 (96)
63 PRK09781 hypothetical protein; 26.0 40 0.00087 27.4 1.4 21 81-101 14-35 (181)
64 PRK14593 rimM 16S rRNA-process 25.8 1.2E+02 0.0025 23.2 3.9 14 99-112 119-132 (184)
65 PF00199 Catalase: Catalase; 25.3 56 0.0012 27.6 2.2 11 115-125 79-89 (384)
66 PF01957 NfeD: NfeD-like C-ter 25.1 46 0.001 22.6 1.4 14 82-95 122-135 (144)
67 PF13856 Gifsy-2: ATP-binding 25.1 36 0.00079 23.1 0.9 18 82-100 66-83 (95)
68 COG3364 Zn-ribbon containing p 25.1 1.4E+02 0.003 22.9 4.1 32 86-120 62-99 (112)
69 PRK13829 rimM 16S rRNA-process 24.8 1.2E+02 0.0026 22.7 3.7 30 83-112 69-117 (162)
70 TIGR00531 BCCP acetyl-CoA carb 24.6 2.3E+02 0.0049 21.3 5.2 30 81-110 85-114 (156)
71 PF11717 Tudor-knot: RNA bindi 24.2 1.9E+02 0.0041 18.0 4.3 39 83-125 2-40 (55)
72 PRK09752 adhesin; Provisional 24.2 99 0.0021 31.6 3.9 6 89-94 952-957 (1250)
73 PF00018 SH3_1: SH3 domain; I 24.0 64 0.0014 18.9 1.7 22 77-98 11-33 (48)
74 PF05257 CHAP: CHAP domain; I 24.0 90 0.0019 21.3 2.7 33 79-111 60-92 (124)
75 PRK07772 single-stranded DNA-b 23.5 1.9E+02 0.004 22.9 4.7 17 81-97 70-89 (186)
76 PRK08559 nusG transcription an 23.4 2.2E+02 0.0047 21.1 4.8 31 79-111 92-122 (153)
77 cd08152 y4iL_like Catalase-lik 23.0 67 0.0015 26.1 2.2 11 115-125 39-49 (305)
78 cd04454 S1_Rrp4_like S1_Rrp4_l 22.9 93 0.002 19.9 2.5 21 82-102 4-27 (82)
79 KOG2310 DNA repair exonuclease 22.9 39 0.00085 32.1 0.9 15 86-100 197-214 (646)
80 PF04076 BOF: Bacterial OB fol 22.8 57 0.0012 23.5 1.6 27 83-109 39-67 (103)
81 PF04023 FeoA: FeoA domain; I 21.7 59 0.0013 20.3 1.3 18 79-96 30-47 (74)
82 PRK14639 hypothetical protein; 21.4 1.8E+02 0.004 21.6 4.1 42 82-125 85-131 (140)
83 PRK09918 putative fimbrial cha 21.2 64 0.0014 25.4 1.7 20 80-99 80-107 (230)
84 PRK14635 hypothetical protein; 21.0 2E+02 0.0044 21.8 4.3 30 83-112 97-129 (162)
85 COG3121 FimC P pilus assembly 20.3 76 0.0016 25.2 2.0 21 79-99 84-113 (235)
86 PLN00129 succinate dehydrogena 20.1 98 0.0021 25.8 2.6 20 74-93 30-51 (276)
No 1
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=100.00 E-value=1.4e-36 Score=222.07 Aligned_cols=54 Identities=63% Similarity=1.034 Sum_probs=51.7
Q ss_pred CCCCCCCCCCCCCCCeeEEeeccceeccccceEEEEccCCceeeeeEEEEeeecC
Q 033136 72 APKPKPPPIGPKRGAKVKILRRESYWYNGIGSVVAVDQVRLFSIFLVYVTFNHFK 126 (126)
Q Consensus 72 a~k~kpppigp~RGskVrIlR~ESYWyn~vGtVvsVDq~~~~~rYPVvVRF~kv~ 126 (126)
++++|||||||+|||||||||+||||||++|+|++|||+.+ +||||+|||||||
T Consensus 30 ~~~~kpp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~~g-irYPVvVRF~kvN 83 (101)
T PLN00045 30 AAKPKPPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQDPG-VRYPVVVRFEKVN 83 (101)
T ss_pred cccCCCCCcccCCCCEEEEccccceeecCcceEEEEeCCCC-cccceEEEeeeee
Confidence 78999999999999999999999999999999999999955 7999999999997
No 2
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=99.96 E-value=1.6e-30 Score=177.95 Aligned_cols=44 Identities=52% Similarity=0.857 Sum_probs=42.2
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEccCCceeeeeEEEEeeecC
Q 033136 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQVRLFSIFLVYVTFNHFK 126 (126)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDq~~~~~rYPVvVRF~kv~ 126 (126)
+++||||||||||||||||++|||++|||+| +||||+|||||||
T Consensus 1 mi~rGskVrIlR~ESYWyn~vGtV~svd~~g--i~YPV~VRF~kvN 44 (64)
T CHL00125 1 MVKRGSKVRILRKESYWYNEIGTVATVDQSG--IRYPVLVRFEKVN 44 (64)
T ss_pred CcccCCEEEEccccceeecCcceEEEEcCCC--CCccEEEEEeeee
Confidence 5799999999999999999999999999997 5999999999997
No 3
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=99.96 E-value=4.1e-30 Score=178.75 Aligned_cols=44 Identities=45% Similarity=0.815 Sum_probs=42.3
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEccCCceeeeeEEEEeeecC
Q 033136 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQVRLFSIFLVYVTFNHFK 126 (126)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDq~~~~~rYPVvVRF~kv~ 126 (126)
+++|||||||||||||||||+|||++|||+| +||||+|||||||
T Consensus 2 ~i~rGskVrIlR~ESYWyn~vGtV~svD~sg--i~YPV~VRF~kvN 45 (71)
T PRK02749 2 AISRGDKVRILRPESYWYNEVGTVASVDKSG--IKYPVIVRFDKVN 45 (71)
T ss_pred ccccCCEEEEccccceeecCcceEEEEccCC--CeeeEEEEeeeee
Confidence 5899999999999999999999999999998 5999999999997
No 4
>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=99.96 E-value=2.4e-30 Score=175.73 Aligned_cols=43 Identities=51% Similarity=0.896 Sum_probs=37.9
Q ss_pred CCCCCeeEEeeccceeccccceEEEEccCCceeeeeEEEEeeecC
Q 033136 82 PKRGAKVKILRRESYWYNGIGSVVAVDQVRLFSIFLVYVTFNHFK 126 (126)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDq~~~~~rYPVvVRF~kv~ 126 (126)
++||||||||||||||||++|+|++|||+| +||||+|||||||
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~--i~YPV~VRF~kvN 43 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSG--IRYPVVVRFDKVN 43 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSS--SSSSEEEE-SSS-
T ss_pred CCCCCEEEEccccceeecccceEEEEccCC--ccccEEEEEEEec
Confidence 589999999999999999999999999999 5999999999996
No 5
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=86.18 E-value=1.5 Score=23.15 Aligned_cols=27 Identities=22% Similarity=0.405 Sum_probs=22.4
Q ss_pred CCCCCeeEEeeccceeccccceEEEEccC
Q 033136 82 PKRGAKVKILRRESYWYNGIGSVVAVDQV 110 (126)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDq~ 110 (126)
++.|++|+|+.-. |-..+|.|..+|..
T Consensus 2 ~~~G~~V~I~~G~--~~g~~g~i~~i~~~ 28 (28)
T smart00739 2 FEVGDTVRVIAGP--FKGKVGKVLEVDGE 28 (28)
T ss_pred CCCCCEEEEeECC--CCCcEEEEEEEcCC
Confidence 5789999999855 77788999999863
No 6
>COG3758 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.56 E-value=1.1 Score=36.26 Aligned_cols=36 Identities=39% Similarity=0.597 Sum_probs=28.8
Q ss_pred CeeEEeeccce----eccccc---------------------eEEEEccCCceeeeeEEEE
Q 033136 86 AKVKILRRESY----WYNGIG---------------------SVVAVDQVRLFSIFLVYVT 121 (126)
Q Consensus 86 skVrIlR~ESY----Wyn~vG---------------------tVvsVDq~~~~~rYPVvVR 121 (126)
+++||||+|.| |=|.=| ++++|.++|-|++||=+=|
T Consensus 2 t~m~il~~~dy~~mPWkNgGG~T~EIav~P~~a~~~dF~WRiS~AtVa~~G~FS~fpGidR 62 (193)
T COG3758 2 TMMRILRAEDYRRMPWKNGGGETNEIAVYPEGAAKRDFDWRISIATVAADGPFSLFPGIDR 62 (193)
T ss_pred cceEeecccccccCCcccCCCceEEEEEcCCCccccccceEEEEEeeccCCCccccCCcce
Confidence 46889999988 887665 5788999999999985544
No 7
>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=76.27 E-value=10 Score=22.61 Aligned_cols=37 Identities=27% Similarity=0.406 Sum_probs=27.8
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEccCCceeeeeEEEEeee
Q 033136 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQVRLFSIFLVYVTFNH 124 (126)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDq~~~~~rYPVvVRF~k 124 (126)
.++.|+.|...-.+.-||. |+|..++.++ . +.|+|.+
T Consensus 2 ~~~~G~~~~a~~~d~~wyr--a~I~~~~~~~---~--~~V~f~D 38 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYR--ARIIKVDGEQ---L--YEVFFID 38 (57)
T ss_pred CCCCCCEEEEEeCCCCEEE--EEEEEECCCC---E--EEEEEEC
Confidence 4678988888767899998 5899999863 2 3566654
No 8
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=75.33 E-value=9.5 Score=23.49 Aligned_cols=35 Identities=23% Similarity=0.444 Sum_probs=25.3
Q ss_pred CCCCCeeEEee--ccceeccccceEEEEccCCceeeeeEEEEeee
Q 033136 82 PKRGAKVKILR--RESYWYNGIGSVVAVDQVRLFSIFLVYVTFNH 124 (126)
Q Consensus 82 p~RGskVrIlR--~ESYWyn~vGtVvsVDq~~~~~rYPVvVRF~k 124 (126)
.+.|+.|.++. .-+|| -|+|..++..+ +| .|+|..
T Consensus 3 ~~~G~~Ve~~~~~~~~W~---~a~V~~~~~~~---~~--~V~~~~ 39 (61)
T smart00743 3 FKKGDRVEVFSKEEDSWW---EAVVTKVLGDG---KY--LVRYLT 39 (61)
T ss_pred cCCCCEEEEEECCCCEEE---EEEEEEECCCC---EE--EEEECC
Confidence 57899999998 44544 48999999843 55 566653
No 9
>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=75.06 E-value=4.3 Score=22.72 Aligned_cols=24 Identities=21% Similarity=0.668 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCeeEEeec-cceecc
Q 033136 76 KPPPIGPKRGAKVKILRR-ESYWYN 99 (126)
Q Consensus 76 kpppigp~RGskVrIlR~-ESYWyn 99 (126)
.+..+..++|++|.|+.. +..|+.
T Consensus 15 ~~~~l~~~~Gd~v~v~~~~~~~w~~ 39 (58)
T smart00326 15 DPDELSFKKGDIITVLEKSDDGWWK 39 (58)
T ss_pred CCCCCCCCCCCEEEEEEcCCCCeEE
Confidence 345678899999999988 788874
No 10
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=72.82 E-value=14 Score=26.94 Aligned_cols=33 Identities=21% Similarity=0.336 Sum_probs=27.5
Q ss_pred CCCCCCCCCeeEEeeccceeccccceEEEEccCCc
Q 033136 78 PPIGPKRGAKVKILRRESYWYNGIGSVVAVDQVRL 112 (126)
Q Consensus 78 ppigp~RGskVrIlR~ESYWyn~vGtVvsVDq~~~ 112 (126)
+..+.+.|++|||. +--|-+-.|.|+.+|.+..
T Consensus 123 ~~~~~~~Gd~VrI~--~GPf~G~~g~v~~i~~~~~ 155 (181)
T PRK05609 123 PKVDFEVGEMVRVI--DGPFADFNGTVEEVDYEKS 155 (181)
T ss_pred cccCCCCCCEEEEe--ccCCCCCEEEEEEEeCCCC
Confidence 45788999999998 5578889999999997653
No 11
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=72.69 E-value=1.9 Score=28.71 Aligned_cols=32 Identities=25% Similarity=0.229 Sum_probs=21.7
Q ss_pred eEEeeccceeccccceEEEEc-----cCCceeeeeEEEEe
Q 033136 88 VKILRRESYWYNGIGSVVAVD-----QVRLFSIFLVYVTF 122 (126)
Q Consensus 88 VrIlR~ESYWyn~vGtVvsVD-----q~~~~~rYPVvVRF 122 (126)
...-.++.+| -||++++|- .+|. -|+|+.+||
T Consensus 29 ~td~~R~~~~--~iG~iit~ky~~~t~~g~-pRfP~f~~~ 65 (66)
T PF14743_consen 29 FTDEEREEPP--YIGKIITVKYQGLTKDGS-PRFPVFVRV 65 (66)
T ss_dssp --HHHHHHHH--HTT-EEEEEEE-TTSSSS--EEEEEEEE
T ss_pred CCHHHHhcCC--CCCCEEEEEEEccCCCCc-cccCEEEEe
Confidence 3335567788 799999984 3555 799999997
No 12
>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=69.18 E-value=6.7 Score=27.61 Aligned_cols=31 Identities=29% Similarity=0.488 Sum_probs=24.7
Q ss_pred CCCCCeeEEee---------------ccceeccccceEEEEccCCc
Q 033136 82 PKRGAKVKILR---------------RESYWYNGIGSVVAVDQVRL 112 (126)
Q Consensus 82 p~RGskVrIlR---------------~ESYWyn~vGtVvsVDq~~~ 112 (126)
+|+|+.||+.| .-+|-|..-|.|..|..+=.
T Consensus 1 lKKG~lVrv~re~~~nSlEa~ASD~~~P~Yife~~GEvl~ikgdYa 46 (67)
T PF11910_consen 1 LKKGSLVRVNREKYENSLEAKASDPRPPSYIFEGPGEVLDIKGDYA 46 (67)
T ss_pred CCcceEEEeehHhhcCchhhhhcCCCCCcceecCCCeEEEecCCEE
Confidence 47888888875 34899999999999986543
No 13
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=66.41 E-value=4.6 Score=28.55 Aligned_cols=15 Identities=47% Similarity=0.835 Sum_probs=14.0
Q ss_pred CCCCCCCCeeEEeec
Q 033136 79 PIGPKRGAKVKILRR 93 (126)
Q Consensus 79 pigp~RGskVrIlR~ 93 (126)
..|.++|+.|||.|+
T Consensus 49 ~~g~k~GdVvkI~R~ 63 (79)
T PRK09570 49 AIGAKPGDVIKIVRK 63 (79)
T ss_pred hcCCCCCCEEEEEEC
Confidence 679999999999998
No 14
>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=65.62 E-value=4.7 Score=28.03 Aligned_cols=16 Identities=44% Similarity=0.719 Sum_probs=12.1
Q ss_pred CCCCCCCCeeEEeecc
Q 033136 79 PIGPKRGAKVKILRRE 94 (126)
Q Consensus 79 pigp~RGskVrIlR~E 94 (126)
..|.++|+.|||.|+-
T Consensus 46 ~~g~k~GdVvkI~R~S 61 (74)
T PF01191_consen 46 YLGAKPGDVVKIIRKS 61 (74)
T ss_dssp HTT--TTSEEEEEEEE
T ss_pred hcCCCCCCEEEEEecC
Confidence 4699999999999983
No 15
>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=65.31 E-value=9.9 Score=28.23 Aligned_cols=31 Identities=32% Similarity=0.469 Sum_probs=24.4
Q ss_pred CCCCCCCCeeEEeeccceeccccceEEEEccCC
Q 033136 79 PIGPKRGAKVKILRRESYWYNGIGSVVAVDQVR 111 (126)
Q Consensus 79 pigp~RGskVrIlR~ESYWyn~vGtVvsVDq~~ 111 (126)
-+-+++||+|+|++-.- =...|+|..||...
T Consensus 39 ~~~IkkGD~V~Vi~Gk~--KGk~GkV~~V~~~~ 69 (114)
T TIGR01080 39 ALPVRKGDKVRIMRGDF--KGHEGKVSKVDLKR 69 (114)
T ss_pred cceeecCCEEEEecCCC--CCCEEEEEEEEcCC
Confidence 34689999999999872 24569999999654
No 16
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=64.25 E-value=11 Score=34.94 Aligned_cols=27 Identities=26% Similarity=0.324 Sum_probs=22.7
Q ss_pred CCCCCCCeeEEeeccceeccccceEEEEccCC
Q 033136 80 IGPKRGAKVKILRRESYWYNGIGSVVAVDQVR 111 (126)
Q Consensus 80 igp~RGskVrIlR~ESYWyn~vGtVvsVDq~~ 111 (126)
--++.|++|+|.. ||..|+|++|+.++
T Consensus 635 ~~~~~Gd~V~v~~-----~~~~g~v~~i~~~~ 661 (782)
T PRK00409 635 EELKVGDEVKYLS-----LGQKGEVLSIPDDK 661 (782)
T ss_pred cCCCCCCEEEEcc-----CCceEEEEEEcCCC
Confidence 4488999999976 89999999998543
No 17
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=63.73 E-value=13 Score=26.63 Aligned_cols=30 Identities=20% Similarity=0.217 Sum_probs=24.9
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEccCCc
Q 033136 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQVRL 112 (126)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDq~~~ 112 (126)
-+++||.|.|++--. -..+|+|..||....
T Consensus 4 ~i~kGD~V~Vi~G~d--KGk~G~V~~V~~~~~ 33 (105)
T PRK00004 4 KIKKGDTVIVIAGKD--KGKRGKVLKVLPKKN 33 (105)
T ss_pred cccCCCEEEEeEcCC--CCcEEEEEEEEcCCC
Confidence 468999999999764 588999999998743
No 18
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=63.48 E-value=14 Score=25.33 Aligned_cols=30 Identities=27% Similarity=0.273 Sum_probs=24.7
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEccCCc
Q 033136 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQVRL 112 (126)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDq~~~ 112 (126)
-+++||+|.|++-. .-..+|+|..||....
T Consensus 6 ~I~kGD~V~Vi~G~--dKGK~G~V~~V~~~~~ 35 (76)
T PRK12281 6 KVKKGDMVKVIAGD--DKGKTGKVLAVLPKKN 35 (76)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCCC
Confidence 57899999999965 3477899999998743
No 19
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=63.47 E-value=19 Score=28.02 Aligned_cols=35 Identities=26% Similarity=0.369 Sum_probs=28.9
Q ss_pred CCCCCCCCCCCCeeEEeeccceeccccceEEEEccCC
Q 033136 75 PKPPPIGPKRGAKVKILRRESYWYNGIGSVVAVDQVR 111 (126)
Q Consensus 75 ~kpppigp~RGskVrIlR~ESYWyn~vGtVvsVDq~~ 111 (126)
++++-+.++.|++|||.. .=.-+..|+|..||.+.
T Consensus 117 ~~~~~~~~e~Gd~VrI~~--GpFa~f~g~V~evd~ek 151 (178)
T COG0250 117 PKKPKVDFEPGDVVRIID--GPFAGFKAKVEEVDEEK 151 (178)
T ss_pred CCcccccCCCCCEEEEec--cCCCCccEEEEEEcCcC
Confidence 566679999999999984 45667889999999983
No 20
>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=60.84 E-value=12 Score=34.31 Aligned_cols=38 Identities=18% Similarity=0.254 Sum_probs=28.7
Q ss_pred CCCCCCCeeEEeec--cceecc-ccceEEEEccCCceeeeeEEEEee
Q 033136 80 IGPKRGAKVKILRR--ESYWYN-GIGSVVAVDQVRLFSIFLVYVTFN 123 (126)
Q Consensus 80 igp~RGskVrIlR~--ESYWyn-~vGtVvsVDq~~~~~rYPVvVRF~ 123 (126)
.....|++|.++|. +.-||| ++|+|+.|+.+. ++|+|+
T Consensus 606 ~~~~~GDrV~~~~N~~~~gv~NGd~g~V~~i~~~~------i~v~~~ 646 (744)
T TIGR02768 606 RKFAAGDRIVFLENNRDLGVKNGMLGTVEEIEDGR------LVVQLD 646 (744)
T ss_pred ceecCCCEEEEEecccccCCcCCCEEEEEEecCCe------EEEEEC
Confidence 45789999999976 335776 799999998653 456775
No 21
>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=60.55 E-value=14 Score=20.46 Aligned_cols=21 Identities=19% Similarity=0.640 Sum_probs=17.2
Q ss_pred CCCCCCCCCeeEEeec-cceec
Q 033136 78 PPIGPKRGAKVKILRR-ESYWY 98 (126)
Q Consensus 78 ppigp~RGskVrIlR~-ESYWy 98 (126)
-.+..++|+.|.|+.. +..|+
T Consensus 14 ~~l~~~~Gd~v~v~~~~~~~w~ 35 (54)
T cd00174 14 DELSFKKGDIIEVLEKSDDGWW 35 (54)
T ss_pred CCCCCCCCCEEEEEEcCCCCeE
Confidence 4678899999999988 56665
No 22
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=57.43 E-value=21 Score=24.85 Aligned_cols=30 Identities=27% Similarity=0.286 Sum_probs=24.9
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEccCCc
Q 033136 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQVRL 112 (126)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDq~~~ 112 (126)
-+.+||.|.|++-.. -...|+|..||....
T Consensus 8 ~I~~GD~V~Vi~G~d--KGK~G~V~~V~~~~~ 37 (83)
T CHL00141 8 HVKIGDTVKIISGSD--KGKIGEVLKIIKKSN 37 (83)
T ss_pred cccCCCEEEEeEcCC--CCcEEEEEEEEcCCC
Confidence 578999999999763 478899999998743
No 23
>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=55.69 E-value=43 Score=24.37 Aligned_cols=31 Identities=26% Similarity=0.318 Sum_probs=25.4
Q ss_pred CCCCCCCCeeEEeeccceeccccceEEEEccCC
Q 033136 79 PIGPKRGAKVKILRRESYWYNGIGSVVAVDQVR 111 (126)
Q Consensus 79 pigp~RGskVrIlR~ESYWyn~vGtVvsVDq~~ 111 (126)
...++.|++|+|. +--|-+-.|.|..+|.+.
T Consensus 117 ~~~~~~G~~V~I~--~Gpf~G~~g~v~~~~~~~ 147 (172)
T TIGR00922 117 KIDFEVGEQVRVN--DGPFANFTGTVEEVDYEK 147 (172)
T ss_pred ccCCCCCCEEEEe--ecCCCCcEEEEEEEcCCC
Confidence 3668999999998 556778889999999654
No 24
>COG1596 Wza Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]
Probab=54.90 E-value=22 Score=28.18 Aligned_cols=44 Identities=14% Similarity=0.004 Sum_probs=32.9
Q ss_pred CCCCCCCCCCCCCeeEEeeccceeccccceEE--EEccCCceeeeeEE
Q 033136 74 KPKPPPIGPKRGAKVKILRRESYWYNGIGSVV--AVDQVRLFSIFLVY 119 (126)
Q Consensus 74 k~kpppigp~RGskVrIlR~ESYWyn~vGtVv--sVDq~~~~~rYPVv 119 (126)
....++.....||+|+|...|.==+... ... +||++|. +-||.|
T Consensus 40 ~~~~~~y~lg~GD~l~I~v~e~~~l~~~-~~~~~tV~~~G~-i~~P~i 85 (239)
T COG1596 40 AAAASAYRLGPGDVLRITVFEAPELTGF-VYRSGTVDPDGN-ISIPLI 85 (239)
T ss_pred ccCCCceeecCCCEEEEEecccCCcccc-cceeeEECCCCc-Eeeeee
Confidence 4455677888999999999886544443 232 6999998 999976
No 25
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=54.39 E-value=18 Score=28.13 Aligned_cols=29 Identities=21% Similarity=0.278 Sum_probs=24.0
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEccCC
Q 033136 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQVR 111 (126)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDq~~ 111 (126)
-+++||+|.|++-.. =...|+|..||...
T Consensus 46 ~IkkGD~V~Vi~Gk~--KGk~GkV~~V~~k~ 74 (143)
T PTZ00194 46 PVRKDDEVMVVRGHH--KGREGKVTAVYRKK 74 (143)
T ss_pred eeecCCEEEEecCCC--CCCceEEEEEEcCC
Confidence 579999999999872 35679999999874
No 26
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=54.12 E-value=9.5 Score=27.58 Aligned_cols=15 Identities=47% Similarity=0.815 Sum_probs=13.9
Q ss_pred CCCCCCCCeeEEeec
Q 033136 79 PIGPKRGAKVKILRR 93 (126)
Q Consensus 79 pigp~RGskVrIlR~ 93 (126)
.+|-++|+.|||.|+
T Consensus 52 ~lgak~GdvVkIvRk 66 (80)
T COG2012 52 ALGAKPGDVVKIVRK 66 (80)
T ss_pred HccCCCCcEEEEEec
Confidence 689999999999997
No 27
>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=50.12 E-value=34 Score=22.10 Aligned_cols=35 Identities=20% Similarity=0.472 Sum_probs=23.0
Q ss_pred CCCCeeEEeeccc----eeccccceEEEEccCCceeeeeEEEEeee
Q 033136 83 KRGAKVKILRRES----YWYNGIGSVVAVDQVRLFSIFLVYVTFNH 124 (126)
Q Consensus 83 ~RGskVrIlR~ES----YWyn~vGtVvsVDq~~~~~rYPVvVRF~k 124 (126)
++|++|.|++.|. =||. ++|.+...+. + ++|+|++
T Consensus 2 ~~G~~VEV~s~e~g~~gaWf~--a~V~~~~~~~---~--~~V~Y~~ 40 (68)
T PF05641_consen 2 KKGDEVEVSSDEDGFRGAWFP--ATVLKENGDD---K--YLVEYDD 40 (68)
T ss_dssp -TT-EEEEEE-SBTT--EEEE--EEEEEEETT----E--EEEEETT
T ss_pred CCCCEEEEEEcCCCCCcEEEE--EEEEEeCCCc---E--EEEEECC
Confidence 6899999999773 5885 7899988874 2 4566643
No 28
>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=49.73 E-value=31 Score=27.30 Aligned_cols=42 Identities=14% Similarity=0.263 Sum_probs=28.9
Q ss_pred CCCCCeeEEeeccceeccc----cceEEEEccCCc------eeeeeEEEEeee
Q 033136 82 PKRGAKVKILRRESYWYNG----IGSVVAVDQVRL------FSIFLVYVTFNH 124 (126)
Q Consensus 82 p~RGskVrIlR~ESYWyn~----vGtVvsVDq~~~------~~rYPVvVRF~k 124 (126)
++.|++|+| +-++|=+.. -|+|..|+.+.. -..|+|.|++++
T Consensus 324 i~~G~~v~v-~~~~~~~~~~~~~~g~V~~i~~~~~~~~~~~~~~~~v~i~l~~ 375 (423)
T TIGR01843 324 VHVGQPAEI-KFSAFPYRRYGILNGKVKSISPDTFTDERGGGPYYRVRISIDQ 375 (423)
T ss_pred hCCCCceEE-EEecCCCcccCCccEEEEEECCCcccCccCCcceEEEEEEECH
Confidence 568999998 556653332 699999975321 135999999874
No 29
>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=48.99 E-value=32 Score=24.81 Aligned_cols=29 Identities=24% Similarity=0.291 Sum_probs=23.7
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEccCC
Q 033136 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQVR 111 (126)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDq~~ 111 (126)
-+++||+|.|++-.. -..+|+|..||...
T Consensus 3 ~ikkGD~V~Vi~G~d--KGK~G~V~~V~~~~ 31 (104)
T TIGR01079 3 KIKKGDTVKVISGKD--KGKRGKVLKVLPKT 31 (104)
T ss_pred cccCCCEEEEeEcCC--CCcEEEEEEEEcCC
Confidence 368999999999763 36789999999874
No 30
>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []. These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.
Probab=48.85 E-value=20 Score=26.02 Aligned_cols=15 Identities=20% Similarity=0.436 Sum_probs=11.9
Q ss_pred ccCCceeeeeEEEEeee
Q 033136 108 DQVRLFSIFLVYVTFNH 124 (126)
Q Consensus 108 Dq~~~~~rYPVvVRF~k 124 (126)
|..+. ||-|+++|++
T Consensus 49 d~~pn--rymVLikF~~ 63 (110)
T PF07576_consen 49 DGTPN--RYMVLIKFRD 63 (110)
T ss_pred CCCCc--eEEEEEEECC
Confidence 55554 9999999975
No 31
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=47.47 E-value=32 Score=33.44 Aligned_cols=32 Identities=22% Similarity=0.272 Sum_probs=25.6
Q ss_pred CCCCCCeeEEeecc--ceecc-ccceEEEEccCCc
Q 033136 81 GPKRGAKVKILRRE--SYWYN-GIGSVVAVDQVRL 112 (126)
Q Consensus 81 gp~RGskVrIlR~E--SYWyn-~vGtVvsVDq~~~ 112 (126)
....|++|.++|.+ -.+|| ++|+|..||.+..
T Consensus 600 ~~~vGDrVm~~rNd~~lgV~NGd~GtV~~I~~~~i 634 (988)
T PRK13889 600 SFASGDRVMFLQNERGLGVKNGTLGTIEQVSAQSM 634 (988)
T ss_pred cccCCCEEEEeecCCcCCEeCCCeEEEEEecCCeE
Confidence 46899999999964 34777 6999999998643
No 32
>PF14334 DUF4390: Domain of unknown function (DUF4390)
Probab=47.32 E-value=17 Score=26.91 Aligned_cols=28 Identities=14% Similarity=0.445 Sum_probs=19.9
Q ss_pred CeeEEeeccceeccccceEEEEccCCceeee
Q 033136 86 AKVKILRRESYWYNGIGSVVAVDQVRLFSIF 116 (126)
Q Consensus 86 skVrIlR~ESYWyn~vGtVvsVDq~~~~~rY 116 (126)
-.++|.|+..||+++ +|+.+...-. ++|
T Consensus 48 ~~~~l~r~R~~w~d~--~v~~~~~~~~-L~Y 75 (165)
T PF14334_consen 48 FEIELYRPRWYWWDE--TVASATRRYR-LSY 75 (165)
T ss_pred EEEEEEeecccccCC--eeEEEEEEEE-EEE
Confidence 457899999999986 5666665533 444
No 33
>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=47.28 E-value=14 Score=22.44 Aligned_cols=26 Identities=19% Similarity=0.588 Sum_probs=16.9
Q ss_pred CCCCCCCCCCCeeEEe---eccceecccc
Q 033136 76 KPPPIGPKRGAKVKIL---RRESYWYNGI 101 (126)
Q Consensus 76 kpppigp~RGskVrIl---R~ESYWyn~v 101 (126)
.+.++..++|+.|+|+ ..+.+|+-..
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 3456999999999999 2355676543
No 34
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=45.93 E-value=13 Score=30.90 Aligned_cols=15 Identities=60% Similarity=0.871 Sum_probs=13.3
Q ss_pred CCCCCCCeeEEeecc
Q 033136 80 IGPKRGAKVKILRRE 94 (126)
Q Consensus 80 igp~RGskVrIlR~E 94 (126)
-|.|||+.|||.|+-
T Consensus 181 yGLKrGqVVKI~r~s 195 (208)
T KOG3218|consen 181 YGLKRGQVVKIIRRS 195 (208)
T ss_pred hccccCcEEEEEecC
Confidence 499999999999973
No 35
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=45.34 E-value=15 Score=30.02 Aligned_cols=16 Identities=38% Similarity=0.565 Sum_probs=14.2
Q ss_pred CCCCCCCCeeEEeecc
Q 033136 79 PIGPKRGAKVKILRRE 94 (126)
Q Consensus 79 pigp~RGskVrIlR~E 94 (126)
-.|.++|+.|||.|+-
T Consensus 177 y~g~k~G~vvkI~R~S 192 (205)
T PTZ00061 177 YFGLSKGQVVKIIRPS 192 (205)
T ss_pred hcCCCCCCEEEEEECC
Confidence 5699999999999973
No 36
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=44.32 E-value=16 Score=29.85 Aligned_cols=15 Identities=53% Similarity=0.674 Sum_probs=13.9
Q ss_pred CCCCCCCCeeEEeec
Q 033136 79 PIGPKRGAKVKILRR 93 (126)
Q Consensus 79 pigp~RGskVrIlR~ 93 (126)
-.|.++|+.|||.|+
T Consensus 178 y~g~k~G~vvkI~R~ 192 (206)
T PLN03111 178 YYGLKRGQVVKIIRP 192 (206)
T ss_pred hcCCCCCCEEEEEEC
Confidence 579999999999998
No 37
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=43.95 E-value=1e+02 Score=27.95 Aligned_cols=49 Identities=14% Similarity=0.116 Sum_probs=32.6
Q ss_pred CCCCCCCCCCCCeeEEeec-cceeccccceEEEEccCC--ceeeeeEEEEeeec
Q 033136 75 PKPPPIGPKRGAKVKILRR-ESYWYNGIGSVVAVDQVR--LFSIFLVYVTFNHF 125 (126)
Q Consensus 75 ~kpppigp~RGskVrIlR~-ESYWyn~vGtVvsVDq~~--~~~rYPVvVRF~kv 125 (126)
.++...-.+.|++|...+. +.=||. ++|+.+.... ..-.|-..|.|...
T Consensus 47 ~~~~~~~~~VGekVla~~~~Dg~~~~--A~VI~~R~~~~~~~~~~~YYVHY~g~ 98 (450)
T PLN00104 47 RPGVMLPLEVGTRVMCRWRFDGKYHP--VKVIERRRGGSGGPNDYEYYVHYTEF 98 (450)
T ss_pred CCCccceeccCCEEEEEECCCCCEEE--EEEEEEeccCCCCCCCceEEEEEecC
Confidence 3444455689999999998 677884 8898888632 10134556777654
No 38
>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=43.46 E-value=75 Score=20.34 Aligned_cols=27 Identities=22% Similarity=0.239 Sum_probs=20.9
Q ss_pred CCCCCCCeeEEeeccceeccccceEEEE--ccCCc
Q 033136 80 IGPKRGAKVKILRRESYWYNGIGSVVAV--DQVRL 112 (126)
Q Consensus 80 igp~RGskVrIlR~ESYWyn~vGtVvsV--Dq~~~ 112 (126)
-|...|+.|++.= -+||+|.+| +.++.
T Consensus 13 ~GL~~gs~V~~~G------v~VG~V~~i~l~~~~~ 41 (81)
T PF02470_consen 13 GGLSVGSPVRYRG------VEVGKVTSIELDPDGN 41 (81)
T ss_pred CCCCCcCEEEECC------EEEEEEEEEEEcCCCC
Confidence 5788999998754 368999999 66654
No 39
>PF11347 DUF3148: Protein of unknown function (DUF3148); InterPro: IPR021495 This family of proteins has no known function.
Probab=43.30 E-value=63 Score=22.42 Aligned_cols=21 Identities=19% Similarity=0.248 Sum_probs=14.5
Q ss_pred cccceEEEEccCCceeeeeEEEEeee
Q 033136 99 NGIGSVVAVDQVRLFSIFLVYVTFNH 124 (126)
Q Consensus 99 n~vGtVvsVDq~~~~~rYPVvVRF~k 124 (126)
.|+|+|++.-..+- .-|||.+
T Consensus 33 ge~G~i~~rrp~~~-----w~VRf~~ 53 (63)
T PF11347_consen 33 GEVGRIVDRRPGDY-----WAVRFRR 53 (63)
T ss_pred CCcEEEEEecCCCE-----EEEEEec
Confidence 57888887777653 5677764
No 40
>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=42.32 E-value=18 Score=22.06 Aligned_cols=21 Identities=19% Similarity=0.618 Sum_probs=16.4
Q ss_pred CCCCCCCCeeEEeec-cceecc
Q 033136 79 PIGPKRGAKVKILRR-ESYWYN 99 (126)
Q Consensus 79 pigp~RGskVrIlR~-ESYWyn 99 (126)
....++|+.|.|+++ ++.|+.
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 477899999999998 788876
No 41
>PRK15208 long polar fimbrial chaperone LpfB; Provisional
Probab=42.03 E-value=18 Score=28.59 Aligned_cols=20 Identities=40% Similarity=0.964 Sum_probs=16.1
Q ss_pred CCCCCCCeeEEee--------ccc-eecc
Q 033136 80 IGPKRGAKVKILR--------RES-YWYN 99 (126)
Q Consensus 80 igp~RGskVrIlR--------~ES-YWyn 99 (126)
+.|..+..|||++ +|| ||+|
T Consensus 78 l~p~~~q~lRIi~~~~~lP~DrESlf~ln 106 (228)
T PRK15208 78 LDPTKNNVLRIVNITNTLPQDRESVYWIN 106 (228)
T ss_pred ECCCCccEEEEEECCCCCCCCeeEEEEEE
Confidence 5788888999987 366 9987
No 42
>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=41.07 E-value=70 Score=18.32 Aligned_cols=33 Identities=18% Similarity=0.261 Sum_probs=22.2
Q ss_pred CCeeEEeecc-ceeccccceEEEEccCCceeeeeEEEEeee
Q 033136 85 GAKVKILRRE-SYWYNGIGSVVAVDQVRLFSIFLVYVTFNH 124 (126)
Q Consensus 85 GskVrIlR~E-SYWyn~vGtVvsVDq~~~~~rYPVvVRF~k 124 (126)
|+.+-.+-+| .-||. ++|..++.++. +.|+|..
T Consensus 1 G~~c~a~~~~d~~wyr--a~V~~~~~~~~-----~~V~f~D 34 (48)
T cd04508 1 GDLCLAKYSDDGKWYR--AKITSILSDGK-----VEVFFVD 34 (48)
T ss_pred CCEEEEEECCCCeEEE--EEEEEECCCCc-----EEEEEEc
Confidence 5566666666 88986 78999987432 4566653
No 43
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=41.03 E-value=48 Score=25.06 Aligned_cols=31 Identities=32% Similarity=0.439 Sum_probs=24.4
Q ss_pred CCCCCCCeeEEeeccceeccccceEEEEccCCc
Q 033136 80 IGPKRGAKVKILRRESYWYNGIGSVVAVDQVRL 112 (126)
Q Consensus 80 igp~RGskVrIlR~ESYWyn~vGtVvsVDq~~~ 112 (126)
.-+++||+|.|++-.. =...|+|..||....
T Consensus 44 ~~IkkGD~V~VisG~~--KGk~GkV~~V~~~~~ 74 (120)
T PRK01191 44 LPVRKGDTVKVMRGDF--KGEEGKVVEVDLKRG 74 (120)
T ss_pred ceEeCCCEEEEeecCC--CCceEEEEEEEcCCC
Confidence 3589999999999772 246799999998743
No 44
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=40.69 E-value=34 Score=31.84 Aligned_cols=23 Identities=30% Similarity=0.387 Sum_probs=20.0
Q ss_pred CCCCeeEEeeccceeccccceEEEEccC
Q 033136 83 KRGAKVKILRRESYWYNGIGSVVAVDQV 110 (126)
Q Consensus 83 ~RGskVrIlR~ESYWyn~vGtVvsVDq~ 110 (126)
+.|++|+|.. +|..|+|++|+..
T Consensus 626 ~~Gd~V~v~~-----~~~~g~v~~i~~~ 648 (771)
T TIGR01069 626 KIGDKVRIRY-----FGQKGKIVQILGG 648 (771)
T ss_pred CCCCEEEEcc-----CCceEEEEEEcCC
Confidence 8899999964 7999999999753
No 45
>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=39.43 E-value=37 Score=19.26 Aligned_cols=27 Identities=26% Similarity=0.569 Sum_probs=20.6
Q ss_pred CCCeeEEeeccceeccccceEEEEccCCc
Q 033136 84 RGAKVKILRRESYWYNGIGSVVAVDQVRL 112 (126)
Q Consensus 84 RGskVrIlR~ESYWyn~vGtVvsVDq~~~ 112 (126)
+|+.|+|++-- .-..+|+|..||++..
T Consensus 1 ~Gd~V~V~~G~--~~G~~G~I~~i~~~~~ 27 (32)
T PF00467_consen 1 VGDTVKVISGP--FKGKIGKIVEIDRSKV 27 (32)
T ss_dssp TTSEEEESSST--TTTEEEEEEEEETTTT
T ss_pred CCCEEEEeEcC--CCCceEEEEEEECCCC
Confidence 48888888643 2467899999999863
No 46
>PRK15249 fimbrial chaperone protein StbB; Provisional
Probab=38.38 E-value=21 Score=28.70 Aligned_cols=21 Identities=43% Similarity=0.937 Sum_probs=16.4
Q ss_pred CCCCCCCeeEEeec---------cc-eeccc
Q 033136 80 IGPKRGAKVKILRR---------ES-YWYNG 100 (126)
Q Consensus 80 igp~RGskVrIlR~---------ES-YWyn~ 100 (126)
+.|+.+..|||++. || ||+|=
T Consensus 90 l~p~~~q~lRI~~~~~~~lP~DRESlf~lnv 120 (253)
T PRK15249 90 IQPKAGQVVRVIYNNTKKLPQDRESVFWFNV 120 (253)
T ss_pred ecCCCceEEEEEEcCCCCCCCCceEEEEEEe
Confidence 57888889999875 55 99863
No 47
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=38.29 E-value=27 Score=24.99 Aligned_cols=22 Identities=18% Similarity=0.430 Sum_probs=19.1
Q ss_pred CCCCCCCeeEEeec-cceecccc
Q 033136 80 IGPKRGAKVKILRR-ESYWYNGI 101 (126)
Q Consensus 80 igp~RGskVrIlR~-ESYWyn~v 101 (126)
.|..+||.|++.+. +.|||+++
T Consensus 24 ~glA~gDvV~~~~~~g~~~~~~~ 46 (117)
T PF14085_consen 24 YGLALGDVVRAEPDDGELWFQKV 46 (117)
T ss_pred CCCCCCCEEEEEeCCCeEEEEEE
Confidence 48899999999998 58999875
No 48
>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=37.67 E-value=35 Score=22.67 Aligned_cols=27 Identities=33% Similarity=0.555 Sum_probs=19.2
Q ss_pred CCCCCeeEEeeccceeccccceEEEEccC
Q 033136 82 PKRGAKVKILRRESYWYNGIGSVVAVDQV 110 (126)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDq~ 110 (126)
.++|++||+||...-=| .|+|.++...
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 57899999999864222 4788877643
No 49
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=37.06 E-value=48 Score=32.76 Aligned_cols=31 Identities=29% Similarity=0.288 Sum_probs=24.7
Q ss_pred CCCCCCeeEEeeccc--eecc-ccceEEEEccCC
Q 033136 81 GPKRGAKVKILRRES--YWYN-GIGSVVAVDQVR 111 (126)
Q Consensus 81 gp~RGskVrIlR~ES--YWyn-~vGtVvsVDq~~ 111 (126)
....|++|.++|.+- .++| ++|+|+.+|.+.
T Consensus 633 ~f~vGDrV~f~rNd~~lgV~NGd~GtV~~i~~~~ 666 (1102)
T PRK13826 633 RFAAGDQIVFLKNEGSLGVKNGMIGKVVEAAPNR 666 (1102)
T ss_pred cccCCCEEEEeeecCccCccCCCeEEEEEecCCe
Confidence 468899999999753 5677 699999998653
No 50
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=36.75 E-value=81 Score=19.17 Aligned_cols=24 Identities=17% Similarity=0.232 Sum_probs=19.0
Q ss_pred CCeeEEee-ccceeccccceEEEEccCCc
Q 033136 85 GAKVKILR-RESYWYNGIGSVVAVDQVRL 112 (126)
Q Consensus 85 GskVrIlR-~ESYWyn~vGtVvsVDq~~~ 112 (126)
|..|+|.. .+.+ .|.+..||.+|.
T Consensus 3 G~~V~v~~~~~~~----~G~~~gId~~G~ 27 (48)
T PF02237_consen 3 GQEVRVETGDGEI----EGIAEGIDDDGA 27 (48)
T ss_dssp TSEEEEEETSCEE----EEEEEEEETTSE
T ss_pred CCEEEEEECCeEE----EEEEEEECCCCE
Confidence 77888887 3333 799999999986
No 51
>PRK15195 fimbrial chaperone protein FimC; Provisional
Probab=34.87 E-value=25 Score=27.94 Aligned_cols=21 Identities=33% Similarity=0.656 Sum_probs=15.9
Q ss_pred CCCCCCCeeEEeec--------cc-eeccc
Q 033136 80 IGPKRGAKVKILRR--------ES-YWYNG 100 (126)
Q Consensus 80 igp~RGskVrIlR~--------ES-YWyn~ 100 (126)
+.|+.+..+||++. || ||+|=
T Consensus 82 l~p~~~q~lRIi~~~~~LP~DrESlf~Lnv 111 (229)
T PRK15195 82 SEPKSENTLRIIYAGPPLAADRESLFWMNV 111 (229)
T ss_pred ECCCCceEEEEEECCCCCCCCeeEEEEEEe
Confidence 57788889998873 55 89873
No 52
>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=34.67 E-value=17 Score=27.40 Aligned_cols=27 Identities=19% Similarity=0.384 Sum_probs=21.0
Q ss_pred CCCCeeEEeeccceeccc-cce-EEEEcc
Q 033136 83 KRGAKVKILRRESYWYNG-IGS-VVAVDQ 109 (126)
Q Consensus 83 ~RGskVrIlR~ESYWyn~-vGt-VvsVDq 109 (126)
=+|..|+-|+.|.|+|.| .|+ .|.||.
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 464 345555
No 53
>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=34.14 E-value=96 Score=24.38 Aligned_cols=42 Identities=12% Similarity=0.078 Sum_probs=25.9
Q ss_pred CCCCCeeEEeeccceeccccceEEEEcc------------C--CceeeeeEEEEeee
Q 033136 82 PKRGAKVKILRRESYWYNGIGSVVAVDQ------------V--RLFSIFLVYVTFNH 124 (126)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDq------------~--~~~~rYPVvVRF~k 124 (126)
++.|.+|+|.-. +|=..--|+|..|.. . ..--.|||.|+|+.
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 456999998543 332233688888842 1 11025999999974
No 54
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=33.38 E-value=1.1e+02 Score=25.52 Aligned_cols=43 Identities=19% Similarity=0.247 Sum_probs=27.9
Q ss_pred CCCCCCeeEEeeccceecc--ccceEEEEc--------------cCCce----eeeeEEEEeee
Q 033136 81 GPKRGAKVKILRRESYWYN--GIGSVVAVD--------------QVRLF----SIFLVYVTFNH 124 (126)
Q Consensus 81 gp~RGskVrIlR~ESYWyn--~vGtVvsVD--------------q~~~~----~rYPVvVRF~k 124 (126)
.++.|++|+|. -.+|=+. --|+|..|+ .+|.| -+|||-+.+++
T Consensus 265 ~v~~Gq~V~I~-~da~p~~~~~~G~V~~I~~~~~~~~~~lp~~~~~g~~~~~~qr~~Vri~l~~ 327 (390)
T PRK15136 265 NMRIGQPATIT-SDIYGDDVVYTGKVVGLDMGTGSAFSLLPAQNATGNWIKVVQRLPVRIELDA 327 (390)
T ss_pred cCCCCCEEEEE-EecCCCCceEEEEEEEECCcccccccCCCCccCCCCeEEEEEEEeEEEEECC
Confidence 35679999984 2333111 258898885 23433 38999999975
No 55
>PF13437 HlyD_3: HlyD family secretion protein
Probab=32.55 E-value=1.2e+02 Score=19.71 Aligned_cols=42 Identities=14% Similarity=0.045 Sum_probs=29.0
Q ss_pred CCCeeEEeeccceeccccceEEEEccCCc--eeeeeEEEEeeec
Q 033136 84 RGAKVKILRRESYWYNGIGSVVAVDQVRL--FSIFLVYVTFNHF 125 (126)
Q Consensus 84 RGskVrIlR~ESYWyn~vGtVvsVDq~~~--~~rYPVvVRF~kv 125 (126)
.|+.|+|.=.-.=.+.--|+|..|+.... --.|+|.+++++-
T Consensus 53 ~g~~v~v~~~~~~~~~~~g~V~~I~~~~~~~~~~~~v~~~i~~~ 96 (105)
T PF13437_consen 53 PGQKVTVRLDPGPEKTIEGKVSSISPSPDPQGGTYRVEISIDNP 96 (105)
T ss_pred CCCEEEEEECCCCCcEEEEEEEEEeCcccCCCcEEEEEEEECCC
Confidence 79999987552213466799999987311 1379999998763
No 56
>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=31.69 E-value=12 Score=28.08 Aligned_cols=17 Identities=41% Similarity=0.984 Sum_probs=11.8
Q ss_pred CCeeEEee---ccceecccc
Q 033136 85 GAKVKILR---RESYWYNGI 101 (126)
Q Consensus 85 GskVrIlR---~ESYWyn~v 101 (126)
-+..|||| +|||||..+
T Consensus 28 ~EE~kvlrEC~~ESFwyRsl 47 (111)
T PF07051_consen 28 EEERKVLRECNEESFWYRSL 47 (111)
T ss_pred HHHHHHHHHHHHhhhHhccC
Confidence 34556664 799999764
No 57
>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=31.31 E-value=1e+02 Score=24.34 Aligned_cols=51 Identities=22% Similarity=0.264 Sum_probs=25.3
Q ss_pred ceeEEEEeccccCCCCCccccCCCCCCCCCCCCCCCCCCCCCCCeeEEeecc
Q 033136 43 SFRLVVRASEEAAAPPAAATTAAPAEGEAAPKPKPPPIGPKRGAKVKILRRE 94 (126)
Q Consensus 43 ~~rlvvRA~e~~aa~~~~a~~aap~~~~~a~k~kpppigp~RGskVrIlR~E 94 (126)
.-+|++|...+...+.++.......... ....+.......|...|+|.|-.
T Consensus 206 ~l~lvLr~~~d~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~V~~~~g~ 256 (261)
T TIGR03177 206 TLSLALRNAADTDEAAATAVLAATLSLA-PALAKAVDAAAPRRAAVEVIRGG 256 (261)
T ss_pred eEEEEeeCcccccccccccccccccccc-ccccccccCCCCCCceEEEEeCc
Confidence 4788998866654322111111111111 22233334444567888888854
No 58
>TIGR00998 8a0101 efflux pump membrane protein (multidrug resistance protein A).
Probab=30.39 E-value=1.6e+02 Score=23.00 Aligned_cols=42 Identities=17% Similarity=0.191 Sum_probs=28.0
Q ss_pred CCCCCeeEEeeccceeccc--cceEEEEccCC--------------ce----eeeeEEEEeee
Q 033136 82 PKRGAKVKILRRESYWYNG--IGSVVAVDQVR--------------LF----SIFLVYVTFNH 124 (126)
Q Consensus 82 p~RGskVrIlR~ESYWyn~--vGtVvsVDq~~--------------~~----~rYPVvVRF~k 124 (126)
++.|++|+|.- ..|-++. -|+|.+|+... .+ .+|||.|++++
T Consensus 255 i~~G~~v~v~~-~~~~~~~~~~G~V~~Is~~~~~~~~~~p~~~~~~~~~~~~~~~~v~i~l~~ 316 (334)
T TIGR00998 255 VRIGQPVTIRS-DLYGSDVVFEGKVTGISMGTGSAFSLLPAQNATGNWIKVVQRLPVRIKLDP 316 (334)
T ss_pred CCCCCEEEEEE-ecCCCCCEEEEEEEEECCCcccccccCCCCCCCcCeEEEEEEEeEEEEEcC
Confidence 56799999862 3333322 59999998642 22 25999998875
No 59
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by Pfam model pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=30.05 E-value=73 Score=23.37 Aligned_cols=35 Identities=11% Similarity=-0.066 Sum_probs=25.6
Q ss_pred CCCCCeeEEeeccceeccccceEEEEccCCceeeeeEEE
Q 033136 82 PKRGAKVKILRRESYWYNGIGSVVAVDQVRLFSIFLVYV 120 (126)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDq~~~~~rYPVvV 120 (126)
+..||+++|.=-+ ..+...-..||++|. +.+|.+=
T Consensus 3 l~pGD~l~i~v~~---~~~~~~~~~V~~dG~-I~lP~iG 37 (165)
T TIGR03027 3 IGPGDSLNINVWR---NPELSGSVPVRPDGK-ITTPLVG 37 (165)
T ss_pred cCCCCEEEEEEcC---CcccccceEECCCCe-EeecccC
Confidence 3568998885433 356666789999987 9999763
No 60
>COG1463 Ttg2C ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=29.66 E-value=71 Score=26.49 Aligned_cols=36 Identities=19% Similarity=0.087 Sum_probs=26.3
Q ss_pred CCCCCCCeeEEeeccceeccccceEEEEccCCceeeeeEEEEee
Q 033136 80 IGPKRGAKVKILRRESYWYNGIGSVVAVDQVRLFSIFLVYVTFN 123 (126)
Q Consensus 80 igp~RGskVrIlR~ESYWyn~vGtVvsVDq~~~~~rYPVvVRF~ 123 (126)
-|...|++|||.= =.||+|..|.-+.. .|-+.|+|+
T Consensus 51 ~GL~~gs~V~~~G------V~VG~V~~I~~~~~--~~~~~v~~~ 86 (359)
T COG1463 51 GGLYVGSPVRYRG------VKVGKVASISLDPK--PNGARVTLE 86 (359)
T ss_pred ccCCCCCceEEcC------EEeEEEEEEEecCC--CCceEEEEE
Confidence 4788999999753 24899998876543 567777774
No 61
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=26.71 E-value=1e+02 Score=22.96 Aligned_cols=29 Identities=31% Similarity=0.407 Sum_probs=18.8
Q ss_pred CCCeeEEeec--------cceecc------------ccceEEEEccCCc
Q 033136 84 RGAKVKILRR--------ESYWYN------------GIGSVVAVDQVRL 112 (126)
Q Consensus 84 RGskVrIlR~--------ESYWyn------------~vGtVvsVDq~~~ 112 (126)
||..+.|-|. |-||+. .+|+|..|+..|.
T Consensus 61 ~g~~l~i~~~~lp~l~e~e~y~~dLiG~~V~d~~g~~lG~V~~V~~~ga 109 (161)
T PRK13828 61 RGLELYVPRDRLPELDDDEFYHADLIGLAAVDTGGALLGRVKAVHNFGA 109 (161)
T ss_pred cCCEEEEEHHHCCCCCCCCEEhhhccCCEEEeCCCCEEEEEEEEccCCC
Confidence 5666666653 556663 3678888877664
No 62
>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=26.52 E-value=66 Score=23.59 Aligned_cols=22 Identities=32% Similarity=0.391 Sum_probs=14.3
Q ss_pred ccceEEEEccCCc-eeeeeEEEE
Q 033136 100 GIGSVVAVDQVRL-FSIFLVYVT 121 (126)
Q Consensus 100 ~vGtVvsVDq~~~-~~rYPVvVR 121 (126)
-+|+||+|+.+.. -.-||.+|-
T Consensus 7 llGkVV~V~~~~~k~~W~PALVV 29 (96)
T PF08169_consen 7 LLGKVVCVESTKKKTSWFPALVV 29 (96)
T ss_dssp STTSEEEEE-SS-SS-EEEEEEE
T ss_pred hcCcEEEEEcCCCCCceeeEEEE
Confidence 3899999987533 146998874
No 63
>PRK09781 hypothetical protein; Provisional
Probab=25.97 E-value=40 Score=27.39 Aligned_cols=21 Identities=48% Similarity=0.879 Sum_probs=16.6
Q ss_pred CCCCCCeeEEeeccc-eecccc
Q 033136 81 GPKRGAKVKILRRES-YWYNGI 101 (126)
Q Consensus 81 gp~RGskVrIlR~ES-YWyn~v 101 (126)
-|--|.-++|-|.|| ||-.+|
T Consensus 14 DP~sG~DI~IA~~~St~W~~~I 35 (181)
T PRK09781 14 DPASGADIRIARRESTSWHKDI 35 (181)
T ss_pred CCCCCceeEEEecccccchHHH
Confidence 456788999999998 887654
No 64
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=25.84 E-value=1.2e+02 Score=23.17 Aligned_cols=14 Identities=14% Similarity=0.458 Sum_probs=10.4
Q ss_pred cccceEEEEccCCc
Q 033136 99 NGIGSVVAVDQVRL 112 (126)
Q Consensus 99 n~vGtVvsVDq~~~ 112 (126)
..+|+|..|+..|.
T Consensus 119 ~~lG~V~~v~~~ga 132 (184)
T PRK14593 119 EILGKVIEIQRISQ 132 (184)
T ss_pred EEeEEEEEEccCCC
Confidence 45788888888765
No 65
>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=25.28 E-value=56 Score=27.60 Aligned_cols=11 Identities=27% Similarity=0.452 Sum_probs=9.8
Q ss_pred eeeEEEEeeec
Q 033136 115 IFLVYVTFNHF 125 (126)
Q Consensus 115 rYPVvVRF~kv 125 (126)
.|||+|||.+.
T Consensus 79 ~~pv~vRFS~~ 89 (384)
T PF00199_consen 79 TYPVIVRFSNA 89 (384)
T ss_dssp EEEEEEEEEES
T ss_pred ccceeeeeccc
Confidence 89999999864
No 66
>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=25.14 E-value=46 Score=22.63 Aligned_cols=14 Identities=21% Similarity=0.489 Sum_probs=10.6
Q ss_pred CCCCCeeEEeeccc
Q 033136 82 PKRGAKVKILRRES 95 (126)
Q Consensus 82 p~RGskVrIlR~ES 95 (126)
+++|++|+|.+-|.
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 67
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=25.08 E-value=36 Score=23.14 Aligned_cols=18 Identities=39% Similarity=0.750 Sum_probs=11.5
Q ss_pred CCCCCeeEEeeccceeccc
Q 033136 82 PKRGAKVKILRRESYWYNG 100 (126)
Q Consensus 82 p~RGskVrIlR~ESYWyn~ 100 (126)
|++|+.| ++..++||-++
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 56689998554
No 68
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=25.07 E-value=1.4e+02 Score=22.86 Aligned_cols=32 Identities=25% Similarity=0.347 Sum_probs=25.2
Q ss_pred CeeEEeeccceecc------ccceEEEEccCCceeeeeEEE
Q 033136 86 AKVKILRRESYWYN------GIGSVVAVDQVRLFSIFLVYV 120 (126)
Q Consensus 86 skVrIlR~ESYWyn------~vGtVvsVDq~~~~~rYPVvV 120 (126)
..|||||+-+|=.| +-+-|+++-.+| +|=+.+
T Consensus 62 etIrI~~pG~YeiNl~~Lld~~~iVval~EeG---~Y~I~L 99 (112)
T COG3364 62 ETIRILRPGVYEINLESLLDRDEIVVALQEEG---RYFIHL 99 (112)
T ss_pred eEEEEecCceEEEehhhhccCCceEEEEccCC---eEEEEC
Confidence 78999999999655 667799988887 665543
No 69
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=24.77 E-value=1.2e+02 Score=22.69 Aligned_cols=30 Identities=23% Similarity=0.312 Sum_probs=20.4
Q ss_pred CCCCeeEEeec--------cceec-----------cccceEEEEccCCc
Q 033136 83 KRGAKVKILRR--------ESYWY-----------NGIGSVVAVDQVRL 112 (126)
Q Consensus 83 ~RGskVrIlR~--------ESYWy-----------n~vGtVvsVDq~~~ 112 (126)
=||..+.|-|. |-||+ +.+|+|..|++.|.
T Consensus 69 l~g~~l~v~~~~lp~L~e~EyY~~dLiG~~V~~~g~~lG~V~~v~~~ga 117 (162)
T PRK13829 69 LVGLRVYADDADLPPLEEGSYYYHELRGLPVYVDGEPLGEVVDVEDAGA 117 (162)
T ss_pred hcCCEEEEEHHHCCCCCCCCEEehhccCeEEEECCEeeEEEEEEecCCC
Confidence 35666666652 55666 44799999988765
No 70
>TIGR00531 BCCP acetyl-CoA carboxylase, biotin carboxyl carrier protein. The gene name is accB or fabE.
Probab=24.59 E-value=2.3e+02 Score=21.33 Aligned_cols=30 Identities=17% Similarity=0.228 Sum_probs=21.9
Q ss_pred CCCCCCeeEEeeccceeccccceEEEEccC
Q 033136 81 GPKRGAKVKILRRESYWYNGIGSVVAVDQV 110 (126)
Q Consensus 81 gp~RGskVrIlR~ESYWyn~vGtVvsVDq~ 110 (126)
-|--|...+.--++.=||-++|..+..+|.
T Consensus 85 sp~~G~~~~~~~P~~~~~v~~Gd~V~~Gq~ 114 (156)
T TIGR00531 85 SPMVGTFYRAPSPDAKPFVEVGDKVKKGQI 114 (156)
T ss_pred CCCCEEEEecCCCCCCccccCCCEeCCCCE
Confidence 355566666666788899999988877664
No 71
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=24.20 E-value=1.9e+02 Score=18.01 Aligned_cols=39 Identities=18% Similarity=0.383 Sum_probs=28.5
Q ss_pred CCCCeeEEeeccceeccccceEEEEccCCceeeeeEEEEeeec
Q 033136 83 KRGAKVKILRRESYWYNGIGSVVAVDQVRLFSIFLVYVTFNHF 125 (126)
Q Consensus 83 ~RGskVrIlR~ESYWyn~vGtVvsVDq~~~~~rYPVvVRF~kv 125 (126)
+-|++|..++.+.=||. .+|..++..++ .+-..|.|...
T Consensus 2 ~vG~~v~~~~~~~~~y~--A~I~~~r~~~~--~~~YyVHY~g~ 40 (55)
T PF11717_consen 2 EVGEKVLCKYKDGQWYE--AKILDIREKNG--EPEYYVHYQGW 40 (55)
T ss_dssp -TTEEEEEEETTTEEEE--EEEEEEEECTT--CEEEEEEETTS
T ss_pred CcCCEEEEEECCCcEEE--EEEEEEEecCC--CEEEEEEcCCC
Confidence 56899999986666764 78999988765 56667777654
No 72
>PRK09752 adhesin; Provisional
Probab=24.17 E-value=99 Score=31.55 Aligned_cols=6 Identities=17% Similarity=0.412 Sum_probs=4.2
Q ss_pred EEeecc
Q 033136 89 KILRRE 94 (126)
Q Consensus 89 rIlR~E 94 (126)
-++|+|
T Consensus 952 PvlRPE 957 (1250)
T PRK09752 952 PVLNAK 957 (1250)
T ss_pred cccccc
Confidence 467777
No 73
>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=24.05 E-value=64 Score=18.93 Aligned_cols=22 Identities=23% Similarity=0.726 Sum_probs=16.1
Q ss_pred CCCCCCCCCCeeEEeec-cceec
Q 033136 77 PPPIGPKRGAKVKILRR-ESYWY 98 (126)
Q Consensus 77 pppigp~RGskVrIlR~-ESYWy 98 (126)
+-.+..++|+++.|+.+ ++-|+
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 44678999999999985 44476
No 74
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=24.00 E-value=90 Score=21.34 Aligned_cols=33 Identities=18% Similarity=0.089 Sum_probs=21.1
Q ss_pred CCCCCCCCeeEEeeccceeccccceEEEEccCC
Q 033136 79 PIGPKRGAKVKILRRESYWYNGIGSVVAVDQVR 111 (126)
Q Consensus 79 pigp~RGskVrIlR~ESYWyn~vGtVvsVDq~~ 111 (126)
..-|+.||.|-.-....-.|..||-|..|+.++
T Consensus 60 ~~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~ 92 (124)
T PF05257_consen 60 GSTPQPGDIVVWDSGSGGGYGHVAIVESVNDGG 92 (124)
T ss_dssp CS---TTEEEEEEECTTTTT-EEEEEEEE-TTS
T ss_pred CcccccceEEEeccCCCCCCCeEEEEEEECCCC
Confidence 345788999988766777788888888884343
No 75
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=23.46 E-value=1.9e+02 Score=22.92 Aligned_cols=17 Identities=29% Similarity=0.554 Sum_probs=13.9
Q ss_pred CCCCCCeeEE---eecccee
Q 033136 81 GPKRGAKVKI---LRRESYW 97 (126)
Q Consensus 81 gp~RGskVrI---lR~ESYW 97 (126)
-.++|++|.| ||.++|.
T Consensus 70 ~L~KGd~V~V~GrL~~r~we 89 (186)
T PRK07772 70 SLTKGMRVIVTGRLKQRSYE 89 (186)
T ss_pred hcCCCCEEEEEEEEEcCceE
Confidence 4789999998 6888875
No 76
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=23.38 E-value=2.2e+02 Score=21.10 Aligned_cols=31 Identities=26% Similarity=0.322 Sum_probs=24.5
Q ss_pred CCCCCCCCeeEEeeccceeccccceEEEEccCC
Q 033136 79 PIGPKRGAKVKILRRESYWYNGIGSVVAVDQVR 111 (126)
Q Consensus 79 pigp~RGskVrIlR~ESYWyn~vGtVvsVDq~~ 111 (126)
-.+.+.|++|||..- =|=+..|.|..+|...
T Consensus 92 ~~~~~~G~~V~I~~G--pf~g~~g~V~~vd~~k 122 (153)
T PRK08559 92 VEGIKEGDIVELIAG--PFKGEKARVVRVDESK 122 (153)
T ss_pred ccCCCCCCEEEEecc--CCCCceEEEEEEcCCC
Confidence 367999999999873 3556679999999764
No 77
>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=22.97 E-value=67 Score=26.09 Aligned_cols=11 Identities=9% Similarity=0.331 Sum_probs=9.7
Q ss_pred eeeEEEEeeec
Q 033136 115 IFLVYVTFNHF 125 (126)
Q Consensus 115 rYPVvVRF~kv 125 (126)
.|||+|||.+.
T Consensus 39 ~~pv~vRfS~~ 49 (305)
T cd08152 39 TYPAVIRFSNA 49 (305)
T ss_pred eEEEEEEecCC
Confidence 89999999864
No 78
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=22.89 E-value=93 Score=19.88 Aligned_cols=21 Identities=24% Similarity=0.458 Sum_probs=11.9
Q ss_pred CCCCCee--EEee-ccceeccccc
Q 033136 82 PKRGAKV--KILR-RESYWYNGIG 102 (126)
Q Consensus 82 p~RGskV--rIlR-~ESYWyn~vG 102 (126)
|+.|+.| +|.+ .+..|+=++|
T Consensus 4 p~~GdiV~G~V~~v~~~~~~V~i~ 27 (82)
T cd04454 4 PDVGDIVIGIVTEVNSRFWKVDIL 27 (82)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEeC
Confidence 6788887 3333 4455555554
No 79
>KOG2310 consensus DNA repair exonuclease MRE11 [Replication, recombination and repair]
Probab=22.86 E-value=39 Score=32.08 Aligned_cols=15 Identities=53% Similarity=1.028 Sum_probs=12.9
Q ss_pred CeeEEeeccce---eccc
Q 033136 86 AKVKILRRESY---WYNG 100 (126)
Q Consensus 86 skVrIlR~ESY---Wyn~ 100 (126)
-+|+.+|||-| |||=
T Consensus 197 ~~V~f~rPe~~e~dWFNl 214 (646)
T KOG2310|consen 197 GKVTFLRPEEYEDDWFNL 214 (646)
T ss_pred CceEEecCccccccceee
Confidence 37999999998 9983
No 80
>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=22.79 E-value=57 Score=23.52 Aligned_cols=27 Identities=30% Similarity=0.575 Sum_probs=19.1
Q ss_pred CCCCeeEEeeccceecccc-ceE-EEEcc
Q 033136 83 KRGAKVKILRRESYWYNGI-GSV-VAVDQ 109 (126)
Q Consensus 83 ~RGskVrIlR~ESYWyn~v-GtV-vsVDq 109 (126)
-+|-.||-|+.|.|.|.|- |+| +.||.
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 3688999999999999874 544 33444
No 81
>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=21.67 E-value=59 Score=20.27 Aligned_cols=18 Identities=17% Similarity=0.693 Sum_probs=13.8
Q ss_pred CCCCCCCCeeEEeeccce
Q 033136 79 PIGPKRGAKVKILRRESY 96 (126)
Q Consensus 79 pigp~RGskVrIlR~ESY 96 (126)
..|...|++|+|+++..+
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 368899999999987654
No 82
>PRK14639 hypothetical protein; Provisional
Probab=21.44 E-value=1.8e+02 Score=21.62 Aligned_cols=42 Identities=26% Similarity=0.296 Sum_probs=26.7
Q ss_pred CCCCCeeEEeeccceeccccceEEEEccCCceeee-----eEEEEeeec
Q 033136 82 PKRGAKVKILRRESYWYNGIGSVVAVDQVRLFSIF-----LVYVTFNHF 125 (126)
Q Consensus 82 p~RGskVrIlR~ESYWyn~vGtVvsVDq~~~~~rY-----PVvVRF~kv 125 (126)
--.|.+|+|.-.+.=+| .|.+..+|.++..+.+ .+.+.|+++
T Consensus 85 r~~G~~v~v~l~~~~~~--~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I 131 (140)
T PRK14639 85 KSIGELVKITTNEKEKF--EGKIVSVDDENITLENLENKEKTTINFNDI 131 (140)
T ss_pred HhCCCEEEEEECCCcEE--EEEEEEEeCCEEEEEEccCCcEEEEEhHHe
Confidence 34699999965443333 4899999988653323 356666654
No 83
>PRK09918 putative fimbrial chaperone protein; Provisional
Probab=21.22 E-value=64 Score=25.41 Aligned_cols=20 Identities=15% Similarity=0.401 Sum_probs=15.1
Q ss_pred CCCCCCCeeEEeec-------cc-eecc
Q 033136 80 IGPKRGAKVKILRR-------ES-YWYN 99 (126)
Q Consensus 80 igp~RGskVrIlR~-------ES-YWyn 99 (126)
+.|.....|||++. || ||+|
T Consensus 80 l~pg~~q~vRii~~~~lp~drEs~f~l~ 107 (230)
T PRK09918 80 VEPGQSQQVRFILKSGSPLNTEHLLRVS 107 (230)
T ss_pred ECCCCceEEEEEECCCCCCCeeEEEEEE
Confidence 56778889999854 44 8986
No 84
>PRK14635 hypothetical protein; Provisional
Probab=20.97 E-value=2e+02 Score=21.80 Aligned_cols=30 Identities=30% Similarity=0.475 Sum_probs=21.6
Q ss_pred CCCCeeEEeec---cceeccccceEEEEccCCc
Q 033136 83 KRGAKVKILRR---ESYWYNGIGSVVAVDQVRL 112 (126)
Q Consensus 83 ~RGskVrIlR~---ESYWyn~vGtVvsVDq~~~ 112 (126)
-+|.+|+|.-+ ..-|...+|.+.++|.+..
T Consensus 97 ~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~~v 129 (162)
T PRK14635 97 FRGIPVRLVFRSEESEKWQEGIFRLVNRDGDQV 129 (162)
T ss_pred hCCCEEEEEEecCCCcEEEecceEEEEEcCCEE
Confidence 36999987533 2366667789999998765
No 85
>COG3121 FimC P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=20.29 E-value=76 Score=25.23 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=16.8
Q ss_pred CCCCCCCCeeEEeecc---------ceecc
Q 033136 79 PIGPKRGAKVKILRRE---------SYWYN 99 (126)
Q Consensus 79 pigp~RGskVrIlR~E---------SYWyn 99 (126)
-+.|+++..|||++.. -||+|
T Consensus 84 rl~p~~~q~vRi~~~~~~lP~drEslf~ln 113 (235)
T COG3121 84 RLEPGQEQQLRILYTGNKLPADRESLFRLN 113 (235)
T ss_pred EECCCCccEEEEEecCCCCCCCceeEEEEE
Confidence 3688999999999754 58887
No 86
>PLN00129 succinate dehydrogenase [ubiquinone] iron-sulfur subunit
Probab=20.08 E-value=98 Score=25.83 Aligned_cols=20 Identities=25% Similarity=0.327 Sum_probs=11.2
Q ss_pred CCCCCCCCCCCCCe--eEEeec
Q 033136 74 KPKPPPIGPKRGAK--VKILRR 93 (126)
Q Consensus 74 k~kpppigp~RGsk--VrIlR~ 93 (126)
+.|....|++...+ +||.|-
T Consensus 30 ~~~~~~~~~~~~~~~~~~i~R~ 51 (276)
T PLN00129 30 ETKASSKGSKPSNLKEFQIYRW 51 (276)
T ss_pred cccccCCCCCCCceEEEEEEee
Confidence 33444556665554 577873
Done!