Query 045228
Match_columns 146
No_of_seqs 96 out of 98
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 11:06:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045228.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045228hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10063 DUF2301: Uncharacteri 100.0 1.2E-57 2.5E-62 352.6 12.7 123 1-127 13-135 (135)
2 COG5413 Uncharacterized integr 100.0 6.5E-42 1.4E-46 271.3 10.7 105 1-127 64-168 (168)
3 PF11460 DUF3007: Protein of u 67.2 4.1 8.8E-05 31.1 1.9 19 126-144 86-104 (104)
4 PF12650 DUF3784: Domain of un 65.6 8.1 0.00018 27.3 3.1 17 125-141 24-40 (97)
5 PF09776 Mitoc_L55: Mitochondr 58.9 6.8 0.00015 30.3 1.8 18 128-145 75-92 (116)
6 PF03918 CcmH: Cytochrome C bi 53.0 4.5 9.8E-05 31.7 0.0 37 93-139 108-144 (148)
7 PF06945 DUF1289: Protein of u 51.7 15 0.00032 23.9 2.3 22 124-145 27-48 (51)
8 COG3313 Predicted Fe-S protein 51.1 16 0.00034 26.5 2.5 22 123-144 31-52 (74)
9 TIGR02587 putative integral me 47.1 56 0.0012 28.7 5.7 52 10-61 8-59 (271)
10 PF13618 Gluconate_2-dh3: Gluc 43.7 21 0.00045 25.9 2.3 20 126-145 67-86 (131)
11 cd01247 PH_GPBP Goodpasture an 42.2 14 0.00029 26.1 1.1 32 114-145 58-91 (91)
12 cd01226 PH_exo84 Exocyst compl 41.8 17 0.00037 27.2 1.6 25 122-146 74-98 (100)
13 PRK15385 magnesium transport p 40.8 2.3E+02 0.0049 24.1 10.1 35 46-86 66-103 (225)
14 COG2119 Predicted membrane pro 37.9 37 0.0008 28.4 3.1 41 74-116 48-88 (190)
15 PF13902 R3H-assoc: R3H-associ 36.7 29 0.00063 26.0 2.2 20 126-145 77-96 (131)
16 PF13779 DUF4175: Domain of un 36.5 68 0.0015 31.8 5.1 28 91-118 36-63 (820)
17 PF14038 YqzE: YqzE-like prote 35.8 40 0.00086 23.0 2.5 21 125-145 14-34 (54)
18 PF07851 TMPIT: TMPIT-like pro 33.9 98 0.0021 27.7 5.3 48 64-111 255-312 (330)
19 cd01265 PH_PARIS-1 PARIS-1 ple 33.7 28 0.00061 24.5 1.6 23 122-144 70-92 (95)
20 PF04854 DUF624: Protein of un 32.2 1.3E+02 0.0027 20.1 4.5 15 4-18 3-17 (77)
21 PRK12586 putative monovalent c 31.6 2.7E+02 0.0058 22.2 7.2 44 42-85 15-61 (145)
22 PF15405 PH_5: Pleckstrin homo 31.3 31 0.00067 26.4 1.6 34 113-146 100-135 (135)
23 PF10864 DUF2663: Protein of u 30.6 2E+02 0.0043 22.7 6.0 54 3-56 19-75 (130)
24 PF10112 Halogen_Hydrol: 5-bro 30.0 2.1E+02 0.0046 22.5 6.1 12 105-116 47-58 (199)
25 PF06628 Catalase-rel: Catalas 29.7 44 0.00096 22.6 2.0 17 127-143 17-33 (68)
26 PF11304 DUF3106: Protein of u 29.5 37 0.0008 25.1 1.7 15 126-140 91-105 (107)
27 COG5249 RER1 Golgi protein inv 29.3 79 0.0017 26.1 3.7 61 62-122 106-175 (180)
28 cd01223 PH_Vav Vav pleckstrin 29.0 35 0.00076 26.3 1.5 24 122-145 87-110 (116)
29 cd01238 PH_Tec Tec pleckstrin 29.0 38 0.00081 24.3 1.6 20 125-144 86-105 (106)
30 PF13801 Metal_resist: Heavy-m 28.5 67 0.0014 21.7 2.7 41 101-141 8-53 (125)
31 PF12017 Tnp_P_element: Transp 28.1 69 0.0015 27.0 3.3 36 102-144 171-207 (236)
32 cd01228 PH_BCR-related BCR (br 28.1 40 0.00086 25.4 1.6 29 116-144 62-92 (96)
33 PF11014 DUF2852: Protein of u 27.9 2.6E+02 0.0056 21.7 6.1 31 74-105 11-41 (115)
34 PF14012 DUF4229: Protein of u 27.9 63 0.0014 22.3 2.5 35 87-121 30-64 (69)
35 PRK10404 hypothetical protein; 27.8 75 0.0016 23.5 3.1 28 29-56 70-97 (101)
36 PRK10408 putative L-valine exp 27.3 88 0.0019 24.3 3.4 27 32-58 61-87 (111)
37 PRK12574 putative monovalent c 27.3 93 0.002 24.3 3.6 30 27-56 56-85 (141)
38 PF04246 RseC_MucC: Positive r 27.2 2.2E+02 0.0048 21.0 5.5 48 68-115 70-121 (135)
39 PF00034 Cytochrom_C: Cytochro 26.1 79 0.0017 19.7 2.6 18 129-146 74-91 (91)
40 cd01222 PH_clg Clg (common-sit 26.0 33 0.00072 25.1 0.9 23 122-144 71-93 (97)
41 PRK12573 putative monovalent c 25.8 1E+02 0.0023 24.0 3.7 28 29-56 58-85 (140)
42 TIGR00943 2a6301s02 monovalent 25.8 1.1E+02 0.0023 22.9 3.6 29 27-55 31-59 (107)
43 PRK12509 putative monovalent c 25.0 1.1E+02 0.0024 23.8 3.7 30 27-56 54-83 (137)
44 TIGR00439 ftsX putative protei 24.8 1.6E+02 0.0035 25.3 4.9 53 92-145 39-91 (309)
45 cd01261 PH_SOS Son of Sevenles 24.8 48 0.001 24.9 1.6 24 121-144 84-107 (112)
46 PF10003 DUF2244: Integral mem 24.8 61 0.0013 24.7 2.2 16 130-145 124-139 (140)
47 PRK10132 hypothetical protein; 24.5 98 0.0021 23.3 3.2 27 30-56 77-103 (108)
48 PF13864 Enkurin: Calmodulin-b 24.3 68 0.0015 23.0 2.2 18 127-144 34-51 (98)
49 PF10112 Halogen_Hydrol: 5-bro 24.2 2.9E+02 0.0064 21.7 6.0 44 2-55 2-47 (199)
50 PF05957 DUF883: Bacterial pro 24.2 1E+02 0.0022 21.6 3.1 29 28-56 62-90 (94)
51 PRK09570 rpoH DNA-directed RNA 24.1 59 0.0013 23.5 1.9 18 126-143 14-31 (79)
52 smart00398 HMG high mobility g 23.5 67 0.0015 20.0 1.9 20 125-144 38-57 (70)
53 PF00505 HMG_box: HMG (high mo 23.2 32 0.00069 21.9 0.3 27 118-144 30-56 (69)
54 PF10463 Peptidase_U49: Peptid 22.8 85 0.0019 26.1 2.8 18 2-19 5-22 (206)
55 KOG4715 SWI/SNF-related matrix 22.4 44 0.00095 30.6 1.1 28 118-145 94-121 (410)
56 PF14163 SieB: Superinfection 22.3 1.8E+02 0.0038 22.0 4.3 36 8-50 3-43 (151)
57 TIGR03707 PPK2_P_aer polyphosp 22.1 64 0.0014 27.0 2.0 18 127-144 141-158 (230)
58 PF13309 HTH_22: HTH domain 21.7 93 0.002 20.8 2.4 19 128-146 19-37 (64)
59 PRK11026 ftsX cell division AB 21.1 2.1E+02 0.0046 24.5 4.9 48 97-145 44-91 (309)
60 COG2899 Uncharacterized protei 21.0 1.4E+02 0.003 27.1 3.9 49 7-69 294-343 (346)
61 PF11241 DUF3043: Protein of u 21.0 2.7E+02 0.0059 22.7 5.3 14 74-87 81-94 (170)
62 TIGR03180 UraD_2 OHCU decarbox 20.8 79 0.0017 24.9 2.2 9 115-123 60-68 (158)
63 PF03086 DUF240: MG032/MG096/M 20.8 69 0.0015 25.1 1.8 26 121-146 84-116 (120)
64 cd01235 PH_SETbf Set binding f 20.7 70 0.0015 21.7 1.6 24 121-144 76-99 (101)
65 PF14584 DUF4446: Protein of u 20.6 62 0.0013 25.6 1.5 13 128-140 137-149 (151)
66 PF12576 DUF3754: Protein of u 20.1 2.8E+02 0.006 21.2 5.0 27 42-68 95-121 (141)
No 1
>PF10063 DUF2301: Uncharacterized integral membrane protein (DUF2301); InterPro: IPR019275 This family contains uncharacterised integral membrane proteins.
Probab=100.00 E-value=1.2e-57 Score=352.57 Aligned_cols=123 Identities=51% Similarity=0.905 Sum_probs=120.9
Q ss_pred ChHHHHHHHHHHHHHHHHHHhhhhcCCCchhHHHHHhcchhHHHHHHHHHHHhhhhhhhhhccchhhhhhhHHHHHHHHH
Q 045228 1 IKRTLQALWVLGVMGSLATYTALARPAGENLVQYVIDHPTAVWFVGSLFAALTGLVFKEGLCYGKLEAGILTFIIPSVLL 80 (146)
Q Consensus 1 ~hr~LQ~~W~iG~~g~~~~~~~~a~~~~~~l~~~v~~~P~~~l~vG~~FaaLtGi~fKE~FCF~~~e~~~lt~l~P~lll 80 (146)
+||+||.+|.+|+++++++ +.++++|++.+|++||.++|++||+|+|+|||+|||+|||||+|++++|+++|++++
T Consensus 13 l~r~LQ~~w~iG~l~~~~l----~~~~~~~l~~~v~~~P~~~l~vG~~FaaLtGi~fKE~FCF~~~e~~~l~~llp~llL 88 (135)
T PF10063_consen 13 LHRILQLFWWIGLLGSLIL----ALQSGEPLASYVYGQPLWLLAVGPLFAALTGIAFKEYFCFRRPEAKLLTFLLPLLLL 88 (135)
T ss_pred HHHHHHHHHHHHHHHHHHH----HhhcCcchHHHHHcCccHHHHHHHHHHHHHhHHhhchhhhhhHHHhhHHHHHHHHHH
Confidence 5999999999999999988 889889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhchhHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCcchhhhh
Q 045228 81 GHLSGLMDDGVKLSLLGSWMVLFVIFAGRKFTQPIKDDIGDKSVFMF 127 (146)
Q Consensus 81 ghl~g~l~~~~~~~ll~~~~~L~~i~A~rK~~mPl~~DIGDKSvf~y 127 (146)
||++|.++...++.++++|++||++||+||||||+||||||||||+|
T Consensus 89 ghl~g~~~~~~~~~ll~~~~~L~~i~A~rK~~mPl~~DIGDKSvf~~ 135 (135)
T PF10063_consen 89 GHLFGLLPASVELALLGIWALLFLIFAIRKWRMPLHFDIGDKSVFQY 135 (135)
T ss_pred HHHHCCCcHHHHHHHHHHHHHHHHHHHHHHhCCCCCcccCccccccC
Confidence 99999999999999999999999999999999999999999999997
No 2
>COG5413 Uncharacterized integral membrane protein [Function unknown]
Probab=100.00 E-value=6.5e-42 Score=271.31 Aligned_cols=105 Identities=31% Similarity=0.426 Sum_probs=100.5
Q ss_pred ChHHHHHHHHHHHHHHHHHHhhhhcCCCchhHHHHHhcchhHHHHHHHHHHHhhhhhhhhhccchhhhhhhHHHHHHHHH
Q 045228 1 IKRTLQALWVLGVMGSLATYTALARPAGENLVQYVIDHPTAVWFVGSLFAALTGLVFKEGLCYGKLEAGILTFIIPSVLL 80 (146)
Q Consensus 1 ~hr~LQ~~W~iG~~g~~~~~~~~a~~~~~~l~~~v~~~P~~~l~vG~~FaaLtGi~fKE~FCF~~~e~~~lt~l~P~lll 80 (146)
.||.||++|.+| .+||+||.+.+++|++|+||||+||||+|||||+|++.+|+++|.+.+
T Consensus 64 ~~~llQ~~~~Ig--------------------~tvy~qp~t~L~lG~a~atL~Gl~fKE~FCF~~l~~~~~~~~V~~L~l 123 (168)
T COG5413 64 FRLLLQLATWIG--------------------LTVYAQPFTALALGGALATLGGLCFKEYFCFRVLLLNAQPFFVALLWL 123 (168)
T ss_pred HHHHHHHHHHHH--------------------HHHhcCCchHHHHHHHHHHHhhHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 389999999999 579999999999999999999999999999999999999999999888
Q ss_pred HHHHhhchhHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCcchhhhh
Q 045228 81 GHLSGLMDDGVKLSLLGSWMVLFVIFAGRKFTQPIKDDIGDKSVFMF 127 (146)
Q Consensus 81 ghl~g~l~~~~~~~ll~~~~~L~~i~A~rK~~mPl~~DIGDKSvf~y 127 (146)
+.|+.|..++++++.+|++||+|+|+|||+||+|+||||||||.|
T Consensus 124 --l~gl~p~~~~qi~~~~~avLflv~a~rK~~~pl~~DIGDKS~y~y 168 (168)
T COG5413 124 --LVGLNPLLFTQIMSLIVAVLFLVLAFRKWQMPLHFDIGDKSKYQY 168 (168)
T ss_pred --HHHhchHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCccccccC
Confidence 778888899999999999999999999999999999999999987
No 3
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=67.22 E-value=4.1 Score=31.10 Aligned_cols=19 Identities=32% Similarity=0.459 Sum_probs=16.6
Q ss_pred hhhcCCHHHHHHHHHHHHh
Q 045228 126 MFNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 126 ~yl~l~~~e~~~~~~~~~~ 144 (146)
-+.+||+||++++.++.||
T Consensus 86 Rle~l~~eE~~~L~~eiee 104 (104)
T PF11460_consen 86 RLEELSPEELEALQAEIEE 104 (104)
T ss_pred HHHhCCHHHHHHHHHHhcC
Confidence 4678999999999999885
No 4
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=65.57 E-value=8.1 Score=27.32 Aligned_cols=17 Identities=29% Similarity=0.409 Sum_probs=13.0
Q ss_pred hhhhcCCHHHHHHHHHH
Q 045228 125 FMFNALSEDEKKALIEK 141 (146)
Q Consensus 125 f~yl~l~~~e~~~~~~~ 141 (146)
=-||.+|+|||+..-+|
T Consensus 24 aGyntms~eEk~~~D~~ 40 (97)
T PF12650_consen 24 AGYNTMSKEEKEKYDKK 40 (97)
T ss_pred hhcccCCHHHHHHhhHH
Confidence 36999999999865443
No 5
>PF09776 Mitoc_L55: Mitochondrial ribosomal protein L55; InterPro: IPR018615 Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Probab=58.93 E-value=6.8 Score=30.33 Aligned_cols=18 Identities=39% Similarity=0.588 Sum_probs=15.4
Q ss_pred hcCCHHHHHHHHHHHHhc
Q 045228 128 NALSEDEKKALIEKLEQQ 145 (146)
Q Consensus 128 l~l~~~e~~~~~~~~~~~ 145 (146)
..||||||++++++++-+
T Consensus 75 ~~LSeeERk~rl~kR~pk 92 (116)
T PF09776_consen 75 DTLSEEERKARLRKRKPK 92 (116)
T ss_pred ccCCHHHHHHHHHHhCCc
Confidence 479999999999998754
No 6
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=52.98 E-value=4.5 Score=31.74 Aligned_cols=37 Identities=22% Similarity=0.159 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCCCCCCcchhhhhhcCCHHHHHHHH
Q 045228 93 LSLLGSWMVLFVIFAGRKFTQPIKDDIGDKSVFMFNALSEDEKKALI 139 (146)
Q Consensus 93 ~~ll~~~~~L~~i~A~rK~~mPl~~DIGDKSvf~yl~l~~~e~~~~~ 139 (146)
-.+..+.++.+++..+|||+.+-.. ..+++||++++-
T Consensus 108 P~~~l~~g~~~~~~~~rr~~~~~~~----------~~ls~~e~~rl~ 144 (148)
T PF03918_consen 108 PFLLLLLGGALLFRRLRRWRRRAAQ----------EELSEEERRRLD 144 (148)
T ss_dssp -----------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHhcccCCCC----------CCCCHHHHHHHH
Confidence 3455566788888999999987665 678888887653
No 7
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=51.67 E-value=15 Score=23.94 Aligned_cols=22 Identities=23% Similarity=0.610 Sum_probs=18.2
Q ss_pred hhhhhcCCHHHHHHHHHHHHhc
Q 045228 124 VFMFNALSEDEKKALIEKLEQQ 145 (146)
Q Consensus 124 vf~yl~l~~~e~~~~~~~~~~~ 145 (146)
+..+..|+++||+++++++.+.
T Consensus 27 I~~W~~~s~~er~~i~~~l~~R 48 (51)
T PF06945_consen 27 IRDWKSMSDDERRAILARLRAR 48 (51)
T ss_pred HHHHhhCCHHHHHHHHHHHHHH
Confidence 4567899999999999888753
No 8
>COG3313 Predicted Fe-S protein [General function prediction only]
Probab=51.06 E-value=16 Score=26.48 Aligned_cols=22 Identities=32% Similarity=0.706 Sum_probs=18.6
Q ss_pred hhhhhhcCCHHHHHHHHHHHHh
Q 045228 123 SVFMFNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 123 Svf~yl~l~~~e~~~~~~~~~~ 144 (146)
-++....|+++||++.+..+.|
T Consensus 31 Ei~~W~~msd~Er~aVl~~l~q 52 (74)
T COG3313 31 EIFNWSSMSDDERRAVLRLLPQ 52 (74)
T ss_pred HHHHHhhCCHHHHHHHHHHhHH
Confidence 3688999999999998887764
No 9
>TIGR02587 putative integral membrane protein TIGR02587. Members of this family are found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Sinorhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighborhood. This family, as defined, includes some members of COG4711 but is narrower and strictly bacterial. Members appear to span the membrane seven times.
Probab=47.14 E-value=56 Score=28.68 Aligned_cols=52 Identities=21% Similarity=0.235 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHhhhhcCCCchhHHHHHhcchhHHHHHHHHHHHhhhhhhhhh
Q 045228 10 VLGVMGSLATYTALARPAGENLVQYVIDHPTAVWFVGSLFAALTGLVFKEGL 61 (146)
Q Consensus 10 ~iG~~g~~~~~~~~a~~~~~~l~~~v~~~P~~~l~vG~~FaaLtGi~fKE~F 61 (146)
+-|.+|++.+.++++...--..+.+-.+-|+-++.++..+..+-++.|.++|
T Consensus 8 ~r~~~GAllfaipia~T~Evw~ig~~~~p~~lllll~~sl~i~~~lv~~~GF 59 (271)
T TIGR02587 8 VRGTAGALLFAIPLLMTMEVWWLGSLAKPRRLVLLIALMFPVLFLLNYTEGF 59 (271)
T ss_pred HHHHHHHHHHhcccchHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3578899988555544433344455555566666678899999999999998
No 10
>PF13618 Gluconate_2-dh3: Gluconate 2-dehydrogenase subunit 3
Probab=43.69 E-value=21 Score=25.93 Aligned_cols=20 Identities=35% Similarity=0.619 Sum_probs=17.7
Q ss_pred hhhcCCHHHHHHHHHHHHhc
Q 045228 126 MFNALSEDEKKALIEKLEQQ 145 (146)
Q Consensus 126 ~yl~l~~~e~~~~~~~~~~~ 145 (146)
.|.+|+++||.++++++++.
T Consensus 67 ~F~~l~~~~~~~lL~~~~~~ 86 (131)
T PF13618_consen 67 SFAELSPAQREALLDALEKS 86 (131)
T ss_pred ChhhCCHHHHHHHHHHHHhc
Confidence 38999999999999999864
No 11
>cd01247 PH_GPBP Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. The GPBP protein is a kinase that phosphorylates an N-terminal region of the alpha 3 chain of type IV collagen , which is commonly known as the goodpasture antigen. It has has an N-terminal PH domain and a C-terminal START domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cyt
Probab=42.20 E-value=14 Score=26.13 Aligned_cols=32 Identities=13% Similarity=0.257 Sum_probs=25.5
Q ss_pred CCCCCC--CcchhhhhhcCCHHHHHHHHHHHHhc
Q 045228 114 PIKDDI--GDKSVFMFNALSEDEKKALIEKLEQQ 145 (146)
Q Consensus 114 Pl~~DI--GDKSvf~yl~l~~~e~~~~~~~~~~~ 145 (146)
|..|+| ++..+|..-|-+++|++.+++.++++
T Consensus 58 ~~~F~i~~~~~r~~~L~A~s~~e~~~Wi~al~~~ 91 (91)
T cd01247 58 ENRFDISVNENVVWYLRAENSQSRLLWMDSVVRE 91 (91)
T ss_pred CCEEEEEeCCCeEEEEEeCCHHHHHHHHHHHhhC
Confidence 445666 44478888899999999999999874
No 12
>cd01226 PH_exo84 Exocyst complex 84-kDa subunit Pleckstrin Homology (PH) domain. Exocyst complex 84-kDa subunit Pleckstrin Homology (PH) domain. Exo84 is a subunit of the exocyt complex, which is important in intracellular trafficking. In metazoa, Exo84 has a PH domain towards its N-terminus. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=41.76 E-value=17 Score=27.22 Aligned_cols=25 Identities=24% Similarity=0.267 Sum_probs=21.5
Q ss_pred chhhhhhcCCHHHHHHHHHHHHhcC
Q 045228 122 KSVFMFNALSEDEKKALIEKLEQQN 146 (146)
Q Consensus 122 KSvf~yl~l~~~e~~~~~~~~~~~~ 146 (146)
|..+.|.+=+++||+.|+..+|+.+
T Consensus 74 ~~s~i~qaes~~~K~eWl~~le~a~ 98 (100)
T cd01226 74 PESRIYQCESARIKTEWFEELEQAK 98 (100)
T ss_pred CccEEEEeCCHHHHHHHHHHHHHHh
Confidence 5567799999999999999999854
No 13
>PRK15385 magnesium transport protein MgtC; Provisional
Probab=40.77 E-value=2.3e+02 Score=24.06 Aligned_cols=35 Identities=31% Similarity=0.472 Sum_probs=20.3
Q ss_pred HHHHHHHhhhhhhhhhccchhhhhhhH---HHHHHHHHHHHHhh
Q 045228 46 GSLFAALTGLVFKEGLCYGKLEAGILT---FIIPSVLLGHLSGL 86 (146)
Q Consensus 46 G~~FaaLtGi~fKE~FCF~~~e~~~lt---~l~P~lllghl~g~ 86 (146)
|-.|..- |.-+||.- + .+++| -+.-...+|...|.
T Consensus 66 GigFlga-G~I~~~~~--~---v~GlTTaAtlw~taaiG~~~g~ 103 (225)
T PRK15385 66 GIGFLGA-GVIMREGM--N---VRGLNTAATLWCSAGIGVLCGL 103 (225)
T ss_pred HHHHHHh-eeeeccCC--C---CCcHHHHHHHHHHHHHHHHHHc
Confidence 4444443 77788764 3 35556 45555566777666
No 14
>COG2119 Predicted membrane protein [Function unknown]
Probab=37.88 E-value=37 Score=28.41 Aligned_cols=41 Identities=24% Similarity=0.217 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHHHhhhcCCCCC
Q 045228 74 IIPSVLLGHLSGLMDDGVKLSLLGSWMVLFVIFAGRKFTQPIK 116 (146)
Q Consensus 74 l~P~lllghl~g~l~~~~~~~ll~~~~~L~~i~A~rK~~mPl~ 116 (146)
=.--.+.|||...+.. ++.+.-..+++|+++|+.-+.-.-+
T Consensus 48 ~~la~~vG~~~~~~~~--~~~~~~~~~~~Flafav~~l~edk~ 88 (190)
T COG2119 48 HALAVLVGHAAASLLP--ERPLAWASGVLFLAFAVWMLIEDKE 88 (190)
T ss_pred HHHHHHHHHHHhccCc--hhHHHHHHHHHHHHHHHHHhccccc
Confidence 3345678999888533 4566677799999999876544333
No 15
>PF13902 R3H-assoc: R3H-associated N-terminal domain
Probab=36.72 E-value=29 Score=25.97 Aligned_cols=20 Identities=40% Similarity=0.725 Sum_probs=17.4
Q ss_pred hhhcCCHHHHHHHHHHHHhc
Q 045228 126 MFNALSEDEKKALIEKLEQQ 145 (146)
Q Consensus 126 ~yl~l~~~e~~~~~~~~~~~ 145 (146)
+|.+.++|||.++++++++.
T Consensus 77 ~f~~~~~eeQ~~~l~~~~~~ 96 (131)
T PF13902_consen 77 DFRNIDEEEQERLLEKLEKK 96 (131)
T ss_pred HHhhcCHHHHHHHHHHhhhc
Confidence 67899999999999988764
No 16
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=36.51 E-value=68 Score=31.78 Aligned_cols=28 Identities=14% Similarity=0.250 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCCCCCC
Q 045228 91 VKLSLLGSWMVLFVIFAGRKFTQPIKDD 118 (146)
Q Consensus 91 ~~~~ll~~~~~L~~i~A~rK~~mPl~~D 118 (146)
...+++++.++..+++.+|+||.|-..|
T Consensus 36 ~~l~~~~~a~~~al~~~lrrfr~Pt~~e 63 (820)
T PF13779_consen 36 ALLAAFAAAALAALVRGLRRFRWPTRAE 63 (820)
T ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHH
Confidence 3344445555555668899999986544
No 17
>PF14038 YqzE: YqzE-like protein
Probab=35.77 E-value=40 Score=23.03 Aligned_cols=21 Identities=14% Similarity=0.267 Sum_probs=14.9
Q ss_pred hhhhcCCHHHHHHHHHHHHhc
Q 045228 125 FMFNALSEDEKKALIEKLEQQ 145 (146)
Q Consensus 125 f~yl~l~~~e~~~~~~~~~~~ 145 (146)
-.|.+.|.|||++.-++..++
T Consensus 14 V~YmdtPkeERk~~k~~rK~~ 34 (54)
T PF14038_consen 14 VKYMDTPKEERKERKEERKEE 34 (54)
T ss_pred HHHhhCCHHHHHHHHHHHHhc
Confidence 469999999988765544443
No 18
>PF07851 TMPIT: TMPIT-like protein; InterPro: IPR012926 A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this. ; GO: 0016021 integral to membrane
Probab=33.91 E-value=98 Score=27.69 Aligned_cols=48 Identities=21% Similarity=0.220 Sum_probs=32.1
Q ss_pred chhhhhhhHHHHHHHHHHHHHhhchhHHHH----------HHHHHHHHHHHHHHhhhc
Q 045228 64 GKLEAGILTFIIPSVLLGHLSGLMDDGVKL----------SLLGSWMVLFVIFAGRKF 111 (146)
Q Consensus 64 ~~~e~~~lt~l~P~lllghl~g~l~~~~~~----------~ll~~~~~L~~i~A~rK~ 111 (146)
.-.--.+||+++|++..||.+-+-+...-. -=..++|++|+++++..+
T Consensus 255 ~s~~~~~L~fLlPfLf~~~~~q~yn~~~l~~~~~~~~~~ewqv~~~~~~f~~l~~gN~ 312 (330)
T PF07851_consen 255 QSWMWRGLTFLLPFLFFGQFFQLYNAYTLFELSYHPECREWQVFVCGLLFLILFLGNF 312 (330)
T ss_pred ccchhccHHHHHHHHHHHHHHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHHHhhhH
Confidence 344456799999999999998875541111 113457888888887544
No 19
>cd01265 PH_PARIS-1 PARIS-1 pleckstrin homology (PH) domain. PARIS-1 pleckstrin homology (PH) domain. PARIS-1 contains a PH domain and a TBC-type GTPase catalytic domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=33.65 E-value=28 Score=24.46 Aligned_cols=23 Identities=17% Similarity=0.312 Sum_probs=19.9
Q ss_pred chhhhhhcCCHHHHHHHHHHHHh
Q 045228 122 KSVFMFNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 122 KSvf~yl~l~~~e~~~~~~~~~~ 144 (146)
..+|.+-|-||||++.+++.++.
T Consensus 70 ~r~y~l~A~s~~e~~~Wi~al~~ 92 (95)
T cd01265 70 NEVIALKASSDKQMNYWLQALQS 92 (95)
T ss_pred CcEEEEECCCHHHHHHHHHHHHh
Confidence 34799999999999999998875
No 20
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=32.23 E-value=1.3e+02 Score=20.05 Aligned_cols=15 Identities=33% Similarity=0.674 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHH
Q 045228 4 TLQALWVLGVMGSLA 18 (146)
Q Consensus 4 ~LQ~~W~iG~~g~~~ 18 (146)
.|+++|.++++.++.
T Consensus 3 ~ln~lwl~~~l~~l~ 17 (77)
T PF04854_consen 3 VLNLLWLLFTLAGLP 17 (77)
T ss_pred HHHHHHHHHHHHHHH
Confidence 367888877766653
No 21
>PRK12586 putative monovalent cation/H+ antiporter subunit G; Reviewed
Probab=31.61 E-value=2.7e+02 Score=22.20 Aligned_cols=44 Identities=18% Similarity=0.264 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHhhhh---hhhhhccchhhhhhhHHHHHHHHHHHHHh
Q 045228 42 VWFVGSLFAALTGLV---FKEGLCYGKLEAGILTFIIPSVLLGHLSG 85 (146)
Q Consensus 42 ~l~vG~~FaaLtGi~---fKE~FCF~~~e~~~lt~l~P~lllghl~g 85 (146)
.+.+|.+|..++.|+ |...++==.-.+|.-|.-+++.++|...-
T Consensus 15 ll~lG~~f~ligaIGllRfPD~ytRlHAatKa~TlG~~liLlg~~l~ 61 (145)
T PRK12586 15 MILLGSIIALISAIGIVKFQDVFLRSHAATKSSTLSVLLTLIGVLIY 61 (145)
T ss_pred HHHHHHHHHHHHHHHHHhCCcHHHHccccccchhhHHHHHHHHHHHH
Confidence 344555555555444 45555544455666677777777776553
No 22
>PF15405 PH_5: Pleckstrin homology domain; PDB: 2Z0Q_A.
Probab=31.28 E-value=31 Score=26.42 Aligned_cols=34 Identities=26% Similarity=0.464 Sum_probs=23.2
Q ss_pred CCCCC-CCCcchh-hhhhcCCHHHHHHHHHHHHhcC
Q 045228 113 QPIKD-DIGDKSV-FMFNALSEDEKKALIEKLEQQN 146 (146)
Q Consensus 113 mPl~~-DIGDKSv-f~yl~l~~~e~~~~~~~~~~~~ 146 (146)
=|+.+ ..|-+.. |+..|=++.+|+.|+++.|+|.
T Consensus 100 yp~~~~hlG~~~~~~TLyA~s~~~R~~W~e~I~~qq 135 (135)
T PF15405_consen 100 YPFTFRHLGRKGYSYTLYASSAQARQKWLEKIEEQQ 135 (135)
T ss_dssp EEEEE---GGG-EEEEEE-SSHHHHHHHHHHHHHH-
T ss_pred cCEEEEEcCCCceEEEEEeCCHHHHHHHHHHHHhcC
Confidence 34444 5676544 7888999999999999999984
No 23
>PF10864 DUF2663: Protein of unknown function (DUF2663); InterPro: IPR020210 This entry represents a group of uncharacterised transmembrane proteins.
Probab=30.55 E-value=2e+02 Score=22.69 Aligned_cols=54 Identities=11% Similarity=0.157 Sum_probs=33.7
Q ss_pred HHHHHHHH-HHHHHHHHHHhhhhcC--CCchhHHHHHhcchhHHHHHHHHHHHhhhh
Q 045228 3 RTLQALWV-LGVMGSLATYTALARP--AGENLVQYVIDHPTAVWFVGSLFAALTGLV 56 (146)
Q Consensus 3 r~LQ~~W~-iG~~g~~~~~~~~a~~--~~~~l~~~v~~~P~~~l~vG~~FaaLtGi~ 56 (146)
|.+...|+ +.+.+..++|++.... +.+.+.+...+||..++-+=.++.++....
T Consensus 19 ~~~~~~~~~l~~~~~~~~y~~~~~~~~s~~~~~s~~~~~~~~l~~ll~~~~~~~~~~ 75 (130)
T PF10864_consen 19 QHLFWQWLFLFSLFLFFIYFYIKVIGYSFSSFLSAILGSPVHLFWLLALAFSYWAMY 75 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHcChHHHHHHHHHHHHHHHHH
Confidence 44444553 3344444445554444 478899999999998877766666665443
No 24
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=29.98 E-value=2.1e+02 Score=22.50 Aligned_cols=12 Identities=25% Similarity=0.091 Sum_probs=5.6
Q ss_pred HHHhhhcCCCCC
Q 045228 105 IFAGRKFTQPIK 116 (146)
Q Consensus 105 i~A~rK~~mPl~ 116 (146)
++...|+++.-+
T Consensus 47 ~~~~~~~~~~~k 58 (199)
T PF10112_consen 47 VYLFGKRRQRRK 58 (199)
T ss_pred HHHhcccccchh
Confidence 344455555433
No 25
>PF06628 Catalase-rel: Catalase-related immune-responsive; InterPro: IPR010582 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 []. This entry represents a small conserved region within catalase enzymes that carries the immune-responsive amphipathic octa-peptide that is recognised by T cells [].; PDB: 2CAH_A 1NM0_A 1H7K_A 1E93_A 1H6N_A 3HB6_A 2CAG_A 1M85_A 1MQF_A 1A4E_C ....
Probab=29.74 E-value=44 Score=22.56 Aligned_cols=17 Identities=29% Similarity=0.751 Sum_probs=14.2
Q ss_pred hhcCCHHHHHHHHHHHH
Q 045228 127 FNALSEDEKKALIEKLE 143 (146)
Q Consensus 127 yl~l~~~e~~~~~~~~~ 143 (146)
|..|+++||+.+++...
T Consensus 17 y~~l~~~er~~lv~nia 33 (68)
T PF06628_consen 17 YRVLSDEERERLVENIA 33 (68)
T ss_dssp HHHSSHHHHHHHHHHHH
T ss_pred HHHCCHHHHHHHHHHHH
Confidence 66899999999988653
No 26
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=29.55 E-value=37 Score=25.12 Aligned_cols=15 Identities=33% Similarity=0.598 Sum_probs=11.0
Q ss_pred hhhcCCHHHHHHHHH
Q 045228 126 MFNALSEDEKKALIE 140 (146)
Q Consensus 126 ~yl~l~~~e~~~~~~ 140 (146)
.|-.||+|||+++-+
T Consensus 91 ~yq~l~~eeR~~l~~ 105 (107)
T PF11304_consen 91 AYQQLPPEERQALRE 105 (107)
T ss_pred HHHcCCHHHHHHHHh
Confidence 567788888877754
No 27
>COG5249 RER1 Golgi protein involved in Golgi-to-ER retrieval [Intracellular trafficking and secretion]
Probab=29.29 E-value=79 Score=26.14 Aligned_cols=61 Identities=25% Similarity=0.272 Sum_probs=39.3
Q ss_pred ccchhhhhhh---HHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHHHhhhcCC------CCCCCCCcc
Q 045228 62 CYGKLEAGIL---TFIIPSVLLGHLSGLMDDGVKLSLLGSWMVLFVIFAGRKFTQ------PIKDDIGDK 122 (146)
Q Consensus 62 CF~~~e~~~l---t~l~P~lllghl~g~l~~~~~~~ll~~~~~L~~i~A~rK~~m------Pl~~DIGDK 122 (146)
-=|-||-|.- +-..-++++|-.+|+++.++---.+.+--+++..+..|+-.| =.|+|||.|
T Consensus 106 IRrLPEFkFWy~s~rat~~aLi~s~F~IfDvPVfwPILvvYfi~l~f~t~rRqIqHM~KYrY~PfdigKk 175 (180)
T COG5249 106 IRRLPEFKFWYFSTRATGMALIGSYFGIFDVPVFWPILVVYFIFLVFYTARRQIQHMKKYRYNPFDIGKK 175 (180)
T ss_pred HHcCchhHHHHHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhh
Confidence 3355666643 455677888999999888655555555556666666554332 367888866
No 28
>cd01223 PH_Vav Vav pleckstrin homology (PH) domain. Vav pleckstrin homology (PH) domain. Vav acts as a guanosine nucleotide exchange factor(GEF) for Rho/Rac proteins. Mammalian Vav proteins consist of a calponin homology (CH) domain, an acidic region, a rho-GEF (DH)domain, a PH domain, a Zinc finger region and an SH2 domain, flanked by two SH3 domains. In invertebrates such as Drosophila and C.elegans, Vav is missing the N-terminal SH3 domain . PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=29.03 E-value=35 Score=26.28 Aligned_cols=24 Identities=29% Similarity=0.369 Sum_probs=21.4
Q ss_pred chhhhhhcCCHHHHHHHHHHHHhc
Q 045228 122 KSVFMFNALSEDEKKALIEKLEQQ 145 (146)
Q Consensus 122 KSvf~yl~l~~~e~~~~~~~~~~~ 145 (146)
++.|+|.+=+||||++|++.++..
T Consensus 87 ~~~~~f~~Ktee~K~kWm~al~~a 110 (116)
T cd01223 87 KTGFTFYFKTEHLRKKWLKALEMA 110 (116)
T ss_pred CccEEEEeCCHHHHHHHHHHHHHH
Confidence 688999999999999999998864
No 29
>cd01238 PH_Tec Tec pleckstrin homology (PH) domain. Tec pleckstrin homology (PH) domain. Proteins in the Tec family of cytoplasmic protein tyrosine kinases that includes Bruton's tyrosine kinase (BTK), BMX, IL2-inducible T-cell kinase (Itk) and Tec. These proteins generally have an N-terminal PH domain, followed by a Tek homology (TH) domain, a SH3 domain, a SH2 domain and a kinase domain. Tec PH domains tether these proteins to membranes following the activation of PI3K and its subsequent phosphorylation of phosphoinositides. The importance of PH domain membrane anchoring is confirmed by the discovery of a mutation of a critical arginine residue in the BTK PH domain, which causes X-linked agammaglobulinemia (XLA) in humans and a related disorder is mice. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few dis
Probab=29.00 E-value=38 Score=24.33 Aligned_cols=20 Identities=30% Similarity=0.355 Sum_probs=16.2
Q ss_pred hhhhcCCHHHHHHHHHHHHh
Q 045228 125 FMFNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 125 f~yl~l~~~e~~~~~~~~~~ 144 (146)
|-..|-+++|++.|++.+.+
T Consensus 86 ~yl~A~s~~er~~WI~ai~~ 105 (106)
T cd01238 86 LYVFAPTEELRKRWIKALKQ 105 (106)
T ss_pred EEEEcCCHHHHHHHHHHHHh
Confidence 33458899999999998875
No 30
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=28.53 E-value=67 Score=21.70 Aligned_cols=41 Identities=17% Similarity=0.134 Sum_probs=13.6
Q ss_pred HHHHHHHhhhcCCCCCCCCC-----cchhhhhhcCCHHHHHHHHHH
Q 045228 101 VLFVIFAGRKFTQPIKDDIG-----DKSVFMFNALSEDEKKALIEK 141 (146)
Q Consensus 101 ~L~~i~A~rK~~mPl~~DIG-----DKSvf~yl~l~~~e~~~~~~~ 141 (146)
++..+++..-|.-|-+..-| ..-...++.||+|.++.+-+.
T Consensus 8 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~Lt~eQ~~~l~~~ 53 (125)
T PF13801_consen 8 LLAGALAGAAAAGPGPGGPGGPRRRHPMLADMLNLTPEQQAKLRAL 53 (125)
T ss_dssp -------------------TTHHHHHHHHHHHS-TTHHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCCCCCCCCcccchhhhhhcCCCHHHHHHHHHH
Confidence 33444444444444333333 344667889998887755443
No 31
>PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM.
Probab=28.07 E-value=69 Score=27.04 Aligned_cols=36 Identities=33% Similarity=0.483 Sum_probs=26.5
Q ss_pred HHHHHHhh-hcCCCCCCCCCcchhhhhhcCCHHHHHHHHHHHHh
Q 045228 102 LFVIFAGR-KFTQPIKDDIGDKSVFMFNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 102 L~~i~A~r-K~~mPl~~DIGDKSvf~yl~l~~~e~~~~~~~~~~ 144 (146)
++++=+++ +|.||+.+|. |. .+..+.-+.+|+++..
T Consensus 171 v~mvrGl~~~WKQpi~~~f-~t------~m~~~~l~~iI~~l~~ 207 (236)
T PF12017_consen 171 VFMVRGLFKSWKQPIYFDF-DT------SMDADILKNIIEKLHE 207 (236)
T ss_pred HHHHHHHHhcCCccEEEEe-cC------cCCHHHHHHHHHHHHH
Confidence 45666776 8999999988 43 4556666788888765
No 32
>cd01228 PH_BCR-related BCR (breakpoint cluster region)-related pleckstrin homology (PH) domain. BCR (breakpoint cluster region)-related pleckstrin homology (PH) domain. The BCR-related protein has a RhoGEF(DH) domain followed by a PH domain, a C2 domain and a RhoGAP domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinases, tyrosine kinases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=28.05 E-value=40 Score=25.45 Aligned_cols=29 Identities=17% Similarity=0.205 Sum_probs=21.9
Q ss_pred CCCCCc--chhhhhhcCCHHHHHHHHHHHHh
Q 045228 116 KDDIGD--KSVFMFNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 116 ~~DIGD--KSvf~yl~l~~~e~~~~~~~~~~ 144 (146)
++-||+ .--|++++=|++||..|++-+++
T Consensus 62 ~~~~~~~~~KSf~~~asS~~Er~eW~~hI~~ 92 (96)
T cd01228 62 PFRIHNKNGKSYTFLLSSDYERSEWRESIQK 92 (96)
T ss_pred hhhccccCCceEEEEecCHHHHHHHHHHHHH
Confidence 355663 34588889999999999998843
No 33
>PF11014 DUF2852: Protein of unknown function (DUF2852); InterPro: IPR021273 This bacterial family of proteins has no known function.
Probab=27.88 E-value=2.6e+02 Score=21.67 Aligned_cols=31 Identities=19% Similarity=0.249 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHhhchhHHHHHHHHHHHHHHHH
Q 045228 74 IIPSVLLGHLSGLMDDGVKLSLLGSWMVLFVI 105 (146)
Q Consensus 74 l~P~lllghl~g~l~~~~~~~ll~~~~~L~~i 105 (146)
-+++.++|..+ ++|..+......+|+--|--
T Consensus 11 ~Ia~mVlGFi~-fWPlGla~Lay~iw~~rm~~ 41 (115)
T PF11014_consen 11 WIAAMVLGFIV-FWPLGLALLAYMIWGKRMFG 41 (115)
T ss_pred HHHHHHHHHHH-HHHHHHHHHHHHHHHHHhhh
Confidence 46677778776 67777777777777755553
No 34
>PF14012 DUF4229: Protein of unknown function (DUF4229)
Probab=27.86 E-value=63 Score=22.34 Aligned_cols=35 Identities=14% Similarity=-0.020 Sum_probs=27.3
Q ss_pred chhHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCc
Q 045228 87 MDDGVKLSLLGSWMVLFVIFAGRKFTQPIKDDIGD 121 (146)
Q Consensus 87 l~~~~~~~ll~~~~~L~~i~A~rK~~mPl~~DIGD 121 (146)
.|..+...+..+.+..+.++.+||+|.-...||..
T Consensus 30 ~p~~~~~l~A~vis~~lS~~ll~~~R~~~~~~ia~ 64 (69)
T PF14012_consen 30 VPLLVAALLALVISMPLSYVLLRRLRDRASADIAA 64 (69)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44557778888888999999999999877666543
No 35
>PRK10404 hypothetical protein; Provisional
Probab=27.77 E-value=75 Score=23.52 Aligned_cols=28 Identities=25% Similarity=0.270 Sum_probs=21.6
Q ss_pred chhHHHHHhcchhHHHHHHHHHHHhhhh
Q 045228 29 ENLVQYVIDHPTAVWFVGSLFAALTGLV 56 (146)
Q Consensus 29 ~~l~~~v~~~P~~~l~vG~~FaaLtGi~ 56 (146)
+..-.||-+||..-++|+...-.+.|+.
T Consensus 70 ~~td~yV~e~Pw~avGiaagvGlllG~L 97 (101)
T PRK10404 70 YRADDYVHEKPWQGIGVGAAVGLVLGLL 97 (101)
T ss_pred HHHHHHHHhCcHHHHHHHHHHHHHHHHH
Confidence 4557899999999999887766666654
No 36
>PRK10408 putative L-valine exporter; Provisional
Probab=27.33 E-value=88 Score=24.29 Aligned_cols=27 Identities=19% Similarity=0.182 Sum_probs=22.5
Q ss_pred HHHHHhcchhHHHHHHHHHHHhhhhhh
Q 045228 32 VQYVIDHPTAVWFVGSLFAALTGLVFK 58 (146)
Q Consensus 32 ~~~v~~~P~~~l~vG~~FaaLtGi~fK 58 (146)
..-|.+||...+...-=|+++++..||
T Consensus 61 ~P~v~~~~~k~~ptlvGf~~l~~~fyk 87 (111)
T PRK10408 61 APEVMHDPRKLLPTLVGFLVLGACFYK 87 (111)
T ss_pred ChHHHhChHHHHHHHHHHHHHHHHHHH
Confidence 445889999999988889999987766
No 37
>PRK12574 putative monovalent cation/H+ antiporter subunit B; Reviewed
Probab=27.26 E-value=93 Score=24.29 Aligned_cols=30 Identities=13% Similarity=0.288 Sum_probs=23.1
Q ss_pred CCchhHHHHHhcchhHHHHHHHHHHHhhhh
Q 045228 27 AGENLVQYVIDHPTAVWFVGSLFAALTGLV 56 (146)
Q Consensus 27 ~~~~l~~~v~~~P~~~l~vG~~FaaLtGi~ 56 (146)
..++.-..+-.+|..+.++|-++++.||+.
T Consensus 56 G~~~~~~~~~~~~~~l~~~Gll~~~~tgl~ 85 (141)
T PRK12574 56 GVEEVLESLPIDFRKLMIIGLLLSSITAII 85 (141)
T ss_pred CHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 335566666778889999999999988864
No 38
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=27.24 E-value=2.2e+02 Score=21.03 Aligned_cols=48 Identities=19% Similarity=0.289 Sum_probs=30.3
Q ss_pred hhhhHHHHHHHH--HHHHHhh-ch-hHHHHHHHHHHHHHHHHHHhhhcCCCC
Q 045228 68 AGILTFIIPSVL--LGHLSGL-MD-DGVKLSLLGSWMVLFVIFAGRKFTQPI 115 (146)
Q Consensus 68 ~~~lt~l~P~ll--lghl~g~-l~-~~~~~~ll~~~~~L~~i~A~rK~~mPl 115 (146)
+.++..++|++. +|..++. +. .....++.++.++...++.+|+++...
T Consensus 70 aa~l~Y~lPll~li~g~~l~~~~~~~e~~~~l~~l~~l~~~~~~~~~~~~~~ 121 (135)
T PF04246_consen 70 AAFLVYLLPLLALIAGAVLGSYLGGSELWAILGGLLGLALGFLILRLFDRRL 121 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 345566777654 4444444 22 255677777777888888888876543
No 39
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=26.06 E-value=79 Score=19.75 Aligned_cols=18 Identities=28% Similarity=0.307 Sum_probs=16.2
Q ss_pred cCCHHHHHHHHHHHHhcC
Q 045228 129 ALSEDEKKALIEKLEQQN 146 (146)
Q Consensus 129 ~l~~~e~~~~~~~~~~~~ 146 (146)
.|+|+|.++++.=++++|
T Consensus 74 ~ls~~e~~~l~ayl~slk 91 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRSLK 91 (91)
T ss_dssp TSSHHHHHHHHHHHHHTS
T ss_pred CCCHHHHHHHHHHHHHhC
Confidence 799999999999888876
No 40
>cd01222 PH_clg Clg (common-site lymphoma/leukemia guanine nucleotide exchange factor) pleckstrin homology (PH) domain. Clg (common-site lymphoma/leukemia guanine nucleotide exchange factor) pleckstrin homology (PH) domain. Clg contains a RhoGEF (DH) domain and a PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=26.04 E-value=33 Score=25.10 Aligned_cols=23 Identities=22% Similarity=0.417 Sum_probs=20.4
Q ss_pred chhhhhhcCCHHHHHHHHHHHHh
Q 045228 122 KSVFMFNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 122 KSvf~yl~l~~~e~~~~~~~~~~ 144 (146)
|..|.+.|=|+|||+.|++++++
T Consensus 71 ~~~~~l~A~s~e~K~~W~~~i~~ 93 (97)
T cd01222 71 KGALQLTARNREEKRIWTQQLKR 93 (97)
T ss_pred ceEEEEEecCHHHHHHHHHHHHH
Confidence 36899999999999999999875
No 41
>PRK12573 putative monovalent cation/H+ antiporter subunit B; Reviewed
Probab=25.82 E-value=1e+02 Score=24.00 Aligned_cols=28 Identities=25% Similarity=0.199 Sum_probs=21.1
Q ss_pred chhHHHHHhcchhHHHHHHHHHHHhhhh
Q 045228 29 ENLVQYVIDHPTAVWFVGSLFAALTGLV 56 (146)
Q Consensus 29 ~~l~~~v~~~P~~~l~vG~~FaaLtGi~ 56 (146)
++.-..+-.+|..+.++|-+.++.+|+.
T Consensus 58 ~~~~~~~~~~~~~l~~~Gll~~~~~G~~ 85 (140)
T PRK12573 58 KTVRRALPFDFKILAGIGLLFAIATGLA 85 (140)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 4455566677888999999988888864
No 42
>TIGR00943 2a6301s02 monovalent cation:proton antiporter. This family of proteins constists of bacterial multicomponent K+:H+ and Na+:H+ antiporters. The best characterized systems are the PhaABCDEFG system of Rhizobium meliloti which functions in pH adaptation and as a K+ efflux system and the MnhABCDEFG system of Staphylococcus aureus which functions as a Na+:H+ antiporter.This family is specific for the phaB and mnhB proteins.
Probab=25.75 E-value=1.1e+02 Score=22.89 Aligned_cols=29 Identities=24% Similarity=0.267 Sum_probs=22.4
Q ss_pred CCchhHHHHHhcchhHHHHHHHHHHHhhh
Q 045228 27 AGENLVQYVIDHPTAVWFVGSLFAALTGL 55 (146)
Q Consensus 27 ~~~~l~~~v~~~P~~~l~vG~~FaaLtGi 55 (146)
..+.....+-.+|..+.++|-++++.||+
T Consensus 31 g~~~~~~~~~~~~~~l~~~Gll~~~~tgl 59 (107)
T TIGR00943 31 GIETVRKILPLDPKRLIGIGLLLAIATGV 59 (107)
T ss_pred CHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 33455666667788899999999999887
No 43
>PRK12509 putative monovalent cation/H+ antiporter subunit B; Reviewed
Probab=25.01 E-value=1.1e+02 Score=23.80 Aligned_cols=30 Identities=23% Similarity=0.234 Sum_probs=23.1
Q ss_pred CCchhHHHHHhcchhHHHHHHHHHHHhhhh
Q 045228 27 AGENLVQYVIDHPTAVWFVGSLFAALTGLV 56 (146)
Q Consensus 27 ~~~~l~~~v~~~P~~~l~vG~~FaaLtGi~ 56 (146)
..+..-..+-.+|..+.++|-+.++.||+.
T Consensus 54 g~~~~~~~~~~~~~~~~~~Gll~~~~tGl~ 83 (137)
T PRK12509 54 GIAAARRLLRVDPLRLLAAGLLVAVLSGLP 83 (137)
T ss_pred CHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 345566777778888999999888888864
No 44
>TIGR00439 ftsX putative protein insertion permease FtsX. FtsX is an integral membrane protein encoded in the same operon as signal recognition particle docking protein FtsY and FtsE. It belongs to a family of predicted permeases and may play a role in the insertion of proteins required for potassium transport, cell division, and other activities. FtsE is a hydrophilic nucleotide-binding protein that associates with the inner membrane by means of association with FtsX.
Probab=24.83 E-value=1.6e+02 Score=25.25 Aligned_cols=53 Identities=15% Similarity=0.235 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCCCCCCCcchhhhhhcCCHHHHHHHHHHHHhc
Q 045228 92 KLSLLGSWMVLFVIFAGRKFTQPIKDDIGDKSVFMFNALSEDEKKALIEKLEQQ 145 (146)
Q Consensus 92 ~~~ll~~~~~L~~i~A~rK~~mPl~~DIGDKSvf~yl~l~~~e~~~~~~~~~~~ 145 (146)
...+......+++...+++...-+..|. .=++|-=.+++|++++++.+++++.
T Consensus 39 ~i~L~l~g~~~l~~~n~~~~~~~~~~~~-~i~vyl~~~~~~~~~~~l~~~l~~~ 91 (309)
T TIGR00439 39 AVSLTLPLVMYLGIKNGQSALTQLYPSP-QITVYLEKALAQSDADTVVSLLTRD 91 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccCc-eEEEEeCCCCCHHHHHHHHHHHhCC
Confidence 3344444555566666777777776666 4677777788899999999988864
No 45
>cd01261 PH_SOS Son of Sevenless (SOS) Pleckstrin homology (PH) domain. Son of Sevenless (SOS) Pleckstrin homology (PH) domain. SOS is a Ras guanine nucleotide exchange factor. It has a RhoGEF (DbH) domain, a PH domain, and a RasGEF domain. The SOS PH domain can bind to inositol 1,4,5-triphosphate. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=24.81 E-value=48 Score=24.94 Aligned_cols=24 Identities=25% Similarity=0.392 Sum_probs=20.6
Q ss_pred cchhhhhhcCCHHHHHHHHHHHHh
Q 045228 121 DKSVFMFNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 121 DKSvf~yl~l~~~e~~~~~~~~~~ 144 (146)
|+..|.+.+=++|||+.|++.++.
T Consensus 84 ~~~s~~l~Akt~eeK~~Wm~~l~~ 107 (112)
T cd01261 84 DGNSVIFSAKNAEEKNNWMAALIS 107 (112)
T ss_pred CCCEEEEEECCHHHHHHHHHHHHH
Confidence 455699999999999999998764
No 46
>PF10003 DUF2244: Integral membrane protein (DUF2244); InterPro: IPR019253 This entry consists of various bacterial putative membrane proteins with no known function.
Probab=24.80 E-value=61 Score=24.66 Aligned_cols=16 Identities=25% Similarity=0.524 Sum_probs=12.9
Q ss_pred CCHHHHHHHHHHHHhc
Q 045228 130 LSEDEKKALIEKLEQQ 145 (146)
Q Consensus 130 l~~~e~~~~~~~~~~~ 145 (146)
|+||||+++..++++.
T Consensus 124 L~~~eR~~la~~L~~a 139 (140)
T PF10003_consen 124 LNPEEREELARELRRA 139 (140)
T ss_pred CCHHHHHHHHHHHHhh
Confidence 7888898888888763
No 47
>PRK10132 hypothetical protein; Provisional
Probab=24.53 E-value=98 Score=23.27 Aligned_cols=27 Identities=11% Similarity=0.102 Sum_probs=20.8
Q ss_pred hhHHHHHhcchhHHHHHHHHHHHhhhh
Q 045228 30 NLVQYVIDHPTAVWFVGSLFAALTGLV 56 (146)
Q Consensus 30 ~l~~~v~~~P~~~l~vG~~FaaLtGi~ 56 (146)
..-.||-+||....+|+...-.+.|+.
T Consensus 77 ~~~~~V~~~Pw~svgiaagvG~llG~L 103 (108)
T PRK10132 77 CADTFVRERPWCSVGTAAAVGIFIGAL 103 (108)
T ss_pred HHHHHHHhCcHHHHHHHHHHHHHHHHH
Confidence 445699999999999887766666654
No 48
>PF13864 Enkurin: Calmodulin-binding
Probab=24.35 E-value=68 Score=22.97 Aligned_cols=18 Identities=39% Similarity=0.685 Sum_probs=14.6
Q ss_pred hhcCCHHHHHHHHHHHHh
Q 045228 127 FNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 127 yl~l~~~e~~~~~~~~~~ 144 (146)
+--||||||+++++.+.+
T Consensus 34 ~~~l~eeER~~lL~~Lk~ 51 (98)
T PF13864_consen 34 MRLLSEEERQELLEGLKK 51 (98)
T ss_pred cccCCHHHHHHHHHHHHH
Confidence 345899999999988865
No 49
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=24.19 E-value=2.9e+02 Score=21.68 Aligned_cols=44 Identities=18% Similarity=0.125 Sum_probs=20.0
Q ss_pred hHHHHHHH--HHHHHHHHHHHhhhhcCCCchhHHHHHhcchhHHHHHHHHHHHhhh
Q 045228 2 KRTLQALW--VLGVMGSLATYTALARPAGENLVQYVIDHPTAVWFVGSLFAALTGL 55 (146)
Q Consensus 2 hr~LQ~~W--~iG~~g~~~~~~~~a~~~~~~l~~~v~~~P~~~l~vG~~FaaLtGi 55 (146)
+|..+.+| .+|+..++++ -+..+...+...++++....++..+.
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~l~~l~~~~~~~~~ 47 (199)
T PF10112_consen 2 KYIIRFIFRWILGVLIAAIT----------FLVSFFGFDHSFLLSLLIGAVAFAVV 47 (199)
T ss_pred chHHHHHHHHHHHHHHHHHH----------HHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 45555554 5555444433 12233333333444555555554444
No 50
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=24.16 E-value=1e+02 Score=21.55 Aligned_cols=29 Identities=24% Similarity=0.277 Sum_probs=21.5
Q ss_pred CchhHHHHHhcchhHHHHHHHHHHHhhhh
Q 045228 28 GENLVQYVIDHPTAVWFVGSLFAALTGLV 56 (146)
Q Consensus 28 ~~~l~~~v~~~P~~~l~vG~~FaaLtGi~ 56 (146)
.+..-.||-+||..-++++...-.+.|.-
T Consensus 62 ~~~~~~~V~e~P~~svgiAagvG~llG~L 90 (94)
T PF05957_consen 62 AEQTEDYVRENPWQSVGIAAGVGFLLGLL 90 (94)
T ss_pred HHHHHHHHHHChHHHHHHHHHHHHHHHHH
Confidence 35667899999999888877665555543
No 51
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=24.08 E-value=59 Score=23.53 Aligned_cols=18 Identities=33% Similarity=0.462 Sum_probs=14.4
Q ss_pred hhhcCCHHHHHHHHHHHH
Q 045228 126 MFNALSEDEKKALIEKLE 143 (146)
Q Consensus 126 ~yl~l~~~e~~~~~~~~~ 143 (146)
.+--|++||+++++++..
T Consensus 14 kH~iLs~eE~~~lL~~y~ 31 (79)
T PRK09570 14 EHEILSEEEAKKLLKEYG 31 (79)
T ss_pred CeEECCHHHHHHHHHHcC
Confidence 345689999999998753
No 52
>smart00398 HMG high mobility group.
Probab=23.54 E-value=67 Score=20.01 Aligned_cols=20 Identities=35% Similarity=0.375 Sum_probs=15.1
Q ss_pred hhhhcCCHHHHHHHHHHHHh
Q 045228 125 FMFNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 125 f~yl~l~~~e~~~~~~~~~~ 144 (146)
=++..||++||+...++-++
T Consensus 38 ~~W~~l~~~ek~~y~~~a~~ 57 (70)
T smart00398 38 ERWKLLSEEEKAPYEEKAKK 57 (70)
T ss_pred HHHHcCCHHHHHHHHHHHHH
Confidence 36889999999987765443
No 53
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=23.21 E-value=32 Score=21.87 Aligned_cols=27 Identities=33% Similarity=0.437 Sum_probs=17.8
Q ss_pred CCCcchhhhhhcCCHHHHHHHHHHHHh
Q 045228 118 DIGDKSVFMFNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 118 DIGDKSvf~yl~l~~~e~~~~~~~~~~ 144 (146)
||....-=++..||+|||+...++-+.
T Consensus 30 ~i~~~~~~~W~~l~~~eK~~y~~~a~~ 56 (69)
T PF00505_consen 30 EISKILAQMWKNLSEEEKAPYKEEAEE 56 (69)
T ss_dssp HHHHHHHHHHHCSHHHHHHHHHHHHHH
T ss_pred cchhhHHHHHhcCCHHHHHHHHHHHHH
Confidence 444444456788999999876665443
No 54
>PF10463 Peptidase_U49: Peptidase U49; InterPro: IPR019504 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This entry contains peptidases belonging to MEROPS peptidase family U49 (Lit peptidase, clan U-). The Lit peptidase from Escherichia coli functions in bacterial cell death in response to infection by Enterobacteria phage T4. Following binding of Gol peptide to domains II and III of elongation factor Tu, the Lit peptidase cleaves domain I of the elongation factor. This prevents binding of guanine nucleotides, shuts down translation and leads to cell death.
Probab=22.82 E-value=85 Score=26.14 Aligned_cols=18 Identities=28% Similarity=0.600 Sum_probs=15.8
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 045228 2 KRTLQALWVLGVMGSLAT 19 (146)
Q Consensus 2 hr~LQ~~W~iG~~g~~~~ 19 (146)
||.||.+|+.|..+....
T Consensus 5 ~~~L~~lW~f~~~~~~~y 22 (206)
T PF10463_consen 5 ERFLEYLWIFGFAAWVLY 22 (206)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 799999999999888753
No 55
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]
Probab=22.41 E-value=44 Score=30.61 Aligned_cols=28 Identities=25% Similarity=0.407 Sum_probs=23.0
Q ss_pred CCCcchhhhhhcCCHHHHHHHHHHHHhc
Q 045228 118 DIGDKSVFMFNALSEDEKKALIEKLEQQ 145 (146)
Q Consensus 118 DIGDKSvf~yl~l~~~e~~~~~~~~~~~ 145 (146)
|||.+--=+++.|++|||+..+.+-|.+
T Consensus 94 eiGK~Ig~mW~dLpd~EK~ey~~EYeaE 121 (410)
T KOG4715|consen 94 EIGKIIGGMWLDLPDEEKQEYLNEYEAE 121 (410)
T ss_pred HHHHHHHHHHhhCcchHHHHHHHHHHHH
Confidence 6888888899999999999887766544
No 56
>PF14163 SieB: Superinfection exclusion protein B
Probab=22.34 E-value=1.8e+02 Score=22.02 Aligned_cols=36 Identities=22% Similarity=0.235 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHhhhhcCCCchhHHHHHh-----cchhHHHHHHHHH
Q 045228 8 LWVLGVMGSLATYTALARPAGENLVQYVID-----HPTAVWFVGSLFA 50 (146)
Q Consensus 8 ~W~iG~~g~~~~~~~~a~~~~~~l~~~v~~-----~P~~~l~vG~~Fa 50 (146)
+|++-+.|.+.+ .|+++...+.- ++.++.++++.++
T Consensus 3 ~~l~i~~~~llf-------~P~~~~~~l~l~~~~~~y~~~i~~~fl~s 43 (151)
T PF14163_consen 3 LWLIIFSGLLLF-------LPESLLEWLNLDKFEIKYQPWIGLIFLFS 43 (151)
T ss_pred HHHHHHHHHHHH-------CCHHHHHHhCcchHHHhcchHHHHHHHHH
Confidence 566666666655 46677666543 6777777777654
No 57
>TIGR03707 PPK2_P_aer polyphosphate kinase 2, PA0141 family. Members of this protein family are designated polyphosphate kinase 2 (PPK2) after the characterized protein in Pseudomonas aeruginosa. This family comprises one of three well-separated clades in the larger family described by Pfam model pfam03976. PA0141 from this family has been shown capable of operating in reverse, with GDP preferred (over ADP) as a substrate, producing GTP (or ATP) by transfer of a phosphate residue from polyphosphate. Most species with a member of this family also encode a polyphosphate kinase 1 (PPK1).
Probab=22.12 E-value=64 Score=27.03 Aligned_cols=18 Identities=11% Similarity=0.128 Sum_probs=16.1
Q ss_pred hhcCCHHHHHHHHHHHHh
Q 045228 127 FNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 127 yl~l~~~e~~~~~~~~~~ 144 (146)
|+.+|+|||++++++++.
T Consensus 141 flhIsk~eQ~kRl~~r~~ 158 (230)
T TIGR03707 141 WLSVSREEQLRRFKARID 158 (230)
T ss_pred EEECCHHHHHHHHHHHhc
Confidence 789999999999998875
No 58
>PF13309 HTH_22: HTH domain
Probab=21.71 E-value=93 Score=20.83 Aligned_cols=19 Identities=32% Similarity=0.581 Sum_probs=16.2
Q ss_pred hcCCHHHHHHHHHHHHhcC
Q 045228 128 NALSEDEKKALIEKLEQQN 146 (146)
Q Consensus 128 l~l~~~e~~~~~~~~~~~~ 146 (146)
-.|+.+||+.++++|++++
T Consensus 19 ~~l~~~~k~~iV~~L~~~G 37 (64)
T PF13309_consen 19 SRLSKEEKKEIVRQLYEKG 37 (64)
T ss_pred hhCCHHHHHHHHHHHHHCC
Confidence 4688999999999999874
No 59
>PRK11026 ftsX cell division ABC transporter subunit FtsX; Provisional
Probab=21.09 E-value=2.1e+02 Score=24.53 Aligned_cols=48 Identities=15% Similarity=0.169 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCCCcchhhhhhcCCHHHHHHHHHHHHhc
Q 045228 97 GSWMVLFVIFAGRKFTQPIKDDIGDKSVFMFNALSEDEKKALIEKLEQQ 145 (146)
Q Consensus 97 ~~~~~L~~i~A~rK~~mPl~~DIGDKSvf~yl~l~~~e~~~~~~~~~~~ 145 (146)
......++...+++...-+..|. .=++|-=.+++|++.+++.+++++.
T Consensus 44 l~g~~~l~~~n~~~~~~~~~~~~-ei~vyl~~~~~~~~~~~l~~~L~~~ 91 (309)
T PRK11026 44 LPSVCYLVWKNVNQAATQWYPSP-QLTVYLDKTLDDDAANAVVEQLKAE 91 (309)
T ss_pred HHHHHHHHHHHHHHHHHhhccCc-eEEEEECCCCCHHHHHHHHHHHhCC
Confidence 33344444555666666666655 4677777789999999998888764
No 60
>COG2899 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.05 E-value=1.4e+02 Score=27.07 Aligned_cols=49 Identities=18% Similarity=0.249 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHhhhhcCCCchhHHH-HHhcchhHHHHHHHHHHHhhhhhhhhhccchhhhh
Q 045228 7 ALWVLGVMGSLATYTALARPAGENLVQY-VIDHPTAVWFVGSLFAALTGLVFKEGLCYGKLEAG 69 (146)
Q Consensus 7 ~~W~iG~~g~~~~~~~~a~~~~~~l~~~-v~~~P~~~l~vG~~FaaLtGi~fKE~FCF~~~e~~ 69 (146)
++|++|.++-+.+ . ++ .++-|..+-++++ +++-|++|-+++-+||.|-+
T Consensus 294 AhyAI~~Laviml----~--------s~~~~hIpEvvTgL~G--a~fIgls~~sSv~~Nr~~~~ 343 (346)
T COG2899 294 AHYAIGALAVIML----L--------STDRFHIPEVVTGLVG--AVFIGLSLWSSVRYNRREVR 343 (346)
T ss_pred hHHHHHHHHHHHH----H--------hhhheehHHHHHHhhH--HHHHHHHHHHHHHHhHhhcc
Confidence 6899999887754 1 11 4566666666554 57889999999999998853
No 61
>PF11241 DUF3043: Protein of unknown function (DUF3043); InterPro: IPR021403 Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed.
Probab=20.96 E-value=2.7e+02 Score=22.73 Aligned_cols=14 Identities=14% Similarity=0.320 Sum_probs=7.3
Q ss_pred HHHHHHHHHHHhhc
Q 045228 74 IIPSVLLGHLSGLM 87 (146)
Q Consensus 74 l~P~lllghl~g~l 87 (146)
++|++++-+.+.+.
T Consensus 81 fmP~alv~lv~~~v 94 (170)
T PF11241_consen 81 FMPVALVLLVLSFV 94 (170)
T ss_pred HHHHHHHHHHHHHH
Confidence 55555555555544
No 62
>TIGR03180 UraD_2 OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model. This model is a separate (but related) clade from that represented by TIGR3164. This model places a second homolog in streptomyces species which (are not in the vicinity of other urate catabolism associated genes) below the trusted cutoff.
Probab=20.84 E-value=79 Score=24.91 Aligned_cols=9 Identities=33% Similarity=0.446 Sum_probs=7.5
Q ss_pred CCCCCCcch
Q 045228 115 IKDDIGDKS 123 (146)
Q Consensus 115 l~~DIGDKS 123 (146)
-|+|||+|.
T Consensus 60 ~HP~lg~~~ 68 (158)
T TIGR03180 60 GHPRIGEKP 68 (158)
T ss_pred hCCcccCcc
Confidence 499999975
No 63
>PF03086 DUF240: MG032/MG096/MG288 family 2; InterPro: IPR004319 This domain is found entirely in Mycoplasma pneumoniae proteins of unknown function. Another related domain (IPR004306 from INTERPRO) is also found entirely in mycoplasmal proteins of the MG032/MG096/MG288 family and both domains often occur together.
Probab=20.82 E-value=69 Score=25.13 Aligned_cols=26 Identities=23% Similarity=0.225 Sum_probs=18.0
Q ss_pred cchhhhhhcCCHHHHH-------HHHHHHHhcC
Q 045228 121 DKSVFMFNALSEDEKK-------ALIEKLEQQN 146 (146)
Q Consensus 121 DKSvf~yl~l~~~e~~-------~~~~~~~~~~ 146 (146)
.||+|+.+.|.+-|++ -+.+|+|++|
T Consensus 84 ~kSI~~~~~L~~a~~~Fe~~~l~Pf~~eR~~Ak 116 (120)
T PF03086_consen 84 TKSIIDDLNLKEAETRFEQEILQPFKAEREKAK 116 (120)
T ss_pred HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3899999999876654 3556666553
No 64
>cd01235 PH_SETbf Set binding factor Pleckstrin Homology (PH) domain. Set binding factor Pleckstrin Homology (PH) domain. Set binding factor is a myotubularin-related pseudo-phosphatase consisting of a Denn domain, a Gram domain, an inactive phosphatase domain, a SID motif and a C-terminal PH domain. Its PH domain is predicted to bind lipids based upon its ability to respond to phosphatidylinositol 3-kinase .
Probab=20.74 E-value=70 Score=21.66 Aligned_cols=24 Identities=29% Similarity=0.358 Sum_probs=19.9
Q ss_pred cchhhhhhcCCHHHHHHHHHHHHh
Q 045228 121 DKSVFMFNALSEDEKKALIEKLEQ 144 (146)
Q Consensus 121 DKSvf~yl~l~~~e~~~~~~~~~~ 144 (146)
++.+|-+.+=++||++.|++.+++
T Consensus 76 ~~r~~~~~a~s~~e~~~Wi~ai~~ 99 (101)
T cd01235 76 SKRTYNFLAENINEAQRWKEKIQQ 99 (101)
T ss_pred CCceEEEECCCHHHHHHHHHHHHh
Confidence 455677888999999999998875
No 65
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=20.62 E-value=62 Score=25.56 Aligned_cols=13 Identities=54% Similarity=0.624 Sum_probs=9.1
Q ss_pred hcCCHHHHHHHHH
Q 045228 128 NALSEDEKKALIE 140 (146)
Q Consensus 128 l~l~~~e~~~~~~ 140 (146)
..||||||+|+-+
T Consensus 137 ~~LS~EE~eal~~ 149 (151)
T PF14584_consen 137 YPLSEEEKEALEK 149 (151)
T ss_pred ccCCHHHHHHHHH
Confidence 4678888887643
No 66
>PF12576 DUF3754: Protein of unknown function (DUF3754); InterPro: IPR022227 This domain family is found in bacteria, archaea and eukaryotes, and is typically between 135 and 166 amino acids in length. There is a single completely conserved residue P that may be functionally important.
Probab=20.12 E-value=2.8e+02 Score=21.23 Aligned_cols=27 Identities=30% Similarity=0.413 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhhhhhhhhhccchhhh
Q 045228 42 VWFVGSLFAALTGLVFKEGLCYGKLEA 68 (146)
Q Consensus 42 ~l~vG~~FaaLtGi~fKE~FCF~~~e~ 68 (146)
......++++++|.++|.++=|+.--.
T Consensus 95 ~~~~~~~l~~~~~~~~r~~~~~~~~~~ 121 (141)
T PF12576_consen 95 LILILSLLSALGGYAFRQYTGYKNNRA 121 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677778888899999999998876554
Done!