Query psy4447
Match_columns 261
No_of_seqs 198 out of 1374
Neff 8.7
Searched_HMMs 46136
Date Fri Aug 16 17:15:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4447.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4447hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1470|consensus 100.0 6.8E-41 1.5E-45 287.5 17.2 192 2-203 51-243 (324)
2 KOG1471|consensus 100.0 4.4E-38 9.5E-43 278.2 16.6 199 2-206 47-260 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 1.6E-34 3.4E-39 230.3 6.8 153 48-202 3-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 3E-31 6.6E-36 211.1 14.1 141 59-203 14-157 (158)
5 cd00170 SEC14 Sec14p-like lipi 100.0 4.5E-29 9.7E-34 197.1 12.8 146 53-202 9-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.6 2E-15 4.3E-20 119.2 5.1 136 59-204 8-145 (149)
7 KOG4406|consensus 98.3 8.6E-06 1.9E-10 72.5 10.5 137 45-191 71-212 (467)
8 PF03765 CRAL_TRIO_N: CRAL/TRI 98.2 1.1E-06 2.5E-11 57.1 3.4 23 2-24 33-55 (55)
9 PF04838 Baculo_LEF5: Baculovi 76.0 12 0.00025 29.3 6.1 92 127-229 16-124 (159)
10 PF14555 UBA_4: UBA-like domai 69.6 5.5 0.00012 24.0 2.6 18 4-21 19-36 (43)
11 PF03474 DMA: DMRTA motif; In 64.2 10 0.00022 22.6 2.8 20 2-21 19-38 (39)
12 PF14213 DUF4325: Domain of un 58.9 37 0.0008 22.9 5.4 50 105-159 17-68 (74)
13 PF02845 CUE: CUE domain; Int 56.3 13 0.00028 22.1 2.4 21 2-22 19-39 (42)
14 PF00627 UBA: UBA/TS-N domain; 55.9 12 0.00026 21.6 2.2 17 4-20 20-36 (37)
15 PF11964 SpoIIAA-like: SpoIIAA 54.5 41 0.00089 24.0 5.4 76 80-165 11-87 (109)
16 smart00546 CUE Domain that may 51.7 17 0.00037 21.7 2.5 21 2-22 20-40 (43)
17 cd00194 UBA Ubiquitin Associat 47.4 22 0.00047 20.3 2.4 19 3-21 18-36 (38)
18 PF03641 Lysine_decarbox: Poss 44.4 26 0.00057 26.6 3.1 43 145-189 86-133 (133)
19 KOG1838|consensus 44.2 2.6E+02 0.0057 25.8 10.1 84 63-159 123-213 (409)
20 COG2961 ComJ Protein involved 43.6 22 0.00048 30.4 2.7 28 144-171 237-264 (279)
21 smart00165 UBA Ubiquitin assoc 42.9 32 0.00069 19.5 2.6 18 4-21 19-36 (37)
22 PF04378 RsmJ: Ribosomal RNA s 41.9 22 0.00048 30.3 2.5 32 141-172 203-234 (245)
23 TIGR02364 dha_pts dihydroxyace 38.4 93 0.002 23.5 5.2 51 103-165 59-109 (125)
24 PRK14484 phosphotransferase ma 37.2 1.1E+02 0.0024 23.1 5.4 46 104-163 58-103 (124)
25 PF02954 HTH_8: Bacterial regu 36.3 38 0.00083 20.0 2.3 21 2-22 9-29 (42)
26 PRK02399 hypothetical protein; 34.6 3.6E+02 0.0078 24.9 9.1 83 80-167 313-403 (406)
27 PF13466 STAS_2: STAS domain 33.1 1.4E+02 0.003 19.9 5.1 52 105-162 26-77 (80)
28 KOG1534|consensus 32.5 3.1E+02 0.0067 23.2 8.0 88 102-193 95-193 (273)
29 smart00804 TAP_C C-terminal do 30.1 67 0.0015 21.2 2.8 24 2-25 29-52 (63)
30 COG1448 TyrB Aspartate/tyrosin 28.4 3.6E+02 0.0078 24.7 7.9 131 66-227 173-321 (396)
31 COG4545 Glutaredoxin-related p 28.3 88 0.0019 21.6 3.2 52 5-69 20-78 (85)
32 PF03943 TAP_C: TAP C-terminal 28.2 48 0.001 20.8 1.8 22 2-23 17-38 (51)
33 TIGR02886 spore_II_AA anti-sig 25.3 2.5E+02 0.0053 19.8 5.9 51 106-162 40-90 (106)
34 PF01740 STAS: STAS domain; I 24.4 1.2E+02 0.0027 21.8 3.8 49 106-160 49-97 (117)
35 TIGR00730 conserved hypothetic 24.3 2.4E+02 0.0052 22.7 5.7 67 112-189 104-175 (178)
36 PF00561 Abhydrolase_1: alpha/ 23.9 1.2E+02 0.0027 23.9 4.1 17 136-152 62-78 (230)
37 cd07042 STAS_SulP_like_sulfate 23.0 2.4E+02 0.0052 19.5 5.1 50 106-161 42-91 (107)
38 PF08938 HBS1_N: HBS1 N-termin 22.9 42 0.00091 23.1 0.9 23 3-25 49-71 (79)
39 PF08566 Pam17: Mitochondrial 22.5 1.1E+02 0.0023 24.7 3.2 14 151-164 95-108 (173)
40 COG0052 RpsB Ribosomal protein 22.1 1.6E+02 0.0034 25.3 4.3 70 138-211 31-109 (252)
41 COG1219 ClpX ATP-dependent pro 21.7 56 0.0012 29.3 1.6 45 2-49 146-196 (408)
42 cd00006 PTS_IIA_man PTS_IIA, P 20.3 2.2E+02 0.0047 21.0 4.4 64 81-160 39-102 (122)
No 1
>KOG1470|consensus
Probab=100.00 E-value=6.8e-41 Score=287.54 Aligned_cols=192 Identities=17% Similarity=0.277 Sum_probs=174.2
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHHHHHHhhCCccccCCCCCcHHHHHHhhhccccccCCCCCCCCEEEEEecCCCCCCCCC
Q psy4447 2 TLILIHHSCYFDLEASKSCIEVYFTTRTNTPEFFSKRDINRPELLAQSKVVEFGAIAPKTPQGYQVIFHRLQQFEPSKYV 81 (261)
Q Consensus 2 ~L~rFLra~~~dv~~A~~~l~~~~~~R~~~~~~~~~~~~~~~~~~~~l~~g~~~~~l~~D~~G~~V~~~~~~~~d~~~~~ 81 (261)
-++||||||+|||++|.+||.+++.||+++..- .....+++...++.|.++ .+|.|++||||+|+++..+.++..+
T Consensus 51 cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~---~~~~~~Ev~~e~~tGK~y-i~G~D~~gRPVl~~~~~~~~qn~~t 126 (324)
T KOG1470|consen 51 CLLRFLRARKWNVKKASKMLSNTLKWRRSFGPE---EVIEADEVAAELETGKAY-ILGHDKDGRPVLYLRPRPHRQNTKT 126 (324)
T ss_pred HHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCc---cccCHHHHHHHhhcCcEE-EecccCCCCeEEEEecCCCCCCCCC
Confidence 479999999999999999999999999998421 113345688899999999 9999999999999999888889999
Q ss_pred HHHHHHHHHHHHHHHhcc-CCCcCcEEEEEeCCCCCcccccccCHHHHHHHHHHhhccccceeeeeEEEeCchHHHHHHH
Q psy4447 82 FQDSVRLLAMSIDACLHV-EGTVPGYIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKIMF 160 (261)
Q Consensus 82 ~~~~~r~~~~~~e~~~~~-~~~~~g~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~ 160 (261)
..+..|+.+|++|.++.. +..++++++++|++|+|+++ +++...+.++.++|+||||||+..+++|+||+|..+|+
T Consensus 127 ~~~~~r~~Vy~mE~Ai~~lp~~qe~~~~L~D~~~fs~sN---~d~~~~k~~~~~lq~hYPErLg~a~l~~~P~iF~~~wk 203 (324)
T KOG1470|consen 127 QKELERLLVYTLENAILFLPPGQEQFVWLFDLTGFSMSN---PDIKFLKELLHILQDHYPERLGKALLVNAPWIFQPFWK 203 (324)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCcceEEEEEecccCcccC---CCcHHHHHHHHHHHHhChHHhhhhhhcCChHHHHHHHH
Confidence 999999999999999764 33578899999999999995 57889999999999999999999999999999999999
Q ss_pred HhhhcchHHhhcceeeCCCCChhhhhhhcCCCCCCCCCCCCCC
Q psy4447 161 VVKPFMKKDLLSLVHFHPEGDISSVYEFVPPKCIPGGDLKGDL 203 (261)
Q Consensus 161 ~vk~fl~~~~~~ki~~~~~~~~~~L~~~i~~~~LP~~~yGG~~ 203 (261)
++|||++++|++||.|+.+ ...|.+|||+++||. .|||+.
T Consensus 204 iikpflDp~t~~Kv~F~~~--~~~l~~~~d~~~l~s-~~GG~~ 243 (324)
T KOG1470|consen 204 IIKPFLDPKTASKVKFVEP--KDDLSEYFDESQLPS-LFGGKL 243 (324)
T ss_pred HhhhccChhhhceeEEecC--hhHHHhhCCccccch-hhCCCc
Confidence 9999999999999999976 567999999999999 999976
No 2
>KOG1471|consensus
Probab=100.00 E-value=4.4e-38 Score=278.23 Aligned_cols=199 Identities=26% Similarity=0.462 Sum_probs=163.5
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHHHHHHhhC--CccccCCCCCcHHHHHHhhhccccccCCCCCCCCEEEEEecCCCCCCC
Q psy4447 2 TLILIHHSCYFDLEASKSCIEVYFTTRTNT--PEFFSKRDINRPELLAQSKVVEFGAIAPKTPQGYQVIFHRLQQFEPSK 79 (261)
Q Consensus 2 ~L~rFLra~~~dv~~A~~~l~~~~~~R~~~--~~~~~~~~~~~~~~~~~l~~g~~~~~l~~D~~G~~V~~~~~~~~d~~~ 79 (261)
+|+||||||+||+++|++++.+++.||+++ ++++.+.+. .+++.+....+ ..+.|++|+|+.+.+.|..++..
T Consensus 47 ~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~-~~~~~~~~~~~----~~~~~~~g~~v~~~~~g~~~~~~ 121 (317)
T KOG1471|consen 47 NLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEE-DDELLKYYPQG----LHGVDKEGRPVYIERLGKIDPKG 121 (317)
T ss_pred HHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhcccc-chhhhhhcccc----ccccCCCCCEEEEeccCCCCccc
Confidence 799999999999999999999999998886 566665322 12233211111 22389999999999999887654
Q ss_pred C----C--------HHHHHHHHHHHHHHHhccCC-CcCcEEEEEeCCCCCcccccccCHHHHHHHHHHhhccccceeeee
Q psy4447 80 Y----V--------FQDSVRLLAMSIDACLHVEG-TVPGYIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGI 146 (261)
Q Consensus 80 ~----~--------~~~~~r~~~~~~e~~~~~~~-~~~g~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i 146 (261)
+ . ..+..+.+.+.+|.+..+.+ +++|++.|+|++|++++|+++..++.+++++.++|++||++++++
T Consensus 122 l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~ 201 (317)
T KOG1471|consen 122 LLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSHLLKPAPTLLKKILKILQDNYPERLKRI 201 (317)
T ss_pred ceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchhHHHHHHHHHHHHHHHHHHhCHHhhceE
Confidence 3 3 34555555566666665444 599999999999999999998999999999999999999999999
Q ss_pred EEEeCchHHHHHHHHhhhcchHHhhcceeeCCCCChhhhhhhcCCCCCCCCCCCCCCCCh
Q psy4447 147 HILNTRPLIDKIMFVVKPFMKKDLLSLVHFHPEGDISSVYEFVPPKCIPGGDLKGDLPDS 206 (261)
Q Consensus 147 ~iiN~P~~f~~~~~~vk~fl~~~~~~ki~~~~~~~~~~L~~~i~~~~LP~~~yGG~~~~~ 206 (261)
||||+|++|+++|+++||||+++|++||++..+++.++|.++||+++||. +|||+++..
T Consensus 202 ~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~~~~~~~L~k~i~~~~LP~-~yGG~~~~~ 260 (317)
T KOG1471|consen 202 HIINAPTIFSALWKVVKPFLDEKTRKKIHVLHSKDKESLLKYIPPEVLPE-EYGGTCGDL 260 (317)
T ss_pred EEEcCchhHHHHHHHHhccCCHHHHhhheecCCCchhhhhhhCCHhhCcc-ccCCCcccc
Confidence 99999999999999999999999999999443334999999999999999 999999865
No 3
>PF00650 CRAL_TRIO: CRAL/TRIO domain; InterPro: IPR001251 This entry defines the C-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1OLM_E 1O6U_E 3Q8G_A 3B7Q_B 3B7Z_A ....
Probab=100.00 E-value=1.6e-34 Score=230.30 Aligned_cols=153 Identities=25% Similarity=0.440 Sum_probs=125.8
Q ss_pred HhhhccccccCCCCCCCCEEEEEecCCCCCCCCCHHHHHHHHHHHHHHHhcc-C--CCcCcEEEEEeCCCCCcccccccC
Q psy4447 48 QSKVVEFGAIAPKTPQGYQVIFHRLQQFEPSKYVFQDSVRLLAMSIDACLHV-E--GTVPGYIFLFDMAGVRLGHVLRLS 124 (261)
Q Consensus 48 ~l~~g~~~~~l~~D~~G~~V~~~~~~~~d~~~~~~~~~~r~~~~~~e~~~~~-~--~~~~g~v~I~D~~g~s~~~~~~~~ 124 (261)
+.+.+..+ ..|+|++||||++++++++|++.++.+++.+++++++|.+++. + .++.|+++|+|++|++++++....
T Consensus 3 ~~~~~~~~-~~g~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~~~~iiD~~g~~~~~~~~~~ 81 (159)
T PF00650_consen 3 ILKSGPFY-LHGRDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRMPEGGQVEGIVVIIDLSGFSLSNFDWWP 81 (159)
T ss_dssp HHTTSCEE-EEEE-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTHHHTSHHH-EEEEEE-TT--HHHHHCHH
T ss_pred HHCCeeEE-ECCCCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhhcccccceeEEEEEeCCCceEeccccch
Confidence 34555555 5559999999999999999999999999999999999998842 2 358999999999999999887555
Q ss_pred HHHHHHHHHHhhccccceeeeeEEEeCchHHHHHHHHhhhcchHHhhcceeeCCC-CChhhhhhhcCCCCCCCCCCCCC
Q psy4447 125 VGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKIMFVVKPFMKKDLLSLVHFHPE-GDISSVYEFVPPKCIPGGDLKGD 202 (261)
Q Consensus 125 ~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~~vk~fl~~~~~~ki~~~~~-~~~~~L~~~i~~~~LP~~~yGG~ 202 (261)
++.++.+++++|++||+|++++||||+|++|+++|++++|||+++|++||+++++ ++.++|.++||+++||+ +|||+
T Consensus 82 ~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP~-~~GG~ 159 (159)
T PF00650_consen 82 ISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLPV-EYGGT 159 (159)
T ss_dssp HHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSBG-GGTSS
T ss_pred hhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCch-hcCCC
Confidence 8899999999999999999999999999999999999999999999999999954 44579999999999999 99996
No 4
>smart00516 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.97 E-value=3e-31 Score=211.12 Aligned_cols=141 Identities=22% Similarity=0.464 Sum_probs=132.3
Q ss_pred CCCCCCCEEEEEecCCCCCCCCCHHHHHHHHHHHHHHHhcc---CCCcCcEEEEEeCCCCCcccccccCHHHHHHHHHHh
Q psy4447 59 PKTPQGYQVIFHRLQQFEPSKYVFQDSVRLLAMSIDACLHV---EGTVPGYIFLFDMAGVRLGHVLRLSVGQLSKFFLYL 135 (261)
Q Consensus 59 ~~D~~G~~V~~~~~~~~d~~~~~~~~~~r~~~~~~e~~~~~---~~~~~g~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~ 135 (261)
|.|++||||+++++++++++..+.+++++++++++|.++.+ +.++.|+++|+|++|++++| ++++.+|.++.++
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~i~D~~~~~~~~---~~~~~lk~~~~~~ 90 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYVLEKILQREKKTGGIEGFTVIFDLKGLSMSN---PDLSVLRKILKIL 90 (158)
T ss_pred CCCCCcCEEEEEeccccccCcCCHHHHHHHHHHHHHHHHHHHhcCCCeeeEEEEEECCCCCccc---ccHHHHHHHHHHH
Confidence 58999999999999999999999999999999999998865 33589999999999999987 4678999999999
Q ss_pred hccccceeeeeEEEeCchHHHHHHHHhhhcchHHhhcceeeCCCCChhhhhhhcCCCCCCCCCCCCCC
Q psy4447 136 QEGLPVRLKGIHILNTRPLIDKIMFVVKPFMKKDLLSLVHFHPEGDISSVYEFVPPKCIPGGDLKGDL 203 (261)
Q Consensus 136 q~~yP~rl~~i~iiN~P~~f~~~~~~vk~fl~~~~~~ki~~~~~~~~~~L~~~i~~~~LP~~~yGG~~ 203 (261)
|++||+|++++||||+|++++++|+++++|+++++++||+++++++.++|.++||+++||+ +|||++
T Consensus 91 ~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~L~~~i~~~~lP~-~~GG~~ 157 (158)
T smart00516 91 QDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGNDSKEELLEYIDPEQLPE-ELGGTL 157 (158)
T ss_pred HHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCCCHHHHHhhCCHhhCcH-hhCCCC
Confidence 9999999999999999999999999999999999999999997655799999999999999 999986
No 5
>cd00170 SEC14 Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.96 E-value=4.5e-29 Score=197.12 Aligned_cols=146 Identities=23% Similarity=0.422 Sum_probs=130.6
Q ss_pred cccccCC-CCCCCCEEEEEecCCCCCCC-CCHHHHHHHHHHHHHHHhccCCC-cCcEEEEEeCCCCCcccccccCHHHHH
Q psy4447 53 EFGAIAP-KTPQGYQVIFHRLQQFEPSK-YVFQDSVRLLAMSIDACLHVEGT-VPGYIFLFDMAGVRLGHVLRLSVGQLS 129 (261)
Q Consensus 53 ~~~~~l~-~D~~G~~V~~~~~~~~d~~~-~~~~~~~r~~~~~~e~~~~~~~~-~~g~v~I~D~~g~s~~~~~~~~~~~~k 129 (261)
.+. +.+ +|++||||+++++++.++.. .+.++.+++.++.+|.++.++.. ..|+++|+|++|++++++. .+.+.+|
T Consensus 9 ~~~-~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~i~D~~~~~~~~~~-~~~~~~k 86 (157)
T cd00170 9 KVG-YLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQEDDEQVEGFVVIIDLKGLSLSHLL-PDPSLLK 86 (157)
T ss_pred ccc-ccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhhhhhcccceEEEEECCCCChhccc-hhHHHHH
Confidence 444 555 79999999999999766544 34599999999999999876654 5799999999999999886 6778999
Q ss_pred HHHHHhhccccceeeeeEEEeCchHHHHHHHHhhhcchHHhhcceeeCCCCChhhhhhhcCCCCCCCCCCCCC
Q psy4447 130 KFFLYLQEGLPVRLKGIHILNTRPLIDKIMFVVKPFMKKDLLSLVHFHPEGDISSVYEFVPPKCIPGGDLKGD 202 (261)
Q Consensus 130 ~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~~vk~fl~~~~~~ki~~~~~~~~~~L~~~i~~~~LP~~~yGG~ 202 (261)
+++.++|++||++++++||||+|++++++|+++++|+++++++||++++++ .++|.+++|+++||. +|||+
T Consensus 87 ~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~-~~~L~~~i~~~~Lp~-~~GG~ 157 (157)
T cd00170 87 KILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSD-KEELLKYIDKEQLPE-EYGGT 157 (157)
T ss_pred HHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCC-HHHHHhhCChhhCcH-hhCCC
Confidence 999999999999999999999999999999999999999999999999754 799999999999999 99996
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.57 E-value=2e-15 Score=119.19 Aligned_cols=136 Identities=20% Similarity=0.324 Sum_probs=95.1
Q ss_pred CCCCCCCEEEEEecCCCCCCCCCHHHHHHHHHHHHHHHhccCCCcCcEEEEEeCCCCCcccccccCHHHHHHHHHHhhcc
Q psy4447 59 PKTPQGYQVIFHRLQQFEPSKYVFQDSVRLLAMSIDACLHVEGTVPGYIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEG 138 (261)
Q Consensus 59 ~~D~~G~~V~~~~~~~~d~~~~~~~~~~r~~~~~~e~~~~~~~~~~g~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~ 138 (261)
|+|++||||+++...+. ++. .+..+++.|++.....+ -...++++|+|++|.+..+- .+.+.++++...++..
T Consensus 8 G~d~~g~pV~~~~~~~~-~~~---~~~~~ll~yl~~~l~~~-~~~~~f~vVid~~~~~~~~~--~~~~~l~~~~~~l~~~ 80 (149)
T PF13716_consen 8 GRDREGRPVVVFIASRL-PSS---DDLERLLLYLLSTLSEE-VVDKPFSVVIDHTGFSRSSE--PSLSWLKQLYKLLPRK 80 (149)
T ss_dssp EEBTTS-EEEEEEGGG--C-T---THHHHHHHHHHHHH-TT-TTTS-EEEEEE-TT--GGG-----HHHHHHTTTSS-HH
T ss_pred ccCCCcCEEEEEECCcC-cch---hhHHHHHHHHHHhhhHH-hcCCCEEEEEEcCCCccccC--CchHHHHHHHHHHHHH
Confidence 39999999999998777 433 36666666666655332 12467999999999987542 3567899999999999
Q ss_pred ccceeeeeEEEeCchHHHHHH-HHhhhcchHHh-hcceeeCCCCChhhhhhhcCCCCCCCCCCCCCCC
Q psy4447 139 LPVRLKGIHILNTRPLIDKIM-FVVKPFMKKDL-LSLVHFHPEGDISSVYEFVPPKCIPGGDLKGDLP 204 (261)
Q Consensus 139 yP~rl~~i~iiN~P~~f~~~~-~~vk~fl~~~~-~~ki~~~~~~~~~~L~~~i~~~~LP~~~yGG~~~ 204 (261)
|+..+++++|||++++++.+. .+.+++.+++. ..||.++.+ .++|.+|||+++||. ++||+.+
T Consensus 81 ~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~s--l~~L~~~i~~~qL~~-~lp~~~~ 145 (149)
T PF13716_consen 81 YKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSS--LSELSKHIDPSQLPE-SLPGVLQ 145 (149)
T ss_dssp HHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESS--TCGGGGTSGGGG-------HHH-
T ss_pred HhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECC--HHHHHhhCCHHHhcc-cCCCEEe
Confidence 999999999999999999999 56678889988 899999887 999999999999999 9998763
No 7
>KOG4406|consensus
Probab=98.26 E-value=8.6e-06 Score=72.48 Aligned_cols=137 Identities=15% Similarity=0.207 Sum_probs=98.0
Q ss_pred HHHHhhh--ccccccCC--CCCCCCEEEEEecCCCCCC-CCCHHHHHHHHHHHHHHHhccCCCcCcEEEEEeCCCCCccc
Q psy4447 45 LLAQSKV--VEFGAIAP--KTPQGYQVIFHRLQQFEPS-KYVFQDSVRLLAMSIDACLHVEGTVPGYIFLFDMAGVRLGH 119 (261)
Q Consensus 45 ~~~~l~~--g~~~~~l~--~D~~G~~V~~~~~~~~d~~-~~~~~~~~r~~~~~~e~~~~~~~~~~g~v~I~D~~g~s~~~ 119 (261)
+..+.+. +.+. +.+ .|+.||+|+++-..++.+. .+.-..++++.++.++..++++ ++.+.=-.|+...+
T Consensus 71 fyd~~~H~~ei~q-vi~~~~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~~id~~Ve~D-----Yt~vYfh~gl~s~n 144 (467)
T KOG4406|consen 71 FYDIARHEREILQ-VIGDAKDKQGRKIIVVYACRLPSSSELDDIRLISYLVYTIDKYVEND-----YTLVYFHHGLPSDN 144 (467)
T ss_pred HHHHHHhhhheee-eccCcccccCCeeEEEEEecCCchhhhhhHHHHHHHHHHHHHHHhcc-----ceeeehhcCCcccc
Confidence 4344433 6666 777 5999999999988776543 3333448889999999887654 44444445554433
Q ss_pred ccccCHHHHHHHHHHhhccccceeeeeEEEeCchHHHHHHHHhhhcchHHhhcceeeCCCCChhhhhhhcCC
Q psy4447 120 VLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKIMFVVKPFMKKDLLSLVHFHPEGDISSVYEFVPP 191 (261)
Q Consensus 120 ~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~~vk~fl~~~~~~ki~~~~~~~~~~L~~~i~~ 191 (261)
- ...+.+.....-+-.+|---++.+|+|.+-|+..++|+++||+++.|..+||+-+.. .++|.+++.-
T Consensus 145 k--p~l~~l~~aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n~--lseL~~~l~l 212 (467)
T KOG4406|consen 145 K--PYLQLLFDAYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFNS--LSELFEALKL 212 (467)
T ss_pred c--chHHHHHHHHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEeeh--HHHHHHhhhh
Confidence 2 223344443333444577889999999999999999999999999999999988876 8899887653
No 8
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=98.23 E-value=1.1e-06 Score=57.07 Aligned_cols=23 Identities=17% Similarity=0.190 Sum_probs=20.7
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHH
Q psy4447 2 TLILIHHSCYFDLEASKSCIEVY 24 (261)
Q Consensus 2 ~L~rFLra~~~dv~~A~~~l~~~ 24 (261)
+|+||||||+|||++|.+||.+|
T Consensus 33 ~llRFLRARkf~v~~A~~mL~~t 55 (55)
T PF03765_consen 33 FLLRFLRARKFDVEKAFKMLKKT 55 (55)
T ss_dssp HHHHHHHHTTT-HHHHHHHHHHH
T ss_pred HHHHHHHHccCCHHHHHHHHHhC
Confidence 79999999999999999999875
No 9
>PF04838 Baculo_LEF5: Baculoviridae late expression factor 5 ; InterPro: IPR006923 This is a family of Baculoviridae late expression factor 5, required for late and very late gene expression.; GO: 0006355 regulation of transcription, DNA-dependent
Probab=76.04 E-value=12 Score=29.25 Aligned_cols=92 Identities=10% Similarity=0.205 Sum_probs=65.7
Q ss_pred HHHHHHHHhhccccceee--eeEEEeCchHHHHHHHHhhhcchH--Hhhcceee----------C-CCC--Chhhhhhhc
Q psy4447 127 QLSKFFLYLQEGLPVRLK--GIHILNTRPLIDKIMFVVKPFMKK--DLLSLVHF----------H-PEG--DISSVYEFV 189 (261)
Q Consensus 127 ~~k~~~~~~q~~yP~rl~--~i~iiN~P~~f~~~~~~vk~fl~~--~~~~ki~~----------~-~~~--~~~~L~~~i 189 (261)
..+.++.++-.+||.-++ ..-++|+.-.|.++|+-+ |-++. +-|+-|+. . .++ .+++|.+.|
T Consensus 16 ~y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYv-P~~s~~~kERKQIRLs~dcI~kL~~nT~NdfKLY~Elf~~i 94 (159)
T PF04838_consen 16 DYKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYV-PSVSNVEKERKQIRLSEDCIEKLFVNTINDFKLYEELFDMI 94 (159)
T ss_pred CHHHHHHHHHhhcccccccCeeecCCCchhhhhhhhcc-CCCchHhHHHHHhhhhHHHHHHHHHhcCchHHHHHHHHHHH
Confidence 356789999999999999 999999999999999876 55554 33443443 2 233 478899999
Q ss_pred CCCCCCCCCCCCCCCChHHHHHHHHHHHHHhHHHHHhhcc
Q psy4447 190 PPKCIPGGDLKGDLPDSKTLHNEYVEWMKNLVEFFLQDEK 229 (261)
Q Consensus 190 ~~~~LP~~~yGG~~~~~~~~~~~w~~~l~~~~~~~~~~~~ 229 (261)
..+.++. ++| .+...+.+.+...|......
T Consensus 95 ~~~~~~~-----~CP-----Cell~~r~~~~~~Yv~~l~~ 124 (159)
T PF04838_consen 95 DDNKLKE-----KCP-----CELLQQRLNEIKSYVNNLNN 124 (159)
T ss_pred HccCCCC-----CCC-----HHHHHHHHHHHHHHHHHhcc
Confidence 8765555 554 24555677777777776544
No 10
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=69.65 E-value=5.5 Score=23.95 Aligned_cols=18 Identities=28% Similarity=0.307 Sum_probs=14.5
Q ss_pred HHHHHhCCCCHHHHHHHH
Q psy4447 4 ILIHHSCYFDLEASKSCI 21 (261)
Q Consensus 4 ~rFLra~~~dv~~A~~~l 21 (261)
..||.+++||++.|...+
T Consensus 19 ~~~L~~~~wdle~Av~~y 36 (43)
T PF14555_consen 19 IQYLEANNWDLEAAVNAY 36 (43)
T ss_dssp HHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 578999999999998754
No 11
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=64.23 E-value=10 Score=22.56 Aligned_cols=20 Identities=25% Similarity=0.260 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCCHHHHHHHH
Q psy4447 2 TLILIHHSCYFDLEASKSCI 21 (261)
Q Consensus 2 ~L~rFLra~~~dv~~A~~~l 21 (261)
.|..-|++|++||-+|.+.+
T Consensus 19 ~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 19 VLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred HHHHHHHHcCCcHHHHHHHh
Confidence 35667999999999998864
No 12
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=58.94 E-value=37 Score=22.91 Aligned_cols=50 Identities=20% Similarity=0.265 Sum_probs=34.5
Q ss_pred cEEEEEeCCCCCcccccccCHHHHHHHHHHhhcccc--ceeeeeEEEeCchHHHHHH
Q psy4447 105 GYIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEGLP--VRLKGIHILNTRPLIDKIM 159 (261)
Q Consensus 105 g~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~yP--~rl~~i~iiN~P~~f~~~~ 159 (261)
|-.+++|++|+.. ++.+++-.++.-+...|| +.-+++.++|+......+.
T Consensus 17 ~~~V~lDF~gv~~-----~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I 68 (74)
T PF14213_consen 17 GEKVVLDFEGVES-----ITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMI 68 (74)
T ss_pred CCeEEEECCCccc-----ccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHH
Confidence 4448899999953 345677777777777777 4445788888876654443
No 13
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=56.27 E-value=13 Score=22.13 Aligned_cols=21 Identities=14% Similarity=0.105 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCCHHHHHHHHH
Q psy4447 2 TLILIHHSCYFDLEASKSCIE 22 (261)
Q Consensus 2 ~L~rFLra~~~dv~~A~~~l~ 22 (261)
.+..-|.++++|++.|...|-
T Consensus 19 ~I~~~L~~~~~~ve~ai~~LL 39 (42)
T PF02845_consen 19 VIEAVLQANNGDVEAAIDALL 39 (42)
T ss_dssp HHHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHH
Confidence 467789999999999998774
No 14
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=55.95 E-value=12 Score=21.55 Aligned_cols=17 Identities=12% Similarity=0.092 Sum_probs=11.5
Q ss_pred HHHHHhCCCCHHHHHHH
Q psy4447 4 ILIHHSCYFDLEASKSC 20 (261)
Q Consensus 4 ~rFLra~~~dv~~A~~~ 20 (261)
.+=|+.+++|+++|..-
T Consensus 20 ~~AL~~~~~nve~A~~~ 36 (37)
T PF00627_consen 20 REALRACNGNVERAVDW 36 (37)
T ss_dssp HHHHHHTTTSHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHh
Confidence 34577777777777654
No 15
>PF11964 SpoIIAA-like: SpoIIAA-like; InterPro: IPR021866 This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important. ; PDB: 2Q3L_B 2OOK_A 3BL4_A.
Probab=54.47 E-value=41 Score=24.02 Aligned_cols=76 Identities=13% Similarity=0.079 Sum_probs=49.6
Q ss_pred CCHHHHHHHHHHHHHHHhccCCCcCcEEEEEeCC-CCCcccccccCHHHHHHHHHHhhccccceeeeeEEEeCchHHHHH
Q psy4447 80 YVFQDSVRLLAMSIDACLHVEGTVPGYIFLFDMA-GVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKI 158 (261)
Q Consensus 80 ~~~~~~~r~~~~~~e~~~~~~~~~~g~v~I~D~~-g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~ 158 (261)
++.+++.++.- .++..+.. -..+.+++|+. ++. .+++.......++... ....++++-+|-.+.+...+
T Consensus 11 ~t~ed~~~~~~-~~~~~~~~---~~~~~ll~d~~~~~~-----~~~~~a~~~~~~~~~~-~~~~~~r~AvV~~~~~~~~~ 80 (109)
T PF11964_consen 11 LTEEDYKELLP-ALEELIAD---HGKIRLLVDLRRDFE-----GWSPEARWEDAKFGLK-HLKHFRRIAVVGDSEWIRMI 80 (109)
T ss_dssp E-HHHHHHHHH-HHHHHHTT---SSSEEEEEEEC-CEE-----EEHHHHHHHHHHHHCC-CCGGEEEEEEE-SSCCCHHH
T ss_pred eCHHHHHHHHH-HHHHHHhc---CCceEEEEEecCccC-----CCCHHHHHHHHHhchh-hhcccCEEEEEECcHHHHHH
Confidence 56677777443 34444432 24588888888 652 1234445555544444 88889999999999999999
Q ss_pred HHHhhhc
Q psy4447 159 MFVVKPF 165 (261)
Q Consensus 159 ~~~vk~f 165 (261)
.+++.++
T Consensus 81 ~~~~~~~ 87 (109)
T PF11964_consen 81 ANFFAAF 87 (109)
T ss_dssp HHHHHHH
T ss_pred HHHHHhc
Confidence 9988886
No 16
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=51.66 E-value=17 Score=21.66 Aligned_cols=21 Identities=10% Similarity=0.039 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCCHHHHHHHHH
Q psy4447 2 TLILIHHSCYFDLEASKSCIE 22 (261)
Q Consensus 2 ~L~rFLra~~~dv~~A~~~l~ 22 (261)
.+.+.|+++++|++.|...|-
T Consensus 20 ~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 20 VIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred HHHHHHHHcCCCHHHHHHHHH
Confidence 466889999999999998764
No 17
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=47.39 E-value=22 Score=20.35 Aligned_cols=19 Identities=5% Similarity=-0.055 Sum_probs=14.2
Q ss_pred HHHHHHhCCCCHHHHHHHH
Q psy4447 3 LILIHHSCYFDLEASKSCI 21 (261)
Q Consensus 3 L~rFLra~~~dv~~A~~~l 21 (261)
..+-|+.+++|+++|...|
T Consensus 18 ~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 18 ARKALRATNNNVERAVEWL 36 (38)
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 4566888888888887655
No 18
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=44.43 E-value=26 Score=26.65 Aligned_cols=43 Identities=26% Similarity=0.454 Sum_probs=35.1
Q ss_pred eeEEEeCchHHHHHHHHh-----hhcchHHhhcceeeCCCCChhhhhhhc
Q psy4447 145 GIHILNTRPLIDKIMFVV-----KPFMKKDLLSLVHFHPEGDISSVYEFV 189 (261)
Q Consensus 145 ~i~iiN~P~~f~~~~~~v-----k~fl~~~~~~ki~~~~~~~~~~L~~~i 189 (261)
-+.++|..-+++.+++.+ ..|++++..+.++++.+ .+++.++|
T Consensus 86 Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d~--~~e~~~~i 133 (133)
T PF03641_consen 86 PIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVDD--PEEALEYI 133 (133)
T ss_dssp EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEESS--HHHHHHHH
T ss_pred CEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeCC--HHHHHhhC
Confidence 599999887878888866 56889999999999877 78877664
No 19
>KOG1838|consensus
Probab=44.17 E-value=2.6e+02 Score=25.81 Aligned_cols=84 Identities=10% Similarity=0.045 Sum_probs=54.3
Q ss_pred CCCEEEEEecCCCCCCCCCHHHHHHHHHHHHHHHhccCCCcCc-EEEEEeCCCCCcccccc------cCHHHHHHHHHHh
Q psy4447 63 QGYQVIFHRLQQFEPSKYVFQDSVRLLAMSIDACLHVEGTVPG-YIFLFDMAGVRLGHVLR------LSVGQLSKFFLYL 135 (261)
Q Consensus 63 ~G~~V~~~~~~~~d~~~~~~~~~~r~~~~~~e~~~~~~~~~~g-~v~I~D~~g~s~~~~~~------~~~~~~k~~~~~~ 135 (261)
...|++++-+|.-.. +.+..+|.++.... + .| -++|++-+|++-+.+.. -....++.+++.+
T Consensus 123 ~~~P~vvilpGltg~---S~~~YVr~lv~~a~---~-----~G~r~VVfN~RG~~g~~LtTpr~f~ag~t~Dl~~~v~~i 191 (409)
T KOG1838|consen 123 GTDPIVVILPGLTGG---SHESYVRHLVHEAQ---R-----KGYRVVVFNHRGLGGSKLTTPRLFTAGWTEDLREVVNHI 191 (409)
T ss_pred CCCcEEEEecCCCCC---ChhHHHHHHHHHHH---h-----CCcEEEEECCCCCCCCccCCCceeecCCHHHHHHHHHHH
Confidence 455888888775433 45677777654332 1 23 48889999976555532 1356799999999
Q ss_pred hccccceeeeeEEEeCchHHHHHH
Q psy4447 136 QEGLPVRLKGIHILNTRPLIDKIM 159 (261)
Q Consensus 136 q~~yP~rl~~i~iiN~P~~f~~~~ 159 (261)
...||.+ .++.|-.+.=..+++
T Consensus 192 ~~~~P~a--~l~avG~S~Gg~iL~ 213 (409)
T KOG1838|consen 192 KKRYPQA--PLFAVGFSMGGNILT 213 (409)
T ss_pred HHhCCCC--ceEEEEecchHHHHH
Confidence 9999997 555555444444444
No 20
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=43.65 E-value=22 Score=30.43 Aligned_cols=28 Identities=14% Similarity=0.304 Sum_probs=24.3
Q ss_pred eeeEEEeCchHHHHHHHHhhhcchHHhh
Q psy4447 144 KGIHILNTRPLIDKIMFVVKPFMKKDLL 171 (261)
Q Consensus 144 ~~i~iiN~P~~f~~~~~~vk~fl~~~~~ 171 (261)
.+++|||+||-+..-...+-|+|...+.
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~L~ 264 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTLLA 264 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHHhc
Confidence 4899999999999999999999877654
No 21
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=42.87 E-value=32 Score=19.51 Aligned_cols=18 Identities=6% Similarity=0.073 Sum_probs=12.0
Q ss_pred HHHHHhCCCCHHHHHHHH
Q psy4447 4 ILIHHSCYFDLEASKSCI 21 (261)
Q Consensus 4 ~rFLra~~~dv~~A~~~l 21 (261)
.+-|+.+++|+++|...|
T Consensus 19 ~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 19 LKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHhCCCHHHHHHHH
Confidence 456777777777776543
No 22
>PF04378 RsmJ: Ribosomal RNA small subunit methyltransferase D, RsmJ; InterPro: IPR007473 This is a bacterial protein of unknown function, possibly secreted.; PDB: 2OO3_A.
Probab=41.92 E-value=22 Score=30.33 Aligned_cols=32 Identities=19% Similarity=0.315 Sum_probs=22.5
Q ss_pred ceeeeeEEEeCchHHHHHHHHhhhcchHHhhc
Q psy4447 141 VRLKGIHILNTRPLIDKIMFVVKPFMKKDLLS 172 (261)
Q Consensus 141 ~rl~~i~iiN~P~~f~~~~~~vk~fl~~~~~~ 172 (261)
..=.+++|||+||-+....+-+-|+|.+.+.+
T Consensus 203 m~GSGm~iiNPPw~l~~~l~~~l~~L~~~L~~ 234 (245)
T PF04378_consen 203 MNGSGMLIINPPWTLDEELEEILPWLAETLAQ 234 (245)
T ss_dssp --EEEEEEES--TTHHHHHHHHHHHHHHHSST
T ss_pred eecceEEEEcCCccHHHHHHHHHHHHHHHhCc
Confidence 33458999999999999888888887766543
No 23
>TIGR02364 dha_pts dihydroxyacetone kinase, phosphotransfer subunit. In E. coli and many other bacteria, unlike the yeasts and a few bacteria such as Citrobacter freundii, the dihydroxyacetone kinase (also called glycerone kinase) transfers a phosphate from a phosphoprotein rather than from ATP and contains multiple subunits. This protein, which resembles proteins of PTS transport systems, is found with its gene adjacent to
Probab=38.42 E-value=93 Score=23.50 Aligned_cols=51 Identities=12% Similarity=0.217 Sum_probs=34.8
Q ss_pred cCcEEEEEeCCCCCcccccccCHHHHHHHHHHhhccccceeeeeEEEeCchHHHHHHHHhhhc
Q psy4447 103 VPGYIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKIMFVVKPF 165 (261)
Q Consensus 103 ~~g~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~~vk~f 165 (261)
-+|++++.|+ |-|..+ ...++..++ ++..+.+..+|.|.+-.++-..+..-
T Consensus 59 ~dgVlvl~DL-Ggs~~n--------~e~a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~~ 109 (125)
T TIGR02364 59 ADGVLIFYDL-GSAVMN--------AEMAVELLE---DEDRDKVHLVDAPLVEGAFAAAVEAQ 109 (125)
T ss_pred CCCEEEEEcC-CCcHhH--------HHHHHHHhc---cccccEEEEechhHHHHHHHHHHHHc
Confidence 4799999999 655322 112333433 35557899999999998888777543
No 24
>PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional
Probab=37.23 E-value=1.1e+02 Score=23.14 Aligned_cols=46 Identities=20% Similarity=0.209 Sum_probs=30.1
Q ss_pred CcEEEEEeCCCCCcccccccCHHHHHHHHHHhhccccceeeeeEEEeCchHHHHHHHHhh
Q psy4447 104 PGYIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKIMFVVK 163 (261)
Q Consensus 104 ~g~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~~vk 163 (261)
+|++++.|+ |-+..+ ....+..+. +- ++++++++|..=..+-..+.
T Consensus 58 dGVlVltDL-Gssp~n--------~~~a~e~~~----~~-~~v~~~daPlVEGa~~Aav~ 103 (124)
T PRK14484 58 DGVLIFFDL-GSAEMN--------AEMAIEMLD----GE-KKIIIIDAPIVEGAFTAAVL 103 (124)
T ss_pred CCeEEEEeC-CChHHH--------HHHHHHhcC----CC-CcEEEECCcHHHHHHHHHHH
Confidence 899999999 655332 222334332 22 89999999987666555554
No 25
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=36.31 E-value=38 Score=20.03 Aligned_cols=21 Identities=5% Similarity=0.036 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCCHHHHHHHHH
Q psy4447 2 TLILIHHSCYFDLEASKSCIE 22 (261)
Q Consensus 2 ~L~rFLra~~~dv~~A~~~l~ 22 (261)
+|..-|..+++|+.+|.+.|.
T Consensus 9 ~i~~aL~~~~gn~~~aA~~Lg 29 (42)
T PF02954_consen 9 LIRQALERCGGNVSKAARLLG 29 (42)
T ss_dssp HHHHHHHHTTT-HHHHHHHHT
T ss_pred HHHHHHHHhCCCHHHHHHHHC
Confidence 567789999999999998773
No 26
>PRK02399 hypothetical protein; Provisional
Probab=34.61 E-value=3.6e+02 Score=24.92 Aligned_cols=83 Identities=13% Similarity=0.083 Sum_probs=60.5
Q ss_pred CCHHHHHHHHHHHHHHHhccCCCcCcEEEEEeCCCCCccccc---ccCHHHHHHHHHHhhccccceeeeeEE-----EeC
Q psy4447 80 YVFQDSVRLLAMSIDACLHVEGTVPGYIFLFDMAGVRLGHVL---RLSVGQLSKFFLYLQEGLPVRLKGIHI-----LNT 151 (261)
Q Consensus 80 ~~~~~~~r~~~~~~e~~~~~~~~~~g~v~I~D~~g~s~~~~~---~~~~~~~k~~~~~~q~~yP~rl~~i~i-----iN~ 151 (261)
.+.+|..+.--++.+.+-.. ..-+.+++=++|+|.-... -.++..-..++..+++..+..+. .+ ||.
T Consensus 313 Tt~eE~~~~g~~ia~kLn~a---~gpv~vllP~~G~S~~D~~G~~f~Dpead~alf~~l~~~l~~~~~--v~~~~~hIND 387 (406)
T PRK02399 313 TTPEENRQIGRWIAEKLNRA---KGPVAFLIPLGGVSALDRPGQPFHDPEADAAFFDALEETVTETRR--LIEVPAHIND 387 (406)
T ss_pred cCHHHHHHHHHHHHHHHhcC---CCCeEEEEeCCCCccccCCCCCccChhHHHHHHHHHHHhCCCCce--EEECCCCCCC
Confidence 46788888777777776332 2458899999999875422 13677778889999998877654 44 799
Q ss_pred chHHHHHHHHhhhcch
Q psy4447 152 RPLIDKIMFVVKPFMK 167 (261)
Q Consensus 152 P~~f~~~~~~vk~fl~ 167 (261)
|.|...+...+..++.
T Consensus 388 ~~FA~a~~~~l~~~~~ 403 (406)
T PRK02399 388 PEFAEAAVEAFEELMA 403 (406)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999988877755543
No 27
>PF13466 STAS_2: STAS domain
Probab=33.12 E-value=1.4e+02 Score=19.85 Aligned_cols=52 Identities=15% Similarity=0.332 Sum_probs=33.4
Q ss_pred cEEEEEeCCCCCcccccccCHHHHHHHHHHhhccccceeeeeEEEeCchHHHHHHHHh
Q psy4447 105 GYIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKIMFVV 162 (261)
Q Consensus 105 g~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~~v 162 (261)
+-.+++|+++++.-+. ..+. ++-.++.....+=+.+.+.|+|.-+..++.+.
T Consensus 26 ~~~v~lDls~v~~iDs-----agl~-lL~~~~~~~~~~g~~~~l~~~~~~~~~ll~~~ 77 (80)
T PF13466_consen 26 GRPVVLDLSGVEFIDS-----AGLQ-LLLAAARRARARGRQLRLTGPSPALRRLLELL 77 (80)
T ss_pred CCeEEEECCCCCeecH-----HHHH-HHHHHHHHHHHCCCeEEEEcCCHHHHHHHHHh
Confidence 3678999999986432 2233 22233334444557899999998887776654
No 28
>KOG1534|consensus
Probab=32.51 E-value=3.1e+02 Score=23.24 Aligned_cols=88 Identities=13% Similarity=0.236 Sum_probs=52.9
Q ss_pred CcCcEEEEEeCCCCCcccccccCHHHHHHHHHHhhccccceeeeeEEEeCch------HHHHHHHHhhhcch-----HHh
Q psy4447 102 TVPGYIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRP------LIDKIMFVVKPFMK-----KDL 170 (261)
Q Consensus 102 ~~~g~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~------~f~~~~~~vk~fl~-----~~~ 170 (261)
-+++--+|+||-|= ..-.++ ...+++++.-++. .-.++..+|++.++. +|+.+++.+..++. -.+
T Consensus 95 d~eddylifDcPGQ-IELytH--~pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~KfiSG~lsAlsAMi~lE~P~INv 170 (273)
T KOG1534|consen 95 DVEDDYLIFDCPGQ-IELYTH--LPVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDSTKFISGCLSALSAMISLEVPHINV 170 (273)
T ss_pred CccCCEEEEeCCCe-eEEeec--ChhHHHHHHHHhc-ccCceeEEEEeccchhhhHHHHHHHHHHHHHHHHHhcCcchhh
Confidence 47888999999983 111122 2467888888876 445666777776664 55555555544433 223
Q ss_pred hcceeeCCCCChhhhhhhcCCCC
Q psy4447 171 LSLVHFHPEGDISSVYEFVPPKC 193 (261)
Q Consensus 171 ~~ki~~~~~~~~~~L~~~i~~~~ 193 (261)
..|.-.+++...++|.++++++.
T Consensus 171 lsKMDLlk~~~k~~l~~Fl~~d~ 193 (273)
T KOG1534|consen 171 LSKMDLLKDKNKKELERFLNPDE 193 (273)
T ss_pred hhHHHHhhhhhHHHHHHhcCCch
Confidence 45555554322577778877663
No 29
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=30.12 E-value=67 Score=21.19 Aligned_cols=24 Identities=8% Similarity=-0.054 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHHH
Q psy4447 2 TLILIHHSCYFDLEASKSCIEVYF 25 (261)
Q Consensus 2 ~L~rFLra~~~dv~~A~~~l~~~~ 25 (261)
|=.++|...+||.++|.+.+.+-.
T Consensus 29 ~s~~cLe~~~Wd~~~Al~~F~~lk 52 (63)
T smart00804 29 YSQMCLEDNNWDYERALKNFTELK 52 (63)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHH
Confidence 446899999999999999887643
No 30
>COG1448 TyrB Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=28.39 E-value=3.6e+02 Score=24.74 Aligned_cols=131 Identities=14% Similarity=0.069 Sum_probs=70.2
Q ss_pred EEEEEecCCCCCCCC--CHHHHHHHHHHHHHHHhccCCCcCcEEEEEeCCCCCcccccccCHHHHHHHHHHhh-------
Q psy4447 66 QVIFHRLQQFEPSKY--VFQDSVRLLAMSIDACLHVEGTVPGYIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQ------- 136 (261)
Q Consensus 66 ~V~~~~~~~~d~~~~--~~~~~~r~~~~~~e~~~~~~~~~~g~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q------- 136 (261)
-|+++..-.+||... +.++.....-.+-| .+++.++|+.=-++.+-..-+...++.++....
T Consensus 173 ~vvLLH~CcHNPTG~D~t~~qW~~l~~~~~~---------r~lip~~D~AYQGF~~GleeDa~~lR~~a~~~~~~lva~S 243 (396)
T COG1448 173 SVVLLHGCCHNPTGIDPTEEQWQELADLIKE---------RGLIPFFDIAYQGFADGLEEDAYALRLFAEVGPELLVASS 243 (396)
T ss_pred CEEEEecCCCCCCCCCCCHHHHHHHHHHHHH---------cCCeeeeehhhhhhccchHHHHHHHHHHHHhCCcEEEEeh
Confidence 467777778888765 44555444433322 578889997655554322123334454443332
Q ss_pred -----ccccceeeeeEEEeCchHHHHHHHHhhhcchHHhhcceeeCCCCChhhhhhhcCCCCCCCCCCCCCCC----ChH
Q psy4447 137 -----EGLPVRLKGIHILNTRPLIDKIMFVVKPFMKKDLLSLVHFHPEGDISSVYEFVPPKCIPGGDLKGDLP----DSK 207 (261)
Q Consensus 137 -----~~yP~rl~~i~iiN~P~~f~~~~~~vk~fl~~~~~~ki~~~~~~~~~~L~~~i~~~~LP~~~yGG~~~----~~~ 207 (261)
..|-||++.+++|-...-. -.-+...|....| -. -.-|+ .+|...- +-.
T Consensus 244 ~SKnfgLYgERVGa~~vva~~~~~---a~~v~sqlk~~iR----~~--------------ySnPP-~~Ga~vva~IL~~p 301 (396)
T COG1448 244 FSKNFGLYGERVGALSVVAEDAEE---ADRVLSQLKAIIR----TN--------------YSNPP-AHGAAVVATILNNP 301 (396)
T ss_pred hhhhhhhhhhccceeEEEeCCHHH---HHHHHHHHHHHHH----hc--------------cCCCc-hhhHHHHHHHhCCH
Confidence 3577888887777433211 1111111111111 11 12366 7777631 124
Q ss_pred HHHHHHHHHHHHhHHHHHhh
Q psy4447 208 TLHNEYVEWMKNLVEFFLQD 227 (261)
Q Consensus 208 ~~~~~w~~~l~~~~~~~~~~ 227 (261)
++.+.|.+.+...++-..+.
T Consensus 302 ~Lra~W~~El~~Mr~Ri~~m 321 (396)
T COG1448 302 ELRAEWEQELEEMRQRILEM 321 (396)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 67899999888877766653
No 31
>COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=28.35 E-value=88 Score=21.58 Aligned_cols=52 Identities=21% Similarity=0.215 Sum_probs=33.5
Q ss_pred HHHHhCCCCH-----HHHHHHHHHHHHHHhhCCccccCCCCCcHHHHHHhhhccccccCC--CCCCCCEEEE
Q psy4447 5 LIHHSCYFDL-----EASKSCIEVYFTTRTNTPEFFSKRDINRPELLAQSKVVEFGAIAP--KTPQGYQVIF 69 (261)
Q Consensus 5 rFLra~~~dv-----~~A~~~l~~~~~~R~~~~~~~~~~~~~~~~~~~~l~~g~~~~~l~--~D~~G~~V~~ 69 (261)
-+|+.-+.|. ..+.+.|++++..|-+.|++ .+.-..|+++ +| ...+|..|+-
T Consensus 20 eyl~rl~v~yd~VeIt~Sm~NlKrFl~lRDs~~~F-----------d~vk~~gyiG--IPall~~d~~vVl~ 78 (85)
T COG4545 20 EYLERLNVDYDFVEITESMANLKRFLHLRDSRPEF-----------DEVKSNGYIG--IPALLTDDGKVVLG 78 (85)
T ss_pred HHHHHcCCCceeeehhhhhhhHHHHHhhhccchhH-----------HhhhhcCccc--ceEEEeCCCcEEEe
Confidence 3455555443 46778889999998887642 2333567776 44 6778887764
No 32
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=28.18 E-value=48 Score=20.76 Aligned_cols=22 Identities=14% Similarity=-0.055 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCCHHHHHHHHHH
Q psy4447 2 TLILIHHSCYFDLEASKSCIEV 23 (261)
Q Consensus 2 ~L~rFLra~~~dv~~A~~~l~~ 23 (261)
|=.++|..++||.++|.+.+..
T Consensus 17 ~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 17 WSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp HHHHHHHHTTT-CCHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHH
Confidence 5578999999999999987754
No 33
>TIGR02886 spore_II_AA anti-sigma F factor antagonist. The anti-sigma F factor antagonist, also called stage II sporulation protein AA, is a protein universal among endospore-forming bacteria, all of which belong to the Firmcutes
Probab=25.31 E-value=2.5e+02 Score=19.76 Aligned_cols=51 Identities=8% Similarity=0.181 Sum_probs=32.5
Q ss_pred EEEEEeCCCCCcccccccCHHHHHHHHHHhhccccceeeeeEEEeCchHHHHHHHHh
Q psy4447 106 YIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKIMFVV 162 (261)
Q Consensus 106 ~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~~v 162 (261)
-.+|+||++++.-..+ ....+..+...++ .+=.+++++|.+.-+..++...
T Consensus 40 ~~vilDls~v~~iDss--gi~~L~~~~~~~~----~~g~~l~l~~~~~~v~~~l~~~ 90 (106)
T TIGR02886 40 KHLILNLKNVTFMDSS--GLGVILGRYKKIK----NEGGEVIVCNVSPAVKRLFELS 90 (106)
T ss_pred CEEEEECCCCcEecch--HHHHHHHHHHHHH----HcCCEEEEEeCCHHHHHHHHHh
Confidence 4799999999864322 2333444444333 2446899999988877766544
No 34
>PF01740 STAS: STAS domain; InterPro: IPR002645 The STAS (Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. The establishment of differential gene expression in sporulating Bacillus subtilis involves four protein components one of which is SpoIIAA (P10727 from SWISSPROT). The four components regulate the sporulation sigma factor F. Early in sporulation, SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase SpoIIAB (P10728 from SWISSPROT). The site at which this protein is a conserved serine. SpoIIAB is an anti-sigma factor that in its free form inhibits F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases Sigma F activity []. The STAS domain is found in the anti-sigma factor antagonist SpoIIAA.; PDB: 3T6O_B 3LKL_B 1H4Z_A 1H4Y_B 1H4X_B 3NY7_A 3OIZ_A 1T6R_A 1VC1_B 1SBO_A ....
Probab=24.40 E-value=1.2e+02 Score=21.75 Aligned_cols=49 Identities=16% Similarity=0.206 Sum_probs=31.9
Q ss_pred EEEEEeCCCCCcccccccCHHHHHHHHHHhhccccceeeeeEEEeCchHHHHHHH
Q psy4447 106 YIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKIMF 160 (261)
Q Consensus 106 ~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~ 160 (261)
-.+|+||++++.- +.+.+..+..+.+..- .+=..++++|.+.-....+.
T Consensus 49 ~~vIlD~s~v~~i-----Dssgi~~L~~~~~~~~-~~g~~~~l~~~~~~v~~~l~ 97 (117)
T PF01740_consen 49 KNVILDMSGVSFI-----DSSGIQALVDIIKELR-RRGVQLVLVGLNPDVRRILE 97 (117)
T ss_dssp SEEEEEETTESEE-----SHHHHHHHHHHHHHHH-HTTCEEEEESHHHHHHHHHH
T ss_pred eEEEEEEEeCCcC-----CHHHHHHHHHHHHHHH-HCCCEEEEEECCHHHHHHHH
Confidence 6899999998643 3344444444444443 44568999999877766544
No 35
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=24.31 E-value=2.4e+02 Score=22.66 Aligned_cols=67 Identities=22% Similarity=0.322 Sum_probs=45.9
Q ss_pred CCCCCcccccccCHHHHHHHHHHhhccccceeeeeEEEeCchHHHHHHHHhh-----hcchHHhhcceeeCCCCChhhhh
Q psy4447 112 MAGVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKIMFVVK-----PFMKKDLLSLVHFHPEGDISSVY 186 (261)
Q Consensus 112 ~~g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~~vk-----~fl~~~~~~ki~~~~~~~~~~L~ 186 (261)
-.|++ ++.-+-.++...|-... -+-+.++|..-+++.+.++++ .|++++-.+.+.+..+ .+++.
T Consensus 104 PGG~G-------TL~El~e~~~~~qlg~~--~kPiil~n~~g~~~~l~~~l~~~~~~gfi~~~~~~~~~~~d~--~~e~~ 172 (178)
T TIGR00730 104 PGGFG-------TLEELFEVLTWAQLGIH--QKPIILFNVNGHFDGLVEWLKYSIQEGFISESHLKLIHVVSR--PDELI 172 (178)
T ss_pred CCCcc-------hHHHHHHHHHHHHcCCC--CCCEEEECCcchHHHHHHHHHHHHHCCCCCHHHcCcEEEcCC--HHHHH
Confidence 36765 34455555555554433 357899998777787776543 5778888888888877 78887
Q ss_pred hhc
Q psy4447 187 EFV 189 (261)
Q Consensus 187 ~~i 189 (261)
+++
T Consensus 173 ~~i 175 (178)
T TIGR00730 173 EQV 175 (178)
T ss_pred HHH
Confidence 766
No 36
>PF00561 Abhydrolase_1: alpha/beta hydrolase fold A web page of Esterases and alpha/beta hydrolases.; InterPro: IPR000073 The alpha/beta hydrolase fold [] is common to a number of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is an alpha/beta-sheet (rather than a barrel), containing 8 strands connected by helices []. The enzymes are believed to have diverged from a common ancestor, preserving the arrangement of the catalytic residues. All have a catalytic triad, the elements of which are borne on loops, which are the best conserved structural features of the fold. Esterase (EST) from Pseudomonas putida is a member of the alpha/beta hydrolase fold superfamily of enzymes []. In most of the family members the beta-strands are parallels, but some have an inversion of the first strands, which gives it an antiparallel orientation. The catalytic triad residues are presented on loops. One of these is the nucleophile elbow and is the most conserved feature of the fold. Some other members lack one or all of the catalytic residues. Some members are therefore inactive but others are involved in surface recognition. The ESTHER database [] gathers and annotates all the published information related to gene and protein sequences of this superfamily []. This entry represents fold-1 of alpha/beta hydrolase.; PDB: 2VAT_E 2VAX_C 2VAV_H 2PSJ_A 2PSH_B 2PSE_A 2PSF_A 2PSD_A 2EDA_A 1CIJ_A ....
Probab=23.87 E-value=1.2e+02 Score=23.94 Aligned_cols=17 Identities=18% Similarity=0.385 Sum_probs=14.7
Q ss_pred hccccceeeeeEEEeCc
Q psy4447 136 QEGLPVRLKGIHILNTR 152 (261)
Q Consensus 136 q~~yP~rl~~i~iiN~P 152 (261)
...||++++++.++++|
T Consensus 62 a~~~p~~v~~lvl~~~~ 78 (230)
T PF00561_consen 62 AAQYPERVKKLVLISPP 78 (230)
T ss_dssp HHHSGGGEEEEEEESES
T ss_pred HHHCchhhcCcEEEeee
Confidence 35699999999999997
No 37
>cd07042 STAS_SulP_like_sulfate_transporter Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
Probab=23.02 E-value=2.4e+02 Score=19.45 Aligned_cols=50 Identities=10% Similarity=0.150 Sum_probs=30.2
Q ss_pred EEEEEeCCCCCcccccccCHHHHHHHHHHhhccccceeeeeEEEeCchHHHHHHHH
Q psy4447 106 YIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKIMFV 161 (261)
Q Consensus 106 ~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~~ 161 (261)
-.+|+|+++++.- +.+.+..+..+.+ .+-.+=..+.+.|++.-...++..
T Consensus 42 ~~lilD~~~v~~i-----Dss~~~~L~~~~~-~~~~~~~~~~l~~~~~~~~~~l~~ 91 (107)
T cd07042 42 KVVILDLSAVNFI-----DSTAAEALEELVK-DLRKRGVELYLAGLNPQVRELLER 91 (107)
T ss_pred eEEEEECCCCchh-----hHHHHHHHHHHHH-HHHHCCCEEEEecCCHHHHHHHHH
Confidence 5688999998753 3333444444433 223334678999998766555543
No 38
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=22.87 E-value=42 Score=23.08 Aligned_cols=23 Identities=22% Similarity=0.307 Sum_probs=17.0
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHH
Q psy4447 3 LILIHHSCYFDLEASKSCIEVYF 25 (261)
Q Consensus 3 L~rFLra~~~dv~~A~~~l~~~~ 25 (261)
|.-=|..+.|||++|...|.+-.
T Consensus 49 i~eal~~~~fDvekAl~~Ll~~~ 71 (79)
T PF08938_consen 49 IKEALWHYYFDVEKALDYLLSKF 71 (79)
T ss_dssp HHHHHHHTTT-CCHHHHHHHHCC
T ss_pred HHHHHHHHcCCHHHHHHHHHHhc
Confidence 44557889999999999887643
No 39
>PF08566 Pam17: Mitochondrial import protein Pam17; InterPro: IPR013875 The presequence translocase-associated motor (PAM) drives the completion of preprotein translocation into the mitochondrial matrix. The Pam17 subunit is required for formation of a stable complex between cochaperones Pam16 and Pam18 and promotes the association of Pam16-Pam18 with the presequence translocase []. Mitochondria lacking Pam17 are selectively impaired in the import of matrix proteins [].
Probab=22.54 E-value=1.1e+02 Score=24.72 Aligned_cols=14 Identities=7% Similarity=0.159 Sum_probs=11.4
Q ss_pred CchHHHHHHHHhhh
Q psy4447 151 TRPLIDKIMFVVKP 164 (261)
Q Consensus 151 ~P~~f~~~~~~vk~ 164 (261)
-|.+.+.+|++...
T Consensus 95 GP~~G~~vf~l~~r 108 (173)
T PF08566_consen 95 GPSLGNQVFRLLNR 108 (173)
T ss_pred cchHHHHHHHHHhH
Confidence 58899999998754
No 40
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=22.10 E-value=1.6e+02 Score=25.27 Aligned_cols=70 Identities=17% Similarity=0.232 Sum_probs=44.3
Q ss_pred cccceeeeeEEEeCchHHH---HHHHHhhhcchHHhhcceeeCCC-C----ChhhhhhhcCCCCCCCCCC-CCCCCChHH
Q psy4447 138 GLPVRLKGIHILNTRPLID---KIMFVVKPFMKKDLLSLVHFHPE-G----DISSVYEFVPPKCIPGGDL-KGDLPDSKT 208 (261)
Q Consensus 138 ~yP~rl~~i~iiN~P~~f~---~~~~~vk~fl~~~~~~ki~~~~~-~----~~~~L~~~i~~~~LP~~~y-GG~~~~~~~ 208 (261)
-|.+| .+|||||--.... .++++++..... -.+|-|++. . ...+..+....-.+.. .| ||++.+...
T Consensus 31 If~~R-ngihIIDL~kT~~~l~~A~~~v~~~~~~--~g~ILfVgTK~~a~~~V~~~A~r~g~~yV~~-RwLgG~LTN~~t 106 (252)
T COG0052 31 IFGER-NGIHIIDLQKTLERLREAYKFLRRIAAN--GGKILFVGTKKQAQEPVKEFAERTGAYYVNG-RWLGGMLTNFKT 106 (252)
T ss_pred ceeec-CCcEEEEHHHHHHHHHHHHHHHHHHHcC--CCEEEEEechHHHHHHHHHHHHHhCCceecC-cccCccccCchh
Confidence 58999 9999999876544 344444433211 357888863 1 2344456677777777 55 999987665
Q ss_pred HHH
Q psy4447 209 LHN 211 (261)
Q Consensus 209 ~~~ 211 (261)
...
T Consensus 107 i~~ 109 (252)
T COG0052 107 IRK 109 (252)
T ss_pred HHH
Confidence 433
No 41
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=21.70 E-value=56 Score=29.32 Aligned_cols=45 Identities=16% Similarity=0.367 Sum_probs=29.3
Q ss_pred HHHHHHHhCCCCHHHHHHHH------HHHHHHHhhCCccccCCCCCcHHHHHHh
Q psy4447 2 TLILIHHSCYFDLEASKSCI------EVYFTTRTNTPEFFSKRDINRPELLAQS 49 (261)
Q Consensus 2 ~L~rFLra~~~dv~~A~~~l------~~~~~~R~~~~~~~~~~~~~~~~~~~~l 49 (261)
.|+|-|.+++|||++|.+-+ ++ ..-..++|.+ -+|.+.+-++..+
T Consensus 146 illkLlqaadydV~rAerGIIyIDEIDK-IarkSeN~SI--TRDVSGEGVQQAL 196 (408)
T COG1219 146 ILLKLLQAADYDVERAERGIIYIDEIDK-IARKSENPSI--TRDVSGEGVQQAL 196 (408)
T ss_pred HHHHHHHHcccCHHHHhCCeEEEechhh-hhccCCCCCc--ccccCchHHHHHH
Confidence 47999999999999998754 22 2222335544 3566666666554
No 42
>cd00006 PTS_IIA_man PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate.
Probab=20.25 E-value=2.2e+02 Score=21.00 Aligned_cols=64 Identities=14% Similarity=0.067 Sum_probs=38.4
Q ss_pred CHHHHHHHHHHHHHHHhccCCCcCcEEEEEeCCCCCcccccccCHHHHHHHHHHhhccccceeeeeEEEeCchHHHHHHH
Q psy4447 81 VFQDSVRLLAMSIDACLHVEGTVPGYIFLFDMAGVRLGHVLRLSVGQLSKFFLYLQEGLPVRLKGIHILNTRPLIDKIMF 160 (261)
Q Consensus 81 ~~~~~~r~~~~~~e~~~~~~~~~~g~v~I~D~~g~s~~~~~~~~~~~~k~~~~~~q~~yP~rl~~i~iiN~P~~f~~~~~ 160 (261)
+++++.+-..-.++.. ...++++++.|+-|=|..+. ...+.... .++..|.-+|.|....++..
T Consensus 39 ~~~~~~~~i~~~i~~~----~~~~~viil~Dl~GGSp~n~----------~~~~~~~~--~~~~visG~nlpmlle~~~~ 102 (122)
T cd00006 39 SPDDLLEKIKAALAEL----DSGEGVLILTDLFGGSPNNA----------AARLSMEH--PPVEVIAGVNLPMLLEAARA 102 (122)
T ss_pred CHHHHHHHHHHHHHHh----CCCCcEEEEEeCCCCCHHHH----------HHHHHhcC--CCEEEEEccCHHHHHHHHHc
Confidence 4555555443333321 22478999999987664431 22222222 56778888999999877643
Done!