Query psy15877
Match_columns 517
No_of_seqs 113 out of 126
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 23:53:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15877.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15877hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1866|consensus 99.2 1E-11 2.3E-16 136.9 5.4 98 419-517 2-103 (944)
2 PF12755 Vac14_Fab1_bd: Vacuol 83.2 20 0.00044 31.3 10.8 22 268-289 36-57 (97)
3 PF10165 Ric8: Guanine nucleot 81.8 52 0.0011 36.1 15.9 34 220-253 40-73 (446)
4 cd00020 ARM Armadillo/beta-cat 79.6 6.9 0.00015 32.7 6.6 61 224-289 19-79 (120)
5 PF02985 HEAT: HEAT repeat; I 74.2 3.3 7.1E-05 28.4 2.5 21 268-288 9-29 (31)
6 KOG0212|consensus 65.8 13 0.00027 42.4 6.1 66 268-343 93-158 (675)
7 cd03569 VHS_Hrs_Vps27p VHS dom 54.6 54 0.0012 30.5 7.4 65 221-289 50-115 (142)
8 KOG1866|consensus 53.0 47 0.001 39.1 7.9 71 260-337 567-640 (944)
9 PF08045 CDC14: Cell division 51.0 89 0.0019 32.3 8.9 64 221-289 101-164 (257)
10 cd00020 ARM Armadillo/beta-cat 48.2 60 0.0013 26.9 6.2 61 222-287 59-119 (120)
11 cd03568 VHS_STAM VHS domain fa 46.7 94 0.002 29.0 7.7 65 221-289 46-111 (144)
12 PF00514 Arm: Armadillo/beta-c 46.3 79 0.0017 22.5 5.7 39 244-287 2-40 (41)
13 PF00790 VHS: VHS domain; Int 44.4 98 0.0021 28.3 7.4 65 221-289 51-119 (140)
14 cd03561 VHS VHS domain family; 43.2 97 0.0021 28.1 7.1 65 221-289 46-113 (133)
15 PF12463 DUF3689: Protein of u 42.2 35 0.00075 36.0 4.5 38 445-482 151-188 (303)
16 cd03565 VHS_Tom1 VHS domain fa 42.2 1.3E+02 0.0029 27.9 7.9 64 223-289 50-116 (141)
17 KOG2171|consensus 40.7 8.1E+02 0.018 30.5 15.7 32 258-289 79-110 (1075)
18 PF13513 HEAT_EZ: HEAT-like re 38.8 98 0.0021 23.2 5.5 49 231-285 6-54 (55)
19 PF12460 MMS19_C: RNAPII trans 38.3 5.4E+02 0.012 27.7 14.5 126 274-423 17-145 (415)
20 PF01602 Adaptin_N: Adaptin N 37.2 5.6E+02 0.012 27.6 13.7 32 452-483 468-501 (526)
21 KOG1059|consensus 36.6 7.1E+02 0.015 29.8 13.9 32 453-486 351-382 (877)
22 smart00288 VHS Domain present 35.1 1.7E+02 0.0036 26.8 7.3 64 221-288 46-111 (133)
23 PF06371 Drf_GBD: Diaphanous G 32.7 1.8E+02 0.0038 27.1 7.3 61 223-288 127-187 (187)
24 PF14663 RasGEF_N_2: Rapamycin 31.0 74 0.0016 28.5 4.2 34 257-290 3-39 (115)
25 PF11707 Npa1: Ribosome 60S bi 29.9 5.1E+02 0.011 27.2 10.9 78 382-472 69-148 (330)
26 cd00197 VHS_ENTH_ANTH VHS, ENT 29.1 2.8E+02 0.006 24.2 7.5 62 222-286 47-113 (115)
27 KOG2199|consensus 28.9 2.2E+02 0.0047 31.5 7.9 85 220-315 53-138 (462)
28 PF11864 DUF3384: Domain of un 28.6 5.6E+02 0.012 28.2 11.3 121 261-401 31-166 (464)
29 PF10508 Proteasom_PSMB: Prote 27.4 9E+02 0.019 27.0 16.7 32 257-289 76-107 (503)
30 PF14222 MOR2-PAG1_N: Cell mor 27.2 4.6E+02 0.0099 29.9 10.5 148 258-428 129-279 (552)
31 PF13646 HEAT_2: HEAT repeats; 26.6 89 0.0019 25.0 3.6 28 258-286 31-58 (88)
32 PF10508 Proteasom_PSMB: Prote 25.8 3.3E+02 0.0071 30.4 9.0 65 220-290 127-191 (503)
33 cd00870 PI3Ka_III Phosphoinosi 25.3 94 0.002 29.8 4.1 17 271-287 90-106 (166)
34 COG5077 Ubiquitin carboxyl-ter 24.7 30 0.00066 40.7 0.7 23 493-515 177-199 (1089)
35 KOG4199|consensus 23.9 3.2E+02 0.0069 30.0 7.9 65 222-291 340-406 (461)
36 smart00185 ARM Armadillo/beta- 23.1 2.3E+02 0.0049 19.3 4.8 24 263-287 17-40 (41)
37 PF03224 V-ATPase_H_N: V-ATPas 22.9 3.2E+02 0.0069 28.2 7.7 65 223-289 68-135 (312)
38 KOG1848|consensus 22.0 8.9E+02 0.019 31.1 12.0 126 264-400 1003-1135(1610)
39 PF12348 CLASP_N: CLASP N term 21.8 2.1E+02 0.0045 27.5 5.8 59 225-289 66-124 (228)
40 PF12719 Cnd3: Nuclear condens 21.3 8.9E+02 0.019 24.8 11.8 65 224-289 76-144 (298)
41 PF12825 DUF3818: Domain of un 21.3 8.6E+02 0.019 26.1 10.7 46 219-267 198-244 (341)
42 PTZ00429 beta-adaptin; Provisi 20.7 1.5E+03 0.032 27.1 18.1 29 453-483 348-376 (746)
43 cd03567 VHS_GGA VHS domain fam 20.3 4.6E+02 0.0099 24.4 7.5 64 221-288 47-116 (139)
No 1
>KOG1866|consensus
Probab=99.21 E-value=1e-11 Score=136.92 Aligned_cols=98 Identities=44% Similarity=0.772 Sum_probs=85.1
Q ss_pred HhccCCCChhhhHhhhhcCCCCccCcCCCccCCHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHhccCC----CCCCCCCC
Q psy15877 419 INDYLFPTSKLMLKLEKTGEISFNEIAPAVCQSPESISAGFSLLIGLCTGSVPNLKLLVAMLTDMFYP----DCAEPLTE 494 (517)
Q Consensus 419 f~dfLFPas~~~~~~~~~~e~~~~d~~~PkCKS~~SR~AAfdLLveL~k~c~~Nl~~Lle~L~emh~s----~~~~~~~e 494 (517)
.++|+||+++.++++++.+..+ +++..|+|.++.|..|+|++|+++|.+|+.|++.+++.++++.+. -..+..+|
T Consensus 2 ~~d~~~~a~~~~l~~m~~~~lP-E~p~lPvcrsp~tIr~~~qllvA~~~~cV~nlkrs~~~~~tl~l~~k~~~s~q~lyE 80 (944)
T KOG1866|consen 2 IDDFHFPASFVGLKNMRLGPLP-EEPALPVCRSPYTIRAGFQLLVALAIGCVYNLKRSVDCLMTLYYMFKATTSCQALYE 80 (944)
T ss_pred CccccccHHHHHHHHHhcCCCc-ccCCCcccCCCcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccC
Confidence 4689999999999999998875 344888999999999999999999999999999999977776332 12257899
Q ss_pred CcccCCCCCCCCCCcccccCCCC
Q psy15877 495 WDYLPPIGPKPPKGFVWPKSKVK 517 (517)
Q Consensus 495 WdYlP~~~~RS~cGYVGLKNa~~ 517 (517)
|+|+|+++.|++-||||||||-|
T Consensus 81 ~~YlppVgsRpp~gfVGLKNaga 103 (944)
T KOG1866|consen 81 WEYLPPVGSRPPEGFVGLKNAGA 103 (944)
T ss_pred cccCCCcCCCCCcceeeecCCCc
Confidence 99999999999999999999865
No 2
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=83.17 E-value=20 Score=31.32 Aligned_cols=22 Identities=14% Similarity=0.010 Sum_probs=20.5
Q ss_pred cCCCChHHHHHHHHHHHHHhcc
Q psy15877 268 LLCDEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 268 L~sP~~~VR~~a~~~L~~Lc~~ 289 (517)
+.+++..||..+|+.||.+++.
T Consensus 36 ~~D~d~rVRy~AcEaL~ni~k~ 57 (97)
T PF12755_consen 36 FDDQDSRVRYYACEALYNISKV 57 (97)
T ss_pred cCCCcHHHHHHHHHHHHHHHHH
Confidence 6999999999999999999865
No 3
>PF10165 Ric8: Guanine nucleotide exchange factor synembryn; InterPro: IPR019318 Ric8 is involved in the EGL-30 neurotransmitter signalling pathway []. It is a guanine nucleotide exchange factor [] that regulates neurotransmitter secretion.
Probab=81.85 E-value=52 Score=36.15 Aligned_cols=34 Identities=24% Similarity=0.280 Sum_probs=27.3
Q ss_pred CCCchhHHHHHHHHHHHHHHHHhCHHHHHHHHcC
Q psy15877 220 DIDLDDILVCKEALELLTVCFLLNNSLLKALLKE 253 (517)
Q Consensus 220 ~l~~eD~~V~~eALeLLv~cL~l~~~~l~sL~~~ 253 (517)
..+..|.-++.|||.+|.-++.+++.....|...
T Consensus 40 ~~~~~~~~v~~EALKCL~N~lf~s~~aR~~~~~~ 73 (446)
T PF10165_consen 40 EFESPDPDVSREALKCLCNALFLSPSARQIFVDL 73 (446)
T ss_pred cccCCChHHHHHHHHHHHHHHhCCHHHHHHHHHc
Confidence 4566789999999999999999887777666654
No 4
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=79.57 E-value=6.9 Score=32.72 Aligned_cols=61 Identities=16% Similarity=0.047 Sum_probs=45.6
Q ss_pred hhHHHHHHHHHHHHHHHHhCHHHHHHHHcCcccchHHHHHHHHhcCCCChHHHHHHHHHHHHHhcc
Q psy15877 224 DDILVCKEALELLTVCFLLNNSLLKALLKEPKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 224 eD~~V~~eALeLLv~cL~l~~~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~ 289 (517)
.|..+.+.|+..|.......++....+.+. .-++.++ .+ |.++++.||..++..|..++..
T Consensus 19 ~~~~~~~~a~~~l~~l~~~~~~~~~~~~~~---~~i~~l~-~~-l~~~~~~v~~~a~~~L~~l~~~ 79 (120)
T cd00020 19 SDENVQREAAWALSNLSAGNNDNIQAVVEA---GGLPALV-QL-LKSEDEEVVKAALWALRNLAAG 79 (120)
T ss_pred CCHHHHHHHHHHHHHHhcCCHHHHHHHHHC---CChHHHH-HH-HhCCCHHHHHHHHHHHHHHccC
Confidence 346777888888754433447888888887 5666555 44 5788999999999999999876
No 5
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=74.16 E-value=3.3 Score=28.39 Aligned_cols=21 Identities=19% Similarity=0.052 Sum_probs=18.2
Q ss_pred cCCCChHHHHHHHHHHHHHhc
Q psy15877 268 LLCDEKIIRACVQEQLTLSVT 288 (517)
Q Consensus 268 L~sP~~~VR~~a~~~L~~Lc~ 288 (517)
|.||++.||..++..|-.++.
T Consensus 9 l~D~~~~VR~~a~~~l~~i~~ 29 (31)
T PF02985_consen 9 LNDPSPEVRQAAAECLGAIAE 29 (31)
T ss_dssp HT-SSHHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHHHHHHHHh
Confidence 699999999999999998874
No 6
>KOG0212|consensus
Probab=65.84 E-value=13 Score=42.36 Aligned_cols=66 Identities=11% Similarity=0.136 Sum_probs=49.2
Q ss_pred cCCCChHHHHHHHHHHHHHhcccccccchhHHhHHHHHHHHHHhhhhhhhhhccCCCCCHHHHHHHHHHhhhhccc
Q psy15877 268 LLCDEKIIRACVQEQLTLSVTLSYAYASNAEQACLVAFLQLLFPLLTSDALETRVYTKSAEYFQLFCRTLNFVSSS 343 (517)
Q Consensus 268 L~sP~~~VR~~a~~~L~~Lc~~s~s~~~~~~~~pllffL~lLl~~L~~~a~e~~~~~~C~EYF~LLCrLLd~l~~s 343 (517)
+.+++-.||-.+|+.+|.+++- +.+. ..-+-..+|..|.....+. -..++.=++|+-||+...-..
T Consensus 93 f~D~d~~vRyyACEsLYNiaKv---~k~~-----v~~~Fn~iFdvL~klsaDs--d~~V~~~aeLLdRLikdIVte 158 (675)
T KOG0212|consen 93 FSDQDSQVRYYACESLYNIAKV---AKGE-----VLVYFNEIFDVLCKLSADS--DQNVRGGAELLDRLIKDIVTE 158 (675)
T ss_pred ccCccceeeeHhHHHHHHHHHH---hccC-----cccchHHHHHHHHHHhcCC--ccccccHHHHHHHHHHHhccc
Confidence 6899999999999999999985 2111 1223466667677665555 678999999999999776543
No 7
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=54.56 E-value=54 Score=30.50 Aligned_cols=65 Identities=17% Similarity=0.078 Sum_probs=48.8
Q ss_pred CCchhHHHHHHHHHHHHHHHHhCH-HHHHHHHcCcccchHHHHHHHHhcCCCChHHHHHHHHHHHHHhcc
Q psy15877 221 IDLDDILVCKEALELLTVCFLLNN-SLLKALLKEPKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 221 l~~eD~~V~~eALeLLv~cL~l~~-~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~ 289 (517)
+...+.-+...||.||-.|...|. .|...+... .|-+-+++++-..+.+.||..+.+.|..-+..
T Consensus 50 l~~~n~~vql~AL~LLe~~vkNCG~~fh~evas~----~fl~~l~~l~~~~~~~~Vk~kil~li~~W~~~ 115 (142)
T cd03569 50 LLSKNPNVQLYALLLLESCVKNCGTHFHDEVASR----EFMDELKDLIKTTKNEEVRQKILELIQAWALA 115 (142)
T ss_pred HcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhhH----HHHHHHHHHHcccCCHHHHHHHHHHHHHHHHH
Confidence 444678889999999999999884 455555544 55555667776678899999998888877643
No 8
>KOG1866|consensus
Probab=52.96 E-value=47 Score=39.05 Aligned_cols=71 Identities=21% Similarity=0.301 Sum_probs=40.7
Q ss_pred HHHHHHHhcCCCChHHHHHHHHHHHHHhcccc-c--ccchhHHhHHHHHHHHHHhhhhhhhhhccCCCCCHHHHHHHHHH
Q psy15877 260 AHFLCDTLLLCDEKIIRACVQEQLTLSVTLSY-A--YASNAEQACLVAFLQLLFPLLTSDALETRVYTKSAEYFQLFCRT 336 (517)
Q Consensus 260 ~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~s~-s--~~~~~~~~pllffL~lLl~~L~~~a~e~~~~~~C~EYF~LLCrL 336 (517)
..++. .+|++|+ || +...+.-++.... + +..-+........+..++..|...+.++ ..+|.|||.|+.--
T Consensus 567 sel~~-~~L~~~~--vR--f~~~~v~~~~~~~ld~~~~~~D~~~l~d~~le~~l~lld~d~~e~--~k~~~qyF~lf~m~ 639 (944)
T KOG1866|consen 567 SELSE-YLLECPS--VR--FVKLIVFIAHFSLLDGPLPSYDNLSLSDQLLEAVLNLLDRDVSEH--GKHLQQYFNLFVMY 639 (944)
T ss_pred HHHHH-HHHhCcc--hh--hHHHHHHHHHHHHhcCCCCCCccccchHHHHHHHHHHHhhhhhhh--hhhHHHHHHHHHhh
Confidence 34444 4468888 88 6666666655311 0 0000001122335566666667777777 99999999998643
Q ss_pred h
Q psy15877 337 L 337 (517)
Q Consensus 337 L 337 (517)
+
T Consensus 640 ~ 640 (944)
T KOG1866|consen 640 V 640 (944)
T ss_pred c
Confidence 3
No 9
>PF08045 CDC14: Cell division control protein 14, SIN component; InterPro: IPR012535 Cdc14 is a component of the septation initiation network (SIN) and is required for the localisation and activity of Sid1. Sid1 is a protein kinase that localises asymmetrically to one spindle pole body (SPB) in anaphase disappears prior to cell separation [], [].
Probab=51.00 E-value=89 Score=32.26 Aligned_cols=64 Identities=22% Similarity=0.176 Sum_probs=48.8
Q ss_pred CCchhHHHHHHHHHHHHHHHHhCHHHHHHHHcCcccchHHHHHHHHhcCCCChHHHHHHHHHHHHHhcc
Q psy15877 221 IDLDDILVCKEALELLTVCFLLNNSLLKALLKEPKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 221 l~~eD~~V~~eALeLLv~cL~l~~~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~ 289 (517)
..+.|..|+ -|+.+|-.|+.++|.-...|... .+-..++++|=.+..+.|...+-..+..+..+
T Consensus 101 ~~~~~~li~-~aL~vLQGl~LLHp~Sr~lF~r~----~~m~lll~LL~~~~~~~i~~a~L~tLv~iLld 164 (257)
T PF08045_consen 101 SPSNDSLIA-LALRVLQGLCLLHPPSRKLFHRE----QNMELLLDLLSPSNPPAIQSACLDTLVCILLD 164 (257)
T ss_pred ccchhHHHH-HHHHHHHHHHHcCchHHHHHhhh----hhHHHHHHHhccCCCchHHHHHHHHHHHHHHc
Confidence 445566654 49999999999999888877766 77777889974555688888888887777665
No 10
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=48.24 E-value=60 Score=26.93 Aligned_cols=61 Identities=16% Similarity=0.011 Sum_probs=41.9
Q ss_pred CchhHHHHHHHHHHHHHHHHhCHHHHHHHHcCcccchHHHHHHHHhcCCCChHHHHHHHHHHHHHh
Q psy15877 222 DLDDILVCKEALELLTVCFLLNNSLLKALLKEPKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSV 287 (517)
Q Consensus 222 ~~eD~~V~~eALeLLv~cL~l~~~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc 287 (517)
..+|..|.++|+..|.......+...+.+.+. .-...++ .+ |.+.+..+|+.++..|..+|
T Consensus 59 ~~~~~~v~~~a~~~L~~l~~~~~~~~~~~~~~---g~l~~l~-~~-l~~~~~~~~~~a~~~l~~l~ 119 (120)
T cd00020 59 KSEDEEVVKAALWALRNLAAGPEDNKLIVLEA---GGVPKLV-NL-LDSSNEDIQKNATGALSNLA 119 (120)
T ss_pred hCCCHHHHHHHHHHHHHHccCcHHHHHHHHHC---CChHHHH-HH-HhcCCHHHHHHHHHHHHHhh
Confidence 34578899999999754333344556666665 3444444 44 46779999999999998886
No 11
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=46.75 E-value=94 Score=29.03 Aligned_cols=65 Identities=15% Similarity=0.078 Sum_probs=49.5
Q ss_pred CCchhHHHHHHHHHHHHHHHHhCH-HHHHHHHcCcccchHHHHHHHHhcCCCChHHHHHHHHHHHHHhcc
Q psy15877 221 IDLDDILVCKEALELLTVCFLLNN-SLLKALLKEPKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 221 l~~eD~~V~~eALeLLv~cL~l~~-~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~ 289 (517)
+...|.-+.-.||.||-.|...|. .|...+... .|-+=|++++-...++.||..+.+.|..-+..
T Consensus 46 l~~~n~~v~l~AL~LLe~~vkNCG~~fh~evask----~Fl~eL~kl~~~~~~~~Vk~kil~li~~W~~~ 111 (144)
T cd03568 46 LNHKDPNVQLRALTLLDACAENCGKRFHQEVASR----DFTQELKKLINDRVHPTVKEKLREVVKQWADE 111 (144)
T ss_pred HcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHhhH----HHHHHHHHHhcccCCHHHHHHHHHHHHHHHHH
Confidence 445678899999999999999985 455666554 55555777776658899999999888877643
No 12
>PF00514 Arm: Armadillo/beta-catenin-like repeat; InterPro: IPR000225 The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. Animal Arm-repeat proteins function in various processes, including intracellular signalling and cytoskeletal regulation, and include such proteins as beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumour suppressor protein, and the nuclear transport factor importin-alpha, amongst others []. A subset of these proteins is conserved across eukaryotic kingdoms. In higher plants, some Arm-repeat proteins function in intracellular signalling like their mammalian counterparts, while others have novel functions []. The 3-dimensional fold of an armadillo repeat is known from the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit []. The cylindrical structure features a positively charged grove, which presumably interacts with the acidic surfaces of the known interaction partners of beta-catenin.; GO: 0005515 protein binding; PDB: 2Z6G_A 1IQ1_C 3RZX_A 2C1M_A 3BTR_C 3OQS_A 3TPO_A 1IAL_A 1Q1S_C 1PJM_B ....
Probab=46.28 E-value=79 Score=22.51 Aligned_cols=39 Identities=8% Similarity=-0.032 Sum_probs=28.6
Q ss_pred HHHHHHHHcCcccchHHHHHHHHhcCCCChHHHHHHHHHHHHHh
Q psy15877 244 NSLLKALLKEPKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSV 287 (517)
Q Consensus 244 ~~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc 287 (517)
++....+.+. .-++.+ +++ |.++++.||+.++-.|..||
T Consensus 2 ~~~~~~i~~~---g~i~~L-v~l-l~~~~~~v~~~a~~al~nl~ 40 (41)
T PF00514_consen 2 PENKQAIVEA---GGIPPL-VQL-LKSPDPEVQEEAAWALGNLA 40 (41)
T ss_dssp HHHHHHHHHT---THHHHH-HHH-TTSSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHc---ccHHHH-HHH-HcCCCHHHHHHHHHHHHHHh
Confidence 4555666666 445554 455 47999999999999998886
No 13
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=44.40 E-value=98 Score=28.31 Aligned_cols=65 Identities=14% Similarity=0.029 Sum_probs=48.7
Q ss_pred CCchhHHHHHHHHHHHHHHHHhCH-HHHHHHHcCcccchHHHHHHHHhcCCCChH---HHHHHHHHHHHHhcc
Q psy15877 221 IDLDDILVCKEALELLTVCFLLNN-SLLKALLKEPKERLFAHFLCDTLLLCDEKI---IRACVQEQLTLSVTL 289 (517)
Q Consensus 221 l~~eD~~V~~eALeLLv~cL~l~~-~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~---VR~~a~~~L~~Lc~~ 289 (517)
+...+.-+.-.||.||-.|...+. .|...+... .|-+-+..++-..+... ||+.+.+.|..-...
T Consensus 51 l~~~~~~vq~~aL~lld~lvkNcg~~f~~ev~~~----~fl~~l~~l~~~~~~~~~~~Vk~k~l~ll~~W~~~ 119 (140)
T PF00790_consen 51 LKHGNPNVQLLALTLLDALVKNCGPRFHREVASK----EFLDELVKLIKSKKTDPETPVKEKILELLQEWAEA 119 (140)
T ss_dssp HTTSSHHHHHHHHHHHHHHHHHSHHHHHHHHTSH----HHHHHHHHHHHHTTTHHHSHHHHHHHHHHHHHHHH
T ss_pred HhCCCHHHHHHHHHHHHHHHHcCCHHHHHHHhHH----HHHHHHHHHHccCCCCchhHHHHHHHHHHHHHHHH
Confidence 334678888999999999999995 555555554 67777888877666665 898888888777654
No 14
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=43.24 E-value=97 Score=28.14 Aligned_cols=65 Identities=14% Similarity=0.011 Sum_probs=49.1
Q ss_pred CCchhHHHHHHHHHHHHHHHHhCHH-HHHHHHcCcccchHHHHHHHHhcC--CCChHHHHHHHHHHHHHhcc
Q psy15877 221 IDLDDILVCKEALELLTVCFLLNNS-LLKALLKEPKERLFAHFLCDTLLL--CDEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 221 l~~eD~~V~~eALeLLv~cL~l~~~-~l~sL~~~~~~~~~~~fL~dLLL~--sP~~~VR~~a~~~L~~Lc~~ 289 (517)
+...+.-+.-.||.||-.|+..+.. |...+... +.+.. ++.++.. ..++.||..+.+.|..-...
T Consensus 46 l~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s~---~fl~~-l~~l~~~~~~~~~~Vk~kil~ll~~W~~~ 113 (133)
T cd03561 46 IKYGNPHVQLLALTLLELLVKNCGKPFHLQVADK---EFLLE-LVKIAKNSPKYDPKVREKALELILAWSES 113 (133)
T ss_pred HcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhhH---HHHHH-HHHHhCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 3344678888999999999988855 66777766 56667 6677665 46789999999888877653
No 15
>PF12463 DUF3689: Protein of unknown function (DUF3689) ; InterPro: IPR022162 This family of proteins is found in eukaryotes. Proteins in this family are typically between 399 and 797 amino acids in length.
Probab=42.22 E-value=35 Score=35.99 Aligned_cols=38 Identities=24% Similarity=0.267 Sum_probs=34.2
Q ss_pred CCCccCCHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHh
Q psy15877 445 APAVCQSPESISAGFSLLIGLCTGSVPNLKLLVAMLTD 482 (517)
Q Consensus 445 ~~PkCKS~~SR~AAfdLLveL~k~c~~Nl~~Lle~L~e 482 (517)
..+.|.+.+..+.+||||=||+|+++.+|+.+...|..
T Consensus 151 l~~~~~~~~v~Q~~FDLLGELiK~n~~~f~~l~~~l~~ 188 (303)
T PF12463_consen 151 LSDGCMSQEVLQSNFDLLGELIKFNRDAFQRLNKYLNN 188 (303)
T ss_pred hcCccchHHHHHHHHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 44778889999999999999999999999999988773
No 16
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=42.21 E-value=1.3e+02 Score=27.88 Aligned_cols=64 Identities=11% Similarity=0.055 Sum_probs=47.1
Q ss_pred chhHHHHHHHHHHHHHHHHhC-HHHHHHHHcCcccchHHHHHHHHhcCC--CChHHHHHHHHHHHHHhcc
Q psy15877 223 LDDILVCKEALELLTVCFLLN-NSLLKALLKEPKERLFAHFLCDTLLLC--DEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 223 ~eD~~V~~eALeLLv~cL~l~-~~~l~sL~~~~~~~~~~~fL~dLLL~s--P~~~VR~~a~~~L~~Lc~~ 289 (517)
..|..++..||.||-.|...| ..|...+... ...+..+++++-.. +...||..+.+.|..-+..
T Consensus 50 ~~n~~v~l~aL~LLe~~vkNCG~~fh~eiask---~Fl~e~L~~~i~~~~~~~~~Vk~kil~li~~W~~~ 116 (141)
T cd03565 50 NKNHKEVMLTLTVLETCVKNCGHRFHVLVAKK---DFIKDVLVKLINPKNNPPTIVQEKVLALIQAWADA 116 (141)
T ss_pred CCCHHHHHHHHHHHHHHHHHccHHHHHHHHHH---HhhhHHHHHHHcccCCCcHHHHHHHHHHHHHHHHH
Confidence 357889999999999999998 5677777666 45555566776432 4468999988888877643
No 17
>KOG2171|consensus
Probab=40.65 E-value=8.1e+02 Score=30.46 Aligned_cols=32 Identities=9% Similarity=0.004 Sum_probs=26.5
Q ss_pred hHHHHHHHHhcCCCChHHHHHHHHHHHHHhcc
Q psy15877 258 LFAHFLCDTLLLCDEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 258 ~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~ 289 (517)
.+.+-|...++..+.+.||+..|+.+-.+++.
T Consensus 79 siks~lL~~~~~E~~~~vr~k~~dviAeia~~ 110 (1075)
T KOG2171|consen 79 SIKSSLLEIIQSETEPSVRHKLADVIAEIARN 110 (1075)
T ss_pred HHHHHHHHHHHhccchHHHHHHHHHHHHHHHh
Confidence 45556667778899999999999999999875
No 18
>PF13513 HEAT_EZ: HEAT-like repeat; PDB: 2Z5J_A 2OT8_B 2Z5O_A 2H4M_A 2QMR_A 1QBK_B 2Z5M_A 2Z5K_A 2Z5N_A 1GCJ_B ....
Probab=38.80 E-value=98 Score=23.17 Aligned_cols=49 Identities=22% Similarity=0.024 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhCHHHHHHHHcCcccchHHHHHHHHhcCCCChHHHHHHHHHHHH
Q psy15877 231 EALELLTVCFLLNNSLLKALLKEPKERLFAHFLCDTLLLCDEKIIRACVQEQLTL 285 (517)
Q Consensus 231 eALeLLv~cL~l~~~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~ 285 (517)
.|...|.......+..+..+.. ..-..+..+ |.|+++.||..++..|-+
T Consensus 6 ~A~~aLg~l~~~~~~~~~~~~~-----~~~~~L~~~-L~d~~~~VR~~A~~aLg~ 54 (55)
T PF13513_consen 6 AAAWALGRLAEGCPELLQPYLP-----ELLPALIPL-LQDDDDSVRAAAAWALGN 54 (55)
T ss_dssp HHHHHHHCTTTTTHHHHHHHHH-----HHHHHHHHH-TTSSSHHHHHHHHHHHHC
T ss_pred HHHHHHhhHhcccHHHHHHHHH-----HHHHHHHHH-HcCCCHHHHHHHHHHHhc
Confidence 3444443222234555555442 334444455 588999999999988754
No 19
>PF12460 MMS19_C: RNAPII transcription regulator C-terminal; InterPro: IPR024687 This domain, approximately 60 amino acids in length, is found in the N-terminal region of MMS19 proteins. MMS19 is required for both nucleotide excision repair (NER) and RNA polymerase II (RNAP II) transcription [].
Probab=38.30 E-value=5.4e+02 Score=27.73 Aligned_cols=126 Identities=18% Similarity=0.136 Sum_probs=70.2
Q ss_pred HHHHHHHHHHHHHhcccccccchhHHhHHHHHHHHHHhhhhhhhhhccCCCCCHHHHHHHHHHhhhhccccccccCCCcc
Q psy15877 274 IIRACVQEQLTLSVTLSYAYASNAEQACLVAFLQLLFPLLTSDALETRVYTKSAEYFQLFCRTLNFVSSSVWIGAGSVLS 353 (517)
Q Consensus 274 ~VR~~a~~~L~~Lc~~s~s~~~~~~~~pllffL~lLl~~L~~~a~e~~~~~~C~EYF~LLCrLLd~l~~s~~~~~gs~~~ 353 (517)
.-++.+-+.|-.+|.... -+.-....|++.|.... + .....+|+.++++-+.++-...... .
T Consensus 17 ~~~~~~L~~l~~ls~~~~---------i~~~~~~~ll~kl~~~~-~---~~~~~~~~~~il~tl~~~~~~~~~~-----~ 78 (415)
T PF12460_consen 17 SNYERILEALAALSTSPQ---------ILETLSIRLLNKLSIVC-Q---SESSSDYCHAILSTLQSLLEKKQED-----K 78 (415)
T ss_pred hHHHHHHHHHHHHHCChh---------HHHHHHHHHHHHHHHHh-c---CCCChHHHHHHHHHHHHHHHhcccc-----c
Confidence 456666777778876521 11222233333333332 2 2338889999888777765443300 0
Q ss_pred cccCHHHHHHH-HHHHHhccccccccCC--CCcchHhhHHHHHHHHHhccCCcchhccCCccchHHHHHhccC
Q psy15877 354 TGIDVEKYLTQ-ELAVLKRLSVGAKKSG--QRDILLQGHLSIVKELVCFLNSEKKMEFGVTNGLIRDLINDYL 423 (517)
Q Consensus 354 ~~iDie~LL~q-eI~~L~~~~~~e~~t~--e~D~lL~GlLnL~k~Ll~~l~~~Kk~~iGs~~~LIkeLf~dfL 423 (517)
+..+.....+. .+.+|.+.-....... .++.+|.=.-++++.++++++.++.. .++.+++.-|+
T Consensus 79 ~~~~~~~y~~~~lv~~l~~~~~~~~~~~~~~~~~~L~~~~~l~~~iv~~l~~~~q~------~~~~~~~~lf~ 145 (415)
T PF12460_consen 79 QFEDNSWYFHRILVPRLFELALQASDQSSDLDDRVLELLSRLINLIVRSLSPEKQQ------EILDELYSLFL 145 (415)
T ss_pred ccchHHHHHHhHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHhCCHHHHH------HHHHHHHHHHc
Confidence 12343333332 4444444322211111 25788888889999999999877762 37888887666
No 20
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=37.18 E-value=5.6e+02 Score=27.63 Aligned_cols=32 Identities=16% Similarity=0.135 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHhhCCHH--HHHHHHHHHHhc
Q psy15877 452 PESISAGFSLLIGLCTGSVP--NLKLLVAMLTDM 483 (517)
Q Consensus 452 ~~SR~AAfdLLveL~k~c~~--Nl~~Lle~L~em 483 (517)
...|..+...+..+....+. ....+.+.+..+
T Consensus 468 ~~vk~~ilt~~~Kl~~~~~~~~~~~~i~~~~~~~ 501 (526)
T PF01602_consen 468 PEVKLQILTALAKLFKRNPENEVQNEILQFLLSL 501 (526)
T ss_dssp HHHHHHHHHHHHHHHHHSCSTTHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHHHHhhCCchhhHHHHHHHHHHH
Confidence 36777777777777777663 334666665555
No 21
>KOG1059|consensus
Probab=36.64 E-value=7.1e+02 Score=29.84 Aligned_cols=32 Identities=22% Similarity=0.220 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHHHhccCC
Q psy15877 453 ESISAGFSLLIGLCTGSVPNLKLLVAMLTDMFYP 486 (517)
Q Consensus 453 ~SR~AAfdLLveL~k~c~~Nl~~Lle~L~emh~s 486 (517)
.-|..|.|||..+|.. +|++.|+..||.++..
T Consensus 351 SIRlrALdLl~gmVsk--kNl~eIVk~LM~~~~~ 382 (877)
T KOG1059|consen 351 SIRLRALDLLYGMVSK--KNLMEIVKTLMKHVEK 382 (877)
T ss_pred hhHHHHHHHHHHHhhh--hhHHHHHHHHHHHHHh
Confidence 6789999999999987 8999999999998543
No 22
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=35.07 E-value=1.7e+02 Score=26.76 Aligned_cols=64 Identities=14% Similarity=0.072 Sum_probs=45.5
Q ss_pred CCchhHHHHHHHHHHHHHHHHhCH-HHHHHHHcCcccchHHHHHHHHhcCCCChH-HHHHHHHHHHHHhc
Q psy15877 221 IDLDDILVCKEALELLTVCFLLNN-SLLKALLKEPKERLFAHFLCDTLLLCDEKI-IRACVQEQLTLSVT 288 (517)
Q Consensus 221 l~~eD~~V~~eALeLLv~cL~l~~-~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~-VR~~a~~~L~~Lc~ 288 (517)
+...+.-+...||.||-.|...|. .|...+... .|-+-++.++-..+... ||..+.+.+..-..
T Consensus 46 l~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~s~----~fl~~L~~l~~~~~~~~~Vk~kil~li~~W~~ 111 (133)
T smart00288 46 LNNKNPHVALLALTLLDACVKNCGSKFHLEVASK----EFLNELVKLIKPKYPLPLVKKRILELIQEWAD 111 (133)
T ss_pred HcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHhH----HHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHH
Confidence 445678889999999999999884 555555544 55556667765555544 89888888776654
No 23
>PF06371 Drf_GBD: Diaphanous GTPase-binding Domain; InterPro: IPR010473 Diaphanous-related formins (Drfs) are a family of formin homology (FH) proteins that act as effectors of Rho small GTPases during growth factor-induced cytoskeletal remodelling, stress fibre formation, and cell division []. Drf proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 (IPR003104 from INTERPRO) and FH3 (IPR010472 from INTERPRO), and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD. This entry represents the GBD, which is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [].; GO: 0003779 actin binding, 0017048 Rho GTPase binding, 0030036 actin cytoskeleton organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=32.75 E-value=1.8e+02 Score=27.08 Aligned_cols=61 Identities=20% Similarity=0.115 Sum_probs=45.7
Q ss_pred chhHHHHHHHHHHHHHHHHhCHHHHHHHHcCcccchHHHHHHHHhcCCCChHHHHHHHHHHHHHhc
Q psy15877 223 LDDILVCKEALELLTVCFLLNNSLLKALLKEPKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSVT 288 (517)
Q Consensus 223 ~eD~~V~~eALeLLv~cL~l~~~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~ 288 (517)
.+|..+.++.+..| -++.-+..-++.+... +..-..|... |.+++..+|..+.+.|-.+|.
T Consensus 127 ~~~~~~~~~~l~Cl-kal~n~~~G~~~v~~~---~~~v~~i~~~-L~s~~~~~r~~~leiL~~lc~ 187 (187)
T PF06371_consen 127 EEDIDIEHECLRCL-KALMNTKYGLEAVLSH---PDSVNLIALS-LDSPNIKTRKLALEILAALCL 187 (187)
T ss_dssp TTCHHHHHHHHHHH-HHHTSSHHHHHHHHCS---SSHHHHHHHT---TTSHHHHHHHHHHHHHHHT
T ss_pred chhHHHHHHHHHHH-HHHHccHHHHHHHHcC---cHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHC
Confidence 57788888888876 4555566667888887 6666666666 579999999999999988873
No 24
>PF14663 RasGEF_N_2: Rapamycin-insensitive companion of mTOR RasGEF_N domain
Probab=31.01 E-value=74 Score=28.50 Aligned_cols=34 Identities=18% Similarity=0.055 Sum_probs=27.7
Q ss_pred chHHHHHHHHh---cCCCChHHHHHHHHHHHHHhccc
Q psy15877 257 RLFAHFLCDTL---LLCDEKIIRACVQEQLTLSVTLS 290 (517)
Q Consensus 257 ~~~~~fL~dLL---L~sP~~~VR~~a~~~L~~Lc~~s 290 (517)
+.|++|.+++| |.||++.|+..|.+.|++.|...
T Consensus 3 ~~f~~w~i~lLv~QL~D~~~~V~~~A~~iL~e~c~~~ 39 (115)
T PF14663_consen 3 PDFEDWGIELLVTQLYDPSPEVVAAALEILEEACEDK 39 (115)
T ss_pred cHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhch
Confidence 45666666665 57999999999999999999873
No 25
>PF11707 Npa1: Ribosome 60S biogenesis N-terminal; InterPro: IPR021714 Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits []. The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre []. The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length.
Probab=29.91 E-value=5.1e+02 Score=27.16 Aligned_cols=78 Identities=18% Similarity=0.314 Sum_probs=47.9
Q ss_pred CcchHhhHHHHHHHHHhccCCcchhccCCccchHHHHHhccCCCChhhhHhhhhc--CCCCccCcCCCccCCHHHHHHHH
Q psy15877 382 RDILLQGHLSIVKELVCFLNSEKKMEFGVTNGLIRDLINDYLFPTSKLMLKLEKT--GEISFNEIAPAVCQSPESISAGF 459 (517)
Q Consensus 382 ~D~lL~GlLnL~k~Ll~~l~~~Kk~~iGs~~~LIkeLf~dfLFPas~~~~~~~~~--~e~~~~d~~~PkCKS~~SR~AAf 459 (517)
...+...-|+|+++++.+.+ | .++++++..|=|....+ .++... .+.. ......+=+ +..|.+..
T Consensus 69 ~~~~~~~~LrLL~~iv~f~~-------g---~~a~~v~~~fd~~~~~l-~kll~~~~~~~~-~~~~~~~~~-~siR~~fI 135 (330)
T PF11707_consen 69 KPSLTNPALRLLTAIVSFDG-------G---ALAREVLRSFDFSLKSL-PKLLTPRKKEKE-KDSESSKSK-PSIRTNFI 135 (330)
T ss_pred cHHHHHHHHHHHHHHHccCC-------H---HHHHHHHHhcCCchhhH-HHHhcccccccc-ccccccccC-cCHHHHHH
Confidence 34466699999999998741 1 28899998887765432 111111 0111 000122222 49999999
Q ss_pred HHHHHHhhCCHHH
Q psy15877 460 SLLIGLCTGSVPN 472 (517)
Q Consensus 460 dLLveL~k~c~~N 472 (517)
+.++.+.+....-
T Consensus 136 ~F~Lsfl~~~~~~ 148 (330)
T PF11707_consen 136 RFWLSFLSSGDPE 148 (330)
T ss_pred HHHHHHHccCCHH
Confidence 9999999977543
No 26
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=29.15 E-value=2.8e+02 Score=24.15 Aligned_cols=62 Identities=18% Similarity=0.102 Sum_probs=41.7
Q ss_pred CchhHHHHHHHHHHHHHHHHhC-HHHHHHHHcCcccchHHHHHH----HHhcCCCChHHHHHHHHHHHHH
Q psy15877 222 DLDDILVCKEALELLTVCFLLN-NSLLKALLKEPKERLFAHFLC----DTLLLCDEKIIRACVQEQLTLS 286 (517)
Q Consensus 222 ~~eD~~V~~eALeLLv~cL~l~-~~~l~sL~~~~~~~~~~~fL~----dLLL~sP~~~VR~~a~~~L~~L 286 (517)
...+.-++-.||.||-.|+..+ ..+...+... .....++. +..-......||..+.+.+...
T Consensus 47 ~~~~~~~~lkaL~lLe~lvkN~g~~f~~~i~~~---~~~~~l~~~~~~~~~~~~~~~~Vr~k~~~l~~~w 113 (115)
T cd00197 47 NNKNPHVVLKALTLLEYCVKNCGERFHQEVASN---DFAVELLKFDKSKLLGDDVSTNVREKAIELVQLW 113 (115)
T ss_pred cCCcHHHHHHHHHHHHHHHHHccHHHHHHHHHh---HHHHHHHHhhccccccCCCChHHHHHHHHHHHHH
Confidence 3348889999999999888887 4666666655 33333322 1223456889999988877654
No 27
>KOG2199|consensus
Probab=28.91 E-value=2.2e+02 Score=31.52 Aligned_cols=85 Identities=14% Similarity=0.134 Sum_probs=58.7
Q ss_pred CCCchhHHHHHHHHHHHHHHHHhCHH-HHHHHHcCcccchHHHHHHHHhcCCCChHHHHHHHHHHHHHhcccccccchhH
Q psy15877 220 DIDLDDILVCKEALELLTVCFLLNNS-LLKALLKEPKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSVTLSYAYASNAE 298 (517)
Q Consensus 220 ~l~~eD~~V~~eALeLLv~cL~l~~~-~l~sL~~~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~s~s~~~~~~ 298 (517)
-++..|.-|+--||.|+..|+..|.. |...+.. .+|..-+..|+=..-++.||..+...+...+.. +-
T Consensus 53 Rln~~dphV~L~AlTLlda~~~NCg~~~r~EVsS----r~F~~el~al~~~~~h~kV~~k~~~lv~eWsee---~K---- 121 (462)
T KOG2199|consen 53 RLNHKDPHVVLQALTLLDACVANCGKRFRLEVSS----RDFTTELRALIESKAHPKVCEKMRDLVKEWSEE---FK---- 121 (462)
T ss_pred HhcCCCcchHHHHHHHHHHHHHhcchHHHHHHhh----hhHHHHHHHHHhhcccHHHHHHHHHHHHHHHHH---hc----
Confidence 47778988999999999999999854 4444444 488888888864477788888776666655432 21
Q ss_pred HhHHHHHHHHHHhhhhh
Q psy15877 299 QACLVAFLQLLFPLLTS 315 (517)
Q Consensus 299 ~~pllffL~lLl~~L~~ 315 (517)
.-|.+.++..|.+.|..
T Consensus 122 ~Dp~lsLi~~l~~klk~ 138 (462)
T KOG2199|consen 122 KDPSLSLISALYKKLKE 138 (462)
T ss_pred cCcchhHHHHHHHHHHH
Confidence 22445566777666543
No 28
>PF11864 DUF3384: Domain of unknown function (DUF3384); InterPro: IPR024584 This entry represents the N-terminal domain of tuberin which is functionally uncharacterised.
Probab=28.60 E-value=5.6e+02 Score=28.23 Aligned_cols=121 Identities=12% Similarity=-0.007 Sum_probs=68.8
Q ss_pred HHHHHHhcCCCChHHHHHHHHHHHHHhcccccccchhHHhHHHHHHHHHHhhhhhhhhhccCCCCCHHHHHHHHHHhhhh
Q psy15877 261 HFLCDTLLLCDEKIIRACVQEQLTLSVTLSYAYASNAEQACLVAFLQLLFPLLTSDALETRVYTKSAEYFQLFCRTLNFV 340 (517)
Q Consensus 261 ~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~s~s~~~~~~~~pllffL~lLl~~L~~~a~e~~~~~~C~EYF~LLCrLLd~l 340 (517)
...+||+-....+.+|+.+.+.+..+++....- ... .| ..||- .+ . .+...+.|.+....|..+
T Consensus 31 ~~~~DLi~~~~p~e~R~~~~~ll~~~i~~~~~~-~~~-~R-~~fF~-~I---------~---~~~~~~d~~~~l~aL~~L 94 (464)
T PF11864_consen 31 YAAKDLIDPNQPSEARRAALELLIACIKRQDSS-SGL-MR-AEFFR-DI---------S---DPSNDDDFDLRLEALIAL 94 (464)
T ss_pred HHHhhhcCCCCCHHHHHHHHHHHHHHHHccccc-cHH-HH-HHHHH-HH---------h---cCCCchhHHHHHHHHHHH
Confidence 345678766666889999999988888763210 110 11 22332 21 1 346677788888888888
Q ss_pred ccccccccCCCcccccCHHHHHHHHHHHHh----cccc-------cc-c--cCCC-CcchHhhHHHHHHHHHhccC
Q psy15877 341 SSSVWIGAGSVLSTGIDVEKYLTQELAVLK----RLSV-------GA-K--KSGQ-RDILLQGHLSIVKELVCFLN 401 (517)
Q Consensus 341 ~~s~~~~~gs~~~~~iDie~LL~qeI~~L~----~~~~-------~e-~--~t~e-~D~lL~GlLnL~k~Ll~~l~ 401 (517)
..... .+ .....++..++.+++.-+. ..+. .. . ..-+ ++..+..+|.++..++++..
T Consensus 95 T~~Gr-di---~~~~~~i~~~L~~wl~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~l~nviKfn~ 166 (464)
T PF11864_consen 95 TDNGR-DI---DFFEYEIGPFLLSWLEPSYQAARSARRKAKKSSSSKSKGLSNLDNEESNLSDLLQFLVNVIKFNF 166 (464)
T ss_pred HcCCc-Cc---hhcccchHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccchhhhHHHHHHHHHHHHhcCC
Confidence 75433 11 1123344445444443222 0000 00 0 0101 78889999999999999864
No 29
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=27.39 E-value=9e+02 Score=26.96 Aligned_cols=32 Identities=19% Similarity=0.124 Sum_probs=27.4
Q ss_pred chHHHHHHHHhcCCCChHHHHHHHHHHHHHhcc
Q psy15877 257 RLFAHFLCDTLLLCDEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 257 ~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~ 289 (517)
+....++...| ..|++.||+.++++|.++...
T Consensus 76 ~~~~~~L~~gL-~h~~~~Vr~l~l~~l~~~~~~ 107 (503)
T PF10508_consen 76 PQYQPFLQRGL-THPSPKVRRLALKQLGRIARH 107 (503)
T ss_pred HHHHHHHHHHh-cCCCHHHHHHHHHHHHHHhcC
Confidence 57788888884 789999999999999988755
No 30
>PF14222 MOR2-PAG1_N: Cell morphogenesis N-terminal
Probab=27.21 E-value=4.6e+02 Score=29.93 Aligned_cols=148 Identities=16% Similarity=0.135 Sum_probs=80.6
Q ss_pred hHHHHHHHHhcCC-CChHHHHHHHHHHHHHhcccccccchhHHhHHHH-HHHHHHhhhhhhhhhccCCCCCHHHHHHHHH
Q psy15877 258 LFAHFLCDTLLLC-DEKIIRACVQEQLTLSVTLSYAYASNAEQACLVA-FLQLLFPLLTSDALETRVYTKSAEYFQLFCR 335 (517)
Q Consensus 258 ~~~~fL~dLLL~s-P~~~VR~~a~~~L~~Lc~~s~s~~~~~~~~pllf-fL~lLl~~L~~~a~e~~~~~~C~EYF~LLCr 335 (517)
+|-+=+.++...+ .+..|++..|+.|-.|-..=......+.+.|.+. ++..|...+.....+ +.+..--|-|.+-
T Consensus 129 ~Fm~~l~~~f~~~h~~~~ik~A~~~~l~~lLlPvA~~~~~evn~P~W~~~v~~i~~~~~~~~~K---~khw~~afPL~t~ 205 (552)
T PF14222_consen 129 EFMQSLAKFFLEAHKKSDIKHAYCEVLVELLLPVAATATAEVNHPKWKEAVETIYPRAAKMMSK---PKHWNVAFPLVTT 205 (552)
T ss_pred HHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHHHhhcccccccccHHHHHHHHHHHHHHHHHhC---cchhhhHHHHHHH
Confidence 3344444555777 6777999999999888653001111223567433 555555443333322 5666667999999
Q ss_pred HhhhhccccccccCCCcccccCHHHHHHHHH-HHHhccccccccCCCCcchHhhHHHHHHHHHhccCCcchhccCCccch
Q psy15877 336 TLNFVSSSVWIGAGSVLSTGIDVEKYLTQEL-AVLKRLSVGAKKSGQRDILLQGHLSIVKELVCFLNSEKKMEFGVTNGL 414 (517)
Q Consensus 336 LLd~l~~s~~~~~gs~~~~~iDie~LL~qeI-~~L~~~~~~e~~t~e~D~lL~GlLnL~k~Ll~~l~~~Kk~~iGs~~~L 414 (517)
||+-.. -+-.++++. +.+......-++....-..|.|+.+|+-.=+.+...+..... ..=
T Consensus 206 lLCvS~----------------~e~F~~~W~~~~i~~~~~klKdk~~r~~~l~~l~RLlWvYL~~r~~Es~n~T---~kr 266 (552)
T PF14222_consen 206 LLCVSP----------------KEFFLSNWLPSLIESLISKLKDKETRPVALECLSRLLWVYLVYRCPESLNNT---TKR 266 (552)
T ss_pred HHhcCc----------------HHHHHHHHHHHHHHHHHhhcCChhhhHHHHHHHHHHHHHHHhcccCCCchHH---HHH
Confidence 985432 233455555 344332222122222567899999997666633222221000 024
Q ss_pred HHHHHhccCCCChh
Q psy15877 415 IRDLINDYLFPTSK 428 (517)
Q Consensus 415 IkeLf~dfLFPas~ 428 (517)
+.+++ +.|||..+
T Consensus 267 L~~i~-~~lfp~~k 279 (552)
T PF14222_consen 267 LDSIF-KLLFPKGK 279 (552)
T ss_pred HHHHH-HHHccCCC
Confidence 56666 58887754
No 31
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=26.55 E-value=89 Score=25.05 Aligned_cols=28 Identities=14% Similarity=0.094 Sum_probs=21.0
Q ss_pred hHHHHHHHHhcCCCChHHHHHHHHHHHHH
Q psy15877 258 LFAHFLCDTLLLCDEKIIRACVQEQLTLS 286 (517)
Q Consensus 258 ~~~~fL~dLLL~sP~~~VR~~a~~~L~~L 286 (517)
.....+..++ .++++.||+.++..|-.+
T Consensus 31 ~~~~~L~~~l-~d~~~~vr~~a~~aL~~i 58 (88)
T PF13646_consen 31 EAIPALIELL-KDEDPMVRRAAARALGRI 58 (88)
T ss_dssp HHHHHHHHHH-TSSSHHHHHHHHHHHHCC
T ss_pred hHHHHHHHHH-cCCCHHHHHHHHHHHHHh
Confidence 4455555654 889999999999888766
No 32
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=25.83 E-value=3.3e+02 Score=30.37 Aligned_cols=65 Identities=22% Similarity=0.153 Sum_probs=50.6
Q ss_pred CCCchhHHHHHHHHHHHHHHHHhCHHHHHHHHcCcccchHHHHHHHHhcCCCChHHHHHHHHHHHHHhccc
Q psy15877 220 DIDLDDILVCKEALELLTVCFLLNNSLLKALLKEPKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSVTLS 290 (517)
Q Consensus 220 ~l~~eD~~V~~eALeLLv~cL~l~~~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~s 290 (517)
-+..+|..|.+.|+.+|. .+..++..++.++.. ....-|.+++ ..++..||.++.+.+..++..+
T Consensus 127 ~L~~~d~~Va~~A~~~L~-~l~~~~~~~~~l~~~----~~~~~L~~l~-~~~~~~vR~Rv~el~v~i~~~S 191 (503)
T PF10508_consen 127 CLRDPDLSVAKAAIKALK-KLASHPEGLEQLFDS----NLLSKLKSLM-SQSSDIVRCRVYELLVEIASHS 191 (503)
T ss_pred HHcCCcHHHHHHHHHHHH-HHhCCchhHHHHhCc----chHHHHHHHH-hccCHHHHHHHHHHHHHHHhcC
Confidence 366789999999999974 676777788888877 3355555664 6678999999999999998763
No 33
>cd00870 PI3Ka_III Phosphoinositide 3-kinase (PI3K) class III, accessory domain (PIK domain); PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, PI3Ks class III phosphorylate phosphoinositol (PtdIns) only. The prototypical PI3K class III, yeast Vps34, is involved in trafficking proteins from Golgi to the vacuole.
Probab=25.33 E-value=94 Score=29.83 Aligned_cols=17 Identities=18% Similarity=0.370 Sum_probs=14.0
Q ss_pred CChHHHHHHHHHHHHHh
Q psy15877 271 DEKIIRACVQEQLTLSV 287 (517)
Q Consensus 271 P~~~VR~~a~~~L~~Lc 287 (517)
+++.||+.|.+.|..+.
T Consensus 90 ~~~~VR~yAV~~L~~~s 106 (166)
T cd00870 90 TNPVVRKYAVSRLKLAS 106 (166)
T ss_pred CCHHHHHHHHHHHHhCC
Confidence 56899999999988753
No 34
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=24.75 E-value=30 Score=40.74 Aligned_cols=23 Identities=17% Similarity=0.362 Sum_probs=18.1
Q ss_pred CCCcccCCCCCCCCCCcccccCC
Q psy15877 493 TEWDYLPPIGPKPPKGFVWPKSK 515 (517)
Q Consensus 493 ~eWdYlP~~~~RS~cGYVGLKNa 515 (517)
.-|.-.-..+.|-..|||||||+
T Consensus 177 VLWHsF~nYnSKkeTGYVGlrNq 199 (1089)
T COG5077 177 VLWHSFLNYNSKKETGYVGLRNQ 199 (1089)
T ss_pred ceeecccccccccceeeeeeccC
Confidence 34765555788889999999997
No 35
>KOG4199|consensus
Probab=23.93 E-value=3.2e+02 Score=29.96 Aligned_cols=65 Identities=14% Similarity=0.096 Sum_probs=42.6
Q ss_pred CchhHHHHHHHHHHHHHHHHhC-HHHHHHHHcCcccchHHHHHHHHhcCCCC-hHHHHHHHHHHHHHhcccc
Q psy15877 222 DLDDILVCKEALELLTVCFLLN-NSLLKALLKEPKERLFAHFLCDTLLLCDE-KIIRACVQEQLTLSVTLSY 291 (517)
Q Consensus 222 ~~eD~~V~~eALeLLv~cL~l~-~~~l~sL~~~~~~~~~~~fL~dLLL~sP~-~~VR~~a~~~L~~Lc~~s~ 291 (517)
.++|.+||+++|..+. .+.++ |+--..++.- ...+....-+=.-|. ..|.|.+|++|..|+.++.
T Consensus 340 h~~~p~Vi~~~~a~i~-~l~LR~pdhsa~~ie~----G~a~~avqAmkahP~~a~vQrnac~~IRNiv~rs~ 406 (461)
T KOG4199|consen 340 HSDDPLVIQEVMAIIS-ILCLRSPDHSAKAIEA----GAADLAVQAMKAHPVAAQVQRNACNMIRNIVVRSA 406 (461)
T ss_pred cCCChHHHHHHHHHHH-HHHhcCcchHHHHHhc----chHHHHHHHHHhCcHHHHHHHHHHHHHHHHHHhhh
Confidence 4678999999998863 44444 4444444443 333344444434444 5699999999999998753
No 36
>smart00185 ARM Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
Probab=23.06 E-value=2.3e+02 Score=19.25 Aligned_cols=24 Identities=13% Similarity=0.055 Sum_probs=19.5
Q ss_pred HHHHhcCCCChHHHHHHHHHHHHHh
Q psy15877 263 LCDTLLLCDEKIIRACVQEQLTLSV 287 (517)
Q Consensus 263 L~dLLL~sP~~~VR~~a~~~L~~Lc 287 (517)
+..+ |.++++.|++.++..|+.|+
T Consensus 17 L~~l-l~~~~~~i~~~a~~aL~nl~ 40 (41)
T smart00185 17 LVEL-LKSEDEEVVKEAAWALSNLS 40 (41)
T ss_pred HHHH-HcCCCHHHHHHHHHHHHHHc
Confidence 3445 56889999999999999886
No 37
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=22.91 E-value=3.2e+02 Score=28.18 Aligned_cols=65 Identities=17% Similarity=0.102 Sum_probs=44.2
Q ss_pred chhHHHHHHHHHHHHHHHHhCHHHHHHHHcC---cccchHHHHHHHHhcCCCChHHHHHHHHHHHHHhcc
Q psy15877 223 LDDILVCKEALELLTVCFLLNNSLLKALLKE---PKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 223 ~eD~~V~~eALeLLv~cL~l~~~~l~sL~~~---~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~ 289 (517)
..+..+++|.+.++.-.+.-++...+.|... ++..-|..|+. +|..++..|+..++..+-.+...
T Consensus 68 ~~~~d~v~yvL~li~dll~~~~~~~~~~~~~~~~~~~~~~~~fl~--ll~~~D~~i~~~a~~iLt~Ll~~ 135 (312)
T PF03224_consen 68 SSNDDTVQYVLTLIDDLLSDDPSRVELFLELAKQDDSDPYSPFLK--LLDRNDSFIQLKAAFILTSLLSQ 135 (312)
T ss_dssp ---HHHHHHHHHHHHHHHH-SSSSHHHHHHHHH-TTH--HHHHHH--H-S-SSHHHHHHHHHHHHHHHTS
T ss_pred cCcHHHHHHHHHHHHHHHhcCHHHHHHHHHhcccccchhHHHHHH--HhcCCCHHHHHHHHHHHHHHHHc
Confidence 3678899999999988777765555544442 22236888887 67999999999999999888765
No 38
>KOG1848|consensus
Probab=22.05 E-value=8.9e+02 Score=31.12 Aligned_cols=126 Identities=17% Similarity=0.040 Sum_probs=64.9
Q ss_pred HHHhcCCCChHHHHHHHHHHHHHhcccccccchhHHhHHHHHHHHHHhhhhhhh-------hhccCCCCCHHHHHHHHHH
Q psy15877 264 CDTLLLCDEKIIRACVQEQLTLSVTLSYAYASNAEQACLVAFLQLLFPLLTSDA-------LETRVYTKSAEYFQLFCRT 336 (517)
Q Consensus 264 ~dLLL~sP~~~VR~~a~~~L~~Lc~~s~s~~~~~~~~pllffL~lLl~~L~~~a-------~e~~~~~~C~EYF~LLCrL 336 (517)
.++ -++-+.+||.-|+..|++|......+-+. ..=..-+|.++++.|.... ..+-..++=+|+|.|.-.=
T Consensus 1003 ~~~-~~dsr~eVRngAvqtlfri~~Shg~~l~~--~aW~s~~w~vi~pLLd~~~~q~~~ewngkeiqkqwtet~~ltisg 1079 (1610)
T KOG1848|consen 1003 ADL-CEDSRAEVRNGAVQTLFRIFNSHGSKLGT--NAWASCCWLVIMPLLDSQPIQNVSEWNGKEIQKQWTETSCLTISG 1079 (1610)
T ss_pred HHH-hccchHHHhhhHHHHHHHHHhhhcccCCh--hHHHHHHHHHHHHHhccccccchhhhcchhHhhhhhhhhhhhHHH
Confidence 344 37888999999999999998653222111 0012347888888776321 1111246667777776554
Q ss_pred hhhhccccccccCCCcccccCHHHHHHHHHHHHhccccccccCCCCcchHhhHHHHHHHHHhcc
Q psy15877 337 LNFVSSSVWIGAGSVLSTGIDVEKYLTQELAVLKRLSVGAKKSGQRDILLQGHLSIVKELVCFL 400 (517)
Q Consensus 337 Ld~l~~s~~~~~gs~~~~~iDie~LL~qeI~~L~~~~~~e~~t~e~D~lL~GlLnL~k~Ll~~l 400 (517)
+-.++.++.+..-. .....+..+.+-+-++|+..... ...-+....++=+.|+.+.
T Consensus 1080 Iaklf~e~fk~lln-ln~f~~vwe~ll~flkrl~s~~s-------~e~slsai~~~qell~sii 1135 (1610)
T KOG1848|consen 1080 IAKLFSENFKLLLN-LNGFLDVWEELLQFLKRLHSDIS-------PEISLSAIKALQELLFSII 1135 (1610)
T ss_pred HHHHHHHHHHHHHh-cccHHHHHHHHHHHHHHHHhcCC-------hHhHHHHHHHHHHHHHHHh
Confidence 44444333211000 00122344455555666655433 3334555555544444443
No 39
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=21.78 E-value=2.1e+02 Score=27.51 Aligned_cols=59 Identities=22% Similarity=0.163 Sum_probs=35.3
Q ss_pred hHHHHHHHHHHHHHHHHhCHHHHHHHHcCcccchHHHHHHHHhcCCCChHHHHHHHHHHHHHhcc
Q psy15877 225 DILVCKEALELLTVCFLLNNSLLKALLKEPKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 225 D~~V~~eALeLLv~cL~l~~~~l~sL~~~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~ 289 (517)
=..|+++|+.++......-..-++.+... .++.++ +. +.+....||..+.+.|..|+..
T Consensus 66 Rs~v~~~A~~~l~~l~~~l~~~~~~~~~~----~l~~Ll-~~-~~~~~~~i~~~a~~~L~~i~~~ 124 (228)
T PF12348_consen 66 RSKVSKTACQLLSDLARQLGSHFEPYADI----LLPPLL-KK-LGDSKKFIREAANNALDAIIES 124 (228)
T ss_dssp ---HHHHHHHHHHHHHHHHGGGGHHHHHH----HHHHHH-HG-GG---HHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHhHhHHHHHHH----HHHHHH-HH-HccccHHHHHHHHHHHHHHHHH
Confidence 35689999988766555533334444322 333333 22 4777889999999999999876
No 40
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=21.33 E-value=8.9e+02 Score=24.75 Aligned_cols=65 Identities=18% Similarity=0.107 Sum_probs=44.6
Q ss_pred hhHHHHHHHHHHHHHHHHhC-HHHHHHHHc---CcccchHHHHHHHHhcCCCChHHHHHHHHHHHHHhcc
Q psy15877 224 DDILVCKEALELLTVCFLLN-NSLLKALLK---EPKERLFAHFLCDTLLLCDEKIIRACVQEQLTLSVTL 289 (517)
Q Consensus 224 eD~~V~~eALeLLv~cL~l~-~~~l~sL~~---~~~~~~~~~fL~dLLL~sP~~~VR~~a~~~L~~Lc~~ 289 (517)
+|..|.-.|+..+...+... .+..+.... ......+.+++.+.| .+-++.||..++++|-++...
T Consensus 76 ~~~~v~~~al~~l~Dll~~~g~~~~~~~~~~~~~~~~~~l~~~l~~~l-~~~~~~~~~~a~EGl~KLlL~ 144 (298)
T PF12719_consen 76 DDEEVKITALKALFDLLLTHGIDIFDSESDNDESVDSKSLLKILTKFL-DSENPELQAIAVEGLCKLLLS 144 (298)
T ss_pred CCHHHHHHHHHHHHHHHHHcCchhccchhccCccchHhHHHHHHHHHH-hcCCHHHHHHHHHHHHHHHhc
Confidence 46667777888877766664 344444443 111246777777775 555999999999999998765
No 41
>PF12825 DUF3818: Domain of unknown function in PX-proteins (DUF3818); InterPro: IPR024554 The function of this domain is not known, but it is almost always found C-terminal to a PX-domain (IPR001683 from INTERPRO).
Probab=21.30 E-value=8.6e+02 Score=26.12 Aligned_cols=46 Identities=15% Similarity=0.172 Sum_probs=37.6
Q ss_pred CCCCchhHHHHHHHHHHHHHHHHhC-HHHHHHHHcCcccchHHHHHHHHh
Q psy15877 219 KDIDLDDILVCKEALELLTVCFLLN-NSLLKALLKEPKERLFAHFLCDTL 267 (517)
Q Consensus 219 ~~l~~eD~~V~~eALeLLv~cL~l~-~~~l~sL~~~~~~~~~~~fL~dLL 267 (517)
...+.+|+.......+++..++..+ .+.+..++.. +.+.++|++++
T Consensus 198 ~~~~~~~a~lf~~lk~yl~l~~r~RDk~~~~~l~~e---~~~~qllkd~v 244 (341)
T PF12825_consen 198 DGEENEDAWLFSDLKEYLKLYLRKRDKEQMIQLWCE---PELTQLLKDLV 244 (341)
T ss_pred CCccchhhHHHHHHHHHHHHHHHHhhHHHHHHHHcC---hhHHHHHHHHH
Confidence 4466788999999999988887776 6778888888 78899988876
No 42
>PTZ00429 beta-adaptin; Provisional
Probab=20.73 E-value=1.5e+03 Score=27.07 Aligned_cols=29 Identities=17% Similarity=0.107 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHHHhc
Q psy15877 453 ESISAGFSLLIGLCTGSVPNLKLLVAMLTDM 483 (517)
Q Consensus 453 ~SR~AAfdLLveL~k~c~~Nl~~Lle~L~em 483 (517)
.-|....++|+.||.. +|...|++.|.+.
T Consensus 348 yIK~~KLeIL~~Lane--~Nv~~IL~EL~eY 376 (746)
T PTZ00429 348 FVKLEKLRLLLKLVTP--SVAPEILKELAEY 376 (746)
T ss_pred HHHHHHHHHHHHHcCc--ccHHHHHHHHHHH
Confidence 4578888899988855 7888888877764
No 43
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=20.31 E-value=4.6e+02 Score=24.43 Aligned_cols=64 Identities=16% Similarity=0.106 Sum_probs=45.7
Q ss_pred CCchhHHHHHHHHHHHHHHHHhC-HHHHHHHHcCcccchHHHHHHHHhcC-----CCChHHHHHHHHHHHHHhc
Q psy15877 221 IDLDDILVCKEALELLTVCFLLN-NSLLKALLKEPKERLFAHFLCDTLLL-----CDEKIIRACVQEQLTLSVT 288 (517)
Q Consensus 221 l~~eD~~V~~eALeLLv~cL~l~-~~~l~sL~~~~~~~~~~~fL~dLLL~-----sP~~~VR~~a~~~L~~Lc~ 288 (517)
+...+.-+.-.||.||-.|..-| ..|...+... +.+.. +++++-. .+.+.||.++.+.|..-..
T Consensus 47 l~~~n~~v~l~AL~LLe~~vkNCG~~fh~evas~---~Fl~e-l~kl~~~k~~~~~~~~~Vk~kil~li~~W~~ 116 (139)
T cd03567 47 IQSPQEKEALQALTVLEACMKNCGERFHSEVGKF---RFLNE-LIKLVSPKYLGSRTSEKVKTKIIELLYSWTL 116 (139)
T ss_pred HcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHHhH---HHHHH-HHHHhccccCCCCCCHHHHHHHHHHHHHHHH
Confidence 44566778899999999999988 5677777766 45555 4455521 2568899998888776653
Done!