Query psy9200
Match_columns 120
No_of_seqs 105 out of 139
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 21:28:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9200.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9200hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01207 Ena-Vasp Enabled-VASP- 100.0 3.4E-37 7.5E-42 224.2 10.4 81 34-120 1-82 (111)
2 cd01206 Homer Homer type EVH1 100.0 3.6E-37 7.8E-42 224.6 9.0 79 32-120 1-80 (111)
3 KOG4590|consensus 99.9 6.9E-27 1.5E-31 199.9 4.3 70 45-120 1-72 (409)
4 smart00461 WH1 WASP homology r 99.9 4.7E-25 1E-29 156.8 10.7 81 32-120 1-81 (106)
5 cd00837 EVH1 EVH1 (Enabled, Va 99.9 9.7E-25 2.1E-29 154.3 11.4 79 34-120 1-79 (104)
6 PF00568 WH1: WH1 domain; Int 99.9 1.6E-21 3.5E-26 138.6 11.3 79 33-120 7-86 (111)
7 cd00835 RanBD Ran-binding doma 99.1 2.2E-09 4.7E-14 77.1 10.3 76 33-118 9-86 (122)
8 smart00160 RanBD Ran-binding d 99.1 1.9E-09 4.2E-14 79.1 9.9 75 32-116 17-92 (130)
9 PF00638 Ran_BP1: RanBP1 domai 98.4 4.5E-06 9.7E-11 59.2 9.3 69 33-111 8-76 (122)
10 cd01205 WASP WASP-type EVH1 do 95.4 0.23 4.9E-06 36.1 8.9 74 35-118 5-78 (105)
11 PF01344 Kelch_1: Kelch motif; 58.0 13 0.00027 21.3 2.5 18 41-58 27-44 (47)
12 COG5171 YRB1 Ran GTPase-activa 52.4 4.4 9.6E-05 32.8 -0.1 63 34-106 89-151 (211)
13 PF13964 Kelch_6: Kelch motif 48.2 19 0.00042 21.1 2.3 22 38-59 24-45 (50)
14 smart00612 Kelch Kelch domain. 43.2 22 0.00047 19.5 1.9 18 41-58 14-31 (47)
15 cd01716 Hfq Hfq, an abundant, 40.9 34 0.00074 22.7 2.8 36 75-115 20-56 (61)
16 TIGR01640 F_box_assoc_1 F-box 40.5 64 0.0014 24.4 4.6 42 42-83 14-61 (230)
17 PF06058 DCP1: Dcp1-like decap 38.2 43 0.00092 24.5 3.2 60 38-109 25-86 (122)
18 PF04939 RRS1: Ribosome biogen 34.0 12 0.00026 29.1 -0.2 26 34-59 89-114 (164)
19 PRK00395 hfq RNA-binding prote 33.0 53 0.0011 23.0 2.8 36 75-115 28-64 (79)
20 KOG3671|consensus 32.5 68 0.0015 29.7 4.1 56 52-118 55-112 (569)
21 TIGR02383 Hfq RNA chaperone Hf 31.5 62 0.0013 21.5 2.8 35 75-114 24-59 (61)
22 KOG0864|consensus 31.3 15 0.00033 29.1 -0.1 69 33-110 55-124 (215)
23 KOG1708|consensus 30.5 87 0.0019 26.0 4.1 36 31-68 127-167 (236)
24 PF07443 HARP: HepA-related pr 30.0 18 0.0004 23.6 0.1 10 46-55 22-31 (55)
25 PF08553 VID27: VID27 cytoplas 29.1 3.8E+02 0.0082 25.9 8.5 59 35-106 248-307 (794)
26 COG5225 RRS1 Uncharacterized p 29.1 32 0.00069 27.1 1.3 19 41-59 107-125 (172)
27 KOG1690|consensus 26.0 3.1E+02 0.0068 22.6 6.5 61 20-84 26-86 (215)
28 KOG1765|consensus 23.7 34 0.00074 27.4 0.6 15 45-59 112-126 (181)
29 cd01735 LSm12_N LSm12 belongs 22.3 2.4E+02 0.0052 18.6 4.5 31 40-70 19-53 (61)
30 PF13418 Kelch_4: Galactose ox 21.6 1.1E+02 0.0025 17.5 2.5 20 39-58 26-45 (49)
31 PRK14091 RNA-binding protein H 21.5 1E+02 0.0022 24.3 2.9 36 75-115 33-69 (165)
No 1
>cd01207 Ena-Vasp Enabled-VASP-type homology (EVH1) domain. Enabled-VASP-type homology (EVH1) domain. The EVH1 domain binds to other proteins at proline rich sequences. It is found in proteins involved in cytoskeletal reorganization such as Enabled and VASP. Ena-VASP type EVH1 domains specifically recognize FPPPP motifs in the focal adhesion proteins zyxin and vinculin, and the ActA surface protein of Listeria monocytogenes. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=100.00 E-value=3.4e-37 Score=224.18 Aligned_cols=81 Identities=53% Similarity=0.854 Sum_probs=78.5
Q ss_pred ccceEEEEEEEEEEeCCCCCeEECCC-CCCeEEEEEEEeCCCCceEEEEeeeccccccccceEEEeeecCCCCeeeeecC
Q psy9200 34 EQSIASARASVMIYDDVNKKWIPSGS-SSGLSKVHVFQHQVNNTFRVVGRKLQNQEYKADYTVSINIPNKKGSNMNITIT 112 (120)
Q Consensus 34 E~~I~~vrA~VM~yDd~tk~WvP~gg-~~glS~V~i~~~~~~n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~Ynkatp 112 (120)
|++||++||+||+|||++|+|+|+|| ++|+|+|+||+++.+|+|||||+|++|+ +++|||.|+++|+||+++|
T Consensus 1 e~~i~~~rA~Vm~~d~~tk~W~P~~~~~~~ls~V~~~~~~~~~~yrIvg~~~~~~------~~v~e~~l~~~l~y~k~~p 74 (111)
T cd01207 1 EQSICQARASVMVYDDSNKKWVPAGGGSQGFSRVQIYHHPRNNTFRVVGRKLQDH------QVVINCAIVKGLKYNQATP 74 (111)
T ss_pred CCceEEEEEEeeEEcCCCCcEEcCCCCCCCcceEEEEEcCCCCEEEEEEeecCCC------cEEEEEEecCCceeeecCC
Confidence 89999999999999999999999997 5699999999999999999999999999 9999999999999999999
Q ss_pred cceeeccC
Q psy9200 113 SYHYSKSK 120 (120)
Q Consensus 113 tFHqWrD~ 120 (120)
+||||+|.
T Consensus 75 ~Fh~w~~~ 82 (111)
T cd01207 75 TFHQWRDA 82 (111)
T ss_pred cceeeecC
Confidence 99999984
No 2
>cd01206 Homer Homer type EVH1 domain. Homer type EVH1 domain. Homer is a synaptic scaffolding protein, involved in neuronal signaling. It contains an EVH1 domain, which binds to both neurotransmitter receptors, such as the metabotropic glutamate receptor (mGluR) and to other scaffolding proteins via PPXXF motifs, in order to target them to the synaptic junction. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=100.00 E-value=3.6e-37 Score=224.63 Aligned_cols=79 Identities=24% Similarity=0.320 Sum_probs=74.1
Q ss_pred ccccceEEEEEEEEEEeCCCC-CeEECCCCCCeEEEEEEEeCCCCceEEEEeeeccccccccceEEEeeecCCCCeeeee
Q psy9200 32 ATEQSIASARASVMIYDDVNK-KWIPSGSSSGLSKVHVFQHQVNNTFRVVGRKLQNQEYKADYTVSINIPNKKGSNMNIT 110 (120)
Q Consensus 32 ~~E~~I~~vrA~VM~yDd~tk-~WvP~gg~~glS~V~i~~~~~~n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~Ynka 110 (120)
|+|+|||++||+||+|||.|| +|+|+|+ ++++|++|||+++|+|||||++ |. +|||||+|.++|+|+||
T Consensus 1 m~E~~I~~arA~V~~yd~~tKk~WvPs~~--~~~~V~~y~~~~~ntfRIi~~~--~~------~~iINc~i~~~~~y~ka 70 (111)
T cd01206 1 MGEQPIFSTRAHVFQIDPKTKKNWIPASK--HAVTVSYFYDSTRNVYRIISVG--GT------KAIINSTITPNMTFTKT 70 (111)
T ss_pred CCccccceeeeEEEEECCCCcceeEeCCC--CceeEEEEecCCCcEEEEEEec--Cc------EEEEeccccCCcceeec
Confidence 899999999999999999997 6999997 5789999999999999999973 44 99999999999999999
Q ss_pred cCcceeeccC
Q psy9200 111 ITSYHYSKSK 120 (120)
Q Consensus 111 tptFHqWrD~ 120 (120)
+|+||||||.
T Consensus 71 s~~FhQWrD~ 80 (111)
T cd01206 71 SQKFGQWADS 80 (111)
T ss_pred cccccccccc
Confidence 9999999995
No 3
>KOG4590|consensus
Probab=99.93 E-value=6.9e-27 Score=199.89 Aligned_cols=70 Identities=43% Similarity=0.722 Sum_probs=67.4
Q ss_pred EEEeCCCCCeEECC-CCCCeEEEEEEEeCCCCceEEEEeeecc-ccccccceEEEeeecCCCCeeeeecCcceeeccC
Q psy9200 45 MIYDDVNKKWIPSG-SSSGLSKVHVFQHQVNNTFRVVGRKLQN-QEYKADYTVSINIPNKKGSNMNITITSYHYSKSK 120 (120)
Q Consensus 45 M~yDd~tk~WvP~g-g~~glS~V~i~~~~~~n~fRIvG~rlqD-~~~~~~~~VvINc~I~~~l~YnkatptFHqWrD~ 120 (120)
|+|||++|+|+|++ |..|+|+|++|+|..+|+|||||+++|| + +|||||.|.+||+|||||||||||||.
T Consensus 1 M~ydd~~k~W~p~g~g~~~~s~V~~~~h~~~n~frVvg~k~qdd~------~vVlnC~I~kGlkYnkatptFHqWR~a 72 (409)
T KOG4590|consen 1 MTYDDSQKGWLPAGGGGAALSKVRIYHHTSGNTFRVVGRKSQDDQ------QVVLNCLILKGLKYNKATPTFHQWRDA 72 (409)
T ss_pred CcccccccccccccccCcccceeEEEeeccCCceeEEeeecccCc------ccccccccccCcceeecccchhhhhhh
Confidence 89999999999999 5789999999999999999999999997 8 999999999999999999999999983
No 4
>smart00461 WH1 WASP homology region 1. Region of the Wiskott-Aldrich syndrome protein (WASp) that contains point mutations in the majority of patients with WAS. Unknown function. Ena-like WH1 domains bind polyproline-containing peptides, and that Homer contains a WH1 domain.
Probab=99.92 E-value=4.7e-25 Score=156.77 Aligned_cols=81 Identities=32% Similarity=0.441 Sum_probs=76.5
Q ss_pred ccccceEEEEEEEEEEeCCCCCeEECCCCCCeEEEEEEEeCCCCceEEEEeeeccccccccceEEEeeecCCCCeeeeec
Q psy9200 32 ATEQSIASARASVMIYDDVNKKWIPSGSSSGLSKVHVFQHQVNNTFRVVGRKLQNQEYKADYTVSINIPNKKGSNMNITI 111 (120)
Q Consensus 32 ~~E~~I~~vrA~VM~yDd~tk~WvP~gg~~glS~V~i~~~~~~n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~Ynkat 111 (120)
|+|++++.++|+||+||+.+++|+|.++ +|++.|.+++++.++.|||++++.+|+ |++||.|.++|+||+++
T Consensus 1 ~~~~~~~~~~avV~~y~~~~~~W~~~~~-gg~~~~~~~~~~~~~~~ri~~~~~~~~-------vv~e~ely~~~~y~~~~ 72 (106)
T smart00461 1 LGSQCIILARAVVQLYDADTKKWVPTGE-GGAANLVIDKNQRSYFFRIVGIKGQDK-------VIWNQELYKNFKYNQAT 72 (106)
T ss_pred CCCCCEEEEEEEEEEEeCCCCCeEECCC-CCEEEEEEEecCCeEEEEEEEecCCCe-------EEEEEeccCCCEEeecC
Confidence 6899999999999999999999999997 669999999999999999999998765 99999999999999999
Q ss_pred CcceeeccC
Q psy9200 112 TSYHYSKSK 120 (120)
Q Consensus 112 ptFHqWrD~ 120 (120)
|+||||++.
T Consensus 73 ~~Fh~f~~~ 81 (106)
T smart00461 73 PTFHQWADD 81 (106)
T ss_pred CceEEEEeC
Confidence 999999974
No 5
>cd00837 EVH1 EVH1 (Enabled, Vasp-Homology) or WASP Homology (WH1) domain. EVH1 (Enabled, Vasp-Homology) or WASP Homology (WH1) domain. The EVH1 domain binds to other proteins at proline rich sequences in either FPPPP or PPXXF motifs. It is found in the cytoskeletal reorganization proteins Enabled VASP, and WASP, and in the synaptic scaffolding protein Homer. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=99.92 E-value=9.7e-25 Score=154.26 Aligned_cols=79 Identities=29% Similarity=0.429 Sum_probs=75.3
Q ss_pred ccceEEEEEEEEEEeCCCCCeEECCCCCCeEEEEEEEeCCCCceEEEEeeeccccccccceEEEeeecCCCCeeeeecCc
Q psy9200 34 EQSIASARASVMIYDDVNKKWIPSGSSSGLSKVHVFQHQVNNTFRVVGRKLQNQEYKADYTVSINIPNKKGSNMNITITS 113 (120)
Q Consensus 34 E~~I~~vrA~VM~yDd~tk~WvP~gg~~glS~V~i~~~~~~n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~Ynkatpt 113 (120)
|++|++++|+||++||++++|+|.|| +++.|.+++|+.+++|||++++++|+ +|+|||.|.++|.|++++|+
T Consensus 1 ~~~l~~~~a~v~~~~~~~~~W~~~~~--~~g~v~~~~d~~~~~y~i~~~~~~~~------~vv~~~~l~~~~~y~~~~~~ 72 (104)
T cd00837 1 EQIISTAVAQVYTADPSTGKWVPASG--GTGAVSLVKDSTRNTYRIRGVDIQDQ------KVIWNQEIYKGLKYTQATPF 72 (104)
T ss_pred CceEEEEEEEEEEECCCCCceEECCC--CeEEEEEEEECCCCEEEEEEEecCCC------eEEEEEEecCCcEEeecCCe
Confidence 68999999999999999999999973 78999999999999999999999999 99999999999999999999
Q ss_pred ceeeccC
Q psy9200 114 YHYSKSK 120 (120)
Q Consensus 114 FHqWrD~ 120 (120)
||+|++.
T Consensus 73 Fh~w~~~ 79 (104)
T cd00837 73 FHQWEDD 79 (104)
T ss_pred EEEEEcC
Confidence 9999974
No 6
>PF00568 WH1: WH1 domain; InterPro: IPR000697 The EVH1 (WH1, RanBP1-WASP) domain is found in multi-domain proteins implicated in a diverse range of signalling, nuclear transport and cytoskeletal events. This domain of around 115 amino acids is present in species ranging from yeast to mammals. Many EVH1-containing proteins associate with actin-based structures and play a role in cytoskeletal organisation. EVH1 domains recognise and bind the proline-rich motif FPPPP with low-affinity, further interactions then form between flanking residues [][]. WASP family proteins contain a EVH1 (WH1) in their N-terminals which bind proline-rich sequences in the WASP interacting protein. Proteins of the RanBP1 family contain a WH1 domain in their N-terminal region, which seems to bind a different sequence motif present in the C-terminal part of RanGTP protein [,]. Tertiary structure of the WH1 domain of the Mena protein revealed structure similarities with the pleckstrin homology (PH) domain. The overall fold consists of a compact parallel beta-sandwich, closed along one edge by a long alpha-helix. A highly conserved cluster of three surface-exposed aromatic side-chains forms the recognition site for the molecules target ligands. [].; GO: 0005515 protein binding; PDB: 1I2H_A 1DDV_A 1DDW_A 1EGX_A 3SYX_A 1TJ6_B 1XOD_B 1EVH_A 1I7A_B 2JP2_A ....
Probab=99.87 E-value=1.6e-21 Score=138.57 Aligned_cols=79 Identities=23% Similarity=0.212 Sum_probs=72.3
Q ss_pred cccceEEEEEEEEEEeCCCCC-eEECCCCCCeEEEEEEEeCCCCceEEEEeeeccccccccceEEEeeecCCCCeeeeec
Q psy9200 33 TEQSIASARASVMIYDDVNKK-WIPSGSSSGLSKVHVFQHQVNNTFRVVGRKLQNQEYKADYTVSINIPNKKGSNMNITI 111 (120)
Q Consensus 33 ~E~~I~~vrA~VM~yDd~tk~-WvP~gg~~glS~V~i~~~~~~n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~Ynkat 111 (120)
+.++|++++|+||++||.+++ |+|++ +...|.+++|..+++|||++..++|+ ++++||.|.++|+|++++
T Consensus 7 ~~~~i~~~vA~v~~~~p~~~~~W~~~~---~~g~v~~v~d~~~~~y~I~~~~~~~~------~~v~e~~l~~~~~Y~~~~ 77 (111)
T PF00568_consen 7 RCQSIATAVAQVYQADPDTKRQWSPVK---GTGVVCFVKDNSRRSYFIRLYDLQDG------KVVWEQELYPGFVYTKAR 77 (111)
T ss_dssp -EEEEEEEEEEEEEEETTTSESEEESS---SEEEEEEEEETTTTEEEEEEEETTTT------EEEEEEEESTT-EEEEES
T ss_pred CceEEEEEEEEEEEEEcCCCCcEeeCC---eEEEEEEEEECCCCEEEEEEEEcccc------EEEEEeEecCCCEEEeCC
Confidence 358999999999999999998 99983 46789999999999999999999999 999999999999999999
Q ss_pred CcceeeccC
Q psy9200 112 TSYHYSKSK 120 (120)
Q Consensus 112 ptFHqWrD~ 120 (120)
|+||||+|.
T Consensus 78 ~~Fh~f~~~ 86 (111)
T PF00568_consen 78 PFFHQFEDD 86 (111)
T ss_dssp SSEEEEEET
T ss_pred CcEEEEEeC
Confidence 999999974
No 7
>cd00835 RanBD Ran-binding domain. Ran-binding domain; This domain of approximately 150 residues shares structural similarity to the PH domain, but lacks detectable sequence similarity. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran . The Ran-binding domain is found in multiple copies in Nuclear pore complex proteins.
Probab=99.06 E-value=2.2e-09 Score=77.12 Aligned_cols=76 Identities=21% Similarity=0.326 Sum_probs=68.2
Q ss_pred cccceEEEEEEEEEEeCCCCCeEECCCCCCeEEEEEEEeCCCCceEEEEeeeccccccccceEEEeeecCCCCeeeeec-
Q psy9200 33 TEQSIASARASVMIYDDVNKKWIPSGSSSGLSKVHVFQHQVNNTFRVVGRKLQNQEYKADYTVSINIPNKKGSNMNITI- 111 (120)
Q Consensus 33 ~E~~I~~vrA~VM~yDd~tk~WvP~gg~~glS~V~i~~~~~~n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~Ynkat- 111 (120)
.|..|+++||-+|.||++++.|..-| .-.+.|.++...+.|||+-|+-+.+ +++||+.|.++|+|.++.
T Consensus 9 ~E~~if~~r~KLy~~~~~~~~WkerG----~G~lki~~~k~~~~~RivmR~d~~~------kv~lN~~i~~~~~~~~~~~ 78 (122)
T cd00835 9 DEEVIFSVRAKLYRFDDETKEWKERG----VGELKILKHKDTGKYRLLMRRDQVL------KLCLNHKLVPGMKLQPMGN 78 (122)
T ss_pred CcEEEEEEEeEEEEEcCCCCCCeece----EEEEEEEEcCCCCcEEEEEEeCCcc------EEEEeeEecCCcEEeecCC
Confidence 58899999999999999999999866 3358999999999999999987777 999999999999999998
Q ss_pred -Ccceeec
Q psy9200 112 -TSYHYSK 118 (120)
Q Consensus 112 -ptFHqWr 118 (120)
.++..|-
T Consensus 79 ~~k~~~~~ 86 (122)
T cd00835 79 SDKSIVWA 86 (122)
T ss_pred CCcEEEEE
Confidence 7888883
No 8
>smart00160 RanBD Ran-binding domain. Domain of apporximately 150 residues that stabilises the GTP-bound form of Ran (the Ras-like nuclear small GTPase).
Probab=99.06 E-value=1.9e-09 Score=79.06 Aligned_cols=75 Identities=24% Similarity=0.316 Sum_probs=65.0
Q ss_pred ccccceEEEEEEEEEEeCCCCCeEECCCCCCeEEEEEEEeCCC-CceEEEEeeeccccccccceEEEeeecCCCCeeeee
Q psy9200 32 ATEQSIASARASVMIYDDVNKKWIPSGSSSGLSKVHVFQHQVN-NTFRVVGRKLQNQEYKADYTVSINIPNKKGSNMNIT 110 (120)
Q Consensus 32 ~~E~~I~~vrA~VM~yDd~tk~WvP~gg~~glS~V~i~~~~~~-n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~Ynka 110 (120)
..|..|+++||.+|.||+.++.|..-| ...+.|+++... +.|||+.|+-+.+ +|+||+.|.++|+|..+
T Consensus 17 E~E~~lf~~r~KL~~~~~~~~~WkerG----~G~lki~~~~~~~~~~RivmR~~~~~------kv~lN~~i~~~~~~~~~ 86 (130)
T smart00160 17 EDEEVIFSARAKLYRFANDKKEWKERG----VGDLKILKSKDNGGKVRIVMRRDGVL------KVCANHPIFKSMTLKPL 86 (130)
T ss_pred cCeEEEEEEEeEEEEEcCCCCCCeecc----EEEEEEEEcCCCCCeEEEEEEECCCc------eEEeccEecCCcEEeec
Confidence 468999999999999999999999865 446999999888 9999999977667 89999999999999987
Q ss_pred cCccee
Q psy9200 111 ITSYHY 116 (120)
Q Consensus 111 tptFHq 116 (120)
.+...-
T Consensus 87 ~~~~~~ 92 (130)
T smart00160 87 AGSNRA 92 (130)
T ss_pred CCCcce
Confidence 665433
No 9
>PF00638 Ran_BP1: RanBP1 domain; InterPro: IPR000156 Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran Binding Protein 1 (RanBP1) has guanine nucleotide dissociation inhibitory activity, specific for the GTP form of Ran and also functions to stimulate Ran GTPase activating protein(GAP)-mediated GTP hydrolysis by Ran. RanBP1 contributes to maintaining the gradient of RanGTP across the nuclear envelope high (GDI activity) or the cytoplasmic levels of RanGTP low (GAP cofactor) []. All RanBP1 proteins contain an approx 150 amino acid residue Ran binding domain. Ran BP1 binds directly to RanGTP with high affinity. There are four sites of contact between Ran and the Ran binding domain. One of these involves binding of the C-terminal segment of Ran to a groove on the Ran binding domain that is analogous to the surface utilised in the EVH1-peptide interaction []. Nup358 contains four Ran binding domains. The structure of the first of these is known [].; GO: 0046907 intracellular transport; PDB: 2Y8F_A 2Y8G_B 2CRF_A 1XKE_A 1RRP_D 2EC1_A 3M1I_B 1K5D_E 3OAN_A 3N7C_A ....
Probab=98.37 E-value=4.5e-06 Score=59.23 Aligned_cols=69 Identities=23% Similarity=0.435 Sum_probs=57.5
Q ss_pred cccceEEEEEEEEEEeCCCCCeEECCCCCCeEEEEEEEeCCCCceEEEEeeeccccccccceEEEeeecCCCCeeeeec
Q psy9200 33 TEQSIASARASVMIYDDVNKKWIPSGSSSGLSKVHVFQHQVNNTFRVVGRKLQNQEYKADYTVSINIPNKKGSNMNITI 111 (120)
Q Consensus 33 ~E~~I~~vrA~VM~yDd~tk~WvP~gg~~glS~V~i~~~~~~n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~Ynkat 111 (120)
.|..+++.||-+|.+|..++.|.-.| ...+.|.++...+.+||+=|+-+-+ +|+||..|.++|+|....
T Consensus 8 ~E~~l~~~r~Kl~~~~~~~~~W~erG----~G~l~i~~~k~~~~~RlvmR~d~~~------kv~lN~~i~~~m~~~~~~ 76 (122)
T PF00638_consen 8 DEEILFEVRAKLYRFDKEDKEWKERG----VGTLKILKHKETGKYRLVMRRDGTG------KVLLNHPIFKGMKLKPMK 76 (122)
T ss_dssp SEEEEEEEEEEEEEEETTTTEEEEEE----EEEEEEEEETTSCEEEEEEEETTTT------EEEEEEE--TTC-EEEST
T ss_pred CcEEEEEEEEEEEEEeCCCCCccccc----eeEEEEEEccCCcceEEEEEEcccC------ceeEEEEecCCceecccc
Confidence 68899999999999999999997744 5678999998889999999977667 899999999999997543
No 10
>cd01205 WASP WASP-type EVH1 domain. WASP-type EVH1 domain. Wiskott-Aldrich syndrome (WAS) is an X-linked recessive disease, characterized by eczema, immunodeficiency, and thrombocytopenia. The majority of patients with WAS, or a milder version of the disorder, X-linked thrombocytopenia (XLT), have point mutations in the EVH1 domain of WASP (Wiskott-Aldrich syndrome protein). WASP is an actin regulatory protein consisting of an N-terminal EVH1 domain, a basic region, a GTP binding domain, a proline rich region and a WH2 acidic region. Yeast members lack the GTP binding domain. WASP binds a 25 residue proline rich motif from the WASP Interacting Protein (WIP) via its N-terminal EVH1 domain.
Probab=95.37 E-value=0.23 Score=36.14 Aligned_cols=74 Identities=9% Similarity=0.112 Sum_probs=54.4
Q ss_pred cceEEEEEEEEEEeCCCCCeEECCCCCCeEEEEEEEeCCCCceEEEEeeeccccccccceEEEeeecCCCCeeeeecCcc
Q psy9200 35 QSIASARASVMIYDDVNKKWIPSGSSSGLSKVHVFQHQVNNTFRVVGRKLQNQEYKADYTVSINIPNKKGSNMNITITSY 114 (120)
Q Consensus 35 ~~I~~vrA~VM~yDd~tk~WvP~gg~~glS~V~i~~~~~~n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~YnkatptF 114 (120)
..++.+=|++..=+|...+|.-. . .|+ +.+-+|...++|=|-=..+..+ .++.+--|..++.|++..|.|
T Consensus 5 ~il~~aVvqlY~a~p~~~~W~~~-~-~Gv--l~~vkD~~~~sy~lrl~D~~~~------~v~weqElY~~f~y~~~r~fF 74 (105)
T cd01205 5 KILATAVVQLYKAYPDPGRWTKT-L-TGA--VCLVKDNVQKSYFIRLFDIKAN------RIIWEQELYDNFEYQQPRPFF 74 (105)
T ss_pred eEEEEEEEEEEEecCCCCeeEEE-e-EEE--EEEEEECCCCEEEEEEEEccCC------cEEEEEEcccCcEEccCCCcE
Confidence 35677778888887777889987 4 454 5566776666654422223334 899999999999999999999
Q ss_pred eeec
Q psy9200 115 HYSK 118 (120)
Q Consensus 115 HqWr 118 (120)
|-+.
T Consensus 75 htFe 78 (105)
T cd01205 75 HTFE 78 (105)
T ss_pred EEEe
Confidence 9763
No 11
>PF01344 Kelch_1: Kelch motif; InterPro: IPR006652 Kelch is a 50-residue motif, named after the Drosophila mutant in which it was first identified []. This sequence motif represents one beta-sheet blade, and several of these repeats can associate to form a beta-propeller. For instance, the motif appears 6 times in Drosophila egg-chamber regulatory protein, creating a 6-bladed beta-propeller. The motif is also found in mouse protein MIPP [] and in a number of poxviruses. In addition, kelch repeats have been recognised in alpha- and beta-scruin [, ], and in galactose oxidase from the fungus Dactylium dendroides [, ]. The structure of galactose oxidase reveals that the repeated sequence corresponds to a 4-stranded anti-parallel beta-sheet motif that forms the repeat unit in a super-barrel structural fold []. The known functions of kelch-containing proteins are diverse: scruin is an actin cross-linking protein; galactose oxidase catalyses the oxidation of the hydroxyl group at the C6 position in D-galactose; neuraminidase hydrolyses sialic acid residues from glycoproteins; and kelch may have a cytoskeletal function, as it is localised to the actin-rich ring canals that connect the 15 nurse cells to the developing oocyte in Drosophila []. Nevertheless, based on the location of the kelch pattern in the catalytic unit in galactose oxidase, functionally important residues have been predicted in glyoxal oxidase []. This entry represents a type of kelch sequence motif that comprises one beta-sheet blade.; GO: 0005515 protein binding; PDB: 2XN4_A 2WOZ_A 3II7_A 4ASC_A 1U6D_X 1ZGK_A 2FLU_X 2VPJ_A 2DYH_A 1X2R_A ....
Probab=58.00 E-value=13 Score=21.32 Aligned_cols=18 Identities=28% Similarity=0.460 Sum_probs=15.2
Q ss_pred EEEEEEEeCCCCCeEECC
Q psy9200 41 RASVMIYDDVNKKWIPSG 58 (120)
Q Consensus 41 rA~VM~yDd~tk~WvP~g 58 (120)
...|..||+.+++|.+..
T Consensus 27 ~~~v~~yd~~~~~W~~~~ 44 (47)
T PF01344_consen 27 TNSVEVYDPETNTWEELP 44 (47)
T ss_dssp EEEEEEEETTTTEEEEEE
T ss_pred eeeEEEEeCCCCEEEEcC
Confidence 467999999999998754
No 12
>COG5171 YRB1 Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
Probab=52.42 E-value=4.4 Score=32.78 Aligned_cols=63 Identities=22% Similarity=0.375 Sum_probs=47.2
Q ss_pred ccceEEEEEEEEEEeCCCCCeEECCCCCCeEEEEEEEeCCCCceEEEEeeeccccccccceEEEeeecCCCCe
Q psy9200 34 EQSIASARASVMIYDDVNKKWIPSGSSSGLSKVHVFQHQVNNTFRVVGRKLQNQEYKADYTVSINIPNKKGSN 106 (120)
Q Consensus 34 E~~I~~vrA~VM~yDd~tk~WvP~gg~~glS~V~i~~~~~~n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~ 106 (120)
|.-+|.+||-.|-+|..+|-|---|- | ..-|..|...|--||+=+|-+-. ++--|..|.|.++
T Consensus 89 E~vlfK~RaKLfrFd~~akewkERgt--G--d~~~lkhkktnk~ri~MrRDktl------klcaNH~i~Pe~k 151 (211)
T COG5171 89 ETVLFKARAKLFRFDEEAKEWKERGT--G--DMIILKHKKTNKARITMRRDKTL------KLCANHFINPEFK 151 (211)
T ss_pred hhhhhhhhhhheeehHHHHHHHhcCC--C--cEEEEeccccCceEEEEeechhh------hhhhhhccCccee
Confidence 66899999999999999999977663 2 46788899999999998874433 3444555555544
No 13
>PF13964 Kelch_6: Kelch motif
Probab=48.17 E-value=19 Score=21.10 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=17.8
Q ss_pred EEEEEEEEEEeCCCCCeEECCC
Q psy9200 38 ASARASVMIYDDVNKKWIPSGS 59 (120)
Q Consensus 38 ~~vrA~VM~yDd~tk~WvP~gg 59 (120)
...-..|..||+.|++|.....
T Consensus 24 ~~~~~~v~~yd~~t~~W~~~~~ 45 (50)
T PF13964_consen 24 GKYSNDVERYDPETNTWEQLPP 45 (50)
T ss_pred CCccccEEEEcCCCCcEEECCC
Confidence 4456789999999999987763
No 14
>smart00612 Kelch Kelch domain.
Probab=43.19 E-value=22 Score=19.55 Aligned_cols=18 Identities=39% Similarity=0.667 Sum_probs=14.6
Q ss_pred EEEEEEEeCCCCCeEECC
Q psy9200 41 RASVMIYDDVNKKWIPSG 58 (120)
Q Consensus 41 rA~VM~yDd~tk~WvP~g 58 (120)
-..|..||+.+..|....
T Consensus 14 ~~~v~~yd~~~~~W~~~~ 31 (47)
T smart00612 14 LKSVEVYDPETNKWTPLP 31 (47)
T ss_pred eeeEEEECCCCCeEccCC
Confidence 456889999999997554
No 15
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=40.88 E-value=34 Score=22.68 Aligned_cols=36 Identities=17% Similarity=0.239 Sum_probs=28.8
Q ss_pred CceEEEEeeec-cccccccceEEEeeecCCCCeeeeecCcce
Q psy9200 75 NTFRVVGRKLQ-NQEYKADYTVSINIPNKKGSNMNITITSYH 115 (120)
Q Consensus 75 n~fRIvG~rlq-D~~~~~~~~VvINc~I~~~l~YnkatptFH 115 (120)
|.||+-|.=.. |+ ..|+|++.-++.|.|..|-.|+-
T Consensus 20 NG~~l~G~I~~fD~-----ftVll~~~g~qqLIYKhAISTI~ 56 (61)
T cd01716 20 NGVQLKGQIESFDN-----FTVLLESDGKQQLVYKHAISTIT 56 (61)
T ss_pred CCcEEEEEEEEEcc-----eEEEEEECCcEEEEEeeeeEEEe
Confidence 67788886554 77 89999999888999999876653
No 16
>TIGR01640 F_box_assoc_1 F-box protein interaction domain. This model describes a large family of plant domains, with several hundred members in Arabidopsis thaliana. Most examples are found C-terminal to an F-box (pfam00646), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes. Some members have two copies of this domain.
Probab=40.48 E-value=64 Score=24.35 Aligned_cols=42 Identities=10% Similarity=0.339 Sum_probs=26.5
Q ss_pred EEEEEEeCCCCC--eEECCCC----CCeEEEEEEEeCCCCceEEEEee
Q psy9200 42 ASVMIYDDVNKK--WIPSGSS----SGLSKVHVFQHQVNNTFRVVGRK 83 (120)
Q Consensus 42 A~VM~yDd~tk~--WvP~gg~----~glS~V~i~~~~~~n~fRIvG~r 83 (120)
..+++.||.|+. +||.... .+.....+-+++..++|.|+--.
T Consensus 14 ~~~~V~NP~T~~~~~LP~~~~~~~~~~~~~~~~G~d~~~~~YKVv~~~ 61 (230)
T TIGR01640 14 KRLVVWNPSTGQSRWLPTPKSRRSNKESDTYFLGYDPIEKQYKVLCFS 61 (230)
T ss_pred CcEEEECCCCCCEEecCCCCCcccccccceEEEeecccCCcEEEEEEE
Confidence 358899999997 5543321 11113566667778889887653
No 17
>PF06058 DCP1: Dcp1-like decapping family; InterPro: IPR010334 An essential step in mRNA turnover is decapping. In yeast, two proteins have been identified that are essential for decapping, Dcp1 (this family) and Dcp2 (IPR007722 from INTERPRO). The precise role of these proteins in the decapping reaction has not been established. Evidence suggests that the Dcp1 may enhance the function of Dcp2 [].; PDB: 1Q67_A 2QKM_C 2QKL_A.
Probab=38.25 E-value=43 Score=24.47 Aligned_cols=60 Identities=12% Similarity=0.298 Sum_probs=35.4
Q ss_pred EEEEEEEEEEeCCCCCeEECCCCCCeEEEEEEEeCC--CCceEEEEeeeccccccccceEEEeeecCCCCeeee
Q psy9200 38 ASARASVMIYDDVNKKWIPSGSSSGLSKVHVFQHQV--NNTFRVVGRKLQNQEYKADYTVSINIPNKKGSNMNI 109 (120)
Q Consensus 38 ~~vrA~VM~yDd~tk~WvP~gg~~glS~V~i~~~~~--~n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~Ynk 109 (120)
..+-|+|..+|+.++.|.-.+-+| ..-+|+... +..+-|.-|+..+. .++ .|.+++.+..
T Consensus 25 ~a~~v~vY~f~~~~~~W~K~~iEG---~LFv~~r~~~p~~~~~vlNR~~~~n-------~~~--~i~~~~~~e~ 86 (122)
T PF06058_consen 25 TASHVVVYKFDHETNEWEKTDIEG---TLFVYKRSSSPRYGLIVLNRRSTEN-------FVE--PITPDLDFEL 86 (122)
T ss_dssp EEEEEEEEEEETTTTEEEEEEEEE---EEEEEEEETTS-ECEEEEESSSS---------EEE--EE-SGGGEEE
T ss_pred hCCeEEEEeecCCCCcEeecCcEe---eEEEEEeecccceEEEEecCCCCCc-------eee--ecCCCcEEEE
Confidence 346788888999999999988423 255776533 34455556554433 333 3666666553
No 18
>PF04939 RRS1: Ribosome biogenesis regulatory protein (RRS1); InterPro: IPR007023 This is a family of eukaryotic ribosomal biogenesis regulatory proteins.; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=34.04 E-value=12 Score=29.15 Aligned_cols=26 Identities=23% Similarity=0.640 Sum_probs=20.0
Q ss_pred ccceEEEEEEEEEEeCCCCCeEECCC
Q psy9200 34 EQSIASARASVMIYDDVNKKWIPSGS 59 (120)
Q Consensus 34 E~~I~~vrA~VM~yDd~tk~WvP~gg 59 (120)
+.=|-.-+=.=|+||+.++.|+|-=|
T Consensus 89 ~KGI~K~Kk~~lv~DE~~~eW~prwG 114 (164)
T PF04939_consen 89 KKGIKKRKKSKLVYDEETGEWVPRWG 114 (164)
T ss_pred HcCCccccCcCccccccccchhhccc
Confidence 33355555677999999999999876
No 19
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=33.01 E-value=53 Score=22.98 Aligned_cols=36 Identities=14% Similarity=0.197 Sum_probs=28.5
Q ss_pred CceEEEEeeec-cccccccceEEEeeecCCCCeeeeecCcce
Q psy9200 75 NTFRVVGRKLQ-NQEYKADYTVSINIPNKKGSNMNITITSYH 115 (120)
Q Consensus 75 n~fRIvG~rlq-D~~~~~~~~VvINc~I~~~l~YnkatptFH 115 (120)
|.||+-|.=.. |+ ..|+|++.=+..|.|..|--|+-
T Consensus 28 NG~~l~G~I~~fD~-----ftVll~~~gkqqLIYKHAISTI~ 64 (79)
T PRK00395 28 NGIKLQGQIESFDN-----FVVLLRNTGKSQLVYKHAISTVV 64 (79)
T ss_pred CCcEEEEEEEEEcc-----EEEEEEECCcEEEEEEeeeEEEe
Confidence 56777776544 77 89999999889999999876653
No 20
>KOG3671|consensus
Probab=32.49 E-value=68 Score=29.68 Aligned_cols=56 Identities=14% Similarity=0.239 Sum_probs=38.4
Q ss_pred CCeEECCCCCCeEEEEEEEeCCCCc--eEEEEeeeccccccccceEEEeeecCCCCeeeeecCcceeec
Q psy9200 52 KKWIPSGSSSGLSKVHVFQHQVNNT--FRVVGRKLQNQEYKADYTVSINIPNKKGSNMNITITSYHYSK 118 (120)
Q Consensus 52 k~WvP~gg~~glS~V~i~~~~~~n~--fRIvG~rlqD~~~~~~~~VvINc~I~~~l~YnkatptFHqWr 118 (120)
..|-=-+- .|+ |.+-+|...+. +||+.. .++ .+|++.-|+.+|.|.+-..-||-+.
T Consensus 55 ~~W~~~~~-~Ga--l~lVkD~~~rsyFlrl~di--~~~------rliWdqELY~nf~y~q~r~ffhtFe 112 (569)
T KOG3671|consen 55 NHWNKTGL-CGA--LCLVKDNAQRSYFLRLVDI--VNN------RLIWDQELYQNFEYRQPRTFFHTFE 112 (569)
T ss_pred hhhccccC-cee--EEEeeccccceeeeEEeee--cCc------eeeehHHhhhhceeccCccceeeec
Confidence 45855443 333 44455554444 566654 455 7999999999999999988888753
No 21
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=31.53 E-value=62 Score=21.53 Aligned_cols=35 Identities=17% Similarity=0.214 Sum_probs=27.8
Q ss_pred CceEEEEeeec-cccccccceEEEeeecCCCCeeeeecCcc
Q psy9200 75 NTFRVVGRKLQ-NQEYKADYTVSINIPNKKGSNMNITITSY 114 (120)
Q Consensus 75 n~fRIvG~rlq-D~~~~~~~~VvINc~I~~~l~YnkatptF 114 (120)
|.||+.|.=.. |+ ..|+|++.=+..|.|..|-.|+
T Consensus 24 nG~~l~G~I~~fD~-----ftVll~~~g~qqLIYKhAISTI 59 (61)
T TIGR02383 24 NGVQLKGVIESFDN-----FTVLLESQGKQQLIYKHAISTI 59 (61)
T ss_pred CCcEEEEEEEEEee-----eEEEEEECCcEEEEEEEEEEEE
Confidence 56788886554 77 8899999988889999886654
No 22
>KOG0864|consensus
Probab=31.30 E-value=15 Score=29.12 Aligned_cols=69 Identities=19% Similarity=0.298 Sum_probs=54.7
Q ss_pred cccceEEEEE-EEEEEeCCCCCeEECCCCCCeEEEEEEEeCCCCceEEEEeeeccccccccceEEEeeecCCCCeeeee
Q psy9200 33 TEQSIASARA-SVMIYDDVNKKWIPSGSSSGLSKVHVFQHQVNNTFRVVGRKLQNQEYKADYTVSINIPNKKGSNMNIT 110 (120)
Q Consensus 33 ~E~~I~~vrA-~VM~yDd~tk~WvP~gg~~glS~V~i~~~~~~n~fRIvG~rlqD~~~~~~~~VvINc~I~~~l~Ynka 110 (120)
.|..|+..+| .++.+|..++.|---| .-.+-+++|-..+..|+.=+|-+-. ..+.-|..|.++|.+...
T Consensus 55 ~e~~~~~~~s~~l~~f~~~~kq~kerG----~g~~~~~kn~~~g~~r~~m~rdst~-----~~v~sn~~~~~~~~~~p~ 124 (215)
T KOG0864|consen 55 DEEIIFDQRSEKLYVFDNETKQWKERG----TGKVKLLKNKDTGSTRDLMRRDSTK-----LKVCSNHFIGPSFKLEPP 124 (215)
T ss_pred hhhhhhhhhhhhHHhhhhhhhhhhccC----CcceEeeecCCCCcceeeeeecccc-----hhhcccccccCcccccCC
Confidence 3778899998 9999999999997764 2368899999999999987753320 158889999999988753
No 23
>KOG1708|consensus
Probab=30.52 E-value=87 Score=25.97 Aligned_cols=36 Identities=17% Similarity=0.333 Sum_probs=25.2
Q ss_pred CccccceEEEEEEEEEEeCCCC-----CeEECCCCCCeEEEEE
Q psy9200 31 YATEQSIASARASVMIYDDVNK-----KWIPSGSSSGLSKVHV 68 (120)
Q Consensus 31 ~~~E~~I~~vrA~VM~yDd~tk-----~WvP~gg~~glS~V~i 68 (120)
--+|+||-..+ +||.+||+.. +|--.+. |--.+|++
T Consensus 127 vk~EaPlhvsk-~VmLvdp~d~q~te~~wr~~e~-GekVRvst 167 (236)
T KOG1708|consen 127 VKSEAPLHVSK-QVMLVDPEDDQPTEVEWRFTED-GEKVRVST 167 (236)
T ss_pred EeecCCceecc-eeEEECccccCCceeeEEEcCC-CcEEEEEe
Confidence 35799998878 9999999874 3877764 22334443
No 24
>PF07443 HARP: HepA-related protein (HARP); InterPro: IPR010003 This entry represents a conserved region approximately 60 residues long within eukaryotic HepA-related protein (HARP). This exhibits single-stranded DNA-dependent ATPase activity, and is ubiquitously expressed in human and mouse tissues []. Family members may contain more than one copy of this region.; GO: 0004386 helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0016568 chromatin modification, 0005634 nucleus
Probab=30.03 E-value=18 Score=23.59 Aligned_cols=10 Identities=40% Similarity=0.836 Sum_probs=8.4
Q ss_pred EEeCCCCCeE
Q psy9200 46 IYDDVNKKWI 55 (120)
Q Consensus 46 ~yDd~tk~Wv 55 (120)
.||+.||+|=
T Consensus 22 ~YD~~Tr~W~ 31 (55)
T PF07443_consen 22 NYDPKTRKWN 31 (55)
T ss_pred ccCccceeee
Confidence 4899999993
No 25
>PF08553 VID27: VID27 cytoplasmic protein; InterPro: IPR013863 This entry represents fungal and plant proteins and contains many hypothetical proteins. Vid27p is a cytoplasmic protein of unknown function, possibly regulates import of fructose-1,6-bisphosphatase into Vacuolar Import and Degradation (Vid) vesicles and is not essential for proteasome-dependent degradation of fructose-1,6-bisphosphatase (FBPase) [, ].
Probab=29.13 E-value=3.8e+02 Score=25.87 Aligned_cols=59 Identities=17% Similarity=0.312 Sum_probs=41.6
Q ss_pred cceEEEEEEEEEEeCCCCCeEECCCCCCeEEEEEEEeCCCCc-eEEEEeeeccccccccceEEEeeecCCCCe
Q psy9200 35 QSIASARASVMIYDDVNKKWIPSGSSSGLSKVHVFQHQVNNT-FRVVGRKLQNQEYKADYTVSINIPNKKGSN 106 (120)
Q Consensus 35 ~~I~~vrA~VM~yDd~tk~WvP~gg~~glS~V~i~~~~~~n~-fRIvG~rlqD~~~~~~~~VvINc~I~~~l~ 106 (120)
..+++..|.+..||+.+++|+..+. ...+.|.....-.- ..|.|. | ..+|+..|..+|.
T Consensus 248 ~~~~~~~~~L~l~d~~~~~f~lq~~---~v~~~i~~~~~~~y~l~i~~~---~-------~~~l~~~v~s~mN 307 (794)
T PF08553_consen 248 EILASESAELYLYDPPTGKFVLQDS---SVTAKIIETGKWEYWLQIEGK---D-------KIWLGQPVSSDMN 307 (794)
T ss_pred ceeeeeeEEEEEEcCCCceEEEecC---cEEEEEEEcCCeEEEEEEecC---C-------ceEEeeeccCCcC
Confidence 3899999999999999999999875 45788887644222 233332 2 3457777777765
No 26
>COG5225 RRS1 Uncharacterized protein involved in ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=29.09 E-value=32 Score=27.10 Aligned_cols=19 Identities=26% Similarity=0.842 Sum_probs=16.5
Q ss_pred EEEEEEEeCCCCCeEECCC
Q psy9200 41 RASVMIYDDVNKKWIPSGS 59 (120)
Q Consensus 41 rA~VM~yDd~tk~WvP~gg 59 (120)
|+-=|+||.+++-|+|-=|
T Consensus 107 r~g~lvyDEasGEwvPkwG 125 (172)
T COG5225 107 RSGPLVYDEASGEWVPKWG 125 (172)
T ss_pred cCCCceeeccccccccccC
Confidence 5668999999999999776
No 27
>KOG1690|consensus
Probab=25.96 E-value=3.1e+02 Score=22.55 Aligned_cols=61 Identities=15% Similarity=0.235 Sum_probs=38.6
Q ss_pred CcceeeecCCCCccccceEEEEEEEEEEeCCCCCeEECCCCCCeEEEEEEEeCCCCceEEEEeee
Q psy9200 20 SSYVATVNTSHYATEQSIASARASVMIYDDVNKKWIPSGSSSGLSKVHVFQHQVNNTFRVVGRKL 84 (120)
Q Consensus 20 ~~~~~~~~~~~~~~E~~I~~vrA~VM~yDd~tk~WvP~gg~~glS~V~i~~~~~~n~fRIvG~rl 84 (120)
+.+--||+.+....| .++..---+=+|||..++|....+ -|+ .|.| .++-.|.-||+....
T Consensus 26 ~~~e~KCF~eelpk~-tmv~G~yk~qlyd~~~~~y~~~p~-~gm-~VeV-~e~fdnnh~Vl~q~~ 86 (215)
T KOG1690|consen 26 AGTEKKCFIEELPKG-TMVTGNYKAQLYDDQLKGYGSYPN-IGM-HVEV-KETFDNNHVVLSQQY 86 (215)
T ss_pred cCCcccchhhhCCCC-cEEEeeeeeeeecchhcccccCCC-ceE-EEEe-ecCCCCceEEEeecC
Confidence 344557888877777 566664445579999999983333 333 4443 455666667777643
No 28
>KOG1765|consensus
Probab=23.69 E-value=34 Score=27.37 Aligned_cols=15 Identities=27% Similarity=0.846 Sum_probs=13.9
Q ss_pred EEEeCCCCCeEECCC
Q psy9200 45 MIYDDVNKKWIPSGS 59 (120)
Q Consensus 45 M~yDd~tk~WvP~gg 59 (120)
|+||.+||.|+|-=|
T Consensus 112 lV~DEasgew~pr~G 126 (181)
T KOG1765|consen 112 LVYDEASGEWKPRWG 126 (181)
T ss_pred cceeccccccccccC
Confidence 999999999999876
No 29
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=22.26 E-value=2.4e+02 Score=18.56 Aligned_cols=31 Identities=16% Similarity=0.326 Sum_probs=19.7
Q ss_pred EEEEEEEEeCCCCCe-E--EC-CCCCCeEEEEEEE
Q psy9200 40 ARASVMIYDDVNKKW-I--PS-GSSSGLSKVHVFQ 70 (120)
Q Consensus 40 vrA~VM~yDd~tk~W-v--P~-gg~~glS~V~i~~ 70 (120)
.+..|+.||.++|-= + |. ++..+.+.|.|..
T Consensus 19 ieGEV~afD~~tk~lIlk~~s~~~~~~~~dv~ivn 53 (61)
T cd01735 19 LQGEVVAFDYPSKMLILKCPSSSGKPNHADILLVN 53 (61)
T ss_pred EEEEEEEecCCCcEEEEECccccCCCCcceEEEEE
Confidence 367899999998763 3 55 3334566666543
No 30
>PF13418 Kelch_4: Galactose oxidase, central domain; PDB: 2UVK_B.
Probab=21.61 E-value=1.1e+02 Score=17.46 Aligned_cols=20 Identities=20% Similarity=0.332 Sum_probs=13.1
Q ss_pred EEEEEEEEEeCCCCCeEECC
Q psy9200 39 SARASVMIYDDVNKKWIPSG 58 (120)
Q Consensus 39 ~vrA~VM~yDd~tk~WvP~g 58 (120)
+.-..+..||..+++|-..+
T Consensus 26 ~~~~d~~~~d~~~~~W~~~~ 45 (49)
T PF13418_consen 26 SPLNDLWIFDIETNTWTRLP 45 (49)
T ss_dssp EE---EEEEETTTTEEEE--
T ss_pred cccCCEEEEECCCCEEEECC
Confidence 45677889999999998774
No 31
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=21.53 E-value=1e+02 Score=24.33 Aligned_cols=36 Identities=6% Similarity=0.114 Sum_probs=28.6
Q ss_pred CceEEEEeeec-cccccccceEEEeeecCCCCeeeeecCcce
Q psy9200 75 NTFRVVGRKLQ-NQEYKADYTVSINIPNKKGSNMNITITSYH 115 (120)
Q Consensus 75 n~fRIvG~rlq-D~~~~~~~~VvINc~I~~~l~YnkatptFH 115 (120)
|.||+-|.=.. |+ ..|+|++.=+..|.|..|-.|+-
T Consensus 33 nG~rl~G~I~~fD~-----ftVlL~~~gkqqLIYKHAISTI~ 69 (165)
T PRK14091 33 KGVKLQGIITWFDN-----FSILLRRDGQSQLVYKHAISTIM 69 (165)
T ss_pred cCcEEEEEEEEEcc-----eEEEEEeCCceEEEEeeeeeeec
Confidence 44888886554 77 89999999889999999877653
Done!