Query psy4906
Match_columns 144
No_of_seqs 106 out of 147
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 20:52:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4906.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4906hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04065 Not3: Not1 N-terminal 100.0 1.5E-68 3.2E-73 440.6 16.0 141 3-143 1-141 (233)
2 KOG2150|consensus 100.0 8E-66 1.7E-70 464.0 15.4 141 3-143 1-141 (575)
3 COG5665 NOT5 CCR4-NOT transcri 100.0 6.3E-47 1.4E-51 333.0 11.3 131 13-143 1-131 (548)
4 KOG0963|consensus 75.5 54 0.0012 31.7 11.6 31 8-38 71-101 (629)
5 PF09745 DUF2040: Coiled-coil 68.0 43 0.00092 25.7 7.7 29 9-38 4-32 (127)
6 PF15188 CCDC-167: Coiled-coil 63.5 49 0.0011 24.0 6.9 43 8-50 3-46 (85)
7 cd07675 F-BAR_FNBP1L The F-BAR 63.2 62 0.0014 27.5 8.5 49 39-92 79-132 (252)
8 PF06657 Cep57_MT_bd: Centroso 62.7 20 0.00044 25.2 4.7 55 12-66 15-76 (79)
9 cd07594 BAR_Endophilin_B The B 61.0 98 0.0021 25.9 10.5 88 10-97 133-220 (229)
10 cd07598 BAR_FAM92 The Bin/Amph 60.0 90 0.0019 25.6 8.7 78 9-93 78-166 (211)
11 PF10368 YkyA: Putative cell-w 57.4 1E+02 0.0023 25.0 9.7 118 20-143 57-183 (204)
12 PF00435 Spectrin: Spectrin re 56.4 24 0.00052 22.9 4.0 58 53-110 3-61 (105)
13 PF14523 Syntaxin_2: Syntaxin- 56.0 35 0.00075 23.6 5.0 57 8-64 38-95 (102)
14 smart00503 SynN Syntaxin N-ter 55.3 69 0.0015 22.3 10.6 93 9-101 10-114 (117)
15 PF04799 Fzo_mitofusin: fzo-li 54.8 57 0.0012 26.5 6.6 62 7-93 102-164 (171)
16 PF05082 Rop-like: Rop-like; 53.5 19 0.00042 25.1 3.2 22 47-68 5-26 (66)
17 PRK05287 hypothetical protein; 53.2 40 0.00086 28.7 5.7 46 47-93 57-103 (250)
18 cd07593 BAR_MUG137_fungi The B 52.7 1.3E+02 0.0029 24.8 10.5 87 10-98 114-200 (215)
19 PF03938 OmpH: Outer membrane 51.7 84 0.0018 23.3 6.7 62 7-68 40-104 (158)
20 PF02185 HR1: Hr1 repeat; Int 49.2 54 0.0012 21.8 4.9 58 8-70 6-63 (70)
21 cd00179 SynN Syntaxin N-termin 47.7 1.1E+02 0.0024 22.4 10.9 94 10-103 9-115 (151)
22 PF07072 DUF1342: Protein of u 46.9 40 0.00087 27.8 4.7 62 24-94 24-86 (211)
23 cd07671 F-BAR_PSTPIP1 The F-BA 46.7 1.7E+02 0.0037 24.3 10.5 77 6-90 109-195 (242)
24 PF00804 Syntaxin: Syntaxin; 45.4 91 0.002 20.8 7.9 30 10-39 10-39 (103)
25 PF11166 DUF2951: Protein of u 43.2 1E+02 0.0022 23.2 5.8 57 10-69 21-78 (98)
26 PF00489 IL6: Interleukin-6/G- 41.5 1.7E+02 0.0036 22.8 7.3 51 13-65 53-104 (154)
27 cd07655 F-BAR_PACSIN The F-BAR 39.5 1.3E+02 0.0029 24.8 6.7 58 7-64 123-192 (258)
28 PF12729 4HB_MCP_1: Four helix 37.3 1.5E+02 0.0032 20.9 10.7 35 36-70 71-105 (181)
29 smart00126 IL6 Interleukin-6 h 36.6 2.2E+02 0.0047 22.7 8.0 53 13-67 53-106 (154)
30 PF03114 BAR: BAR domain; Int 36.0 1.9E+02 0.004 21.7 9.4 84 10-93 131-215 (229)
31 TIGR02449 conserved hypothetic 35.9 50 0.0011 22.9 3.1 39 59-98 26-64 (65)
32 cd07600 BAR_Gvp36 The Bin/Amph 35.7 2.7E+02 0.0058 23.4 9.8 88 10-98 147-234 (242)
33 PF10400 Vir_act_alpha_C: Viru 33.6 1.5E+02 0.0032 19.8 5.4 62 78-139 26-89 (90)
34 TIGR03185 DNA_S_dndD DNA sulfu 32.9 1.5E+02 0.0032 27.7 6.6 58 8-70 235-292 (650)
35 PF02646 RmuC: RmuC family; I 31.0 2.5E+02 0.0054 23.9 7.1 47 9-60 1-47 (304)
36 cd00176 SPEC Spectrin repeats, 30.9 2.1E+02 0.0045 20.8 10.5 89 17-109 75-165 (213)
37 cd07654 F-BAR_FCHSD The F-BAR 29.8 1.5E+02 0.0033 25.1 5.6 37 6-47 120-156 (264)
38 cd00890 Prefoldin Prefoldin is 29.1 2.1E+02 0.0046 20.3 7.1 22 47-68 9-30 (129)
39 PF06730 FAM92: FAM92 protein; 28.8 3.6E+02 0.0078 22.8 8.6 78 9-92 85-172 (219)
40 cd01111 HTH_MerD Helix-Turn-He 28.5 2E+02 0.0043 20.8 5.4 29 39-67 79-107 (107)
41 cd00176 SPEC Spectrin repeats, 28.0 1.7E+02 0.0037 21.3 5.0 55 55-110 4-60 (213)
42 PF09597 IGR: IGR protein moti 28.0 1.4E+02 0.0031 20.0 4.2 24 70-93 32-55 (57)
43 PF10458 Val_tRNA-synt_C: Valy 27.9 1.8E+02 0.004 19.2 5.9 45 48-92 8-55 (66)
44 PF03528 Rabaptin: Rabaptin; 27.8 39 0.00084 25.5 1.6 53 2-58 16-70 (106)
45 PF14282 FlxA: FlxA-like prote 27.7 2E+02 0.0044 20.9 5.4 27 43-72 18-44 (106)
46 COG2924 Uncharacterized protei 27.3 52 0.0011 24.3 2.1 15 79-93 60-74 (90)
47 KOG2117|consensus 27.3 1.6E+02 0.0035 26.8 5.6 83 22-105 67-178 (379)
48 PRK09793 methyl-accepting prot 27.2 3.7E+02 0.0079 24.2 7.9 64 10-73 81-145 (533)
49 PTZ00473 Plasmodium Vir superf 27.0 1.5E+02 0.0033 27.4 5.4 100 21-141 75-184 (420)
50 PRK13182 racA polar chromosome 26.9 2.7E+02 0.0059 22.3 6.4 25 77-101 119-143 (175)
51 cd07673 F-BAR_FCHO2 The F-BAR 26.8 3.8E+02 0.0083 22.5 9.3 75 8-87 155-240 (269)
52 PRK13415 flagella biosynthesis 26.3 2E+02 0.0044 24.3 5.7 52 10-63 144-206 (219)
53 COG5606 Uncharacterized conser 24.6 1.1E+02 0.0025 22.6 3.5 43 22-74 2-44 (91)
54 PRK10361 DNA recombination pro 24.3 3.6E+02 0.0079 25.2 7.4 75 9-88 135-217 (475)
55 COG4079 Uncharacterized protei 24.3 2.1E+02 0.0045 25.2 5.5 48 18-65 147-205 (293)
56 PF01806 Paramyxo_P: Paramyxov 24.2 97 0.0021 26.5 3.4 32 10-45 69-100 (248)
57 KOG0804|consensus 23.9 6.3E+02 0.014 24.0 9.0 30 18-47 329-358 (493)
58 PF08439 Peptidase_M3_N: Oligo 23.8 74 0.0016 20.8 2.2 30 7-36 37-66 (70)
59 cd04786 HTH_MerR-like_sg7 Heli 23.4 1E+02 0.0022 23.2 3.1 23 47-69 88-110 (131)
60 KOG3364|consensus 23.2 69 0.0015 25.7 2.3 67 18-89 50-118 (149)
61 PF12220 U1snRNP70_N: U1 small 22.7 2.6E+02 0.0056 19.9 5.0 51 21-71 38-93 (94)
62 PF04362 Iron_traffic: Bacteri 22.1 77 0.0017 23.3 2.2 14 79-92 60-73 (88)
63 PF07139 DUF1387: Protein of u 21.9 86 0.0019 27.7 2.8 34 42-90 148-181 (302)
64 PF06729 CENP-R: Kinetochore c 21.7 4.1E+02 0.009 21.1 6.3 57 10-66 59-124 (139)
65 cd00089 HR1 Protein kinase C-r 21.5 2.6E+02 0.0056 18.6 7.8 59 6-67 5-69 (72)
66 PF05008 V-SNARE: Vesicle tran 21.4 2.6E+02 0.0055 18.5 7.0 51 13-63 24-77 (79)
67 cd07616 BAR_Endophilin_B1 The 21.3 5E+02 0.011 21.8 10.3 85 11-97 134-220 (229)
68 PF05263 DUF722: Protein of un 21.0 2E+02 0.0042 22.3 4.3 26 42-69 56-81 (130)
69 cd01107 HTH_BmrR Helix-Turn-He 20.9 1.8E+02 0.0038 20.8 3.9 24 45-68 83-106 (108)
70 smart00787 Spc7 Spc7 kinetocho 20.8 1.6E+02 0.0034 25.6 4.2 22 47-68 249-270 (312)
71 PRK05408 oxidative damage prot 20.7 83 0.0018 23.2 2.1 15 78-92 59-73 (90)
72 PF07851 TMPIT: TMPIT-like pro 20.2 6.3E+02 0.014 22.5 9.9 55 45-99 37-91 (330)
No 1
>PF04065 Not3: Not1 N-terminal domain, CCR4-Not complex component ; InterPro: IPR007207 The Ccr4-Not complex (Not1, Not2, Not3, Not4 and Not5) is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID []. This domain is the N-terminal region of the Not proteins.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=100.00 E-value=1.5e-68 Score=440.58 Aligned_cols=141 Identities=66% Similarity=0.924 Sum_probs=139.8
Q ss_pred CCcCchhhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhhHHHH
Q psy4906 3 RTYPGRQGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYR 82 (144)
Q Consensus 3 ~~~RKLQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L~e~R 82 (144)
|++||||+|||+|||||+|||+.||+||+||++++|+|||||||+|||||||||||||||||+|+++||||||++|+++|
T Consensus 1 m~~RKLQ~Eid~~lKkv~EG~~~F~~i~~K~~~~~n~~QKEK~E~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L~e~R 80 (233)
T PF04065_consen 1 MAKRKLQQEIDRTLKKVQEGVEEFDEIYEKVESATNQNQKEKLEADLKKEIKKLQRLRDQIKTWLSSNDIKDKKKLLENR 80 (233)
T ss_pred CCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHccCcccccHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcccchhhhcccccCCCchHHHHHHHHHHHHHHHHHHHHhhhhc
Q psy4906 83 KLIETQMERFKVVERETKTKAYSKEGLGAVQKMDPAQKEKEEISTWLVTSIDALNIQVSSV 143 (144)
Q Consensus 83 k~IE~~MErFK~~Eke~KtK~fSkegL~~~~~~dp~~~~k~e~~~wl~~~id~L~~QiE~~ 143 (144)
++||++||+||+|||+||||||||+||++++++||.++++.+++.||+++|++|+.|||.|
T Consensus 81 k~IE~~MErFK~vEkesKtKafSkeGL~~~~k~dp~e~ek~e~~~wl~~~Id~L~~QiE~~ 141 (233)
T PF04065_consen 81 KLIEEQMERFKVVEKESKTKAFSKEGLMAASKLDPKEKEKEEARDWLKDSIDELNRQIEQL 141 (233)
T ss_pred HHHHHHHHHHHHHHHHhcccccchhhhhcccccCcchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999986
No 2
>KOG2150|consensus
Probab=100.00 E-value=8e-66 Score=463.98 Aligned_cols=141 Identities=61% Similarity=0.919 Sum_probs=139.8
Q ss_pred CCcCchhhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhhHHHH
Q psy4906 3 RTYPGRQGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYR 82 (144)
Q Consensus 3 ~~~RKLQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L~e~R 82 (144)
|++||||+|||||||||+|||+.||+||+||++++|.|||||||+|||||||||||||||||||++++|||||+.|++||
T Consensus 1 ~~~RKLq~eIdr~lkKv~Egve~Fd~i~ek~~~~~n~sqkeK~e~DLKkEIKKLQRlRdQIKtW~ss~dIKDK~~L~d~R 80 (575)
T KOG2150|consen 1 MAKRKLQQEIDRCLKKVDEGVEIFDEIYEKLHSANNVSQKEKLESDLKKEIKKLQRLRDQIKTWQSSSDIKDKDSLLDNR 80 (575)
T ss_pred CchhHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcccchhhhcccccCCCchHHHHHHHHHHHHHHHHHHHHhhhhc
Q psy4906 83 KLIETQMERFKVVERETKTKAYSKEGLGAVQKMDPAQKEKEEISTWLVTSIDALNIQVSSV 143 (144)
Q Consensus 83 k~IE~~MErFK~~Eke~KtK~fSkegL~~~~~~dp~~~~k~e~~~wl~~~id~L~~QiE~~ 143 (144)
|+||.+|||||+|||+||||||||+||+.+.++||++++|.|+.+||+++||+|++|+|+|
T Consensus 81 rlIE~~MErfK~vEke~KtKa~SkegL~~~~klDPkEkek~d~~~wi~~~ideLe~q~d~~ 141 (575)
T KOG2150|consen 81 RLIEQRMERFKAVEKEMKTKAFSKEGLSAAEKLDPKEKEKRDTMDWISNQIDELERQVDSF 141 (575)
T ss_pred HHHHHHHHHHHHHHHHhhccccchhhccccccCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999986
No 3
>COG5665 NOT5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=100.00 E-value=6.3e-47 Score=333.00 Aligned_cols=131 Identities=46% Similarity=0.743 Sum_probs=128.4
Q ss_pred HHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhhHHHHHHHHHHHHHH
Q psy4906 13 DRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERF 92 (144)
Q Consensus 13 Dr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~MErF 92 (144)
+++|++|-|||+.||+||+|+++++|.+||||||+|||++||||||+|||||||++++|||||..|++||++||..||+|
T Consensus 1 ~~~~~~~~e~i~~fd~iyek~~~s~~~s~~ekle~dlk~~ikklq~~rdqiktw~s~~dikdk~~l~~nrrlie~~me~f 80 (548)
T COG5665 1 DKLLKKVKEGIEDFDDIYEKFQSTDNSSHREKLESDLKREIKKLQKHRDQIKTWLSKEDVKDKQVLMTNRRLIENGMERF 80 (548)
T ss_pred ChhHHHHHhhhhhHHHHHHHHhccCchhHHHHHhhHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHhHHHHHhHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcccchhhhcccccCCCchHHHHHHHHHHHHHHHHHHHHhhhhc
Q psy4906 93 KVVERETKTKAYSKEGLGAVQKMDPAQKEKEEISTWLVTSIDALNIQVSSV 143 (144)
Q Consensus 93 K~~Eke~KtK~fSkegL~~~~~~dp~~~~k~e~~~wl~~~id~L~~QiE~~ 143 (144)
|+|||+||||+||+|||+.+..+||++.++.++..||.+|+++|.+|.|.+
T Consensus 81 k~ve~~mk~k~fske~ls~~~~~dpke~~k~d~i~~i~~~~~el~~q~e~~ 131 (548)
T COG5665 81 KSVEKLMKTKQFSKEALTNPDIIDPKELKKRDQVLFIHDCLDELQKQLEQY 131 (548)
T ss_pred HHHHHHHHHHHhhHhhccCcccCChhHhccccceehHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999864
No 4
>KOG0963|consensus
Probab=75.51 E-value=54 Score=31.67 Aligned_cols=31 Identities=29% Similarity=0.405 Sum_probs=28.9
Q ss_pred hhhhHHHHHHhHHHhHHHHHHHHHHHhhcCC
Q psy4906 8 RQGEIDRCLKKVSEGVETFEDIWQKVHNATN 38 (144)
Q Consensus 8 LQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~ 38 (144)
-|.|||-+.++-..|...|=+||+++..++.
T Consensus 71 yQ~EiD~LtkRsk~aE~afl~vye~L~eaPD 101 (629)
T KOG0963|consen 71 YQSEIDNLTKRSKFAEAAFLDVYEKLIEAPD 101 (629)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHhhCCC
Confidence 3899999999999999999999999998865
No 5
>PF09745 DUF2040: Coiled-coil domain-containing protein 55 (DUF2040); InterPro: IPR018612 This entry represents a conserved domain of approximately 130 residues of proteins conserved from fungi to humans. Some proteins containing this domain are described as coiled-coil domain-containing protein 55, but the function is unknown.
Probab=68.04 E-value=43 Score=25.72 Aligned_cols=29 Identities=10% Similarity=0.353 Sum_probs=18.7
Q ss_pred hhhHHHHHHhHHHhHHHHHHHHHHHhhcCC
Q psy4906 9 QGEIDRCLKKVSEGVETFEDIWQKVHNATN 38 (144)
Q Consensus 9 Q~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~ 38 (144)
+.++.+.|. ..-.|=.||++|+-+..+..
T Consensus 4 ~~~~~~A~~-~DptvfdYD~vYD~m~~~~~ 32 (127)
T PF09745_consen 4 KKEAQKALE-EDPTVFDYDEVYDDMKAKKE 32 (127)
T ss_pred HHHHHHHhc-cCChHhhHHHHHHHHhhhhH
Confidence 344444443 45567789999999985533
No 6
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=63.45 E-value=49 Score=24.03 Aligned_cols=43 Identities=19% Similarity=0.234 Sum_probs=37.8
Q ss_pred hhhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcc-hHHHHHHHHH
Q psy4906 8 RQGEIDRCLKKVSEGVETFEDIWQKVHNATNSN-QKEKYEADLK 50 (144)
Q Consensus 8 LQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~-QKEKlE~DLK 50 (144)
++.|||++=.++..+....+.+=.++.....++ +|+-+|.++.
T Consensus 3 V~~eId~lEekl~~cr~~le~ve~rL~~~eLs~e~R~~lE~E~~ 46 (85)
T PF15188_consen 3 VAKEIDGLEEKLAQCRRRLEAVESRLRRRELSPEARRSLEKELN 46 (85)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHHcccCCChHHHHHHHHHHH
Confidence 578999999999999999999999999997655 8999996654
No 7
>cd07675 F-BAR_FNBP1L The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Formin Binding Protein 1-Like. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FormiN Binding Protein 1-Like (FNBP1L), also known as Toca-1 (Transducer of Cdc42-dependent actin assembly), forms a complex with neural Wiskott-Aldrich syndrome protein (N-WASP). The FNBP1L/N-WASP complex induces the formation of filopodia and endocytic vesicles. FNBP1L is required for Cdc42-induced actin assembly and is essential for autophagy of intracellular pathogens. It contains an N-terminal F-BAR domain, a central Cdc42-binding HR1 domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=63.18 E-value=62 Score=27.47 Aligned_cols=49 Identities=14% Similarity=0.256 Sum_probs=30.6
Q ss_pred cchHHHHHHHHHHHH-----HHHHHHHHHHHHhhccccccchhhhHHHHHHHHHHHHHH
Q psy4906 39 SNQKEKYEADLKKEI-----KKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERF 92 (144)
Q Consensus 39 ~~QKEKlE~DLKkEI-----KKLQR~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~MErF 92 (144)
+.|+|.+..+|...| ...+.++.++|.++ .+-..|+..+......|++-
T Consensus 79 a~q~e~~a~~l~~~v~~~l~~~~~~l~~~rk~~~-----~~~~klqk~l~~~~~~leks 132 (252)
T cd07675 79 AGQREVVAEEMGHRVYGELMRYSHDLKGERKMHL-----QEGRKAQQYLDMCWKQMDNS 132 (252)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHH
Confidence 567888888885432 44578888888887 33344555555555555543
No 8
>PF06657 Cep57_MT_bd: Centrosome microtubule-binding domain of Cep57; InterPro: IPR010597 This entry is thought to represent a centrosomal protein of 57 kDa (Cep57-related protein). It is required for spindle microtubule attachment to both kinetochores and centrosomes and functions to tether minus-ends of spindle microtubules to centrosomes. It may act by forming ring-like structures around microtubules, or by serving as a cross-linker or scaffold at the attachment site [].
Probab=62.72 E-value=20 Score=25.22 Aligned_cols=55 Identities=15% Similarity=0.381 Sum_probs=40.2
Q ss_pred HHHHHHhHHHhHHH----HHHH---HHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy4906 12 IDRCLKKVSEGVET----FEDI---WQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSW 66 (144)
Q Consensus 12 IDr~lKkV~EGi~~----Fd~i---~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W 66 (144)
.-.+|+.+.+-+.. |..+ |..+..+.+...|.-|++.|+.=+++|-.--|||-..
T Consensus 15 Ls~vl~~LqDE~~hm~~e~~~L~~~~~~~d~s~~~~~R~~L~~~l~~lv~~mE~K~dQI~~L 76 (79)
T PF06657_consen 15 LSEVLKALQDEFGHMKMEHQELQDEYKQMDPSLGRRKRRDLEQELEELVKRMEAKADQIYKL 76 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445554444433 3333 7777778888899999999999999999999999653
No 9
>cd07594 BAR_Endophilin_B The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Vertebrates contain two endophilin-B isoforms. Endophilin-B proteins are cytoplasmic proteins expressed mainly in the heart, placenta, and skeletal muscle.
Probab=61.03 E-value=98 Score=25.87 Aligned_cols=88 Identities=17% Similarity=0.200 Sum_probs=70.3
Q ss_pred hhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhhHHHHHHHHHHH
Q psy4906 10 GEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQM 89 (144)
Q Consensus 10 ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~M 89 (144)
.+|-+.-|+|.--.-.||..-.++..+.++.....++.+|+.---|..+.-+--..-+.+---.+..+|.....+|+.++
T Consensus 133 k~i~k~RKkLe~rRLd~D~~k~r~~kAk~~~~~~~~e~elr~Ae~kF~~~~E~a~~~M~~i~~~~~~~~~~L~~lv~AQl 212 (229)
T cd07594 133 KTISKERKLLENKRLDLDACKTRVKKAKSAEAIEQAEQDLRVAQSEFDRQAEITKLLLEGISSTHANHLRCLRDFVEAQM 212 (229)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCCccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 36778889999999999999999988877766678899999888888888887776666422224567999999999999
Q ss_pred HHHHHHHH
Q psy4906 90 ERFKVVER 97 (144)
Q Consensus 90 ErFK~~Ek 97 (144)
+=|+.|=.
T Consensus 213 ~Yh~q~~e 220 (229)
T cd07594 213 TYYAQCYQ 220 (229)
T ss_pred HHHHHHHH
Confidence 98887643
No 10
>cd07598 BAR_FAM92 The Bin/Amphiphysin/Rvs (BAR) domain of Family with sequence similarity 92 (FAM92). BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of proteins from the family with sequence similarity 92 (FAM92), which were originally identified by the presence of the unknown domain DUF1208. This domain shows similarity to the BAR domains of sorting nexins. Mammals contain at least two member types, FAM92A and FAM92B, which may exist in many variants. The Xenopus homolog of FAM92A1, xVAP019, is essential for embryo survival and cell differentiation. FAM92A1 may be involved in regulating cell proliferation and apoptosis. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=59.98 E-value=90 Score=25.61 Aligned_cols=78 Identities=21% Similarity=0.289 Sum_probs=45.2
Q ss_pred hhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc-----------chhh
Q psy4906 9 QGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIK-----------DKST 77 (144)
Q Consensus 9 Q~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diK-----------dk~~ 77 (144)
|.++++.+.+|.|.+..|..+..-+...-...+ . -.+-+-+...+|-|+| +.++++-. -+..
T Consensus 78 q~qv~~l~~~v~epLk~Y~~l~k~~k~~~K~~~-~-ar~~~~~~~~~leklk-----~~~~~d~~~i~eaE~~l~~a~~d 150 (211)
T cd07598 78 QAEVERLEAKVVQPLALYGTICKHARDDLKNTF-T-ARNKELKQLKQLEKLR-----QKNPSDRQIISQAESELQKASVD 150 (211)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-H-HHHHHHHHHHHHHHHH-----hcCCchhhHHHHHHHHHHHHHHH
Confidence 568999999999999999998844432211000 0 1222333446666665 22322211 1113
Q ss_pred hHHHHHHHHHHHHHHH
Q psy4906 78 LLDYRKLIETQMERFK 93 (144)
Q Consensus 78 L~e~Rk~IE~~MErFK 93 (144)
.....+.|++.|.+|.
T Consensus 151 ~~r~s~~l~ee~~rFe 166 (211)
T cd07598 151 ANRSTKELEEQMDNFE 166 (211)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4556788888998884
No 11
>PF10368 YkyA: Putative cell-wall binding lipoprotein; InterPro: IPR019454 The YkyA family of proteins contain a lipoprotein signal and a hydrolase domain. They are similar to cell wall binding proteins and might also be recognisable by a host immune defence system. It is thus likely that they function in pathways important for pathogenicity []. ; PDB: 2AP3_A.
Probab=57.36 E-value=1e+02 Score=25.04 Aligned_cols=118 Identities=21% Similarity=0.266 Sum_probs=58.6
Q ss_pred HHhHHHHHHHHHHHhhc-CCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcc-ccccchhhhHHHHHHHHHHHHHHHHHHH
Q psy4906 20 SEGVETFEDIWQKVHNA-TNSNQKEKYEADLKKEIKKLQRLRDQIKSWIAS-AEIKDKSTLLDYRKLIETQMERFKVVER 97 (144)
Q Consensus 20 ~EGi~~Fd~i~~K~~~~-~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~-~diKdk~~L~e~Rk~IE~~MErFK~~Ek 97 (144)
.+|.+.|+.|=.....+ .|..+|++ -|++|=+-|+...+.++.--+. +.|+|+.+-.+.-.+++.=.+||+....
T Consensus 57 ~~~~~d~~~v~~~~~~a~~nv~~R~k---~l~~Ek~ai~~a~~e~~~~~~~i~ki~d~~~k~qa~~l~~~~~~ry~~~~~ 133 (204)
T PF10368_consen 57 QLGKDDNDEVKKLSDEALKNVDEREK---ELKKEKEAIEKAKEEFKKAKKYIDKIEDEKLKKQAKELNEAMKKRYKSYDK 133 (204)
T ss_dssp --G-SSHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHTT----------HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccCcchHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444444444433 23444544 4666666677777777765554 4688887666666666665557765544
Q ss_pred hhhcccchhhhcccc-------cCCCchHHHHHHHHHHHHHHHHHHHHhhhhc
Q psy4906 98 ETKTKAYSKEGLGAV-------QKMDPAQKEKEEISTWLVTSIDALNIQVSSV 143 (144)
Q Consensus 98 e~KtK~fSkegL~~~-------~~~dp~~~~k~e~~~wl~~~id~L~~QiE~~ 143 (144)
-. .+.+.+|... ...|+....-.+-..=|+.+-+++..+.+.|
T Consensus 134 l~---~~Y~~~l~~ekely~~L~~~d~~~~~l~~ki~~iN~~y~~~~~~~~~f 183 (204)
T PF10368_consen 134 LY---KAYKKALELEKELYEMLKDKDTTQKQLDEKIKAINQSYKEVNKQKEKF 183 (204)
T ss_dssp HH---HHHHHHHHHHHHHHHHHTSTT--HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HH---HHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33 3456666543 1233444445555556666666666666554
No 12
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=56.43 E-value=24 Score=22.94 Aligned_cols=58 Identities=21% Similarity=0.358 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHhhcccccc-chhhhHHHHHHHHHHHHHHHHHHHhhhcccchhhhcc
Q psy4906 53 IKKLQRLRDQIKSWIASAEIK-DKSTLLDYRKLIETQMERFKVVERETKTKAYSKEGLG 110 (144)
Q Consensus 53 IKKLQR~RdQIK~W~~~~diK-dk~~L~e~Rk~IE~~MErFK~~Eke~KtK~fSkegL~ 110 (144)
....++--+.+..|+...+-. ........-.-++..|..++.++.++....=.-+.|.
T Consensus 3 ~~~f~~~~~~l~~Wl~~~e~~l~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~l~~l~ 61 (105)
T PF00435_consen 3 LQQFQQEADELLDWLQETEAKLSSSEPGSDLEELEEQLKKHKELQEEIESRQERLESLN 61 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCSCTHSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHhhhhhHHHHHHHHHHHHH
Confidence 344555566777888774443 1111244445677888888888888877665555553
No 13
>PF14523 Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A.
Probab=56.03 E-value=35 Score=23.65 Aligned_cols=57 Identities=16% Similarity=0.322 Sum_probs=35.3
Q ss_pred hhhhHHHHHHhHHHhHHHHHHH-HHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHH
Q psy4906 8 RQGEIDRCLKKVSEGVETFEDI-WQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIK 64 (144)
Q Consensus 8 LQ~EIDr~lKkV~EGi~~Fd~i-~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK 64 (144)
++.++-.+++.+++.+..+..+ .....+...--+.+||-.|.+.-+...|+.-..+.
T Consensus 38 ~~~~~~~l~k~~~~~l~~l~~~~~~~~~~~~~k~~~~KL~~df~~~l~~fq~~q~~~~ 95 (102)
T PF14523_consen 38 LIQKTNQLIKEISELLKKLNSLSSDRSNDRQQKLQREKLSRDFKEALQEFQKAQRRYA 95 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHSH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666666666666655 11111111224699999999999999988766553
No 14
>smart00503 SynN Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p
Probab=55.29 E-value=69 Score=22.31 Aligned_cols=93 Identities=17% Similarity=0.294 Sum_probs=58.5
Q ss_pred hhhHHHHHHhHHHhHHHHHHHHHHHhhcCCc--chHHHHHHHHHHHHHHHHHHHHHHHHhhccc---------cccc-hh
Q psy4906 9 QGEIDRCLKKVSEGVETFEDIWQKVHNATNS--NQKEKYEADLKKEIKKLQRLRDQIKSWIASA---------EIKD-KS 76 (144)
Q Consensus 9 Q~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~--~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~---------diKd-k~ 76 (144)
-.+|...+..|+.-+..+...+..+.++..+ .-++++......=-..-+..+..||.--..+ +..- +.
T Consensus 10 v~~I~~~I~~i~~~v~~l~~l~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~~i~~~lk~l~~~~~~~~~~~~~~~r~~~~ 89 (117)
T smart00503 10 VEEIRANIQKISQNVAELQKLHEELLTPPDADKELREKLERLIDDIKRLAKEIRAKLKELEKENLENRASGSASDRTRKA 89 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhcccCCHhhhHHHH
Confidence 4678889999999999999999999887653 3466666543333333344444444432222 1111 12
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhhc
Q psy4906 77 TLLDYRKLIETQMERFKVVERETKT 101 (144)
Q Consensus 77 ~L~e~Rk~IE~~MErFK~~Eke~Kt 101 (144)
...-..+..-..|..|-.+++..+.
T Consensus 90 q~~~L~~~f~~~m~~fq~~Q~~~~~ 114 (117)
T smart00503 90 QTEKLRKKFKEVMNEFQRLQRKYRE 114 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444566667788899988887664
No 15
>PF04799 Fzo_mitofusin: fzo-like conserved region; InterPro: IPR006884 This entry represents the heptad repeat domain which is conserved at the C terminus of Fzo/mitofusion family of GTPases. Fzo is a mediator of mitochondrial fusion during spermatogenesis []. This conserved region is also found in the human mitofusin protein []. This domain forms a dimeric antiparallel coiled coil structure, which has been proposed to act as a mitochodrial tether before vesicle fusion [].; GO: 0003924 GTPase activity, 0006184 GTP catabolic process, 0008053 mitochondrial fusion, 0005741 mitochondrial outer membrane, 0016021 integral to membrane; PDB: 1T3J_A.
Probab=54.79 E-value=57 Score=26.55 Aligned_cols=62 Identities=21% Similarity=0.470 Sum_probs=33.8
Q ss_pred chhhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcc-ccccchhhhHHHHHHH
Q psy4906 7 GRQGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIAS-AEIKDKSTLLDYRKLI 85 (144)
Q Consensus 7 KLQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~-~diKdk~~L~e~Rk~I 85 (144)
.+|+|++-+|.+...-++ -..+||+.||+.|..-=+++..-+.. ..+++|. -.+
T Consensus 102 QVqqeL~~tf~rL~~~Vd-------------------~~~~eL~~eI~~L~~~i~~le~~~~~~k~LrnKa------~~L 156 (171)
T PF04799_consen 102 QVQQELSSTFARLCQQVD-------------------QTKNELEDEIKQLEKEIQRLEEIQSKSKTLRNKA------NWL 156 (171)
T ss_dssp --------HHHHHHHHHH-------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHH
T ss_pred HHHHHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHH
Confidence 345666666666554443 45678888998888766666555443 3333333 456
Q ss_pred HHHHHHHH
Q psy4906 86 ETQMERFK 93 (144)
Q Consensus 86 E~~MErFK 93 (144)
+.+.++|.
T Consensus 157 ~~eL~~F~ 164 (171)
T PF04799_consen 157 ESELERFQ 164 (171)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 77788886
No 16
>PF05082 Rop-like: Rop-like; InterPro: IPR007774 This family contains several uncharacterised bacterial proteins. These proteins are found in nitrogen fixation operons, so are likely to play a role in this process.; PDB: 3CSX_A 2JS5_B.
Probab=53.51 E-value=19 Score=25.10 Aligned_cols=22 Identities=45% Similarity=0.507 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhc
Q psy4906 47 ADLKKEIKKLQRLRDQIKSWIA 68 (144)
Q Consensus 47 ~DLKkEIKKLQR~RdQIK~W~~ 68 (144)
.+||++||||+|.=-|.|.=++
T Consensus 5 ~eLk~evkKL~~~A~~~kmdLH 26 (66)
T PF05082_consen 5 EELKKEVKKLNRKATQAKMDLH 26 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999998888776554
No 17
>PRK05287 hypothetical protein; Provisional
Probab=53.21 E-value=40 Score=28.72 Aligned_cols=46 Identities=22% Similarity=0.477 Sum_probs=35.1
Q ss_pred HHHHHH-HHHHHHHHHHHHHhhccccccchhhhHHHHHHHHHHHHHHH
Q psy4906 47 ADLKKE-IKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERFK 93 (144)
Q Consensus 47 ~DLKkE-IKKLQR~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~MErFK 93 (144)
+|||.| ||-|.|.+-.++.|..+++|- ...|......|+.....-.
T Consensus 57 ~DlKsdLlKeLerq~~~L~~~~~~p~vd-~~~l~~~l~~l~~~~~~L~ 103 (250)
T PRK05287 57 GDLKSDLLKELERQRQKLQKWRGNPGVD-QEALEALLQELEQASAALN 103 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCcC-HHHHHHHHHHHHHHHHHHH
Confidence 577776 578999999999999999885 4447777777777665544
No 18
>cd07593 BAR_MUG137_fungi The Bin/Amphiphysin/Rvs (BAR) domain of Schizosaccharomyces pombe Meiotically Up-regulated Gene 137 protein and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This subfamily is composed predominantly of uncharacterized fungal proteins with similarity to Schizosaccharomyces pombe Meiotically Up-regulated Gene 137 protein (MUG137), which may play a role in meiosis and sporulation in fission yeast. MUG137 contains an N-terminal BAR domain and a C-terminal SH3 domain, similar to endophilins. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be invol
Probab=52.74 E-value=1.3e+02 Score=24.82 Aligned_cols=87 Identities=11% Similarity=0.242 Sum_probs=70.2
Q ss_pred hhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhhHHHHHHHHHHH
Q psy4906 10 GEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQM 89 (144)
Q Consensus 10 ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~M 89 (144)
.+|-+..|+|.--.-.||..-.++..+.++. ..++.+|+.-=-|.-+..+....=+.+=--.+..++.....+|+.++
T Consensus 114 k~i~k~RKkLe~rRLdyD~~ksk~~kak~~~--~~~eeElr~Ae~kfees~E~a~~~M~~i~~~e~e~~~~L~~lv~AQl 191 (215)
T cd07593 114 KEYHSARKKLESRRLAYDAALTKSQKAKKED--SRLEEELRRAKAKYEESSEDVEARMVAIKESEADQYRDLTDLLDAEL 191 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhccccc--hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHH
Confidence 4778888999999999999999999886553 46888898888999999999888887433334567999999999999
Q ss_pred HHHHHHHHh
Q psy4906 90 ERFKVVERE 98 (144)
Q Consensus 90 ErFK~~Eke 98 (144)
+-|+.|=..
T Consensus 192 ~Yh~q~~e~ 200 (215)
T cd07593 192 DYHQQSLDV 200 (215)
T ss_pred HHHHHHHHH
Confidence 988866443
No 19
>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others. OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.
Probab=51.70 E-value=84 Score=23.32 Aligned_cols=62 Identities=15% Similarity=0.287 Sum_probs=41.4
Q ss_pred chhhhHHHHHHhHHHhHHHHHHHHHHHhhc---CCcchHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy4906 7 GRQGEIDRCLKKVSEGVETFEDIWQKVHNA---TNSNQKEKYEADLKKEIKKLQRLRDQIKSWIA 68 (144)
Q Consensus 7 KLQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~---~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~ 68 (144)
+|+.+.+..-+.+..--..|...+.++... -++.++...+.+|......|+++..++..=+.
T Consensus 40 ~l~~~~~~~~~~l~~~~~el~~~~~~l~~~~~~ls~~~~~~~~~~l~~~~~~l~~~~~~~~~~l~ 104 (158)
T PF03938_consen 40 KLQEKFKALQKELQAKQKELQKLQQKLQSQKATLSEEERQKRQQELQQKEQELQQFQQQAQQQLQ 104 (158)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS----SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444455555555666666666663 45677899999999988888888888775433
No 20
>PF02185 HR1: Hr1 repeat; InterPro: IPR000861 The HR1 repeat was first described as a three times repeated homology region of the N-terminal non-catalytic part of protein kinase PRK1(PKN) []. The first two of these repeats were later shown to bind the small G protein rho [, ] known to activate PKN in its GTP-bound form. Similar rho-binding domains also occur in a number of other protein kinases and in the rho-binding proteins rhophilin and rhotekin. Recently, the structure of the N-terminal HR1 repeat complexed with RhoA has been determined by X-ray crystallography []. It forms an antiparallel coiled-coil fold termed an ACC finger. This entry includes domains found within rho-associated protein kinases.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1CXZ_B 3O0Z_C 2RMK_B 1URF_A.
Probab=49.20 E-value=54 Score=21.83 Aligned_cols=58 Identities=22% Similarity=0.367 Sum_probs=42.7
Q ss_pred hhhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q psy4906 8 RQGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASA 70 (144)
Q Consensus 8 LQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~ 70 (144)
|+.+|++= .+|.+|.+..=.+| ++.+...+...++.|.---.|+.-||.+|..+....
T Consensus 6 L~~~i~~E-~ki~~Gae~m~~~~----~t~~~~~~~~~~~~l~~s~~kI~~L~~~L~~l~~~~ 63 (70)
T PF02185_consen 6 LQKKIDKE-LKIKEGAENMLQAY----STDKKKVLSEAESQLRESNQKIELLREQLEKLQQRS 63 (70)
T ss_dssp HHHHHHHH-HHHHHHHHHHHHHH----CCHHCH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_pred HHHHHHHH-HHHHHHHHHHHHHH----ccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 44555544 36889998888877 333333588999999999999999999998877653
No 21
>cd00179 SynN Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain
Probab=47.73 E-value=1.1e+02 Score=22.41 Aligned_cols=94 Identities=19% Similarity=0.258 Sum_probs=56.6
Q ss_pred hhHHHHHHhHHHhHHHHHHHHHHHhhcCC--cchHHHHHHHHHHHHHHHHHHHHHHHHhhcc----------ccccc-hh
Q psy4906 10 GEIDRCLKKVSEGVETFEDIWQKVHNATN--SNQKEKYEADLKKEIKKLQRLRDQIKSWIAS----------AEIKD-KS 76 (144)
Q Consensus 10 ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~--~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~----------~diKd-k~ 76 (144)
++|...+..|+..|..+...+..+.++.+ +.-+++++.-...=-..-...+..|+.--.. ++..- +.
T Consensus 9 ~~I~~~i~~i~~~v~~l~~l~~~~~t~~~~~~~~~~~l~~~~~~~~~~~~~ik~~lk~l~~~~~~~~~~~~s~~~r~~~~ 88 (151)
T cd00179 9 EEIRGNIDKISEDVEELQKLHSQLLTAPDADPELKQELESLVQEIKKLAKEIKGKLKELEESNEQNEALNGSSVDRIRKT 88 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHH
Confidence 57888899999999999999999988875 2236666543221111112222222222111 12222 22
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhhccc
Q psy4906 77 TLLDYRKLIETQMERFKVVERETKTKA 103 (144)
Q Consensus 77 ~L~e~Rk~IE~~MErFK~~Eke~KtK~ 103 (144)
...-..+.+-..|..|-.++...+.+.
T Consensus 89 q~~~L~~~f~~~m~~fq~~Q~~~~~~~ 115 (151)
T cd00179 89 QHSGLSKKFVEVMTEFNKAQRKYRERY 115 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566777888999999998887543
No 22
>PF07072 DUF1342: Protein of unknown function (DUF1342); InterPro: IPR009777 This family consists of several hypothetical bacterial proteins of around 250 residues in length. Members of this family are often known as YacF after the Escherichia coli protein P36680 from SWISSPROT. The function of this family is unknown.; PDB: 2OEZ_A.
Probab=46.95 E-value=40 Score=27.82 Aligned_cols=62 Identities=18% Similarity=0.422 Sum_probs=39.2
Q ss_pred HHHHHHHHHHhhcCCcchHHHHHHHHHHH-HHHHHHHHHHHHHhhccccccchhhhHHHHHHHHHHHHHHHH
Q psy4906 24 ETFEDIWQKVHNATNSNQKEKYEADLKKE-IKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERFKV 94 (144)
Q Consensus 24 ~~Fd~i~~K~~~~~~~~QKEKlE~DLKkE-IKKLQR~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~MErFK~ 94 (144)
..|..+++=+.-++. +|||.| ||-|.|++-.+..|..+++|-.. .|......|+.....-..
T Consensus 24 ~al~~Lfellev~~R--------~DlK~eLlKELeRq~~~L~~~~~~p~vd~~-~l~~~l~~l~~~~~~L~~ 86 (211)
T PF07072_consen 24 AALRALFELLEVLER--------ADLKSELLKELERQRQKLNQWRDNPGVDQE-ALDALLQELDQALQALQQ 86 (211)
T ss_dssp HHHHHHHHHHHHHCC--------S-HHHHHHHHHHHHHHHHHCTTT-TTS-HH-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhhh--------HHHHHHHHHHHHHHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHHHHHHh
Confidence 344555554444432 356665 57799999999999999998544 477766777666555443
No 23
>cd07671 F-BAR_PSTPIP1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine Phosphatase-Interacting Protein 1. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Proline-Serine-Threonine Phosphatase-Interacting Protein 1 (PSTPIP1), also known as CD2 Binding Protein 1 (CD2BP1), is mainly expressed in hematopoietic cells. It is a binding partner of the cell surface receptor CD2 and PTP-PEST, a tyrosine phosphatase which functions in cell motility and Rac1 regulation. It also plays a role in the activation of the Wiskott-Aldrich syndrome protein (WASP), which couples actin rearrangement and T cell activation. Mutations in the gene encoding PSTPIP1 cause the autoinflammatory disorder known as PAPA (pyogenic sterile arthritis, pyoderma gangrenosum, and acne) syndrome. PSTPIP1 contains an N-terminal F-BAR domain, PEST motifs, and a C-terminal SH3 domain. F-BAR
Probab=46.66 E-value=1.7e+02 Score=24.32 Aligned_cols=77 Identities=22% Similarity=0.120 Sum_probs=48.9
Q ss_pred CchhhhHHHHHHhHHHhHHHHHHHHHHHh----------hcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccccccch
Q psy4906 6 PGRQGEIDRCLKKVSEGVETFEDIWQKVH----------NATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDK 75 (144)
Q Consensus 6 RKLQ~EIDr~lKkV~EGi~~Fd~i~~K~~----------~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diKdk 75 (144)
+|+|.=....+++|...-..|+.-+.... +..++.+-||+++-+++.-.-+++.++.-..-+.
T Consensus 109 eK~qk~~~~~~k~l~ksKk~Ye~~Cke~~~a~q~~~k~~~~~t~keleK~~~K~~k~~~~~~~a~~~Y~~~v~------- 181 (242)
T cd07671 109 ERVQKSKVSLYKKTMESKKTYEQRCREADEAEQTFERSSSTGNPKQSEKSQNKAKQCRDAATEAERVYKQNIE------- 181 (242)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------
Confidence 34555555567777777788876664443 2344556777777777777777666655544332
Q ss_pred hhhHHHHHHHHHHHH
Q psy4906 76 STLLDYRKLIETQME 90 (144)
Q Consensus 76 ~~L~e~Rk~IE~~ME 90 (144)
.|.+.|-.-+..|.
T Consensus 182 -~l~~~~~~w~~~~~ 195 (242)
T cd07671 182 -QLDKARTEWETEHI 195 (242)
T ss_pred -HHHHHHHHHHHHHH
Confidence 36677777777775
No 24
>PF00804 Syntaxin: Syntaxin; InterPro: IPR006011 Syntaxins A and B are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins are a family of receptors for intracellular transport vesicles. Each target membrane may be identified by a specific member of the syntaxin family []. Members of the syntaxin family [, ] have a size ranging from 30 Kd to 40 Kd; a C-terminal extremity which is highly hydrophobic and anchors the protein on the cytoplasmic surface of cellular membranes; a central, well conserved region, which seems to be in a coiled-coil conformation. ; GO: 0016020 membrane; PDB: 1S94_B 1EZ3_A 3C98_B 1BR0_A 1FIO_A 2XHE_B.
Probab=45.43 E-value=91 Score=20.82 Aligned_cols=30 Identities=17% Similarity=0.375 Sum_probs=26.9
Q ss_pred hhHHHHHHhHHHhHHHHHHHHHHHhhcCCc
Q psy4906 10 GEIDRCLKKVSEGVETFEDIWQKVHNATNS 39 (144)
Q Consensus 10 ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~ 39 (144)
++|...+.+|..-+..+...+.++...+++
T Consensus 10 ~~i~~~i~~i~~~~~~l~~l~~~~l~~~~~ 39 (103)
T PF00804_consen 10 QEIREDIDKIKEKLNELRKLHKKILSSPDQ 39 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTSSSH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence 578889999999999999999999988874
No 25
>PF11166 DUF2951: Protein of unknown function (DUF2951); InterPro: IPR021337 This family of proteins has no known function. It has a highly conserved sequence.
Probab=43.17 E-value=1e+02 Score=23.22 Aligned_cols=57 Identities=25% Similarity=0.310 Sum_probs=38.4
Q ss_pred hhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHH-HHHHHHhhcc
Q psy4906 10 GEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRL-RDQIKSWIAS 69 (144)
Q Consensus 10 ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~-RdQIK~W~~~ 69 (144)
..|...|-.|.+|+..-+.+++|+.-+-.+=+||+ ++-+|.|+.-+- =-+||.|+-+
T Consensus 21 k~i~~~L~~Ik~gq~~qe~v~~kld~tlD~i~reR---e~dee~k~~n~Knir~~KmwilG 78 (98)
T PF11166_consen 21 KTIFNKLDEIKDGQHDQELVNQKLDRTLDEINRER---EEDEENKKKNDKNIRDIKMWILG 78 (98)
T ss_pred HHHHHHHHHHHHhHhhHHHHHHHHHhhHHHHHHHH---HHHHHHHHHHHhhHHHHHHHHHH
Confidence 35778889999999999999999965544444553 344455544332 3358888754
No 26
>PF00489 IL6: Interleukin-6/G-CSF/MGF family; InterPro: IPR003573 Interleukin-6 (IL6), also refered to as B-cell stimulatory factor-2 (BSF-2) and interferon beta-2, is a cytokine involved in a wide variety of biological functions []. It plays an essential role in the final differentiation of B-cells into IG-secreting cells, as well as inducing myeloma/plasmacytoma growth, nerve cell differentiation and, in hepatocytes, acute phase reactants [, ]. A number of other cytokines may be grouped with IL6 on the basis of sequence similarity [, , ]: these include granulocyte colony-stimulating factor (GCSF) and myelomonocytic growth factor (MGF). GCSF acts in hematopoiesis by affecting the production, differentiation and function of 2 related white cell groups in the blood []. MGF also acts in hematopoiesis, stimulating proliferation and colony formation of normal and transformed avian cells of the myeloid lineage. Cytokines of the IL6/GCSF/MGF family are glycoproteins of about 170 to 180 amino acid residues that contains four conserved cysteine residues involved in two disulphide bonds []. They have a compact, globular fold (similar to other interleukins), stabilised by the 2 disulphide bonds. One half of the structure is dominated by a 4 alpha-helix bundle with a left-handed twist []: the helices are anti-parallel, with 2 overhand connections, which fall into a 2-stranded anti-parallel beta-sheet. The fourth alpha-helix is important to the biological activity of the molecule []. It has been said [] that this family can be extended by the adjunction of LIF and OSM (see the relevant entry IPR001581 from INTERPRO) which seem to be structurally related.; GO: 0005125 cytokine activity, 0006955 immune response, 0005576 extracellular region; PDB: 1P9M_B 2IL6_A 1IL6_A 1ALU_A 3QWR_B 3DUH_C 3D85_C 3D87_C 1BGC_A 2L3Y_A ....
Probab=41.51 E-value=1.7e+02 Score=22.77 Aligned_cols=51 Identities=20% Similarity=0.480 Sum_probs=33.1
Q ss_pred HHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHH-HHHHHHHHH
Q psy4906 13 DRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKL-QRLRDQIKS 65 (144)
Q Consensus 13 Dr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKL-QR~RdQIK~ 65 (144)
|.||.++..|+..|..+.+-+.+--..+ ++.. .+|+--++-| +-++.+++.
T Consensus 53 e~CL~ri~~GL~~yq~lL~~l~~~~~~~-~~~v-~~Lq~~~~~L~~~i~~~~~~ 104 (154)
T PF00489_consen 53 ETCLSRIHSGLQEYQILLKYLQGEFPGL-KENV-ESLQLDTKDLAQTIKQKMKN 104 (154)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTTSSTTT-HHHH-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCccc-hhHH-HHHHHHHHHHHHHHHHHhhc
Confidence 7899999999999999998776643333 3332 3445444444 344445554
No 27
>cd07655 F-BAR_PACSIN The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins, also called Synaptic dynamin-associated proteins (Syndapins), act as regulators of cytoskeletal and membrane dynamics. They bind both dynamin and Wiskott-Aldrich syndrome protein (WASP), and may provide direct links between the actin cytoskeletal machinery through WASP and dynamin-dependent endocytosis. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSINs contain an N-terminal F-BAR domain and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce
Probab=39.45 E-value=1.3e+02 Score=24.82 Aligned_cols=58 Identities=17% Similarity=0.278 Sum_probs=32.9
Q ss_pred chhhhHHHHHHhHHHhHHHHHHHHHHHhhcCC------------cchHHHHHHHHHHHHHHHHHHHHHHH
Q psy4906 7 GRQGEIDRCLKKVSEGVETFEDIWQKVHNATN------------SNQKEKYEADLKKEIKKLQRLRDQIK 64 (144)
Q Consensus 7 KLQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~------------~~QKEKlE~DLKkEIKKLQR~RdQIK 64 (144)
|+|+-+...+++|...-..|+.......++.. +.+-+|+++-|.+-...+...++.-.
T Consensus 123 kaqk~~~~~~~~l~kaKk~Y~~~cke~e~a~~~~~~~~~d~~~~~~eleK~~~k~~k~~~~~~~~~~~Y~ 192 (258)
T cd07655 123 KAQKPWAKLLKKVEKAKKAYHAACKAEKSAQKQENNAKSDTSLSPDQVKKLQDKVEKCKQEVSKTKDKYE 192 (258)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555566677777777777777666544321 23345666666655555555444433
No 28
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=37.34 E-value=1.5e+02 Score=20.89 Aligned_cols=35 Identities=14% Similarity=0.326 Sum_probs=19.3
Q ss_pred cCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q psy4906 36 ATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASA 70 (144)
Q Consensus 36 ~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~ 70 (144)
.+++..++.+..++......+...-+.+.....++
T Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 105 (181)
T PF12729_consen 71 ATDPEERQEIEKEIDEARAEIDEALEEYEKLILSP 105 (181)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCH
Confidence 34455566666666666665555555555544333
No 29
>smart00126 IL6 Interleukin-6 homologues. Family includes granulocyte colony-stimulating factor (G-CSF) and myelomonocytic growth factor (MGF). IL-6 is also known as B-cell stimulatory factor 2.
Probab=36.59 E-value=2.2e+02 Score=22.69 Aligned_cols=53 Identities=25% Similarity=0.429 Sum_probs=36.1
Q ss_pred HHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHH-HHHHHHHHHhh
Q psy4906 13 DRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKL-QRLRDQIKSWI 67 (144)
Q Consensus 13 Dr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKL-QR~RdQIK~W~ 67 (144)
+.||.++..|+-.|..+++-+++--..+ ++..+. |---++=| |-+|++++.|-
T Consensus 53 e~CL~ri~~GL~~yq~~L~~l~~~f~~~-~~~v~~-l~~~~~~L~~~l~~k~k~~~ 106 (154)
T smart00126 53 EICLVKITAGLLEYQVYLEYLQNEFPEN-KENVDT-LQLDTKTLIQIIQQEMKDLG 106 (154)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCccc-cccHHH-HHHHHHHHHHHHHHHhhCcC
Confidence 6799999999999999999776553322 443332 33333333 66788888885
No 30
>PF03114 BAR: BAR domain; InterPro: IPR004148 Endocytosis and intracellular transport involve several mechanistic steps: (1) for the internalisation of cargo molecules, the membrane needs to bend to form a vesicular structure, which requires membrane curvature and a rearrangement of the cytoskeleton; (2) following its formation, the vesicle has to be pinched off the membrane; (3) the cargo has to be subsequently transported through the cell and the vesicle must fuse with the correct cellular compartment. Members of the Amphiphysin protein family are key regulators in the early steps of endocytosis, involved in the formation of clathrin-coated vesicles by promoting the assembly of a protein complex at the plasma membrane and directly assist in the induction of the high curvature of the membrane at the neck of the vesicle. Amphiphysins contain a characteristic domain, known as the BAR (Bin-Amphiphysin-Rvs)-domain, which is required for their in vivo function and their ability to tubulate membranes []. The crystal structure of these proteins suggest the domain forms a crescent-shaped dimer of a three-helix coiled coil with a characteristic set of conserved hydrophobic, aromatic and hydrophilic amino acids. Proteins containing this domain have been shown to homodimerise, heterodimerise or, in a few cases, interact with small GTPases. ; GO: 0005515 protein binding, 0005737 cytoplasm; PDB: 4AVM_A 2D4C_C 1X03_A 1X04_A 2RND_A 2RMY_A 2FIC_A 2C08_A 2Z0V_A 3SOG_A ....
Probab=35.97 E-value=1.9e+02 Score=21.68 Aligned_cols=84 Identities=19% Similarity=0.301 Sum_probs=54.3
Q ss_pred hhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhh-HHHHHHHHHH
Q psy4906 10 GEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTL-LDYRKLIETQ 88 (144)
Q Consensus 10 ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L-~e~Rk~IE~~ 88 (144)
.+|.+..++...-...||....++..+.+...+..-+.+|..--.+...+.++++..++.=--.-..-| ......|+.+
T Consensus 131 ~~i~~~~kkr~~~~ldyd~~~~k~~k~~~~~~~~~~~~~l~~a~~~f~~~~~~l~~~l~~l~~~~~~~l~~~l~~~i~~q 210 (229)
T PF03114_consen 131 KEIKKLIKKREKKRLDYDSARSKLEKLRKKKSKSSKEEKLEEAKEEFEALNEELKEELPKLFAKRQDILEPCLQSFIEAQ 210 (229)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCHTTSSBTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467777788888888888888888877543322222778888888888888888888875211111223 4445555555
Q ss_pred HHHHH
Q psy4906 89 MERFK 93 (144)
Q Consensus 89 MErFK 93 (144)
+.=|.
T Consensus 211 ~~~~~ 215 (229)
T PF03114_consen 211 LQYFQ 215 (229)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 54443
No 31
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=35.94 E-value=50 Score=22.86 Aligned_cols=39 Identities=26% Similarity=0.342 Sum_probs=26.7
Q ss_pred HHHHHHHhhccccccchhhhHHHHHHHHHHHHHHHHHHHh
Q psy4906 59 LRDQIKSWIASAEIKDKSTLLDYRKLIETQMERFKVVERE 98 (144)
Q Consensus 59 ~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~MErFK~~Eke 98 (144)
+|.|+.+|.+-.+- =..+..-+|..||.=+.|+|.+|.+
T Consensus 26 Lr~q~~~~~~ER~~-L~ekne~Ar~rvEamI~RLk~leq~ 64 (65)
T TIGR02449 26 LRAQEKTWREERAQ-LLEKNEQARQKVEAMITRLKALEQH 64 (65)
T ss_pred HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhhhhhccC
Confidence 56666666653221 1123566899999999999999865
No 32
>cd07600 BAR_Gvp36 The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Golgi vesicle protein of 36 kDa and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Proteomic analysis shows that Golgi vesicle protein of 36 kDa (Gvp36) may be involved in vesicular trafficking and nutritional adaptation. A Saccharomyces cerevisiae strain deficient in Gvp36 shows defects in growth, in actin cytoskeleton polarization, in endocytosis, in vacuolar biogenesis, and in the cell cycle. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=35.70 E-value=2.7e+02 Score=23.44 Aligned_cols=88 Identities=10% Similarity=0.186 Sum_probs=56.4
Q ss_pred hhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhhHHHHHHHHHHH
Q psy4906 10 GEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQM 89 (144)
Q Consensus 10 ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~M 89 (144)
.+|-+.-|+|..-.-.||..-.++..+.++..++-+..++..-=.++--..+--..-+.+ -+.....+...+.+|+.++
T Consensus 147 k~i~k~RKkle~~RLd~D~~K~~~~ka~~~~k~~~~~~e~E~aEdef~~a~E~a~~~M~~-il~~~e~i~~L~~fv~AQl 225 (242)
T cd07600 147 QKAHKARKKVEDKRLQLDTARAELKSAEPAEKQEAARVEVETAEDEFVSATEEAVELMKE-VLDNPEPLQLLKELVKAQL 225 (242)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHhHHHHHHHHHH-HHhhhHHHHHHHHHHHHHH
Confidence 367788888888889999998888887665544444444443333333344433333322 1334447888888999999
Q ss_pred HHHHHHHHh
Q psy4906 90 ERFKVVERE 98 (144)
Q Consensus 90 ErFK~~Eke 98 (144)
+-|+.|=..
T Consensus 226 ~Yh~~~~e~ 234 (242)
T cd07600 226 AYHKTAAEL 234 (242)
T ss_pred HHHHHHHHH
Confidence 888876443
No 33
>PF10400 Vir_act_alpha_C: Virulence activator alpha C-term; InterPro: IPR018309 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response []. This entry represents the C-terminal domain.; PDB: 1YG2_A.
Probab=33.61 E-value=1.5e+02 Score=19.82 Aligned_cols=62 Identities=15% Similarity=0.227 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhcccch--hhhcccccCCCchHHHHHHHHHHHHHHHHHHHHh
Q psy4906 78 LLDYRKLIETQMERFKVVERETKTKAYS--KEGLGAVQKMDPAQKEKEEISTWLVTSIDALNIQ 139 (144)
Q Consensus 78 L~e~Rk~IE~~MErFK~~Eke~KtK~fS--kegL~~~~~~dp~~~~k~e~~~wl~~~id~L~~Q 139 (144)
|.+.+...+..+..|..++......+.. ......-..++-.-.--.-..+|+..+|+.|+..
T Consensus 26 l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ltl~~Gi~~~~~~i~W~~~~~~~L~~~ 89 (90)
T PF10400_consen 26 LEERREQHEERLAEYEEIEQEIFSDPDELDPEAFYWYLTLEYGIRYEQAEIEWCEEAIEELEKR 89 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHSS-GGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 6666777777777777766543333111 1111111111111112234678999999999863
No 34
>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
Probab=32.85 E-value=1.5e+02 Score=27.72 Aligned_cols=58 Identities=16% Similarity=0.221 Sum_probs=0.0
Q ss_pred hhhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q psy4906 8 RQGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASA 70 (144)
Q Consensus 8 LQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~ 70 (144)
++.+++.+-.++.+-...|.. ..+.-..+|+.++.+++..-..+.+.+++++.+++++
T Consensus 235 l~~ele~a~~~l~~l~~~~~~-----~GG~~~~~r~~Le~ei~~le~e~~e~~~~l~~l~~~~ 292 (650)
T TIGR03185 235 LRNELEEAQRSLESLEKKFRS-----EGGDLFEEREQLERQLKEIEAARKANRAQLRELAADP 292 (650)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-----hcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
No 35
>PF02646 RmuC: RmuC family; InterPro: IPR003798 This protein contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures []. Proteins in this family are predicted to contain a central endonuclease-like fold domain, surrounded by coiled coils, consistent with a direct role in DNA cleavage [, ].
Probab=30.98 E-value=2.5e+02 Score=23.94 Aligned_cols=47 Identities=23% Similarity=0.398 Sum_probs=33.6
Q ss_pred hhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHH
Q psy4906 9 QGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLR 60 (144)
Q Consensus 9 Q~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~R 60 (144)
|+.|+.+++-|.|-++.|...-+..+.. .-+--+.|..+|+.|....
T Consensus 1 ~~~l~~l~~pl~e~l~~~~~~l~~~~~~-----~~~~~~~L~~~l~~l~~~~ 47 (304)
T PF02646_consen 1 QEQLEQLLKPLKEQLEKFEKRLEESFEQ-----RSEEFGSLKEQLKQLSEAN 47 (304)
T ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHhh
Confidence 5678999999999999888655555433 2233477888887776666
No 36
>cd00176 SPEC Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here
Probab=30.86 E-value=2.1e+02 Score=20.76 Aligned_cols=89 Identities=15% Similarity=0.327 Sum_probs=52.4
Q ss_pred HhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc--chhhhHHHHHHHHHHHHHHHH
Q psy4906 17 KKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIK--DKSTLLDYRKLIETQMERFKV 94 (144)
Q Consensus 17 KkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diK--dk~~L~e~Rk~IE~~MErFK~ 94 (144)
..|..-++..+..|+.+... .......|+.-+ ...+.++.+++ +-.|+...+-. +-.+.. .-..++..+..++.
T Consensus 75 ~~i~~~~~~l~~~w~~l~~~-~~~r~~~L~~~~-~~~~~~~~~~~-l~~wl~~~e~~l~~~~~~~-~~~~~~~~l~~~~~ 150 (213)
T cd00176 75 EEIQERLEELNQRWEELREL-AEERRQRLEEAL-DLQQFFRDADD-LEQWLEEKEAALASEDLGK-DLESVEELLKKHKE 150 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH-HHHHHHHHHHH-HHHHHHHHHHHhcCcccCC-CHHHHHHHHHHHHH
Confidence 34555555666666666443 222355555555 34567777777 89999885443 211111 44567777777887
Q ss_pred HHHhhhcccchhhhc
Q psy4906 95 VERETKTKAYSKEGL 109 (144)
Q Consensus 95 ~Eke~KtK~fSkegL 109 (144)
+..+.......-+.+
T Consensus 151 ~~~~~~~~~~~~~~~ 165 (213)
T cd00176 151 LEEELEAHEPRLKSL 165 (213)
T ss_pred HHHHHHhchHHHHHH
Confidence 777776555555544
No 37
>cd07654 F-BAR_FCHSD The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains proteins (FCHSD). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of FCH and double SH3 domain (FCHSD) proteins, so named as they contain an N-terminal F-BAR domain and two SH3 domains at the C-terminus. Vertebrates harbor two subfamily members, FCHSD1 and FCHSD2, which have been characterized only in silico. Their biological function is still unknown. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=29.83 E-value=1.5e+02 Score=25.09 Aligned_cols=37 Identities=24% Similarity=0.305 Sum_probs=26.2
Q ss_pred CchhhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHH
Q psy4906 6 PGRQGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEA 47 (144)
Q Consensus 6 RKLQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~ 47 (144)
.+||+|++++++-+.-.--.|+.......++ ++|++.
T Consensus 120 ~~lq~el~~~~~eL~ksKK~Y~~~~~~~~~a-----r~K~~~ 156 (264)
T cd07654 120 QRAQAEVQQTVRELSKSRKTYFEREQVAHLA-----REKAAD 156 (264)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH-----HHHHHH
Confidence 5788899999888888888887655543333 677763
No 38
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=29.10 E-value=2.1e+02 Score=20.26 Aligned_cols=22 Identities=14% Similarity=0.389 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhc
Q psy4906 47 ADLKKEIKKLQRLRDQIKSWIA 68 (144)
Q Consensus 47 ~DLKkEIKKLQR~RdQIK~W~~ 68 (144)
..|..+|..|+..+.++..|++
T Consensus 9 ~~l~~~i~~l~~~~~~l~~~~~ 30 (129)
T cd00890 9 QQLQQQLEALQQQLQKLEAQLT 30 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3467777788888877777765
No 39
>PF06730 FAM92: FAM92 protein; InterPro: IPR009602 This family consists of several eukaryotic sequences of around 270 residues in length. Members of this family are found in mouse, human and Drosophila melanogaster. The function of this family is unknown.
Probab=28.76 E-value=3.6e+02 Score=22.78 Aligned_cols=78 Identities=26% Similarity=0.407 Sum_probs=43.5
Q ss_pred hhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcccc--c--------cchhhh
Q psy4906 9 QGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAE--I--------KDKSTL 78 (144)
Q Consensus 9 Q~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~d--i--------Kdk~~L 78 (144)
|.+|+|+--||-+-+..|..+-...-.- =.+...--.+|||++..| |.+++=-+++- | +-+...
T Consensus 85 qa~v~RlE~KVv~pL~~Y~~~cK~~r~e-----lK~~~~ar~kEikq~~~L-eklr~k~psdr~~isqae~el~kas~~~ 158 (219)
T PF06730_consen 85 QAEVERLEAKVVEPLSQYGTICKHARDE-----LKKFNKARNKEIKQLKQL-EKLRQKNPSDRQIISQAESELQKASVDA 158 (219)
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHH-HHHHccCCccchhhhHHHHHHHHHHHHH
Confidence 5788888888888888888665443110 112334456777777643 23333333322 1 112234
Q ss_pred HHHHHHHHHHHHHH
Q psy4906 79 LDYRKLIETQMERF 92 (144)
Q Consensus 79 ~e~Rk~IE~~MErF 92 (144)
...-+.+|+.|+.|
T Consensus 159 ~rt~~~Lee~i~~F 172 (219)
T PF06730_consen 159 TRTTKQLEETIDNF 172 (219)
T ss_pred HHHHHHHHHHHHHH
Confidence 45557778888877
No 40
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=28.51 E-value=2e+02 Score=20.83 Aligned_cols=29 Identities=10% Similarity=0.100 Sum_probs=25.2
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy4906 39 SNQKEKYEADLKKEIKKLQRLRDQIKSWI 67 (144)
Q Consensus 39 ~~QKEKlE~DLKkEIKKLQR~RdQIK~W~ 67 (144)
..+.+.+.+.|...+..|.+++.++..|.
T Consensus 79 ~~~~~~~~~~l~~~~~~L~~l~~~L~~~~ 107 (107)
T cd01111 79 EACLAQLRQKIEVRRAALNALTTQLAEMA 107 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 34688888999999999999999999883
No 41
>cd00176 SPEC Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here
Probab=28.04 E-value=1.7e+02 Score=21.26 Aligned_cols=55 Identities=16% Similarity=0.247 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHhhcccccc--chhhhHHHHHHHHHHHHHHHHHHHhhhcccchhhhcc
Q psy4906 55 KLQRLRDQIKSWIASAEIK--DKSTLLDYRKLIETQMERFKVVERETKTKAYSKEGLG 110 (144)
Q Consensus 55 KLQR~RdQIK~W~~~~diK--dk~~L~e~Rk~IE~~MErFK~~Eke~KtK~fSkegL~ 110 (144)
++++--+.+-.|+...+.. +..+.. .-..++..+++|+.+.+++..+...-+++.
T Consensus 4 ~f~~~~~~l~~Wl~~~e~~l~~~~~~~-d~~~~~~~l~~~~~~~~e~~~~~~~~~~l~ 60 (213)
T cd00176 4 QFLRDADELEAWLSEKEELLSSTDYGD-DLESVEALLKKHEALEAELAAHEERVEALN 60 (213)
T ss_pred HHHHhHHHHHHHHHHHHHHhcCcccCC-CHHHHHHHHHHHHHHHHHHHHCHHHHHHHH
Confidence 3444556677888775443 222222 344778888888888888877666666664
No 42
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=27.97 E-value=1.4e+02 Score=20.02 Aligned_cols=24 Identities=17% Similarity=0.325 Sum_probs=17.3
Q ss_pred ccccchhhhHHHHHHHHHHHHHHH
Q psy4906 70 AEIKDKSTLLDYRKLIETQMERFK 93 (144)
Q Consensus 70 ~diKdk~~L~e~Rk~IE~~MErFK 93 (144)
...|+..-=...||.|=..||+|+
T Consensus 32 ~~LK~~GIp~r~RryiL~~~ek~r 55 (57)
T PF09597_consen 32 KQLKELGIPVRQRRYILRWREKYR 55 (57)
T ss_pred HHHHHCCCCHHHHHHHHHHHHHHh
Confidence 445555555668889999999886
No 43
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=27.92 E-value=1.8e+02 Score=19.19 Aligned_cols=45 Identities=20% Similarity=0.359 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhccccccchhh---hHHHHHHHHHHHHHH
Q psy4906 48 DLKKEIKKLQRLRDQIKSWIASAEIKDKST---LLDYRKLIETQMERF 92 (144)
Q Consensus 48 DLKkEIKKLQR~RdQIK~W~~~~diKdk~~---L~e~Rk~IE~~MErF 92 (144)
-|.++|.||+..-+.+..=++|+..-.+.| ....|...+.-....
T Consensus 8 rL~Kel~kl~~~i~~~~~kL~n~~F~~kAP~eVve~er~kl~~~~~~~ 55 (66)
T PF10458_consen 8 RLEKELEKLEKEIERLEKKLSNENFVEKAPEEVVEKEREKLEELEEEL 55 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCSTTHHHHS-CCHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHcCccccccCCHHHHHHHHHHHHHHHHHH
Confidence 345566666666666666667666655543 444454444443333
No 44
>PF03528 Rabaptin: Rabaptin; InterPro: IPR018514 Regeneration of injured axons at neuromuscular junctions has been assumed to be regulated by extra-cellular factors that promote neurite outgrowth. A novel neurite outgrowth factor from chick denervated skeletal muscle has been cloned and characterised. The protein, termed neurocrescin (rabaptin), has been shown to be secreted in an activity-dependent fashion [].Rabaptin is a 100kDa coiled-coil protein that interacts with the GTP form of the small GTPase Rab5, a potent regulator of endocytic transport []. It is mainly cytosolic, but a fraction co-localises with Rab5 to early endosomes. Rab5 recruits rabaptin-5 to purified early endosomes in a GTP-dependent manner, demonstrating functional similarities with other members of the Ras superfamily. Immunodepletion of rabaptin-5 from cytosol strongly inhibits Rab5-dependent early endosome fusion. Thus, rabaptin-5 is a Rab effector required for membrane docking and fusion.; GO: 0005096 GTPase activator activity, 0008083 growth factor activity; PDB: 1X79_C.
Probab=27.83 E-value=39 Score=25.51 Aligned_cols=53 Identities=25% Similarity=0.314 Sum_probs=4.9
Q ss_pred CCCcCchhhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcch--HHHHHHHHHHHHHHHHH
Q psy4906 2 YRTYPGRQGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQ--KEKYEADLKKEIKKLQR 58 (144)
Q Consensus 2 ~~~~RKLQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~Q--KEKlE~DLKkEIKKLQR 58 (144)
..+.|+=|.||--+.--|.+++..|+.-|..++.-..+.+ ++..+-+ +++||+
T Consensus 16 ~~~~r~~qEEvASLq~i~k~tv~~ye~~~~~LeqEr~Q~~q~~e~~~Re----v~~L~~ 70 (106)
T PF03528_consen 16 IEVQRQWQEEVASLQAILKETVSEYETQWSLLEQERLQWQQYRESEERE----VAKLQR 70 (106)
T ss_dssp ----------------------------------------------HHH----HHHHHH
T ss_pred HHHHhHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH----HHHhcc
Confidence 3567889999999999999999999998888765533332 4444433 666664
No 45
>PF14282 FlxA: FlxA-like protein
Probab=27.71 E-value=2e+02 Score=20.90 Aligned_cols=27 Identities=26% Similarity=0.487 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccccc
Q psy4906 43 EKYEADLKKEIKKLQRLRDQIKSWIASAEI 72 (144)
Q Consensus 43 EKlE~DLKkEIKKLQR~RdQIK~W~~~~di 72 (144)
+..=..|++.|+.|+ ++|+.+..+.+.
T Consensus 18 ~~~I~~L~~Qi~~Lq---~ql~~l~~~~~~ 44 (106)
T PF14282_consen 18 DSQIEQLQKQIKQLQ---EQLQELSQDSDL 44 (106)
T ss_pred HHHHHHHHHHHHHHH---HHHHHHHcccCC
Confidence 555667888887777 788888885443
No 46
>COG2924 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.34 E-value=52 Score=24.31 Aligned_cols=15 Identities=40% Similarity=0.598 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHH
Q psy4906 79 LDYRKLIETQMERFK 93 (144)
Q Consensus 79 ~e~Rk~IE~~MErFK 93 (144)
.++|+++|..|+.|=
T Consensus 60 ~e~Rk~Leqem~~fl 74 (90)
T COG2924 60 AEHRKLLEQEMVNFL 74 (90)
T ss_pred HHHHHHHHHHHHHHh
Confidence 589999999999993
No 47
>KOG2117|consensus
Probab=27.30 E-value=1.6e+02 Score=26.84 Aligned_cols=83 Identities=20% Similarity=0.332 Sum_probs=50.5
Q ss_pred hHHHHHHHHHHHhhcCC-----------------------cchHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc----c
Q psy4906 22 GVETFEDIWQKVHNATN-----------------------SNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIK----D 74 (144)
Q Consensus 22 Gi~~Fd~i~~K~~~~~~-----------------------~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diK----d 74 (144)
+|=.||++|+-+++..+ +.-|-++|-.|.-| ++|||=|+-=..-....+.= .
T Consensus 67 tif~YDe~YDdmq~kk~e~~~~~~~~~~r~kPkYi~nLie~aerRkkE~e~r~E-Rkl~KeREkEg~~fdDkekfVTgAY 145 (379)
T KOG2117|consen 67 TIFGYDEVYDDMQSKKREQLPRLRLREKRRKPKYIENLIEAAERRKKEQELRYE-RKLLKEREKEGDEFDDKEKFVTGAY 145 (379)
T ss_pred chhccchhhHHHHHHHhhhhHhhhhhccccccHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhhccccccchhhhhHHH
Confidence 56778999999975533 22234444444443 57777777544444333321 5
Q ss_pred hhhhHHHHHHHHHHHH--HHHHHHHhhhcccch
Q psy4906 75 KSTLLDYRKLIETQME--RFKVVERETKTKAYS 105 (144)
Q Consensus 75 k~~L~e~Rk~IE~~ME--rFK~~Eke~KtK~fS 105 (144)
+..|.|-++-+|..=+ -|-+|---+|.|-||
T Consensus 146 KKklEE~~k~~e~Ek~~e~~e~~ddVTKqKDls 178 (379)
T KOG2117|consen 146 KKKLEEVKKWLEQEKEEEALEATDDVTKQKDLS 178 (379)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhcchhhhhhHH
Confidence 5677787777776443 455666667777766
No 48
>PRK09793 methyl-accepting protein IV; Provisional
Probab=27.15 E-value=3.7e+02 Score=24.19 Aligned_cols=64 Identities=8% Similarity=0.260 Sum_probs=48.7
Q ss_pred hhHHHHHHhHHHhHHHHHHHHHHHhhcC-CcchHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc
Q psy4906 10 GEIDRCLKKVSEGVETFEDIWQKVHNAT-NSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIK 73 (144)
Q Consensus 10 ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~-~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diK 73 (144)
.++.+.+..+.+.+..++..|+.|.... ++..-..+-.++..-........+++-.|+..+++.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~~l~~~~~~~~~~~~~~~~l~~~~~~~ 145 (533)
T PRK09793 81 DDIKTLMTTARASLTQSTTLFKSFMAMTAGNEHVRALQKETEKSFARWHNDLEHQATWLESNQLS 145 (533)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhcccCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH
Confidence 4567888889999999999999998653 334444566778888888888888899998776654
No 49
>PTZ00473 Plasmodium Vir superfamily; Provisional
Probab=27.04 E-value=1.5e+02 Score=27.36 Aligned_cols=100 Identities=15% Similarity=0.151 Sum_probs=63.8
Q ss_pred HhHHHHHHHHHHHhhcCC---------cchHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhhHHHHHHHHHHHHH
Q psy4906 21 EGVETFEDIWQKVHNATN---------SNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMER 91 (144)
Q Consensus 21 EGi~~Fd~i~~K~~~~~~---------~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~MEr 91 (144)
+++-.=+.||+.+-...- ++-=+++=.|+.+.|+| .+++.-+.++.--+.
T Consensus 75 g~l~~n~~iw~~~~ew~y~~~~~~~v~s~~l~~f~~~~~~li~k---------------------~il~~f~kfk~~~~~ 133 (420)
T PTZ00473 75 GDLKKNDDIWKDFVEWFYNKQEKFDVFSNHLESFNYDFEYLIQK---------------------NILKNFNKFKKLYEN 133 (420)
T ss_pred ccccchhHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHHH---------------------HhhhhHhhccccccc
Confidence 445555666666544322 22245666677776643 255556667777788
Q ss_pred HHHHHHhhhcccchhhhcc-cccCCCchHHHHHHHHHHHHHHHHHHHHhhh
Q psy4906 92 FKVVERETKTKAYSKEGLG-AVQKMDPAQKEKEEISTWLVTSIDALNIQVS 141 (144)
Q Consensus 92 FK~~Eke~KtK~fSkegL~-~~~~~dp~~~~k~e~~~wl~~~id~L~~QiE 141 (144)
++++|..||.=-|+--.-. ..-...|........|+|+++|||--++=+.
T Consensus 134 ~~e~e~ImKL~yFteNig~Ik~lm~~~~~~~y~s~C~fvn~CidIYrk~i~ 184 (420)
T PTZ00473 134 NYELEDIMKLFYFTENVGDIKSLMGAPDNEHYASSCKFVNDCLDIYRKYKD 184 (420)
T ss_pred chhHHHHHHHHHHHhhhHHHHHHhcCCcchhHHHHHHHHHHHHHHHHHHHH
Confidence 8889999998877643322 2212235556677899999999998877663
No 50
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=26.92 E-value=2.7e+02 Score=22.28 Aligned_cols=25 Identities=32% Similarity=0.486 Sum_probs=22.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhhc
Q psy4906 77 TLLDYRKLIETQMERFKVVERETKT 101 (144)
Q Consensus 77 ~L~e~Rk~IE~~MErFK~~Eke~Kt 101 (144)
.|+-+|+-||+-|.+-..+|--++-
T Consensus 119 qll~hr~e~ee~~~~l~~le~~~~~ 143 (175)
T PRK13182 119 QLLQHRREMEEMLERLQKLEARLKK 143 (175)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 5999999999999999999987764
No 51
>cd07673 F-BAR_FCHO2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only 2 protein. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. The specific function of FCH domain Only 2 (FCHO2) is still unknown. It contains an N-terminal F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in FCHO1 and endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=26.81 E-value=3.8e+02 Score=22.46 Aligned_cols=75 Identities=21% Similarity=0.270 Sum_probs=52.4
Q ss_pred hhhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHH----HHHHHHhhcc--cc-----ccchh
Q psy4906 8 RQGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRL----RDQIKSWIAS--AE-----IKDKS 76 (144)
Q Consensus 8 LQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~----RdQIK~W~~~--~d-----iKdk~ 76 (144)
-+.+||++..++.-.-+.|....+++... +..++.++..-..++|.+ -+.+|.++.. +. +.+-.
T Consensus 155 t~k~leK~~~k~~ka~~~Y~~~v~~l~~~-----~~~~~~~m~~~~~~~Q~~Ee~Ri~~~k~~l~~y~~~~s~~~~~~~~ 229 (269)
T cd07673 155 TQREIEKAAVKSKKATESYKLYVEKYALA-----KADFEQKMTETAQKFQDIEETHLIRIKEIIGSYSNSVKEIHIQIGQ 229 (269)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHH
Confidence 47889999888888888877777777533 558999999999998876 3456666654 22 22344
Q ss_pred hhHHHHHHHHH
Q psy4906 77 TLLDYRKLIET 87 (144)
Q Consensus 77 ~L~e~Rk~IE~ 87 (144)
...+-|+.||.
T Consensus 230 ~~e~ir~~le~ 240 (269)
T cd07673 230 VHEEFINNMAN 240 (269)
T ss_pred HHHHHHHHHHh
Confidence 56666666654
No 52
>PRK13415 flagella biosynthesis protein FliZ; Provisional
Probab=26.31 E-value=2e+02 Score=24.28 Aligned_cols=52 Identities=29% Similarity=0.466 Sum_probs=34.6
Q ss_pred hhHHHHHHhHHHhHHHHHHHH----HHH----hhc---CCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy4906 10 GEIDRCLKKVSEGVETFEDIW----QKV----HNA---TNSNQKEKYEADLKKEIKKLQRLRDQI 63 (144)
Q Consensus 10 ~EIDr~lKkV~EGi~~Fd~i~----~K~----~~~---~~~~QKEKlE~DLKkEIKKLQR~RdQI 63 (144)
+||+.++..=.+..+...+ | .++ ... .+++ =.-+..-|++||+.|.+-|+.+
T Consensus 144 ~eve~il~~~e~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~-~~sF~~~l~~ql~~l~~~r~e~ 206 (219)
T PRK13415 144 KEIEEILAQHEERLESKAE-WSRWGQKLRDQWKGKSKQKQTT-LPSFSALLKEELKELKEKRSEG 206 (219)
T ss_pred HHHHHHHHHHHHhhhhhhc-hHHHHHHHHHhhhccccCCCCC-CccHHHHHHHHHHHHHHHHHHH
Confidence 5888888877777654443 3 221 111 1222 3678999999999999999876
No 53
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=24.62 E-value=1.1e+02 Score=22.64 Aligned_cols=43 Identities=23% Similarity=0.538 Sum_probs=28.3
Q ss_pred hHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhccccccc
Q psy4906 22 GVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKD 74 (144)
Q Consensus 22 Gi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diKd 74 (144)
|.+.|+++|+-+..++.+. -+++==+.+=.+|+.|+..+-.+-
T Consensus 2 ~~~vF~s~~~~~~D~~e~a----------~~m~ir~~l~~~i~~~i~q~~l~Q 44 (91)
T COG5606 2 SNEVFTSVWDAIEDTPEAA----------ENMKIRSALMMAIKQWIEQAALSQ 44 (91)
T ss_pred CCchhhhHHHHHhccHHHH----------HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578999999998886222 123333556678888887655443
No 54
>PRK10361 DNA recombination protein RmuC; Provisional
Probab=24.34 E-value=3.6e+02 Score=25.18 Aligned_cols=75 Identities=17% Similarity=0.275 Sum_probs=53.3
Q ss_pred hhhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcc------ccccchhhhHH--
Q psy4906 9 QGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIAS------AEIKDKSTLLD-- 80 (144)
Q Consensus 9 Q~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~------~diKdk~~L~e-- 80 (144)
+.-|+.+|+=+.|-|+.|..--+.+++. .. +--+.|+.+|+.|+.+-.+|-.=..+ .+.|.....-|
T Consensus 135 ~~~l~~ll~Pl~e~l~~f~~~v~~~~~~---~~--~~~~~L~~qi~~L~~~n~~i~~ea~nLt~ALkgd~K~rG~WGE~q 209 (475)
T PRK10361 135 RQSLNSLLSPLREQLDGFRRQVQDSFGK---EA--QERHTLAHEIRNLQQLNAQMAQEAINLTRALKGDNKTQGNWGEVV 209 (475)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHH---HH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCcCcchHHHH
Confidence 4678999999999999999755555433 22 33389999999999998888765444 34444444545
Q ss_pred HHHHHHHH
Q psy4906 81 YRKLIETQ 88 (144)
Q Consensus 81 ~Rk~IE~~ 88 (144)
.++.+|..
T Consensus 210 LerILE~s 217 (475)
T PRK10361 210 LTRVLEAS 217 (475)
T ss_pred HHHHHHHh
Confidence 66777764
No 55
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.32 E-value=2.1e+02 Score=25.19 Aligned_cols=48 Identities=21% Similarity=0.404 Sum_probs=33.5
Q ss_pred hHHHhHHHHHHHHHHHhhcCCc-----------chHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4906 18 KVSEGVETFEDIWQKVHNATNS-----------NQKEKYEADLKKEIKKLQRLRDQIKS 65 (144)
Q Consensus 18 kV~EGi~~Fd~i~~K~~~~~~~-----------~QKEKlE~DLKkEIKKLQR~RdQIK~ 65 (144)
+++.-.+.|.++++.+.+.+++ +-=++..--+++.|.-||.+|.|++.
T Consensus 147 ~lqd~~dal~elfe~vss~tpsVskeydiy~vs~~~d~~~rl~kkDie~L~k~R~~L~~ 205 (293)
T COG4079 147 KLQDAVDALMELFETVSSKTPSVSKEYDIYQVSSNVDPVLRLVKKDIETLRKHRRRLAE 205 (293)
T ss_pred CHHHHHHHHHHHHHHhhcCCCcccceeEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3667788999999998755441 11223566677888888888888764
No 56
>PF01806 Paramyxo_P: Paramyxovirinae P phosphoprotein C-terminal region; InterPro: IPR002693 Sendai virus is a member of the Paramyxovirinae family. Its negative-sense ssRNA genome is packaged by the viral nucleoprotein (N) within a helical nucleocapsid. Paramyxovirinae use this N-RNA (nucleoprotein-RNA) complex as a template for both transcription and replication. During viral genome replication, the synthesis of viral RNA and its encapsidation by N are concomitant. Viral transcription and replication are carried out by viral RNA-dependent RNA polymerase, which consists of two proteins: L polymerase and phosphoprotein P. The L polymerase carries the enzyme activity. Phosphoprotein P binds the viral nucleocapsid, and positions the L polymerase on the template for transcription and replication formed by nucleoprotein-RNA (N-RNA) []. This entry represents phosphoprotein P from Sendai virus as well as from close family members. Phosphoprotein P, an indispensable subunit of the viral polymerase complex, is a modular protein organised into two moieties that are both functionally and structurally distinct: a well-conserved C-terminal moiety that contains all the regions required for transcription, and a poorly conserved, intrinsically unstructured N-terminal moiety that provides several additional functions required for replication. The N-terminal moiety is responsible for binding to newly synthesized free N(0) (nucleoprotein that has not yet bound RNA), in order to prevent the binding of N(0) to cellular RNA. The C-terminal moiety consists of an oligomerisation domain, an N-RNA (nucleoprotein-RNA)-binding domain and an L polymerase-binding domain [, ]. ; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0019079 viral genome replication; PDB: 1R4G_A 1EZJ_A.
Probab=24.22 E-value=97 Score=26.50 Aligned_cols=32 Identities=25% Similarity=0.456 Sum_probs=26.0
Q ss_pred hhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHH
Q psy4906 10 GEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKY 45 (144)
Q Consensus 10 ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKl 45 (144)
-||-..++-+.+.+..|+++|.+| ..+|||-+
T Consensus 69 ~q~q~~l~~ik~~~~~~~e~hrR~----~E~QkEQ~ 100 (248)
T PF01806_consen 69 NQIQQELKQIKEDLKKMDESHRRF----IENQKEQN 100 (248)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHH
Confidence 367788999999999999999998 44566643
No 57
>KOG0804|consensus
Probab=23.94 E-value=6.3e+02 Score=23.96 Aligned_cols=30 Identities=23% Similarity=0.355 Sum_probs=18.5
Q ss_pred hHHHhHHHHHHHHHHHhhcCCcchHHHHHH
Q psy4906 18 KVSEGVETFEDIWQKVHNATNSNQKEKYEA 47 (144)
Q Consensus 18 kV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~ 47 (144)
++.--...|++++.++..+.-.|||+.||.
T Consensus 329 qleSqr~y~e~~~~e~~qsqlen~k~~~e~ 358 (493)
T KOG0804|consen 329 QLESQRKYYEQIMSEYEQSQLENQKQYYEL 358 (493)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 344445566677777766555666666653
No 58
>PF08439 Peptidase_M3_N: Oligopeptidase F; InterPro: IPR013647 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain is found towards the N terminus of metallopeptidases belonging to MEROPS peptidase subfamily M3B (oligopeptidase F, clan MA). An example protein is Lactococcus lactisPepF []. The function of this N-terminal domain is unknown.; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2QR4_B 3CE2_A.
Probab=23.82 E-value=74 Score=20.83 Aligned_cols=30 Identities=20% Similarity=0.454 Sum_probs=24.6
Q ss_pred chhhhHHHHHHhHHHhHHHHHHHHHHHhhc
Q psy4906 7 GRQGEIDRCLKKVSEGVETFEDIWQKVHNA 36 (144)
Q Consensus 7 KLQ~EIDr~lKkV~EGi~~Fd~i~~K~~~~ 36 (144)
.|-.+.+++|-.+..|...+..+|+-+.++
T Consensus 37 ~Ls~~~E~lLa~~~~~~~a~~~~y~~l~~~ 66 (70)
T PF08439_consen 37 TLSEEEEKLLAKLSPGLSAWSNLYDTLSNS 66 (70)
T ss_dssp ---HHHHHHHHHCCCHHHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHHhhhHHhhHHHHHHHHHHc
Confidence 355789999999999999999999998755
No 59
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=23.44 E-value=1e+02 Score=23.25 Aligned_cols=23 Identities=22% Similarity=0.226 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcc
Q psy4906 47 ADLKKEIKKLQRLRDQIKSWIAS 69 (144)
Q Consensus 47 ~DLKkEIKKLQR~RdQIK~W~~~ 69 (144)
.++..+|+.|++.+++|..+++.
T Consensus 88 ~~i~~~i~~L~~~~~~L~~~i~~ 110 (131)
T cd04786 88 ADIEALEARLAQNKAQLLVLIDL 110 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 57889999999999999988755
No 60
>KOG3364|consensus
Probab=23.23 E-value=69 Score=25.69 Aligned_cols=67 Identities=18% Similarity=0.308 Sum_probs=36.6
Q ss_pred hHHHhHHHHHHHHHHHhhcCCcchHHHHH--HHHHHHHHHHHHHHHHHHHhhccccccchhhhHHHHHHHHHHH
Q psy4906 18 KVSEGVETFEDIWQKVHNATNSNQKEKYE--ADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQM 89 (144)
Q Consensus 18 kV~EGi~~Fd~i~~K~~~~~~~~QKEKlE--~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~M 89 (144)
-|++||..|+++|. ++.+...||.+= +==---||---+.|.-+-+.+... .|-.+-.+.++.||.+|
T Consensus 50 dv~~GI~iLe~l~~---~~~~~~rRe~lyYLAvg~yRlkeY~~s~~yvd~ll~~e--~~n~Qa~~Lk~~ied~i 118 (149)
T KOG3364|consen 50 DVQEGIVILEDLLK---SAHPERRRECLYYLAVGHYRLKEYSKSLRYVDALLETE--PNNRQALELKETIEDKI 118 (149)
T ss_pred HHHHhHHHHHHHhh---hcCcccchhhhhhhHHHHHHHhhHHHHHHHHHHHHhhC--CCcHHHHHHHHHHHHHH
Confidence 58999999999998 555666676642 000111222333333444444321 02234666777888777
No 61
>PF12220 U1snRNP70_N: U1 small nuclear ribonucleoprotein of 70kDa MW N terminal; InterPro: IPR022023 This domain is found in eukaryotes. This domain is about 90 amino acids in length. This domain is found associated with PF00076 from PFAM. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition.
Probab=22.73 E-value=2.6e+02 Score=19.87 Aligned_cols=51 Identities=14% Similarity=0.371 Sum_probs=30.6
Q ss_pred HhHHHHHHHHHHHhhcC----Ccc-hHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q psy4906 21 EGVETFEDIWQKVHNAT----NSN-QKEKYEADLKKEIKKLQRLRDQIKSWIASAE 71 (144)
Q Consensus 21 EGi~~Fd~i~~K~~~~~----~~~-QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~d 71 (144)
-||..|=..++...... ..+ .--+...-..|..+.-+.++.+|.+|=..+|
T Consensus 38 tGvs~~l~~~~~~~~~~~~~~~et~~e~~~r~~~ek~~~~~~~l~~~l~~w~P~~D 93 (94)
T PF12220_consen 38 TGVSQYLSEFEDYKDEPPPEPTETKEERRERKRKEKKEKNEEKLEEELKEWDPHED 93 (94)
T ss_pred CcHHHHHHHHhccccCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 47777777776665331 122 1223333344555666888999999977654
No 62
>PF04362 Iron_traffic: Bacterial Fe(2+) trafficking; InterPro: IPR007457 The protein represented by this entry, YggX, serves to protect Fe-S clusters from oxidative damage []. The effect is two-fold: proteins that rely on Fe-S clusters do not become inactivated, and the release of free iron and hydrogen peroxide--a DNA damaging agent--is prevented. These observations are consistent with the hypothesis that YggX chelates free iron, and recent experiments show that YggX can indeed bind Fe(II) in vitro and in vivo []. Furthermore, YggX has a positive effect on the action of at least one Fe(II)-responsive protein. The combined actions of YggX is reminiscent of iron trafficking proteins [], and YggX is therefore proposed to play a role in Fe(II) trafficking []. In Escherichia coli, YggX was shown to be under the transcriptional control of the redox-sensing SoxRS system []. ; GO: 0005506 iron ion binding; PDB: 1YHD_A 1T07_A 1XS8_A.
Probab=22.14 E-value=77 Score=23.26 Aligned_cols=14 Identities=50% Similarity=0.826 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHH
Q psy4906 79 LDYRKLIETQMERF 92 (144)
Q Consensus 79 ~e~Rk~IE~~MErF 92 (144)
-+.|+.++.+|+.|
T Consensus 60 p~~R~~L~~qM~~F 73 (88)
T PF04362_consen 60 PEARKFLEEQMEKF 73 (88)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 46899999999999
No 63
>PF07139 DUF1387: Protein of unknown function (DUF1387); InterPro: IPR009816 This family represents a conserved region approximately 300 residues long within a number of hypothetical proteins of unknown function that seem to be restricted to mammals.
Probab=21.86 E-value=86 Score=27.69 Aligned_cols=34 Identities=29% Similarity=0.578 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhhHHHHHHHHHHHH
Q psy4906 42 KEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQME 90 (144)
Q Consensus 42 KEKlE~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~ME 90 (144)
.-|+..-|.|-+|.|||+= ..|..||-.|++.|+
T Consensus 148 ~KKlg~nIEKSvKDLqRct---------------vSL~RYr~~lkee~d 181 (302)
T PF07139_consen 148 NKKLGPNIEKSVKDLQRCT---------------VSLTRYRVVLKEEMD 181 (302)
T ss_pred ccccCccHHHHHHHHHHHH---------------HHHHhhhhHHHHHHH
Confidence 3466677888888888762 247777777777776
No 64
>PF06729 CENP-R: Kinetochore component, CENP-R; InterPro: IPR009601 This family consists of mammalian nuclear receptor co-activator NRIF3 proteins. NRIF3 exhibits a distinct receptor specificity in interacting with and potentiating the activity of only TRs and RXRs but not other examined nuclear receptors. NRIF3 as a coregulator that possesses both transactivation and transrepression domains and/or functions. Collectively, the NRIF3 family of coregulators may play dual roles in mediating both positive and negative regulatory effects on gene expression [].
Probab=21.70 E-value=4.1e+02 Score=21.11 Aligned_cols=57 Identities=25% Similarity=0.352 Sum_probs=42.7
Q ss_pred hhHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHH---------HHHHHHHHHHHHHHHHHHHh
Q psy4906 10 GEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYE---------ADLKKEIKKLQRLRDQIKSW 66 (144)
Q Consensus 10 ~EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE---------~DLKkEIKKLQR~RdQIK~W 66 (144)
.++.-++-+|.-..+.|=.+++.+.+-....-=-.|| .+||.|++|-+-|=-++..|
T Consensus 59 D~fm~L~SkvekS~eeime~~qnL~slQALeGsreLEnLiGvs~sSc~Lk~ElqKTkeLmtkv~k~ 124 (139)
T PF06729_consen 59 DEFMVLLSKVEKSLEEIMEIRQNLSSLQALEGSRELENLIGVSCSSCDLKRELQKTKELMTKVEKQ 124 (139)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHhccccchHHHHHHHHHHHHHHHHHHHH
Confidence 5788899999999999999999987654333222455 37999999988776665544
No 65
>cd00089 HR1 Protein kinase C-related kinase homology region 1 domain; also known as the ACC (antiparallel coiled-coil) finger domain or Rho-binding domain. Found in vertebrate PRK1 and yeast PKC1 protein kinases C; those found in rhophilin bind RhoGTP; those in PRK1 bind RhoA and RhoB. Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 repeats often occur in tandem repeat arrangments, seperated by a short linker region.
Probab=21.52 E-value=2.6e+02 Score=18.60 Aligned_cols=59 Identities=22% Similarity=0.311 Sum_probs=37.1
Q ss_pred CchhhhHHHHHHh------HHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy4906 6 PGRQGEIDRCLKK------VSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWI 67 (144)
Q Consensus 6 RKLQ~EIDr~lKk------V~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~ 67 (144)
++++.-|+.+-++ |.+|.+..-.+|.. ..........++.|.---.||+.+|.+|....
T Consensus 5 ~~~~~~l~~L~~~l~~E~~~r~Gaenm~~~~~~---~~~~~~~~~~~~~l~es~~ki~~Lr~~L~k~~ 69 (72)
T cd00089 5 SKLQSRLERLEKELSIELKVKEGAENLLRLYSD---EKKKKLLAEAEQMLRESKQKLELLKMQLEKLK 69 (72)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666666554 55666665555541 11122466777778878888888888887554
No 66
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=21.44 E-value=2.6e+02 Score=18.54 Aligned_cols=51 Identities=10% Similarity=0.408 Sum_probs=27.1
Q ss_pred HHHHHhHHHhHHHHHHHHHHHhh---cCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy4906 13 DRCLKKVSEGVETFEDIWQKVHN---ATNSNQKEKYEADLKKEIKKLQRLRDQI 63 (144)
Q Consensus 13 Dr~lKkV~EGi~~Fd~i~~K~~~---~~~~~QKEKlE~DLKkEIKKLQR~RdQI 63 (144)
..++..|...++..+++.+.|.- ..+++.|-.|.+.|+.-=..|..++.++
T Consensus 24 ~~~i~~~e~~l~ea~~~l~qMe~E~~~~p~s~r~~~~~kl~~yr~~l~~lk~~l 77 (79)
T PF05008_consen 24 KSLIREIERDLDEAEELLKQMELEVRSLPPSERNQYKSKLRSYRSELKKLKKEL 77 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34455555555555555555432 1245667777776655444444444443
No 67
>cd07616 BAR_Endophilin_B1 The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Endophilin-B proteins are cytoplasmic proteins expressed mainly in the heart, placenta, and skeletal muscle. Endophilin-B1, also called Bax-interacting factor 1 (Bif-1) or SH3GLB1 (SH3-domain GRB2-like endophilin B1), is localized mainly to the Golgi apparatus. It is involved in the regulation of many biological events including autophagy, tumorigenesis, nerve growth fact
Probab=21.29 E-value=5e+02 Score=21.82 Aligned_cols=85 Identities=13% Similarity=0.177 Sum_probs=51.8
Q ss_pred hHHHHHHhHHHhHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc--chhhhHHHHHHHHHH
Q psy4906 11 EIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIK--DKSTLLDYRKLIETQ 88 (144)
Q Consensus 11 EIDr~lKkV~EGi~~Fd~i~~K~~~~~~~~QKEKlE~DLKkEIKKLQR~RdQIK~W~~~~diK--dk~~L~e~Rk~IE~~ 88 (144)
+|-+.-|+|.--.-.||..-.++..+.++..+--.|.+|+.-=-|+-+.-+--..-+ ..|. +..++...+.+|+.+
T Consensus 134 ~i~k~RKkLe~rRLdyD~~K~r~~kAk~~~~~~~~e~elr~ae~efees~E~a~~~m--~~i~~~~~e~~~~L~~lv~AQ 211 (229)
T cd07616 134 TITKERKLLQNKRLDLDAAKTRLKKAKVAEARAAAEQELRITQSEFDRQAEITRLLL--EGISSTHAHHLRCLNDFVEAQ 211 (229)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhcchHHHHHHHHHHHHHHHHHHHHHH--HhhhhcChHHHHHHHHHHHHH
Confidence 566677777777777888877777765544444445555544444444444333322 2233 555788888888888
Q ss_pred HHHHHHHHH
Q psy4906 89 MERFKVVER 97 (144)
Q Consensus 89 MErFK~~Ek 97 (144)
++=|+.|=.
T Consensus 212 l~Yh~~~~e 220 (229)
T cd07616 212 MTYYAQCYQ 220 (229)
T ss_pred HHHHHHHHH
Confidence 887776643
No 68
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.03 E-value=2e+02 Score=22.28 Aligned_cols=26 Identities=35% Similarity=0.829 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy4906 42 KEKYEADLKKEIKKLQRLRDQIKSWIAS 69 (144)
Q Consensus 42 KEKlE~DLKkEIKKLQR~RdQIK~W~~~ 69 (144)
+|++|+| ++|.+|.+.++.|..|+++
T Consensus 56 ~e~~e~D--~~L~~L~~~k~~id~~~~~ 81 (130)
T PF05263_consen 56 KERLESD--EELQSLKRQKEAIDRWLET 81 (130)
T ss_pred HHHHHhh--HHHHHHHHHHHHHHHHHHh
Confidence 5556666 7899999999999999984
No 69
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.89 E-value=1.8e+02 Score=20.82 Aligned_cols=24 Identities=29% Similarity=0.423 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhc
Q psy4906 45 YEADLKKEIKKLQRLRDQIKSWIA 68 (144)
Q Consensus 45 lE~DLKkEIKKLQR~RdQIK~W~~ 68 (144)
-...|..+|..|+..++.|+.++.
T Consensus 83 ~~~~l~~~i~~l~~~~~~l~~~l~ 106 (108)
T cd01107 83 KLAELEAEIEELQRILRLLEDRLK 106 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 346788899999999999988764
No 70
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=20.75 E-value=1.6e+02 Score=25.64 Aligned_cols=22 Identities=18% Similarity=0.367 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhc
Q psy4906 47 ADLKKEIKKLQRLRDQIKSWIA 68 (144)
Q Consensus 47 ~DLKkEIKKLQR~RdQIK~W~~ 68 (144)
+++..+|..+++.+++++.|-.
T Consensus 249 ~e~~~~I~~ae~~~~~~r~~t~ 270 (312)
T smart00787 249 SELNTEIAEAEKKLEQCRGFTF 270 (312)
T ss_pred HHHHHHHHHHHHHHHhcCCCCH
Confidence 5677888889999999998865
No 71
>PRK05408 oxidative damage protection protein; Provisional
Probab=20.68 E-value=83 Score=23.24 Aligned_cols=15 Identities=47% Similarity=0.682 Sum_probs=13.1
Q ss_pred hHHHHHHHHHHHHHH
Q psy4906 78 LLDYRKLIETQMERF 92 (144)
Q Consensus 78 L~e~Rk~IE~~MErF 92 (144)
--++|+.++.+|+.|
T Consensus 59 dp~ar~~L~~qMekF 73 (90)
T PRK05408 59 DPEARKFLEEQMEKF 73 (90)
T ss_pred CHHHHHHHHHHHHHH
Confidence 346899999999999
No 72
>PF07851 TMPIT: TMPIT-like protein; InterPro: IPR012926 A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this. ; GO: 0016021 integral to membrane
Probab=20.16 E-value=6.3e+02 Score=22.54 Aligned_cols=55 Identities=13% Similarity=0.175 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccccccchhhhHHHHHHHHHHHHHHHHHHHhh
Q psy4906 45 YEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERFKVVERET 99 (144)
Q Consensus 45 lE~DLKkEIKKLQR~RdQIK~W~~~~diKdk~~L~e~Rk~IE~~MErFK~~Eke~ 99 (144)
--+.+.+.++.|..+.+-++.--.+..-.+...+.+.+..|.++=-.|.++|...
T Consensus 37 C~ssI~~QkkrLk~L~~sLk~~~~~~~~e~~~~i~~L~~~Ik~r~~~l~DmEa~L 91 (330)
T PF07851_consen 37 CSSSISHQKKRLKELKKSLKRCKKSLSAEERELIEKLEEDIKERRCQLFDMEAFL 91 (330)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHHhhHHHHHhhC
Confidence 3356777788888888888888766555666677777777777777777777444
Done!