Query psy17564
Match_columns 109
No_of_seqs 103 out of 159
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 16:48:12 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17564hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02724 CDC45: CDC45-like pro 100.0 1.3E-31 2.8E-36 230.2 8.3 109 1-109 348-460 (622)
2 KOG2475|consensus 99.9 3.3E-27 7.2E-32 199.6 6.0 92 1-109 334-425 (587)
3 PF08369 PCP_red: Proto-chloro 77.8 3.2 7E-05 24.6 2.9 36 4-39 3-38 (45)
4 KOG4634|consensus 69.1 5.7 0.00012 27.8 2.8 26 13-38 57-82 (105)
5 PF03748 FliL: Flagellar basal 56.8 6.5 0.00014 25.5 1.3 30 16-45 70-99 (99)
6 PRK07718 fliL flagellar basal 56.4 7.1 0.00015 28.0 1.5 30 16-45 113-142 (142)
7 PRK08455 fliL flagellar basal 54.7 7.9 0.00017 29.1 1.5 30 16-45 153-182 (182)
8 PRK07021 fliL flagellar basal 50.6 12 0.00026 27.2 2.0 29 17-45 130-162 (162)
9 PRK05696 fliL flagellar basal 45.4 16 0.00035 26.8 1.9 14 32-45 157-170 (170)
10 PF13702 Lysozyme_like: Lysozy 44.6 44 0.00096 24.9 4.2 17 20-36 7-23 (160)
11 PF14622 Ribonucleas_3_3: Ribo 44.0 25 0.00055 24.2 2.7 48 22-69 62-111 (128)
12 PRK12785 fliL flagellar basal 42.2 15 0.00032 27.1 1.3 30 16-45 137-166 (166)
13 PF10978 DUF2785: Protein of u 42.2 42 0.0009 24.8 3.7 61 5-69 28-104 (175)
14 PRK05697 flagellar basal body- 41.0 15 0.00032 26.5 1.1 29 17-45 105-137 (137)
15 PF07498 Rho_N: Rho terminatio 37.8 62 0.0013 18.6 3.3 34 17-62 2-35 (43)
16 PF05511 ATP-synt_F6: Mitochon 35.8 25 0.00055 24.4 1.6 32 12-43 61-96 (99)
17 PF05190 MutS_IV: MutS family 35.3 19 0.00041 22.6 0.9 49 3-56 6-54 (92)
18 PHA00099 minor capsid protein 34.4 47 0.001 24.5 2.9 44 25-68 31-74 (147)
19 cd07321 Extradiol_Dioxygenase_ 34.2 36 0.00078 22.1 2.1 25 12-36 13-37 (77)
20 cd00593 RIBOc RIBOc. Ribonucle 33.3 45 0.00097 22.3 2.5 48 22-69 62-111 (133)
21 PF12415 rpo132: Poxvirus DNA 32.4 23 0.0005 20.0 0.8 16 55-70 13-28 (33)
22 PF07841 DM4_12: DM4/DM12 fami 32.0 41 0.0009 21.5 2.1 19 18-36 1-19 (82)
23 COG1510 Predicted transcriptio 31.8 75 0.0016 24.3 3.7 47 16-62 6-52 (177)
24 cd07588 BAR_Amphiphysin The Bi 30.1 34 0.00073 26.4 1.6 27 3-29 148-174 (211)
25 PF03081 Exo70: Exo70 exocyst 30.1 39 0.00085 26.9 2.0 29 4-32 310-339 (371)
26 cd08531 SAM_PNT-ERG_FLI-1 Ster 29.2 66 0.0014 20.9 2.7 49 18-66 10-70 (75)
27 cd07923 Gallate_dioxygenase_C 28.2 50 0.0011 22.7 2.0 26 11-36 14-39 (94)
28 cd07589 BAR_DNMBP The Bin/Amph 28.2 43 0.00094 25.0 1.9 27 3-29 135-161 (195)
29 PF14206 Cys_rich_CPCC: Cystei 28.1 24 0.00051 23.4 0.4 20 1-20 47-69 (78)
30 KOG1241|consensus 27.9 52 0.0011 30.6 2.6 52 4-70 74-125 (859)
31 PF07746 LigA: Aromatic-ring-o 27.1 55 0.0012 22.0 2.1 26 11-36 7-32 (88)
32 CHL00076 chlB photochlorophyll 26.7 71 0.0015 27.5 3.2 36 4-39 466-501 (513)
33 cd02879 GH18_plant_chitinase_c 25.8 67 0.0015 25.3 2.7 32 8-39 81-114 (299)
34 PF15583 Imm41: Immunity prote 25.6 58 0.0012 24.5 2.1 44 25-69 34-88 (158)
35 PRK10870 transcriptional repre 25.4 75 0.0016 23.2 2.7 61 2-62 7-82 (176)
36 PRK14129 heat shock protein Hs 24.6 10 0.00022 26.7 -1.9 32 28-62 2-33 (105)
37 cd07612 BAR_Bin2 The Bin/Amphi 24.5 46 0.001 25.9 1.5 27 3-29 148-174 (211)
38 PF03598 CdhC: CO dehydrogenas 24.0 51 0.0011 28.3 1.8 26 12-37 352-377 (411)
39 smart00398 HMG high mobility g 23.5 1E+02 0.0022 18.0 2.6 30 4-33 34-63 (70)
40 PF13354 Beta-lactamase2: Beta 23.1 1.3E+02 0.0029 21.4 3.6 47 22-68 89-140 (197)
41 smart00535 RIBOc Ribonuclease 23.0 82 0.0018 21.0 2.4 47 23-69 61-109 (129)
42 PF12645 HTH_16: Helix-turn-he 22.8 90 0.002 19.6 2.4 28 5-32 37-64 (65)
43 cd07591 BAR_Rvs161p The Bin/Am 22.8 56 0.0012 25.1 1.7 27 3-29 153-179 (224)
44 PF09388 SpoOE-like: Spo0E lik 22.4 1.1E+02 0.0023 17.6 2.5 18 19-36 7-24 (45)
45 cd07590 BAR_Bin3 The Bin/Amphi 22.4 39 0.00085 26.3 0.7 39 3-47 154-192 (225)
46 cd07611 BAR_Amphiphysin_I_II T 22.3 56 0.0012 25.4 1.6 28 3-30 148-175 (211)
47 PF06628 Catalase-rel: Catalas 22.2 1.1E+02 0.0024 19.0 2.7 26 4-29 11-36 (68)
48 smart00545 JmjN Small domain f 22.0 56 0.0012 19.1 1.2 21 21-41 18-38 (42)
49 PF02285 COX8: Cytochrome oxid 21.5 94 0.002 18.5 2.1 18 49-66 7-24 (44)
50 cd02876 GH18_SI-CLP Stabilin-1 21.2 1E+02 0.0023 24.2 2.9 30 10-39 83-114 (318)
51 cd02878 GH18_zymocin_alpha Zym 21.1 1E+02 0.0023 24.7 3.0 31 9-39 82-113 (345)
52 PRK09529 bifunctional acetyl-C 20.9 71 0.0015 29.3 2.1 27 12-38 652-678 (711)
53 cd08536 SAM_PNT-Mae Sterile al 20.8 1.2E+02 0.0026 19.2 2.6 26 18-43 7-32 (66)
54 COG1580 FliL Flagellar basal b 20.6 68 0.0015 23.8 1.7 31 15-45 128-159 (159)
55 PRK12371 ribonuclease III; Rev 20.6 2E+02 0.0043 22.2 4.3 62 9-70 68-137 (235)
56 cd00598 GH18_chitinase-like Th 20.5 1.2E+02 0.0026 21.6 3.0 26 14-39 85-110 (210)
57 TIGR02191 RNaseIII ribonucleas 20.4 1.2E+02 0.0026 22.3 3.0 48 23-70 77-126 (220)
No 1
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=99.97 E-value=1.3e-31 Score=230.24 Aligned_cols=109 Identities=35% Similarity=0.437 Sum_probs=90.1
Q ss_pred CchhhhhhchhcCCHHHHhHHHHHHHHHhhhCCCCCcccchhheeecCCCccchhhHHHHHHHHhccCcchh---ccccc
Q psy17564 1 MPLLQSKQLYNSMDLSIRRELPTMLSKMAADHQLDELIMPSFTLLHGYRTKIQASDYVYAMLALLESPVRIL---CRMDD 77 (109)
Q Consensus 1 isL~q~kQ~y~~Md~~lK~~L~~~le~~a~~ygL~dl~~~SF~r~~Gy~~~lSA~D~vyav~ALLE~~~~~~---~~~~~ 77 (109)
|||+||||+|.|||+++|++|+++|+++||+|||++++|+||+|+|||+++|||+||||||+||||+++... ...+.
T Consensus 348 isL~~~~Q~y~~Md~~~K~~L~~~l~~~a~~ygL~dl~~~sF~r~~Gy~~~lSA~D~v~al~ALLE~~~~~~~~~~~~~~ 427 (622)
T PF02724_consen 348 ISLKQAQQKYSYMDMELKRELREKLEKYAPKYGLDDLVFPSFVRTYGYRGKLSASDVVYALTALLEVGKSSSNVNNASNP 427 (622)
T ss_pred CcHHHHcCCchhCCHHHHHHHHHHHHHHHHhcCCCCceeeeEEEEecCCCceeHHHHHHHHHHHhcCCccccccccccCc
Confidence 799999999999999999999999999999999999999999999999999999999999999999985311 01111
Q ss_pred ccc-cCccchhhhhhhccCChhhHHHHHhhhcC
Q psy17564 78 VEL-ENIPEYNQIFEHQEKKPSDCFLDAAYCLA 109 (109)
Q Consensus 78 ~~~-~~~~~~~~~~~~~~~~~~~~Fw~AyDaLs 109 (109)
... ....+..+.....++.|.+|||.|||||+
T Consensus 428 ~~~~~~~~~~~~~~~~~~~~~~~nF~~A~DaL~ 460 (622)
T PF02724_consen 428 ENDSDEEEDNEEDEEKEEESWVDNFWRAYDALS 460 (622)
T ss_pred ccccccchhhhhhcccccccHHHHHHHHHHHhC
Confidence 111 12233344446667899999999999996
No 2
>KOG2475|consensus
Probab=99.94 E-value=3.3e-27 Score=199.62 Aligned_cols=92 Identities=39% Similarity=0.610 Sum_probs=83.6
Q ss_pred CchhhhhhchhcCCHHHHhHHHHHHHHHhhhCCCCCcccchhheeecCCCccchhhHHHHHHHHhccCcchhcccccccc
Q psy17564 1 MPLLQSKQLYNSMDLSIRRELPTMLSKMAADHQLDELIMPSFTLLHGYRTKIQASDYVYAMLALLESPVRILCRMDDVEL 80 (109)
Q Consensus 1 isL~q~kQ~y~~Md~~lK~~L~~~le~~a~~ygL~dl~~~SF~r~~Gy~~~lSA~D~vyav~ALLE~~~~~~~~~~~~~~ 80 (109)
|||.||||+|.+||+++||.|++++++.||+|||.|++|.||+|++||++++||||||||++||||+++.
T Consensus 334 l~L~e~kQkf~aMd~~lk~~l~~~~er~a~~ygl~D~~~~tF~rt~Gy~~~~sAsDvvyA~talLEs~ns---------- 403 (587)
T KOG2475|consen 334 LPLVEAKQKFEAMDLELKRELKSMFERFAPKYGLMDIIFATFTRTLGYRGKLSASDVVYALTALLESGNS---------- 403 (587)
T ss_pred CcHHHHHHHhhhcCHHHHHHHHHHHHhhcccccchhhhhhhhhhhccccccccHHHHHHHHHHHHhcCcc----------
Confidence 7999999999999999999999999999999999999999999999999999999999999999999765
Q ss_pred cCccchhhhhhhccCChhhHHHHHhhhcC
Q psy17564 81 ENIPEYNQIFEHQEKKPSDCFLDAAYCLA 109 (109)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~Fw~AyDaLs 109 (109)
++......+.+++|.+|+|+|+
T Consensus 404 -------kt~~~~~~s~ed~f~ea~d~ls 425 (587)
T KOG2475|consen 404 -------KTIMNSFDSGEDIFLEALDALS 425 (587)
T ss_pred -------ccccCCCCChHHHHHHHHHHHH
Confidence 2222234566889999999985
No 3
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=77.78 E-value=3.2 Score=24.60 Aligned_cols=36 Identities=17% Similarity=0.306 Sum_probs=28.7
Q ss_pred hhhhhchhcCCHHHHhHHHHHHHHHhhhCCCCCccc
Q psy17564 4 LQSKQLYNSMDLSIRRELPTMLSKMAADHQLDELIM 39 (109)
Q Consensus 4 ~q~kQ~y~~Md~~lK~~L~~~le~~a~~ygL~dl~~ 39 (109)
.+|++....++.=+|+.++...|++|.+-|.+.|+.
T Consensus 3 ~eA~~~L~~iP~fvR~~~r~~~E~~Ar~~G~~~IT~ 38 (45)
T PF08369_consen 3 DEAEARLDRIPFFVRKKLRDAAEKYARERGYDEITV 38 (45)
T ss_dssp HHHHHHHCTS-HHHHHHHHHHHHHHHHHCT-SEE-H
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHcCCCeECH
Confidence 367777778888899999999999999999998764
No 4
>KOG4634|consensus
Probab=69.05 E-value=5.7 Score=27.84 Aligned_cols=26 Identities=23% Similarity=0.202 Sum_probs=22.4
Q ss_pred CCHHHHhHHHHHHHHHhhhCCCCCcc
Q psy17564 13 MDLSIRRELPTMLSKMAADHQLDELI 38 (109)
Q Consensus 13 Md~~lK~~L~~~le~~a~~ygL~dl~ 38 (109)
=++++++.|++.+.+.|.+||+.+.-
T Consensus 57 s~pe~e~eLk~el~rla~qfg~~~~D 82 (105)
T KOG4634|consen 57 SDPEYEQELKEELFRLAQQFGLANAD 82 (105)
T ss_pred CCHHHHHHHHHHHHHHHHHhCccCch
Confidence 47889999999999999999976543
No 5
>PF03748 FliL: Flagellar basal body-associated protein FliL; InterPro: IPR005503 This FliL protein controls the rotational direction of the flagella during chemotaxis []. FliL is a cytoplasmic membrane protein associated with the basal body [].; GO: 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009425 bacterial-type flagellum basal body
Probab=56.83 E-value=6.5 Score=25.51 Aligned_cols=30 Identities=13% Similarity=0.402 Sum_probs=23.6
Q ss_pred HHHhHHHHHHHHHhhhCCCCCcccchhhee
Q psy17564 16 SIRRELPTMLSKMAADHQLDELIMPSFTLL 45 (109)
Q Consensus 16 ~lK~~L~~~le~~a~~ygL~dl~~~SF~r~ 45 (109)
.+|+.|++.+.+..+.=.+.++.|.+|+.|
T Consensus 70 ~Lk~~l~~~in~~l~~~~V~~V~ft~fviQ 99 (99)
T PF03748_consen 70 RLKDELKDRINKILGKGKVKDVYFTDFVIQ 99 (99)
T ss_pred HHHHHHHHHHHHhhccCcEEEEEEEEEEEC
Confidence 567777777777777777899999999865
No 6
>PRK07718 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=56.43 E-value=7.1 Score=28.00 Aligned_cols=30 Identities=13% Similarity=0.448 Sum_probs=24.1
Q ss_pred HHHhHHHHHHHHHhhhCCCCCcccchhhee
Q psy17564 16 SIRRELPTMLSKMAADHQLDELIMPSFTLL 45 (109)
Q Consensus 16 ~lK~~L~~~le~~a~~ygL~dl~~~SF~r~ 45 (109)
.+|..+++++.++.++-...++.|.+|+-|
T Consensus 113 ~Lr~el~~~in~~l~~g~V~~Vyft~fViQ 142 (142)
T PRK07718 113 ALKEQLKEKINNLMQEGKVEKVYITSFILQ 142 (142)
T ss_pred HHHHHHHHHHHHhhccCceEEEEEEeeeeC
Confidence 567777777777777778999999999865
No 7
>PRK08455 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=54.73 E-value=7.9 Score=29.14 Aligned_cols=30 Identities=13% Similarity=0.334 Sum_probs=25.2
Q ss_pred HHHhHHHHHHHHHhhhCCCCCcccchhhee
Q psy17564 16 SIRRELPTMLSKMAADHQLDELIMPSFTLL 45 (109)
Q Consensus 16 ~lK~~L~~~le~~a~~ygL~dl~~~SF~r~ 45 (109)
.+|+.+.+++.+....=.+.+++|.+|+.|
T Consensus 153 ~Lk~ei~~~iN~~L~~g~V~~VyFT~FViQ 182 (182)
T PRK08455 153 RLKDEIVGKLNEFLIDGFIKNVFFTDFVVQ 182 (182)
T ss_pred HHHHHHHHHHHHHhccCceeEEEeEeeeeC
Confidence 577778888888888888999999999865
No 8
>PRK07021 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=50.60 E-value=12 Score=27.22 Aligned_cols=29 Identities=17% Similarity=0.324 Sum_probs=18.4
Q ss_pred HHhHHHHHHHHHhhhC----CCCCcccchhhee
Q psy17564 17 IRRELPTMLSKMAADH----QLDELIMPSFTLL 45 (109)
Q Consensus 17 lK~~L~~~le~~a~~y----gL~dl~~~SF~r~ 45 (109)
+|+.+++.+.+....- .+.++.|.+|+.|
T Consensus 130 Lk~ei~~~in~~l~~~~~~~~V~~VlFt~fVvQ 162 (162)
T PRK07021 130 LAAEIKQTLSQPLVPGQPPQVVTDVLFTAFILQ 162 (162)
T ss_pred HHHHHHHHHHHHHhccCCCCceeEEeeeeceeC
Confidence 4444444555544332 4889999999865
No 9
>PRK05696 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=45.36 E-value=16 Score=26.78 Aligned_cols=14 Identities=7% Similarity=0.430 Sum_probs=11.8
Q ss_pred CCCCCcccchhhee
Q psy17564 32 HQLDELIMPSFTLL 45 (109)
Q Consensus 32 ygL~dl~~~SF~r~ 45 (109)
=.++++.|.+|+.|
T Consensus 157 ~~V~~VlFt~fVvQ 170 (170)
T PRK05696 157 PVVEKVLFTGFVMQ 170 (170)
T ss_pred CceeEEeeeeceeC
Confidence 36889999999865
No 10
>PF13702 Lysozyme_like: Lysozyme-like
Probab=44.61 E-value=44 Score=24.94 Aligned_cols=17 Identities=24% Similarity=0.343 Sum_probs=14.9
Q ss_pred HHHHHHHHHhhhCCCCC
Q psy17564 20 ELPTMLSKMAADHQLDE 36 (109)
Q Consensus 20 ~L~~~le~~a~~ygL~d 36 (109)
+.+..++++|.+||+++
T Consensus 7 ~y~~~V~k~a~e~gi~~ 23 (160)
T PF13702_consen 7 QYRPMVEKYAKEYGIPE 23 (160)
T ss_pred HHHHHHHHHHHHcCChh
Confidence 46789999999999986
No 11
>PF14622 Ribonucleas_3_3: Ribonuclease-III-like; PDB: 1O0W_A 2A11_A 3N3W_B.
Probab=44.05 E-value=25 Score=24.25 Aligned_cols=48 Identities=19% Similarity=0.075 Sum_probs=30.2
Q ss_pred HHHHHHHhhhCCCCCcccchh-heeecCCCcc-chhhHHHHHHHHhccCc
Q psy17564 22 PTMLSKMAADHQLDELIMPSF-TLLHGYRTKI-QASDYVYAMLALLESPV 69 (109)
Q Consensus 22 ~~~le~~a~~ygL~dl~~~SF-~r~~Gy~~~l-SA~D~vyav~ALLE~~~ 69 (109)
++.|.++|.++||+++.+++- ...-+.+..- --+|+++|+.+-+-.+.
T Consensus 62 ~~~La~~a~~lgL~~~i~~~~~~~~~~~~~~~~vlad~feAliGAiyld~ 111 (128)
T PF14622_consen 62 NETLAEIAKQLGLDKLIRWGPGEEKSGGSGSDKVLADVFEALIGAIYLDS 111 (128)
T ss_dssp HHHHHHHHHHTTCGGC-B--HHHHHTTGGG-HHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHCCHHHHHHhCccHhhcCCCCCccHHHhHHHHHHHHHHHHc
Confidence 567899999999999999743 1222222221 26799999987766543
No 12
>PRK12785 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=42.23 E-value=15 Score=27.06 Aligned_cols=30 Identities=13% Similarity=0.256 Sum_probs=22.9
Q ss_pred HHHhHHHHHHHHHhhhCCCCCcccchhhee
Q psy17564 16 SIRRELPTMLSKMAADHQLDELIMPSFTLL 45 (109)
Q Consensus 16 ~lK~~L~~~le~~a~~ygL~dl~~~SF~r~ 45 (109)
.+|..+.+++......=.++++.|.+|+.|
T Consensus 137 ~Lr~ei~~~in~~l~~~~V~~VlFt~FVvQ 166 (166)
T PRK12785 137 RLKEELLRRVNVALAPAQVNAVLFKEVVIQ 166 (166)
T ss_pred HHHHHHHHHHHhhcCCCceeEEEEEeeEEC
Confidence 466667777777666667899999999865
No 13
>PF10978 DUF2785: Protein of unknown function (DUF2785); InterPro: IPR021247 Some members in this family are annotated as hypothetical membrane spanning proteins however this cannot be confirmed. The family has no known function.
Probab=42.16 E-value=42 Score=24.78 Aligned_cols=61 Identities=20% Similarity=0.198 Sum_probs=48.9
Q ss_pred hhhhchhcCCHHHHhHHHHHHHHHhhhCCCCCcccchhheeecCC----------------CccchhhHHHHHHHHhccC
Q psy17564 5 QSKQLYNSMDLSIRRELPTMLSKMAADHQLDELIMPSFTLLHGYR----------------TKIQASDYVYAMLALLESP 68 (109)
Q Consensus 5 q~kQ~y~~Md~~lK~~L~~~le~~a~~ygL~dl~~~SF~r~~Gy~----------------~~lSA~D~vyav~ALLE~~ 68 (109)
.+...+..|+.+.+..+.+++..|.. .+--+.||+-..||- +.++.+|+...+.++.+.-
T Consensus 28 ~~d~~~~fL~~~~~~~~~~~~~~Yl~----~E~D~RGfv~~~GWaHa~AH~aD~l~el~~~p~~~~~~~~~lL~~i~~~~ 103 (175)
T PF10978_consen 28 YADRNYPFLSQEERQELIDQLIRYLL----LEKDTRGFVEEKGWAHAFAHGADLLDELVQHPELDRADKIELLAAILEKY 103 (175)
T ss_pred hcCCcccCCCHHHHHHHHHHHHHHHH----HccccccCCccCcHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 45556899999999999999999884 367789999999997 5667777777777777654
Q ss_pred c
Q psy17564 69 V 69 (109)
Q Consensus 69 ~ 69 (109)
.
T Consensus 104 ~ 104 (175)
T PF10978_consen 104 K 104 (175)
T ss_pred c
Confidence 4
No 14
>PRK05697 flagellar basal body-associated protein FliL-like protein; Validated
Probab=40.96 E-value=15 Score=26.50 Aligned_cols=29 Identities=14% Similarity=0.295 Sum_probs=18.8
Q ss_pred HHhHHHHHHHHHhh----hCCCCCcccchhhee
Q psy17564 17 IRRELPTMLSKMAA----DHQLDELIMPSFTLL 45 (109)
Q Consensus 17 lK~~L~~~le~~a~----~ygL~dl~~~SF~r~ 45 (109)
+|+.+.+.+.+... +-+++++.|.+|+.|
T Consensus 105 Lr~eil~~in~~L~~~~g~~~V~~VlFT~FVvQ 137 (137)
T PRK05697 105 IRQECLKQVNELLEQETGKPLVVDLLFTKYIYQ 137 (137)
T ss_pred HHHHHHHHHHHHHhhccCCCceeEEeeeeeeeC
Confidence 44444444455443 456899999999865
No 15
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=37.85 E-value=62 Score=18.56 Aligned_cols=34 Identities=15% Similarity=0.390 Sum_probs=22.8
Q ss_pred HHhHHHHHHHHHhhhCCCCCcccchhheeecCCCccchhhHHHHHH
Q psy17564 17 IRRELPTMLSKMAADHQLDELIMPSFTLLHGYRTKIQASDYVYAML 62 (109)
Q Consensus 17 lK~~L~~~le~~a~~ygL~dl~~~SF~r~~Gy~~~lSA~D~vyav~ 62 (109)
+++.-...|.+.|.++|+.+ ...+.=.|.|++|.
T Consensus 2 L~~~~~~eL~~iAk~lgI~~------------~~~~~K~eLI~~Il 35 (43)
T PF07498_consen 2 LKSMTLSELREIAKELGIEG------------YSKMRKQELIFAIL 35 (43)
T ss_dssp HHCS-HHHHHHHHHCTT-TT------------GCCS-HHHHHHHHH
T ss_pred cccCCHHHHHHHHHHcCCCC------------CCcCCHHHHHHHHH
Confidence 45555678899999999996 34566677777765
No 16
>PF05511 ATP-synt_F6: Mitochondrial ATP synthase coupling factor 6; InterPro: IPR008387 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit F6 (or coupling factor 6) found in the F0 complex of F-ATPases in mitochondria. The F6 subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. There is no homologue of subunit F6 in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); PDB: 2WSS_V 2CLY_C 1VZS_A.
Probab=35.79 E-value=25 Score=24.43 Aligned_cols=32 Identities=22% Similarity=0.328 Sum_probs=23.7
Q ss_pred cCCHHHHhHHHHHHHHHhhhCCCC---Cc-ccchhh
Q psy17564 12 SMDLSIRRELPTMLSKMAADHQLD---EL-IMPSFT 43 (109)
Q Consensus 12 ~Md~~lK~~L~~~le~~a~~ygL~---dl-~~~SF~ 43 (109)
-.++++.+.|.+.|++.+..||.. |+ .||.|.
T Consensus 61 D~~Pe~~kel~eel~kL~r~YG~g~~~Dm~kFP~Fk 96 (99)
T PF05511_consen 61 DAGPEYEKELNEELEKLARQYGGGSGVDMTKFPTFK 96 (99)
T ss_dssp T--THHHHHHHHHHHHHHHHHHSS---TTTS-SS--
T ss_pred CCCHHHHHHHHHHHHHHHHHhCCcccccHHhCCCCC
Confidence 457899999999999999999998 54 567664
No 17
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=35.33 E-value=19 Score=22.62 Aligned_cols=49 Identities=22% Similarity=0.391 Sum_probs=34.9
Q ss_pred hhhhhhchhcCCHHHHhHHHHHHHHHhhhCCCCCcccchhheeecCCCccchhh
Q psy17564 3 LLQSKQLYNSMDLSIRRELPTMLSKMAADHQLDELIMPSFTLLHGYRTKIQASD 56 (109)
Q Consensus 3 L~q~kQ~y~~Md~~lK~~L~~~le~~a~~ygL~dl~~~SF~r~~Gy~~~lSA~D 56 (109)
|.++++.|. ++.+.|.+.+.+++.++|+..|.+. +..+.||--.+...+
T Consensus 6 Ld~~~~~~~----~~~~~l~~~~~~~~~~~~~~~lk~~-~~~~~gy~i~v~~~~ 54 (92)
T PF05190_consen 6 LDELREEYE----EIEEELEELLEEIRKKLGIPSLKLV-YIPKRGYLIEVPKSD 54 (92)
T ss_dssp HHHHHHHHH----HHHHHHHHHHHHHHHHCT-TTBEEE-EETTTEEEEEEETCC
T ss_pred HHHHHHHHH----HHHHHHHHHHHHHHHHcCCCcEEEE-EcCceEEEEEEEccc
Confidence 445555554 4566788888899999999888874 466788887777666
No 18
>PHA00099 minor capsid protein
Probab=34.43 E-value=47 Score=24.49 Aligned_cols=44 Identities=11% Similarity=0.152 Sum_probs=30.9
Q ss_pred HHHHhhhCCCCCcccchhheeecCCCccchhhHHHHHHHHhccC
Q psy17564 25 LSKMAADHQLDELIMPSFTLLHGYRTKIQASDYVYAMLALLESP 68 (109)
Q Consensus 25 le~~a~~ygL~dl~~~SF~r~~Gy~~~lSA~D~vyav~ALLE~~ 68 (109)
|++++.+++-......-=.|+--|-.+.|-.|+-.|+.++.|.-
T Consensus 31 In~ivkk~n~t~~l~h~~rRq~~ygdc~sp~D~qeAl~~V~~~q 74 (147)
T PHA00099 31 INNIVKKLNATGVLEHVERRQPRYGDCMSPMDYQEALNVVIEAQ 74 (147)
T ss_pred HHHHHHHHhcchhhhhhhhhCCccccCCCchhHHHHHHHHHHHH
Confidence 44455555555444444566777778889999999999999863
No 19
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=34.24 E-value=36 Score=22.11 Aligned_cols=25 Identities=8% Similarity=0.093 Sum_probs=23.0
Q ss_pred cCCHHHHhHHHHHHHHHhhhCCCCC
Q psy17564 12 SMDLSIRRELPTMLSKMAADHQLDE 36 (109)
Q Consensus 12 ~Md~~lK~~L~~~le~~a~~ygL~d 36 (109)
.++++.|..+++-=+.+..+|||++
T Consensus 13 ~~~~~~re~f~~dp~a~~~~~~Lt~ 37 (77)
T cd07321 13 LVKPEVKERFKADPEAVLAEYGLTP 37 (77)
T ss_pred hcCHHHHHHHHhCHHHHHHHcCCCH
Confidence 5689999999999999999999986
No 20
>cd00593 RIBOc RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.
Probab=33.29 E-value=45 Score=22.26 Aligned_cols=48 Identities=13% Similarity=0.042 Sum_probs=33.0
Q ss_pred HHHHHHHhhhCCCCCcccchhheee--cCCCccchhhHHHHHHHHhccCc
Q psy17564 22 PTMLSKMAADHQLDELIMPSFTLLH--GYRTKIQASDYVYAMLALLESPV 69 (109)
Q Consensus 22 ~~~le~~a~~ygL~dl~~~SF~r~~--Gy~~~lSA~D~vyav~ALLE~~~ 69 (109)
.+.+-+.+.++||.+..+.+-.... +-...-.-+|+++|+.+.+=...
T Consensus 62 n~~l~~~a~~~gl~~~i~~~~~~~~~~~~~~~k~~ad~~eAliGAiyld~ 111 (133)
T cd00593 62 NETLARLARELGLGKYLRLGKGEEKSGGRLRPKILADVFEALIGAIYLDG 111 (133)
T ss_pred HHHHHHHHHHcCcHHHhccCchHhhcCCcccccHHHHHHHHHHHHHHHhC
Confidence 4567789999999977665433221 23456677999999987765544
No 21
>PF12415 rpo132: Poxvirus DNA dependent RNA polymerase; InterPro: IPR024390 All three classes of poxvirus genes - early, intermediate and late - are transcribed by the viral RNA polymerase compex []. This complex is composed of nine distinct subunits which total more than 500kDa in mass. The two largest subunits (147 and 136kDa) are homologous to the largest subunits of eukaryotic and prokaryotic RNA polymerases and, like them, are thought to form a claw-shaped structure whose cleft is the site of template interaction and phosphodiester bond formation. While the smaller subunits of poxvirus RNA polymerase show much less similarity, if any, to the smaller subunits of the eukaryotic and prokaryotic enzymes, it is thought that they may play a similar role in interacting with transcription factors. The 132kDa subunit is the second largest subunit of the poxvirus DNA dependent RNA polymerase and shows structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.
Probab=32.38 E-value=23 Score=20.01 Aligned_cols=16 Identities=38% Similarity=0.600 Sum_probs=13.4
Q ss_pred hhHHHHHHHHhccCcc
Q psy17564 55 SDYVYAMLALLESPVR 70 (109)
Q Consensus 55 ~D~vyav~ALLE~~~~ 70 (109)
.+++|-|+||+|+.+.
T Consensus 13 ~ei~ylvnalIestk~ 28 (33)
T PF12415_consen 13 PEIIYLVNALIESTKR 28 (33)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3789999999998665
No 22
>PF07841 DM4_12: DM4/DM12 family; InterPro: IPR006631 This domain of unknown function is found in primarily in Drosophila melanogaster (Fruit fly) proteins of unknown function.
Probab=31.98 E-value=41 Score=21.51 Aligned_cols=19 Identities=32% Similarity=0.398 Sum_probs=16.8
Q ss_pred HhHHHHHHHHHhhhCCCCC
Q psy17564 18 RRELPTMLSKMAADHQLDE 36 (109)
Q Consensus 18 K~~L~~~le~~a~~ygL~d 36 (109)
|+.|.++||+....+|++.
T Consensus 1 R~~lY~~lE~~l~~~G~~g 19 (82)
T PF07841_consen 1 RRDLYKKLEDMLQRMGFDG 19 (82)
T ss_pred CHHHHHHHHHHHHHcCCCc
Confidence 6789999999999999975
No 23
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=31.78 E-value=75 Score=24.31 Aligned_cols=47 Identities=6% Similarity=0.070 Sum_probs=34.4
Q ss_pred HHHhHHHHHHHHHhhhCCCCCcccchhheeecCCCccchhhHHHHHH
Q psy17564 16 SIRRELPTMLSKMAADHQLDELIMPSFTLLHGYRTKIQASDYVYAML 62 (109)
Q Consensus 16 ~lK~~L~~~le~~a~~ygL~dl~~~SF~r~~Gy~~~lSA~D~vyav~ 62 (109)
+.|+.+-+.+.+.+..||++..+-.=+-.-|-=+.++++.+.+++++
T Consensus 6 qak~~~Ie~fae~m~r~G~nrtVG~iYgilyls~~Pmtl~Ei~E~lg 52 (177)
T COG1510 6 QAKDIFIEHFAETMSRWGINRTVGQIYGILYLSRKPLTLDEIAEALG 52 (177)
T ss_pred HHHHHHHHHHHHHHHHhCCcchHHHHhhhheecCCCccHHHHHHHHC
Confidence 45777889999999999998644322222333378999999999875
No 24
>cd07588 BAR_Amphiphysin The Bin/Amphiphysin/Rvs (BAR) domain of Amphiphysins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Amphiphysins function primarily in endocytosis and other membrane remodeling events. They contain an N-terminal BAR domain with an additional N-terminal amphipathic helix (an N-BAR), a variable central domain, and a C-terminal SH3 domain. This subfamily is composed of different isoforms of amphiphysin and Bridging integrator 2 (Bin2). Amphiphysin I proteins, enriched in the brain and nervous system, contain domains that bind clathrin, Adaptor Protein complex 2 (AP2), dynamin and synaptojanin. They function in synaptic vesicle endocytosis. Some amphiphysin II isoforms, also called Bridging integrator 1 (Bin1), are localized in many different tissues and may function in intracellular vesicle trafficking. In skeletal muscle, Bin1 plays a role in the organization and maintenance of th
Probab=30.13 E-value=34 Score=26.38 Aligned_cols=27 Identities=26% Similarity=0.569 Sum_probs=24.6
Q ss_pred hhhhhhchhcCCHHHHhHHHHHHHHHh
Q psy17564 3 LLQSKQLYNSMDLSIRRELPTMLSKMA 29 (109)
Q Consensus 3 L~q~kQ~y~~Md~~lK~~L~~~le~~a 29 (109)
|.+|+|.|.+++-++++.|+..+..-.
T Consensus 148 l~~Ak~~Ye~lN~~L~~ELP~L~~~ri 174 (211)
T cd07588 148 LQQAKKVYEELNTELHEELPALYDSRI 174 (211)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHhh
Confidence 578999999999999999999988766
No 25
>PF03081 Exo70: Exo70 exocyst complex subunit; InterPro: IPR004140 The Exo70 protein forms one subunit of the exocyst complex. First discovered in Saccharomyces cerevisiae [], Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localized at the tip of the bud, the major site of exocytosis in yeast []. Exo70 interacts with the Rho3 GTPase []. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud) []. In humans, the functions of Exo70 and the exocyst complex are less well characterised: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis [].; GO: 0006887 exocytosis, 0000145 exocyst; PDB: 2PFV_A 2B7M_B 2B1E_A 2PFT_A.
Probab=30.11 E-value=39 Score=26.92 Aligned_cols=29 Identities=14% Similarity=0.282 Sum_probs=19.5
Q ss_pred hhhhhchhcCCHHHHhHHHHHHHH-HhhhC
Q psy17564 4 LQSKQLYNSMDLSIRRELPTMLSK-MAADH 32 (109)
Q Consensus 4 ~q~kQ~y~~Md~~lK~~L~~~le~-~a~~y 32 (109)
-+.|+.|.--|+++|+.|+..+.+ ..|.|
T Consensus 310 ~~~q~~~~vpD~~LR~~Lr~~i~~~v~p~Y 339 (371)
T PF03081_consen 310 YKAQKTWKVPDPELREELRREIKEKVVPAY 339 (371)
T ss_dssp HHHHTT---S-HHHHHHHHHHHHHHHHHHH
T ss_pred HHcCcceecCCHHHHHHHHHHHHHHHHHHH
Confidence 467889988899999999998865 45544
No 26
>cd08531 SAM_PNT-ERG_FLI-1 Sterile alpha motif (SAM)/Pointed domain of ERG (Ets related gene) and FLI-1 (Friend leukemia integration 1) transcription factors. SAM Pointed domain of ERG/FLI-1 subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. The ERG and FLI regulators are involved in endothelial cell differentiation, bone morphogenesis and neural crest development. They are proto-oncogenes implicated in cancer development such as myeloid leukemia, Ewing's sarcoma and erythroleukemia. Members of this subfamily are potential targets for cancer therapy.
Probab=29.18 E-value=66 Score=20.93 Aligned_cols=49 Identities=18% Similarity=0.303 Sum_probs=33.2
Q ss_pred HhHHHHHHHHHhhhCCCCCcccchhheeec----------CC--CccchhhHHHHHHHHhc
Q psy17564 18 RRELPTMLSKMAADHQLDELIMPSFTLLHG----------YR--TKIQASDYVYAMLALLE 66 (109)
Q Consensus 18 K~~L~~~le~~a~~ygL~dl~~~SF~r~~G----------y~--~~lSA~D~vyav~ALLE 66 (109)
+..+.+.|+=...+|+|.++.+..|..-=| |. .+--..|+.+.-..+|-
T Consensus 10 ~~~V~~WL~Wa~~ef~L~~i~~~~F~~m~Gk~LC~lt~edF~~~~~~~~GdiL~~hL~~Lr 70 (75)
T cd08531 10 REHVRQWLEWAVKEYGLQDVDVSRFQNIDGKELCKMTKEDFLRLTSAYNADVLLSHLSYLR 70 (75)
T ss_pred HHHHHHHHHHHHHHcCCCCCChhhccCCChHHHHcCCHHHHHHHcCCCcchHHHHHHHHHH
Confidence 567889999999999999998888833223 21 22224577766666653
No 27
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=28.24 E-value=50 Score=22.72 Aligned_cols=26 Identities=12% Similarity=0.109 Sum_probs=23.6
Q ss_pred hcCCHHHHhHHHHHHHHHhhhCCCCC
Q psy17564 11 NSMDLSIRRELPTMLSKMAADHQLDE 36 (109)
Q Consensus 11 ~~Md~~lK~~L~~~le~~a~~ygL~d 36 (109)
+-++.+.|..+++--+.+..+|||.+
T Consensus 14 sL~~a~~RerF~~D~ea~~~e~gLt~ 39 (94)
T cd07923 14 RLIEPAHRERFLEDPEALFDEAGLTE 39 (94)
T ss_pred HHCCHHHHHHHHhCHHHHHHHcCCCH
Confidence 34799999999999999999999996
No 28
>cd07589 BAR_DNMBP The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. DyNamin Binding Protein (DNMBP), also called Tuba, is a Cdc42-specific Guanine nucleotide Exchange Factor (GEF) that binds dynamin and various actin regulatory proteins. It serves as a link between dynamin function, Rho GTPase signaling, and actin dynamics. It plays an important role in regulating cell junction configuration. DNMBP contains BAR and SH3 domains as well as a Dbl Homology domain (DH domain), which harbors GEF activity. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of DNMBP may be involved in binding to membranes. The gene encoding DNMBP is a candidate gene for late onset Alzheimer's disease.
Probab=28.16 E-value=43 Score=25.03 Aligned_cols=27 Identities=22% Similarity=0.448 Sum_probs=24.1
Q ss_pred hhhhhhchhcCCHHHHhHHHHHHHHHh
Q psy17564 3 LLQSKQLYNSMDLSIRRELPTMLSKMA 29 (109)
Q Consensus 3 L~q~kQ~y~~Md~~lK~~L~~~le~~a 29 (109)
+.++++.|..++..+|+.|+.-+..-.
T Consensus 135 l~~a~~~y~~lN~~L~~ELP~l~~~~~ 161 (195)
T cd07589 135 LEEAANQYEALNAQLKEELPKFNQLTA 161 (195)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 578999999999999999999887765
No 29
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=28.11 E-value=24 Score=23.43 Aligned_cols=20 Identities=15% Similarity=0.365 Sum_probs=13.4
Q ss_pred Cchhhhhhchh---cCCHHHHhH
Q psy17564 1 MPLLQSKQLYN---SMDLSIRRE 20 (109)
Q Consensus 1 isL~q~kQ~y~---~Md~~lK~~ 20 (109)
+||.|||++|. .|..+.++.
T Consensus 47 ~SL~eAr~ny~~~GA~e~~~~~~ 69 (78)
T PF14206_consen 47 MSLNEARENYKKFGACEERMLKH 69 (78)
T ss_pred HHHHHHHHHHHHHCcccHHHHhh
Confidence 58999999886 344444443
No 30
>KOG1241|consensus
Probab=27.90 E-value=52 Score=30.62 Aligned_cols=52 Identities=23% Similarity=0.238 Sum_probs=37.1
Q ss_pred hhhhhchhcCCHHHHhHHHHHHHHHhhhCCCCCcccchhheeecCCCccchhhHHHHHHHHhccCcc
Q psy17564 4 LQSKQLYNSMDLSIRRELPTMLSKMAADHQLDELIMPSFTLLHGYRTKIQASDYVYAMLALLESPVR 70 (109)
Q Consensus 4 ~q~kQ~y~~Md~~lK~~L~~~le~~a~~ygL~dl~~~SF~r~~Gy~~~lSA~D~vyav~ALLE~~~~ 70 (109)
.||+|.|..|+++.|+.+|..+.+-. |=..- +.+=+|+-+|-+| |-.|-+.+
T Consensus 74 ~~~~qRWl~l~~e~reqVK~~il~tL---~~~ep-----------~~~s~Aaq~va~I-A~~ElP~n 125 (859)
T KOG1241|consen 74 QQYQQRWLQLPAEIREQVKNNILRTL---GSPEP-----------RRPSSAAQCVAAI-ACIELPQN 125 (859)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHc---CCCCC-----------CccchHHHHHHHH-HHhhCchh
Confidence 58999999999999999999988765 11111 3455677777665 45666654
No 31
>PF07746 LigA: Aromatic-ring-opening dioxygenase LigAB, LigA subunit; InterPro: IPR011986 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A (IPR004183 from INTERPRO) and B (IPR004183 from INTERPRO). LigAB is a protocatechuate 4,5-dioxygenase (1.13.11.8 from EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [].; PDB: 1BOU_A 1B4U_A.
Probab=27.09 E-value=55 Score=21.98 Aligned_cols=26 Identities=15% Similarity=0.029 Sum_probs=20.5
Q ss_pred hcCCHHHHhHHHHHHHHHhhhCCCCC
Q psy17564 11 NSMDLSIRRELPTMLSKMAADHQLDE 36 (109)
Q Consensus 11 ~~Md~~lK~~L~~~le~~a~~ygL~d 36 (109)
+-++.+.|..+++-=+.+..+|||++
T Consensus 7 ~L~~~~~r~~F~~D~~a~~~~~~Lt~ 32 (88)
T PF07746_consen 7 SLNDPENRERFLADPEAYLDEYGLTE 32 (88)
T ss_dssp GGGSHHHHHHHHH-HHHHHHCCT--H
T ss_pred HHcCHHHHHHHHHCHHHHHHHcCCCH
Confidence 34799999999999999999999986
No 32
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=26.71 E-value=71 Score=27.49 Aligned_cols=36 Identities=11% Similarity=0.143 Sum_probs=32.2
Q ss_pred hhhhhchhcCCHHHHhHHHHHHHHHhhhCCCCCccc
Q psy17564 4 LQSKQLYNSMDLSIRRELPTMLSKMAADHQLDELIM 39 (109)
Q Consensus 4 ~q~kQ~y~~Md~~lK~~L~~~le~~a~~ygL~dl~~ 39 (109)
.||++....++.=.|+++|.+.|++|.+-|.+.|+-
T Consensus 466 ~ea~~~l~~iP~f~r~~~r~~~e~~a~~~g~~~it~ 501 (513)
T CHL00076 466 PESQLELSKIPGFVRGKVKRNTEKFARQNGITNITV 501 (513)
T ss_pred HHHHHHHHhCCHHhHHHHHHHHHHHHHHcCCCeEcH
Confidence 467888888899999999999999999999998875
No 33
>cd02879 GH18_plant_chitinase_class_V The class V plant chitinases have a glycosyl hydrolase family 18 (GH18) domain, but lack the chitin-binding domain present in other GH18 enzymes. The GH18 domain of the class V chitinases has endochitinase activity in some cases and no catalytic activity in others. Included in this family is a lectin found in black locust (Robinia pseudoacacia) bark, which binds chitin but lacks chitinase activity. Also included is a chitinase-related receptor-like kinase (CHRK1) from tobacco (Nicotiana tabacum), with an N-terminal GH18 domain and a C-terminal kinase domain, which is thought to be part of a plant signaling pathway. The GH18 domain of CHRK1 is expressed extracellularly where it binds chitin but lacks chitinase activity.
Probab=25.83 E-value=67 Score=25.31 Aligned_cols=32 Identities=22% Similarity=0.284 Sum_probs=26.6
Q ss_pred hchhcC--CHHHHhHHHHHHHHHhhhCCCCCccc
Q psy17564 8 QLYNSM--DLSIRRELPTMLSKMAADHQLDELIM 39 (109)
Q Consensus 8 Q~y~~M--d~~lK~~L~~~le~~a~~ygL~dl~~ 39 (109)
+.|+.| +.+.|+.+-+.+.+++.+||++.|-.
T Consensus 81 ~~fs~~~~~~~~R~~fi~siv~~l~~~~fDGidi 114 (299)
T cd02879 81 SAFAAMASDPTARKAFINSSIKVARKYGFDGLDL 114 (299)
T ss_pred chhhHHhCCHHHHHHHHHHHHHHHHHhCCCceee
Confidence 345555 78899999999999999999996655
No 34
>PF15583 Imm41: Immunity protein 41
Probab=25.58 E-value=58 Score=24.49 Aligned_cols=44 Identities=36% Similarity=0.443 Sum_probs=29.8
Q ss_pred HHHHhhhCCCCCcccchhhee---------ecCCCcc-chhhHHHHHHHH-hccCc
Q psy17564 25 LSKMAADHQLDELIMPSFTLL---------HGYRTKI-QASDYVYAMLAL-LESPV 69 (109)
Q Consensus 25 le~~a~~ygL~dl~~~SF~r~---------~Gy~~~l-SA~D~vyav~AL-LE~~~ 69 (109)
+.++-.++||+.+ -++|.+. -||...+ .|.|+|-.+.|| |||-.
T Consensus 34 l~eIF~d~gLdkl-~~nfr~t~~~l~~~~~~G~e~~f~~aid~V~DLaallLEc~~ 88 (158)
T PF15583_consen 34 LSEIFADLGLDKL-NGNFRQTDENLKFTESDGFEHEFDFAIDLVTDLAALLLECKK 88 (158)
T ss_pred HHHHHHhcCchhh-ccccccccccceeecccchHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445567788877 5566655 3555554 499999999997 56643
No 35
>PRK10870 transcriptional repressor MprA; Provisional
Probab=25.42 E-value=75 Score=23.22 Aligned_cols=61 Identities=20% Similarity=0.255 Sum_probs=40.0
Q ss_pred chhhhhhchhc--------------CCHHHHhHHHHHHHHHhhhCCCCCcccchhheeecC-CCccchhhHHHHHH
Q psy17564 2 PLLQSKQLYNS--------------MDLSIRRELPTMLSKMAADHQLDELIMPSFTLLHGY-RTKIQASDYVYAML 62 (109)
Q Consensus 2 sL~q~kQ~y~~--------------Md~~lK~~L~~~le~~a~~ygL~dl~~~SF~r~~Gy-~~~lSA~D~vyav~ 62 (109)
|+++.-++|.. +-..+.+.+...+.+....|||..--|.-...-+.. ...++..|.+..+.
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~l~~~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~ 82 (176)
T PRK10870 7 PIEQMLKFRASRHEDFPYQEILLTRLCMHMQSKLLENRNKMLKAQGINETLFMALITLESQENHSIQPSELSCALG 82 (176)
T ss_pred hHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHC
Confidence 56666666665 344556677778888899999987655554444433 34577777766543
No 36
>PRK14129 heat shock protein HspQ; Provisional
Probab=24.56 E-value=10 Score=26.70 Aligned_cols=32 Identities=19% Similarity=0.283 Sum_probs=27.0
Q ss_pred HhhhCCCCCcccchhheeecCCCccchhhHHHHHH
Q psy17564 28 MAADHQLDELIMPSFTLLHGYRTKIQASDYVYAML 62 (109)
Q Consensus 28 ~a~~ygL~dl~~~SF~r~~Gy~~~lSA~D~vyav~ 62 (109)
++.||||-+++. .|.+||++-+--.|-+|+.+
T Consensus 2 i~akF~IGQ~Vr---Hrl~~yrGVV~DVDP~fs~~ 33 (105)
T PRK14129 2 IASKFGIGQQVR---HSLLGYLGVVVDIDPEYSLE 33 (105)
T ss_pred ccccccCCcEEE---EeecCCCeEEEeeCCCcCCC
Confidence 467899999888 57899999999999888754
No 37
>cd07612 BAR_Bin2 The Bin/Amphiphysin/Rvs (BAR) domain of Bridging integrator 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Bridging integrator 2 (Bin2) is a BAR domain containing protein that is mainly expressed in hematopoietic cells. It is upregulated during granulocyte differentiation and is thought to function primarily in this lineage. The BAR domain of Bin2 is closely related to the BAR domains of amphiphysins, which function primarily in endocytosis and other membrane remodeling events. Amphiphysins contain an N-terminal BAR domain with an additional N-terminal amphipathic helix (an N-BAR), a variable central domain, and a C-terminal SH3 domain. Unlike amphiphysins, Bin2 does not appear to contain a C-terminal SH3 domain. Amphiphysin I proteins, enriched in the brain and nervous system, function in synaptic vesicle endocytosis. Some amphiphysin II isoforms, also called Bridging integrator 1 (
Probab=24.53 E-value=46 Score=25.87 Aligned_cols=27 Identities=15% Similarity=0.445 Sum_probs=24.0
Q ss_pred hhhhhhchhcCCHHHHhHHHHHHHHHh
Q psy17564 3 LLQSKQLYNSMDLSIRRELPTMLSKMA 29 (109)
Q Consensus 3 L~q~kQ~y~~Md~~lK~~L~~~le~~a 29 (109)
|.+|||.|.+++-.|+..|+..+.-=.
T Consensus 148 l~~Ak~~ye~lN~~L~~ELP~L~~~Ri 174 (211)
T cd07612 148 FNRAQVVFEDINRELREELPILYDSRI 174 (211)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 678999999999999999999887655
No 38
>PF03598 CdhC: CO dehydrogenase/acetyl-CoA synthase complex beta subunit; InterPro: IPR004461 The carbon monoxide dehydrogenase alpha subunit (1.2.99.2 from EC) catalyses the interconversion of CO and CO2 and the synthesis of acteyl-coA from the methylated corrinoid/iron sulphur protein, CO and CoA. Nomenclature follows the description for Methanosarcina thermophila. The complex is also found in Archaeoglobus fulgidus, not considered a methanogen, but is otherwise generally associated with methanogenesis.; GO: 0018492 carbon-monoxide dehydrogenase (acceptor) activity, 0006084 acetyl-CoA metabolic process; PDB: 2Z8Y_O 1MJG_N 3GIT_A 3S2X_B 3I01_O 3I04_N 1OAO_C 1RU3_A.
Probab=24.03 E-value=51 Score=28.25 Aligned_cols=26 Identities=19% Similarity=0.325 Sum_probs=22.2
Q ss_pred cCCHHHHhHHHHHHHHHhhhCCCCCc
Q psy17564 12 SMDLSIRRELPTMLSKMAADHQLDEL 37 (109)
Q Consensus 12 ~Md~~lK~~L~~~le~~a~~ygL~dl 37 (109)
-|+.++|..+++.|.+-+.+-|++|+
T Consensus 352 WmPk~lKe~v~~~i~~~~~e~~~~~~ 377 (411)
T PF03598_consen 352 WMPKELKEEVKERIPKRAKELGLEDF 377 (411)
T ss_dssp E--HHHHHHCHHHHHHHHHHTTSTTH
T ss_pred ECCHHHHHHHHHHHHHHhhhccchHH
Confidence 59999999999999999999999775
No 39
>smart00398 HMG high mobility group.
Probab=23.53 E-value=1e+02 Score=17.97 Aligned_cols=30 Identities=3% Similarity=-0.064 Sum_probs=23.5
Q ss_pred hhhhhchhcCCHHHHhHHHHHHHHHhhhCC
Q psy17564 4 LQSKQLYNSMDLSIRRELPTMLSKMAADHQ 33 (109)
Q Consensus 4 ~q~kQ~y~~Md~~lK~~L~~~le~~a~~yg 33 (109)
..+-+.|..|+.+.|....+.-++....|.
T Consensus 34 ~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~ 63 (70)
T smart00398 34 KKLGERWKLLSEEEKAPYEEKAKKDKERYE 63 (70)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence 356788999999999998888777665553
No 40
>PF13354 Beta-lactamase2: Beta-lactamase enzyme family; PDB: 1G6A_A 1G68_A 3NIA_A 3NI9_B 1BUL_A 1BUE_A 4EUZ_A 4EV4_A 4EQI_A 1O7E_B ....
Probab=23.06 E-value=1.3e+02 Score=21.44 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=36.9
Q ss_pred HHHHHHHhhhCCCCCcccchhhe-----eecCCCccchhhHHHHHHHHhccC
Q psy17564 22 PTMLSKMAADHQLDELIMPSFTL-----LHGYRTKIQASDYVYAMLALLESP 68 (109)
Q Consensus 22 ~~~le~~a~~ygL~dl~~~SF~r-----~~Gy~~~lSA~D~vyav~ALLE~~ 68 (109)
.+.+.+++.++|+.+..+..-.. ..++.+..|+.|++.-+..|....
T Consensus 89 ~~~v~~~~~~~G~~~t~~~~~~~~~~~~~~~~~n~~T~~d~~~ll~~l~~~~ 140 (197)
T PF13354_consen 89 PDAVNAWLKRLGLTDTRINRPLPDPEAIDGGYRNTTTARDMARLLEQLYQGE 140 (197)
T ss_dssp HHHHHHHHHHTTHSSGBGGSCTTGGGGCTTCSTTEEEHHHHHHHHHHHHTSS
T ss_pred ccchhhhHHHcCCccEEeccccccccccccCCCCcCCHHHHHHHHHHHhhcc
Confidence 46678889999999876654332 247789999999999999998864
No 41
>smart00535 RIBOc Ribonuclease III family.
Probab=23.00 E-value=82 Score=20.99 Aligned_cols=47 Identities=17% Similarity=0.143 Sum_probs=32.2
Q ss_pred HHHHHHhhhCCCCCcccchhhe-ee-cCCCccchhhHHHHHHHHhccCc
Q psy17564 23 TMLSKMAADHQLDELIMPSFTL-LH-GYRTKIQASDYVYAMLALLESPV 69 (109)
Q Consensus 23 ~~le~~a~~ygL~dl~~~SF~r-~~-Gy~~~lSA~D~vyav~ALLE~~~ 69 (109)
+.+-+.+.++||+++...+... .- +-..+-.-+|+++|+.+-+-...
T Consensus 61 ~~la~~a~~~~l~~~i~~~~~~~~~~~~~~~k~~a~~~eAliGAi~ld~ 109 (129)
T smart00535 61 ETLARLAKKLGLGEFIRLGRGEAISGGRDKPSILADVFEALIGAIYLDS 109 (129)
T ss_pred HHHHHHHHHCCcHHHHccCchHhhcCCcccchHHHHHHHHHHHHHHHhC
Confidence 5678899999999877754321 11 12345568899999987766544
No 42
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=22.81 E-value=90 Score=19.56 Aligned_cols=28 Identities=14% Similarity=0.258 Sum_probs=22.7
Q ss_pred hhhhchhcCCHHHHhHHHHHHHHHhhhC
Q psy17564 5 QSKQLYNSMDLSIRRELPTMLSKMAADH 32 (109)
Q Consensus 5 q~kQ~y~~Md~~lK~~L~~~le~~a~~y 32 (109)
+.-+.+.+.|.++|+.|..+|-+...+|
T Consensus 37 ~~g~~~~~vDedl~q~l~~kLi~~I~~F 64 (65)
T PF12645_consen 37 EYGNVYGYVDEDLKQRLEIKLIEAILKF 64 (65)
T ss_pred ccCCcCceeCHHHHHHHHHHHHHHHHcc
Confidence 4456677899999999999998877665
No 43
>cd07591 BAR_Rvs161p The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 161 and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 161 (Rvs161p) and Schizosaccharomyces pombe Hob3 (homolog of Bin3). S. cerevisiae Rvs161p plays a role in regulating cell polarity, actin cytoskeleton polarization, vesicle trafficking, endocytosis, bud formation, and the mating response. It forms a heterodimer with another BAR domain protein Rvs167p. Rvs161p and Rvs167p share common functions but are not interchangeable. Their BAR domains cannot be replaced with each other and the overexpression of one cannot suppress the mutant phenotypes of the other. S. pombe Hob3 is important in regulating filamentous actin localization an
Probab=22.78 E-value=56 Score=25.12 Aligned_cols=27 Identities=22% Similarity=0.518 Sum_probs=24.2
Q ss_pred hhhhhhchhcCCHHHHhHHHHHHHHHh
Q psy17564 3 LLQSKQLYNSMDLSIRRELPTMLSKMA 29 (109)
Q Consensus 3 L~q~kQ~y~~Md~~lK~~L~~~le~~a 29 (109)
|.+|++.|..++..+|..|+..+.--.
T Consensus 153 l~~a~~~Ye~lN~~Lk~ELP~l~~~r~ 179 (224)
T cd07591 153 LDEAKEVYETLNDQLKTELPQLVDLRI 179 (224)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 578999999999999999999888665
No 44
>PF09388 SpoOE-like: Spo0E like sporulation regulatory protein; InterPro: IPR018540 Spore formation is an extreme response to starvation and can also be a component of disease transmission. Sporulation is controlled by an expanded two-component system where starvation signals result in sensor kinase activation and phosphorylation of the master sporulation response regulator Spo0A. Phosphatases such as Spo0E dephosphorylate Spo0A thereby inhibiting sporulation. This is a family of Spo0E-like phosphatases. The structure of a Bacillus anthracis member of this family has revealed an anti-parallel alpha-helical structure []. ; PDB: 2BZB_B 2C0S_A.
Probab=22.43 E-value=1.1e+02 Score=17.60 Aligned_cols=18 Identities=28% Similarity=0.431 Sum_probs=14.3
Q ss_pred hHHHHHHHHHhhhCCCCC
Q psy17564 19 RELPTMLSKMAADHQLDE 36 (109)
Q Consensus 19 ~~L~~~le~~a~~ygL~d 36 (109)
..+|..|.+.+.++||.+
T Consensus 7 e~~R~~L~~~~~~~~l~~ 24 (45)
T PF09388_consen 7 EELRQELNELAEKKGLTD 24 (45)
T ss_dssp HHHHHHHHHHHHHCCTTC
T ss_pred HHHHHHHHHHHHHcCCCC
Confidence 457888888888888876
No 45
>cd07590 BAR_Bin3 The Bin/Amphiphysin/Rvs (BAR) domain of Bridging integrator 3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Bridging integrator 3 (Bin3) is widely expressed in many tissues except in the brain. It plays roles in regulating filamentous actin localization and in cell division. In humans, the Bin3 gene is located in chromosome 8p21.3, a region that is implicated in cancer suppression. Homozygous inactivation of the Bin3 gene in mice led to the development of cataracts and an increased likelihood of lymphomas during aging, suggesting a role for Bin3 in lens development and cancer suppression. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=22.36 E-value=39 Score=26.29 Aligned_cols=39 Identities=18% Similarity=0.393 Sum_probs=30.2
Q ss_pred hhhhhhchhcCCHHHHhHHHHHHHHHhhhCCCCCcccchhheeec
Q psy17564 3 LLQSKQLYNSMDLSIRRELPTMLSKMAADHQLDELIMPSFTLLHG 47 (109)
Q Consensus 3 L~q~kQ~y~~Md~~lK~~L~~~le~~a~~ygL~dl~~~SF~r~~G 47 (109)
+..|++.|.+++..++..|+..+..-. ..+-|+|..-+.
T Consensus 154 l~~Ak~~ye~~N~~L~~ELP~l~~~r~------~f~~p~Fqsl~~ 192 (225)
T cd07590 154 LAAARADFEKQNIKLLEELPKFYNGRT------DYFQPCFEALIK 192 (225)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHcc------HHHHHHHHHHHH
Confidence 578999999999999999999988776 344455554433
No 46
>cd07611 BAR_Amphiphysin_I_II The Bin/Amphiphysin/Rvs (BAR) domain of Amphiphysin I and II. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Amphiphysins function primarily in endocytosis and other membrane remodeling events. They contain an N-terminal BAR domain with an additional N-terminal amphipathic helix (an N-BAR), a variable central domain, and a C-terminal SH3 domain. Amphiphysin I proteins, enriched in the brain and nervous system, contain domains that bind clathrin, Adaptor Protein complex 2 (AP2), dynamin and synaptojanin. They function in synaptic vesicle endocytosis. Some amphiphysin II isoforms, also called Bridging integrator 1 (Bin1), are localized in many different tissues and may function in intracellular vesicle trafficking. In skeletal muscle, Bin1 plays a role in the organization and maintenance of the T-tubule network. The N-BAR domain of amphiphysin forms a curved dimer with a posit
Probab=22.28 E-value=56 Score=25.40 Aligned_cols=28 Identities=14% Similarity=0.565 Sum_probs=24.6
Q ss_pred hhhhhhchhcCCHHHHhHHHHHHHHHhh
Q psy17564 3 LLQSKQLYNSMDLSIRRELPTMLSKMAA 30 (109)
Q Consensus 3 L~q~kQ~y~~Md~~lK~~L~~~le~~a~ 30 (109)
|.+|+|.|.+++-.||..|+..+.--.|
T Consensus 148 l~~Ak~~ye~lN~~Lk~ELP~L~~~Ri~ 175 (211)
T cd07611 148 FQKAQKVFEEFNVDLQEELPSLWSRRVG 175 (211)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence 6789999999999999999998876553
No 47
>PF06628 Catalase-rel: Catalase-related immune-responsive; InterPro: IPR010582 Catalases (1.11.1.6 from EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects []. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (IPR000763 from INTERPRO) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (IPR007760 from INTERPRO) that are found in bacteria []. This entry represents a small conserved region within catalase enzymes that carries the immune-responsive amphipathic octa-peptide that is recognised by T cells [].; PDB: 2CAH_A 1NM0_A 1H7K_A 1E93_A 1H6N_A 3HB6_A 2CAG_A 1M85_A 1MQF_A 1A4E_C ....
Probab=22.17 E-value=1.1e+02 Score=19.04 Aligned_cols=26 Identities=19% Similarity=0.244 Sum_probs=23.0
Q ss_pred hhhhhchhcCCHHHHhHHHHHHHHHh
Q psy17564 4 LQSKQLYNSMDLSIRRELPTMLSKMA 29 (109)
Q Consensus 4 ~q~kQ~y~~Md~~lK~~L~~~le~~a 29 (109)
.|++.-|..|+..-|..|-..|-...
T Consensus 11 ~Qa~~ly~~l~~~er~~lv~nia~~l 36 (68)
T PF06628_consen 11 SQARDLYRVLSDEERERLVENIAGHL 36 (68)
T ss_dssp HHHHHHHHHSSHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHCCHHHHHHHHHHHHHHH
Confidence 58899999999999999998887766
No 48
>smart00545 JmjN Small domain found in the jumonji family of transcription factors. To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).
Probab=21.99 E-value=56 Score=19.09 Aligned_cols=21 Identities=10% Similarity=0.148 Sum_probs=16.7
Q ss_pred HHHHHHHHhhhCCCCCcccch
Q psy17564 21 LPTMLSKMAADHQLDELIMPS 41 (109)
Q Consensus 21 L~~~le~~a~~ygL~dl~~~S 41 (109)
.-++++..+.+||+--|+.+.
T Consensus 18 yi~~i~~~~~~yGi~KIvPP~ 38 (42)
T smart00545 18 YISKIRPQAEKYGICKVVPPK 38 (42)
T ss_pred HHHHHHHHHhhCCEEEEECCC
Confidence 445688889999998888764
No 49
>PF02285 COX8: Cytochrome oxidase c subunit VIII; InterPro: IPR003205 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits.This family is composed of cytochrome c oxidase subunit VIII. ; GO: 0004129 cytochrome-c oxidase activity; PDB: 3AG3_Z 3ABM_M 1OCC_Z 3ASO_Z 3AG2_Z 3ABL_M 3AG4_M 3AG1_M 3ASN_M 1OCZ_M ....
Probab=21.47 E-value=94 Score=18.54 Aligned_cols=18 Identities=6% Similarity=0.178 Sum_probs=12.2
Q ss_pred CCccchhhHHHHHHHHhc
Q psy17564 49 RTKIQASDYVYAMLALLE 66 (109)
Q Consensus 49 ~~~lSA~D~vyav~ALLE 66 (109)
+.++|++|.+.+++.+.-
T Consensus 7 ~~~~s~~e~aigltv~f~ 24 (44)
T PF02285_consen 7 REPLSPAEQAIGLTVCFV 24 (44)
T ss_dssp SS---HHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHH
Confidence 568999999999987754
No 50
>cd02876 GH18_SI-CLP Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl hydrolase family 18 (GH18) domain but lacks a chitin-binding domain. The catalytic amino acids of the GH18 domain are not conserved in SI-CLP, similar to the chitolectins YKL-39, YKL-40, and YM1/2. Human SI-CLP is sorted to late endosomes and secretory lysosomes in alternatively activated macrophages.
Probab=21.16 E-value=1e+02 Score=24.20 Aligned_cols=30 Identities=23% Similarity=0.420 Sum_probs=25.7
Q ss_pred hhcC--CHHHHhHHHHHHHHHhhhCCCCCccc
Q psy17564 10 YNSM--DLSIRRELPTMLSKMAADHQLDELIM 39 (109)
Q Consensus 10 y~~M--d~~lK~~L~~~le~~a~~ygL~dl~~ 39 (109)
|+.| +.+.|+++-..+.+++.+||++.|..
T Consensus 83 f~~~~~~~~~R~~fi~s~~~~~~~~~~DGidi 114 (318)
T cd02876 83 LQSLLNDEQEREKLIKLLVTTAKKNHFDGIVL 114 (318)
T ss_pred HHHHHcCHHHHHHHHHHHHHHHHHcCCCcEEE
Confidence 5555 88899999999999999999997754
No 51
>cd02878 GH18_zymocin_alpha Zymocin, alpha subunit. Zymocin is a heterotrimeric enzyme that inhibits yeast cell cycle progression. The zymocin alpha subunit has a chitinase activity that is essential for holoenzyme action from the cell exterior while the gamma subunit contains the intracellular toxin responsible for G1 phase cell cycle arrest. The zymocin alpha and beta subunits are thought to act from the cell's exterior by docking to the cell wall-associated chitin, thus mediating gamma-toxin translocation. The alpha subunit has an eight-stranded TIM barrel fold similar to that of family 18 glycosyl hydrolases such as hevamine, chitolectin, and chitobiase.
Probab=21.12 E-value=1e+02 Score=24.74 Aligned_cols=31 Identities=10% Similarity=0.205 Sum_probs=25.5
Q ss_pred chhcC-CHHHHhHHHHHHHHHhhhCCCCCccc
Q psy17564 9 LYNSM-DLSIRRELPTMLSKMAADHQLDELIM 39 (109)
Q Consensus 9 ~y~~M-d~~lK~~L~~~le~~a~~ygL~dl~~ 39 (109)
.|..| +.+.|+.+-..+.+++.+||++.|-.
T Consensus 82 ~f~~~~~~~~R~~Fi~si~~~~~~~~fDGidi 113 (345)
T cd02878 82 IFRDAVKPANRDTFANNVVNFVNKYNLDGVDF 113 (345)
T ss_pred hhHhhcCHHHHHHHHHHHHHHHHHcCCCceee
Confidence 45555 78999999999999999999995543
No 52
>PRK09529 bifunctional acetyl-CoA decarbonylase/synthase complex subunit alpha/beta; Reviewed
Probab=20.85 E-value=71 Score=29.26 Aligned_cols=27 Identities=22% Similarity=0.295 Sum_probs=24.4
Q ss_pred cCCHHHHhHHHHHHHHHhhhCCCCCcc
Q psy17564 12 SMDLSIRRELPTMLSKMAADHQLDELI 38 (109)
Q Consensus 12 ~Md~~lK~~L~~~le~~a~~ygL~dl~ 38 (109)
-|+.++|..+++.|.+-|.+-|++|++
T Consensus 652 WmPk~lKe~v~~~i~~~~~e~g~~~~~ 678 (711)
T PRK09529 652 WMPKELKEELKDRLNARAKEEGLPDFY 678 (711)
T ss_pred ECCHHHHHHHHHHhhhhhhhccchHHH
Confidence 599999999999999999999998753
No 53
>cd08536 SAM_PNT-Mae Sterile alpha motif (SAM)/Pointed domain of Mae protein homolog. Mae (Modulator of the Activity of ETS) subfamily represents a group of SAM Pointed monodomain proteins. SAM Pointed domain is a protein-protein interaction domain. It can interact with other SAM pointed domains forming head-to-tail heterodimers and also provides a kinase docking site. For example, in Drosophila Mae is required for facilitating phosphorylation of the Yan factor and for blocking phosphorylation of the ETS-2 regulator. Mae interacts with the SAM Pointed domains of Yan and ETS-2. Binding enhances access of the kinase to the Yan phosphorylation site by providing a kinase docking site, or inhibits phosphorylation of ETS-2 by blocking its docking site. This type of factors participates in regulation of kinase signaling particularly during embryogenesis.
Probab=20.75 E-value=1.2e+02 Score=19.17 Aligned_cols=26 Identities=27% Similarity=0.312 Sum_probs=22.1
Q ss_pred HhHHHHHHHHHhhhCCCCCcccchhh
Q psy17564 18 RRELPTMLSKMAADHQLDELIMPSFT 43 (109)
Q Consensus 18 K~~L~~~le~~a~~ygL~dl~~~SF~ 43 (109)
+..+.+.|+-...+|+|+.+....|.
T Consensus 7 ~~~V~~WL~w~~~ef~L~~~~~~~F~ 32 (66)
T cd08536 7 REHVRTWLRWVSARYQLEVVDLDKFL 32 (66)
T ss_pred HHHHHHHHHHHHHHhCCCCCCccccC
Confidence 46788899999999999998887774
No 54
>COG1580 FliL Flagellar basal body-associated protein [Cell motility and secretion]
Probab=20.64 E-value=68 Score=23.76 Aligned_cols=31 Identities=6% Similarity=0.330 Sum_probs=24.9
Q ss_pred HHHHhHHHHHHHHHhhhC-CCCCcccchhhee
Q psy17564 15 LSIRRELPTMLSKMAADH-QLDELIMPSFTLL 45 (109)
Q Consensus 15 ~~lK~~L~~~le~~a~~y-gL~dl~~~SF~r~ 45 (109)
..+|+++++.+..+...= +..|+.|..|+.+
T Consensus 128 e~Lk~ei~~~in~~L~~g~~V~dV~fT~fiiq 159 (159)
T COG1580 128 EKLKAEIKDRINTILKEGQVVKDVLFTNFIIQ 159 (159)
T ss_pred HHHHHHHHHHHHHHHhcCCeeEEEeeehhhcC
Confidence 367888888888888777 8889999988753
No 55
>PRK12371 ribonuclease III; Reviewed
Probab=20.62 E-value=2e+02 Score=22.19 Aligned_cols=62 Identities=15% Similarity=0.035 Sum_probs=35.9
Q ss_pred chhcCCHH----HHhHHH--HHHHHHhhhCCCCCcccchhh-eeecCCC-ccchhhHHHHHHHHhccCcc
Q psy17564 9 LYNSMDLS----IRRELP--TMLSKMAADHQLDELIMPSFT-LLHGYRT-KIQASDYVYAMLALLESPVR 70 (109)
Q Consensus 9 ~y~~Md~~----lK~~L~--~~le~~a~~ygL~dl~~~SF~-r~~Gy~~-~lSA~D~vyav~ALLE~~~~ 70 (109)
+|..|+.. +|..+. +.|-+.|.++||++....+-- ...+-+. .=.=+|+|+|+.+.+=.+.+
T Consensus 68 ~~p~~~eG~Lt~~rs~lV~n~~La~ia~~lgL~~~i~~~~~~~~~~~~~~~~ilad~~EAliGAiylD~G 137 (235)
T PRK12371 68 AFPDASEGELSVRLNQLVNAETCAAIADEIGLHDLIRTGSDVKKLTGKRLLNVRADVVEALIAAIYLDGG 137 (235)
T ss_pred hCCCCCHHHHHHHHHHHhChHHHHHHHHHCCcHHHhccCcchhhcCCcccchHHHHHHHHHHHHHHHcCC
Confidence 44456544 333333 566789999999988764421 1111111 11228999999877665544
No 56
>cd00598 GH18_chitinase-like The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel. The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins. The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are inclu
Probab=20.48 E-value=1.2e+02 Score=21.61 Aligned_cols=26 Identities=15% Similarity=0.175 Sum_probs=22.6
Q ss_pred CHHHHhHHHHHHHHHhhhCCCCCccc
Q psy17564 14 DLSIRRELPTMLSKMAADHQLDELIM 39 (109)
Q Consensus 14 d~~lK~~L~~~le~~a~~ygL~dl~~ 39 (109)
+.+.|+++-+.+.++..+||++.|.+
T Consensus 85 ~~~~~~~f~~~~~~~v~~~~~DGidi 110 (210)
T cd00598 85 DPASRAAFANSLVSFLKTYGFDGVDI 110 (210)
T ss_pred CHHHHHHHHHHHHHHHHHcCCCceEE
Confidence 66788999999999999999996655
No 57
>TIGR02191 RNaseIII ribonuclease III, bacterial. This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family.
Probab=20.42 E-value=1.2e+02 Score=22.25 Aligned_cols=48 Identities=15% Similarity=0.131 Sum_probs=31.3
Q ss_pred HHHHHHhhhCCCCCcccch--hheeecCCCccchhhHHHHHHHHhccCcc
Q psy17564 23 TMLSKMAADHQLDELIMPS--FTLLHGYRTKIQASDYVYAMLALLESPVR 70 (109)
Q Consensus 23 ~~le~~a~~ygL~dl~~~S--F~r~~Gy~~~lSA~D~vyav~ALLE~~~~ 70 (109)
..+-+.|.++||++....+ .....|...+=--+|+++|+.+.+=.+.+
T Consensus 77 ~~la~~a~~~gl~~~i~~~~~~~~~~~~~~~k~~ad~~eAliGAiyld~g 126 (220)
T TIGR02191 77 ESLAEVARELGLGKFLLLGKGEEKSGGRRRESILADAFEALIGAIYLDSG 126 (220)
T ss_pred HHHHHHHHHCCcHHHhccCchHhhcCCcccchHHHHHHHHHHHHHHHhCC
Confidence 5677899999999876643 32333444344469999998766544443
Done!