Query 034650
Match_columns 88
No_of_seqs 11 out of 13
Neff 1.7
Searched_HMMs 46136
Date Fri Mar 29 05:04:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034650.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034650hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13232 Complex1_LYR_1: Compl 98.4 1.3E-06 2.8E-11 51.9 5.5 60 17-79 2-61 (61)
2 PF05347 Complex1_LYR: Complex 98.1 8.4E-06 1.8E-10 47.2 4.9 57 17-76 2-58 (59)
3 PF13233 Complex1_LYR_2: Compl 89.4 0.18 3.9E-06 32.1 1.0 14 18-31 1-14 (104)
4 PF04716 ETC_C1_NDUFA5: ETC co 87.8 1.3 2.7E-05 27.5 4.0 53 15-69 4-56 (57)
5 KOG3801 Uncharacterized conser 48.4 15 0.00032 25.8 2.0 63 14-80 5-68 (94)
6 PF09373 PMBR: Pseudomurein-bi 47.9 33 0.00071 18.8 3.0 24 64-87 7-31 (33)
7 KOG4620 Uncharacterized conser 46.9 15 0.00032 25.3 1.8 58 15-83 8-74 (80)
8 PF06426 SATase_N: Serine acet 46.5 57 0.0012 21.6 4.5 53 9-71 9-62 (105)
9 cd00159 RhoGAP RhoGAP: GTPase- 46.4 76 0.0017 20.2 5.3 32 14-45 51-82 (169)
10 cd04385 RhoGAP_ARAP RhoGAP_ARA 42.6 58 0.0013 22.8 4.3 48 16-69 70-117 (184)
11 cd04400 RhoGAP_fBEM3 RhoGAP_fB 41.9 88 0.0019 21.8 5.1 30 15-44 78-107 (190)
12 PRK08392 hypothetical protein; 41.9 14 0.00031 26.1 1.2 40 39-84 166-205 (215)
13 PRK09248 putative hydrolase; V 41.0 21 0.00045 25.5 1.9 44 35-84 173-216 (246)
14 KOG3466 NADH:ubiquinone oxidor 41.0 22 0.00048 26.9 2.0 65 5-72 3-67 (157)
15 PF09268 Clathrin-link: Clathr 38.0 13 0.00028 20.4 0.3 18 24-41 7-24 (24)
16 PF11946 DUF3463: Domain of un 37.8 28 0.0006 25.5 2.1 32 6-37 11-43 (138)
17 PF15224 SCRG1: Scrapie-respon 37.5 28 0.0006 23.8 2.0 49 19-67 6-56 (78)
18 TIGR02607 antidote_HigA addict 37.5 33 0.00072 19.9 2.1 48 8-57 20-68 (78)
19 PF06021 Gly_acyl_tr_N: Aralky 35.8 19 0.00041 27.5 1.1 31 34-70 172-202 (205)
20 PRK08609 hypothetical protein; 35.4 23 0.0005 29.5 1.5 61 18-84 477-549 (570)
21 PF12399 BCA_ABC_TP_C: Branche 34.5 25 0.00054 18.6 1.1 15 8-22 7-21 (23)
22 cd04373 RhoGAP_p190 RhoGAP_p19 33.3 96 0.0021 21.7 4.2 47 16-68 69-115 (185)
23 PF03695 UPF0149: Uncharacteri 31.6 44 0.00095 22.1 2.2 30 8-37 55-91 (177)
24 smart00324 RhoGAP GTPase-activ 31.4 1.4E+02 0.003 19.6 4.5 33 14-46 55-87 (174)
25 TIGR03791 TTQ_mauG tryptophan 30.6 1E+02 0.0022 23.9 4.3 61 15-75 70-137 (291)
26 PF13547 GTA_TIM: GTA TIM-barr 29.6 19 0.00041 29.4 0.1 41 38-78 9-59 (299)
27 TIGR02292 ygfB_yecA yecA famil 29.5 45 0.00097 22.3 1.9 20 13-32 63-82 (150)
28 PF03800 Nuf2: Nuf2 family; I 28.1 57 0.0012 21.9 2.3 25 3-28 25-51 (146)
29 cd06259 YdcF-like YdcF-like. Y 27.8 28 0.0006 22.4 0.7 20 37-56 24-43 (150)
30 cd04406 RhoGAP_myosin_IXA RhoG 27.6 1.6E+02 0.0035 20.7 4.6 30 16-45 68-97 (186)
31 COG1392 Phosphate transport re 27.3 61 0.0013 24.2 2.5 27 61-87 86-114 (217)
32 PF14769 CLAMP: Flagellar C1a 26.8 1.3E+02 0.0027 19.4 3.6 43 3-46 3-48 (101)
33 PRK05590 hypothetical protein; 26.6 51 0.0011 24.8 2.0 35 20-56 33-67 (166)
34 PF06971 Put_DNA-bind_N: Putat 25.9 56 0.0012 19.7 1.7 32 19-50 11-42 (50)
35 PF13884 Peptidase_S74: Chaper 25.9 29 0.00063 20.0 0.5 15 56-71 1-15 (58)
36 PF07002 Copine: Copine; Inte 25.6 36 0.00078 23.9 1.0 24 16-40 67-90 (146)
37 cd07556 Nucleotidyl_cyc_III Cl 25.6 42 0.00091 19.7 1.1 23 61-83 110-132 (133)
38 cd04382 RhoGAP_MgcRacGAP RhoGA 25.6 1.5E+02 0.0033 21.1 4.2 29 16-44 70-98 (193)
39 PF14805 THDPS_N_2: Tetrahydro 25.3 1.1E+02 0.0025 19.6 3.2 26 58-83 13-42 (70)
40 PF12450 vWF_A: von Willebrand 24.5 38 0.00081 23.3 0.9 17 68-84 35-53 (99)
41 cd00076 H4 Histone H4, one of 23.8 96 0.0021 20.6 2.7 51 23-74 4-61 (85)
42 PF02609 Exonuc_VII_S: Exonucl 23.0 1.2E+02 0.0027 17.6 2.8 28 19-46 5-32 (53)
43 PF02049 FliE: Flagellar hook- 22.8 69 0.0015 20.7 1.8 15 13-27 79-93 (96)
44 PF14929 TAF1_subA: TAF RNA Po 22.6 1.5E+02 0.0033 25.5 4.3 16 69-84 135-150 (547)
45 COG0133 TrpB Tryptophan syntha 22.3 1E+02 0.0023 26.3 3.2 38 11-48 34-71 (396)
46 KOG4100 Uncharacterized conser 21.8 70 0.0015 23.5 1.9 66 9-79 3-69 (125)
47 PF00620 RhoGAP: RhoGAP domain 21.8 2.2E+02 0.0048 18.0 4.8 30 14-43 52-81 (151)
48 PF05377 FlaC_arch: Flagella a 21.8 84 0.0018 19.9 2.0 23 8-30 29-52 (55)
49 PF00990 GGDEF: GGDEF domain; 21.8 1E+02 0.0023 18.3 2.4 22 59-80 135-156 (161)
50 PF03872 RseA_N: Anti sigma-E 20.7 2.3E+02 0.0049 18.2 3.9 39 10-48 27-65 (87)
No 1
>PF13232 Complex1_LYR_1: Complex1_LYR-like
Probab=98.38 E-value=1.3e-06 Score=51.89 Aligned_cols=60 Identities=27% Similarity=0.304 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHhcCCCcccchHHHHHhHHHHHHHHHHhccchhhhccHHHHHHhHHHHHHHhh
Q 034650 17 RVLSLYRQILRSLNSPKLELSLAARLAKKAEARAIFMVGSEERSIHNIQDLIDTAEYALSLLK 79 (88)
Q Consensus 17 ~VlSLYRqiLRslnSp~L~L~~AarlaKKae~RaiF~~gseErS~HNI~dLid~aey~Ls~L~ 79 (88)
.||||||++||.-+. +|..-+. -.-+..||.-|--...+.+.+.|+.++..|+..|++|+
T Consensus 2 ~vL~LYR~lLR~~~~--~~~~~~r-~~~~~~ir~~Fr~~~~~td~~~i~~~l~~~~~~L~~l~ 61 (61)
T PF13232_consen 2 QVLSLYRQLLREASK--FPDYNFR-SYFRRRIRDRFRRNKNVTDPEKIAKLLKEGRKELELLR 61 (61)
T ss_pred hHHHHHHHHHHHhhh--cCCcchH-HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 589999999998654 5544333 34466799999999999999999999999999999885
No 2
>PF05347 Complex1_LYR: Complex 1 protein (LYR family); InterPro: IPR008011 This family of short proteins includes proteins from the NADH-ubiquinone oxidoreductase complex I. The family includes the B14 subunit from bovine NADH-ubiquinone oxidoreductase B14 subunit Q02366 from SWISSPROT, and the B22 subunit from the human enzyme Q9Y6M9 from SWISSPROT. The family has been named LYR after a highly conserved tripeptide motif close to the N terminus of these proteins. Members of this family also found in yeast which do contain this complex. In these organisms they are believed to be be required for iron-sulphur custer biogenesis.
Probab=98.11 E-value=8.4e-06 Score=47.19 Aligned_cols=57 Identities=37% Similarity=0.464 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHhcCCCcccchHHHHHhHHHHHHHHHHhccchhhhccHHHHHHhHHHHHH
Q 034650 17 RVLSLYRQILRSLNSPKLELSLAARLAKKAEARAIFMVGSEERSIHNIQDLIDTAEYALS 76 (88)
Q Consensus 17 ~VlSLYRqiLRslnSp~L~L~~AarlaKKae~RaiF~~gseErS~HNI~dLid~aey~Ls 76 (88)
.||+|||++||+..+ +|-.- .+-.-+..+|.-|--...|.+...|..++..|+-.|.
T Consensus 2 ~vl~LYR~lLR~~~~--~~~~~-~r~~~~~~iR~~Fr~n~~~~d~~~I~~~l~~g~~~l~ 58 (59)
T PF05347_consen 2 RVLSLYRQLLRAARS--FPDDS-EREYIRAEIRQEFRKNRNETDPEKIEELLKKGEEELE 58 (59)
T ss_pred hHHHHHHHHHHHHHH--cCCcc-hHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhc
Confidence 599999999999844 44433 5666689999999999999999999999999987764
No 3
>PF13233 Complex1_LYR_2: Complex1_LYR-like
Probab=89.40 E-value=0.18 Score=32.06 Aligned_cols=14 Identities=64% Similarity=1.001 Sum_probs=12.8
Q ss_pred HHHHHHHHHHhcCC
Q 034650 18 VLSLYRQILRSLNS 31 (88)
Q Consensus 18 VlSLYRqiLRslnS 31 (88)
|+||||.|||.|..
T Consensus 1 V~~lYR~lLRel~~ 14 (104)
T PF13233_consen 1 VLSLYRSLLRELRR 14 (104)
T ss_pred ChHHHHHHHHHHHh
Confidence 78999999999975
No 4
>PF04716 ETC_C1_NDUFA5: ETC complex I subunit conserved region; InterPro: IPR006806 This is a family of eukaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC) (1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 29.9 kDa protein. The conserved region is found at the N terminus of the member proteins [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022904 respiratory electron transport chain, 0005743 mitochondrial inner membrane
Probab=87.80 E-value=1.3 Score=27.55 Aligned_cols=53 Identities=26% Similarity=0.384 Sum_probs=43.4
Q ss_pred hhHHHHHHHHHHHhcCCCcccchHHHHHhHHHHHHHHHHhccchhhhccHHHHHH
Q 034650 15 QKRVLSLYRQILRSLNSPKLELSLAARLAKKAEARAIFMVGSEERSIHNIQDLID 69 (88)
Q Consensus 15 r~~VlSLYRqiLRslnSp~L~L~~AarlaKKae~RaiF~~gseErS~HNI~dLid 69 (88)
|+...+||.++|+.|. .+|=+-+-|.+-.+=++.-+-+--+|-.+.-|++-|.
T Consensus 4 r~~L~~lY~~~L~~L~--~~P~~a~YR~~tE~it~~Rl~iv~~~~d~~~iE~~i~ 56 (57)
T PF04716_consen 4 REALISLYNKTLKALK--KIPEDAAYRQYTEAITKHRLKIVEEEEDIEKIEKKIG 56 (57)
T ss_pred HHHHHHHHHHHHHHHH--hCCCccHHHHHHHHHHHHHHHHHHccccHHHHHHHhC
Confidence 6788999999999999 8999999999888877777766666767766766654
No 5
>KOG3801 consensus Uncharacterized conserved protein BCN92 [RNA processing and modification]
Probab=48.38 E-value=15 Score=25.79 Aligned_cols=63 Identities=25% Similarity=0.419 Sum_probs=41.1
Q ss_pred chhHHHHHHHHHHHhcCCCccc-chHHHHHhHHHHHHHHHHhccchhhhccHHHHHHhHHHHHHHhhc
Q 034650 14 HQKRVLSLYRQILRSLNSPKLE-LSLAARLAKKAEARAIFMVGSEERSIHNIQDLIDTAEYALSLLKE 80 (88)
Q Consensus 14 nr~~VlSLYRqiLRslnSp~L~-L~~AarlaKKae~RaiF~~gseErS~HNI~dLid~aey~Ls~L~~ 80 (88)
+|--|+||||-+||. |-.+| .++=.-- +--.|--|-.---+...--|..++.-|+--|..+++
T Consensus 5 sr~qvlsLyr~~lr~--s~qfp~YNyReY~--~RrtRD~Fr~Nkn~~Dp~e~~~l~~eakk~LevikR 68 (94)
T KOG3801|consen 5 SRRQVLSLYRNLLRE--SKQFPQYNYREYF--QRRTRDTFRANKNVCDPAEIKKLYKEAKKQLEVIKR 68 (94)
T ss_pred cHHHHHHHHHHHHHH--HhhCCcccHHHHH--HHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHH
Confidence 567899999999995 44555 3332211 123455566555555666677888888888877765
No 6
>PF09373 PMBR: Pseudomurein-binding repeat; InterPro: IPR018975 Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins.
Probab=47.94 E-value=33 Score=18.75 Aligned_cols=24 Identities=17% Similarity=0.451 Sum_probs=18.8
Q ss_pred HHHHHHhHHHHHHHh-hcCCCCCCC
Q 034650 64 IQDLIDTAEYALSLL-KEGKIPKHI 87 (88)
Q Consensus 64 I~dLid~aey~Ls~L-~~G~iP~~~ 87 (88)
..+++|.|.-..++. ++|+.|+++
T Consensus 7 ~~~~~d~a~rv~~f~~~ngRlPnyV 31 (33)
T PF09373_consen 7 KEEYLDMASRVNNFYESNGRLPNYV 31 (33)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCee
Confidence 467888888888776 579999875
No 7
>KOG4620 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.87 E-value=15 Score=25.27 Aligned_cols=58 Identities=33% Similarity=0.395 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHHHhcCCCcccchHHHHHhHHHHHHHHHHhccchhhh---------ccHHHHHHhHHHHHHHhhcCCC
Q 034650 15 QKRVLSLYRQILRSLNSPKLELSLAARLAKKAEARAIFMVGSEERSI---------HNIQDLIDTAEYALSLLKEGKI 83 (88)
Q Consensus 15 r~~VlSLYRqiLRslnSp~L~L~~AarlaKKae~RaiF~~gseErS~---------HNI~dLid~aey~Ls~L~~G~i 83 (88)
+--||+|||..||+- +---+++.+--..|--+|--. --|+-|..-+.--+..+..++.
T Consensus 8 QrqVlhlYR~~lraa-----------~~Kp~~~~~~~m~fvh~EFrk~~~lpr~Df~~IEhLlRvG~rq~~~~s~pe~ 74 (80)
T KOG4620|consen 8 QRQVLHLYRDLLRAA-----------RGKPGAEARRWMAFVHAEFRKHAGLPRSDFLRIEHLLRVGRRQLQLLSSPEA 74 (80)
T ss_pred HHHHHHHHHHHHHHh-----------cCCCchHHHHHHHHHHHHHHHhcCCcHhHHHHHHHHHHHhHHHHHHhcCcch
Confidence 346999999999853 333345555444444444333 3467777777776666666554
No 8
>PF06426 SATase_N: Serine acetyltransferase, N-terminal ; InterPro: IPR010493 The N-terminal domain of serine acetyltransferase has a sequence that is conserved in plants [] and bacteria [].; GO: 0009001 serine O-acetyltransferase activity, 0006535 cysteine biosynthetic process from serine, 0005737 cytoplasm; PDB: 1T3D_C 3MC4_B 3P47_A 3P1B_A 3Q1X_A 1SSM_A 1S80_C 1SSQ_D 1SST_A 3GVD_L ....
Probab=46.55 E-value=57 Score=21.63 Aligned_cols=53 Identities=26% Similarity=0.345 Sum_probs=35.9
Q ss_pred hhhh-hchhHHHHHHHHHHHhcCCCcccchHHHHHhHHHHHHHHHHhccchhhhccHHHHHHhH
Q 034650 9 AVDS-KHQKRVLSLYRQILRSLNSPKLELSLAARLAKKAEARAIFMVGSEERSIHNIQDLIDTA 71 (88)
Q Consensus 9 Aedl-rnr~~VlSLYRqiLRslnSp~L~L~~AarlaKKae~RaiF~~gseErS~HNI~dLid~a 71 (88)
|++. ++.|..-+.|..-+ |+.+++.-.++.+||.| +++.+.+-+-+++++..+
T Consensus 9 A~~~~~~eP~La~~l~~~i--L~h~s~~~ALa~~La~k--------L~~~~~~~~~l~~~~~~~ 62 (105)
T PF06426_consen 9 AEEAAASEPLLASFLHATI--LSHDSFEDALAFRLANK--------LADPTLSADQLRDLFRDA 62 (105)
T ss_dssp HHHHHHH-GGGHHHHHHHT--TTSSSHHHHHHHHHHHH--------H-BTTS-HHHHHHHHHHH
T ss_pred HHHHHHhCchHHHHHHHHh--hcccCHHHHHHHHHHHh--------cCccccCHHHHHHHHHHH
Confidence 5666 77888877766533 78999999999999998 444555555555655544
No 9
>cd00159 RhoGAP RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins.
Probab=46.37 E-value=76 Score=20.23 Aligned_cols=32 Identities=25% Similarity=0.339 Sum_probs=25.5
Q ss_pred chhHHHHHHHHHHHhcCCCcccchHHHHHhHH
Q 034650 14 HQKRVLSLYRQILRSLNSPKLELSLAARLAKK 45 (88)
Q Consensus 14 nr~~VlSLYRqiLRslnSp~L~L~~AarlaKK 45 (88)
+--.|-++.+++||+|..|=+|-.+..++-+.
T Consensus 51 ~~~~va~~lK~~l~~Lp~pli~~~~~~~~~~~ 82 (169)
T cd00159 51 DVHDVASLLKLYLRELPEPLIPFELYDEFIEL 82 (169)
T ss_pred CHHHHHHHHHHHHHcCCCccCCHHHHHHHHHH
Confidence 34457899999999999999999877666543
No 10
>cd04385 RhoGAP_ARAP RhoGAP_ARAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) contain, besides the RhoGAP domain, an Arf GAP, ankyrin repeat ras-associating, and PH domains. Since their ArfGAP activity is PIP3-dependent, ARAPs are considered integration points for phosphoinositide, Arf and Rho signaling. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=42.64 E-value=58 Score=22.75 Aligned_cols=48 Identities=27% Similarity=0.413 Sum_probs=33.0
Q ss_pred hHHHHHHHHHHHhcCCCcccchHHHHHhHHHHHHHHHHhccchhhhccHHHHHH
Q 034650 16 KRVLSLYRQILRSLNSPKLELSLAARLAKKAEARAIFMVGSEERSIHNIQDLID 69 (88)
Q Consensus 16 ~~VlSLYRqiLRslnSp~L~L~~AarlaKKae~RaiF~~gseErS~HNI~dLid 69 (88)
-.|-++-+++||.|-.|=+|-.+-..+..-++. .+++..+..++++++
T Consensus 70 ~~va~llK~yLreLP~pLi~~~~~~~~~~~~~~------~~~~~~i~~l~~~i~ 117 (184)
T cd04385 70 HDVADVLKRFLRDLPDPLLTSELHAEWIEAAEL------ENKDERIARYKELIR 117 (184)
T ss_pred HHHHHHHHHHHHhCCCccCCHHHHHHHHHHHhC------CCHHHHHHHHHHHHH
Confidence 458899999999999999998887766543321 234444555555554
No 11
>cd04400 RhoGAP_fBEM3 RhoGAP_fBEM3: RhoGAP (GTPase-activator [GAP] protein for Rho-like small GTPases) domain of fungal BEM3-like proteins. Bem3 is a GAP protein of Cdc42, and is specifically involved in the control of the initial assembly of the septin ring in yeast bud formation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=41.94 E-value=88 Score=21.80 Aligned_cols=30 Identities=23% Similarity=0.234 Sum_probs=25.4
Q ss_pred hhHHHHHHHHHHHhcCCCcccchHHHHHhH
Q 034650 15 QKRVLSLYRQILRSLNSPKLELSLAARLAK 44 (88)
Q Consensus 15 r~~VlSLYRqiLRslnSp~L~L~~AarlaK 44 (88)
-..|-|+.++.||.|-.|=+|..+...+-+
T Consensus 78 ~h~va~lLK~flreLP~PLi~~~~~~~~~~ 107 (190)
T cd04400 78 VHTVAGLLKLYLRELPTLILGGELHNDFKR 107 (190)
T ss_pred HHHHHHHHHHHHHhCCcccCCHHHHHHHHH
Confidence 347889999999999999999988876644
No 12
>PRK08392 hypothetical protein; Provisional
Probab=41.91 E-value=14 Score=26.06 Aligned_cols=40 Identities=18% Similarity=0.241 Sum_probs=32.1
Q ss_pred HHHHhHHHHHHHHHHhccchhhhccHHHHHHhHHHHHHHhhcCCCC
Q 034650 39 AARLAKKAEARAIFMVGSEERSIHNIQDLIDTAEYALSLLKEGKIP 84 (88)
Q Consensus 39 AarlaKKae~RaiF~~gseErS~HNI~dLid~aey~Ls~L~~G~iP 84 (88)
-.+++++.+++ |.+||+ -|+..|+-+ -++++.++++-.+|
T Consensus 166 ~l~~~~~~G~~--~~igSD---AH~~~~vg~-~~~a~~~~~~~g~~ 205 (215)
T PRK08392 166 FIRECIKRGIK--LTFASD---AHRPEDVGN-VSWSLKVFKKAGGK 205 (215)
T ss_pred HHHHHHHcCCE--EEEeCC---CCChHHCCc-HHHHHHHHHHcCCC
Confidence 36677777865 899998 588888876 77899999988777
No 13
>PRK09248 putative hydrolase; Validated
Probab=40.99 E-value=21 Score=25.51 Aligned_cols=44 Identities=34% Similarity=0.345 Sum_probs=31.8
Q ss_pred cchHHHHHhHHHHHHHHHHhccchhhhccHHHHHHhHHHHHHHhhcCCCC
Q 034650 35 ELSLAARLAKKAEARAIFMVGSEERSIHNIQDLIDTAEYALSLLKEGKIP 84 (88)
Q Consensus 35 ~L~~AarlaKKae~RaiF~~gseErS~HNI~dLid~aey~Ls~L~~G~iP 84 (88)
|....++++++.++. |.+||+ -|+..|+- ..+.++.++++.-++
T Consensus 173 ~~~~~~~~~~~~g~~--~~~gSD---AH~~~~vg-~~~~~~~~~~~~g~~ 216 (246)
T PRK09248 173 NCRAIAALCKKAGVW--VALGSD---AHIAFDIG-NFEEALKILDEVGFP 216 (246)
T ss_pred hHHHHHHHHHHcCCe--EEEeCC---CCChhhhc-cHHHHHHHHHHcCCC
Confidence 455677888888774 888987 47777776 456677777776665
No 14
>KOG3466 consensus NADH:ubiquinone oxidoreductase, NDUFB9/B22 subunit [Energy production and conversion]
Probab=40.98 E-value=22 Score=26.95 Aligned_cols=65 Identities=23% Similarity=0.287 Sum_probs=40.2
Q ss_pred hhhhhhhhhchhHHHHHHHHHHHhcCCCcccchHHHHHhHHHHHHHHHHhccchhhhccHHHHHHhHH
Q 034650 5 IWATAVDSKHQKRVLSLYRQILRSLNSPKLELSLAARLAKKAEARAIFMVGSEERSIHNIQDLIDTAE 72 (88)
Q Consensus 5 iwaTAedlrnr~~VlSLYRqiLRslnSp~L~L~~AarlaKKae~RaiF~~gseErS~HNI~dLid~ae 72 (88)
-|+.+--|-++-+|.+||+.-||-|.|=-..-++ -|. .+--.||=|---.+ ..+--+..|+.-+|
T Consensus 3 a~~f~~~lshkqkV~rLYKRaLR~lenWy~~rn~-yRy-~ac~~RARFden~~-kD~~k~~~LLa~ge 67 (157)
T KOG3466|consen 3 AAYFARRLSHKQKVRRLYKRALRDLENWYVHRNI-YRY-QACIIRARFDENDE-KDVDKAIRLLAEGE 67 (157)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchH-HHH-HHHHHHHHhhhhhh-hhHHHHHHHHHHHH
Confidence 5667777888999999999999999886655554 221 22345666643333 33333444444444
No 15
>PF09268 Clathrin-link: Clathrin, heavy-chain linker; InterPro: IPR015348 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the core motif for the alpha-helical zigzag linker region connecting the conserved N-terminal beta-propeller region to the C-terminal alpha-alpha-superhelical region in clathrin heavy chains []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030130 clathrin coat of trans-Golgi network vesicle, 0030132 clathrin coat of coated pit; PDB: 1C9I_A 1BPO_B 1C9L_A 1UTC_B 3GD1_I 3GC3_B 2XZG_A 2XZH_A.
Probab=38.01 E-value=13 Score=20.38 Aligned_cols=18 Identities=50% Similarity=0.774 Sum_probs=12.6
Q ss_pred HHHHhcCCCcccchHHHH
Q 034650 24 QILRSLNSPKLELSLAAR 41 (88)
Q Consensus 24 qiLRslnSp~L~L~~Aar 41 (88)
-|+..|+.|.|-|.+|.|
T Consensus 7 yi~~~L~N~~LAl~lA~R 24 (24)
T PF09268_consen 7 YILNTLQNPDLALRLASR 24 (24)
T ss_dssp HHHHTT--HHHHHHHHHH
T ss_pred HHHhccCCHHHHHHHhcC
Confidence 367789999988888875
No 16
>PF11946 DUF3463: Domain of unknown function (DUF3463); InterPro: IPR022563 This functionally uncharacterised domain is found in bacteria and archaea, which is about 140 amino acids in length and is found C-terminal to PF04055 from PFAM. It contains two conserved sequence motifs: CTPWG and PCYL. This domain is associated with hopanoid biosynthesis associated radical SAM proteins.
Probab=37.81 E-value=28 Score=25.48 Aligned_cols=32 Identities=19% Similarity=0.346 Sum_probs=25.1
Q ss_pred hhhhhhh-hchhHHHHHHHHHHHhcCCCcccch
Q 034650 6 WATAVDS-KHQKRVLSLYRQILRSLNSPKLELS 37 (88)
Q Consensus 6 waTAedl-rnr~~VlSLYRqiLRslnSp~L~L~ 37 (88)
||+++|+ -+|...-.|+|+|++....-+-|++
T Consensus 11 ~ap~q~~fl~r~~t~~lfr~i~~~~~~k~w~f~ 43 (138)
T PF11946_consen 11 YAPDQDHFLNREQTRELFRKIFAKGKKKKWRFN 43 (138)
T ss_pred CCchhhccCCHHHHHHHHHHHHHhcccCCcccc
Confidence 7889999 8999999999999965544444443
No 17
>PF15224 SCRG1: Scrapie-responsive protein 1
Probab=37.55 E-value=28 Score=23.82 Aligned_cols=49 Identities=27% Similarity=0.327 Sum_probs=34.4
Q ss_pred HHHHHHHHHhcCCCcccchHHHHHhHHHHHHHHHHhcc--chhhhccHHHH
Q 034650 19 LSLYRQILRSLNSPKLELSLAARLAKKAEARAIFMVGS--EERSIHNIQDL 67 (88)
Q Consensus 19 lSLYRqiLRslnSp~L~L~~AarlaKKae~RaiF~~gs--eErS~HNI~dL 67 (88)
||-||.+|+.=|--.+|-|.|.----...+.--||=|- |-.-.-|..+|
T Consensus 6 lsCyrk~L~D~nCH~iPeG~~~L~~id~~lqdHFW~GkgCEmiCYCNf~EL 56 (78)
T PF15224_consen 6 LSCYRKILKDHNCHNIPEGVADLRQIDVNLQDHFWEGKGCEMICYCNFSEL 56 (78)
T ss_pred hhHHHHHhccCCcCcCchhhhhhhhhccchhhhcccCCCceEEEEeCchHh
Confidence 79999999999999999998865444456666677653 33333444444
No 18
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=37.54 E-value=33 Score=19.91 Aligned_cols=48 Identities=19% Similarity=0.142 Sum_probs=33.9
Q ss_pred hhhhh-hchhHHHHHHHHHHHhcCCCcccchHHHHHhHHHHHHHHHHhccc
Q 034650 8 TAVDS-KHQKRVLSLYRQILRSLNSPKLELSLAARLAKKAEARAIFMVGSE 57 (88)
Q Consensus 8 TAedl-rnr~~VlSLYRqiLRslnSp~L~L~~AarlaKKae~RaiF~~gse 57 (88)
|.+|+ +.-|.--+-+.+++..-. .++...+.++++.-+|..-|+++-.
T Consensus 20 t~~~lA~~~gis~~tis~~~~g~~--~~~~~~~~~l~~~l~v~~~~l~~~~ 68 (78)
T TIGR02607 20 SIRALAKALGVSRSTLSRIVNGRR--GITADMALRLAKALGTSPEFWLNLQ 68 (78)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC--CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 55666 555555566677777544 3467889999999999888887743
No 19
>PF06021 Gly_acyl_tr_N: Aralkyl acyl-CoA:amino acid N-acyltransferase; InterPro: IPR015938 This entry represents mammalian-specific glycine N-acyltransferase (also called aralkyl acyl-CoA:amino acid N-acyltransferase; 2.3.1.13 from EC). Mitochondrial acyltransferases catalyse the transfer of an acyl group from acyl-CoA to the N terminus of glycine to produce N-acylglycine. These enzymes can conjugate a multitude of substrates to form a variety of N-acylglycines. The CoA derivatives of a number of aliphatic and aromatic acids, but not phenylacetyl-CoA or (indol-3-yl)acetyl-CoA, can act as donor [, ].; GO: 0047961 glycine N-acyltransferase activity, 0005739 mitochondrion
Probab=35.84 E-value=19 Score=27.53 Aligned_cols=31 Identities=29% Similarity=0.450 Sum_probs=22.3
Q ss_pred ccchHHHHHhHHHHHHHHHHhccchhhhccHHHHHHh
Q 034650 34 LELSLAARLAKKAEARAIFMVGSEERSIHNIQDLIDT 70 (88)
Q Consensus 34 L~L~~AarlaKKae~RaiF~~gseErS~HNI~dLid~ 70 (88)
|-.++|+-+ -.-.-||+.|||+..|+.+|..
T Consensus 172 LdvsHA~LV------N~tW~fGgNErslryI~~~I~~ 202 (205)
T PF06021_consen 172 LDVSHADLV------NKTWKFGGNERSLRYIERCIQN 202 (205)
T ss_pred cChHHHHHH------hccccCCCcHHHHHHHHHHHHh
Confidence 344566543 3345599999999999999964
No 20
>PRK08609 hypothetical protein; Provisional
Probab=35.36 E-value=23 Score=29.52 Aligned_cols=61 Identities=20% Similarity=0.270 Sum_probs=44.6
Q ss_pred HHHHHHHHHHh---------cCCCcccc---hHHHHHhHHHHHHHHHHhccchhhhccHHHHHHhHHHHHHHhhcCCCC
Q 034650 18 VLSLYRQILRS---------LNSPKLEL---SLAARLAKKAEARAIFMVGSEERSIHNIQDLIDTAEYALSLLKEGKIP 84 (88)
Q Consensus 18 VlSLYRqiLRs---------lnSp~L~L---~~AarlaKKae~RaiF~~gseErS~HNI~dLid~aey~Ls~L~~G~iP 84 (88)
+-..+..+++. +|+-.+.+ .--.+.+++.++ .|.+||+ -|+..|+ ..-+|+..++++|-+|
T Consensus 477 ~~~d~~~i~~~a~~~G~~lEINa~~~r~~~~~~~~~~~~e~Gv--~i~igSD---AH~~~~l-~~~~~~v~~ar~~~~~ 549 (570)
T PRK08609 477 YDVNIDQLIELAKETNTALELNANPNRLDLSAEHLKKAQEAGV--KLAINTD---AHHTEML-DDMKYGVATARKGWIQ 549 (570)
T ss_pred chHHHHHHHHHHHHhCCEEEEcCCccccCccHHHHHHHHHcCC--EEEEECC---CCChhhh-CcHHHHHHHHHHcCCC
Confidence 33445666666 67754433 234567777777 4889997 5999998 6699999999999998
No 21
>PF12399 BCA_ABC_TP_C: Branched-chain amino acid ATP-binding cassette transporter
Probab=34.53 E-value=25 Score=18.61 Aligned_cols=15 Identities=20% Similarity=0.273 Sum_probs=13.0
Q ss_pred hhhhhhchhHHHHHH
Q 034650 8 TAVDSKHQKRVLSLY 22 (88)
Q Consensus 8 TAedlrnr~~VlSLY 22 (88)
|.++.++.+.|...|
T Consensus 7 ~p~~i~~n~~V~~aY 21 (23)
T PF12399_consen 7 TPEEIRANPEVREAY 21 (23)
T ss_pred CHHHHhcCHHHHHhh
Confidence 678888999998887
No 22
>cd04373 RhoGAP_p190 RhoGAP_p190: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p190-like proteins. p190, also named RhoGAP5, plays a role in neuritogenesis and axon branch stability. p190 shows a preference for Rho, over Rac and Cdc42, and consists of an N-terminal GTPase domain and a C-terminal GAP domain. The central portion of p190 contains important regulatory phosphorylation sites. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=33.25 E-value=96 Score=21.73 Aligned_cols=47 Identities=17% Similarity=0.389 Sum_probs=31.4
Q ss_pred hHHHHHHHHHHHhcCCCcccchHHHHHhHHHHHHHHHHhccchhhhccHHHHH
Q 034650 16 KRVLSLYRQILRSLNSPKLELSLAARLAKKAEARAIFMVGSEERSIHNIQDLI 68 (88)
Q Consensus 16 ~~VlSLYRqiLRslnSp~L~L~~AarlaKKae~RaiF~~gseErS~HNI~dLi 68 (88)
-.|-|+.++.||.|-.|=+|-.+..++-. +.-..+++-.+..+.+++
T Consensus 69 ~~va~~lK~fLreLPePlip~~~~~~~~~------~~~~~~~~~~i~~l~~li 115 (185)
T cd04373 69 NAVAGALKSFFSELPDPLIPYSMHLELVE------AAKINDREQRLHALKELL 115 (185)
T ss_pred HHHHHHHHHHHhcCCchhccHHHHHHHHH------HHhCCCHHHHHHHHHHHH
Confidence 46889999999999999999887765432 222333333445555554
No 23
>PF03695 UPF0149: Uncharacterised protein family (UPF0149); InterPro: IPR011978 This group of proteins includes the Escherichia coli proteins YgfB and YecA. The function of these proteins is unknown. The crystal structure is known for the member from Haemophilus influenzae (YgfB, P44882 from SWISSPROT), revealing a multi-helical protein consisting of two tightly associated 3-helical bundles with different twists.; PDB: 1IZM_A.
Probab=31.65 E-value=44 Score=22.10 Aligned_cols=30 Identities=23% Similarity=0.423 Sum_probs=17.2
Q ss_pred hhhhh-hchhHHHHHHHHHHHhcC------CCcccch
Q 034650 8 TAVDS-KHQKRVLSLYRQILRSLN------SPKLELS 37 (88)
Q Consensus 8 TAedl-rnr~~VlSLYRqiLRsln------Sp~L~L~ 37 (88)
+.+.. +-...|..+|.+|.+.|+ .|-+|-.
T Consensus 55 ~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~p~lp~~ 91 (177)
T PF03695_consen 55 SEEQAERFLELLMALYNEIAEQLNDDDFAFQPLLPDD 91 (177)
T ss_dssp T----TTTHHHHHHHHHHHHHHHTTTS----------
T ss_pred ChhhHHHHHHHHHHHHHHHHHHHccCCccccccCccc
Confidence 33444 777899999999999999 5555554
No 24
>smart00324 RhoGAP GTPase-activator protein for Rho-like GTPases. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. etter domain limits and outliers.
Probab=31.39 E-value=1.4e+02 Score=19.63 Aligned_cols=33 Identities=24% Similarity=0.352 Sum_probs=26.7
Q ss_pred chhHHHHHHHHHHHhcCCCcccchHHHHHhHHH
Q 034650 14 HQKRVLSLYRQILRSLNSPKLELSLAARLAKKA 46 (88)
Q Consensus 14 nr~~VlSLYRqiLRslnSp~L~L~~AarlaKKa 46 (88)
+-..|-++..++||+|..|=+|-.+...+-+-.
T Consensus 55 ~~~~va~~lK~~Lr~Lp~pli~~~~~~~~~~~~ 87 (174)
T smart00324 55 DVHDVAGLLKLFLRELPEPLIPYELYEEFIEAA 87 (174)
T ss_pred CHHHHHHHHHHHHHhCCCccCCHHHHHHHHHHH
Confidence 445688999999999999999998877765433
No 25
>TIGR03791 TTQ_mauG tryptophan tryptophylquinone biosynthesis enzyme MauG. Members of this protein family are the tryptophan tryptophylquinone biosynthesis (TTQ) enzyme MauG, as found in Methylobacterium extorquens and related species. This protein is required to complete the maturation of the TTQ cofactor in the methylamine dehydrogenase light (beta) chain.
Probab=30.60 E-value=1e+02 Score=23.90 Aligned_cols=61 Identities=20% Similarity=0.194 Sum_probs=42.9
Q ss_pred hhHHHHHHHHHHHhcCCCcc----cchHHHHHhHHHHHHHHHH--hccch-hhhccHHHHHHhHHHHH
Q 034650 15 QKRVLSLYRQILRSLNSPKL----ELSLAARLAKKAEARAIFM--VGSEE-RSIHNIQDLIDTAEYAL 75 (88)
Q Consensus 15 r~~VlSLYRqiLRslnSp~L----~L~~AarlaKKae~RaiF~--~gseE-rS~HNI~dLid~aey~L 75 (88)
.||+-+|..|++..+-+|.- +-.+.+||.+..+-+..|- ||.++ .+.-||..-|.+=+-+|
T Consensus 70 DGr~~~Le~Qa~~pi~~p~EM~~~~~~v~~rl~~~~~Y~~~F~~~f~~~~~i~~~~i~~Alaafertl 137 (291)
T TIGR03791 70 DGRADSLEAQAILPITAADEMNFEMDLLLERLKAVAGYAPLFANAFGDAEPIGAKHLTAALASFQRTL 137 (291)
T ss_pred ccChhhHHHHHhccccChhhhCCCHHHHHHHHHhChHHHHHHHHHcCCcCCCCHHHHHHHHHHHHHhc
Confidence 46777999999998887721 1236778887666666663 57665 78888888776655554
No 26
>PF13547 GTA_TIM: GTA TIM-barrel-like domain
Probab=29.58 E-value=19 Score=29.42 Aligned_cols=41 Identities=34% Similarity=0.374 Sum_probs=32.9
Q ss_pred HHHHHhHHHHHHHHHHhccchhhhccHHH----------HHHhHHHHHHHh
Q 034650 38 LAARLAKKAEARAIFMVGSEERSIHNIQD----------LIDTAEYALSLL 78 (88)
Q Consensus 38 ~AarlaKKae~RaiF~~gseErS~HNI~d----------Lid~aey~Ls~L 78 (88)
|-|.||+.++-=..|++|||=|.+-.|++ |+.-|...-.+|
T Consensus 9 HYA~La~~aggVdaF~IGSEl~gLT~iR~~~~~fPaV~~l~~LAa~VR~il 59 (299)
T PF13547_consen 9 HYAHLAAAAGGVDAFCIGSELRGLTRIRDGAGSFPAVEALRALAADVRAIL 59 (299)
T ss_pred HHHHHHHhcCCCcEEEEchhhhhheeecCCCCCCcHHHHHHHHHHHHHHHh
Confidence 56789987877799999999999988884 777777666665
No 27
>TIGR02292 ygfB_yecA yecA family protein. This family resembles PFAM model pfam03695 (version pfam03695.3), uncharacterised protein family UPF0149, but is broader in scope and includes additional proteins. It includes E. coli proteins YgfB and YecA. The function of this family of proteins is unknown. The crystal structure is known for the member from Haemophilus influenzae (Ygfb, HI0817).
Probab=29.48 E-value=45 Score=22.27 Aligned_cols=20 Identities=20% Similarity=0.286 Sum_probs=16.6
Q ss_pred hchhHHHHHHHHHHHhcCCC
Q 034650 13 KHQKRVLSLYRQILRSLNSP 32 (88)
Q Consensus 13 rnr~~VlSLYRqiLRslnSp 32 (88)
+-.+.|..+|.+|.+.|+++
T Consensus 63 ~~~~~l~~~~~~i~~~L~~~ 82 (150)
T TIGR02292 63 RIIDLIVQHYNQIAAQLSDG 82 (150)
T ss_pred HHHHHHHHHHHHHHHHHhcC
Confidence 33477899999999999875
No 28
>PF03800 Nuf2: Nuf2 family; InterPro: IPR005549 Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex []. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein has been included in this family that has previously not been identified as a member of this family, Q9C953 from SWISSPROT. The match is not strong, but in common with other members of this family contains coiled-coil to the C terminus of this region.; GO: 0007067 mitosis, 0000775 chromosome, centromeric region; PDB: 2VE7_D 3IZ0_D.
Probab=28.15 E-value=57 Score=21.87 Aligned_cols=25 Identities=28% Similarity=0.395 Sum_probs=16.6
Q ss_pred cchhhhhhhh--hchhHHHHHHHHHHHh
Q 034650 3 GLIWATAVDS--KHQKRVLSLYRQILRS 28 (88)
Q Consensus 3 gliwaTAedl--rnr~~VlSLYRqiLRs 28 (88)
|+- +|+||+ =+-..|..+|.++|..
T Consensus 25 ~~~-~t~~dl~kPt~e~v~~ly~~~L~~ 51 (146)
T PF03800_consen 25 GIP-VTEEDLKKPTPEFVQKLYERFLET 51 (146)
T ss_dssp T---HHHHC--G--HHHHHHHHHHHHHH
T ss_pred CCC-cCHHHHcCCCHHHHHHHHHHHHHH
Confidence 344 799999 3456799999999974
No 29
>cd06259 YdcF-like YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX, which are involved in vancomycin resistance; sfiX may also be involved in murein synthesis.
Probab=27.83 E-value=28 Score=22.44 Aligned_cols=20 Identities=25% Similarity=0.353 Sum_probs=8.8
Q ss_pred hHHHHHhHHHHHHHHHHhcc
Q 034650 37 SLAARLAKKAEARAIFMVGS 56 (88)
Q Consensus 37 ~~AarlaKKae~RaiF~~gs 56 (88)
-.|++|.|+--+.-|++-|+
T Consensus 24 ~~a~~l~~~~~~~~ii~sGg 43 (150)
T cd06259 24 DAAAELYRAGPAPKLIVSGG 43 (150)
T ss_pred HHHHHHHHhCCCCEEEEcCC
Confidence 34444444444444444443
No 30
>cd04406 RhoGAP_myosin_IXA RhoGAP_myosin_IXA: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXA. Class IX myosins contain a characteristic head domain, a neck domain and a tail domain which contains a C6H2-zinc binding motif and a Rho-GAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell prolife
Probab=27.64 E-value=1.6e+02 Score=20.72 Aligned_cols=30 Identities=23% Similarity=0.469 Sum_probs=25.8
Q ss_pred hHHHHHHHHHHHhcCCCcccchHHHHHhHH
Q 034650 16 KRVLSLYRQILRSLNSPKLELSLAARLAKK 45 (88)
Q Consensus 16 ~~VlSLYRqiLRslnSp~L~L~~AarlaKK 45 (88)
-.|-|+..++||.|-.|=+|..+...+.+.
T Consensus 68 h~va~lLK~fLReLPePLi~~~~y~~~~~~ 97 (186)
T cd04406 68 HVIASVFKQWLRDLPNPLMTFELYEEFLRA 97 (186)
T ss_pred HHHHHHHHHHHHhCCCccCCHHHHHHHHHH
Confidence 468899999999999999999988876553
No 31
>COG1392 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]
Probab=27.33 E-value=61 Score=24.22 Aligned_cols=27 Identities=41% Similarity=0.521 Sum_probs=21.8
Q ss_pred hccHHHHHHhHHHHHHHhhcCC--CCCCC
Q 034650 61 IHNIQDLIDTAEYALSLLKEGK--IPKHI 87 (88)
Q Consensus 61 ~HNI~dLid~aey~Ls~L~~G~--iP~~~ 87 (88)
++-++|++|.+|.+...+.-++ ||..+
T Consensus 86 ~~~~D~i~D~~ed~A~~l~l~~~~ip~~~ 114 (217)
T COG1392 86 IESQDDIADAAEDAAKLLLLRKPFIPEEL 114 (217)
T ss_pred HHHHHHHHHHHHHHHHHHHccccCCCcch
Confidence 5667889999999999988888 88543
No 32
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=26.84 E-value=1.3e+02 Score=19.38 Aligned_cols=43 Identities=14% Similarity=0.286 Sum_probs=34.4
Q ss_pred cchhhhhhhh--hchhHHHHHHHHHHH-hcCCCcccchHHHHHhHHH
Q 034650 3 GLIWATAVDS--KHQKRVLSLYRQILR-SLNSPKLELSLAARLAKKA 46 (88)
Q Consensus 3 gliwaTAedl--rnr~~VlSLYRqiLR-slnSp~L~L~~AarlaKKa 46 (88)
+++||.-.+. ..-..++++..+++. +++ |..++.=+-..-|+.
T Consensus 3 ~~~Fa~~~~fs~~q~s~~~~i~~~ll~~~i~-~~~~~~~~~~~fk~~ 48 (101)
T PF14769_consen 3 TFLFAKEQGFSWEQTSAFLSILKELLEKNIE-KGMSLEDSFKYFKEL 48 (101)
T ss_pred hhHhHhhCCCCHHHHHHHHHHHHHHHHHHHH-ccCCHHHHHHHHHHH
Confidence 6788888887 777889999999999 777 888877766666554
No 33
>PRK05590 hypothetical protein; Provisional
Probab=26.63 E-value=51 Score=24.80 Aligned_cols=35 Identities=26% Similarity=0.423 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCCCcccchHHHHHhHHHHHHHHHHhcc
Q 034650 20 SLYRQILRSLNSPKLELSLAARLAKKAEARAIFMVGS 56 (88)
Q Consensus 20 SLYRqiLRslnSp~L~L~~AarlaKKae~RaiF~~gs 56 (88)
+.|.|||.. -+..-=|--.-||+|-++-.+||+|-
T Consensus 33 ~iy~~iL~~--~~~~~~gtv~ela~k~~~~~~~~~Gf 67 (166)
T PRK05590 33 NIYTQILAN--HKEVVEGTVKELAEKFGTSVVFFMGF 67 (166)
T ss_pred HHHHHHHcC--CCceeeeeHHHHHHHhCCChhhhhhh
Confidence 578888853 23444577789999999999999983
No 34
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=25.94 E-value=56 Score=19.74 Aligned_cols=32 Identities=25% Similarity=0.300 Sum_probs=21.2
Q ss_pred HHHHHHHHHhcCCCcccchHHHHHhHHHHHHH
Q 034650 19 LSLYRQILRSLNSPKLELSLAARLAKKAEARA 50 (88)
Q Consensus 19 lSLYRqiLRslnSp~L~L~~AarlaKKae~Ra 50 (88)
|++|-++|+.|..-...---...||+..++-+
T Consensus 11 L~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~ 42 (50)
T PF06971_consen 11 LPLYLRYLEQLKEEGVERVSSQELAEALGITP 42 (50)
T ss_dssp HHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-H
T ss_pred HHHHHHHHHHHHHcCCeeECHHHHHHHHCCCH
Confidence 78899999988776665556667777666543
No 35
>PF13884 Peptidase_S74: Chaperone of endosialidase; PDB: 3GUD_A.
Probab=25.90 E-value=29 Score=19.96 Aligned_cols=15 Identities=47% Similarity=0.665 Sum_probs=6.0
Q ss_pred cchhhhccHHHHHHhH
Q 034650 56 SEERSIHNIQDLIDTA 71 (88)
Q Consensus 56 seErS~HNI~dLid~a 71 (88)
|++|-.+||.++ +.+
T Consensus 1 SD~R~K~nI~~i-~~~ 15 (58)
T PF13884_consen 1 SDRRLKTNIKDI-DNA 15 (58)
T ss_dssp --STT--S--S--HHH
T ss_pred CchhhhCCCeec-hhH
Confidence 678999999999 544
No 36
>PF07002 Copine: Copine; InterPro: IPR010734 This represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca2+-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth [].
Probab=25.63 E-value=36 Score=23.86 Aligned_cols=24 Identities=25% Similarity=0.300 Sum_probs=16.9
Q ss_pred hHHHHHHHHHHHhcCCCcccchHHH
Q 034650 16 KRVLSLYRQILRSLNSPKLELSLAA 40 (88)
Q Consensus 16 ~~VlSLYRqiLRslnSp~L~L~~Aa 40 (88)
--|+..||+.++.+ .++=|-.||-
T Consensus 67 ~gvl~~Y~~~~~~v-~l~GPT~fap 90 (146)
T PF07002_consen 67 DGVLEAYRKALPKV-QLSGPTNFAP 90 (146)
T ss_pred HHHHHHHHHHhhhe-EECCCccHHH
Confidence 35899999999975 3455555543
No 37
>cd07556 Nucleotidyl_cyc_III Class III nucleotidyl cyclases. Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's). The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways.
Probab=25.61 E-value=42 Score=19.70 Aligned_cols=23 Identities=22% Similarity=0.198 Sum_probs=19.4
Q ss_pred hccHHHHHHhHHHHHHHhhcCCC
Q 034650 61 IHNIQDLIDTAEYALSLLKEGKI 83 (88)
Q Consensus 61 ~HNI~dLid~aey~Ls~L~~G~i 83 (88)
.++..+++..|.-+++.-++|+|
T Consensus 110 ~~~~~~~~~~a~~a~~~a~~~~i 132 (133)
T cd07556 110 YDVWGALVNLASRMESQAKAGQV 132 (133)
T ss_pred ceEEcHHHHHHHHHHhcCCCCCc
Confidence 36889999999999988887765
No 38
>cd04382 RhoGAP_MgcRacGAP RhoGAP_MgcRacGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in MgcRacGAP proteins. MgcRacGAP plays an important dual role in cytokinesis: i) it is part of centralspindlin-complex, together with the mitotic kinesin MKLP1, which is critical for the structure of the central spindle by promoting microtuble bundling. ii) after phosphorylation by aurora B MgcRacGAP becomes an effective regulator of RhoA and plays an important role in the assembly of the contractile ring and the initiation of cytokinesis. MgcRacGAP-like proteins contain a N-terminal C1-like domain, and a C-terminal RhoGAP domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway
Probab=25.58 E-value=1.5e+02 Score=21.11 Aligned_cols=29 Identities=21% Similarity=0.390 Sum_probs=24.2
Q ss_pred hHHHHHHHHHHHhcCCCcccchHHHHHhH
Q 034650 16 KRVLSLYRQILRSLNSPKLELSLAARLAK 44 (88)
Q Consensus 16 ~~VlSLYRqiLRslnSp~L~L~~AarlaK 44 (88)
-.|-|+-++.||.|..|=+|-.+-.++-+
T Consensus 70 h~vaslLK~fLReLPePLi~~~~y~~~~~ 98 (193)
T cd04382 70 HVICGCLKDFLRSLKEPLITFALWKEFME 98 (193)
T ss_pred HHHHHHHHHHHHhCCCcCCCHHHHHHHHH
Confidence 46789999999999999999987666543
No 39
>PF14805 THDPS_N_2: Tetrahydrodipicolinate N-succinyltransferase N-terminal; PDB: 3EG4_A 3TDT_A 2TDT_A 1KGT_A 1TDT_A 1KGQ_A 3BXY_A 3GOS_A 3TK8_A.
Probab=25.31 E-value=1.1e+02 Score=19.59 Aligned_cols=26 Identities=27% Similarity=0.399 Sum_probs=19.7
Q ss_pred hhhhcc----HHHHHHhHHHHHHHhhcCCC
Q 034650 58 ERSIHN----IQDLIDTAEYALSLLKEGKI 83 (88)
Q Consensus 58 ErS~HN----I~dLid~aey~Ls~L~~G~i 83 (88)
.|...+ =.++-++-+.++.+|.+|+|
T Consensus 13 ~r~~l~~~~~~~~~~~av~~~i~~Ld~G~l 42 (70)
T PF14805_consen 13 NRDELTPSNADPELRDAVEEVIELLDSGEL 42 (70)
T ss_dssp GGGG-BTTT--HHHHHHHHHHHHHHHTTSS
T ss_pred hHhhCCCccCCHHHHHHHHHHHHHhcCCCe
Confidence 345555 46788899999999999987
No 40
>PF12450 vWF_A: von Willebrand factor ; InterPro: IPR022156 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00092 from PFAM. There are two conserved sequence motifs: STF and DVD. There are two completely conserved residues (E and N) that may be functionally important. In hemostasis, platelet adhesion to the damaged vessel wall is mediated by several proteins, including von Willebrand factor. In solution vWF becomes immobilized via its A3 domain on the fibrillar collagen of the vessel wall and acts as an intermediary between collagen and the platelet receptor glycoprotein Ibalpha (GPIbalpha), which is the only platelet receptor that does not require prior activation for bond formation.
Probab=24.53 E-value=38 Score=23.33 Aligned_cols=17 Identities=41% Similarity=0.894 Sum_probs=14.2
Q ss_pred HHhHHHHH--HHhhcCCCC
Q 034650 68 IDTAEYAL--SLLKEGKIP 84 (88)
Q Consensus 68 id~aey~L--s~L~~G~iP 84 (88)
+|+|-|+. ++|++|+.|
T Consensus 35 VDtaSYs~vRr~L~~G~lP 53 (99)
T PF12450_consen 35 VDTASYSNVRRFLNQGQLP 53 (99)
T ss_pred cCcccHHHHHHHHHCCCCC
Confidence 57888875 789999999
No 41
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=23.85 E-value=96 Score=20.56 Aligned_cols=51 Identities=25% Similarity=0.245 Sum_probs=32.0
Q ss_pred HHHHHhcCCCcccchHHHHHhHHHHHHHHHHhccch-------hhhccHHHHHHhHHHH
Q 034650 23 RQILRSLNSPKLELSLAARLAKKAEARAIFMVGSEE-------RSIHNIQDLIDTAEYA 74 (88)
Q Consensus 23 RqiLRslnSp~L~L~~AarlaKKae~RaiF~~gseE-------rS~HNI~dLid~aey~ 74 (88)
|.+||. |...+|..--.|||++++|.-|.--.-+| .-..=++|.+.-++||
T Consensus 4 r~~~~~-~~~gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha 61 (85)
T cd00076 4 RKVLRD-NIKGITKPAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHA 61 (85)
T ss_pred hHHHHH-hhccCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 455664 34468888889999999887776444333 2233345666555554
No 42
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=22.99 E-value=1.2e+02 Score=17.61 Aligned_cols=28 Identities=21% Similarity=0.348 Sum_probs=20.6
Q ss_pred HHHHHHHHHhcCCCcccchHHHHHhHHH
Q 034650 19 LSLYRQILRSLNSPKLELSLAARLAKKA 46 (88)
Q Consensus 19 lSLYRqiLRslnSp~L~L~~AarlaKKa 46 (88)
+.-..+|++.|.|+.+||-=+..+-+++
T Consensus 5 ~~~Le~Iv~~Le~~~~sLdes~~lyeeg 32 (53)
T PF02609_consen 5 MERLEEIVEKLESGELSLDESLKLYEEG 32 (53)
T ss_dssp HHHHHHHHHHHHTT-S-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence 3446789999999999998887776665
No 43
>PF02049 FliE: Flagellar hook-basal body complex protein FliE; InterPro: IPR001624 Four genes from the major Bacillus subtilis chemotaxis locus have been shown to encode proteins that are similar to the Salmonella typhimurium FlgB, FlgC, FlgG and FliF proteins; a further gene product is similar to the Escherichia coli FliE protein []. All of these proteins are thought to form part of the hook-basal body complex of the bacterial flagella []. The FlgB, FlgC and FlgG proteins are components of the proximal and distal rods; FliF forms the M-ring that anchors the rod assembly to the membrane; but the role of FliE has not yet been determined []. The similarity between the proteins in these two organisms suggests that the structures of the M-ring and the rod may be similar []. Nevertheless, some differences in size and amino acid composition between some of the homologues suggest the basal body proteins may be organised slightly differently within B. subtilis []. From gel electrophoresis and autoradiography of 35S-labelled S. typhimurium hook-basal body complexes and the deduced number of sulphur-containing residues in FliE, the stoichiometry of the protein in the hook-basal body complex has been estimated to be about nine subunits []. FliE does not undergo cleavage of a signal peptide, nor does it show any similarity to the axial components like the rod or hook proteins, which are thought to be exported by the flagellum-specific export pathway []. On this evidence, it has been suggested that FliE may be in the vicinity of the MS ring, perhaps acting as an adaptor protein between ring and rod substructures [].; GO: 0003774 motor activity, 0005198 structural molecule activity, 0001539 ciliary or flagellar motility, 0009288 bacterial-type flagellum
Probab=22.82 E-value=69 Score=20.70 Aligned_cols=15 Identities=20% Similarity=0.620 Sum_probs=12.7
Q ss_pred hchhHHHHHHHHHHH
Q 034650 13 KHQKRVLSLYRQILR 27 (88)
Q Consensus 13 rnr~~VlSLYRqiLR 27 (88)
-=|-|+++.|..|.|
T Consensus 79 qVRnK~v~AYqEImr 93 (96)
T PF02049_consen 79 QVRNKAVEAYQEIMR 93 (96)
T ss_pred HHHHHHHHHHHHHHh
Confidence 347899999999987
No 44
>PF14929 TAF1_subA: TAF RNA Polymerase I subunit A
Probab=22.64 E-value=1.5e+02 Score=25.46 Aligned_cols=16 Identities=44% Similarity=0.482 Sum_probs=12.6
Q ss_pred HhHHHHHHHhhcCCCC
Q 034650 69 DTAEYALSLLKEGKIP 84 (88)
Q Consensus 69 d~aey~Ls~L~~G~iP 84 (88)
=.-|++|..|.+|.|-
T Consensus 135 V~LE~al~ll~qG~ie 150 (547)
T PF14929_consen 135 VSLEHALFLLSQGNIE 150 (547)
T ss_pred HHHHHHHHHHhCCchH
Confidence 4568899999999874
No 45
>COG0133 TrpB Tryptophan synthase beta chain [Amino acid transport and metabolism]
Probab=22.30 E-value=1e+02 Score=26.26 Aligned_cols=38 Identities=18% Similarity=0.232 Sum_probs=33.5
Q ss_pred hhhchhHHHHHHHHHHHhcCCCcccchHHHHHhHHHHH
Q 034650 11 DSKHQKRVLSLYRQILRSLNSPKLELSLAARLAKKAEA 48 (88)
Q Consensus 11 dlrnr~~VlSLYRqiLRslnSp~L~L~~AarlaKKae~ 48 (88)
+.++.+....-|.++||.----.-||-+|.||.++.++
T Consensus 34 ~~~~D~~F~~el~~~l~~Y~GRptpLy~a~~Lt~~~ga 71 (396)
T COG0133 34 KAKNDPEFQAELDYLLKDYAGRPTPLYFAERLTEHLGA 71 (396)
T ss_pred HHhcCHHHHHHHHHHHHHhCCCCChhHHHHHHHHhhCc
Confidence 44788889999999999888888899999999999884
No 46
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.83 E-value=70 Score=23.51 Aligned_cols=66 Identities=30% Similarity=0.280 Sum_probs=34.3
Q ss_pred hhhhhchhHHHHHHHHHHHhcCC-CcccchHHHHHhHHHHHHHHHHhccchhhhccHHHHHHhHHHHHHHhh
Q 034650 9 AVDSKHQKRVLSLYRQILRSLNS-PKLELSLAARLAKKAEARAIFMVGSEERSIHNIQDLIDTAEYALSLLK 79 (88)
Q Consensus 9 Aedlrnr~~VlSLYRqiLRslnS-p~L~L~~AarlaKKae~RaiF~~gseErS~HNI~dLid~aey~Ls~L~ 79 (88)
+..+.+-++|--||+.|||.=.- |. ++-.---.=-|.|.|-=--++.+ |-..=|-+-..|+-.+.+
T Consensus 3 ~~~~~~p~rvrlLYkriLrlHr~lp~-~~R~lGD~YVkdEFrrHk~vnp~----~~~~FlteW~~Ya~~l~q 69 (125)
T KOG4100|consen 3 ASQLLHPPRVRLLYKRILRLHRGLPA-ELRALGDQYVKDEFRRHKTVNPL----EAQGFLTEWERYAVALSQ 69 (125)
T ss_pred ccccCCcchHHHHHHHHHHHHccCCh-HHHHHHHHHHHHHHHHhccCChH----HHHHHHHHHHHHHHHHHH
Confidence 34457778887799999986321 11 11111112234555544444433 333445556667655544
No 47
>PF00620 RhoGAP: RhoGAP domain; InterPro: IPR000198 Members of the Rho family of small G proteins transduce signals from plasma-membrane receptors and control cell adhesion, motility and shape by actin cytoskeleton formation. Like all other GTPases, Rho proteins act as molecular switches, with an active GTP-bound form and an inactive GDP-bound form. The active conformation is promoted by guanine-nucleotide exchange factors, and the inactive state by GTPase-activating proteins (GAPs) which stimulate the intrinsic GTPase activity of small G proteins. This entry is a Rho/Rac/Cdc42-like GAP domain, that is found in a wide variety of large, multi-functional proteins []. A number of structure are known for this family [, , ]. The domain is composed of seven alpha helices. This domain is also known as the breakpoint cluster region-homology (BH) domain.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1RGP_A 1AM4_B 1GRN_B 2NGR_B 1OW3_A 1TX4_A 3BYI_B 1XA6_A 3FK2_B 1F7C_A ....
Probab=21.79 E-value=2.2e+02 Score=17.99 Aligned_cols=30 Identities=27% Similarity=0.404 Sum_probs=24.4
Q ss_pred chhHHHHHHHHHHHhcCCCcccchHHHHHh
Q 034650 14 HQKRVLSLYRQILRSLNSPKLELSLAARLA 43 (88)
Q Consensus 14 nr~~VlSLYRqiLRslnSp~L~L~~Aarla 43 (88)
+-..|-++.+.+||.|..|=+|-.+-..+-
T Consensus 52 ~~~~va~~lK~~L~~lp~pli~~~~~~~~~ 81 (151)
T PF00620_consen 52 DVHDVASLLKRFLRELPEPLIPSELYDKFI 81 (151)
T ss_dssp THHHHHHHHHHHHHHSSSTSTTHHHHHHHH
T ss_pred ChhhccccceeeeeccccchhhhhHHHHHh
Confidence 345678999999999999999988766555
No 48
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=21.79 E-value=84 Score=19.87 Aligned_cols=23 Identities=26% Similarity=0.421 Sum_probs=19.3
Q ss_pred hhhhh-hchhHHHHHHHHHHHhcC
Q 034650 8 TAVDS-KHQKRVLSLYRQILRSLN 30 (88)
Q Consensus 8 TAedl-rnr~~VlSLYRqiLRsln 30 (88)
+-|++ .|=-.|++||..+-+.+|
T Consensus 29 ~ve~i~envk~ll~lYE~Vs~~iN 52 (55)
T PF05377_consen 29 SVEKIEENVKDLLSLYEVVSNQIN 52 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHccCC
Confidence 45677 788899999999988887
No 49
>PF00990 GGDEF: GGDEF domain; InterPro: IPR000160 This domain appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain. Its function is to synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria [,]. Enzymatic activity can be strongly influenced by the adjacent domains. Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation. Structural studies of PleD from Caulobacter crescentus show that this domain forms a five-stranded beta sheet surrounded by helices, similar to the catalytic core of adenylate cyclase [].; PDB: 3IGN_A 3BRE_B 3EZU_A 3ICL_B 3PJX_A 3PJW_A 3HVW_A 3HVA_B 3I5C_B 3I5B_B ....
Probab=21.79 E-value=1e+02 Score=18.28 Aligned_cols=22 Identities=27% Similarity=0.345 Sum_probs=18.7
Q ss_pred hhhccHHHHHHhHHHHHHHhhc
Q 034650 59 RSIHNIQDLIDTAEYALSLLKE 80 (88)
Q Consensus 59 rS~HNI~dLid~aey~Ls~L~~ 80 (88)
..-.|+.+|+..|+.||...++
T Consensus 135 ~~~~~~~~ll~~a~~al~~ak~ 156 (161)
T PF00990_consen 135 NDGQDADELLKKADQALQEAKE 156 (161)
T ss_dssp STTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHH
Confidence 3567999999999999988765
No 50
>PF03872 RseA_N: Anti sigma-E protein RseA, N-terminal domain; InterPro: IPR005572 Sigma-E is important for the induction of proteins involved in heat shock response. RseA binds sigma-E via its N-terminal domain, sequestering sigma-E and preventing transcription from heat-shock promoters []. The C-terminal domain is located in the periplasm, and may interact with other protein that signal periplasmic stress.; GO: 0016989 sigma factor antagonist activity; PDB: 1OR7_F 1YFN_G.
Probab=20.74 E-value=2.3e+02 Score=18.24 Aligned_cols=39 Identities=23% Similarity=0.320 Sum_probs=26.4
Q ss_pred hhhhchhHHHHHHHHHHHhcCCCcccchHHHHHhHHHHH
Q 034650 10 VDSKHQKRVLSLYRQILRSLNSPKLELSLAARLAKKAEA 48 (88)
Q Consensus 10 edlrnr~~VlSLYRqiLRslnSp~L~L~~AarlaKKae~ 48 (88)
++++..=....|.+..||+=.+...+..|++|++.+-+.
T Consensus 27 ~e~~~~W~rYhlIgd~lR~~~~~~~~~d~s~~V~a~L~~ 65 (87)
T PF03872_consen 27 PELRQTWQRYHLIGDVLRGEDPVALSLDFSARVSAALEA 65 (87)
T ss_dssp HHHHHHHHHHHHHHHHHHT-S-SEEES-HHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHhccCCCCCChhHHHHHHHHHHc
Confidence 345555556677788899877788999999998776543
Done!