Query psy4706
Match_columns 163
No_of_seqs 59 out of 61
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 23:47:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4706.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4706hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11701 UNC45-central: Myosin 99.8 5E-20 1.1E-24 144.4 7.2 97 60-161 15-118 (157)
2 KOG4151|consensus 99.5 5.6E-14 1.2E-18 134.2 5.9 140 19-158 151-297 (748)
3 KOG2758|consensus 93.2 0.2 4.4E-06 46.1 5.8 81 10-102 227-322 (432)
4 PF08167 RIX1: rRNA processing 76.5 17 0.00037 28.7 7.5 99 8-122 37-143 (165)
5 cd00020 ARM Armadillo/beta-cat 63.2 44 0.00096 22.6 6.4 107 37-157 5-117 (120)
6 PF01099 Uteroglobin: Uteroglo 63.1 5.2 0.00011 27.5 1.7 23 61-83 45-67 (67)
7 PF06371 Drf_GBD: Diaphanous G 57.7 84 0.0018 24.0 8.7 101 15-120 83-185 (187)
8 PF11698 V-ATPase_H_C: V-ATPas 56.4 48 0.001 25.9 6.2 83 27-122 26-115 (119)
9 KOG1517|consensus 55.4 25 0.00054 37.1 5.6 60 65-126 615-675 (1387)
10 KOG1241|consensus 54.8 21 0.00046 36.1 4.9 58 65-127 341-398 (859)
11 PF10897 DUF2713: Protein of u 54.2 6.4 0.00014 34.2 1.1 51 67-117 118-172 (246)
12 PF13646 HEAT_2: HEAT repeats; 53.4 20 0.00043 23.8 3.2 74 64-155 14-87 (88)
13 KOG0888|consensus 50.9 17 0.00038 29.6 3.1 57 74-138 49-108 (156)
14 PF07571 DUF1546: Protein of u 50.7 62 0.0013 23.5 5.7 56 67-127 23-81 (92)
15 PF01152 Bac_globin: Bacterial 49.7 18 0.00038 26.4 2.7 44 73-127 15-59 (120)
16 cd07922 CarBa CarBa is the A s 48.6 21 0.00046 26.2 2.9 30 74-103 6-36 (81)
17 PF10296 DUF2404: Putative int 45.2 38 0.00082 24.2 3.8 57 72-138 2-59 (91)
18 COG5215 KAP95 Karyopherin (imp 44.8 1.1E+02 0.0023 30.9 7.8 99 18-128 298-401 (858)
19 PF13174 TPR_6: Tetratricopept 44.4 25 0.00055 19.1 2.3 24 74-97 6-30 (33)
20 KOG1822|consensus 37.3 1.6E+02 0.0036 32.9 8.3 92 16-121 29-121 (2067)
21 PF00505 HMG_box: HMG (high mo 35.7 76 0.0016 20.5 3.9 30 67-97 28-57 (69)
22 cd01493 APPBP1_RUB Ubiquitin a 33.2 1.5E+02 0.0032 27.5 6.5 63 32-100 286-351 (425)
23 PF11864 DUF3384: Domain of un 32.2 2.5E+02 0.0054 25.7 7.8 41 77-117 420-461 (464)
24 KOG0211|consensus 31.8 2.7E+02 0.0057 28.1 8.4 107 12-122 534-664 (759)
25 PF07746 LigA: Aromatic-ring-o 30.5 72 0.0016 23.6 3.4 29 74-103 1-30 (88)
26 smart00540 LEM in nuclear memb 28.3 43 0.00092 22.0 1.6 23 40-69 10-32 (44)
27 COG2406 Protein distantly rela 28.1 2.1E+02 0.0045 24.0 6.0 57 9-87 11-82 (172)
28 PF05205 COMPASS-Shg1: COMPASS 28.0 1.5E+02 0.0032 22.2 4.7 50 77-128 20-70 (106)
29 PF13335 Mg_chelatase_2: Magne 27.9 36 0.00077 25.0 1.4 24 39-64 63-86 (96)
30 cd00256 VATPase_H VATPase_H, r 27.8 1.7E+02 0.0037 27.4 6.0 87 25-124 334-427 (429)
31 TIGR00247 conserved hypothetic 27.0 55 0.0012 29.0 2.6 68 13-85 179-250 (342)
32 smart00265 BH4 BH4 Bcl-2 homol 26.5 54 0.0012 19.7 1.7 18 91-108 6-23 (27)
33 TIGR03628 arch_S11P archaeal r 25.8 67 0.0014 24.9 2.6 21 2-22 75-95 (114)
34 PF04532 DUF587: Protein of un 25.7 64 0.0014 27.9 2.6 39 83-127 50-91 (215)
35 PF06743 FAST_1: FAST kinase-l 25.7 1.3E+02 0.0028 20.7 3.8 55 78-132 8-63 (71)
36 PF08349 DUF1722: Protein of u 25.6 1.5E+02 0.0033 22.1 4.4 42 61-102 45-86 (117)
37 cd01068 sensor_globin Globin d 25.3 1.6E+02 0.0034 21.8 4.5 18 69-86 30-47 (147)
38 COG3499 Phage protein U [Gener 25.1 39 0.00085 27.7 1.2 29 128-159 46-74 (147)
39 PF00233 PDEase_I: 3'5'-cyclic 24.0 3.9E+02 0.0084 22.3 7.0 101 40-160 48-152 (237)
40 PF13513 HEAT_EZ: HEAT-like re 23.0 2E+02 0.0043 17.8 4.1 52 65-118 2-53 (55)
41 PF11460 DUF3007: Protein of u 22.8 52 0.0011 25.5 1.4 25 78-102 59-83 (104)
42 smart00398 HMG high mobility g 21.4 1.8E+02 0.004 18.3 3.7 31 67-98 29-59 (70)
43 cd00454 Trunc_globin Truncated 21.1 1.5E+02 0.0033 21.1 3.6 44 72-126 14-58 (116)
44 PF14664 RICTOR_N: Rapamycin-i 20.2 1.8E+02 0.004 26.2 4.6 89 25-130 76-166 (371)
No 1
>PF11701 UNC45-central: Myosin-binding striated muscle assembly central; InterPro: IPR024660 The UNC-45 or small muscle protein 1 of Caenorhabditis elegans is expressed in two forms from different genomic positions in mammals: as a general tissue protein (UNC-45a) and as a specific form (UNC-45b) expressed only in striated and skeletal muscle. Myofibril formation requires both UNC-45 forms, consistent with the fact that the cytoskeleton is necessary for the development and maintenance of organised myofibrils []. Rng3 (Ring assembly protein 3), the homologue in Schizosaccharomyces pombe, is crucial for cell shape, normal actin cytoskeleton, and contractile ring assembly, and is essential for assembly of the myosin II-containing progenitors of the contractile ring. Widespread defects in the cytoskeleton are found in null mutants of all three fungal proteins []. Mammalian Unc45 is found to act as a specific chaperone during the folding of myosin and the assembly of striated muscle by forming a stable complex with the general chaperone Hsp90 []. All members carry up to three amino-terminal tetratricopeptide repeat (TPR) and a UCS domain at the C terminus that contains a number of Arm repeats. ; PDB: 3OPB_A 3NOW_A.
Probab=99.81 E-value=5e-20 Score=144.44 Aligned_cols=97 Identities=16% Similarity=0.202 Sum_probs=91.3
Q ss_pred ccCCcchhHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHhhhhhhhhhcccCCCCccc-
Q psy4706 60 MEITEDTHTLASLCLARIFENMYYDQARERYLESIMEFIKDKLLSPDIESKVRVTVAITCLLLASLVSLEGSAPRSRVR- 138 (163)
Q Consensus 60 lpvT~nTRm~aSV~LskLYDdm~~D~~Re~F~~~ce~fik~~~~~~d~eskvrai~~is~LLqGP~DVGn~~l~~~gv~- 138 (163)
++.|+|||++++|||+|+. |.+|+.|++.|++||++++.++++++++++++++++|++||.|+|+.++..+|++
T Consensus 15 ~~~~~~~r~~a~v~l~k~l-----~~~~~~~~~~~~~~i~~~~~~~~~d~~i~~~~~l~~lfp~~~dv~~~l~~~eg~~~ 89 (157)
T PF11701_consen 15 LRQPEEVRSHALVILSKLL-----DAAREEFKEKISDFIESLLDEGEMDSLIIAFSALTALFPGPPDVGSELFLSEGFLE 89 (157)
T ss_dssp TTTSCCHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHCCHHCCHHHHHHHHHHHHCTTTHHHHHHHCCTTTHHH
T ss_pred cCCCHhHHHHHHHHHHHHH-----HHhHHHHHHHHHHHHHHHHccccchhHHHHHHHHHHHhCCCHHHHHHHHhhhhHHH
Confidence 4889999999999999993 9999999999999999999999999999999999999999999999999999997
Q ss_pred ----cCC--chhHHHHHHHHHHHHHHhcc
Q psy4706 139 ----FPP--RANFVLNRRTCQVYLIVAGE 161 (163)
Q Consensus 139 ----~~~--s~~~~~q~va~ea~i~aa~k 161 (163)
++. +.+...|.+++|+++||+.+
T Consensus 90 ~l~~~~~~~~~~~~~~~~~lell~aAc~d 118 (157)
T PF11701_consen 90 SLLPLASRKSKDRKVQKAALELLSAACID 118 (157)
T ss_dssp HHHHHHH-CTS-HHHHHHHHHHHHHHTTS
T ss_pred HHHHHHhcccCCHHHHHHHHHHHHHHHcc
Confidence 556 89999999999999999875
No 2
>KOG4151|consensus
Probab=99.46 E-value=5.6e-14 Score=134.23 Aligned_cols=140 Identities=13% Similarity=0.179 Sum_probs=127.6
Q ss_pred HHHHhhcccccchHHHHHHHHhHHHHHHhhhccccccccCcccCCcchhHHHHHHHHHHHhhhhccHHHHHHHHHHHHHH
Q psy4706 19 LITRNVHYKAINWAERLIEIRGLQRLMEVASELQEYKYESSMEITEDTHTLASLCLARIFENMYYDQARERYLESIMEFI 98 (163)
Q Consensus 19 LL~KnVp~~~~~~~~~~~~~~GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~LskLYDdm~~D~~Re~F~~~ce~fi 98 (163)
.++.++....+.|++.|++++|+-+++.+++.-.+++++..+||+.++++++++||.|||.+|++|..|..|.+..+.|+
T Consensus 151 ~i~~~~~p~~~~~~eif~elk~ll~~~d~~s~~~~~~~~~~~~vg~~~~~~~~i~l~rl~~~~~~~~~~~~~~~~~~~~~ 230 (748)
T KOG4151|consen 151 RIVEKMDPSNVSASEIFEELKGLLELKDLASDESELPLEAVAPVGASPALIAKICLQRLYKSKKTDCVEAFLTKDGERLF 230 (748)
T ss_pred HHHhcCCCCcchHHHHHHHHHHHHhhcCCccccccCChhhhccccCchHHHHHHHHHHHhhhccchhHHhhcCCcHHhhh
Confidence 44556677888999999999999999999996666555788999999999999999999999999999999999999999
Q ss_pred HhhcCC--CCcchhHHHHHHHHHhhhhhhhhhcccCCCCccc-----cCCchhHHHHHHHHHHHHHH
Q psy4706 99 KDKLLS--PDIESKVRVTVAITCLLLASLVSLEGSAPRSRVR-----FPPRANFVLNRRTCQVYLIV 158 (163)
Q Consensus 99 k~~~~~--~d~eskvrai~~is~LLqGP~DVGn~~l~~~gv~-----~~~s~~~~~q~va~ea~i~a 158 (163)
+++... .|++.+++.-..+++.++||+|+|+......+++ +++|.++..|+.+++.++|.
T Consensus 231 ~~~v~~~~~d~~~~~~~~~~l~a~~~~~v~~~~~~~~~e~l~~~~l~~~~~~~e~~~~~~~~~~v~~ 297 (748)
T KOG4151|consen 231 KERVFEDPSDLKFKKKSKCKLKAAQEDPVSDTVKVMDKEQLLEEILAVGGSQDELAQVWRTLKLVYG 297 (748)
T ss_pred hhhhccCcccchhhhhhhhhhhhhcCCcccchhhhhhHHHHHHHhhcccccchHHhhhhhhhhhhhc
Confidence 999853 5999999999999999999999999998888776 77999999999999999987
No 3
>KOG2758|consensus
Probab=93.20 E-value=0.2 Score=46.11 Aligned_cols=81 Identities=26% Similarity=0.426 Sum_probs=60.0
Q ss_pred cchhHHHHHHHHHhhcc-----cccchHHHHHHH----------HhHHHHHHhhhccccccccCcccCCcchhHHHHHHH
Q psy4706 10 LSGRDAIIQLITRNVHY-----KAINWAERLIEI----------RGLQRLMEVASELQEYKYESSMEITEDTHTLASLCL 74 (163)
Q Consensus 10 g~gRD~~i~LL~KnVp~-----~~~~~~~~~~~~----------~GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~L 74 (163)
+.|||.+|+++...-|| ..-.|..|.... +-||.|.+|-.|= .|.|.+ |||+ .|
T Consensus 227 pkgrd~iid~fly~p~YLNaIQt~cPhllRYLatAvvtnk~~rr~~lkdlvkVIqqE-~ysYkD--Pite--------Fl 295 (432)
T KOG2758|consen 227 PKGRDTIIDMFLYQPPYLNAIQTSCPHLLRYLATAVVTNKRRRRNRLKDLVKVIQQE-SYSYKD--PITE--------FL 295 (432)
T ss_pred CChhhHHHHHHccCHHHHHHHHhhCHHHHHHHHHHhhcchHhhHHHHHHHHHHHHHh-ccccCC--cHHH--------HH
Confidence 67999999999877766 234566655444 4799999998662 333432 7776 47
Q ss_pred HHHHhhhhccHHHHHHHHHHHHHHHhhc
Q psy4706 75 ARIFENMYYDQARERYLESIMEFIKDKL 102 (163)
Q Consensus 75 skLYDdm~~D~~Re~F~~~ce~fik~~~ 102 (163)
+-||=+.-||.++...++ ||+.+..-|
T Consensus 296 ~clyvn~DFdgAq~kl~e-CeeVl~nDf 322 (432)
T KOG2758|consen 296 ECLYVNYDFDGAQKKLRE-CEEVLVNDF 322 (432)
T ss_pred HHHhhccchHHHHHHHHH-HHHHHhcch
Confidence 779999999999999888 988776543
No 4
>PF08167 RIX1: rRNA processing/ribosome biogenesis
Probab=76.47 E-value=17 Score=28.67 Aligned_cols=99 Identities=22% Similarity=0.191 Sum_probs=64.8
Q ss_pred CCcchhHHHHHHHHHhhcccccchHHHH-----HHHHhHHHHHHhhhccccccccCcccCCcchhHHHHHHHHHHHhhhh
Q psy4706 8 RLLSGRDAIIQLITRNVHYKAINWAERL-----IEIRGLQRLMEVASELQEYKYESSMEITEDTHTLASLCLARIFENMY 82 (163)
Q Consensus 8 vSg~gRD~~i~LL~KnVp~~~~~~~~~~-----~~~~GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~LskLYDdm~ 82 (163)
-+..+|-..+.|+.-.|.+-+ .+.| .++++|-++|+- ++ .+.+.-.+-.+|++||+-+.
T Consensus 37 ~~~~~rw~G~~Ll~~~~~~~~---~e~l~~~~~~W~~~Ll~~L~~----~~---------~~~~~~~ai~~L~~l~~~~~ 100 (165)
T PF08167_consen 37 KSAYSRWAGLCLLKVTVEQCS---WEILLSHGSQWLRALLSILEK----PD---------PPSVLEAAIITLTRLFDLIR 100 (165)
T ss_pred CChhhHHHHHHHHHHHHHHhh---HHHHHHHHHHHHHHHHHHHcC----CC---------CHHHHHHHHHHHHHHHHHhc
Confidence 346777777777766664421 1222 122444444443 33 45667788889999999998
Q ss_pred ccHH--HHHHHHHHHHHHHhhcC-CCCcchhHHHHHHHHHhhh
Q psy4706 83 YDQA--RERYLESIMEFIKDKLL-SPDIESKVRVTVAITCLLL 122 (163)
Q Consensus 83 ~D~~--Re~F~~~ce~fik~~~~-~~d~eskvrai~~is~LLq 122 (163)
.-++ ||.-....-.||+..+. ..+..-...++.++++|++
T Consensus 101 ~~p~l~Rei~tp~l~~~i~~ll~l~~~~~~~~~~l~~L~~ll~ 143 (165)
T PF08167_consen 101 GKPTLTREIATPNLPKFIQSLLQLLQDSSCPETALDALATLLP 143 (165)
T ss_pred CCCchHHHHhhccHHHHHHHHHHHHhccccHHHHHHHHHHHHH
Confidence 8887 88888888899988884 2224455567777777765
No 5
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=63.22 E-value=44 Score=22.62 Aligned_cols=107 Identities=14% Similarity=0.037 Sum_probs=62.6
Q ss_pred HHHhHHHHHHhhhccccccccCcccCCcchhHHHHHHHHHHHhhhhccHHHHHHHH-HHHHHHHhhcCCCCcchhHHHHH
Q psy4706 37 EIRGLQRLMEVASELQEYKYESSMEITEDTHTLASLCLARIFENMYYDQARERYLE-SIMEFIKDKLLSPDIESKVRVTV 115 (163)
Q Consensus 37 ~~~GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~LskLYDdm~~D~~Re~F~~-~ce~fik~~~~~~d~eskvrai~ 115 (163)
+.++++.|++.-..- +++.|-.+..+|..+-.+ .+..+..|.+ -+=+.+-..+.+++.+-...++.
T Consensus 5 ~~~~i~~l~~~l~~~-----------~~~~~~~a~~~l~~l~~~--~~~~~~~~~~~~~i~~l~~~l~~~~~~v~~~a~~ 71 (120)
T cd00020 5 QAGGLPALVSLLSSS-----------DENVQREAAWALSNLSAG--NNDNIQAVVEAGGLPALVQLLKSEDEEVVKAALW 71 (120)
T ss_pred HcCChHHHHHHHHcC-----------CHHHHHHHHHHHHHHhcC--CHHHHHHHHHCCChHHHHHHHhCCCHHHHHHHHH
Confidence 345666666654321 256677888888888765 2344444433 33344444556678888889999
Q ss_pred HHHHhhhhhhhhhcccCCCCccc-----cCCchhHHHHHHHHHHHHH
Q psy4706 116 AITCLLLASLVSLEGSAPRSRVR-----FPPRANFVLNRRTCQVYLI 157 (163)
Q Consensus 116 ~is~LLqGP~DVGn~~l~~~gv~-----~~~s~~~~~q~va~ea~i~ 157 (163)
+++-|.+++-..=..+ -..|++ ...+.+.--++.|+.++-+
T Consensus 72 ~L~~l~~~~~~~~~~~-~~~g~l~~l~~~l~~~~~~~~~~a~~~l~~ 117 (120)
T cd00020 72 ALRNLAAGPEDNKLIV-LEAGGVPKLVNLLDSSNEDIQKNATGALSN 117 (120)
T ss_pred HHHHHccCcHHHHHHH-HHCCChHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 9999999885432222 223333 2233345555666666544
No 6
>PF01099 Uteroglobin: Uteroglobin family; InterPro: IPR006038 Uteroglobin (or blastokinin) is a mammalian steroid-inducible secreted protein originally isolated from the uterus of rabbits during early pregnancy. The mucosal epithelia of several organs that communicate with the external environment express uteroglobin. Its tissue-specific expression is regulated by steroid hormones, and is augmented in the uterus by non-steroidal prolactin. Uteroglobin may be a multi-functional protein with anti-inflammatory/immunomodulatory properties, acting to inhibit phospholipase A2 activity, and binding to (and possibly sequestering) several hydrophobic ligands such as progesterone, retinols, polychlorinated biphenyls, phospholipids and prostaglandins. In addition, uteroglobin has anti-chemotactic, anti-allergic, anti-tumourigenic and embryo growth-stimulatory properties. Uteroglobin may have a homeostatic role against oxidative damage, inflammation, autoimmunity and cancer [, , , ]. Uteroglobin consists of a disulphide-linked dimer of two identical polypeptides, each polypeptide being composed of four helices. It is a member of the secretoglobin superfamily. This entry represents uteroglobin proteins from several mammalian species, as well as other members of the secretoglobin superfamily, such as lipophilin B [], prostatic steroid-binding protein [], mammaglobin [], and the related allergen Fel d 1 (Felis domesticus allergen 1) [].; GO: 0005488 binding, 0005576 extracellular region; PDB: 1UTR_B 1CCD_A 1UTG_A 2UTG_A 1ZKR_B 1PUO_B 2EJN_B.
Probab=63.15 E-value=5.2 Score=27.54 Aligned_cols=23 Identities=13% Similarity=0.252 Sum_probs=19.5
Q ss_pred cCCcchhHHHHHHHHHHHhhhhc
Q psy4706 61 EITEDTHTLASLCLARIFENMYY 83 (163)
Q Consensus 61 pvT~nTRm~aSV~LskLYDdm~~ 83 (163)
.+|++||.++..+|.+||++..|
T Consensus 45 ~ls~e~~~~i~~~l~~I~~S~~C 67 (67)
T PF01099_consen 45 KLSNETRENILKLLEKIYNSPLC 67 (67)
T ss_dssp TS-HHHHHHHHHHHHHHHTSCCC
T ss_pred hCCHHHHHHHHHHHHHHHcCCCC
Confidence 67999999999999999987655
No 7
>PF06371 Drf_GBD: Diaphanous GTPase-binding Domain; InterPro: IPR010473 Diaphanous-related formins (Drfs) are a family of formin homology (FH) proteins that act as effectors of Rho small GTPases during growth factor-induced cytoskeletal remodelling, stress fibre formation, and cell division []. Drf proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 (IPR003104 from INTERPRO) and FH3 (IPR010472 from INTERPRO), and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD. This entry represents the GBD, which is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [].; GO: 0003779 actin binding, 0017048 Rho GTPase binding, 0030036 actin cytoskeleton organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=57.65 E-value=84 Score=24.03 Aligned_cols=101 Identities=23% Similarity=0.378 Sum_probs=55.7
Q ss_pred HHHHHHHHhhcccccchHHHHHHHHhHHHHHHhhhccccccccCcccCCcchhHHHHHHHHHHHhhhhccHHHHHHHH--
Q psy4706 15 AIIQLITRNVHYKAINWAERLIEIRGLQRLMEVASELQEYKYESSMEITEDTHTLASLCLARIFENMYYDQARERYLE-- 92 (163)
Q Consensus 15 ~~i~LL~KnVp~~~~~~~~~~~~~~GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~LskLYDdm~~D~~Re~F~~-- 92 (163)
..+.-|....-..++.|...|+..+|+..|+++-..+.+++.. +++--.....||.=|.-=|-...-++.+.+
T Consensus 83 ~~L~~L~v~Lrt~~~~Wv~~Fl~~~G~~~L~~~L~~~~~~~~~-----~~~~~~~~~~~l~Clkal~n~~~G~~~v~~~~ 157 (187)
T PF06371_consen 83 KILKSLRVSLRTNPISWVQEFLELGGLEALLNVLSKLNKKKEK-----SEEDIDIEHECLRCLKALMNTKYGLEAVLSHP 157 (187)
T ss_dssp HHHHHHHHHHHHS-HHHHHHH-HHHHHHHHHHHHHHHHTHHCT-----CTTCHHHHHHHHHHHHHHTSSHHHHHHHHCSS
T ss_pred HHHHHHHHHhccCCchHHHHhccCCCHHHHHHHHHHhhhhhhh-----cchhHHHHHHHHHHHHHHHccHHHHHHHHcCc
Confidence 4455555555567889999999999999999999888651111 122222222333333333333333333322
Q ss_pred HHHHHHHhhcCCCCcchhHHHHHHHHHh
Q psy4706 93 SIMEFIKDKLLSPDIESKVRVTVAITCL 120 (163)
Q Consensus 93 ~ce~fik~~~~~~d~eskvrai~~is~L 120 (163)
.+=..|-.-+.++++..+.-|+..++++
T Consensus 158 ~~v~~i~~~L~s~~~~~r~~~leiL~~l 185 (187)
T PF06371_consen 158 DSVNLIALSLDSPNIKTRKLALEILAAL 185 (187)
T ss_dssp SHHHHHHHT--TTSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 1223333445678888888888877765
No 8
>PF11698 V-ATPase_H_C: V-ATPase subunit H; InterPro: IPR011987 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C-terminal domain of subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=56.41 E-value=48 Score=25.92 Aligned_cols=83 Identities=16% Similarity=0.173 Sum_probs=56.6
Q ss_pred cccchHHHHHHH-----HhHHHHHHhhhccccccccCcccCCcchhHHHHHHHHHHHhhhhccHHHHHHHH--HHHHHHH
Q psy4706 27 KAINWAERLIEI-----RGLQRLMEVASELQEYKYESSMEITEDTHTLASLCLARIFENMYYDQARERYLE--SIMEFIK 99 (163)
Q Consensus 27 ~~~~~~~~~~~~-----~GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~LskLYDdm~~D~~Re~F~~--~ce~fik 99 (163)
...=|.+|...+ .-||+|.++-....+ -...||++.=|.+=.++.++-..+-+ .+.+-|-
T Consensus 26 se~FW~ENa~kf~~~~~~llk~L~~lL~~s~d-------------~~~laVac~Dig~~vr~~p~gr~ii~~lg~K~~vM 92 (119)
T PF11698_consen 26 SEKFWRENADKFEENNFELLKKLIKLLDKSDD-------------PTTLAVACHDIGEFVRHYPNGRNIIEKLGAKERVM 92 (119)
T ss_dssp -HHHHHHHSGGGSSGGGHHHHHHHHHH-SHHH-------------HHHHHHHHHHHHHHHHH-GGGHHHHHHHSHHHHHH
T ss_pred CccHHHHHHHHHHHcccHHHHHHHHHHccCCC-------------cceeehhhcchHHHHHHChhHHHHHHhcChHHHHH
Confidence 355566665555 357777776643323 56788889988888888887533332 2566788
Q ss_pred hhcCCCCcchhHHHHHHHHHhhh
Q psy4706 100 DKLLSPDIESKVRVTVAITCLLL 122 (163)
Q Consensus 100 ~~~~~~d~eskvrai~~is~LLq 122 (163)
+++..+|-+-+-+|+.++..|+.
T Consensus 93 ~Lm~h~d~eVr~eAL~avQklm~ 115 (119)
T PF11698_consen 93 ELMNHEDPEVRYEALLAVQKLMV 115 (119)
T ss_dssp HHTS-SSHHHHHHHHHHHHHHHH
T ss_pred HHhcCCCHHHHHHHHHHHHHHHH
Confidence 88889999999999999988875
No 9
>KOG1517|consensus
Probab=55.45 E-value=25 Score=37.11 Aligned_cols=60 Identities=23% Similarity=0.303 Sum_probs=41.9
Q ss_pred chhHHHHHHHHHHHhhhhccHHH-HHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHhhhhhhh
Q psy4706 65 DTHTLASLCLARIFENMYYDQAR-ERYLESIMEFIKDKLLSPDIESKVRVTVAITCLLLASLV 126 (163)
Q Consensus 65 nTRm~aSV~LskLYDdm~~D~~R-e~F~~~ce~fik~~~~~~d~eskvrai~~is~LLqGP~D 126 (163)
==|+=+.+||.|||+| ||.+| ---++.+-|=.-..+.++-.|.+--|+-+++|+|.+-.|
T Consensus 615 LLrQW~~icLG~LW~d--~~~Arw~G~r~~AhekL~~~LsD~vpEVRaAAVFALgtfl~~~~d 675 (1387)
T KOG1517|consen 615 LLRQWLCICLGRLWED--YDEARWSGRRDNAHEKLILLLSDPVPEVRAAAVFALGTFLSNGSD 675 (1387)
T ss_pred HHHHHHHHHHHHHhhh--cchhhhccccccHHHHHHHHhcCccHHHHHHHHHHHHHHhccccc
Confidence 3589999999999998 57774 111122222233344568888888889999999998855
No 10
>KOG1241|consensus
Probab=54.78 E-value=21 Score=36.11 Aligned_cols=58 Identities=19% Similarity=0.405 Sum_probs=46.9
Q ss_pred chhHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHhhhhhhhh
Q psy4706 65 DTHTLASLCLARIFENMYYDQARERYLESIMEFIKDKLLSPDIESKVRVTVAITCLLLASLVS 127 (163)
Q Consensus 65 nTRm~aSV~LskLYDdm~~D~~Re~F~~~ce~fik~~~~~~d~eskvrai~~is~LLqGP~DV 127 (163)
|-.|.|++||- +|--...|+- ...+=.||++.+..||...+=-|+-++++.|-||--.
T Consensus 341 np~kAAg~CL~-l~A~~~~D~I----v~~Vl~Fiee~i~~pdwr~reaavmAFGSIl~gp~~~ 398 (859)
T KOG1241|consen 341 NPAKAAGVCLM-LFAQCVGDDI----VPHVLPFIEENIQNPDWRNREAAVMAFGSILEGPEPD 398 (859)
T ss_pred cHHHHHHHHHH-HHHHHhcccc----hhhhHHHHHHhcCCcchhhhhHHHHHHHhhhcCCchh
Confidence 55788888885 4444444444 4578899999999999999999999999999999764
No 11
>PF10897 DUF2713: Protein of unknown function (DUF2713); InterPro: IPR020404 This entry contains proteins with no known function. In some organisms this represents the C-terminal domain of a fusion protein with YjbL.
Probab=54.25 E-value=6.4 Score=34.22 Aligned_cols=51 Identities=18% Similarity=0.234 Sum_probs=42.6
Q ss_pred hHHHHHHHHHHHhhhhccHH-HHHHHHHHHHHHHhhcC---CCCcchhHHHHHHH
Q psy4706 67 HTLASLCLARIFENMYYDQA-RERYLESIMEFIKDKLL---SPDIESKVRVTVAI 117 (163)
Q Consensus 67 Rm~aSV~LskLYDdm~~D~~-Re~F~~~ce~fik~~~~---~~d~eskvrai~~i 117 (163)
..-||++++-=|.+-+-|-. |.+-.+-||.||+++|. +++|.+.++-+--+
T Consensus 118 KplAsll~S~sy~Sa~AD~~gav~ineycenyit~q~k~LSqq~MKK~L~eMK~L 172 (246)
T PF10897_consen 118 KPLASLLISFSYGSAYADIIGAVNINEYCENYITSQFKILSQQDMKKNLGEMKRL 172 (246)
T ss_pred hHHHHHHHHHHHhHHHHHhhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35789999999999888876 78899999999999994 88898888766544
No 12
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=53.37 E-value=20 Score=23.83 Aligned_cols=74 Identities=8% Similarity=0.056 Sum_probs=45.2
Q ss_pred cchhHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHhhhhhhhhhcccCCCCccccCCch
Q psy4706 64 EDTHTLASLCLARIFENMYYDQARERYLESIMEFIKDKLLSPDIESKVRVTVAITCLLLASLVSLEGSAPRSRVRFPPRA 143 (163)
Q Consensus 64 ~nTRm~aSV~LskLYDdm~~D~~Re~F~~~ce~fik~~~~~~d~eskvrai~~is~LLqGP~DVGn~~l~~~gv~~~~s~ 143 (163)
+..|..+.-+|.++.+. ....++.+.+.+++...+..|+.+++.+ |.-++-..+.. ++-.+.
T Consensus 14 ~~vr~~a~~~L~~~~~~------------~~~~~L~~~l~d~~~~vr~~a~~aL~~i--~~~~~~~~L~~----~l~~~~ 75 (88)
T PF13646_consen 14 PQVRAEAARALGELGDP------------EAIPALIELLKDEDPMVRRAAARALGRI--GDPEAIPALIK----LLQDDD 75 (88)
T ss_dssp HHHHHHHHHHHHCCTHH------------HHHHHHHHHHTSSSHHHHHHHHHHHHCC--HHHHTHHHHHH----HHTC-S
T ss_pred HHHHHHHHHHHHHcCCH------------hHHHHHHHHHcCCCHHHHHHHHHHHHHh--CCHHHHHHHHH----HHcCCC
Confidence 45688888888855332 3566677777888999999999999876 32111111100 122344
Q ss_pred hHHHHHHHHHHH
Q psy4706 144 NFVLNRRTCQVY 155 (163)
Q Consensus 144 ~~~~q~va~ea~ 155 (163)
+..-+..|++||
T Consensus 76 ~~~vr~~a~~aL 87 (88)
T PF13646_consen 76 DEVVREAAAEAL 87 (88)
T ss_dssp SHHHHHHHHHHH
T ss_pred cHHHHHHHHhhc
Confidence 555577777775
No 13
>KOG0888|consensus
Probab=50.89 E-value=17 Score=29.65 Aligned_cols=57 Identities=11% Similarity=0.142 Sum_probs=43.6
Q ss_pred HHHHHhhhhccHHHHHHHHHHHHHHHhhcCCCCcch---hHHHHHHHHHhhhhhhhhhcccCCCCccc
Q psy4706 74 LARIFENMYYDQARERYLESIMEFIKDKLLSPDIES---KVRVTVAITCLLLASLVSLEGSAPRSRVR 138 (163)
Q Consensus 74 LskLYDdm~~D~~Re~F~~~ce~fik~~~~~~d~es---kvrai~~is~LLqGP~DVGn~~l~~~gv~ 138 (163)
|.++|++++ .|..|..+++ |+.+ .|.+.. .-.|++..-. |.||.++.......||..
T Consensus 49 ~e~~Y~~~~---~~~Ff~~Lv~-~m~S---GPvvamv~~g~~~V~~~r~-llG~t~~~~a~~~~pgsi 108 (156)
T KOG0888|consen 49 LEEHYSDLK---SKPFFPGLVE-YMSS---GPVVAMVLEGDNVVQYWRA-LLGPTNPAAARAAAPGSI 108 (156)
T ss_pred HHHHHHHhc---CCccHHHHHH-HHhc---CcceehhhcCCCHHHHHHH-HhCCCCcccccccCCCCe
Confidence 889999998 7889999999 8776 233322 2237777777 889999999988888876
No 14
>PF07571 DUF1546: Protein of unknown function (DUF1546); InterPro: IPR011442 These proteins are associated with IPR004823 from INTERPRO in transcription initiation factor TFIID subunit 6 (TAF6).; GO: 0051090 regulation of sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=50.74 E-value=62 Score=23.50 Aligned_cols=56 Identities=16% Similarity=0.190 Sum_probs=40.9
Q ss_pred hHHHHHHHHHHHhhhh--ccHHHHHHHHHHHHHHHhhcC-CCCcchhHHHHHHHHHhhhhhhhh
Q psy4706 67 HTLASLCLARIFENMY--YDQARERYLESIMEFIKDKLL-SPDIESKVRVTVAITCLLLASLVS 127 (163)
Q Consensus 67 Rm~aSV~LskLYDdm~--~D~~Re~F~~~ce~fik~~~~-~~d~eskvrai~~is~LLqGP~DV 127 (163)
|..||-+|+.|.+... |..=+ .++..-|.+.+++ +..+.+...|+..++.| ||-=|
T Consensus 23 Rd~AA~lL~~I~~~~~~~~~~L~---~Ri~~tl~k~l~d~~~~~~t~YGAi~gL~~l--G~~~v 81 (92)
T PF07571_consen 23 RDFAASLLAQICRKFSSSYPTLQ---PRITRTLLKALLDPKKPLGTHYGAIVGLSAL--GPEAV 81 (92)
T ss_pred HHHHHHHHHHHHHHhccccchHH---HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH--HHHHH
Confidence 7888999999998754 22233 4566667777764 56778999999999998 87544
No 15
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=49.74 E-value=18 Score=26.38 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=30.7
Q ss_pred HHHHHHhhhhccHHHHHHHHHHHHHHHhhcCCCCcch-hHHHHHHHHHhhhhhhhh
Q psy4706 73 CLARIFENMYYDQARERYLESIMEFIKDKLLSPDIES-KVRVTVAITCLLLASLVS 127 (163)
Q Consensus 73 ~LskLYDdm~~D~~Re~F~~~ce~fik~~~~~~d~es-kvrai~~is~LLqGP~DV 127 (163)
+..++|+-+.-|+. ++..|...+++. +-+-...++.++-||..=
T Consensus 15 lv~~fY~rv~~d~~-----------l~~~F~~~d~~~~~~~~~~fl~~~~GGp~~Y 59 (120)
T PF01152_consen 15 LVDAFYDRVLADPR-----------LKPFFEGIDLEKHKEKQAEFLSQLLGGPPLY 59 (120)
T ss_dssp HHHHHHHHHHT-TT-----------TGGGGTTSCHHHHHHHHHHHHHHHTTSSSHH
T ss_pred HHHHHHHHHHcCHH-----------HHhhcCCCCHHHHHHHHHHHHHHHhCCCCCC
Confidence 35556666666555 556667778885 677788899999999754
No 16
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=48.57 E-value=21 Score=26.17 Aligned_cols=30 Identities=17% Similarity=0.385 Sum_probs=26.5
Q ss_pred HHHHHhhhhccHH-HHHHHHHHHHHHHhhcC
Q psy4706 74 LARIFENMYYDQA-RERYLESIMEFIKDKLL 103 (163)
Q Consensus 74 LskLYDdm~~D~~-Re~F~~~ce~fik~~~~ 103 (163)
++|+..+|..|++ |++|++-=+.++++.=+
T Consensus 6 ~nrli~~L~~dp~~rerF~~DPea~~~~~gL 36 (81)
T cd07922 6 VNRLIQELFKDPGLIERFQDDPSAVFEEYGL 36 (81)
T ss_pred HHHHHHHHhcCHHHHHHHHHCHHHHHHHcCC
Confidence 6999999999997 99999999988887643
No 17
>PF10296 DUF2404: Putative integral membrane protein conserved region (DUF2404); InterPro: IPR019411 This is entry represents a domain of unknown function found in mitochondrial distribution and morphology proteins Mdm12 and Mdm34, and in maintenance of mitochondrial morphology protein Mmm1. These proteins are components of the ERMES/MDM complex, which serves as a molecular tether to connect the endoplasmic reticulum and mitochondria [].
Probab=45.15 E-value=38 Score=24.25 Aligned_cols=57 Identities=21% Similarity=0.261 Sum_probs=30.6
Q ss_pred HHHHHHHhhhhccHH-HHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHhhhhhhhhhcccCCCCccc
Q psy4706 72 LCLARIFENMYYDQA-RERYLESIMEFIKDKLLSPDIESKVRVTVAITCLLLASLVSLEGSAPRSRVR 138 (163)
Q Consensus 72 V~LskLYDdm~~D~~-Re~F~~~ce~fik~~~~~~d~eskvrai~~is~LLqGP~DVGn~~l~~~gv~ 138 (163)
++++|+|-+++.|++ ++.+++..+..+++.- .|+.-+.++. -=+|+|...=.-+++.
T Consensus 2 ~ll~R~f~~~~~t~~~~~~i~~~L~~kL~~i~-~P~fl~~i~v---------~~~~lG~~~P~i~~~~ 59 (91)
T PF10296_consen 2 ALLGRLFFDFRRTEAFRDKIKEKLQKKLNKIK-LPSFLDEISV---------TELDLGDSPPIISNVR 59 (91)
T ss_pred hHHHHHHHHHhcCHHHHHHHHHHHHHHHcccc-CCCccCcEEE---------EEEECCCCCCEEEecc
Confidence 479999999999887 4444444444444322 2333233322 2356666654444443
No 18
>COG5215 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]
Probab=44.81 E-value=1.1e+02 Score=30.95 Aligned_cols=99 Identities=14% Similarity=0.209 Sum_probs=66.9
Q ss_pred HHHHHhhc---ccccchHHHHH--HHHhHHHHHHhhhccccccccCcccCCcchhHHHHHHHHHHHhhhhccHHHHHHHH
Q psy4706 18 QLITRNVH---YKAINWAERLI--EIRGLQRLMEVASELQEYKYESSMEITEDTHTLASLCLARIFENMYYDQARERYLE 92 (163)
Q Consensus 18 ~LL~KnVp---~~~~~~~~~~~--~~~GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~LskLYDdm~~D~~Re~F~~ 92 (163)
++-.|..| -.+.+.+.-.+ .+.-|-+||+=-++=|+ ++ .=|-+|.||-||. +|-.+..|+--++
T Consensus 298 ~~e~~~~pe~p~qn~~fa~aav~dvlP~lL~LL~~q~ed~~---~D----dWn~smaA~sCLq-lfaq~~gd~i~~p--- 366 (858)
T COG5215 298 EMEDKYLPEVPAQNHGFARAAVADVLPELLSLLEKQGEDYY---GD----DWNPSMAASSCLQ-LFAQLKGDKIMRP--- 366 (858)
T ss_pred HHHHhhcccCchhhcchHHHHHHHHHHHHHHHHHhcCCCcc---cc----ccchhhhHHHHHH-HHHHHhhhHhHHH---
Confidence 34445544 34445555555 33556666654444332 33 2345899999995 7888888887444
Q ss_pred HHHHHHHhhcCCCCcchhHHHHHHHHHhhhhhhhhh
Q psy4706 93 SIMEFIKDKLLSPDIESKVRVTVAITCLLLASLVSL 128 (163)
Q Consensus 93 ~ce~fik~~~~~~d~eskvrai~~is~LLqGP~DVG 128 (163)
+=+||..-+..++-.-.=-|+.++++.+.||..+-
T Consensus 367 -Vl~FvEqni~~~~w~nreaavmAfGSvm~gp~~~~ 401 (858)
T COG5215 367 -VLGFVEQNIRSESWANREAAVMAFGSVMHGPCEDC 401 (858)
T ss_pred -HHHHHHHhccCchhhhHHHHHHHhhhhhcCccHHH
Confidence 77888888887887777778899999999998753
No 19
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=44.39 E-value=25 Score=19.10 Aligned_cols=24 Identities=33% Similarity=0.544 Sum_probs=17.7
Q ss_pred HHHHHhhh-hccHHHHHHHHHHHHH
Q psy4706 74 LARIFENM-YYDQARERYLESIMEF 97 (163)
Q Consensus 74 LskLYDdm-~~D~~Re~F~~~ce~f 97 (163)
+.++|..+ .+|.+++.|.+.+++|
T Consensus 6 ~a~~~~~~g~~~~A~~~~~~~~~~~ 30 (33)
T PF13174_consen 6 LARCYYKLGDYDEAIEYFQRLIKRY 30 (33)
T ss_dssp HHHHHHHHCHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHC
Confidence 56677777 6777888888877765
No 20
>KOG1822|consensus
Probab=37.29 E-value=1.6e+02 Score=32.91 Aligned_cols=92 Identities=20% Similarity=0.205 Sum_probs=58.9
Q ss_pred HHHHHHHhhcccccchHHHHHHHHhHHHHHHhhhccccccccCcccCCcchhHHHHHHHHHHHhhhhccHH-HHHHHHHH
Q psy4706 16 IIQLITRNVHYKAINWAERLIEIRGLQRLMEVASELQEYKYESSMEITEDTHTLASLCLARIFENMYYDQA-RERYLESI 94 (163)
Q Consensus 16 ~i~LL~KnVp~~~~~~~~~~~~~~GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~LskLYDdm~~D~~-Re~F~~~c 94 (163)
.|..+.||.|...... .--.+.+-.++|.++-...++ +.||.-+|+|+.|+|+. .|-= --.|-..|
T Consensus 29 ~l~~l~~~l~~~~ke~-~l~tQ~~~~~~l~s~~~~~~~----------~p~rkL~s~~i~rl~~~--gd~f~~~~~l~~c 95 (2067)
T KOG1822|consen 29 WLRYLERNLNEEQKED-LLVTQLKLEQQLISRLTNGAG----------PPTRKLISVAIARLISN--GDSFSLYSRLNSC 95 (2067)
T ss_pred HHHHHHhcCCcchhHH-HHHHhHHHHHHHHHHHccCCC----------chhHHHHHHHHHHHHhc--cchhhHHHHHHHh
Confidence 4556667776543221 111122455556666555554 34689999999999997 3321 11235589
Q ss_pred HHHHHhhcCCCCcchhHHHHHHHHHhh
Q psy4706 95 MEFIKDKLLSPDIESKVRVTVAITCLL 121 (163)
Q Consensus 95 e~fik~~~~~~d~eskvrai~~is~LL 121 (163)
++|+++ -.+.+...|+.|.+.++.++
T Consensus 96 ~d~l~d-~~~~~~q~k~~a~~~l~~~y 121 (2067)
T KOG1822|consen 96 NDFLSD-GSPSDPQRKLAALSCLGSLY 121 (2067)
T ss_pred hhhhhc-CCCccHHHHHhhccchHHHH
Confidence 999993 35688889999988888776
No 21
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=35.73 E-value=76 Score=20.47 Aligned_cols=30 Identities=23% Similarity=0.326 Sum_probs=22.5
Q ss_pred hHHHHHHHHHHHhhhhccHHHHHHHHHHHHH
Q psy4706 67 HTLASLCLARIFENMYYDQARERYLESIMEF 97 (163)
Q Consensus 67 Rm~aSV~LskLYDdm~~D~~Re~F~~~ce~f 97 (163)
-..++-.|++.|.+| .|.+|+.|.+..++=
T Consensus 28 ~~~i~~~~~~~W~~l-~~~eK~~y~~~a~~~ 57 (69)
T PF00505_consen 28 NKEISKILAQMWKNL-SEEEKAPYKEEAEEE 57 (69)
T ss_dssp HHHHHHHHHHHHHCS-HHHHHHHHHHHHHHH
T ss_pred cccchhhHHHHHhcC-CHHHHHHHHHHHHHH
Confidence 445566699999998 677888888876653
No 22
>cd01493 APPBP1_RUB Ubiquitin activating enzyme (E1) subunit APPBP1. APPBP1 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by Rub family of ubiquitin-like proteins (Ublps) activates SCF ubiquitin ligases and is involved in cell cycle control, signaling and embryogenesis. ABPP1 contains part of the adenylation domain.
Probab=33.17 E-value=1.5e+02 Score=27.49 Aligned_cols=63 Identities=16% Similarity=0.289 Sum_probs=38.4
Q ss_pred HHHHHHH-HhHHHHHHh-hhccccccccCcc-cCCcchhHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHHh
Q psy4706 32 AERLIEI-RGLQRLMEV-ASELQEYKYESSM-EITEDTHTLASLCLARIFENMYYDQARERYLESIMEFIKD 100 (163)
Q Consensus 32 ~~~~~~~-~GLkrLLeV-a~~~~e~~~~~~l-pvT~nTRm~aSV~LskLYDdm~~D~~Re~F~~~ce~fik~ 100 (163)
+..|+.+ ++||+.++= -|.+|- ++.+ .+|..|... |.|.+||.+= .-+..+.|.+.+.++.++
T Consensus 286 ~~~fwi~~~alk~F~~~~~g~lPl---~G~lPDM~s~t~~Y--i~Lq~iY~~k-a~~D~~~v~~~v~~~~~~ 351 (425)
T cd01493 286 SSSFWIMARALKEFVAEENGLLPL---PGTLPDMTADTEKY--IKLQNIYREK-AEKDAAEVEKYVREILKS 351 (425)
T ss_pred CchHHHHHHHHHHHHHhcCCCCCC---CCCCCCCccCHHHH--HHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 3345555 899999866 666654 4443 467766665 5689999762 222235566666655543
No 23
>PF11864 DUF3384: Domain of unknown function (DUF3384); InterPro: IPR024584 This entry represents the N-terminal domain of tuberin which is functionally uncharacterised.
Probab=32.21 E-value=2.5e+02 Score=25.74 Aligned_cols=41 Identities=7% Similarity=0.237 Sum_probs=35.4
Q ss_pred HHhhhhccHHHHHHHHHHHHHHHhhc-CCCCcchhHHHHHHH
Q psy4706 77 IFENMYYDQARERYLESIMEFIKDKL-LSPDIESKVRVTVAI 117 (163)
Q Consensus 77 LYDdm~~D~~Re~F~~~ce~fik~~~-~~~d~eskvrai~~i 117 (163)
.|+.-.|.+....|.+.|..+++..| .+...+.+++|++++
T Consensus 420 ~~~~~~~~Ps~~~W~~n~~~ll~~F~~~~~~~~vRi~aL~~l 461 (464)
T PF11864_consen 420 FYEERSCSPSNPDWLDNLQKLLDRFYNRDRRSEVRIKALDVL 461 (464)
T ss_pred HHHhcccCCCChHHHHHHHHHHHHHhCCCCCchHHHHHHHHH
Confidence 89999999999999999999999999 566777777787766
No 24
>KOG0211|consensus
Probab=31.79 E-value=2.7e+02 Score=28.15 Aligned_cols=107 Identities=15% Similarity=0.147 Sum_probs=68.4
Q ss_pred hhHHHHHHHHHhhcccccchHHHHHHH------------------HhHHHHHHhhhccc--ccccc----CcccCCcchh
Q psy4706 12 GRDAIIQLITRNVHYKAINWAERLIEI------------------RGLQRLMEVASELQ--EYKYE----SSMEITEDTH 67 (163)
Q Consensus 12 gRD~~i~LL~KnVp~~~~~~~~~~~~~------------------~GLkrLLeVa~~~~--e~~~~----~~lpvT~nTR 67 (163)
-|.+|..-+.+-+.+.+..|+.....- .-+.-|.+|.|+=- ++=+| -.-.-++|=|
T Consensus 534 Ir~~aa~~l~~l~~~~G~~w~~~~~i~k~L~~~~q~~y~~R~t~l~si~~la~v~g~ei~~~~Llp~~~~l~~D~vanVR 613 (759)
T KOG0211|consen 534 IREAAARNLPALVETFGSEWARLEEIPKLLAMDLQDNYLVRMTTLFSIHELAEVLGQEITCEDLLPVFLDLVKDPVANVR 613 (759)
T ss_pred HHHHHHHHhHHHHHHhCcchhHHHhhHHHHHHhcCcccchhhHHHHHHHHHHHHhccHHHHHHHhHHHHHhccCCchhhh
Confidence 466677777777777777776543332 23444555554410 00000 0114468999
Q ss_pred HHHHHHHHHHHhhhhccHHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHhhh
Q psy4706 68 TLASLCLARIFENMYYDQARERYLESIMEFIKDKLLSPDIESKVRVTVAITCLLL 122 (163)
Q Consensus 68 m~aSV~LskLYDdm~~D~~Re~F~~~ce~fik~~~~~~d~eskvrai~~is~LLq 122 (163)
++++-.|.++=--|..+. |+..-..+.+++.+ +++.+.+.+|+.+.+++.+
T Consensus 614 ~nvak~L~~i~~~L~~~~-~~~~v~pll~~L~~---d~~~dvr~~a~~a~~~i~l 664 (759)
T KOG0211|consen 614 INVAKHLPKILKLLDESV-RDEEVLPLLETLSS---DQELDVRYRAILAFGSIEL 664 (759)
T ss_pred hhHHHHHHHHHhhcchHH-HHHHHHHHHHHhcc---CcccchhHHHHHHHHHHHH
Confidence 999999888877776643 55555567777666 8999999999999987754
No 25
>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=30.49 E-value=72 Score=23.57 Aligned_cols=29 Identities=24% Similarity=0.412 Sum_probs=22.8
Q ss_pred HHHHHhhhhccHH-HHHHHHHHHHHHHhhcC
Q psy4706 74 LARIFENMYYDQA-RERYLESIMEFIKDKLL 103 (163)
Q Consensus 74 LskLYDdm~~D~~-Re~F~~~ce~fik~~~~ 103 (163)
|+|+.-+| -|++ |++|++.=+.|+.++=.
T Consensus 1 lNkf~~~L-~~~~~r~~F~~D~~a~~~~~~L 30 (88)
T PF07746_consen 1 LNKFCWSL-NDPENRERFLADPEAYLDEYGL 30 (88)
T ss_dssp HHHHHHGG-GSHHHHHHHHH-HHHHHHCCT-
T ss_pred ChHHHHHH-cCHHHHHHHHHCHHHHHHHcCC
Confidence 68999999 5555 99999999999987643
No 26
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=28.25 E-value=43 Score=22.03 Aligned_cols=23 Identities=22% Similarity=0.134 Sum_probs=14.2
Q ss_pred hHHHHHHhhhccccccccCcccCCcchhHH
Q psy4706 40 GLQRLMEVASELQEYKYESSMEITEDTHTL 69 (163)
Q Consensus 40 GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~ 69 (163)
-|++-|.-.|..| -|||+.||-.
T Consensus 10 eL~~~L~~~G~~~-------gPIt~sTR~v 32 (44)
T smart00540 10 ELRAELKQYGLPP-------GPITDTTRKL 32 (44)
T ss_pred HHHHHHHHcCCCC-------CCcCcchHHH
Confidence 3444454444433 4999999953
No 27
>COG2406 Protein distantly related to bacterial ferritins [General function prediction only]
Probab=28.11 E-value=2.1e+02 Score=23.99 Aligned_cols=57 Identities=25% Similarity=0.350 Sum_probs=41.9
Q ss_pred CcchhHHHHHHHHHhhcccccchHHHHHHH---------------HhHHHHHHhhhccccccccCcccCCcchhHHHHHH
Q psy4706 9 LLSGRDAIIQLITRNVHYKAINWAERLIEI---------------RGLQRLMEVASELQEYKYESSMEITEDTHTLASLC 73 (163)
Q Consensus 9 Sg~gRD~~i~LL~KnVp~~~~~~~~~~~~~---------------~GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~ 73 (163)
+|.--|.+|++|+|+. +..|++- .|++.++|.|-+ +-|.|+-.+
T Consensus 11 ~Gvd~~kli~~Llka~-------AaE~tt~YYYtilr~~l~Gle~e~~keiae~Ar~--------------E~r~H~e~i 69 (172)
T COG2406 11 PGVDKDKLIELLLKAA-------AAEWTTYYYYTILRYALKGLEGEGIKEIAEEARE--------------EDRKHFELI 69 (172)
T ss_pred cCCCHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--------------HHHHHHHHH
Confidence 5677899999999997 2222221 488888888854 128899998
Q ss_pred HHHHHhhhhccHHH
Q psy4706 74 LARIFENMYYDQAR 87 (163)
Q Consensus 74 LskLYDdm~~D~~R 87 (163)
-.|||| +..|.-|
T Consensus 70 ~~Ri~e-lg~~~Pr 82 (172)
T COG2406 70 APRIYE-LGGDLPR 82 (172)
T ss_pred HHHHHH-hCCCCch
Confidence 999996 6777776
No 28
>PF05205 COMPASS-Shg1: COMPASS (Complex proteins associated with Set1p) component shg1
Probab=27.98 E-value=1.5e+02 Score=22.20 Aligned_cols=50 Identities=14% Similarity=0.155 Sum_probs=34.6
Q ss_pred HHhhhhccHHHHHHHHHHHHHHHhhcC-CCCcchhHHHHHHHHHhhhhhhhhh
Q psy4706 77 IFENMYYDQARERYLESIMEFIKDKLL-SPDIESKVRVTVAITCLLLASLVSL 128 (163)
Q Consensus 77 LYDdm~~D~~Re~F~~~ce~fik~~~~-~~d~eskvrai~~is~LLqGP~DVG 128 (163)
++++..-.+...+|+..+++|+.+++. ++.+-++=+ .-.++|++|-++=.
T Consensus 20 ~l~~~~~~~~~~~l~~~v~~~v~~~l~~~~~l~~~nk--~k~~alI~~~i~rs 70 (106)
T PF05205_consen 20 CLADFDTSPAYQNLRQRVEEIVESELERDPWLLSKNK--GKARALIEGAIDRS 70 (106)
T ss_pred HHHhccccHHHHHHHHHHHHHHHHHHhcCcccCCcch--HHHHHHHHHHHHHh
Confidence 445555557889999999999999995 445544444 34677888876643
No 29
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=27.88 E-value=36 Score=25.00 Aligned_cols=24 Identities=38% Similarity=0.632 Sum_probs=19.8
Q ss_pred HhHHHHHHhhhccccccccCcccCCc
Q psy4706 39 RGLQRLMEVASELQEYKYESSMEITE 64 (163)
Q Consensus 39 ~GLkrLLeVa~~~~e~~~~~~lpvT~ 64 (163)
+|..|||+||-++.+ ++.+-.|+.
T Consensus 63 R~~~rilrvARTIAD--L~~~~~I~~ 86 (96)
T PF13335_consen 63 RGYHRILRVARTIAD--LEGSERITR 86 (96)
T ss_pred HHHHHHHHHHHHHHh--HcCCCCCCH
Confidence 899999999999999 766555554
No 30
>cd00256 VATPase_H VATPase_H, regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is that of a superhelical spiral, in part the geometry is similar to superhelices composed of armadillo repeat motifs, as found in importins for example.
Probab=27.80 E-value=1.7e+02 Score=27.37 Aligned_cols=87 Identities=14% Similarity=0.096 Sum_probs=61.7
Q ss_pred cccccchHHHHHHH-----HhHHHHHHhhhccccccccCcccCCcchhHHHHHHHHHHHhhhhccHHHHHHHHH--HHHH
Q psy4706 25 HYKAINWAERLIEI-----RGLQRLMEVASELQEYKYESSMEITEDTHTLASLCLARIFENMYYDQARERYLES--IMEF 97 (163)
Q Consensus 25 p~~~~~~~~~~~~~-----~GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~LskLYDdm~~D~~Re~F~~~--ce~f 97 (163)
|+...=|.+|...+ .-+|+|.+.-... +.-...||+.+=|.+=.++.|+...--+. +.+.
T Consensus 334 H~se~FW~EN~~kf~~~~~~llk~L~~iL~~s-------------~d~~~laVAc~Dige~vr~~P~gr~i~~~lg~K~~ 400 (429)
T cd00256 334 HKSEKFWRENADRLNEKNYELLKILIHLLETS-------------VDPIILAVACHDIGEYVRHYPRGKDVVEQLGGKQR 400 (429)
T ss_pred CCCchHHHHHHHHHHhcchHHHHHHHHHHhcC-------------CCcceeehhhhhHHHHHHHCccHHHHHHHcCcHHH
Confidence 44567888888777 3456666654222 22345688889999888888875333332 5677
Q ss_pred HHhhcCCCCcchhHHHHHHHHHhhhhh
Q psy4706 98 IKDKLLSPDIESKVRVTVAITCLLLAS 124 (163)
Q Consensus 98 ik~~~~~~d~eskvrai~~is~LLqGP 124 (163)
|-+++..+|-+-+-+|+.++.-|+...
T Consensus 401 vM~Lm~h~d~~Vr~eAL~avQklm~~~ 427 (429)
T cd00256 401 VMRLLNHEDPNVRYEALLAVQKLMVHN 427 (429)
T ss_pred HHHHhcCCCHHHHHHHHHHHHHHHHhc
Confidence 888888999999999999999886543
No 31
>TIGR00247 conserved hypothetical protein, YceG family. This uncharacterized protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in E. coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC.
Probab=26.97 E-value=55 Score=28.98 Aligned_cols=68 Identities=21% Similarity=0.324 Sum_probs=42.9
Q ss_pred hHHHHHHHHHhhcccccchHHHHHHHHh--HHHHHHhhhccccccccCcccCCcchhHHHHHHHHHHHhhh--hccH
Q psy4706 13 RDAIIQLITRNVHYKAINWAERLIEIRG--LQRLMEVASELQEYKYESSMEITEDTHTLASLCLARIFENM--YYDQ 85 (163)
Q Consensus 13 RD~~i~LL~KnVp~~~~~~~~~~~~~~G--LkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~LskLYDdm--~~D~ 85 (163)
.+.++..+.++.-.....|..+.-.+.. ..++|.+||=++. |. ...++=.++|+|.++||-.+| ..|+
T Consensus 179 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~ltlASIVEk---E~--~~~~e~~~IA~Vf~NRL~~~M~LQsD~ 250 (342)
T TIGR00247 179 LELLKRAFVKMFKAKLKAWGVRLSDLPSKELYNLVIMASIVEK---ET--RVKSERPKVASVFYNRLKSGMALQTDP 250 (342)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHH---hh--CCchhhhHHHHHHHHhccCCCCcccCH
Confidence 3445555555543333345443222211 4689999998865 32 456777899999999999998 4555
No 32
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=26.51 E-value=54 Score=19.74 Aligned_cols=18 Identities=22% Similarity=0.364 Sum_probs=15.5
Q ss_pred HHHHHHHHHhhcCCCCcc
Q psy4706 91 LESIMEFIKDKLLSPDIE 108 (163)
Q Consensus 91 ~~~ce~fik~~~~~~d~e 108 (163)
++++++||+-|+.+.+.+
T Consensus 6 RelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 6 RELVVDYVTYKLSQNGYE 23 (27)
T ss_pred HHHHHHHHHHHHhhcCCC
Confidence 689999999999887764
No 33
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=25.77 E-value=67 Score=24.94 Aligned_cols=21 Identities=29% Similarity=0.431 Sum_probs=17.2
Q ss_pred CCCCCCCCcchhHHHHHHHHH
Q psy4706 2 GNNNNNRLLSGRDAIIQLITR 22 (163)
Q Consensus 2 ~~~~~~vSg~gRD~~i~LL~K 22 (163)
|.|-.+..|+||+++|.-|.+
T Consensus 75 gg~~~~~~G~Gr~~air~l~~ 95 (114)
T TIGR03628 75 GGNGQKSPGPGAQAAIRALAR 95 (114)
T ss_pred CCCCCCCCCCcHHHHHHHHHH
Confidence 556678899999999988755
No 34
>PF04532 DUF587: Protein of unknown function (DUF587); InterPro: IPR007618 This domain is found at the N-termini of some human herpesvirus U58 proteins, and some cytomegalovirus UL87 proteins. This region is always found N-terminal to the UL87 (IPR004285 from INTERPRO), which has no known function.
Probab=25.71 E-value=64 Score=27.93 Aligned_cols=39 Identities=18% Similarity=0.363 Sum_probs=28.7
Q ss_pred ccHHHHHHHHHHHHHHHhhcC--CCCcch-hHHHHHHHHHhhhhhhhh
Q psy4706 83 YDQARERYLESIMEFIKDKLL--SPDIES-KVRVTVAITCLLLASLVS 127 (163)
Q Consensus 83 ~D~~Re~F~~~ce~fik~~~~--~~d~es-kvrai~~is~LLqGP~DV 127 (163)
-|.+| +++-|+.+|. ++.... +=||=.+++=||.||+-|
T Consensus 50 vd~e~------v~~vf~~L~~a~p~~~~~~~DR~k~vLcRLLLGPvAV 91 (215)
T PF04532_consen 50 VDPER------VRSVFEALYAASPPHVRTERDRAKLVLCRLLLGPVAV 91 (215)
T ss_pred CCHHH------HHHHHHHHHHhCCcccccchhhhhhhhhHhhcCCccc
Confidence 46665 7888888884 334443 667888899999999865
No 35
>PF06743 FAST_1: FAST kinase-like protein, subdomain 1; InterPro: IPR010622 This entry represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis []. Note that many family members are hypothetical proteins.; GO: 0004672 protein kinase activity
Probab=25.69 E-value=1.3e+02 Score=20.68 Aligned_cols=55 Identities=16% Similarity=0.187 Sum_probs=45.9
Q ss_pred HhhhhccHHH-HHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHhhhhhhhhhcccC
Q psy4706 78 FENMYYDQAR-ERYLESIMEFIKDKLLSPDIESKVRVTVAITCLLLASLVSLEGSA 132 (163)
Q Consensus 78 YDdm~~D~~R-e~F~~~ce~fik~~~~~~d~eskvrai~~is~LLqGP~DVGn~~l 132 (163)
|--+-|++.. +.|-+.|.+.+.+.|..-....-+.++-+++.|=+=|.+.=++++
T Consensus 8 fa~LNy~P~~~~~f~~~~~~~L~~~l~~~~p~~ll~~v~Sl~~l~~~p~~~l~~vf 63 (71)
T PF06743_consen 8 FARLNYQPPNAEEFFEKLIERLESYLDEFSPEDLLDLVWSLCLLQRFPEDLLNKVF 63 (71)
T ss_pred HHhcCCCCCCHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHhhCCHHHHHHHc
Confidence 5556688874 889999999999999888888889999999888888888766664
No 36
>PF08349 DUF1722: Protein of unknown function (DUF1722); InterPro: IPR013560 This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from Escherichia coli.
Probab=25.56 E-value=1.5e+02 Score=22.13 Aligned_cols=42 Identities=14% Similarity=0.279 Sum_probs=33.2
Q ss_pred cCCcchhHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHHhhc
Q psy4706 61 EITEDTHTLASLCLARIFENMYYDQARERYLESIMEFIKDKL 102 (163)
Q Consensus 61 pvT~nTRm~aSV~LskLYDdm~~D~~Re~F~~~ce~fik~~~ 102 (163)
|.|..++.+|.-=+.--+-+--...||+.|.+.+++|-+++.
T Consensus 45 ~~~~~~~~Nvl~Hi~Gyfk~~ls~~EK~~~~~~i~~yr~g~i 86 (117)
T PF08349_consen 45 PPTRGSHINVLQHIFGYFKKKLSSEEKQHFLDLIEDYREGKI 86 (117)
T ss_pred CCCchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHcCCc
Confidence 557777777766666667777788899999999999987753
No 37
>cd01068 sensor_globin Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic heme sensors combining a globin with an MCP signaling domain, others function as gene regulators, by direct combination with DNA-binding domains, with domains modulating 2nd messengers, or with domains interacting with transcription factors or regulators.
Probab=25.30 E-value=1.6e+02 Score=21.76 Aligned_cols=18 Identities=11% Similarity=0.202 Sum_probs=14.9
Q ss_pred HHHHHHHHHHhhhhccHH
Q psy4706 69 LASLCLARIFENMYYDQA 86 (163)
Q Consensus 69 ~aSV~LskLYDdm~~D~~ 86 (163)
++.-.+..+||-|..+++
T Consensus 30 ~~~~i~~~FY~~l~~~p~ 47 (147)
T cd01068 30 NADELVDRFYDHLRRTPE 47 (147)
T ss_pred HHHHHHHHHHHHHhcChH
Confidence 445668999999999988
No 38
>COG3499 Phage protein U [General function prediction only]
Probab=25.06 E-value=39 Score=27.67 Aligned_cols=29 Identities=21% Similarity=0.107 Sum_probs=24.4
Q ss_pred hcccCCCCccccCCchhHHHHHHHHHHHHHHh
Q psy4706 128 LEGSAPRSRVRFPPRANFVLNRRTCQVYLIVA 159 (163)
Q Consensus 128 Gn~~l~~~gv~~~~s~~~~~q~va~ea~i~aa 159 (163)
|+-.|.+|||+++ ++.-++.+++||+.+|
T Consensus 46 g~dsItLsGvl~P---e~~GG~~sL~aL~a~A 74 (147)
T COG3499 46 GEDSITLSGVLYP---EETGGESSLDALRALA 74 (147)
T ss_pred CCCeEEEcceecc---hhhCCHhHHHHHHHHH
Confidence 5677889999999 7777888999988776
No 39
>PF00233 PDEase_I: 3'5'-cyclic nucleotide phosphodiesterase; InterPro: IPR002073 The cyclic nucleotide phosphodiesterases (PDE) comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They are divided into 11 families. They regulate the localisation, duration and amplitude of cyclic nucleotide signalling within subcellular domains. PDEs are therefore important for signal transduction. PDE enzymes are often targets for pharmacological inhibition due to their unique tissue distribution, structural properties, and functional properties. Inhibitors include: Roflumilast for chronic obstructive pulmonary disease and asthma [], Sildenafil for erectile dysfunction [] and Cilostazol for peripheral arterial occlusive disease [], amongst others. Retinal 3',5'-cGMP phosphodiesterase is located in photoreceptor outer segments: it is light activated, playing a pivotal role in signal transduction. In rod cells, PDE is oligomeric, comprising an alpha-, a beta- and 2 gamma-subunits, while in cones, PDE is a homodimer of alpha chains, which are associated with several smaller subunits. Both rod and cone PDEs catalyse the hydrolysis of cAMP or cGMP to the corresponding nucleoside 5' monophosphates, both enzymes also binding cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion. This entry represents the catalytic domain of PDE which is multihelical and can be divided into three subdomains.; GO: 0004114 3',5'-cyclic-nucleotide phosphodiesterase activity, 0007165 signal transduction; PDB: 3I8V_A 3TVX_A 2QYK_A 1ZKL_A 3G3N_A 4DFF_B 2OUS_B 3SNL_A 2OUY_A 2OUP_B ....
Probab=23.95 E-value=3.9e+02 Score=22.26 Aligned_cols=101 Identities=14% Similarity=0.146 Sum_probs=54.4
Q ss_pred hHHHHHHhhhcccccc-ccCcccCCcchhHHHHHHHHHHHh---hhhccHHHHHHHHHHHHHHHhhcCCCCcchhHHHHH
Q psy4706 40 GLQRLMEVASELQEYK-YESSMEITEDTHTLASLCLARIFE---NMYYDQARERYLESIMEFIKDKLLSPDIESKVRVTV 115 (163)
Q Consensus 40 GLkrLLeVa~~~~e~~-~~~~lpvT~nTRm~aSV~LskLYD---dm~~D~~Re~F~~~ce~fik~~~~~~d~eskvrai~ 115 (163)
|+--...|-++.|-.. |. ..+.--++|+|++..=|-+ |.-..-.++.|.+ +.++|.+....-||...-+.+.
T Consensus 48 G~~N~flv~~~~~LA~~Y~---d~SvLE~~H~~~~~~lL~~~~~nil~~l~~~~~~~-~r~~ii~~ILaTDm~~h~~~~~ 123 (237)
T PF00233_consen 48 GVNNAFLVKTNSPLAILYN---DRSVLENHHCALAFQLLRKEECNILSNLSEDDYQE-FRKLIIELILATDMSKHFELLS 123 (237)
T ss_dssp SSCHHHHHHTTSHHHHHTT---TSSHHHHHHHHHHHHHHTSTTTTTTTTS-HHHHHH-HHHHHHHHHHTTSGGGHHHHHH
T ss_pred ccccchhhccccchhhhcC---ccCCccccHHHHHHHHHHhhhhhhhcchhhhhhHH-HHHHHHHHHHhcchhhHHHHHH
Confidence 5555555555544211 11 2234447788886654331 1111122223332 5556667777789998888777
Q ss_pred HHHHhhhhhhhhhcccCCCCccccCCchhHHHHHHHHHHHHHHhc
Q psy4706 116 AITCLLLASLVSLEGSAPRSRVRFPPRANFVLNRRTCQVYLIVAG 160 (163)
Q Consensus 116 ~is~LLqGP~DVGn~~l~~~gv~~~~s~~~~~q~va~ea~i~aa~ 160 (163)
.+...++..-. .+..+....++.+||+|+
T Consensus 124 ~~~~~~~~~~~----------------~~~~~r~~~l~~ll~~AD 152 (237)
T PF00233_consen 124 KLQEKLDSGDF----------------LDEDDRQLLLQLLLKAAD 152 (237)
T ss_dssp HHHHHHHTTEB----------------TTTCHHHHHHHHHHHHHH
T ss_pred HHHHHhhhhcc----------------cchHHHHHHHHhcccccc
Confidence 77666654422 111166677788888885
No 40
>PF13513 HEAT_EZ: HEAT-like repeat; PDB: 2Z5J_A 2OT8_B 2Z5O_A 2H4M_A 2QMR_A 1QBK_B 2Z5M_A 2Z5K_A 2Z5N_A 1GCJ_B ....
Probab=23.02 E-value=2e+02 Score=17.83 Aligned_cols=52 Identities=17% Similarity=0.209 Sum_probs=26.7
Q ss_pred chhHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHH
Q psy4706 65 DTHTLASLCLARIFENMYYDQARERYLESIMEFIKDKLLSPDIESKVRVTVAIT 118 (163)
Q Consensus 65 nTRm~aSV~LskLYDdm~~D~~Re~F~~~ce~fik~~~~~~d~eskvrai~~is 118 (163)
..|..|+-+|..+=... +..-+.|...+-..+...+.+++-+.+-.|+-+++
T Consensus 2 ~vR~~A~~aLg~l~~~~--~~~~~~~~~~~~~~L~~~L~d~~~~VR~~A~~aLg 53 (55)
T PF13513_consen 2 RVRRAAAWALGRLAEGC--PELLQPYLPELLPALIPLLQDDDDSVRAAAAWALG 53 (55)
T ss_dssp HHHHHHHHHHHCTTTTT--HHHHHHHHHHHHHHHHHHTTSSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhHhccc--HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 35777888887733222 22222344444444555555555455555555554
No 41
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=22.79 E-value=52 Score=25.50 Aligned_cols=25 Identities=28% Similarity=0.464 Sum_probs=20.7
Q ss_pred HhhhhccHHHHHHHHHHHHHHHhhc
Q psy4706 78 FENMYYDQARERYLESIMEFIKDKL 102 (163)
Q Consensus 78 YDdm~~D~~Re~F~~~ce~fik~~~ 102 (163)
=.+|.|-+.|..|.+..|..-++.+
T Consensus 59 t~~MTy~~Q~k~Ye~a~~~~~~~~l 83 (104)
T PF11460_consen 59 TGKMTYMQQRKDYEEAVDQLTNEEL 83 (104)
T ss_pred cCCCcHHHHHHHHHHHHHHHhHHHH
Confidence 3699999999999999887776643
No 42
>smart00398 HMG high mobility group.
Probab=21.44 E-value=1.8e+02 Score=18.34 Aligned_cols=31 Identities=13% Similarity=0.088 Sum_probs=23.8
Q ss_pred hHHHHHHHHHHHhhhhccHHHHHHHHHHHHHH
Q psy4706 67 HTLASLCLARIFENMYYDQARERYLESIMEFI 98 (163)
Q Consensus 67 Rm~aSV~LskLYDdm~~D~~Re~F~~~ce~fi 98 (163)
...++-.|++.|.+|. |.+|+.|.+.+++--
T Consensus 29 ~~~i~~~~~~~W~~l~-~~ek~~y~~~a~~~~ 59 (70)
T smart00398 29 NAEISKKLGERWKLLS-EEEKAPYEEKAKKDK 59 (70)
T ss_pred HHHHHHHHHHHHHcCC-HHHHHHHHHHHHHHH
Confidence 3445667999999997 788899988877643
No 43
>cd00454 Trunc_globin Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct from the three-over-three pattern found in other globins. A subset of these have been demonstrated to form homodimers.
Probab=21.12 E-value=1.5e+02 Score=21.09 Aligned_cols=44 Identities=14% Similarity=0.172 Sum_probs=26.5
Q ss_pred HHHHHHHhhhhccHHHHHHHHHHHHHHHhhcCCCCcchhH-HHHHHHHHhhhhhhh
Q psy4706 72 LCLARIFENMYYDQARERYLESIMEFIKDKLLSPDIESKV-RVTVAITCLLLASLV 126 (163)
Q Consensus 72 V~LskLYDdm~~D~~Re~F~~~ce~fik~~~~~~d~eskv-rai~~is~LLqGP~D 126 (163)
-+...+|+.+.-|+. |+..|...+++... +....++.++-||..
T Consensus 14 ~lv~~FY~~i~~dp~-----------i~~~F~~~~~~~~~~~~~~fl~~~~gg~~~ 58 (116)
T cd00454 14 ALVDRFYARVAADPR-----------LGPIFPADDLEEHRAKLADFLTQVLGGPGL 58 (116)
T ss_pred HHHHHHHHHHhcChH-----------HHHhcCCcchHHHHHHHHHHHHHHcCCCCC
Confidence 345677777776664 44445444455433 455667788888753
No 44
>PF14664 RICTOR_N: Rapamycin-insensitive companion of mTOR, N-term
Probab=20.20 E-value=1.8e+02 Score=26.23 Aligned_cols=89 Identities=15% Similarity=0.175 Sum_probs=53.3
Q ss_pred cccccchHHHHHHHHhHHHHHHhhhccccccccCcccCCcchhHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHHhhc-C
Q psy4706 25 HYKAINWAERLIEIRGLQRLMEVASELQEYKYESSMEITEDTHTLASLCLARIFENMYYDQARERYLESIMEFIKDKL-L 103 (163)
Q Consensus 25 p~~~~~~~~~~~~~~GLkrLLeVa~~~~e~~~~~~lpvT~nTRm~aSV~LskLYDdm~~D~~Re~F~~~ce~fik~~~-~ 103 (163)
-+......||.--++=+.+++++-....+ ++ ..=.|..+||.- + +.++|+..|=+.+-+.. .
T Consensus 76 ~~~~~~~~ER~QALkliR~~l~~~~~~~~--~~-----~~vvralvaiae-----~-----~~D~lr~~cletL~El~l~ 138 (371)
T PF14664_consen 76 DRDNKNDVEREQALKLIRAFLEIKKGPKE--IP-----RGVVRALVAIAE-----H-----EDDRLRRICLETLCELALL 138 (371)
T ss_pred cccCCChHHHHHHHHHHHHHHHhcCCccc--CC-----HHHHHHHHHHHh-----C-----CchHHHHHHHHHHHHHHhh
Confidence 33333344544445667778887433333 21 122355666532 2 66788888988888887 4
Q ss_pred CCCcchhHHHHHHHHHhhh-hhhhhhcc
Q psy4706 104 SPDIESKVRVTVAITCLLL-ASLVSLEG 130 (163)
Q Consensus 104 ~~d~eskvrai~~is~LLq-GP~DVGn~ 130 (163)
.|++-.+-.++.++.-.+. ||+++...
T Consensus 139 ~P~lv~~~gG~~~L~~~l~d~~~~~~~~ 166 (371)
T PF14664_consen 139 NPELVAECGGIRVLLRALIDGSFSISES 166 (371)
T ss_pred CHHHHHHcCCHHHHHHHHHhccHhHHHH
Confidence 6777777777766665555 77775444
Done!