Query 025586
Match_columns 250
No_of_seqs 57 out of 59
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 07:21:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025586.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025586hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10236 hypothetical protein; 100.0 3.6E-36 7.8E-41 268.8 10.6 125 61-207 8-142 (237)
2 COG4735 Uncharacterized protei 99.6 6E-17 1.3E-21 143.3 -0.2 70 116-196 23-93 (211)
3 COG4735 Uncharacterized protei 98.9 3.4E-10 7.4E-15 100.7 1.6 93 132-240 1-102 (211)
4 PF13099 DUF3944: Domain of un 96.6 0.0023 4.9E-08 43.4 3.0 30 60-89 3-32 (35)
5 PF03250 Tropomodulin: Tropomo 82.9 2 4.3E-05 37.3 4.3 31 53-83 109-139 (147)
6 PF03981 Ubiq_cyt_C_chap: Ubiq 82.2 0.44 9.6E-06 38.2 0.1 51 116-196 5-56 (141)
7 PF02173 pKID: pKID domain; I 60.9 6 0.00013 27.9 1.6 13 138-150 18-30 (41)
8 TIGR00759 aceE pyruvate dehydr 51.2 1.1E+02 0.0024 33.4 9.7 23 57-79 301-323 (885)
9 cd01915 CODH Carbon monoxide d 49.4 61 0.0013 33.8 7.3 92 139-237 105-211 (613)
10 cd02642 R3H_encore_like R3H do 45.5 35 0.00077 24.7 3.7 44 115-158 3-49 (63)
11 PF11248 DUF3046: Protein of u 44.7 47 0.001 25.2 4.3 44 115-158 5-62 (63)
12 PF04542 Sigma70_r2: Sigma-70 44.3 41 0.00088 22.8 3.7 33 142-177 5-37 (71)
13 TIGR02989 Sig-70_gvs1 RNA poly 42.5 34 0.00075 26.9 3.5 36 141-179 9-44 (159)
14 cd06406 PB1_P67 A PB1 domain i 40.5 24 0.00053 27.8 2.3 20 137-156 18-37 (80)
15 PF15008 DUF4518: Domain of un 39.1 75 0.0016 29.9 5.7 85 61-171 7-91 (262)
16 cd06134 RNaseT DEDDh 3'-5' exo 37.2 27 0.00058 29.8 2.3 33 145-177 151-188 (189)
17 PF12616 DUF3775: Protein of u 33.8 95 0.0021 24.0 4.6 31 60-90 3-34 (75)
18 cd02646 R3H_G-patch R3H domain 31.9 61 0.0013 23.1 3.1 44 117-160 1-46 (58)
19 TIGR01702 CO_DH_cata carbon-mo 29.8 1E+02 0.0022 32.4 5.3 50 136-188 101-154 (621)
20 PF02836 Glyco_hydro_2_C: Glyc 28.9 41 0.0009 30.1 2.2 38 118-155 36-73 (298)
21 PRK09405 aceE pyruvate dehydro 28.7 3.5E+02 0.0077 29.7 9.3 132 60-246 344-510 (891)
22 PF07176 DUF1400: Alpha/beta h 28.0 78 0.0017 26.1 3.5 36 55-90 26-61 (127)
23 KOG3708 Uncharacterized conser 26.8 55 0.0012 34.3 2.9 69 97-175 588-665 (681)
24 PF10826 DUF2551: Protein of u 26.0 79 0.0017 25.3 3.0 28 222-250 14-41 (83)
25 KOG3354 Gluconate kinase [Carb 25.2 96 0.0021 28.2 3.8 39 110-148 63-104 (191)
26 PF08708 PriCT_1: Primase C te 24.5 1.2E+02 0.0025 21.9 3.5 54 108-168 7-60 (71)
27 PRK06759 RNA polymerase factor 23.9 1.5E+02 0.0033 23.2 4.3 35 141-179 12-46 (154)
28 PRK12513 RNA polymerase sigma 23.7 75 0.0016 26.2 2.7 36 141-179 34-69 (194)
29 PF01371 Trp_repressor: Trp re 23.7 1.2E+02 0.0025 24.0 3.6 20 65-84 9-28 (87)
30 PF09379 FERM_N: FERM N-termin 22.9 61 0.0013 23.2 1.8 17 140-156 17-33 (80)
31 PF13873 Myb_DNA-bind_5: Myb/S 22.7 2.2E+02 0.0047 20.5 4.7 43 110-153 34-76 (78)
32 COG4840 Uncharacterized protei 22.3 1E+02 0.0022 24.1 2.9 31 57-90 26-56 (71)
33 PRK09643 RNA polymerase sigma 22.2 1.2E+02 0.0025 25.5 3.6 36 141-179 35-70 (192)
34 PF11470 TUG-UBL1: GLUT4 regul 22.1 59 0.0013 24.3 1.6 20 139-158 16-35 (65)
35 PRK07247 DNA polymerase III su 22.1 1.4E+02 0.0031 26.0 4.2 36 140-177 131-168 (195)
36 cd00014 CH Calponin homology d 21.7 1.7E+02 0.0036 21.5 4.0 26 141-167 62-87 (107)
37 KOG2805 tRNA (5-methylaminomet 20.5 79 0.0017 31.3 2.5 33 147-179 60-92 (377)
38 PRK14082 hypothetical protein; 20.5 78 0.0017 24.4 2.0 16 162-177 33-48 (65)
No 1
>PRK10236 hypothetical protein; Provisional
Probab=100.00 E-value=3.6e-36 Score=268.80 Aligned_cols=125 Identities=18% Similarity=0.313 Sum_probs=115.7
Q ss_pred hHHHHHHHhhChHHHHHHHHHhc-----CCCCCCccchhhc-cc---CCcchHHHhhhhHHHHHHHHHHHHHHhhhcccc
Q 025586 61 PELRSVLELATDSELYELERILF-----GPSYFSPLLKSFT-KR---ADVDYVMIEQDLEEREDFIASLESRFLFLAADA 131 (250)
Q Consensus 61 ~ELr~~LeLATdEEL~eL~~ILf-----~~r~fsPLlkS~~-kr---~~~Dy~~~~~~~~~R~~~i~~IE~RfqfLAADs 131 (250)
|++.+||..|++|||.+|++||+ ..|+++.|+++.. |+ +.+||.+ ||+.||+||||||||+
T Consensus 8 D~DL~fL~~cs~edL~~Lv~~Lt~d~dG~~R~te~lt~~~~yk~~~~~~~~~~~----------yw~~Ia~elq~fGgnt 77 (237)
T PRK10236 8 DSDLDFLQHCSEEQLANFARLLTHNEKGKTRLSSVLMRNELFKSMEGHPEQHRR----------NWQLIAGELQHFGGDS 77 (237)
T ss_pred CccHHHHHhCCHHHHHHHHHHHhcCCCCCEeehhhhcccHHHHhhcccchhHHH----------HHHHHHHHHHHhcchH
Confidence 34447999999999999999999 4577888888854 66 8999999 9999999999999999
Q ss_pred -cchhccCCchHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCccccCCchhhhhhhhhhhh
Q 025586 132 -RSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWENSEASDAQNSLELGLS 207 (250)
Q Consensus 132 -~tvLRG~~vsYReVLl~VckkLKI~~s~klsT~dLEaEIFLhLL~~~ss~~~~~~~~aWekm~~~~~~~sl~~~~~ 207 (250)
+|+|||+|++|||||+|||+||||||++++||++||++||+|+|++ +|+||+++ +++++...++
T Consensus 78 ~~n~lRG~Gv~YreIL~DVc~~LKV~y~~~~st~~iE~~il~kll~~-----------a~~kms~e-E~~~L~~~l~ 142 (237)
T PRK10236 78 IANKLRGHGKLYRAILLDVSKRLKLKADKEMSTFEIEQQLLEQFLRN-----------TWKKMDEE-HKQEFLHAVD 142 (237)
T ss_pred HHHHHhcCCccHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHH-----------HHHHCCHH-HHHHHHHHHh
Confidence 5799999999999999999999999999999999999999999999 99999999 9999999998
No 2
>COG4735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.61 E-value=6e-17 Score=143.27 Aligned_cols=70 Identities=16% Similarity=0.338 Sum_probs=68.8
Q ss_pred HHHHHHHHHhhhcccc-cchhccCCchHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCccccCC
Q 025586 116 FIASLESRFLFLAADA-RSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWENSE 194 (250)
Q Consensus 116 ~i~~IE~RfqfLAADs-~tvLRG~~vsYReVLl~VckkLKI~~s~klsT~dLEaEIFLhLL~~~ss~~~~~~~~aWekm~ 194 (250)
||+.|++++|++++|+ .+.|||.|+.||+||+|+|||||++|+++++|.+||+.++++||++ +|+||+
T Consensus 23 y~k~ia~elq~~gg~s~anflr~~G~lyk~il~d~~~~Lk~k~~k~~~tt~Iee~ll~~il~~-----------~l~km~ 91 (211)
T COG4735 23 YLKRIAEELQTTGGLSAANFLRDLGQLYKKILCDEKDKLKVKVQKELGTTEIEEPLLLQILRN-----------PLEKML 91 (211)
T ss_pred HHHhhHHHHHHhccHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhccccccchhHHHHHHh-----------HHHHHh
Confidence 8899999999999999 7999999999999999999999999999999999999999999999 999999
Q ss_pred ch
Q 025586 195 AS 196 (250)
Q Consensus 195 ~~ 196 (250)
..
T Consensus 92 ~~ 93 (211)
T COG4735 92 KG 93 (211)
T ss_pred HH
Confidence 87
No 3
>COG4735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.92 E-value=3.4e-10 Score=100.74 Aligned_cols=93 Identities=23% Similarity=0.258 Sum_probs=87.0
Q ss_pred cchhccC--CchHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCccccCCchhhhhhhhhhhhhH
Q 025586 132 RSTLRGW--RPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWENSEASDAQNSLELGLSQW 209 (250)
Q Consensus 132 ~tvLRG~--~vsYReVLl~VckkLKI~~s~klsT~dLEaEIFLhLL~~~ss~~~~~~~~aWekm~~~~~~~sl~~~~~~w 209 (250)
+|++||+ ..+||+-++||||+++++|..-+.|-++|.++|+|.+++ .|++.+.. +.+.|...++
T Consensus 1 lt~~l~~~~~~k~r~g~~~~~ky~k~ia~elq~~gg~s~anflr~~G~-----------lyk~il~d-~~~~Lk~k~~-- 66 (211)
T COG4735 1 LTVLLGRSEQFKYREGLIQVCKYLKRIAEELQTTGGLSAANFLRDLGQ-----------LYKKILCD-EKDKLKVKVQ-- 66 (211)
T ss_pred CchhhccchhhHHHhhHHHHHHHHHhhHHHHHHhccHHHHHHHHHHHH-----------HHHHcCHH-HHHHHHHHHH--
Confidence 4788996 999999999999999999999999999999999999999 99999998 8999999999
Q ss_pred HHHHhhhcccCc-------hhhHHHHHhccceehHHHH
Q 025586 210 KVQALAAFNAGA-------VELKSMMLKGGGIYTLVKI 240 (250)
Q Consensus 210 ~~~~la~~~lg~-------~~~~~~~lKGgsalavssi 240 (250)
+.++.+.+.+ +|++..++|||++.+++++
T Consensus 67 --k~~~tt~Iee~ll~~il~~~l~km~~~~~~e~~~~l 102 (211)
T COG4735 67 --KELGTTEIEEPLLLQILRNPLEKMLKGGKAEAVDSL 102 (211)
T ss_pred --HhhccccccchhHHHHHHhHHHHHhHHHHHHHHHHh
Confidence 7788888877 9999999999999999987
No 4
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=96.59 E-value=0.0023 Score=43.40 Aligned_cols=30 Identities=17% Similarity=0.018 Sum_probs=25.2
Q ss_pred chHHHHHHHhhChHHHHHHHHHhcCCCCCC
Q 025586 60 DPELRSVLELATDSELYELERILFGPSYFS 89 (250)
Q Consensus 60 d~ELr~~LeLATdEEL~eL~~ILf~~r~fs 89 (250)
-|+..+||..|++|+|.+|++||+.-+-.+
T Consensus 3 ~D~DLeFL~~cs~edL~~L~~~Lt~dkdG~ 32 (35)
T PF13099_consen 3 YDSDLEFLAECSNEDLKDLVDILTHDKDGK 32 (35)
T ss_pred cCcchHHHHHCCHHHHHHHHHHHhcCCCCC
Confidence 367889999999999999999999655333
No 5
>PF03250 Tropomodulin: Tropomodulin; InterPro: IPR004934 Actin filaments have an intrinsic polarity, each with a fast-growing (barbed) end and a slow-growing (pointed) end. To regulate the dynamics at these ends, capping proteins have evolved that specifically bind to either the barbed or the pointed ends of the filament, where they block the association and dissociation of monomers. Pointed ends, for which actin monomers have significantly lower association and dissociation rate-constants than for barbed, are capped by either the Arp2/3 complex or tropomodulins []. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments []. Limited proteolysis shows this protein is composed of two domains. The unstructured tropomyosin-binding region at the N terminus has an actin pointed-end-capping activity that is dramatically up-regulated by tropomyosin coating of the actin filament[]. The second region is found near the C terminus. This tropomyosin-independent capping-domain caps pure actin. ; GO: 0005523 tropomyosin binding, 0005856 cytoskeleton
Probab=82.87 E-value=2 Score=37.34 Aligned_cols=31 Identities=45% Similarity=0.549 Sum_probs=27.1
Q ss_pred cCCCCCCchHHHHHHHhhChHHHHHHHHHhc
Q 025586 53 SKGQGAFDPELRSVLELATDSELYELERILF 83 (250)
Q Consensus 53 ~~~~~~~d~ELr~~LeLATdEEL~eL~~ILf 83 (250)
....-..++||.++|.-|||+||.+|+.||-
T Consensus 109 ~ee~v~ldpeleeaL~~Atd~El~dlAaILG 139 (147)
T PF03250_consen 109 KEEQVTLDPELEEALSNATDAELCDLAAILG 139 (147)
T ss_pred cccccccCHHHHHHHhcCcHHHHHHHHHHHh
Confidence 3445678899999999999999999999995
No 6
>PF03981 Ubiq_cyt_C_chap: Ubiquinol-cytochrome C chaperone ; InterPro: IPR021150 Saccharomyces cerevisiae ubiquinol-cytochrome C chaperone is required for assembly of coenzyme QF-2-cytochrome C reductase. It appears to be found in a number of different organisms including Homo sapiens, Caenorhabditis elegans and Rhizobium meliloti. This entry also contains bacterial proteins belonging to the UPF0174 family.
Probab=82.16 E-value=0.44 Score=38.20 Aligned_cols=51 Identities=18% Similarity=0.220 Sum_probs=41.6
Q ss_pred HHHHHHHHHhhhcccc-cchhccCCchHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCccccCC
Q 025586 116 FIASLESRFLFLAADA-RSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWENSE 194 (250)
Q Consensus 116 ~i~~IE~RfqfLAADs-~tvLRG~~vsYReVLl~VckkLKI~~s~klsT~dLEaEIFLhLL~~~ss~~~~~~~~aWekm~ 194 (250)
+.+.+++||++++... +...| |+..+ -+..++|++||.++.++ ++++|.
T Consensus 5 ~~dt~~~~f~~~~lh~~l~~~R----------------Lk~~~---~~~~~~~q~l~~~~~~d-----------~~~~l~ 54 (141)
T PF03981_consen 5 VPDTFAGRFQMLGLHVWLVLRR----------------LKAEG---KEGKELEQALFDKFFED-----------MDERLR 54 (141)
T ss_pred CccCHHHHHHHHHHHHHHHHHH----------------Hcccc---ccHHHHHHHHHHHHHHH-----------HHHHHH
Confidence 4578999999999988 45444 77766 45699999999999999 888887
Q ss_pred ch
Q 025586 195 AS 196 (250)
Q Consensus 195 ~~ 196 (250)
+.
T Consensus 55 ~~ 56 (141)
T PF03981_consen 55 EM 56 (141)
T ss_pred Hh
Confidence 66
No 7
>PF02173 pKID: pKID domain; InterPro: IPR003102 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB [].; GO: 0005515 protein binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1KDX_B.
Probab=60.87 E-value=6 Score=27.94 Aligned_cols=13 Identities=46% Similarity=0.810 Sum_probs=11.3
Q ss_pred CCchHHHHHHHHH
Q 025586 138 WRPSYRNVLLAVR 150 (250)
Q Consensus 138 ~~vsYReVLl~Vc 150 (250)
+|||||.||-++.
T Consensus 18 RRPSYRKIlndLs 30 (41)
T PF02173_consen 18 RRPSYRKILNDLS 30 (41)
T ss_dssp TSTHHHHHHHHHH
T ss_pred hCchHHHHHHHhc
Confidence 6999999998874
No 8
>TIGR00759 aceE pyruvate dehydrogenase E1 component, homodimeric type. WARNING: This family is classified as subfamily rather than equivalog because it includes a counterexample from Pseudomonas putida, MdeB, that is active as an E1 component of an alpha-ketoglutarate dehydrogenase complex rather than a pyruvate dehydrogase complex. The second pyruvate dehydrogenase complex E1 protein from Alcaligenes eutrophus, PdhE, complements an aceE mutant of E. coli but is not part of a pyruvate dehydrogenase complex operon, is more similar to the Pseudomonas putida MdeB than to E. coli AceE, and may have also have a different primary specificity.
Probab=51.23 E-value=1.1e+02 Score=33.45 Aligned_cols=23 Identities=9% Similarity=0.091 Sum_probs=15.9
Q ss_pred CCCchHHHHHHHhhChHHHHHHH
Q 025586 57 GAFDPELRSVLELATDSELYELE 79 (250)
Q Consensus 57 ~~~d~ELr~~LeLATdEEL~eL~ 79 (250)
.+...-|+..++.|.|.|.|.+.
T Consensus 301 ~d~~g~L~~~m~~~~dg~yq~~~ 323 (885)
T TIGR00759 301 RDTSGVLVKLMNETVDGDYQTYK 323 (885)
T ss_pred CCCccHHHHHHHhcccHHHHHHh
Confidence 34455677777777777777664
No 9
>cd01915 CODH Carbon monoxide dehydrogenase (CODH) is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA, respectively. CODH has two types of metal clusters, a cubane [Fe4-S4] center (B-cluster) similar to that of hybrid cluster protein (HCP) and a Ni-Fe-S center (C-cluster) where carbon monoxide oxidation occurs. Bifunctional CODH forms a heterotetramer with acetyl-CoA synthase (ACS) consisting of two CODH and two ACS subunits while monofunctional CODH forms a homodimer. Bifunctional CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide, CoA, and a methyl group donated by another protein (CoFeSP), while monofunctional CODH oxidizes carbon monoxide to carbon dioxide. CODH and ACS each have a metal cluster referred to as the C- and A-clusters, respectively.
Probab=49.44 E-value=61 Score=33.83 Aligned_cols=92 Identities=18% Similarity=0.158 Sum_probs=61.2
Q ss_pred CchHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCCc-----------cccCCchhhhhhhhhhhh
Q 025586 139 RPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGS-----------WENSEASDAQNSLELGLS 207 (250)
Q Consensus 139 ~vsYReVLl~VckkLKI~~s~klsT~dLEaEIFLhLL~~~ss~~~~~~~~a-----------Wekm~~~~~~~sl~~~~~ 207 (250)
.+.=.+=|..||++|+|+.+. -+..||=.|+=..+|++|.....+...+. |+++.-- ..++-
T Consensus 105 ~I~d~~KL~~~A~~~gi~t~g-~~~~eiA~~va~~~l~d~~~~~~~~~~~~~~~ap~~r~e~w~~lgi~------p~gi~ 177 (613)
T cd01915 105 EIKDEEKLKALAKRLGIDTEG-KSINEIAVEVAEIALEDFGRPREEPSRWVEAFAPEKRLELWEELGIL------PGGID 177 (613)
T ss_pred ccCCHHHHHHHHHHcCCCcCC-CCHHHHHHHHHHHHHHHhcCCCCcchhhHhhhCCHHHHHHHHHcCCC------ChHHH
Confidence 333348899999999999766 78899999999999999987654455554 6665433 11122
Q ss_pred hHHHHHhhhcccCc----hhhHHHHHhccceehH
Q 025586 208 QWKVQALAAFNAGA----VELKSMMLKGGGIYTL 237 (250)
Q Consensus 208 ~w~~~~la~~~lg~----~~~~~~~lKGgsalav 237 (250)
+--..++.....|. .|++...|+-|-+..+
T Consensus 178 ~ei~e~l~~t~~g~d~D~~~ll~~~Lr~Gla~~~ 211 (613)
T cd01915 178 SEIAEAMHRTHTGVDSDPVSLLLHSLRLGLAAGY 211 (613)
T ss_pred HHHHHHHHHHccCCCCCHHHHHHHHHHHhhhccH
Confidence 22236666666663 4555556666765544
No 10
>cd02642 R3H_encore_like R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=45.47 E-value=35 Score=24.71 Aligned_cols=44 Identities=23% Similarity=0.312 Sum_probs=36.3
Q ss_pred HHHHHHHHHHhhhcccc-cch--hccCCchHHHHHHHHHHhcCCCCC
Q 025586 115 DFIASLESRFLFLAADA-RST--LRGWRPSYRNVLLAVRKNLNIPCS 158 (250)
Q Consensus 115 ~~i~~IE~RfqfLAADs-~tv--LRG~~vsYReVLl~VckkLKI~~s 158 (250)
.|+-.||..|.=|..|+ ... |..-...+|.++-+||++.|....
T Consensus 3 ~~~l~~E~~i~~Fi~~~~~~~~~f~pm~sy~RllvH~la~~~gL~s~ 49 (63)
T cd02642 3 LFVLKLEKDLLAFIKDSTRQSLELPPMNSYYRLLAHRVAQYYGLDHN 49 (63)
T ss_pred hHHHHHHHHHHHHHhCCCCCeeEcCCCCcHHHHHHHHHHHHhCCeeE
Confidence 58899999999999998 444 445689999999999999886543
No 11
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=44.71 E-value=47 Score=25.16 Aligned_cols=44 Identities=30% Similarity=0.369 Sum_probs=34.5
Q ss_pred HHHHHHHHHH-----hhhcccc-cchhccC--------CchHHHHHHHHHHhcCCCCC
Q 025586 115 DFIASLESRF-----LFLAADA-RSTLRGW--------RPSYRNVLLAVRKNLNIPCS 158 (250)
Q Consensus 115 ~~i~~IE~Rf-----qfLAADs-~tvLRG~--------~vsYReVLl~VckkLKI~~s 158 (250)
.||++++.+| +.++.|- .+-|-|+ |+.=|+|=..||+-++||-+
T Consensus 5 eFw~~~~~~FG~~~~~~la~dhvL~~LGgrT~~eAL~~G~dpr~VW~AlC~~~dVP~~ 62 (63)
T PF11248_consen 5 EFWQLMEEEFGPAYGRSLARDHVLSELGGRTAAEALEAGVDPRDVWRALCDAFDVPEE 62 (63)
T ss_pred HHHHHHHHHhCchhHHHHHHhcchhhcCCcCHHHHHHcCCCHHHHHHHHHHHcCCCCC
Confidence 4889999888 4455555 3666554 89999999999999999965
No 12
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=44.35 E-value=41 Score=22.79 Aligned_cols=33 Identities=24% Similarity=0.384 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhh
Q 025586 142 YRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQE 177 (250)
Q Consensus 142 YReVLl~VckkLKI~~s~klsT~dLEaEIFLhLL~~ 177 (250)
|...+..+|.+. +......+|+-+|.|+.+++.
T Consensus 5 ~~~~l~~~~~~~---~~~~~~~eD~~qe~~~~l~~~ 37 (71)
T PF04542_consen 5 YYPLLYRYARRY---TGDPEDAEDLVQEAFIKLWRA 37 (71)
T ss_dssp THHHHHHHHHTC---TTCSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH---hCCHhhHHHHhhHHHHHHHhh
Confidence 677788888887 555579999999999999977
No 13
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=42.50 E-value=34 Score=26.91 Aligned_cols=36 Identities=17% Similarity=0.253 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhhhh
Q 025586 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (250)
Q Consensus 141 sYReVLl~VckkLKI~~s~klsT~dLEaEIFLhLL~~~s 179 (250)
.|+..|..+|.++.. ....-+||.+|+|+++++...
T Consensus 9 ~~~~~l~~~~~~~~~---~~~~aEDivQe~~l~l~~~~~ 44 (159)
T TIGR02989 9 RHQRSLRAFVRSLVP---DRDDADDVLQETFVTAWRKFD 44 (159)
T ss_pred HhHHHHHHHHHHHcC---ChhhHHHHHHHHHHHHHHHHH
Confidence 477888888888854 445679999999999998754
No 14
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=40.50 E-value=24 Score=27.76 Aligned_cols=20 Identities=25% Similarity=0.474 Sum_probs=18.9
Q ss_pred cCCchHHHHHHHHHHhcCCC
Q 025586 137 GWRPSYRNVLLAVRKNLNIP 156 (250)
Q Consensus 137 G~~vsYReVLl~VckkLKI~ 156 (250)
..+++|.++.-.|++|||++
T Consensus 18 p~~~~y~~L~~ki~~kLkl~ 37 (80)
T cd06406 18 ARGLSYATLLQKISSKLELP 37 (80)
T ss_pred CCCCCHHHHHHHHHHHhCCC
Confidence 57999999999999999998
No 15
>PF15008 DUF4518: Domain of unknown function (DUF4518)
Probab=39.14 E-value=75 Score=29.90 Aligned_cols=85 Identities=20% Similarity=0.287 Sum_probs=61.4
Q ss_pred hHHHHHHHhhChHHHHHHHHHhcCCCCCCccchhhcccCCcchHHHhhhhHHHHHHHHHHHHHHhhhcccccchhccCCc
Q 025586 61 PELRSVLELATDSELYELERILFGPSYFSPLLKSFTKRADVDYVMIEQDLEEREDFIASLESRFLFLAADARSTLRGWRP 140 (250)
Q Consensus 61 ~ELr~~LeLATdEEL~eL~~ILf~~r~fsPLlkS~~kr~~~Dy~~~~~~~~~R~~~i~~IE~RfqfLAADs~tvLRG~~v 140 (250)
..+|++|.+-++++|..|++.-|.+- ..| - +|+.=++. +.-+-.|+..+||.+ .
T Consensus 7 ~G~rdlL~~l~~~~LlaL~~TVTn~~-i~~----------e----------~~~EAi~a----IL~~s~~a~~LL~rk-k 60 (262)
T PF15008_consen 7 EGCRDLLGLLDNDDLLALADTVTNRL-IKP----------E----------SRQEAIDA----ILLYSQDAEELLRRK-K 60 (262)
T ss_pred HHHHHHHhcCChHHHHHHHHHHhcCc-eec----------C----------CHHHHHHH----HHHhCcCHHHHHhcc-c
Confidence 45899999999999999999999875 555 1 22222222 223445667777765 4
Q ss_pred hHHHHHHHHHHhcCCCCCCCCChHHHHHHHH
Q 025586 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIF 171 (250)
Q Consensus 141 sYReVLl~VckkLKI~~s~klsT~dLEaEIF 171 (250)
-+|+||..--..-+|..+...+-.+|=+.+.
T Consensus 61 V~RelLFkYLa~kgv~v~p~s~K~~LI~~~l 91 (262)
T PF15008_consen 61 VKRELLFKYLASKGVIVPPDSEKADLIQRVL 91 (262)
T ss_pred ccHHHHHHHHHHcCCCCCCCccHHHHHHHHH
Confidence 5899999999999999998888777654443
No 16
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=37.22 E-value=27 Score=29.77 Aligned_cols=33 Identities=24% Similarity=0.309 Sum_probs=25.8
Q ss_pred HHHHHHHhcCCCCC-----CCCChHHHHHHHHHHHHhh
Q 025586 145 VLLAVRKNLNIPCS-----SKLSTEDLEAEIFLHLLQE 177 (250)
Q Consensus 145 VLl~VckkLKI~~s-----~klsT~dLEaEIFLhLL~~ 177 (250)
-|-.+|++++|+.. ..++....-+++|++++++
T Consensus 151 ~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 151 VLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred cHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 48899999999853 2345566778999999987
No 17
>PF12616 DUF3775: Protein of unknown function (DUF3775); InterPro: IPR022254 This domain family is found in bacteria, and is approximately 80 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=33.77 E-value=95 Score=24.01 Aligned_cols=31 Identities=32% Similarity=0.502 Sum_probs=27.4
Q ss_pred chHHHHHHHhhChHHHHHHHHHhc-CCCCCCc
Q 025586 60 DPELRSVLELATDSELYELERILF-GPSYFSP 90 (250)
Q Consensus 60 d~ELr~~LeLATdEEL~eL~~ILf-~~r~fsP 90 (250)
-+||+.+++-.+++|..+|+.+.. ||-=|+|
T Consensus 3 ~~el~~~I~~l~~deqaeLvALmwiGRGd~~~ 34 (75)
T PF12616_consen 3 EEELRSFIEDLNEDEQAELVALMWIGRGDFEA 34 (75)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhcCCCCCH
Confidence 379999999999999999999998 7766666
No 18
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=31.91 E-value=61 Score=23.09 Aligned_cols=44 Identities=16% Similarity=0.208 Sum_probs=34.5
Q ss_pred HHHHHHHHhhhcccccchhcc--CCchHHHHHHHHHHhcCCCCCCC
Q 025586 117 IASLESRFLFLAADARSTLRG--WRPSYRNVLLAVRKNLNIPCSSK 160 (250)
Q Consensus 117 i~~IE~RfqfLAADs~tvLRG--~~vsYReVLl~VckkLKI~~s~k 160 (250)
|+.|+.+|+-|-+|....+.= =.+.-|.++-++|+.+++...+.
T Consensus 1 ~~~i~~~i~~F~~~~~~~~~fppm~~~~R~~vH~lA~~~~L~S~S~ 46 (58)
T cd02646 1 IEDIKDEIEAFLLDSRDSLSFPPMDKHGRKTIHKLANCYNLKSKSR 46 (58)
T ss_pred ChHHHHHHHHHHhCCCceEecCCCCHHHHHHHHHHHHHcCCccccc
Confidence 467899999999888544432 27888999999999999987653
No 19
>TIGR01702 CO_DH_cata carbon-monoxide dehydrogenase, catalytic subunit. This model represents the carbon-monoxide dehydrogenase catalytic subunit. This protein is related to prismane (also called hybrid cluster protein), a complex whose activity is not yet fully described; the two share similar sets of ligands to unusual metal-containing clusters.
Probab=29.81 E-value=1e+02 Score=32.42 Aligned_cols=50 Identities=22% Similarity=0.244 Sum_probs=36.6
Q ss_pred ccCCchHH----HHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhhhhccccCCCCC
Q 025586 136 RGWRPSYR----NVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPG 188 (250)
Q Consensus 136 RG~~vsYR----eVLl~VckkLKI~~s~klsT~dLEaEIFLhLL~~~ss~~~~~~~~ 188 (250)
+|+.+ |+ +=|..+++.++|+... -+. ||=.++=..+|+++.....++..+
T Consensus 101 ~g~~~-y~Ikd~~Kl~~~a~~~gI~te~-~~~-eia~~va~~~l~D~~~~~~~~~~~ 154 (621)
T TIGR01702 101 EGKTP-YSIKDEAKLKWLAKKLGIDTEG-DSN-ELAVEVAEIVLSDFRKPREEKAEL 154 (621)
T ss_pred cCCcc-cccccHHHHHHHHHHCCCCCCC-chH-HHHHHHHHHHHHHhccccccchhh
Confidence 35554 65 8899999999999866 334 898999999999987553334433
No 20
>PF02836 Glyco_hydro_2_C: Glycosyl hydrolases family 2, TIM barrel domain; InterPro: IPR006103 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. Beta-galactosidase from E. coli has a TIM-barrel-like core surrounded by four other largely beta domains [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3CMG_A 3FN9_C 1YQ2_A 3K4D_B 3LPG_B 3LPF_A 3K4A_B 3K46_B 3GM8_A 3DEC_A ....
Probab=28.85 E-value=41 Score=30.08 Aligned_cols=38 Identities=11% Similarity=0.132 Sum_probs=26.8
Q ss_pred HHHHHHHhhhcccccchhccCCchHHHHHHHHHHhcCC
Q 025586 118 ASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNLNI 155 (250)
Q Consensus 118 ~~IE~RfqfLAADs~tvLRG~~vsYReVLl~VckkLKI 155 (250)
+.++..++.+-.=++|.+|-+...+.+-.++.||++||
T Consensus 36 ~~~~~d~~l~k~~G~N~iR~~h~p~~~~~~~~cD~~Gi 73 (298)
T PF02836_consen 36 EAMERDLELMKEMGFNAIRTHHYPPSPRFYDLCDELGI 73 (298)
T ss_dssp HHHHHHHHHHHHTT-SEEEETTS--SHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHhcCcceEEcccccCcHHHHHHHhhcCC
Confidence 45666777776666899997666677888999999998
No 21
>PRK09405 aceE pyruvate dehydrogenase subunit E1; Reviewed
Probab=28.74 E-value=3.5e+02 Score=29.66 Aligned_cols=132 Identities=23% Similarity=0.347 Sum_probs=0.0
Q ss_pred chHHHHHHHhhChHHHHHHHHHhcCCCCCCccchhhcccCCcchHHHhhhhHHHHHHHHHHHHHHhhhcccc---cchhc
Q 025586 60 DPELRSVLELATDSELYELERILFGPSYFSPLLKSFTKRADVDYVMIEQDLEEREDFIASLESRFLFLAADA---RSTLR 136 (250)
Q Consensus 60 d~ELr~~LeLATdEEL~eL~~ILf~~r~fsPLlkS~~kr~~~Dy~~~~~~~~~R~~~i~~IE~RfqfLAADs---~tvLR 136 (250)
++|+.+.++-.|||||..| ++++-|+.. ..+.++.--..=+.=+ +.|++
T Consensus 344 ~~~~~~lv~~~sD~~i~~l------------------~~gGHD~~~----------i~~A~~~A~~~~~~PtvIia~Tvk 395 (891)
T PRK09405 344 YPETKALVADMSDDDIWAL------------------NRGGHDPRK----------VYAAYKAAVEHKGQPTVILAKTIK 395 (891)
T ss_pred CHHHHHHHhhCCHHHHHHh------------------ccCCCCHHH----------HHHHHHHHHhCCCCCEEEEEecee
Q ss_pred cCC---------------chHHHHHHHHHHhcCCCCCCCCChHHHHH-----------HHHHHHHhhhhccccCCCCCcc
Q 025586 137 GWR---------------PSYRNVLLAVRKNLNIPCSSKLSTEDLEA-----------EIFLHLLQEYASEESGVFPGSW 190 (250)
Q Consensus 137 G~~---------------vsYReVLl~VckkLKI~~s~klsT~dLEa-----------EIFLhLL~~~ss~~~~~~~~aW 190 (250)
|+| +.=.+-+.+.++++++| ++-+++|. | +..|.+
T Consensus 396 G~G~~~~~e~~~~~H~~~~l~~e~~~~~r~~~g~~----~~d~~~~~~~~~~~~~~s~e--~~~l~~------------- 456 (891)
T PRK09405 396 GYGMGEAGEGKNIAHQVKKLDLDDLKHFRDRFNIP----ISDEQLEKLPYYKPGEDSPE--IKYLHE------------- 456 (891)
T ss_pred cCCCCcccCCCccccCCCCCCHHHHHHHHHHcCCC----CChhHhccCCCcCCCCCCHH--HHHHHH-------------
Q ss_pred ccCCchhhhhhhhhhhhhHHHHHhhhcccCchhhHHHHHhccc------eehHHHHHHHHHh
Q 025586 191 ENSEASDAQNSLELGLSQWKVQALAAFNAGAVELKSMMLKGGG------IYTLVKIYQLVGE 246 (250)
Q Consensus 191 ekm~~~~~~~sl~~~~~~w~~~~la~~~lg~~~~~~~~lKGgs------alavssi~~~la~ 246 (250)
....|.--+.+=.... .+++++.......++||++ ..|...++..|+|
T Consensus 457 -------~r~~l~g~~p~r~~~~-~~~~~P~~~~~~~~~~~~~~~~~sT~~Afgr~L~~L~~ 510 (891)
T PRK09405 457 -------RRKALGGYLPARRPKF-EPLEVPALSAFEALLKGSGEREISTTMAFVRILNILLK 510 (891)
T ss_pred -------HHHHcCCCCCCCCCCC-CCCCCCChhhHHHhhccCCCCcccHHHHHHHHHHHHHh
No 22
>PF07176 DUF1400: Alpha/beta hydrolase of unknown function (DUF1400); InterPro: IPR010802 This domain is specific to cyanobacterial proteins, its function and the function of the proteins it is associated with, are uncharacterised.
Probab=28.01 E-value=78 Score=26.08 Aligned_cols=36 Identities=28% Similarity=0.421 Sum_probs=32.9
Q ss_pred CCCCCchHHHHHHHhhChHHHHHHHHHhcCCCCCCc
Q 025586 55 GQGAFDPELRSVLELATDSELYELERILFGPSYFSP 90 (250)
Q Consensus 55 ~~~~~d~ELr~~LeLATdEEL~eL~~ILf~~r~fsP 90 (250)
..|...+||+..+.+.+.++.++|-++|..+=.++|
T Consensus 26 ~tG~~~~~L~~~~~ll~~~~~~~lr~~L~~~~~~~~ 61 (127)
T PF07176_consen 26 ETGEISPELAFYLNLLSPQQRQQLRELLNTPIPIDP 61 (127)
T ss_pred HcCCCCHHHHHHHHhcCHhhHHHHHHHHcCCCCCCH
Confidence 467889999999999999999999999998887877
No 23
>KOG3708 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.77 E-value=55 Score=34.27 Aligned_cols=69 Identities=30% Similarity=0.407 Sum_probs=46.7
Q ss_pred ccCCcchHH-------Hhhh-hHHHHHHHHHHHHHHhhhcccccchhccCCchHHHHHHHHHHhcCCCCCCC-CChHHHH
Q 025586 97 KRADVDYVM-------IEQD-LEEREDFIASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNLNIPCSSK-LSTEDLE 167 (250)
Q Consensus 97 kr~~~Dy~~-------~~~~-~~~R~~~i~~IE~RfqfLAADs~tvLRG~~vsYReVLl~VckkLKI~~s~k-lsT~dLE 167 (250)
.-++.||+. .+.+ ++.|++. +.|+ -|++.||+.+|||--|.-|+ ++-+=+|+.. +|+++++
T Consensus 588 afY~~DYv~ARa~l~~~~q~~ee~r~~~-dv~d---~Fl~~~slHvlRaVEP~Lr~------ry~~r~c~ar~l~ee~~~ 657 (681)
T KOG3708|consen 588 AFYNVDYVAARARLAAASQQEEEERENL-DVID---AFLGFSSLHVLRAVEPTLRQ------RYHKRSCSARSLSEELYH 657 (681)
T ss_pred EEechHHHHHHHHhccccCchhhhcCCc-cHHH---HHhhcchhhhhhhcChhhhh------hhhhccCccccCCHHHHH
Confidence 344678887 1222 3344443 4454 38999999999998776654 4456688888 8999999
Q ss_pred HHHHHHHH
Q 025586 168 AEIFLHLL 175 (250)
Q Consensus 168 aEIFLhLL 175 (250)
...-.++-
T Consensus 658 RC~~s~~e 665 (681)
T KOG3708|consen 658 RCLDSKLE 665 (681)
T ss_pred HHHHHHhh
Confidence 87655543
No 24
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=25.97 E-value=79 Score=25.32 Aligned_cols=28 Identities=29% Similarity=0.443 Sum_probs=23.7
Q ss_pred hhhHHHHHhccceehHHHHHHHHHhhcCC
Q 025586 222 VELKSMMLKGGGIYTLVKIYQLVGELLSV 250 (250)
Q Consensus 222 ~~~~~~~lKGgsalavssi~~~la~~ls~ 250 (250)
++++++||++++ +|+..|++.|.++.+|
T Consensus 14 r~vL~~fl~~~~-~T~~di~e~L~~~f~v 41 (83)
T PF10826_consen 14 RAVLKLFLKGKK-FTTDDIYERLKEKFDV 41 (83)
T ss_pred HHHHHHHHhCCC-eeHHHHHHHHHHHcCc
Confidence 678999999875 8999999999988654
No 25
>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]
Probab=25.18 E-value=96 Score=28.15 Aligned_cols=39 Identities=15% Similarity=0.207 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHHHHhhhcccc-cchhccC--CchHHHHHHH
Q 025586 110 LEEREDFIASLESRFLFLAADA-RSTLRGW--RPSYRNVLLA 148 (250)
Q Consensus 110 ~~~R~~~i~~IE~RfqfLAADs-~tvLRG~--~vsYReVLl~ 148 (250)
.+||=.|++.|....+-=.|++ ..+|--- +..||+||..
T Consensus 63 D~DR~pWL~~i~~~~~~~l~~~q~vVlACSaLKk~YRdILr~ 104 (191)
T KOG3354|consen 63 DDDRWPWLKKIAVELRKALASGQGVVLACSALKKKYRDILRH 104 (191)
T ss_pred cccccHHHHHHHHHHHHHhhcCCeEEEEhHHHHHHHHHHHHh
Confidence 4566679999999998877777 3444432 7799999987
No 26
>PF08708 PriCT_1: Primase C terminal 1 (PriCT-1); InterPro: IPR014820 This alpha helical domain is found at the C-terminal of primases.
Probab=24.53 E-value=1.2e+02 Score=21.87 Aligned_cols=54 Identities=19% Similarity=0.279 Sum_probs=40.7
Q ss_pred hhhHHHHHHHHHHHHHHhhhcccccchhccCCchHHHHHHHHHHhcCCCCCCCCChHHHHH
Q 025586 108 QDLEEREDFIASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEA 168 (250)
Q Consensus 108 ~~~~~R~~~i~~IE~RfqfLAADs~tvLRG~~vsYReVLl~VckkLKI~~s~klsT~dLEa 168 (250)
+++-+|..++=.+..++.+-+.+--. ..++.+.+.|..++-.|+..|+-.|+++
T Consensus 7 ~~~g~RN~~lf~~a~~~~~~~v~~~~-------~~~~~v~~~~~~~N~~~~~PL~~~Ev~~ 60 (71)
T PF08708_consen 7 IVEGGRNCTLFRLARRLAYRGVDQEE-------QFRQEVLSLAQAINSNFSPPLPESEVKA 60 (71)
T ss_pred CCCCCcHHHHHHHHHHHHHhCCCHhH-------HHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence 34556777777777666666555433 7788899999999999999999888875
No 27
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=23.94 E-value=1.5e+02 Score=23.21 Aligned_cols=35 Identities=20% Similarity=0.264 Sum_probs=27.5
Q ss_pred hHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhhhh
Q 025586 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (250)
Q Consensus 141 sYReVLl~VckkLKI~~s~klsT~dLEaEIFLhLL~~~s 179 (250)
.|...+..+|.+++. .-..+|+=+|.|+.+.+...
T Consensus 12 ~y~~~l~~~~~~~~~----~~~aeDi~Qe~~l~l~~~~~ 46 (154)
T PRK06759 12 LYEGLIVNQIKKLGI----YQDYEEYYQCGLIGLWHAYE 46 (154)
T ss_pred HHHHHHHHHHHHhCC----cccHHHHHHHHHHHHHHHHH
Confidence 477888889988743 23679999999999997754
No 28
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=23.71 E-value=75 Score=26.22 Aligned_cols=36 Identities=22% Similarity=0.260 Sum_probs=27.4
Q ss_pred hHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhhhh
Q 025586 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (250)
Q Consensus 141 sYReVLl~VckkLKI~~s~klsT~dLEaEIFLhLL~~~s 179 (250)
.|+..|..+|.+.- ......+|+=+|+|+.+++...
T Consensus 34 ~y~~~l~~~~~~~~---~~~~daeDlvQe~fi~l~~~~~ 69 (194)
T PRK12513 34 RHRTGLYRFLLRLA---RDRALAEDIFQETWLRVIRARA 69 (194)
T ss_pred HHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHH
Confidence 57777777777763 3445789999999999998744
No 29
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=23.68 E-value=1.2e+02 Score=24.04 Aligned_cols=20 Identities=25% Similarity=0.406 Sum_probs=10.3
Q ss_pred HHHHhhChHHHHHHHHHhcC
Q 025586 65 SVLELATDSELYELERILFG 84 (250)
Q Consensus 65 ~~LeLATdEEL~eL~~ILf~ 84 (250)
.++.+-+.||.++|-+-|..
T Consensus 9 ~i~~l~~~ee~~~f~~dL~T 28 (87)
T PF01371_consen 9 AILSLKDEEECYDFFEDLCT 28 (87)
T ss_dssp HHHCHHCHHCHHHHHHHHSS
T ss_pred HHHHcCCHHHHHHHHHHhCC
Confidence 34445555555555555543
No 30
>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....
Probab=22.85 E-value=61 Score=23.21 Aligned_cols=17 Identities=18% Similarity=0.260 Sum_probs=14.4
Q ss_pred chHHHHHHHHHHhcCCC
Q 025586 140 PSYRNVLLAVRKNLNIP 156 (250)
Q Consensus 140 vsYReVLl~VckkLKI~ 156 (250)
-+=++++-.||++|+|.
T Consensus 17 ~t~~~l~~~v~~~l~l~ 33 (80)
T PF09379_consen 17 TTGQDLLEQVCDKLGLK 33 (80)
T ss_dssp SBHHHHHHHHHHHHTTS
T ss_pred CcHHHHHHHHHHHcCCC
Confidence 34589999999999996
No 31
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=22.68 E-value=2.2e+02 Score=20.53 Aligned_cols=43 Identities=12% Similarity=0.247 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHHHHhhhcccccchhccCCchHHHHHHHHHHhc
Q 025586 110 LEEREDFIASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNL 153 (250)
Q Consensus 110 ~~~R~~~i~~IE~RfqfLAADs~tvLRG~~vsYReVLl~VckkL 153 (250)
...++..|+.|..+|-=++.- .-....++.-|+++...+.+++
T Consensus 34 ~~~k~~~W~~I~~~lN~~~~~-~Rs~~~lkkkW~nlk~~~Kk~~ 76 (78)
T PF13873_consen 34 NKEKRKAWEEIAEELNALGPG-KRSWKQLKKKWKNLKSKAKKKL 76 (78)
T ss_pred HHHHHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHHHHHHHh
Confidence 566778889999999877763 3333345677788777777664
No 32
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.32 E-value=1e+02 Score=24.14 Aligned_cols=31 Identities=29% Similarity=0.482 Sum_probs=24.1
Q ss_pred CCCchHHHHHHHhhChHHHHHHHHHhcCCCCCCc
Q 025586 57 GAFDPELRSVLELATDSELYELERILFGPSYFSP 90 (250)
Q Consensus 57 ~~~d~ELr~~LeLATdEEL~eL~~ILf~~r~fsP 90 (250)
|.+++|- +..+..|||-++++..-.+..|||
T Consensus 26 gvl~~e~---~d~~~~edLtdiy~mvkkkenfSp 56 (71)
T COG4840 26 GVLDPEK---YDNANYEDLTDIYDMVKKKENFSP 56 (71)
T ss_pred hccCHHh---cccccHHHHHHHHHHHHHhccCCH
Confidence 4444443 356788999999999999999999
No 33
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=22.25 E-value=1.2e+02 Score=25.45 Aligned_cols=36 Identities=14% Similarity=0.141 Sum_probs=26.1
Q ss_pred hHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhhhh
Q 025586 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (250)
Q Consensus 141 sYReVLl~VckkLKI~~s~klsT~dLEaEIFLhLL~~~s 179 (250)
.|+..|..+|.++- ......+|+=+|+|+.+.+...
T Consensus 35 ~y~~~l~~~~~~~~---~~~~~AeDlvQEvfl~l~~~~~ 70 (192)
T PRK09643 35 RHHRRLWAVARRTS---GTREDAADALQDAMLSAHRAAG 70 (192)
T ss_pred HHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHHHH
Confidence 46677777776653 3455679999999999986643
No 34
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=22.10 E-value=59 Score=24.33 Aligned_cols=20 Identities=20% Similarity=0.218 Sum_probs=14.8
Q ss_pred CchHHHHHHHHHHhcCCCCC
Q 025586 139 RPSYRNVLLAVRKNLNIPCS 158 (250)
Q Consensus 139 ~vsYReVLl~VckkLKI~~s 158 (250)
.-+-.+||.++|+|+|++-+
T Consensus 16 ~~~l~~VL~eac~k~~l~~~ 35 (65)
T PF11470_consen 16 NTTLNQVLEEACKKFGLDPS 35 (65)
T ss_dssp TSBHHHHHHHHHHHTT--GG
T ss_pred CCCHHHHHHHHHHHcCCCcc
Confidence 34567999999999998754
No 35
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=22.05 E-value=1.4e+02 Score=26.02 Aligned_cols=36 Identities=25% Similarity=0.326 Sum_probs=29.1
Q ss_pred chHHHHHHHHHHhcCCCCCCCCChHHHH--HHHHHHHHhh
Q 025586 140 PSYRNVLLAVRKNLNIPCSSKLSTEDLE--AEIFLHLLQE 177 (250)
Q Consensus 140 vsYReVLl~VckkLKI~~s~klsT~dLE--aEIFLhLL~~ 177 (250)
.+|| |-.+|++++|++...-.-.|-+ ++||++++..
T Consensus 131 ~~~~--L~~La~~~gi~~~~HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 131 ANLK--LQTVADFLGIKGRGHNSLEDARMTARVYESFLES 168 (195)
T ss_pred CCCC--HHHHHHhcCCCCCCcCCHHHHHHHHHHHHHHHhh
Confidence 4566 8999999999987766666655 8999999977
No 36
>cd00014 CH Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
Probab=21.69 E-value=1.7e+02 Score=21.53 Aligned_cols=26 Identities=27% Similarity=0.442 Sum_probs=21.3
Q ss_pred hHHHHHHHHHHhcCCCCCCCCChHHHH
Q 025586 141 SYRNVLLAVRKNLNIPCSSKLSTEDLE 167 (250)
Q Consensus 141 sYReVLl~VckkLKI~~s~klsT~dLE 167 (250)
.--+..+++|+++|||.. ..+++||-
T Consensus 62 ~Ni~~~l~~~~~~gi~~~-~~~~~Dl~ 87 (107)
T cd00014 62 ENINLALNFAEKLGVPVV-NFDAEDLV 87 (107)
T ss_pred HHHHHHHHHHHHcCCcee-ccCHHHHh
Confidence 344678899999999987 78999986
No 37
>KOG2805 consensus tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=20.53 E-value=79 Score=31.26 Aligned_cols=33 Identities=30% Similarity=0.413 Sum_probs=29.2
Q ss_pred HHHHHhcCCCCCCCCChHHHHHHHHHHHHhhhh
Q 025586 147 LAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (250)
Q Consensus 147 l~VckkLKI~~s~klsT~dLEaEIFLhLL~~~s 179 (250)
-.||++|+||+.+--=+.|-=..+|..+|++|.
T Consensus 60 ~~Vc~~LnI~~~~Vnf~kEYW~~Vfs~~L~~Y~ 92 (377)
T KOG2805|consen 60 KRVCKQLNIPLHQVNFVKEYWNDVFSPFLEEYE 92 (377)
T ss_pred HHHHHHhCCeeEEEeeHHHHHHHHHHHHHHHHh
Confidence 469999999999887788888889999999987
No 38
>PRK14082 hypothetical protein; Provisional
Probab=20.48 E-value=78 Score=24.37 Aligned_cols=16 Identities=31% Similarity=0.640 Sum_probs=14.4
Q ss_pred ChHHHHHHHHHHHHhh
Q 025586 162 STEDLEAEIFLHLLQE 177 (250)
Q Consensus 162 sT~dLEaEIFLhLL~~ 177 (250)
--+|||+||=++++++
T Consensus 33 eREDLeQElk~Ki~eK 48 (65)
T PRK14082 33 EREDLEQELKIKIIEK 48 (65)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 4689999999999987
Done!