Query 031135
Match_columns 165
No_of_seqs 130 out of 307
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 09:44:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031135.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031135hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2240 RNA polymerase II gene 100.0 6.4E-54 1.4E-58 343.7 8.1 156 1-159 6-162 (162)
2 PF01849 NAC: NAC domain; Int 99.8 1.8E-21 3.9E-26 131.9 4.4 57 36-92 1-58 (58)
3 KOG2239 Transcription factor c 99.4 1.6E-12 3.5E-17 108.1 9.1 62 33-94 63-125 (209)
4 PRK06369 nac nascent polypepti 99.1 8.5E-11 1.8E-15 90.5 5.9 60 34-94 5-68 (115)
5 TIGR00264 alpha-NAC-related pr 97.7 8.3E-05 1.8E-09 57.6 6.1 57 37-93 12-71 (116)
6 COG1308 EGD2 Transcription fac 96.5 0.0036 7.8E-08 49.0 4.2 41 34-74 6-48 (122)
7 PF10411 DsbC_N: Disulfide bon 43.7 41 0.0009 22.2 3.6 33 47-88 18-50 (57)
8 PRK10877 protein disulfide iso 43.3 59 0.0013 27.2 5.2 46 33-88 20-72 (232)
9 PF08680 DUF1779: Protein of u 41.4 52 0.0011 26.8 4.5 53 36-88 131-197 (203)
10 PF10512 Borealin: Cell divisi 38.4 29 0.00063 26.7 2.4 45 77-121 64-110 (116)
11 PRK06049 rpl30p 50S ribosomal 32.7 47 0.001 26.8 2.9 54 35-98 14-68 (154)
12 PF03471 CorC_HlyC: Transporte 28.9 71 0.0015 22.0 3.0 36 77-112 3-38 (81)
13 cd04437 DEP_Epac DEP (Dishevel 28.1 45 0.00099 26.0 2.1 46 58-110 73-119 (125)
14 PF03958 Secretin_N: Bacterial 27.2 77 0.0017 21.3 2.9 23 68-90 43-65 (82)
15 PHA00669 hypothetical protein 26.0 78 0.0017 24.7 3.0 28 41-68 42-70 (114)
16 PF15588 Imm7: Immunity protei 22.9 1.6E+02 0.0035 22.2 4.2 53 47-101 62-114 (115)
17 PF08154 NLE: NLE (NUC135) dom 22.7 1.2E+02 0.0027 20.5 3.2 36 66-101 4-39 (65)
18 cd07981 TAF12 TATA Binding Pro 22.7 1E+02 0.0022 21.3 2.9 30 91-120 5-36 (72)
19 TIGR01310 L7 60S ribosomal pro 22.5 75 0.0016 27.4 2.5 53 36-98 87-140 (235)
20 PF05481 Myco_19_kDa: Mycobact 22.1 1.7E+02 0.0036 23.9 4.3 39 52-90 96-139 (160)
21 PF01873 eIF-5_eIF-2B: Domain 22.0 1.1E+02 0.0023 23.7 3.1 30 73-102 61-91 (125)
22 cd01657 Ribosomal_L7_archeal_e 21.9 76 0.0016 25.5 2.3 53 35-97 13-66 (159)
No 1
>KOG2240 consensus RNA polymerase II general transcription factor BTF3 and related proteins [Transcription]
Probab=100.00 E-value=6.4e-54 Score=343.73 Aligned_cols=156 Identities=59% Similarity=0.923 Sum_probs=143.2
Q ss_pred CCHHHHHHHhhccccCCCCccceecccccCCCCcccHHHHHHHhhhCCccCCCccceeeeecC-EEEEeeCCeeeeeecC
Q 031135 1 MNVEKLMKMAGAVRTGGKGSVRRKKKAVHKTTTTDDKRLQSTLKRIGVNAIPAIEEVNIFKDD-VVIQFLNPKVQASIAA 79 (165)
Q Consensus 1 m~~eKL~kl~~~~r~GGkGt~RRKkK~v~k~a~~dDKKlq~~LkKLg~~~I~gIeEVnmfk~d-~vihF~nPkVqaS~~a 79 (165)
|+++||++++..+|||||||+|||++++|++++.||||||+.|+||+|++|+||+||||||++ +||||++|+||+|+++
T Consensus 6 ~~~~kl~k~~a~~r~ggkGt~rrkk~~~~~~~~~ddkKlqs~lkkl~v~~i~~i~evn~~k~~g~Vihf~~~~vqasl~~ 85 (162)
T KOG2240|consen 6 ENLAKLQKLQAVVRIGGKGTARRKKKVVHKTATADDKKLQSSLKKLGVNNIPGIEEVNMFKNDGTVIHFNNPKVQASLAA 85 (162)
T ss_pred hhHHHHhhhhheeeecCCCccccccCCCCCCCCcccchhhhhhhhhccccccchhHhhhccccceeEecCCccccccccC
Confidence 467888888999999999999999999999999999999999999999999999999999999 9999999999999999
Q ss_pred CeEEEecccccchhhhhhhhhhhccchhhHHHHHHHHHHHHhhCCCCCCCCCCCCCCCCCCcccCCCCCChhHHhhcccc
Q 031135 80 NTWVVSGAPQTKKLQDILPGIINQLGPDNLDNLRKLAEQFQKQAPNAGTGAPTTQEDDDDEVPELVAGETFEAAAEEKTE 159 (165)
Q Consensus 80 NTfvV~G~~~~K~lte~lP~Il~QLG~d~l~~L~~lae~~~~~~~~~~~~~~~~~~~ddddVPdLV~genFde~sk~e~~ 159 (165)
|||+||||+++|+|+||||+||+|||++++++||+||++++.+.....+. .+....+||+||+|| |||+++++++++
T Consensus 86 nTf~ItG~~~~k~l~EmlPsilsqLg~~sl~~Lr~La~~l~~~~~~~~~~-~~~~~~~dd~~p~Lv--enf~~~~~~~~~ 162 (162)
T KOG2240|consen 86 NTFTITGHAETKQLTEMLPSILSQLGPDSLTALRRLAEQLPKQDGKEGAD-AATIEDDDDDVPELV--ENFDEAAKNEAN 162 (162)
T ss_pred CeEEEecCCcccchhhhcchhhhhcChhhHHHHHHHHHhcccccccCCCC-ccchhhcccchHHHH--HhHHHHhhhccC
Confidence 99999999999999999999999999999999999999998776555422 223345699999999 799999998764
No 2
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=99.84 E-value=1.8e-21 Score=131.88 Aligned_cols=57 Identities=49% Similarity=0.750 Sum_probs=47.6
Q ss_pred cHHHHHHHhhhCCccCCCccceeeeecC-EEEEeeCCeeeeeecCCeEEEecccccch
Q 031135 36 DKRLQSTLKRIGVNAIPAIEEVNIFKDD-VVIQFLNPKVQASIAANTWVVSGAPQTKK 92 (165)
Q Consensus 36 DKKlq~~LkKLg~~~I~gIeEVnmfk~d-~vihF~nPkVqaS~~aNTfvV~G~~~~K~ 92 (165)
|||+|.+|+|||+++|+||+||+|+++| ++|||+||+||+++++|||+|||++++++
T Consensus 1 ekk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~~~~P~V~~~~~~~tyvV~G~~~~~~ 58 (58)
T PF01849_consen 1 EKKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFVFNNPEVQKSPGSNTYVVFGEAEEED 58 (58)
T ss_dssp -------GHHCT-EEETTEEEEEEEETTTEEEEEESEEEEEETTCCEEEEESEEEEEE
T ss_pred CHHHHHHHHHcCCcccCCcEEEEEEECCceEEEEcCCeEEEcCCCCEEEEEeeeEEcC
Confidence 6899999999999999999999999999 99999999999999999999999999874
No 3
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=99.39 E-value=1.6e-12 Score=108.06 Aligned_cols=62 Identities=19% Similarity=0.463 Sum_probs=59.3
Q ss_pred CcccHHHHHHHhhhCCccCCCccceeeeecC-EEEEeeCCeeeeeecCCeEEEecccccchhh
Q 031135 33 TTDDKRLQSTLKRIGVNAIPAIEEVNIFKDD-VVIQFLNPKVQASIAANTWVVSGAPQTKKLQ 94 (165)
Q Consensus 33 ~~dDKKlq~~LkKLg~~~I~gIeEVnmfk~d-~vihF~nPkVqaS~~aNTfvV~G~~~~K~lt 94 (165)
+..+||.|.++.|||+++|+||.+|+|+|.. .+|.+++|.||.|++++||||||++...+|+
T Consensus 63 srsekKark~m~KLGlk~v~gV~RVti~ksKNilfvI~kPdVyKsp~sdtYiiFGeakiedls 125 (209)
T KOG2239|consen 63 SRSEKKARKAMLKLGLKQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIIFGEAKIEDLS 125 (209)
T ss_pred chHHHHHHHHHHhcCCccccceeEEEEEecccEEEEecCCceeccCCCceEEEecccccchhH
Confidence 4689999999999999999999999999988 9999999999999999999999999998887
No 4
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=99.13 E-value=8.5e-11 Score=90.48 Aligned_cols=60 Identities=25% Similarity=0.506 Sum_probs=55.9
Q ss_pred cccHHHHHHHhhhCCc--cCCCccceeeeecCEEEEeeCCeee--eeecCCeEEEecccccchhh
Q 031135 34 TDDKRLQSTLKRIGVN--AIPAIEEVNIFKDDVVIQFLNPKVQ--ASIAANTWVVSGAPQTKKLQ 94 (165)
Q Consensus 34 ~dDKKlq~~LkKLg~~--~I~gIeEVnmfk~d~vihF~nPkVq--aS~~aNTfvV~G~~~~K~lt 94 (165)
-+.||++..++|||++ +| ||++|+|.+.+..|.|++|.|+ .++.++||+|||.+++.+++
T Consensus 5 ~nprk~rkmmkkmGik~e~i-~v~~V~Ir~~~~~~Vi~~P~V~~m~~~g~~tY~I~Ge~~~e~~~ 68 (115)
T PRK06369 5 MNPRKMKQMMKQMGIDVEEL-DVEEVIIRLKDKEIVFENPQVTVMDAQGQKTYQIVGEPEEVEKE 68 (115)
T ss_pred CCHHHHHHHHHHcCCcchhc-CeEEEEEEeCCEEEEEcCCeEEEEecCCCcEEEEEeccEEeecc
Confidence 4779999999999999 99 9999999998888999999999 79999999999999998755
No 5
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=97.74 E-value=8.3e-05 Score=57.61 Aligned_cols=57 Identities=35% Similarity=0.557 Sum_probs=46.0
Q ss_pred HHHHHHHhhhCCccC-CCccceeeeecCEEEEeeCCeeee--eecCCeEEEecccccchh
Q 031135 37 KRLQSTLKRIGVNAI-PAIEEVNIFKDDVVIQFLNPKVQA--SIAANTWVVSGAPQTKKL 93 (165)
Q Consensus 37 KKlq~~LkKLg~~~I-~gIeEVnmfk~d~vihF~nPkVqa--S~~aNTfvV~G~~~~K~l 93 (165)
|+++..|++||++.. .+|++|.|.+.+.-|.|++|.|.. ....-||.|+|.++++++
T Consensus 12 ~~mkkmMk~MGi~~~eidV~~ViIk~~~k~ivf~~p~V~~m~~~G~~tYqI~G~~~~~~~ 71 (116)
T TIGR00264 12 KQMQKMMKQMGMEMEDLDVEEVIIVFDDEEWIFENPKVQVMDILGVKTYQITGKPKKEKV 71 (116)
T ss_pred HHHHHHHHHcCCCccccccEEEEEEeCCceEEEecCeeEEEecCCcEEEEEecccEEeec
Confidence 489999999997765 449999999988444599997754 467789999999998754
No 6
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=96.51 E-value=0.0036 Score=48.96 Aligned_cols=41 Identities=27% Similarity=0.456 Sum_probs=36.1
Q ss_pred cccHHHHHHHhhhC--CccCCCccceeeeecCEEEEeeCCeee
Q 031135 34 TDDKRLQSTLKRIG--VNAIPAIEEVNIFKDDVVIQFLNPKVQ 74 (165)
Q Consensus 34 ~dDKKlq~~LkKLg--~~~I~gIeEVnmfk~d~vihF~nPkVq 74 (165)
.+-++|+..++.|| +..|+||++|.|...|+.|.|++|.|+
T Consensus 6 mnpr~l~k~mkqmGi~~eeld~v~~V~i~~kd~e~vi~~P~V~ 48 (122)
T COG1308 6 MNPRKLKKLMKQMGIDVEELDGVERVIIKLKDTEYVIENPQVT 48 (122)
T ss_pred CCHHHHHHHHHHhCCCceeccCceEEEEEcCCceEEeeCCcEE
Confidence 35678889999997 999999999999998855999999997
No 7
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=43.68 E-value=41 Score=22.24 Aligned_cols=33 Identities=18% Similarity=0.337 Sum_probs=21.3
Q ss_pred CCccCCCccceeeeecCEEEEeeCCeeeeeecCCeEEEeccc
Q 031135 47 GVNAIPAIEEVNIFKDDVVIQFLNPKVQASIAANTWVVSGAP 88 (165)
Q Consensus 47 g~~~I~gIeEVnmfk~d~vihF~nPkVqaS~~aNTfvV~G~~ 88 (165)
...+|+|+=||.+ +++.+++.+ ....|+|.|+-
T Consensus 18 ~~spi~GlyeV~~-~~~~i~Y~~--------~dg~yli~G~l 50 (57)
T PF10411_consen 18 SPSPIPGLYEVVL-KGGGILYVD--------EDGRYLIQGQL 50 (57)
T ss_dssp EE-SSTTEEEEEE--TTEEEEEE--------TTSSEEEES-E
T ss_pred EcCCCCCeEEEEE-CCCeEEEEc--------CCCCEEEEeEE
Confidence 4568999999998 555655432 35688998863
No 8
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=43.30 E-value=59 Score=27.16 Aligned_cols=46 Identities=20% Similarity=0.437 Sum_probs=29.2
Q ss_pred CcccHHHHHHHhhhCC-------ccCCCccceeeeecCEEEEeeCCeeeeeecCCeEEEeccc
Q 031135 33 TTDDKRLQSTLKRIGV-------NAIPAIEEVNIFKDDVVIQFLNPKVQASIAANTWVVSGAP 88 (165)
Q Consensus 33 ~~dDKKlq~~LkKLg~-------~~I~gIeEVnmfk~d~vihF~nPkVqaS~~aNTfvV~G~~ 88 (165)
.+++..++..|.++|+ .||+|+-||.+ ++.++.+ . ....|+|.|+-
T Consensus 20 ~a~~~~~~~~l~~~~~~v~~v~~sp~~Gl~ev~~--~~~i~Y~-~-------~dg~y~i~G~l 72 (232)
T PRK10877 20 HADDAAIQQTLAKLGIQSADIQPSPVAGMKTVLT--ESGVLYI-T-------DDGKHIIQGPM 72 (232)
T ss_pred ccCHHHHHHHHHHcCCceeEEccCCCCCeEEEEE--CCeEEEE-c-------CCCCEEEeeee
Confidence 4466788888887644 57889999865 2343332 2 24567777753
No 9
>PF08680 DUF1779: Protein of unknown function (DUF1779); InterPro: IPR014794 This entry represents uncharacterised proteins. The structure of the YwmB protein from Bacillus subtilis has shown it to adopt an alpha/beta fold. ; PDB: 2FPN_A.
Probab=41.44 E-value=52 Score=26.77 Aligned_cols=53 Identities=23% Similarity=0.395 Sum_probs=25.7
Q ss_pred cHHHHHHHhhhCCccCCCccceeeee-----cC--EEEEeeC--CeeeeeecCC-----eEEEeccc
Q 031135 36 DKRLQSTLKRIGVNAIPAIEEVNIFK-----DD--VVIQFLN--PKVQASIAAN-----TWVVSGAP 88 (165)
Q Consensus 36 DKKlq~~LkKLg~~~I~gIeEVnmfk-----~d--~vihF~n--PkVqaS~~aN-----TfvV~G~~ 88 (165)
.+++...|++|++++|..+.+-+++- .. ..|.... --||.++..+ ||++-|.|
T Consensus 131 ~~~~~~~l~~l~A~~vE~~~~~~~vSvsaYt~~~~~~i~~~~~k~NlqiAlr~~~~~~~T~I~iGTP 197 (203)
T PF08680_consen 131 EKIAERLLKKLGAKPVESLKDENFVSVSAYTPKWDDSIQTGGKKMNLQIALRYNSYGGKTYITIGTP 197 (203)
T ss_dssp HHHHHHHHHHH---------BTTEEEEEE--TTSS--EEETTEEE-EEEEEE--------EEEEESS
T ss_pred HHHHHHHHHHcCCcEeeEEecccEEEEEEEccchhhhhhcCCeEEEEEEEEEecCCCCCEEEEEEec
Confidence 56788899999999999999988842 22 1222221 2367777666 99999976
No 10
>PF10512 Borealin: Cell division cycle-associated protein 8 ; InterPro: IPR018867 The chromosomal passenger complex of Aurora B kinase, INCENP, and Survivin has essential regulatory roles at centromeres and the central spindle in mitosis. Cell division cycle-associated protein 8, also known as Borealin, is also a member of the complex. Approximately half of Aurora B in mitotic cells is complexed with INCENP, Borealin, and Survivin. Depletion of Borealin by RNA interference delays mitotic progression and results in kinetochore-spindle mis-attachments and an increase in bipolar spindles associated with ectopic asters []. ; PDB: 2KDD_A.
Probab=38.45 E-value=29 Score=26.74 Aligned_cols=45 Identities=27% Similarity=0.402 Sum_probs=29.1
Q ss_pred ecCCeEEEecccccchh--hhhhhhhhhccchhhHHHHHHHHHHHHh
Q 031135 77 IAANTWVVSGAPQTKKL--QDILPGIINQLGPDNLDNLRKLAEQFQK 121 (165)
Q Consensus 77 ~~aNTfvV~G~~~~K~l--te~lP~Il~QLG~d~l~~L~~lae~~~~ 121 (165)
.-+|..|=.|..+...| .|+=+..|.||.+|.|.+|+.|-..|..
T Consensus 64 ~~~~vnIPl~~G~~~~l~~~dl~~~~l~~Ld~~tl~~ik~L~~~L~~ 110 (116)
T PF10512_consen 64 EDANVNIPLGNGKPIRLLASDLDREDLEQLDPETLNQIKTLQANLQK 110 (116)
T ss_dssp -S-EE---SSSSS---EETTT--HHHHHTS-HHHHHHHHHHHHHHHH
T ss_pred CCccEEEecCCCeEEEcchhhcCHHHHHhcCHHHHHHHHHHHHHHHH
Confidence 34566666777788888 8888899999999999999999888754
No 11
>PRK06049 rpl30p 50S ribosomal protein L30P; Reviewed
Probab=32.75 E-value=47 Score=26.76 Aligned_cols=54 Identities=17% Similarity=0.295 Sum_probs=41.2
Q ss_pred ccHHHHHHHhhhCCccCCCccceeeeecCEEEEeeCCeeeeeec-CCeEEEecccccchhhhhhh
Q 031135 35 DDKRLQSTLKRIGVNAIPAIEEVNIFKDDVVIQFLNPKVQASIA-ANTWVVSGAPQTKKLQDILP 98 (165)
Q Consensus 35 dDKKlq~~LkKLg~~~I~gIeEVnmfk~d~vihF~nPkVqaS~~-aNTfvV~G~~~~K~lte~lP 98 (165)
-.++.+.+|+.||+..|.- .|++=.+|-+..-+. ..-||..|++..+.+.+|+=
T Consensus 14 ~~~~~r~tL~~LgL~ki~~----------~V~v~~tp~~~GML~kV~~~V~~ge~~~~tv~~Li~ 68 (154)
T PRK06049 14 VPRDIADTLKMLRLHRVNH----------CVLVPETPSYKGMLQKVKDYVTWGEIDADTLAELLR 68 (154)
T ss_pred CCHHHHHHHHHcCCCcCCC----------EEEEeCCHHHHHHHHhhhceeEEeeCchHHHHHHHH
Confidence 3468899999999987754 666666776555443 56899999999999998863
No 12
>PF03471 CorC_HlyC: Transporter associated domain; InterPro: IPR005170 This small domain is found in a family of proteins with the CBS IPR002550 from INTERPRO domain and two CBS domains with this domain found at the C terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates.; PDB: 3DED_F 2PLI_C 2R2Z_A 2P4P_A 2O3G_A 2P3H_A 3LLB_A 3LAE_A 2P13_B 2NQW_A ....
Probab=28.86 E-value=71 Score=21.98 Aligned_cols=36 Identities=25% Similarity=0.382 Sum_probs=25.8
Q ss_pred ecCCeEEEecccccchhhhhhhhhhhccchhhHHHH
Q 031135 77 IAANTWVVSGAPQTKKLQDILPGIINQLGPDNLDNL 112 (165)
Q Consensus 77 ~~aNTfvV~G~~~~K~lte~lP~Il~QLG~d~l~~L 112 (165)
...|+|+|+|....++|.+.|.-=|+.-..+.+..+
T Consensus 3 ~~~~~~~v~G~~~l~~l~~~~~~~l~~~~~~Tl~G~ 38 (81)
T PF03471_consen 3 LDDGTYIVSGSTPLDDLNELLGLDLPEEDYDTLGGL 38 (81)
T ss_dssp ETTSEEEEETTSBHHHHHHHHTS-TTTTTTSBHHHH
T ss_pred EcCCEEEEEecCCHHHHHHHHCcCCCccchhhHHHH
Confidence 357999999999999999998654544334445544
No 13
>cd04437 DEP_Epac DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in Epac-like proteins. Epac (exchange proteins directly activated by cAMP) proteins are GEFs (guanine-nucleotide-exchange factors) for the small GTPases, Rap1 and Rap2. They are directly regulated by cyclic AMP, a second messenger that plays a role in the control of diverse cellular processes, such as cell adhesion and insulin secretion. Epac-like proteins share a common domain architecture, containing RasGEF, DEP and CAP-effector (cAMP binding) domains. The DEP domain is involved in membrane localization.
Probab=28.13 E-value=45 Score=25.98 Aligned_cols=46 Identities=24% Similarity=0.419 Sum_probs=29.8
Q ss_pred eeeecC-EEEEeeCCeeeeeecCCeEEEecccccchhhhhhhhhhhccchhhHH
Q 031135 58 NIFKDD-VVIQFLNPKVQASIAANTWVVSGAPQTKKLQDILPGIINQLGPDNLD 110 (165)
Q Consensus 58 nmfk~d-~vihF~nPkVqaS~~aNTfvV~G~~~~K~lte~lP~Il~QLG~d~l~ 110 (165)
.-|+|+ ..+.|....-... .+ ....-+.++++-+ .+|.|||||.+-
T Consensus 73 h~F~D~~~fYrF~~d~~~~~----~~--~~~~~eee~~~~v-~~l~q~~p~~~~ 119 (125)
T cd04437 73 LHFQDKYQFYRFSDDECSPA----PL--EKREAEEELQEAV-TLLSQLGPDALL 119 (125)
T ss_pred CccccCCeeEEECCccCCcc----cc--hhhhhHHHHHHHH-HHHHhhCcHHHH
Confidence 468888 7888987743211 11 3344445677765 789999999753
No 14
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=27.22 E-value=77 Score=21.26 Aligned_cols=23 Identities=22% Similarity=0.382 Sum_probs=18.7
Q ss_pred eeCCeeeeeecCCeEEEeccccc
Q 031135 68 FLNPKVQASIAANTWVVSGAPQT 90 (165)
Q Consensus 68 F~nPkVqaS~~aNTfvV~G~~~~ 90 (165)
..++.|.+...+|+.+|+|.++.
T Consensus 43 ~~~~~i~~d~~tNsliv~g~~~~ 65 (82)
T PF03958_consen 43 SSSGRIVADERTNSLIVRGTPED 65 (82)
T ss_dssp HTTTEEEEECTTTEEEEEEEHHH
T ss_pred CCCeEEEEECCCCEEEEEeCHHH
Confidence 45667888899999999997655
No 15
>PHA00669 hypothetical protein
Probab=25.97 E-value=78 Score=24.67 Aligned_cols=28 Identities=32% Similarity=0.635 Sum_probs=23.1
Q ss_pred HHHhhhCCccCCCccceeeeecC-EEEEe
Q 031135 41 STLKRIGVNAIPAIEEVNIFKDD-VVIQF 68 (165)
Q Consensus 41 ~~LkKLg~~~I~gIeEVnmfk~d-~vihF 68 (165)
.+|.|||+..+|.|-++-|+... .|-..
T Consensus 42 etL~kLg~~~lp~VG~~v~l~arA~V~s~ 70 (114)
T PHA00669 42 EALERLGIDALPAVGSVVMITARAVVCSV 70 (114)
T ss_pred HHHHHcCCCCCccCCCeEEEEEEEEEEee
Confidence 58999999999999999998776 55443
No 16
>PF15588 Imm7: Immunity protein 7
Probab=22.87 E-value=1.6e+02 Score=22.16 Aligned_cols=53 Identities=21% Similarity=0.282 Sum_probs=32.3
Q ss_pred CCccCCCccceeeeecCEEEEeeCCeeeeeecCCeEEEecccccchhhhhhhhhh
Q 031135 47 GVNAIPAIEEVNIFKDDVVIQFLNPKVQASIAANTWVVSGAPQTKKLQDILPGII 101 (165)
Q Consensus 47 g~~~I~gIeEVnmfk~d~vihF~nPkVqaS~~aNTfvV~G~~~~K~lte~lP~Il 101 (165)
|..-..||++|.+..+..+|+|+... ...+.-....|.=.. .+.|.++|..||
T Consensus 62 ~~~~Yg~i~~v~L~~~~l~~~~~~~~-~~~l~~~~v~i~~~~-~~~l~~~l~~il 114 (115)
T PF15588_consen 62 GYSCYGGIEKVELTRDLLVFEFDPDA-AIDLGLEEVKIDFNI-IQYLRQILQDIL 114 (115)
T ss_pred CCceeccEEEEEEeCCEEEEEECccc-ceecccceEEEEhHH-HHHHHHHHHHHh
Confidence 44567899999998887888887664 234444444443322 445555555554
No 17
>PF08154 NLE: NLE (NUC135) domain; InterPro: IPR012972 This domain is located N-terminal to WD40 repeats(IPR001680 from INTERPRO). It is found in the microtubule-associated protein Q12024 from SWISSPROT [].
Probab=22.71 E-value=1.2e+02 Score=20.46 Aligned_cols=36 Identities=14% Similarity=0.315 Sum_probs=27.1
Q ss_pred EEeeCCeeeeeecCCeEEEecccccchhhhhhhhhh
Q 031135 66 IQFLNPKVQASIAANTWVVSGAPQTKKLQDILPGII 101 (165)
Q Consensus 66 ihF~nPkVqaS~~aNTfvV~G~~~~K~lte~lP~Il 101 (165)
++|....=.-.+...+|.|-+....++|++|+-.+|
T Consensus 4 v~F~t~~~~~~~~~~~~~VP~~~t~~~Ls~LvN~LL 39 (65)
T PF08154_consen 4 VQFVTEDGEYEVPGTPISVPSNITRKELSELVNQLL 39 (65)
T ss_pred EEEEcCCCCccCCCCCEEEeCCCCHHHHHHHHHHHh
Confidence 455544333345688999999999999999887776
No 18
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=22.68 E-value=1e+02 Score=21.26 Aligned_cols=30 Identities=40% Similarity=0.568 Sum_probs=25.0
Q ss_pred chhhhhhhhhhh--ccchhhHHHHHHHHHHHH
Q 031135 91 KKLQDILPGIIN--QLGPDNLDNLRKLAEQFQ 120 (165)
Q Consensus 91 K~lte~lP~Il~--QLG~d~l~~L~~lae~~~ 120 (165)
..|++|++.|-+ .++++....|..+++.|-
T Consensus 5 ~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv 36 (72)
T cd07981 5 RKLQELLKEIDPREQLDPDVEELLLEIADDFV 36 (72)
T ss_pred HHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHH
Confidence 468888888876 688999999999999873
No 19
>TIGR01310 L7 60S ribosomal protein L7, eukaryotic. Members of this family average ~ 250 residues in length, somewhat longer than the archaeal L30P/L7E homolog (~ 155 residues) and much longer than the related bacterial/organellar form (~ 60 residues).
Probab=22.50 E-value=75 Score=27.38 Aligned_cols=53 Identities=13% Similarity=0.274 Sum_probs=33.7
Q ss_pred cHHHHHHHhhhCCccCCCccceeeeecCEEEEeeCCeeeeee-cCCeEEEecccccchhhhhhh
Q 031135 36 DKRLQSTLKRIGVNAIPAIEEVNIFKDDVVIQFLNPKVQASI-AANTWVVSGAPQTKKLQDILP 98 (165)
Q Consensus 36 DKKlq~~LkKLg~~~I~gIeEVnmfk~d~vihF~nPkVqaS~-~aNTfvV~G~~~~K~lte~lP 98 (165)
-.+++.+|+.|++..|-. ..|.+ .+|....-+ -...||++|.+..+.+.+|+-
T Consensus 87 ~p~v~k~L~lLRL~~in~---~Vfvk-------~~~~~~~ML~~VepYVt~G~p~l~tvr~Li~ 140 (235)
T TIGR01310 87 PPKPRKVLRLLRLKQVHN---GVFVK-------VNKATLQMLRIVEPYVAYGYPNLKSVRELIY 140 (235)
T ss_pred CHHHHHHHHHhCCCccce---EEEEE-------CCHHHHHHHHhcCCeEEEecCCHHHHHHHHH
Confidence 467888888888776643 23332 233221111 146799999999999988763
No 20
>PF05481 Myco_19_kDa: Mycobacterium 19 kDa lipoprotein antigen; InterPro: IPR008691 Most of the antigens of Mycobacterium leprae and Mycobacterium tuberculosis that have been identified are members of stress protein families, which are highly conserved throughout many diverse species. Of the M. leprae and M. tuberculosis antigens identified by monoclonal antibodies, all except the 18 kDa M. leprae antigen and the 19 kDa M. tuberculosis antigen are strongly cross-reactive between these two species and are coded within very similar genes [, ].; GO: 0016020 membrane
Probab=22.13 E-value=1.7e+02 Score=23.85 Aligned_cols=39 Identities=21% Similarity=0.393 Sum_probs=25.1
Q ss_pred CCccceeeeecC-EEEEeeC--C--eeeeeecCCeEEEeccccc
Q 031135 52 PAIEEVNIFKDD-VVIQFLN--P--KVQASIAANTWVVSGAPQT 90 (165)
Q Consensus 52 ~gIeEVnmfk~d-~vihF~n--P--kVqaS~~aNTfvV~G~~~~ 90 (165)
|-++-|.|---+ .-+-|.. | ...+....|||.|+|.+.-
T Consensus 96 p~V~sV~i~~v~G~tl~y~~g~~~g~A~vtkdG~tYtItGtA~G 139 (160)
T PF05481_consen 96 PTVESVGIGNVDGFTLGYSEGVGGGSATVTKDGNTYTITGTATG 139 (160)
T ss_pred ceEEEEEeEccCCeEEEEeCCCCCCceEEEeCCCEEEEEEEEEe
Confidence 445666664333 3344443 2 4667788999999999873
No 21
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=22.00 E-value=1.1e+02 Score=23.74 Aligned_cols=30 Identities=30% Similarity=0.510 Sum_probs=24.9
Q ss_pred eeeeecC-CeEEEecccccchhhhhhhhhhh
Q 031135 73 VQASIAA-NTWVVSGAPQTKKLQDILPGIIN 102 (165)
Q Consensus 73 VqaS~~a-NTfvV~G~~~~K~lte~lP~Il~ 102 (165)
+++++.. +.|+|.|....+.|+++|-..+.
T Consensus 61 t~~~id~~~~lii~G~~~~~~i~~~L~~fI~ 91 (125)
T PF01873_consen 61 TQGSIDGKGRLIINGRFSSKQIQDLLDKFIK 91 (125)
T ss_dssp SEEEEETTTEEEEESSSSCCHHHHHHHHHHC
T ss_pred CceEECCCCEEEEEEecCHHHHHHHHHHHHH
Confidence 5666666 99999999999999999876654
No 22
>cd01657 Ribosomal_L7_archeal_euk Ribosomal protein L7, which is found in archaea and eukaryotes but not in prokaryotes, binds domain II of the 23S rRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L7 members have an N-terminal extension not found in the archeal L7 orthologs. L7 is closely related to the ribosomal L30 protein found in eukaryotes and prokaryotes.
Probab=21.88 E-value=76 Score=25.48 Aligned_cols=53 Identities=17% Similarity=0.326 Sum_probs=38.8
Q ss_pred ccHHHHHHHhhhCCccCCCccceeeeecCEEEEeeCCeeeeeec-CCeEEEecccccchhhhhh
Q 031135 35 DDKRLQSTLKRIGVNAIPAIEEVNIFKDDVVIQFLNPKVQASIA-ANTWVVSGAPQTKKLQDIL 97 (165)
Q Consensus 35 dDKKlq~~LkKLg~~~I~gIeEVnmfk~d~vihF~nPkVqaS~~-aNTfvV~G~~~~K~lte~l 97 (165)
-.++.+.+|+.||++.+.- .|++=++|.+..-+. -.-||..|++..+.+.+|+
T Consensus 13 ~~~~~r~tL~~LgL~k~~~----------~v~~~~t~~~~gmL~kV~~~V~~ge~~~~tv~~Li 66 (159)
T cd01657 13 VPPKIRKTLQLLRLRRINN----------AVFVKLTKATIGMLKKVEPYVTWGEPNLETLRELI 66 (159)
T ss_pred CCHHHHHHHHHcCCCcCCC----------EEEEeCCHHHHHHHHHhhhheEeccCcHHHHHHHH
Confidence 3468999999999987654 556656665444332 4579999999999888875
Done!