Query 031690
Match_columns 155
No_of_seqs 128 out of 291
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:00:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031690.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031690hhsearch_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 2.9E-52 6.2E-57 331.3 7.3 145 2-149 17-162 (162)
2 PF01849 NAC: NAC domain; Int 99.8 1.4E-21 3.1E-26 131.2 4.3 57 26-82 1-58 (58)
3 KOG2239 Transcription factor c 99.4 4.9E-13 1.1E-17 110.2 4.9 62 23-84 63-125 (209)
4 PRK06369 nac nascent polypepti 99.1 1.2E-10 2.6E-15 88.9 5.9 60 24-84 5-68 (115)
5 TIGR00264 alpha-NAC-related pr 97.8 6.9E-05 1.5E-09 57.5 5.9 57 27-83 12-71 (116)
6 COG1308 EGD2 Transcription fac 96.5 0.0036 7.8E-08 48.5 4.1 41 24-64 6-48 (122)
7 PF10512 Borealin: Cell divisi 41.8 25 0.00055 26.8 2.6 45 67-111 64-110 (116)
8 PF08680 DUF1779: Protein of u 40.8 57 0.0012 26.2 4.6 53 26-78 131-197 (203)
9 PRK06049 rpl30p 50S ribosomal 35.9 39 0.00084 27.0 2.9 54 25-88 14-68 (154)
10 PF03958 Secretin_N: Bacterial 34.3 50 0.0011 22.0 2.9 23 58-80 43-65 (82)
11 PRK10877 protein disulfide iso 30.4 1.2E+02 0.0027 24.9 5.1 46 22-77 19-71 (232)
12 cd04437 DEP_Epac DEP (Dishevel 29.8 41 0.00089 26.0 2.0 47 47-100 72-119 (125)
13 cd07981 TAF12 TATA Binding Pro 29.4 66 0.0014 22.0 2.8 30 81-110 5-36 (72)
14 PF10411 DsbC_N: Disulfide bon 29.2 97 0.0021 20.2 3.5 33 37-78 18-50 (57)
15 PHA00669 hypothetical protein 25.9 79 0.0017 24.4 2.9 27 31-57 42-69 (114)
16 cd01657 Ribosomal_L7_archeal_e 24.4 63 0.0014 25.7 2.3 54 25-88 13-67 (159)
17 TIGR01310 L7 60S ribosomal pro 23.4 69 0.0015 27.3 2.5 52 27-88 88-140 (235)
18 TIGR01309 L30P_arch 50S riboso 22.6 65 0.0014 25.7 2.0 54 25-88 12-66 (152)
19 cd08871 START_STARD10-like Lip 22.2 3.5E+02 0.0075 21.6 6.2 68 40-112 138-206 (222)
20 PF08154 NLE: NLE (NUC135) dom 22.2 1.3E+02 0.0027 20.2 3.1 37 55-91 3-39 (65)
21 PF03471 CorC_HlyC: Transporte 21.2 1.2E+02 0.0026 20.6 3.0 36 67-102 3-38 (81)
22 PF00280 potato_inhibit: Potat 21.0 50 0.0011 22.6 1.0 23 130-153 3-26 (63)
23 PF01873 eIF-5_eIF-2B: Domain 20.9 1.1E+02 0.0024 23.4 3.0 30 63-92 61-91 (125)
No 1
>KOG2240 consensus RNA polymerase II general transcription factor BTF3 and related proteins [Transcription]
Probab=100.00 E-value=2.9e-52 Score=331.31 Aligned_cols=145 Identities=57% Similarity=0.862 Sum_probs=134.2
Q ss_pred ccccccCCccccccccccCCCCcccHHHHHHHhhhCCccCCCccceeeeecC-EEEEeeCCeeeeeecCCeEEEeccccc
Q 031690 2 VNSFLTLALNHRKKKAVHKTTTTDDKRLQSTLKRIGVNAIPAIEEVNIFKDD-VVIQFLNPKVQASIAANTWVVSGAPQT 80 (155)
Q Consensus 2 ~~~~ggKGt~RRKkK~v~k~~~~DDKKLq~~LkKLg~~~I~gIeEVnmfk~d-~vihF~nPkVqaS~~aNT~vv~G~~e~ 80 (155)
|+|||||||+|||++++|++++.||||||..|+||+|++|+||+||||||++ +||||++|+||+|+++|||+||||+++
T Consensus 17 ~~r~ggkGt~rrkk~~~~~~~~~ddkKlqs~lkkl~v~~i~~i~evn~~k~~g~Vihf~~~~vqasl~~nTf~ItG~~~~ 96 (162)
T KOG2240|consen 17 VVRIGGKGTARRKKKVVHKTATADDKKLQSSLKKLGVNNIPGIEEVNMFKNDGTVIHFNNPKVQASLAANTFTITGHAET 96 (162)
T ss_pred eeeecCCCccccccCCCCCCCCcccchhhhhhhhhccccccchhHhhhccccceeEecCCccccccccCCeEEEecCCcc
Confidence 7999999999999999999999999999999999999999999999999999 999999999999999999999999999
Q ss_pred chhhhhhhhhhhccchhhHHHHHHHHHHHHhhCCCCCCCCCCCCCCCCCCcccCCCCCChhHHhhcccc
Q 031690 81 KKLQDILPGIINQLGPDNLDNLRKLAEQFQKQAPNAGTGAPTTQEDDDDEVPELVAGETFEAAAEEKTE 149 (155)
Q Consensus 81 K~l~ellP~Il~QLG~d~l~~L~~lae~~~~~~~~~~~~~~~~~~~ddddVPdLV~genFee~sk~e~~ 149 (155)
|+|+||||+||+|||+++|++||+||++++.+.....+.. +....+||+||+|| |||+++++++++
T Consensus 97 k~l~EmlPsilsqLg~~sl~~Lr~La~~l~~~~~~~~~~~-~~~~~~dd~~p~Lv--enf~~~~~~~~~ 162 (162)
T KOG2240|consen 97 KQLTEMLPSILSQLGPDSLTALRRLAEQLPKQDGKEGADA-ATIEDDDDDVPELV--ENFDEAAKNEAN 162 (162)
T ss_pred cchhhhcchhhhhcChhhHHHHHHHHHhcccccccCCCCc-cchhhcccchHHHH--HhHHHHhhhccC
Confidence 9999999999999999999999999999988765555322 33345699999999 799999998763
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=1.4e-21 Score=131.17 Aligned_cols=57 Identities=49% Similarity=0.750 Sum_probs=47.6
Q ss_pred cHHHHHHHhhhCCccCCCccceeeeecC-EEEEeeCCeeeeeecCCeEEEecccccch
Q 031690 26 DKRLQSTLKRIGVNAIPAIEEVNIFKDD-VVIQFLNPKVQASIAANTWVVSGAPQTKK 82 (155)
Q Consensus 26 DKKLq~~LkKLg~~~I~gIeEVnmfk~d-~vihF~nPkVqaS~~aNT~vv~G~~e~K~ 82 (155)
|||+|.+|+|||+++|+||+||+|+++| ++|||+||+||+++++|||+|||++++++
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 99999999999999999999999999864
No 3
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=99.37 E-value=4.9e-13 Score=110.18 Aligned_cols=62 Identities=19% Similarity=0.463 Sum_probs=59.3
Q ss_pred CcccHHHHHHHhhhCCccCCCccceeeeecC-EEEEeeCCeeeeeecCCeEEEecccccchhh
Q 031690 23 TTDDKRLQSTLKRIGVNAIPAIEEVNIFKDD-VVIQFLNPKVQASIAANTWVVSGAPQTKKLQ 84 (155)
Q Consensus 23 ~~DDKKLq~~LkKLg~~~I~gIeEVnmfk~d-~vihF~nPkVqaS~~aNT~vv~G~~e~K~l~ 84 (155)
+..+||.|.++.|||+++|+||.+|+|+|.. ..|.+++|.||.|++++||+|||.+...+++
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 5789999999999999999999999999998 9999999999999999999999999987776
No 4
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=99.12 E-value=1.2e-10 Score=88.87 Aligned_cols=60 Identities=25% Similarity=0.506 Sum_probs=55.9
Q ss_pred cccHHHHHHHhhhCCc--cCCCccceeeeecCEEEEeeCCeee--eeecCCeEEEecccccchhh
Q 031690 24 TDDKRLQSTLKRIGVN--AIPAIEEVNIFKDDVVIQFLNPKVQ--ASIAANTWVVSGAPQTKKLQ 84 (155)
Q Consensus 24 ~DDKKLq~~LkKLg~~--~I~gIeEVnmfk~d~vihF~nPkVq--aS~~aNT~vv~G~~e~K~l~ 84 (155)
-+.||++.+++|||++ .| ||++|.|.+.+..|.|++|.|+ .++.++||+|+|.+++.+++
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 4789999999999999 99 9999999999999999999999 79999999999999998654
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=97.76 E-value=6.9e-05 Score=57.52 Aligned_cols=57 Identities=35% Similarity=0.557 Sum_probs=46.1
Q ss_pred HHHHHHHhhhCCccC-CCccceeeeecCEEEEeeCCeeee--eecCCeEEEecccccchh
Q 031690 27 KRLQSTLKRIGVNAI-PAIEEVNIFKDDVVIQFLNPKVQA--SIAANTWVVSGAPQTKKL 83 (155)
Q Consensus 27 KKLq~~LkKLg~~~I-~gIeEVnmfk~d~vihF~nPkVqa--S~~aNT~vv~G~~e~K~l 83 (155)
|+++..|+++|++.. .+|+||.|.+++.-|.|++|.|+. +...-||.|+|.++++.+
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 499999999997654 449999999988444499997754 567889999999998754
No 6
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=96.51 E-value=0.0036 Score=48.55 Aligned_cols=41 Identities=27% Similarity=0.456 Sum_probs=36.4
Q ss_pred cccHHHHHHHhhhC--CccCCCccceeeeecCEEEEeeCCeee
Q 031690 24 TDDKRLQSTLKRIG--VNAIPAIEEVNIFKDDVVIQFLNPKVQ 64 (155)
Q Consensus 24 ~DDKKLq~~LkKLg--~~~I~gIeEVnmfk~d~vihF~nPkVq 64 (155)
.+-++|+..++.|| +..|+||++|.|...|+.|.|++|.|+
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 46678889999997 999999999999999955999999987
No 7
>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=41.78 E-value=25 Score=26.80 Aligned_cols=45 Identities=27% Similarity=0.402 Sum_probs=29.4
Q ss_pred ecCCeEEEecccccchh--hhhhhhhhhccchhhHHHHHHHHHHHHh
Q 031690 67 IAANTWVVSGAPQTKKL--QDILPGIINQLGPDNLDNLRKLAEQFQK 111 (155)
Q Consensus 67 ~~aNT~vv~G~~e~K~l--~ellP~Il~QLG~d~l~~L~~lae~~~~ 111 (155)
.-+|..|=.|..+...| .|+=+..|.||.++.|.+|+.|-..|..
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 44566666788888888 8988999999999999999999988754
No 8
>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=40.76 E-value=57 Score=26.23 Aligned_cols=53 Identities=23% Similarity=0.395 Sum_probs=25.4
Q ss_pred cHHHHHHHhhhCCccCCCccceeeee-----cC--EEEEeeC--CeeeeeecCC-----eEEEeccc
Q 031690 26 DKRLQSTLKRIGVNAIPAIEEVNIFK-----DD--VVIQFLN--PKVQASIAAN-----TWVVSGAP 78 (155)
Q Consensus 26 DKKLq~~LkKLg~~~I~gIeEVnmfk-----~d--~vihF~n--PkVqaS~~aN-----T~vv~G~~ 78 (155)
.+++...|++|++++|..+++-+++- .. ..|.-.. --||.++..+ ||++-|.|
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 11 1222221 2367777666 99998877
No 9
>PRK06049 rpl30p 50S ribosomal protein L30P; Reviewed
Probab=35.95 E-value=39 Score=26.97 Aligned_cols=54 Identities=17% Similarity=0.295 Sum_probs=40.9
Q ss_pred ccHHHHHHHhhhCCccCCCccceeeeecCEEEEeeCCeeeeeec-CCeEEEecccccchhhhhhh
Q 031690 25 DDKRLQSTLKRIGVNAIPAIEEVNIFKDDVVIQFLNPKVQASIA-ANTWVVSGAPQTKKLQDILP 88 (155)
Q Consensus 25 DDKKLq~~LkKLg~~~I~gIeEVnmfk~d~vihF~nPkVqaS~~-aNT~vv~G~~e~K~l~ellP 88 (155)
-..+.+.+|+.||+..|.- .|++=.+|-++.-+. ..-||..|++..+.+.+|+=
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 3477889999999987754 566666666554433 56899999999999999863
No 10
>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=34.30 E-value=50 Score=21.96 Aligned_cols=23 Identities=22% Similarity=0.382 Sum_probs=19.1
Q ss_pred eeCCeeeeeecCCeEEEeccccc
Q 031690 58 FLNPKVQASIAANTWVVSGAPQT 80 (155)
Q Consensus 58 F~nPkVqaS~~aNT~vv~G~~e~ 80 (155)
..+..|.+-..+|+.+|+|.++.
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 45667888899999999998765
No 11
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=30.35 E-value=1.2e+02 Score=24.95 Aligned_cols=46 Identities=20% Similarity=0.517 Sum_probs=29.1
Q ss_pred CCcccHHHHHHHhhhCC-------ccCCCccceeeeecCEEEEeeCCeeeeeecCCeEEEecc
Q 031690 22 TTTDDKRLQSTLKRIGV-------NAIPAIEEVNIFKDDVVIQFLNPKVQASIAANTWVVSGA 77 (155)
Q Consensus 22 ~~~DDKKLq~~LkKLg~-------~~I~gIeEVnmfk~d~vihF~nPkVqaS~~aNT~vv~G~ 77 (155)
+.+++..++..|.++++ .+|+|+-||.+ +..++ |..+ ...|+|.|+
T Consensus 19 a~a~~~~~~~~l~~~~~~v~~v~~sp~~Gl~ev~~--~~~i~-Y~~~-------dg~y~i~G~ 71 (232)
T PRK10877 19 AHADDAAIQQTLAKLGIQSADIQPSPVAGMKTVLT--ESGVL-YITD-------DGKHIIQGP 71 (232)
T ss_pred cccCHHHHHHHHHHcCCceeEEccCCCCCeEEEEE--CCeEE-EEcC-------CCCEEEeee
Confidence 44567888888888654 56888888865 22433 2223 345777774
No 12
>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=29.76 E-value=41 Score=25.97 Aligned_cols=47 Identities=23% Similarity=0.368 Sum_probs=30.3
Q ss_pred eeeeecC-EEEEeeCCeeeeeecCCeEEEecccccchhhhhhhhhhhccchhhHH
Q 031690 47 VNIFKDD-VVIQFLNPKVQASIAANTWVVSGAPQTKKLQDILPGIINQLGPDNLD 100 (155)
Q Consensus 47 Vnmfk~d-~vihF~nPkVqaS~~aNT~vv~G~~e~K~l~ellP~Il~QLG~d~l~ 100 (155)
=.-|+|+ ..+.|....-.. +......-+..+++-+ .+|+|||||.+-
T Consensus 72 ~h~F~D~~~fYrF~~d~~~~------~~~~~~~~eee~~~~v-~~l~q~~p~~~~ 119 (125)
T cd04437 72 ELHFQDKYQFYRFSDDECSP------APLEKREAEEELQEAV-TLLSQLGPDALL 119 (125)
T ss_pred cCccccCCeeEEECCccCCc------ccchhhhhHHHHHHHH-HHHHhhCcHHHH
Confidence 3468888 889998774221 1113344445666655 789999999753
No 13
>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=29.45 E-value=66 Score=22.04 Aligned_cols=30 Identities=40% Similarity=0.568 Sum_probs=25.4
Q ss_pred chhhhhhhhhhh--ccchhhHHHHHHHHHHHH
Q 031690 81 KKLQDILPGIIN--QLGPDNLDNLRKLAEQFQ 110 (155)
Q Consensus 81 K~l~ellP~Il~--QLG~d~l~~L~~lae~~~ 110 (155)
..|++|+..|-+ +++++....|..+++.|-
T Consensus 5 ~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv 36 (72)
T cd07981 5 RKLQELLKEIDPREQLDPDVEELLLEIADDFV 36 (72)
T ss_pred HHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHH
Confidence 478899988876 688999999999999873
No 14
>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=29.18 E-value=97 Score=20.23 Aligned_cols=33 Identities=18% Similarity=0.337 Sum_probs=20.5
Q ss_pred CCccCCCccceeeeecCEEEEeeCCeeeeeecCCeEEEeccc
Q 031690 37 GVNAIPAIEEVNIFKDDVVIQFLNPKVQASIAANTWVVSGAP 78 (155)
Q Consensus 37 g~~~I~gIeEVnmfk~d~vihF~nPkVqaS~~aNT~vv~G~~ 78 (155)
...+++|+=||.+ ++..++..+ ....|+|.|+-
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 4467899999988 454555433 34578888863
No 15
>PHA00669 hypothetical protein
Probab=25.85 E-value=79 Score=24.44 Aligned_cols=27 Identities=33% Similarity=0.657 Sum_probs=22.7
Q ss_pred HHHhhhCCccCCCccceeeeecC-EEEE
Q 031690 31 STLKRIGVNAIPAIEEVNIFKDD-VVIQ 57 (155)
Q Consensus 31 ~~LkKLg~~~I~gIeEVnmfk~d-~vih 57 (155)
.+|.|||+..+|+|-++-|+... .|--
T Consensus 42 etL~kLg~~~lp~VG~~v~l~arA~V~s 69 (114)
T PHA00669 42 EALERLGIDALPAVGSVVMITARAVVCS 69 (114)
T ss_pred HHHHHcCCCCCccCCCeEEEEEEEEEEe
Confidence 58999999999999999998776 5544
No 16
>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=24.36 E-value=63 Score=25.67 Aligned_cols=54 Identities=17% Similarity=0.301 Sum_probs=38.8
Q ss_pred ccHHHHHHHhhhCCccCCCccceeeeecCEEEEeeCCeeeeeec-CCeEEEecccccchhhhhhh
Q 031690 25 DDKRLQSTLKRIGVNAIPAIEEVNIFKDDVVIQFLNPKVQASIA-ANTWVVSGAPQTKKLQDILP 88 (155)
Q Consensus 25 DDKKLq~~LkKLg~~~I~gIeEVnmfk~d~vihF~nPkVqaS~~-aNT~vv~G~~e~K~l~ellP 88 (155)
-.++.+.+|+.||++.+.- .|++=.+|.+..-+. ..-||..|++..+.+.+|+-
T Consensus 13 ~~~~~r~tL~~LgL~k~~~----------~v~~~~t~~~~gmL~kV~~~V~~ge~~~~tv~~Li~ 67 (159)
T cd01657 13 VPPKIRKTLQLLRLRRINN----------AVFVKLTKATIGMLKKVEPYVTWGEPNLETLRELIY 67 (159)
T ss_pred CCHHHHHHHHHcCCCcCCC----------EEEEeCCHHHHHHHHHhhhheEeccCcHHHHHHHHH
Confidence 3477899999999987754 555555565443332 45799999999999888753
No 17
>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=23.45 E-value=69 Score=27.31 Aligned_cols=52 Identities=13% Similarity=0.284 Sum_probs=33.4
Q ss_pred HHHHHHHhhhCCccCCCccceeeeecCEEEEeeCCeeeeee-cCCeEEEecccccchhhhhhh
Q 031690 27 KRLQSTLKRIGVNAIPAIEEVNIFKDDVVIQFLNPKVQASI-AANTWVVSGAPQTKKLQDILP 88 (155)
Q Consensus 27 KKLq~~LkKLg~~~I~gIeEVnmfk~d~vihF~nPkVqaS~-~aNT~vv~G~~e~K~l~ellP 88 (155)
.+.+.+|+.|++..|.. ..|.+ .+|....-+ -..-||.+|.+..+.+.+|+-
T Consensus 88 p~v~k~L~lLRL~~in~---~Vfvk-------~~~~~~~ML~~VepYVt~G~p~l~tvr~Li~ 140 (235)
T TIGR01310 88 PKPRKVLRLLRLKQVHN---GVFVK-------VNKATLQMLRIVEPYVAYGYPNLKSVRELIY 140 (235)
T ss_pred HHHHHHHHHhCCCccce---EEEEE-------CCHHHHHHHHhcCCeEEEecCCHHHHHHHHH
Confidence 67788888888776643 23333 222221111 145799999999999998863
No 18
>TIGR01309 L30P_arch 50S ribosomal protein L30P, archaeal. This model represents the archaeal ribosomal protein similar to longer (~ 250 residue) eukaryotic 60S ribosomal protein L7 and to the much shorter (~ 60 residue) bacterial 50S ribosomal protein L30. Protein naming follows the SwissProt designation as L30P, while the gene symbol rpmD follows TIGR usage.
Probab=22.61 E-value=65 Score=25.66 Aligned_cols=54 Identities=13% Similarity=0.221 Sum_probs=39.8
Q ss_pred ccHHHHHHHhhhCCccCCCccceeeeecCEEEEeeCCeeeeeec-CCeEEEecccccchhhhhhh
Q 031690 25 DDKRLQSTLKRIGVNAIPAIEEVNIFKDDVVIQFLNPKVQASIA-ANTWVVSGAPQTKKLQDILP 88 (155)
Q Consensus 25 DDKKLq~~LkKLg~~~I~gIeEVnmfk~d~vihF~nPkVqaS~~-aNT~vv~G~~e~K~l~ellP 88 (155)
-..+.+.+|+.||+..+.- .|++=.+|.+..-+. ..-||..|++..+.+.+|+=
T Consensus 12 ~~~~~r~tL~~LrL~ri~~----------~V~v~~tp~~~gML~kV~~yV~~ge~~~~tv~~Li~ 66 (152)
T TIGR01309 12 VPRDIADTLEMLRLHRVNH----------CVLYPETPTYLGMLQKVKDYVTWGEIDEDTLELLIR 66 (152)
T ss_pred CCHHHHHHHHHcCCCcCCC----------EEEEeCCHHHHHHHHHhHhheeEecCCHHHHHHHHH
Confidence 3478899999999987754 566656665544433 56799999999999988863
No 19
>cd08871 START_STARD10-like Lipid-binding START domain of mammalian STARD10 and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD10 (also known as CGI-52, PTCP-like, and SDCCAG28). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD10 binds phophatidylcholine and phosphatidylethanolamine. This protein is widely expressed and is synthesized constitutively in many organs. It may function in the liver in the export of phospholipids into bile. It is concentrated in the sperm flagellum, and may play a role in energy metabolism. In the mammary gland it may participate in the enrichment of lipids in milk, and be a potential marker of differentiation. Its expression is induced in this gland during gestation and lactation. It is overe
Probab=22.23 E-value=3.5e+02 Score=21.62 Aligned_cols=68 Identities=15% Similarity=0.193 Sum_probs=36.0
Q ss_pred cCCCccceeeeecCEEEEeeCC-eeeeeecCCeEEEecccccchhhhhhhhhhhccchhhHHHHHHHHHHHHhh
Q 031690 40 AIPAIEEVNIFKDDVVIQFLNP-KVQASIAANTWVVSGAPQTKKLQDILPGIINQLGPDNLDNLRKLAEQFQKQ 112 (155)
Q Consensus 40 ~I~gIeEVnmfk~d~vihF~nP-kVqaS~~aNT~vv~G~~e~K~l~ellP~Il~QLG~d~l~~L~~lae~~~~~ 112 (155)
.-+|..++.++...-+|.-..| .... ||+.+-.+.-.--+-++..++....+..|.+|++++++|+.=
T Consensus 138 ~~~g~VR~~~~~~g~~i~p~~~~~t~v-----t~~~~~Dp~G~IP~~lvN~~~~~~~~~~l~~l~k~~~~y~~~ 206 (222)
T cd08871 138 PRKGFVRAISLLTGYLIRPTGPKGCTL-----TYVTQNDPKGSLPKWVVNKATTKLAPKVMKKLHKAALKYPEW 206 (222)
T ss_pred CCCCeEEeEEEccEEEEEECCCCCEEE-----EEEEecCCCCCcCHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 3467777777665534432222 1111 344444443332222233333444667899999999999653
No 20
>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=22.18 E-value=1.3e+02 Score=20.19 Aligned_cols=37 Identities=14% Similarity=0.293 Sum_probs=27.9
Q ss_pred EEEeeCCeeeeeecCCeEEEecccccchhhhhhhhhh
Q 031690 55 VIQFLNPKVQASIAANTWVVSGAPQTKKLQDILPGII 91 (155)
Q Consensus 55 vihF~nPkVqaS~~aNT~vv~G~~e~K~l~ellP~Il 91 (155)
.++|....-.-.....+|.|-+...++.|++|+-.+|
T Consensus 3 ~v~F~t~~~~~~~~~~~~~VP~~~t~~~Ls~LvN~LL 39 (65)
T PF08154_consen 3 QVQFVTEDGEYEVPGTPISVPSNITRKELSELVNQLL 39 (65)
T ss_pred EEEEEcCCCCccCCCCCEEEeCCCCHHHHHHHHHHHh
Confidence 3556555443456788999999999999999887776
No 21
>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=21.16 E-value=1.2e+02 Score=20.56 Aligned_cols=36 Identities=25% Similarity=0.382 Sum_probs=25.6
Q ss_pred ecCCeEEEecccccchhhhhhhhhhhccchhhHHHH
Q 031690 67 IAANTWVVSGAPQTKKLQDILPGIINQLGPDNLDNL 102 (155)
Q Consensus 67 ~~aNT~vv~G~~e~K~l~ellP~Il~QLG~d~l~~L 102 (155)
...|+|+|+|...-+++.++|.-=|+.-..+.+..+
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 367999999999999999988654544334445443
No 22
>PF00280 potato_inhibit: Potato inhibitor I family; InterPro: IPR000864 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family of proteinase inhibitors belong to MEROPS inhibitor family I13, clan IG. They inhibit peptidases of the S1 (IPR001254 from INTERPRO) and S8 (IPR000209 from INTERPRO) families []. Potato inhibitor type I sequences are not solely restricted to potatoes but are found in other plant species for example: barley endosperm chymotrypsin inhibitor [], and pumpkin trypsin inhibitor. Exceptions are found in leech's, e.g.Hirudo medicinalis (Medicinal leech), but not other metazoa []. In general, the proteins have retained a specificity towards chymotrypsin-like and elastase-like proteases []. Structurally these inhibitors are small (60 to 90 residues) and in contrast with other families of protease inhibitors, they lack disulphide bonds. The inhibitor is a wedge-shaped molecule, its pointed edge formed by the protease-binding loop, which contains the scissile bond. The loop binds tightly to the protease active site, subsequent cleavage of the scissile bond causing inhibition of the enzyme []. The inhibitors (designated type I and II) are synthesised in potato tubers, increasing in concentration as the tuber develops. Synthesis of the inhibitors throughout the plant is also induced by leaf damage; this systemic response being triggered by the release of a putative plant hormone []. Examples found in the bacteria and archaea are probable false positives.; GO: 0004867 serine-type endopeptidase inhibitor activity, 0009611 response to wounding; PDB: 1TEC_I 1SBN_I 1ACB_I 1EGP_A 3TEC_I 2SEC_I 1EGL_A 2TEC_I 1SIB_I 1MEE_I ....
Probab=21.00 E-value=50 Score=22.58 Aligned_cols=23 Identities=43% Similarity=0.595 Sum_probs=16.0
Q ss_pred CcccCCCCCChhHHhhc-cccCCCC
Q 031690 130 EVPELVAGETFEAAAEE-KTEKPDA 153 (155)
Q Consensus 130 dVPdLV~genFee~sk~-e~~~~~~ 153 (155)
.-|||| |.+.++|... +.+.|+.
T Consensus 3 sWPELV-G~~~~~A~~~I~~e~P~v 26 (63)
T PF00280_consen 3 SWPELV-GKSGEEAKAIIERENPDV 26 (63)
T ss_dssp B-GGGT-TSBHHHHHHHHHHHSTTS
T ss_pred CCchhc-CCCHHHHHHHHHHHCCCC
Confidence 359999 7888888765 6666653
No 23
>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=20.95 E-value=1.1e+02 Score=23.41 Aligned_cols=30 Identities=30% Similarity=0.510 Sum_probs=25.1
Q ss_pred eeeeecC-CeEEEecccccchhhhhhhhhhh
Q 031690 63 VQASIAA-NTWVVSGAPQTKKLQDILPGIIN 92 (155)
Q Consensus 63 VqaS~~a-NT~vv~G~~e~K~l~ellP~Il~ 92 (155)
.|++... +.++|.|....+.|+++|-..+.
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
Done!