Query 040579
Match_columns 72
No_of_seqs 119 out of 590
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 09:45:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040579.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040579hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1724 SCF ubiquitin ligase, 99.9 6.3E-25 1.4E-29 140.2 4.6 72 1-72 8-96 (162)
2 smart00512 Skp1 Found in Skp1 99.9 2.6E-22 5.7E-27 119.3 3.6 67 1-72 5-88 (104)
3 PF03931 Skp1_POZ: Skp1 family 99.8 2.8E-20 6.2E-25 102.1 0.2 45 1-45 4-62 (62)
4 COG5201 SKP1 SCF ubiquitin lig 99.7 3.9E-17 8.4E-22 101.5 2.1 72 1-72 5-91 (158)
5 KOG3473 RNA polymerase II tran 97.7 2.3E-05 4.9E-10 47.0 1.7 45 1-45 20-82 (112)
6 smart00225 BTB Broad-Complex, 89.6 0.43 9.3E-06 25.3 2.5 37 8-44 23-62 (90)
7 cd00068 GGL G protein gamma su 75.5 4.2 9E-05 21.5 2.6 17 30-46 23-39 (57)
8 PF00651 BTB: BTB/POZ domain; 69.1 5 0.00011 22.5 2.2 32 12-43 39-74 (111)
9 PF05871 ESCRT-II: ESCRT-II co 65.9 4.6 9.9E-05 25.3 1.6 13 34-46 27-39 (139)
10 smart00224 GGL G protein gamma 65.7 8.3 0.00018 20.8 2.5 17 30-46 23-39 (63)
11 PF11338 DUF3140: Protein of u 63.9 11 0.00023 22.3 2.8 22 25-46 54-75 (92)
12 COG4565 CitB Response regulato 63.8 9.3 0.0002 25.9 2.9 29 20-49 146-175 (224)
13 PF14716 HHH_8: Helix-hairpin- 54.3 19 0.00042 19.3 2.7 20 22-41 49-68 (68)
14 PRK11566 hdeB acid-resistance 53.9 6.1 0.00013 23.7 0.7 25 21-45 62-86 (102)
15 PF13711 DUF4160: Domain of un 53.7 12 0.00026 20.0 1.8 19 27-45 41-59 (66)
16 PF08727 P3A: Poliovirus 3A pr 51.4 12 0.00026 20.2 1.5 12 34-45 30-41 (57)
17 PF08225 Antimicrobial19: Pseu 48.7 14 0.00031 16.1 1.2 10 31-40 3-12 (23)
18 PF11795 DUF3322: Uncharacteri 46.7 15 0.00034 23.7 1.8 39 26-70 140-178 (190)
19 PF09384 UTP15_C: UTP15 C term 46.6 17 0.00037 22.6 1.9 27 23-49 66-92 (148)
20 PF06411 HdeA: HdeA/HdeB famil 46.6 12 0.00027 21.4 1.2 23 22-45 66-88 (94)
21 KOG4068 Uncharacterized conser 43.5 17 0.00037 23.7 1.5 15 33-47 31-45 (174)
22 KOG3321 Mitochondrial ribosoma 43.3 16 0.00036 23.8 1.4 26 22-47 116-141 (175)
23 PF11165 DUF2949: Protein of u 43.0 24 0.00053 19.0 1.9 15 28-42 44-58 (58)
24 PRK13602 putative ribosomal pr 41.8 36 0.00078 19.1 2.6 20 25-44 34-53 (82)
25 TIGR01689 EcbF-BcbF capsule bi 41.7 23 0.0005 21.6 1.9 18 28-45 61-78 (126)
26 PRK13601 putative L7Ae-like ri 38.9 42 0.00091 19.0 2.6 20 26-45 32-51 (82)
27 PF13727 CoA_binding_3: CoA-bi 37.8 36 0.00078 20.3 2.4 23 22-44 146-168 (175)
28 PF03474 DMA: DMRTA motif; In 37.3 31 0.00068 17.1 1.6 18 25-42 12-29 (39)
29 PRK12271 rps10p 30S ribosomal 36.2 38 0.00083 20.0 2.2 26 1-26 7-41 (102)
30 smart00491 HELICc2 helicase su 35.0 39 0.00084 20.8 2.2 23 22-44 77-99 (142)
31 PRK11675 LexA regulated protei 34.6 44 0.00096 19.5 2.2 22 23-45 53-74 (90)
32 PF07430 PP1: Phloem filament 34.2 32 0.0007 23.0 1.8 23 21-43 9-31 (202)
33 COG2100 Predicted Fe-S oxidore 33.9 37 0.00081 24.8 2.2 25 21-45 261-285 (414)
34 PF03682 UPF0158: Uncharacteri 33.7 33 0.00071 21.8 1.7 20 30-49 124-143 (163)
35 PF06540 GMAP: Galanin message 33.6 52 0.0011 18.0 2.3 16 29-44 22-37 (62)
36 PF00631 G-gamma: GGL domain; 33.4 39 0.00084 18.1 1.8 17 30-47 26-42 (68)
37 TIGR01046 S10_Arc_S20_Euk ribo 33.1 46 0.00099 19.5 2.2 26 1-26 6-40 (99)
38 PRK01018 50S ribosomal protein 32.8 59 0.0013 18.8 2.6 19 26-44 40-58 (99)
39 PF15472 DUF4638: Domain of un 31.1 36 0.00079 23.5 1.7 16 31-46 29-44 (268)
40 PRK06683 hypothetical protein; 30.7 69 0.0015 18.0 2.6 20 26-45 35-54 (82)
41 PF00356 LacI: Bacterial regul 27.9 91 0.002 15.6 2.8 21 26-46 24-44 (46)
42 PRK07714 hypothetical protein; 27.6 78 0.0017 18.2 2.5 20 26-45 42-61 (100)
43 PHA01623 hypothetical protein 27.1 78 0.0017 16.6 2.2 19 27-45 19-37 (56)
44 PF00010 HLH: Helix-loop-helix 26.6 78 0.0017 15.8 2.2 14 29-42 40-53 (55)
45 KOG4119 G protein gamma subuni 26.6 94 0.002 17.4 2.6 17 30-46 31-47 (71)
46 COG1199 DinG Rad3-related DNA 26.0 72 0.0016 24.0 2.7 26 22-47 556-581 (654)
47 PF07818 HCNGP: HCNGP-like pro 25.8 55 0.0012 19.1 1.6 15 29-43 42-56 (96)
48 PF09329 zf-primase: Primase z 25.6 11 0.00023 19.2 -1.3 9 37-45 28-36 (46)
49 PHA02713 hypothetical protein; 25.6 62 0.0013 24.3 2.2 24 21-44 67-90 (557)
50 PF11360 DUF3110: Protein of u 25.4 54 0.0012 18.8 1.5 33 10-46 38-70 (86)
51 smart00668 CTLH C-terminal to 25.4 65 0.0014 15.9 1.7 15 31-45 15-29 (58)
52 PF13315 DUF4085: Protein of u 25.2 95 0.0021 20.9 2.8 26 20-45 69-94 (208)
53 CHL00135 rps10 ribosomal prote 24.9 77 0.0017 18.7 2.2 25 2-26 13-46 (101)
54 smart00229 RasGEFN Guanine nuc 24.8 31 0.00068 20.2 0.5 20 26-45 3-22 (127)
55 COG4849 Predicted nucleotidylt 24.5 95 0.0021 21.4 2.8 27 21-47 136-162 (269)
56 PRK04966 hypothetical protein; 24.5 58 0.0013 18.3 1.5 21 22-42 2-23 (72)
57 COG0051 RpsJ Ribosomal protein 24.4 84 0.0018 18.9 2.3 6 21-26 38-43 (104)
58 PF06303 MatP: Organiser of ma 24.4 52 0.0011 21.0 1.4 13 34-46 52-64 (148)
59 PTZ00039 40S ribosomal protein 24.3 79 0.0017 19.2 2.2 7 20-26 50-56 (115)
60 PTZ00271 hypoxanthine-guanine 24.1 76 0.0017 21.1 2.3 17 29-45 130-146 (211)
61 PTZ00106 60S ribosomal protein 24.1 96 0.0021 18.4 2.5 19 26-44 49-67 (108)
62 COG0634 Hpt Hypoxanthine-guani 24.0 64 0.0014 21.2 1.8 18 29-46 105-122 (178)
63 PF08879 WRC: WRC; InterPro: 23.9 34 0.00074 17.5 0.4 8 38-45 26-33 (46)
64 PF09336 Vps4_C: Vps4 C termin 23.8 95 0.0021 16.5 2.2 18 26-43 44-61 (62)
65 PHA00159 endonuclease I 23.7 40 0.00086 21.5 0.8 9 37-45 110-118 (148)
66 PF03164 Mon1: Trafficking pro 22.9 72 0.0016 23.2 2.1 16 30-45 390-405 (415)
67 PHA03098 kelch-like protein; P 22.9 1.2E+02 0.0027 22.0 3.3 32 12-44 39-70 (534)
68 KOG3977 Troponin I [Cytoskelet 22.9 36 0.00078 22.9 0.5 13 20-32 76-88 (221)
69 smart00740 PASTA PASTA domain. 22.8 52 0.0011 16.2 1.0 22 22-43 4-25 (66)
70 KOG1232 Proteins containing th 22.5 1.8E+02 0.0038 21.9 4.0 29 21-50 91-119 (511)
71 PF01736 Polyoma_agno: Polyoma 22.5 62 0.0013 17.4 1.3 13 31-43 31-43 (62)
72 smart00492 HELICc3 helicase su 22.3 89 0.0019 19.1 2.2 23 22-44 76-98 (141)
73 KOG4441 Proteins containing BT 22.3 97 0.0021 23.5 2.7 26 20-45 75-100 (571)
74 PF06794 UPF0270: Uncharacteri 22.0 60 0.0013 18.1 1.2 20 23-42 3-23 (70)
75 COG4049 Uncharacterized protei 21.8 26 0.00057 19.0 -0.2 11 1-11 8-18 (65)
76 PF04472 DUF552: Protein of un 21.7 1.2E+02 0.0026 16.3 2.4 24 22-45 26-49 (73)
77 PF00307 CH: Calponin homology 21.6 1.6E+02 0.0034 16.2 3.6 43 5-48 29-80 (108)
78 PF01498 HTH_Tnp_Tc3_2: Transp 21.5 78 0.0017 16.6 1.6 20 26-45 53-72 (72)
79 PF01745 IPT: Isopentenyl tran 21.2 76 0.0016 21.7 1.8 21 24-46 168-188 (233)
80 PF02186 TFIIE_beta: TFIIE bet 20.1 1.2E+02 0.0026 16.4 2.2 19 29-48 3-21 (65)
81 PF05321 HHA: Haemolysin expre 20.1 1.3E+02 0.0028 16.2 2.2 17 29-45 8-24 (57)
82 PF05367 Phage_endo_I: Phage e 20.1 54 0.0012 20.9 0.9 9 37-45 110-118 (149)
83 COG5478 Predicted small integr 20.0 1.6E+02 0.0035 18.6 3.0 28 20-47 92-119 (141)
No 1
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=6.3e-25 Score=140.23 Aligned_cols=72 Identities=44% Similarity=0.784 Sum_probs=55.0
Q ss_pred CeecCChhHHH-------------HHHHhc-CCCC--cccCCCCCHHHHHHHHHHHHHcCCCCCCccccC-CCCCCCcCh
Q 040579 1 MLKSSDGEVFE-------------HMIEDD-CAVD--RIPLPNVTIKIFYKAIKYCNKHDEASMFDDLAT-TSIDDDLKA 63 (72)
Q Consensus 1 ~L~SsDg~~f~-------------~~i~~~-~~~~--~IplpnV~~~~L~kViewc~~H~~~~~~~~~~~-~~~~~~i~~ 63 (72)
+|+||||++|+ +++.+. +... +||||||+|.+|+|||+||+||+++++...+.. .+....++.
T Consensus 8 kL~SsDG~~f~ve~~~a~~s~~i~~~~~~~~~~~~~~~IPl~nV~~~iL~kVIewC~~Hk~d~~~~~~~~~~~~~~~i~~ 87 (162)
T KOG1724|consen 8 KLESSDGEIFEVEEEVARQSQTISAHMIEDGCADENDPIPLPNVTSKILKKVIEWCKKHKDDDPANPEDKELPEETDIPE 87 (162)
T ss_pred EEEccCCceeehhHHHHHHhHHHHHHHHHcCCCccCCccccCccCHHHHHHHHHHHHHcccccccccccccccccCCccH
Confidence 58999999999 333333 3444 899999999999999999999999865433211 134445999
Q ss_pred hhhhccccC
Q 040579 64 WDADLVKVD 72 (72)
Q Consensus 64 WD~~F~~~d 72 (72)
||++||++|
T Consensus 88 WD~~Flk~d 96 (162)
T KOG1724|consen 88 WDAEFLKVD 96 (162)
T ss_pred HHHHHHhcC
Confidence 999999864
No 2
>smart00512 Skp1 Found in Skp1 protein family. Family of Skp1 (kinetochore protein required for cell cycle progression) and elongin C (subunit of RNA polymerase II transcription factor SIII) homologues.
Probab=99.86 E-value=2.6e-22 Score=119.32 Aligned_cols=67 Identities=51% Similarity=0.770 Sum_probs=54.2
Q ss_pred CeecCChhHHH-------------HHHHhcCCC----CcccCCCCCHHHHHHHHHHHHHcCCCCCCccccCCCCCCCcCh
Q 040579 1 MLKSSDGEVFE-------------HMIEDDCAV----DRIPLPNVTIKIFYKAIKYCNKHDEASMFDDLATTSIDDDLKA 63 (72)
Q Consensus 1 ~L~SsDg~~f~-------------~~i~~~~~~----~~IplpnV~~~~L~kViewc~~H~~~~~~~~~~~~~~~~~i~~ 63 (72)
+|+|+||++|. +||++.+.. .+||||+|+|.+|+|||+||+||+.++.+..+ ...+++
T Consensus 5 ~L~S~Dg~~f~v~~~~a~~S~~i~~~l~~~~~~~~~~~~Ipl~~v~~~~L~~Vi~yc~~h~~~~~~~~~-----~~~~~~ 79 (104)
T smart00512 5 KLISSDGEVFEVEREVARQSKTIKAMIEDLGVDDENNNPIPLPNVTSKILSKVIEYCEHHVDDPPSVAD-----KDDIPT 79 (104)
T ss_pred EEEeCCCCEEEecHHHHHHHHHHHHHHHccCcccCCCCCccCCCcCHHHHHHHHHHHHHcccCCCCccc-----cccccH
Confidence 58999999999 677665532 48999999999999999999999988654322 146899
Q ss_pred hhhhccccC
Q 040579 64 WDADLVKVD 72 (72)
Q Consensus 64 WD~~F~~~d 72 (72)
||++|++++
T Consensus 80 wD~~F~~~d 88 (104)
T smart00512 80 WDAEFLKID 88 (104)
T ss_pred HHHHHHcCC
Confidence 999999753
No 3
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=99.77 E-value=2.8e-20 Score=102.11 Aligned_cols=45 Identities=49% Similarity=0.806 Sum_probs=38.4
Q ss_pred CeecCChhHHH-------------HHHHhcCCCC-cccCCCCCHHHHHHHHHHHHHcCC
Q 040579 1 MLKSSDGEVFE-------------HMIEDDCAVD-RIPLPNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 1 ~L~SsDg~~f~-------------~~i~~~~~~~-~IplpnV~~~~L~kViewc~~H~~ 45 (72)
+|+|+||++|+ +|+++.+... +||||+|+|++|+||||||+||++
T Consensus 4 ~L~SsDg~~f~V~~~~a~~S~~i~~ml~~~~~~~~~Ipl~~v~~~~L~kViewc~~H~~ 62 (62)
T PF03931_consen 4 KLVSSDGQEFEVSREAAKQSKTIKNMLEDLGDEDEPIPLPNVSSRILKKVIEWCEHHKN 62 (62)
T ss_dssp EEEETTSEEEEEEHHHHTTSHHHHHHHHCTCCCGTEEEETTS-HHHHHHHHHHHHHHHH
T ss_pred EEEcCCCCEEEeeHHHHHHhHHHHHHHhhhcccccccccCccCHHHHHHHHHHHHhcCC
Confidence 58999999999 7777766543 699999999999999999999973
No 4
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=99.65 E-value=3.9e-17 Score=101.54 Aligned_cols=72 Identities=29% Similarity=0.441 Sum_probs=55.0
Q ss_pred CeecCChhHHH-------------HHHHhcCC-CCcccCCCCCHHHHHHHHHHHHHcCCCCCCcccc-CCCCCCCcChhh
Q 040579 1 MLKSSDGEVFE-------------HMIEDDCA-VDRIPLPNVTIKIFYKAIKYCNKHDEASMFDDLA-TTSIDDDLKAWD 65 (72)
Q Consensus 1 ~L~SsDg~~f~-------------~~i~~~~~-~~~IplpnV~~~~L~kViewc~~H~~~~~~~~~~-~~~~~~~i~~WD 65 (72)
.|+|.||++|. +|+.+..+ .-|||+|||.|.+|.||++||+||+....++.++ ..++...+..||
T Consensus 5 ~l~s~dge~F~vd~~iAerSiLikN~l~d~~~~n~p~p~pnVrSsvl~kv~ew~ehh~~s~sede~d~~~rks~p~D~wd 84 (158)
T COG5201 5 ELESIDGEIFRVDENIAERSILIKNMLCDSTACNYPIPAPNVRSSVLMKVQEWMEHHTSSLSEDENDLEIRKSKPSDFWD 84 (158)
T ss_pred EEEecCCcEEEehHHHHHHHHHHHHHhccccccCCCCcccchhHHHHHHHHHHHHhccccCCCccChHhhhccCCccHHH
Confidence 48999999998 55554433 3489999999999999999999999854433321 224567789999
Q ss_pred hhccccC
Q 040579 66 ADLVKVD 72 (72)
Q Consensus 66 ~~F~~~d 72 (72)
+.|+.+|
T Consensus 85 r~Fm~vD 91 (158)
T COG5201 85 RFFMEVD 91 (158)
T ss_pred HHHHHhh
Confidence 9999765
No 5
>KOG3473 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription]
Probab=97.68 E-value=2.3e-05 Score=46.95 Aligned_cols=45 Identities=20% Similarity=0.237 Sum_probs=35.5
Q ss_pred CeecCChhHHH-------------HHHHhcC-----CCCcccCCCCCHHHHHHHHHHHHHcCC
Q 040579 1 MLKSSDGEVFE-------------HMIEDDC-----AVDRIPLPNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 1 ~L~SsDg~~f~-------------~~i~~~~-----~~~~IplpnV~~~~L~kViewc~~H~~ 45 (72)
+|+|+||.+|. .||.+-+ ..+.+-++.+.+-+|.||.+|..+...
T Consensus 20 kLvS~Ddhefiikre~AmtSgTiraml~gpg~~se~~~n~v~f~di~shiLeKvc~Yl~Yk~r 82 (112)
T KOG3473|consen 20 KLVSSDDHEFIIKREHAMTSGTIRAMLSGPGVFSEAEKNEVYFRDIPSHILEKVCEYLAYKVR 82 (112)
T ss_pred EeecCCCcEEEEeehhhhhhhHHHHHHcCCccccccccceEEeccchHHHHHHHHHHhhheee
Confidence 58999999998 4444321 235799999999999999999987654
No 6
>smart00225 BTB Broad-Complex, Tramtrack and Bric a brac. Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures.
Probab=89.55 E-value=0.43 Score=25.32 Aligned_cols=37 Identities=16% Similarity=0.251 Sum_probs=27.3
Q ss_pred hHHHHHHHhcC---CCCcccCCCCCHHHHHHHHHHHHHcC
Q 040579 8 EVFEHMIEDDC---AVDRIPLPNVTIKIFYKAIKYCNKHD 44 (72)
Q Consensus 8 ~~f~~~i~~~~---~~~~IplpnV~~~~L~kViewc~~H~ 44 (72)
.-|..|+.... ....|++++++...+..+++||..-.
T Consensus 23 ~~f~~~~~~~~~~~~~~~i~l~~~~~~~f~~~l~~ly~~~ 62 (90)
T smart00225 23 PYFKALFSGDFKESKKSEIYLDDVSPEDFRALLEFLYTGK 62 (90)
T ss_pred HHHHHHHcCCCccCCCCEEEecCCCHHHHHHHHHeecCce
Confidence 34446665432 24579999999999999999987653
No 7
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=75.52 E-value=4.2 Score=21.54 Aligned_cols=17 Identities=29% Similarity=0.550 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHcCCC
Q 040579 30 IKIFYKAIKYCNKHDEA 46 (72)
Q Consensus 30 ~~~L~kViewc~~H~~~ 46 (72)
|....-+++||+.|...
T Consensus 23 S~a~~~l~~y~e~~~~~ 39 (57)
T cd00068 23 SKAAAELLKYCEQNAEN 39 (57)
T ss_pred HHHHHHHHHHHHhcCCC
Confidence 77888899999999764
No 8
>PF00651 BTB: BTB/POZ domain; InterPro: IPR013069 The BTB (for BR-C, ttk and bab) [] or POZ (for Pox virus and Zinc finger) [] domain is present near the N terminus of a fraction of zinc finger (IPR007087 from INTERPRO) proteins and in proteins that contain the IPR006652 from INTERPRO motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation []. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule []. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [, , ]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.; GO: 0005515 protein binding; PDB: 3M5B_A 1R28_B 3LBZ_A 3E4U_F 3BIM_B 1R2B_A 1R29_A 2VPK_A 2YY9_B 3GA1_A ....
Probab=69.06 E-value=5 Score=22.52 Aligned_cols=32 Identities=22% Similarity=0.361 Sum_probs=23.6
Q ss_pred HHHHhcC-CC---CcccCCCCCHHHHHHHHHHHHHc
Q 040579 12 HMIEDDC-AV---DRIPLPNVTIKIFYKAIKYCNKH 43 (72)
Q Consensus 12 ~~i~~~~-~~---~~IplpnV~~~~L~kViewc~~H 43 (72)
+|+.... .. ..|++++++...+..+++||...
T Consensus 39 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~ 74 (111)
T PF00651_consen 39 NLFEGSKFKESTVPEISLPDVSPEAFEAFLEYMYTG 74 (111)
T ss_dssp HHHTTTTSTTSSEEEEEETTSCHHHHHHHHHHHHHS
T ss_pred hcccccccccccccccccccccccccccccccccCC
Confidence 5665542 22 25889999999999999999533
No 9
>PF05871 ESCRT-II: ESCRT-II complex subunit; InterPro: IPR008570 This entry represents the vps25 subunit (vacuolar protein sorting-associated protein 25) of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs) []. ESCRT-II recruits the transport machinery for protein sorting at MVB []. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo []. ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps35 [].; PDB: 1W7P_B 1U5T_D 1XB4_D 3HTU_E 3CUQ_C 2ZME_D.
Probab=65.86 E-value=4.6 Score=25.29 Aligned_cols=13 Identities=23% Similarity=0.496 Sum_probs=10.1
Q ss_pred HHHHHHHHHcCCC
Q 040579 34 YKAIKYCNKHDEA 46 (72)
Q Consensus 34 ~kViewc~~H~~~ 46 (72)
..|+.||.||+--
T Consensus 27 ~lIl~y~~~~k~~ 39 (139)
T PF05871_consen 27 DLILDYCRHHKIF 39 (139)
T ss_dssp HHHHHHHHHTT-S
T ss_pred HHHHHHHHHhcee
Confidence 3699999999875
No 10
>smart00224 GGL G protein gamma subunit-like motifs.
Probab=65.70 E-value=8.3 Score=20.79 Aligned_cols=17 Identities=29% Similarity=0.569 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHcCCC
Q 040579 30 IKIFYKAIKYCNKHDEA 46 (72)
Q Consensus 30 ~~~L~kViewc~~H~~~ 46 (72)
|....-++.||+.|...
T Consensus 23 S~a~~~li~y~e~~~~~ 39 (63)
T smart00224 23 SKAAEELLAYCEQHAEE 39 (63)
T ss_pred HHHHHHHHHHHHcCCCC
Confidence 77888899999998875
No 11
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=63.86 E-value=11 Score=22.26 Aligned_cols=22 Identities=18% Similarity=0.303 Sum_probs=18.0
Q ss_pred CCCCCHHHHHHHHHHHHHcCCC
Q 040579 25 LPNVTIKIFYKAIKYCNKHDEA 46 (72)
Q Consensus 25 lpnV~~~~L~kViewc~~H~~~ 46 (72)
|..=+-..++||+.||..|...
T Consensus 54 ltddD~~hMrkVV~yv~rhlaq 75 (92)
T PF11338_consen 54 LTDDDYEHMRKVVGYVKRHLAQ 75 (92)
T ss_pred CCHHHHHHHHHHHHHHHHHHhc
Confidence 4444567899999999999987
No 12
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=63.77 E-value=9.3 Score=25.92 Aligned_cols=29 Identities=10% Similarity=0.040 Sum_probs=23.3
Q ss_pred CCcccCC-CCCHHHHHHHHHHHHHcCCCCCC
Q 040579 20 VDRIPLP-NVTIKIFYKAIKYCNKHDEASMF 49 (72)
Q Consensus 20 ~~~Iplp-nV~~~~L~kViewc~~H~~~~~~ 49 (72)
..+.+|| .+++.||.+|.+|.+ +.+.+..
T Consensus 146 ~~~~~LPkGi~~~Tl~~i~~~~~-~~~~~~T 175 (224)
T COG4565 146 QPPDDLPKGLDELTLQKVREALK-EPDQELT 175 (224)
T ss_pred cCcccCCCCcCHHHHHHHHHHHh-CcCCccC
Confidence 4578888 799999999999999 6554443
No 13
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=54.25 E-value=19 Score=19.26 Aligned_cols=20 Identities=20% Similarity=0.089 Sum_probs=17.3
Q ss_pred cccCCCCCHHHHHHHHHHHH
Q 040579 22 RIPLPNVTIKIFYKAIKYCN 41 (72)
Q Consensus 22 ~IplpnV~~~~L~kViewc~ 41 (72)
.--||+|-..+-.+|.||++
T Consensus 49 ~~~l~gIG~~ia~kI~E~le 68 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKIDEILE 68 (68)
T ss_dssp HCTSTTTTHHHHHHHHHHHH
T ss_pred HhhCCCCCHHHHHHHHHHHC
Confidence 45689999999999999975
No 14
>PRK11566 hdeB acid-resistance protein; Provisional
Probab=53.90 E-value=6.1 Score=23.71 Aligned_cols=25 Identities=28% Similarity=0.506 Sum_probs=19.8
Q ss_pred CcccCCCCCHHHHHHHHHHHHHcCC
Q 040579 21 DRIPLPNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 21 ~~IplpnV~~~~L~kViewc~~H~~ 45 (72)
+-+.+..+.-..-.|||+||..|..
T Consensus 62 D~vd~~e~et~~tPkvie~Ckk~P~ 86 (102)
T PRK11566 62 DYVDLNETDTTQVPKVIEYCKKNPQ 86 (102)
T ss_pred ccccccceeeeechHHHHHHHhCCc
Confidence 3477777777668899999999955
No 15
>PF13711 DUF4160: Domain of unknown function (DUF4160)
Probab=53.70 E-value=12 Score=20.04 Aligned_cols=19 Identities=16% Similarity=0.253 Sum_probs=16.7
Q ss_pred CCCHHHHHHHHHHHHHcCC
Q 040579 27 NVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 27 nV~~~~L~kViewc~~H~~ 45 (72)
.++.+.|++|.+|++-|++
T Consensus 41 ~l~~k~l~~i~~~i~~~~~ 59 (66)
T PF13711_consen 41 FLPRKELRKILEWIEENQE 59 (66)
T ss_pred CCCHHHHHHHHHHHHHHHH
Confidence 4789999999999999865
No 16
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=51.42 E-value=12 Score=20.16 Aligned_cols=12 Identities=17% Similarity=0.429 Sum_probs=9.0
Q ss_pred HHHHHHHHHcCC
Q 040579 34 YKAIKYCNKHDE 45 (72)
Q Consensus 34 ~kViewc~~H~~ 45 (72)
.+|++||+...=
T Consensus 30 ~eV~~YC~~~GW 41 (57)
T PF08727_consen 30 PEVREYCEEQGW 41 (57)
T ss_dssp HHHHHHHHHHT-
T ss_pred HHHHHHHHHCCc
Confidence 469999998754
No 17
>PF08225 Antimicrobial19: Pseudin antimicrobial peptide; InterPro: IPR013156 Pseudins are a subfamily of the FSAP family (Frog Secreted Active Peptides) extracted from the skin of the paradoxical frog Pseudis paradoxa (Paradoxical frog). The pseudins belong to the class of cationic, amphipathic-helical antimicrobial peptides [].; GO: 0006952 defense response
Probab=48.69 E-value=14 Score=16.05 Aligned_cols=10 Identities=10% Similarity=0.016 Sum_probs=7.2
Q ss_pred HHHHHHHHHH
Q 040579 31 KIFYKAIKYC 40 (72)
Q Consensus 31 ~~L~kViewc 40 (72)
.+|+||++=+
T Consensus 3 ntlkkv~qgl 12 (23)
T PF08225_consen 3 NTLKKVFQGL 12 (23)
T ss_pred hHHHHHHHHH
Confidence 4788888753
No 18
>PF11795 DUF3322: Uncharacterized protein conserved in bacteria N-term (DUF3322); InterPro: IPR024537 This domain, found in various hypothetical bacterial proteins, has no known function. The family represents just the N terminus.
Probab=46.73 E-value=15 Score=23.67 Aligned_cols=39 Identities=5% Similarity=0.222 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHHHHHHHcCCCCCCccccCCCCCCCcChhhhhccc
Q 040579 26 PNVTIKIFYKAIKYCNKHDEASMFDDLATTSIDDDLKAWDADLVK 70 (72)
Q Consensus 26 pnV~~~~L~kViewc~~H~~~~~~~~~~~~~~~~~i~~WD~~F~~ 70 (72)
+..+-.-|-+|+.|+..|-....+ .+...++-.|.+|++
T Consensus 140 ~~~d~~~l~~vl~wl~~h~~~g~y------lRqlpi~GvDTKfiE 178 (190)
T PF11795_consen 140 SDDDFERLLAVLDWLRPHPRSGLY------LRQLPIPGVDTKFIE 178 (190)
T ss_pred HHhhHHHHHHHHHHHhcCCCCCCc------hhhCCcCCcchHHHH
Confidence 344557788999999888665433 345567777888874
No 19
>PF09384 UTP15_C: UTP15 C terminal; InterPro: IPR018983 This entry represents the C-terminal domain of the U3 small nucleolar RNA-associated protein 15 (UTP15). This protein is involved in nucleolar processing of pre-18S ribosomal RNA, and is required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). UTP15 is a component of the ribosomal small subunit (SSU) processome, which is a large ribonucleoprotein (RNP) required for processing of precursors to the small subunit RNA, the 18S, of the ribosome [, ]. This domain is found C-terminal to the WD40 repeat (IPR001680 from INTERPRO). UTP15 associates with U3 snoRNA, which is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA []. ; GO: 0006364 rRNA processing, 0005730 nucleolus
Probab=46.64 E-value=17 Score=22.64 Aligned_cols=27 Identities=11% Similarity=0.096 Sum_probs=23.0
Q ss_pred ccCCCCCHHHHHHHHHHHHHcCCCCCC
Q 040579 23 IPLPNVTIKIFYKAIKYCNKHDEASMF 49 (72)
Q Consensus 23 IplpnV~~~~L~kViewc~~H~~~~~~ 49 (72)
.=|-+-+..+|..|+.||.+|..+|-.
T Consensus 66 ~AL~~Rde~~L~piL~Fl~k~i~~pr~ 92 (148)
T PF09384_consen 66 AALAGRDEESLEPILKFLIKNITDPRY 92 (148)
T ss_pred HHHHhCCHHHHHHHHHHHHHhCCCccc
Confidence 346688999999999999999988754
No 20
>PF06411 HdeA: HdeA/HdeB family; InterPro: IPR010486 HNS (histone-like nucleoid structuring)-dependent expression A (HdeA) protein is a stress response protein found in highly acid resistant bacteria such as Shigella flexneri and Escherichia coli, but which is lacking in mildly acid tolerant bacteria such as Salmonella []. HdeA is one of the most abundant proteins found in the periplasmic space of E. coli, where it is one of a network of proteins that confer an acid resistance phenotype essential for the pathogenesis of enteric bacteria []. HdeA is thought to act as a chaperone, functioning to prevent the aggregation of periplasmic proteins denatured under acidic conditions. The HNS protein, a chromatin-associated protein that influences the gene expression of several environmentally-induced target genes, represses the expression of HdeA. HdeB, which is encoded within the same operon, may form heterodimers with HdeA. HdeA is a single domain protein with an overall fold that is similar to the fold of the N-terminal subdomain of the GluRS anticodon-binding domain. ; PDB: 1BG8_C 1DJ8_C 2XUV_C.
Probab=46.56 E-value=12 Score=21.42 Aligned_cols=23 Identities=17% Similarity=0.440 Sum_probs=15.2
Q ss_pred cccCCCCCHHHHHHHHHHHHHcCC
Q 040579 22 RIPLPNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 22 ~IplpnV~~~~L~kViewc~~H~~ 45 (72)
.|-+..+... -.+|++||..|..
T Consensus 66 ~vD~~~~~~~-tp~v~~~Ckk~P~ 88 (94)
T PF06411_consen 66 YVDFDGIETV-TPKVVEYCKKNPK 88 (94)
T ss_dssp BB-HHHHHHH-HHHHHHHHHCTTT
T ss_pred eeeHHHHHHh-hHHHHHHHHHCcc
Confidence 4444444444 7899999999954
No 21
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.52 E-value=17 Score=23.67 Aligned_cols=15 Identities=20% Similarity=0.388 Sum_probs=12.1
Q ss_pred HHHHHHHHHHcCCCC
Q 040579 33 FYKAIKYCNKHDEAS 47 (72)
Q Consensus 33 L~kViewc~~H~~~~ 47 (72)
-..|++||.|++--.
T Consensus 31 ~~lil~ycr~~k~~s 45 (174)
T KOG4068|consen 31 IDLILQYCRHNKIWS 45 (174)
T ss_pred HHHHHHHHHhcCeEE
Confidence 357999999999754
No 22
>KOG3321 consensus Mitochondrial ribosomal protein S10 [Translation, ribosomal structure and biogenesis]
Probab=43.27 E-value=16 Score=23.77 Aligned_cols=26 Identities=19% Similarity=0.158 Sum_probs=22.7
Q ss_pred cccCCCCCHHHHHHHHHHHHHcCCCC
Q 040579 22 RIPLPNVTIKIFYKAIKYCNKHDEAS 47 (72)
Q Consensus 22 ~IplpnV~~~~L~kViewc~~H~~~~ 47 (72)
-|.+-+|+|.||...++|..+|.-..
T Consensus 116 ~i~l~~~tgsTl~tfleYI~rn~peg 141 (175)
T KOG3321|consen 116 LIELYSVTGSTLDTFLEYIQRNLPEG 141 (175)
T ss_pred HHHHhhcCchHHHHHHHHHHhhChhh
Confidence 57788999999999999999997653
No 23
>PF11165 DUF2949: Protein of unknown function (DUF2949); InterPro: IPR021336 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=42.97 E-value=24 Score=18.96 Aligned_cols=15 Identities=7% Similarity=0.299 Sum_probs=13.5
Q ss_pred CCHHHHHHHHHHHHH
Q 040579 28 VTIKIFYKAIKYCNK 42 (72)
Q Consensus 28 V~~~~L~kViewc~~ 42 (72)
|+=..|.+|.+|+++
T Consensus 44 ItL~QL~~i~DWl~~ 58 (58)
T PF11165_consen 44 ITLEQLDQIFDWLEN 58 (58)
T ss_pred ccHHHHHHHHHHHhC
Confidence 899999999999874
No 24
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=41.82 E-value=36 Score=19.10 Aligned_cols=20 Identities=10% Similarity=0.086 Sum_probs=17.5
Q ss_pred CCCCCHHHHHHHHHHHHHcC
Q 040579 25 LPNVTIKIFYKAIKYCNKHD 44 (72)
Q Consensus 25 lpnV~~~~L~kViewc~~H~ 44 (72)
=.|++..+.++|..+|+++.
T Consensus 34 A~D~~~~~~~~i~~~c~~~~ 53 (82)
T PRK13602 34 AEDADPRLTEKVEALANEKG 53 (82)
T ss_pred ECCCCHHHHHHHHHHHHHcC
Confidence 34899999999999999885
No 25
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=41.69 E-value=23 Score=21.64 Aligned_cols=18 Identities=22% Similarity=0.366 Sum_probs=15.8
Q ss_pred CCHHHHHHHHHHHHHcCC
Q 040579 28 VTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 28 V~~~~L~kViewc~~H~~ 45 (72)
++..+|..+++||.+|.-
T Consensus 61 i~~~~~~~t~~wL~k~~i 78 (126)
T TIGR01689 61 INIHTLPIIILWLNQHNV 78 (126)
T ss_pred cchhhHHHHHHHHHHcCC
Confidence 788999999999999843
No 26
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=38.88 E-value=42 Score=19.01 Aligned_cols=20 Identities=10% Similarity=0.199 Sum_probs=17.7
Q ss_pred CCCCHHHHHHHHHHHHHcCC
Q 040579 26 PNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 26 pnV~~~~L~kViewc~~H~~ 45 (72)
.+.+..+-+++..+|+++.-
T Consensus 32 ~Da~~~~~k~i~~~c~~~~V 51 (82)
T PRK13601 32 KDAEEHVTKKIKELCEEKSI 51 (82)
T ss_pred CCCCHHHHHHHHHHHHhCCC
Confidence 47899999999999999864
No 27
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=37.83 E-value=36 Score=20.34 Aligned_cols=23 Identities=22% Similarity=0.219 Sum_probs=17.7
Q ss_pred cccCCCCCHHHHHHHHHHHHHcC
Q 040579 22 RIPLPNVTIKIFYKAIKYCNKHD 44 (72)
Q Consensus 22 ~IplpnV~~~~L~kViewc~~H~ 44 (72)
-|=+|......++++++.|+.|.
T Consensus 146 ~ial~~~~~~~i~~ii~~~~~~~ 168 (175)
T PF13727_consen 146 IIALPWSEEEQIKRIIEELENHG 168 (175)
T ss_dssp EE--TTS-HHHHHHHHHHHHTTT
T ss_pred EEEcCccCHHHHHHHHHHHHhCC
Confidence 36688899999999999999884
No 28
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=37.30 E-value=31 Score=17.12 Aligned_cols=18 Identities=17% Similarity=0.432 Sum_probs=15.4
Q ss_pred CCCCCHHHHHHHHHHHHH
Q 040579 25 LPNVTIKIFYKAIKYCNK 42 (72)
Q Consensus 25 lpnV~~~~L~kViewc~~ 42 (72)
.|+-...+|..|++-|.-
T Consensus 12 FP~~kr~~Le~iL~~C~G 29 (39)
T PF03474_consen 12 FPHQKRSVLELILQRCNG 29 (39)
T ss_pred CCCCChHHHHHHHHHcCC
Confidence 578899999999999963
No 29
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=36.17 E-value=38 Score=20.03 Aligned_cols=26 Identities=31% Similarity=0.479 Sum_probs=14.3
Q ss_pred CeecCChhHHH----HHHH---hcCC--CCcccCC
Q 040579 1 MLKSSDGEVFE----HMIE---DDCA--VDRIPLP 26 (72)
Q Consensus 1 ~L~SsDg~~f~----~~i~---~~~~--~~~Iplp 26 (72)
+|.|.|-...+ .+++ ..+. .+|||||
T Consensus 7 ~L~S~d~~~Ld~~~~~I~~~~k~~g~~~~GPipLP 41 (102)
T PRK12271 7 RLSSTNPEDLDEVCDQIKEIAEKTGVDMSGPIPLP 41 (102)
T ss_pred EEEeCCHHHHHHHHHHHHHHHHHcCCeEECCCcCC
Confidence 35666666666 2222 2222 3788888
No 30
>smart00491 HELICc2 helicase superfamily c-terminal domain.
Probab=35.01 E-value=39 Score=20.76 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=20.5
Q ss_pred cccCCCCCHHHHHHHHHHHHHcC
Q 040579 22 RIPLPNVTIKIFYKAIKYCNKHD 44 (72)
Q Consensus 22 ~IplpnV~~~~L~kViewc~~H~ 44 (72)
-+|.|+.+...+....+|.+...
T Consensus 77 glPfp~~~d~~~~~~~~~~~~~~ 99 (142)
T smart00491 77 GIPFPNPDSPILRARLEYLDEKG 99 (142)
T ss_pred ecCCCCCCCHHHHHHHHHHHHhc
Confidence 58999999999999999998775
No 31
>PRK11675 LexA regulated protein; Provisional
Probab=34.58 E-value=44 Score=19.54 Aligned_cols=22 Identities=5% Similarity=0.114 Sum_probs=18.4
Q ss_pred ccCCCCCHHHHHHHHHHHHHcCC
Q 040579 23 IPLPNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 23 IplpnV~~~~L~kViewc~~H~~ 45 (72)
|-| .|+....+++-+||+.|.-
T Consensus 53 veV-Kldedl~ekL~eyAe~~ni 74 (90)
T PRK11675 53 VEL-KLNADLVDALNELAEARNI 74 (90)
T ss_pred EEE-EECHHHHHHHHHHHHHcCC
Confidence 444 6899999999999999954
No 32
>PF07430 PP1: Phloem filament protein PP1; InterPro: IPR009994 This domain represents a conserved region approximately 200 residues long, four copies of which are found within the plant phloem filament protein PP1. This is one of the constituents of the proteinaceous filaments found in the sieve elements of Cucurbita phloem [].
Probab=34.15 E-value=32 Score=22.97 Aligned_cols=23 Identities=17% Similarity=0.346 Sum_probs=19.4
Q ss_pred CcccCCCCCHHHHHHHHHHHHHc
Q 040579 21 DRIPLPNVTIKIFYKAIKYCNKH 43 (72)
Q Consensus 21 ~~IplpnV~~~~L~kViewc~~H 43 (72)
.=||||+|....|.-|++|.-..
T Consensus 9 ~w~~ip~v~~~~~q~v~~~~veq 31 (202)
T PF07430_consen 9 KWIKIPDVKEPCLQEVAKFAVEQ 31 (202)
T ss_pred ccccCCcccchHHHHHHHHHHHH
Confidence 45899999999999999997544
No 33
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=33.90 E-value=37 Score=24.80 Aligned_cols=25 Identities=20% Similarity=0.227 Sum_probs=21.8
Q ss_pred CcccCCCCCHHHHHHHHHHHHHcCC
Q 040579 21 DRIPLPNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 21 ~~IplpnV~~~~L~kViewc~~H~~ 45 (72)
.|+=||+++..-+.+||+|.-.--.
T Consensus 261 aPv~lPG~ND~E~~~iIe~A~~iGa 285 (414)
T COG2100 261 APVWLPGVNDDEMPKIIEWAREIGA 285 (414)
T ss_pred eeeecCCcChHHHHHHHHHHHHhCC
Confidence 5788999999999999999877644
No 34
>PF03682 UPF0158: Uncharacterised protein family (UPF0158); InterPro: IPR005361 This is a small family of hypothetical bacterial proteins of unknown function.
Probab=33.67 E-value=33 Score=21.84 Aligned_cols=20 Identities=15% Similarity=0.326 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHcCCCCCC
Q 040579 30 IKIFYKAIKYCNKHDEASMF 49 (72)
Q Consensus 30 ~~~L~kViewc~~H~~~~~~ 49 (72)
......+++||+.|.=.+..
T Consensus 124 ~~~r~~a~eWleen~I~~~~ 143 (163)
T PF03682_consen 124 ERLRERAIEWLEENGIEPVF 143 (163)
T ss_pred HHHHHHHHHHHHHcCCCccc
Confidence 46678899999999766544
No 35
>PF06540 GMAP: Galanin message associated peptide (GMAP); InterPro: IPR013068 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. This domain represents the galanin message-associated peptide (GMAP) domain which is found C-terminal to the galanin domain in the preprogalanin precursor protein. GMAP sequences in different species show a high degree of homology, but the biological function of the GMAP peptide is not known [].
Probab=33.63 E-value=52 Score=17.96 Aligned_cols=16 Identities=13% Similarity=0.067 Sum_probs=13.9
Q ss_pred CHHHHHHHHHHHHHcC
Q 040579 29 TIKIFYKAIKYCNKHD 44 (72)
Q Consensus 29 ~~~~L~kViewc~~H~ 44 (72)
+..++..||||+.+-+
T Consensus 22 d~nivrTiiEFLtfLh 37 (62)
T PF06540_consen 22 DDNIVRTIIEFLTFLH 37 (62)
T ss_pred hhHHHHHHHHHHHHHH
Confidence 7889999999998754
No 36
>PF00631 G-gamma: GGL domain; InterPro: IPR015898 This entry represents the G protein gamma subunit and the GGL (G protein gamma-like) domain, which are related in sequence and are comprised of an extended alpha-helical polypeptide. The G protein gamma subunit forms a stable dimer with the beta subunit, but it does not make any contact with the alpha subunit, which contacts the opposite face of the beta subunit. The GGL domain is found in several RGS (regulators of G protein signaling) proteins. GGL domains can interact with beta subunits to form novel dimers that prevent gamma subunit binding, and may prevent heterotrimer formation by inhibiting alpha subunit binding. The interaction between G protein beta-5 neuro-specific isoforms and RGS GGL domains may represent a general mode of binding between beta-propeller proteins and their partners [].; GO: 0004871 signal transducer activity, 0007186 G-protein coupled receptor protein signaling pathway, 0005834 heterotrimeric G-protein complex; PDB: 3PSC_G 3SN6_G 1OMW_G 2BCJ_G 1GG2_G 3PVW_G 3PVU_G 3AH8_G 3CIK_G 1GP2_G ....
Probab=33.35 E-value=39 Score=18.15 Aligned_cols=17 Identities=24% Similarity=0.442 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHcCCCC
Q 040579 30 IKIFYKAIKYCNKHDEAS 47 (72)
Q Consensus 30 ~~~L~kViewc~~H~~~~ 47 (72)
|...+.+++||+ -..||
T Consensus 26 S~a~~~li~y~~-~~~DP 42 (68)
T PF00631_consen 26 SKACKELIEYCE-STPDP 42 (68)
T ss_dssp HHHHHHHHHHHH-GTC-H
T ss_pred HHHHHHHHHHhc-CCCCc
Confidence 789999999999 44453
No 37
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=33.09 E-value=46 Score=19.54 Aligned_cols=26 Identities=23% Similarity=0.339 Sum_probs=14.8
Q ss_pred CeecCChhHHH----HHHHh---cC--CCCcccCC
Q 040579 1 MLKSSDGEVFE----HMIED---DC--AVDRIPLP 26 (72)
Q Consensus 1 ~L~SsDg~~f~----~~i~~---~~--~~~~Iplp 26 (72)
+|.|.|-...+ .+++. .+ ..+|||||
T Consensus 6 ~L~S~d~~~Ld~~~~~I~~~ak~~g~~~~GPipLP 40 (99)
T TIGR01046 6 KLTSTNVRSLEKVCAQIKRIAEKTGVRMSGPVPLP 40 (99)
T ss_pred EEEECCHHHHHHHHHHHHHHHHHcCCEEECCccCC
Confidence 36677777666 22222 22 24788888
No 38
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=32.80 E-value=59 Score=18.81 Aligned_cols=19 Identities=16% Similarity=0.046 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHHHHHHHcC
Q 040579 26 PNVTIKIFYKAIKYCNKHD 44 (72)
Q Consensus 26 pnV~~~~L~kViewc~~H~ 44 (72)
.+++..+-+++..||+++.
T Consensus 40 ~D~~~~~~~~i~~~c~~~~ 58 (99)
T PRK01018 40 SNCPKDIKEDIEYYAKLSG 58 (99)
T ss_pred CCCCHHHHHHHHHHHHHcC
Confidence 4788999999999999985
No 39
>PF15472 DUF4638: Domain of unknown function (DUF4638)
Probab=31.09 E-value=36 Score=23.47 Aligned_cols=16 Identities=0% Similarity=0.204 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHcCCC
Q 040579 31 KIFYKAIKYCNKHDEA 46 (72)
Q Consensus 31 ~~L~kViewc~~H~~~ 46 (72)
.-|-+|+||++..++-
T Consensus 29 SDLTRVLEWLERRQGK 44 (268)
T PF15472_consen 29 SDLTRVLEWLERRQGK 44 (268)
T ss_pred hhHHHHHHHHHHhccc
Confidence 3588999999998774
No 40
>PRK06683 hypothetical protein; Provisional
Probab=30.67 E-value=69 Score=18.00 Aligned_cols=20 Identities=10% Similarity=0.205 Sum_probs=17.5
Q ss_pred CCCCHHHHHHHHHHHHHcCC
Q 040579 26 PNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 26 pnV~~~~L~kViewc~~H~~ 45 (72)
.+.+..+.+++..+|+++.-
T Consensus 35 ~Da~~~~~~~i~~~~~~~~V 54 (82)
T PRK06683 35 EDADMRLTHVIIRTALQHNI 54 (82)
T ss_pred CCCCHHHHHHHHHHHHhcCC
Confidence 47899999999999999853
No 41
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=27.90 E-value=91 Score=15.61 Aligned_cols=21 Identities=10% Similarity=0.097 Sum_probs=17.4
Q ss_pred CCCCHHHHHHHHHHHHHcCCC
Q 040579 26 PNVTIKIFYKAIKYCNKHDEA 46 (72)
Q Consensus 26 pnV~~~~L~kViewc~~H~~~ 46 (72)
+.|+..+-++|.+.++.+-.-
T Consensus 24 ~~vs~~tr~rI~~~a~~lgY~ 44 (46)
T PF00356_consen 24 PRVSEETRERILEAAEELGYR 44 (46)
T ss_dssp SSSTHHHHHHHHHHHHHHTB-
T ss_pred CCCCHHHHHHHHHHHHHHCCC
Confidence 579999999999999887553
No 42
>PRK07714 hypothetical protein; Provisional
Probab=27.58 E-value=78 Score=18.20 Aligned_cols=20 Identities=10% Similarity=0.177 Sum_probs=17.4
Q ss_pred CCCCHHHHHHHHHHHHHcCC
Q 040579 26 PNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 26 pnV~~~~L~kViewc~~H~~ 45 (72)
.+++..+-+++..+|+++.-
T Consensus 42 ~D~s~~~~~ki~~~~~~~~v 61 (100)
T PRK07714 42 EDASVNTTKKITDKCTYYNV 61 (100)
T ss_pred CCCCHHHHHHHHHHHHhcCC
Confidence 37999999999999999753
No 43
>PHA01623 hypothetical protein
Probab=27.11 E-value=78 Score=16.59 Aligned_cols=19 Identities=16% Similarity=0.294 Sum_probs=16.5
Q ss_pred CCCHHHHHHHHHHHHHcCC
Q 040579 27 NVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 27 nV~~~~L~kViewc~~H~~ 45 (72)
.++...+.++-.||..|..
T Consensus 19 rldeel~~~Ld~y~~~~g~ 37 (56)
T PHA01623 19 YMDKDLKTRLKVYCAKNNL 37 (56)
T ss_pred EeCHHHHHHHHHHHHHcCC
Confidence 4779999999999999965
No 44
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=26.64 E-value=78 Score=15.82 Aligned_cols=14 Identities=36% Similarity=0.543 Sum_probs=11.7
Q ss_pred CHHHHHHHHHHHHH
Q 040579 29 TIKIFYKAIKYCNK 42 (72)
Q Consensus 29 ~~~~L~kViewc~~ 42 (72)
...+|...|+|+.+
T Consensus 40 K~~iL~~ai~yI~~ 53 (55)
T PF00010_consen 40 KASILQKAIDYIKQ 53 (55)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 36899999999875
No 45
>KOG4119 consensus G protein gamma subunit [Signal transduction mechanisms]
Probab=26.55 E-value=94 Score=17.39 Aligned_cols=17 Identities=24% Similarity=0.511 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHcCCC
Q 040579 30 IKIFYKAIKYCNKHDEA 46 (72)
Q Consensus 30 ~~~L~kViewc~~H~~~ 46 (72)
+..=+.+.+||+.|...
T Consensus 31 S~a~~el~~y~E~~~~~ 47 (71)
T KOG4119|consen 31 SKAAAELLEYCETHATE 47 (71)
T ss_pred HHHHHHHHHHHHhcCcc
Confidence 55566778999999874
No 46
>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]
Probab=25.96 E-value=72 Score=24.02 Aligned_cols=26 Identities=12% Similarity=0.346 Sum_probs=23.1
Q ss_pred cccCCCCCHHHHHHHHHHHHHcCCCC
Q 040579 22 RIPLPNVTIKIFYKAIKYCNKHDEAS 47 (72)
Q Consensus 22 ~IplpnV~~~~L~kViewc~~H~~~~ 47 (72)
.||+|+.+...++...+|++....+|
T Consensus 556 ~lPfp~p~dp~~~~r~~~~~~~g~~~ 581 (654)
T COG1199 556 GLPFPNPDDPLLKARLEFLKRLGGDP 581 (654)
T ss_pred ecCCCCCCCHHHHHHHHHHHHhcCCC
Confidence 69999999999999999999886554
No 47
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=25.76 E-value=55 Score=19.11 Aligned_cols=15 Identities=20% Similarity=0.257 Sum_probs=12.4
Q ss_pred CHHHHHHHHHHHHHc
Q 040579 29 TIKIFYKAIKYCNKH 43 (72)
Q Consensus 29 ~~~~L~kViewc~~H 43 (72)
|..+|.|+|+||.=.
T Consensus 42 NP~i~ekLi~~~~Id 56 (96)
T PF07818_consen 42 NPSILEKLIEFFGID 56 (96)
T ss_pred ChHHHHHHHHHcCCC
Confidence 578999999999653
No 48
>PF09329 zf-primase: Primase zinc finger; InterPro: IPR015408 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger domain is found in Mcm10 proteins and DnaG-type primases []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0006260 DNA replication, 0005634 nucleus; PDB: 3H15_A 3EBE_C.
Probab=25.58 E-value=11 Score=19.18 Aligned_cols=9 Identities=44% Similarity=0.844 Sum_probs=5.6
Q ss_pred HHHHHHcCC
Q 040579 37 IKYCNKHDE 45 (72)
Q Consensus 37 iewc~~H~~ 45 (72)
=+||++|..
T Consensus 28 ~~~C~yH~~ 36 (46)
T PF09329_consen 28 GEYCDYHVE 36 (46)
T ss_dssp -SS-TTTHH
T ss_pred CcccHHHHH
Confidence 378999965
No 49
>PHA02713 hypothetical protein; Provisional
Probab=25.57 E-value=62 Score=24.25 Aligned_cols=24 Identities=13% Similarity=0.217 Sum_probs=21.0
Q ss_pred CcccCCCCCHHHHHHHHHHHHHcC
Q 040579 21 DRIPLPNVTIKIFYKAIKYCNKHD 44 (72)
Q Consensus 21 ~~IplpnV~~~~L~kViewc~~H~ 44 (72)
..|.|.+|+..+|+.||+|+....
T Consensus 67 ~~v~l~~v~~~~~~~ll~y~Yt~~ 90 (557)
T PHA02713 67 TRVNLQMFDKDAVKNIVQYLYNRH 90 (557)
T ss_pred ceEEeccCCHHHHHHHHHHhcCCC
Confidence 468999999999999999987753
No 50
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=25.40 E-value=54 Score=18.81 Aligned_cols=33 Identities=15% Similarity=0.241 Sum_probs=21.9
Q ss_pred HHHHHHhcCCCCcccCCCCCHHHHHHHHHHHHHcCCC
Q 040579 10 FEHMIEDDCAVDRIPLPNVTIKIFYKAIKYCNKHDEA 46 (72)
Q Consensus 10 f~~~i~~~~~~~~IplpnV~~~~L~kViewc~~H~~~ 46 (72)
|-.||+... .|.|.|-.--...|++||..|...
T Consensus 38 Ya~lLEAqd----~~~p~Ve~id~~~i~~fC~~~gy~ 70 (86)
T PF11360_consen 38 YAGLLEAQD----FPDPTVEEIDPEEIEEFCRSAGYE 70 (86)
T ss_pred HHHHHHhcC----CCCCCeEEECHHHHHHHHHHCCce
Confidence 336776542 344556666667788999999775
No 51
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=25.35 E-value=65 Score=15.91 Aligned_cols=15 Identities=7% Similarity=0.118 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHcCC
Q 040579 31 KIFYKAIKYCNKHDE 45 (72)
Q Consensus 31 ~~L~kViewc~~H~~ 45 (72)
.-+..+++||..+..
T Consensus 15 g~~~~a~~~~~~~~~ 29 (58)
T smart00668 15 GDWDEALEWLSSLKP 29 (58)
T ss_pred CCHHHHHHHHHHcCH
Confidence 346788999999975
No 52
>PF13315 DUF4085: Protein of unknown function (DUF4085)
Probab=25.25 E-value=95 Score=20.85 Aligned_cols=26 Identities=15% Similarity=0.203 Sum_probs=21.3
Q ss_pred CCcccCCCCCHHHHHHHHHHHHHcCC
Q 040579 20 VDRIPLPNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 20 ~~~IplpnV~~~~L~kViewc~~H~~ 45 (72)
+..+.++-.+.+..+.+.+||+-...
T Consensus 69 d~~~~~~~~s~~l~~~~~ew~~~~~~ 94 (208)
T PF13315_consen 69 DIRFNLDYPSEKLKKAITEWCEDYEK 94 (208)
T ss_pred cCcccCCCCcHHHHHHHHHHHHHHHH
Confidence 44588888899999999999987644
No 53
>CHL00135 rps10 ribosomal protein S10; Validated
Probab=24.93 E-value=77 Score=18.68 Aligned_cols=25 Identities=44% Similarity=0.603 Sum_probs=13.6
Q ss_pred eecCChhHHH---HHH----HhcC--CCCcccCC
Q 040579 2 LKSSDGEVFE---HMI----EDDC--AVDRIPLP 26 (72)
Q Consensus 2 L~SsDg~~f~---~~i----~~~~--~~~~Iplp 26 (72)
|.|.|-...+ +.| ...+ ..+|||||
T Consensus 13 LkS~d~~~L~~~~~~I~~~~k~~~~~~~GpipLP 46 (101)
T CHL00135 13 LKSFNHELLNSSCKKIIDTASRTNATAVGPIPLP 46 (101)
T ss_pred EEECCHHHHHHHHHHHHHHHHHcCCeEeCCcCCC
Confidence 5666666666 222 1122 24788887
No 54
>smart00229 RasGEFN Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).
Probab=24.81 E-value=31 Score=20.15 Aligned_cols=20 Identities=10% Similarity=-0.092 Sum_probs=17.2
Q ss_pred CCCCHHHHHHHHHHHHHcCC
Q 040579 26 PNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 26 pnV~~~~L~kViewc~~H~~ 45 (72)
+.|.+.+|.++|++|..+..
T Consensus 3 ~~i~~gtl~~Li~~L~~~~~ 22 (127)
T smart00229 3 GLIKGGTLEKLIEHLTEAFD 22 (127)
T ss_pred CeeeeecHHHHHHHHcCCCc
Confidence 45789999999999998865
No 55
>COG4849 Predicted nucleotidyltransferase [General function prediction only]
Probab=24.48 E-value=95 Score=21.41 Aligned_cols=27 Identities=15% Similarity=0.127 Sum_probs=22.6
Q ss_pred CcccCCCCCHHHHHHHHHHHHHcCCCC
Q 040579 21 DRIPLPNVTIKIFYKAIKYCNKHDEAS 47 (72)
Q Consensus 21 ~~IplpnV~~~~L~kViewc~~H~~~~ 47 (72)
-.|+||.+.|-++-|.+.|++.-.+++
T Consensus 136 ~~v~l~~~Pgl~~lKLhAWLDR~~~n~ 162 (269)
T COG4849 136 LTVHLPQPPGLAVLKLHAWLDRADHNY 162 (269)
T ss_pred eeeecCCCCchHHHHHHHHHhhcccCc
Confidence 369999999999999999999854443
No 56
>PRK04966 hypothetical protein; Provisional
Probab=24.46 E-value=58 Score=18.27 Aligned_cols=21 Identities=14% Similarity=0.316 Sum_probs=16.1
Q ss_pred cccCCCCCHHHHHHHHH-HHHH
Q 040579 22 RIPLPNVTIKIFYKAIK-YCNK 42 (72)
Q Consensus 22 ~IplpnV~~~~L~kVie-wc~~ 42 (72)
.||...+++.||..+|+ |...
T Consensus 2 iIP~~~L~~eTL~nLIeefv~R 23 (72)
T PRK04966 2 IIPWQDLAPETLENLIESFVLR 23 (72)
T ss_pred cCChHhCCHHHHHHHHHHHHhc
Confidence 37888899999998885 4444
No 57
>COG0051 RpsJ Ribosomal protein S10 [Translation, ribosomal structure and biogenesis]
Probab=24.42 E-value=84 Score=18.85 Aligned_cols=6 Identities=67% Similarity=1.243 Sum_probs=3.9
Q ss_pred CcccCC
Q 040579 21 DRIPLP 26 (72)
Q Consensus 21 ~~Iplp 26 (72)
+|||||
T Consensus 38 GPiPLP 43 (104)
T COG0051 38 GPIPLP 43 (104)
T ss_pred CCccCC
Confidence 566666
No 58
>PF06303 MatP: Organiser of macrodomain of Terminus of chromosome; InterPro: IPR009390 Many bacteria have circular genomes that are large in comparison to their cellular dimensions; this imposes the necessity for compaction of the chromosome during cellular growth, replication, transcription, and segregation. Compaction of chromosomes results in the formation of structures called nucleoids. Nucleoids can be generated by a number of different processes: they include unrestrained DNA supercoiling, formation of a chromatin-like structure through the interaction of DNA binding proteins, condensation by structural maintenance of chromosomes (SMC)-like proteins, and macromolecular crowding []. Chromosome replication and segregation are intimately linked and tightly controlled to ensure that daughter cells each receive a complete copy of the genome. Chromosomes have replication origin (Ori) and termination (Ter) regions that are diametrically opposed. During the process of chromosome replication and cell division the Ori and Ter regions form two macrodomains (MDs), the Ori MD is centred on migS, a 25 bp sequence, that acts as the cis-acting site for the bipolar positioning of oriC []. The Ter MD is centred on dif (deletion-induced filamentation), which is a resolvase site that reduces chromosome multimers to monomers []. The Ori and Ter MDs are insulated from one and other by non-structural regions and other nucleoids. Chromosome replication initiates bidirectionally from oriC. Within the Ori MD with sister chromatids being located in separate cell halves and with the Ter macrodomain anchored to the cell pole. Cell division occurs with the completion of replication of the Ter region and the subsequent separation of the two sister chromatids [, ]. This entry contains MatP (YcbG), which is a component of the MatP/MatS site-specific system that organises the Ter macrodomain (MD) in Escherichia coli (strain K12) and related enterobacteria during replication of the chromosome. In E. coli there are 23 matS sequences, located in the Ter region which is centred on dif. The matS consensus is a palindromic sequence 5'-GTGAC[AG][CT]GTCAC, which is the recognition sequence for MatP. MatP binds to the matS sequences; and is critical for Ter MD formation. Inactivation of matP causes severe defects in chromosome segregation and cell division revealing its role as a major organiser of the Ter MD [].
Probab=24.37 E-value=52 Score=21.01 Aligned_cols=13 Identities=23% Similarity=0.304 Sum_probs=10.6
Q ss_pred HHHHHHHHHcCCC
Q 040579 34 YKAIKYCNKHDEA 46 (72)
Q Consensus 34 ~kViewc~~H~~~ 46 (72)
.+|.+||..|-..
T Consensus 52 ~~v~~WI~~~m~~ 64 (148)
T PF06303_consen 52 VKVNEWIKKHMNP 64 (148)
T ss_pred HHHHHHHHHHCCH
Confidence 4788999999764
No 59
>PTZ00039 40S ribosomal protein S20; Provisional
Probab=24.31 E-value=79 Score=19.16 Aligned_cols=7 Identities=14% Similarity=0.563 Sum_probs=4.7
Q ss_pred CCcccCC
Q 040579 20 VDRIPLP 26 (72)
Q Consensus 20 ~~~Iplp 26 (72)
.+|||||
T Consensus 50 ~GPipLP 56 (115)
T PTZ00039 50 TGPVRMP 56 (115)
T ss_pred ECCccCC
Confidence 3677777
No 60
>PTZ00271 hypoxanthine-guanine phosphoribosyltransferase; Provisional
Probab=24.15 E-value=76 Score=21.05 Aligned_cols=17 Identities=0% Similarity=0.034 Sum_probs=15.0
Q ss_pred CHHHHHHHHHHHHHcCC
Q 040579 29 TIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 29 ~~~~L~kViewc~~H~~ 45 (72)
+|.||+.++++|..+..
T Consensus 130 TG~TL~~v~~~l~~~~p 146 (211)
T PTZ00271 130 SAITLQYLMRFMLAKKP 146 (211)
T ss_pred CHHHHHHHHHHHHhcCC
Confidence 79999999999998743
No 61
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=24.13 E-value=96 Score=18.38 Aligned_cols=19 Identities=11% Similarity=-0.160 Sum_probs=17.2
Q ss_pred CCCCHHHHHHHHHHHHHcC
Q 040579 26 PNVTIKIFYKAIKYCNKHD 44 (72)
Q Consensus 26 pnV~~~~L~kViewc~~H~ 44 (72)
.+++..+-+++..||+++.
T Consensus 49 ~D~~~~~kkki~~~~~~~~ 67 (108)
T PTZ00106 49 NNCPPIRRSEIEYYAMLSK 67 (108)
T ss_pred CCCCHHHHHHHHHHHhhcC
Confidence 4899999999999999985
No 62
>COG0634 Hpt Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=23.95 E-value=64 Score=21.20 Aligned_cols=18 Identities=6% Similarity=-0.060 Sum_probs=15.3
Q ss_pred CHHHHHHHHHHHHHcCCC
Q 040579 29 TIKIFYKAIKYCNKHDEA 46 (72)
Q Consensus 29 ~~~~L~kViewc~~H~~~ 46 (72)
+|.||+.|.+||.+....
T Consensus 105 sG~TLs~i~~~l~~r~a~ 122 (178)
T COG0634 105 SGLTLSKVRDLLKERGAK 122 (178)
T ss_pred cChhHHHHHHHHHhCCCC
Confidence 689999999999977554
No 63
>PF08879 WRC: WRC; InterPro: IPR014977 WRC is named after the conserved Trp-Arg-Cys motif, it contains two distinctive features: a putative nuclear localisation signal and a zinc-finger motif (C3H). It is suggested that WRC functions in DNA binding []. ; GO: 0005515 protein binding
Probab=23.93 E-value=34 Score=17.51 Aligned_cols=8 Identities=25% Similarity=0.742 Sum_probs=6.4
Q ss_pred HHHHHcCC
Q 040579 38 KYCNKHDE 45 (72)
Q Consensus 38 ewc~~H~~ 45 (72)
.||+||..
T Consensus 26 ~~Ce~H~~ 33 (46)
T PF08879_consen 26 SLCEHHLD 33 (46)
T ss_pred cHHHHHHH
Confidence 47999975
No 64
>PF09336 Vps4_C: Vps4 C terminal oligomerisation domain; InterPro: IPR015415 This domain is found at the C-terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation []. ; PDB: 1XWI_A 3EIH_C 2QPA_C 3EIE_A 2RKO_A 2QP9_X 3MHV_C 3CF3_C 3CF1_A 3CF2_A ....
Probab=23.75 E-value=95 Score=16.51 Aligned_cols=18 Identities=17% Similarity=0.257 Sum_probs=14.3
Q ss_pred CCCCHHHHHHHHHHHHHc
Q 040579 26 PNVTIKIFYKAIKYCNKH 43 (72)
Q Consensus 26 pnV~~~~L~kViewc~~H 43 (72)
|.|+..-|++-.+|-+.+
T Consensus 44 pSVs~~dl~~ye~w~~~F 61 (62)
T PF09336_consen 44 PSVSQEDLKKYEEWTKEF 61 (62)
T ss_dssp GSS-HHHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHHHHHHc
Confidence 689999999999997654
No 65
>PHA00159 endonuclease I
Probab=23.71 E-value=40 Score=21.49 Aligned_cols=9 Identities=33% Similarity=0.870 Sum_probs=7.3
Q ss_pred HHHHHHcCC
Q 040579 37 IKYCNKHDE 45 (72)
Q Consensus 37 iewc~~H~~ 45 (72)
-+||+.|--
T Consensus 110 a~Wc~khG~ 118 (148)
T PHA00159 110 AEWCEKHGI 118 (148)
T ss_pred HHHHHHcCc
Confidence 599999954
No 66
>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole [, ]. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes [, ].
Probab=22.91 E-value=72 Score=23.17 Aligned_cols=16 Identities=31% Similarity=0.383 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHcCC
Q 040579 30 IKIFYKAIKYCNKHDE 45 (72)
Q Consensus 30 ~~~L~kViewc~~H~~ 45 (72)
-+...+|+.||+++..
T Consensus 390 i~~~~~likWikk~e~ 405 (415)
T PF03164_consen 390 IASANKLIKWIKKEEN 405 (415)
T ss_pred HHHHHHHHHHHHhhcC
Confidence 4557899999999854
No 67
>PHA03098 kelch-like protein; Provisional
Probab=22.87 E-value=1.2e+02 Score=22.04 Aligned_cols=32 Identities=22% Similarity=0.324 Sum_probs=23.1
Q ss_pred HHHHhcCCCCcccCCCCCHHHHHHHHHHHHHcC
Q 040579 12 HMIEDDCAVDRIPLPNVTIKIFYKAIKYCNKHD 44 (72)
Q Consensus 12 ~~i~~~~~~~~IplpnV~~~~L~kViewc~~H~ 44 (72)
.|+...-....|.|+. +..+|+.||+|+..-+
T Consensus 39 ~mf~~~~~~~~i~l~~-~~~~~~~~l~y~Ytg~ 70 (534)
T PHA03098 39 KMFKNNFKENEINLNI-DYDSFNEVIKYIYTGK 70 (534)
T ss_pred HHHhCCCCCceEEecC-CHHHHHHHHHHhcCCc
Confidence 5554322245688888 9999999999976654
No 68
>KOG3977 consensus Troponin I [Cytoskeleton]
Probab=22.86 E-value=36 Score=22.88 Aligned_cols=13 Identities=38% Similarity=0.480 Sum_probs=9.9
Q ss_pred CCcccCCCCCHHH
Q 040579 20 VDRIPLPNVTIKI 32 (72)
Q Consensus 20 ~~~IplpnV~~~~ 32 (72)
+..||||+|++--
T Consensus 76 eR~i~lp~~d~l~ 88 (221)
T KOG3977|consen 76 ERTIPLPDVDSLD 88 (221)
T ss_pred HccCCCCCCCccc
Confidence 4689999987643
No 69
>smart00740 PASTA PASTA domain.
Probab=22.79 E-value=52 Score=16.21 Aligned_cols=22 Identities=18% Similarity=0.108 Sum_probs=19.2
Q ss_pred cccCCCCCHHHHHHHHHHHHHc
Q 040579 22 RIPLPNVTIKIFYKAIKYCNKH 43 (72)
Q Consensus 22 ~IplpnV~~~~L~kViewc~~H 43 (72)
.+.+|++.+.++..+.+++...
T Consensus 4 ~~~vp~~~g~~~~~a~~~l~~~ 25 (66)
T smart00740 4 KVEVPDVIGLSKEEAKKLLKAL 25 (66)
T ss_pred eeeCCCcCCCCHHHHHHHHHHC
Confidence 4778999999999999999865
No 70
>KOG1232 consensus Proteins containing the FAD binding domain [Energy production and conversion]
Probab=22.49 E-value=1.8e+02 Score=21.92 Aligned_cols=29 Identities=21% Similarity=0.344 Sum_probs=20.8
Q ss_pred CcccCCCCCHHHHHHHHHHHHHcCCCCCCc
Q 040579 21 DRIPLPNVTIKIFYKAIKYCNKHDEASMFD 50 (72)
Q Consensus 21 ~~IplpnV~~~~L~kViewc~~H~~~~~~~ 50 (72)
.-+-.|+ +..-.+.|++||+..+-.-.|.
T Consensus 91 klvL~Pk-st~eVS~ILkYCn~~kLAVVPQ 119 (511)
T KOG1232|consen 91 KLVLKPK-STEEVSAILKYCNDRKLAVVPQ 119 (511)
T ss_pred eEEecCC-CHHHHHHHHHhhccccEEEecC
Confidence 3466664 5667789999999998764443
No 71
>PF01736 Polyoma_agno: Polyomavirus agnoprotein; InterPro: IPR002643 This family consists of the DNA-binding protein or agnoprotein from various polyomaviruses. This protein is highly basic and can bind single stranded and double stranded DNA []. Mutations in the agnoprotein produce smaller viral plaques, hence its function is not essential for growth in tissue culture cells but something has slowed in the normal replication cycle []. There is also evidence suggesting that the agnogene and agnoprotein act as regulators of structural protein synthesis [].; GO: 0003677 DNA binding
Probab=22.45 E-value=62 Score=17.41 Aligned_cols=13 Identities=15% Similarity=0.434 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHc
Q 040579 31 KIFYKAIKYCNKH 43 (72)
Q Consensus 31 ~~L~kViewc~~H 43 (72)
-+|..+++||.-.
T Consensus 31 FiLElLL~FC~Ge 43 (62)
T PF01736_consen 31 FILELLLEFCRGE 43 (62)
T ss_pred HHHHHHHHHhcCC
Confidence 4788999999753
No 72
>smart00492 HELICc3 helicase superfamily c-terminal domain.
Probab=22.32 E-value=89 Score=19.13 Aligned_cols=23 Identities=13% Similarity=0.296 Sum_probs=20.3
Q ss_pred cccCCCCCHHHHHHHHHHHHHcC
Q 040579 22 RIPLPNVTIKIFYKAIKYCNKHD 44 (72)
Q Consensus 22 ~IplpnV~~~~L~kViewc~~H~ 44 (72)
-+|.|+.+...++.-.+|.+++.
T Consensus 76 glPfp~~~d~~~~~~~~~~~~~~ 98 (141)
T smart00492 76 GLPFPYPDSPILKARLELLRDKG 98 (141)
T ss_pred ecCCCCCCCHHHHHHHHHHHHhC
Confidence 58999999999999999998875
No 73
>KOG4441 consensus Proteins containing BTB/POZ and Kelch domains, involved in regulatory/signal transduction processes [Signal transduction mechanisms; General function prediction only]
Probab=22.28 E-value=97 Score=23.48 Aligned_cols=26 Identities=15% Similarity=0.135 Sum_probs=22.3
Q ss_pred CCcccCCCCCHHHHHHHHHHHHHcCC
Q 040579 20 VDRIPLPNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 20 ~~~IplpnV~~~~L~kViewc~~H~~ 45 (72)
...|.|..|++.+|..+|+|+...+-
T Consensus 75 ~~~i~l~~v~~~~l~~ll~y~Yt~~i 100 (571)
T KOG4441|consen 75 QKEINLEGVDPETLELLLDYAYTGKL 100 (571)
T ss_pred ceEEEEecCCHHHHHHHHHHhhcceE
Confidence 45799999999999999999877654
No 74
>PF06794 UPF0270: Uncharacterised protein family (UPF0270); InterPro: IPR010648 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 1Y0N_A.
Probab=21.98 E-value=60 Score=18.07 Aligned_cols=20 Identities=15% Similarity=0.371 Sum_probs=12.8
Q ss_pred ccCCCCCHHHHHHHHH-HHHH
Q 040579 23 IPLPNVTIKIFYKAIK-YCNK 42 (72)
Q Consensus 23 IplpnV~~~~L~kVie-wc~~ 42 (72)
||...+++.||..+|+ |+..
T Consensus 3 IP~~~L~~eTL~nLIeefv~R 23 (70)
T PF06794_consen 3 IPYQQLPPETLNNLIEEFVLR 23 (70)
T ss_dssp --GGGS-HHHHHHHHHHHHH-
T ss_pred CChHHCCHHHHHHHHHHHHHc
Confidence 7877899999998885 5543
No 75
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=21.81 E-value=26 Score=19.02 Aligned_cols=11 Identities=36% Similarity=0.625 Sum_probs=7.9
Q ss_pred CeecCChhHHH
Q 040579 1 MLKSSDGEVFE 11 (72)
Q Consensus 1 ~L~SsDg~~f~ 11 (72)
++.|.||++|-
T Consensus 8 Kv~~RDGE~~l 18 (65)
T COG4049 8 KVRDRDGEEFL 18 (65)
T ss_pred EeeccCCceee
Confidence 35677888776
No 76
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=21.67 E-value=1.2e+02 Score=16.33 Aligned_cols=24 Identities=8% Similarity=0.027 Sum_probs=17.7
Q ss_pred cccCCCCCHHHHHHHHHHHHHcCC
Q 040579 22 RIPLPNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 22 ~IplpnV~~~~L~kViewc~~H~~ 45 (72)
.+-|.+++.+..+++++|+.--..
T Consensus 26 ivnl~~l~~~~~~Ri~Dfl~G~~~ 49 (73)
T PF04472_consen 26 IVNLENLDDEEAQRILDFLSGAVY 49 (73)
T ss_dssp EEE-TTS-HHHHHHHHHHHHHHHH
T ss_pred EEECCCCCHHHHHHHHHHHhchhe
Confidence 366789999999999999976543
No 77
>PF00307 CH: Calponin homology (CH) domain; InterPro: IPR001715 The calponin homology domain (also known as CH-domain) is a superfamily of actin-binding domains found in both cytoskeletal proteins and signal transduction proteins []. It comprises the following groups of actin-binding domains: Actinin-type (including spectrin, fimbrin, ABP-280) (see IPR001589 from INTERPRO). Calponin-type (see IPR000557 from INTERPRO). A comprehensive review of proteins containing this type of actin-binding domains is given in []. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity []. Most proteins have two copies of the CH domain, however some proteins such as calponin and the human vav proto-oncogene (P15498 from SWISSPROT) have only a single copy. The structure of an example CH-domain has recently been solved []. This entry represents the calponin-homology (CH) domain, a superfamily of actin-binding domains found in cytoskeletal proteins (contain two CH domain in tandem repeat), in regulatory proteins from muscle, and in signal transduction proteins. This domain has a core structure consisting of a 4-helical bundle. This domain is found in: Calponin, which is involved in the regulation of contractility and organisation of the actin cytoskeleton in smooth muscle cells []. Beta-spectrin, a major component of a submembrane cytoskeletal network connecting actin filaments to integral plasma membrane proteins []. The actin-cross-linking domain of the fimbrin/plastin family of actin filament bundling or cross-linking proteins []. Utrophin,a close homologue of dystrophin []. Dystrophin, the protein found to be defective in Duchenne muscular dystrophy; this protein contains a tandem repeat of two CH domains []. Actin-binding domain of plectin, a large and widely expressed cytolinker protein []. The N-terminal microtubule-binding domain of microtubule-associated protein eb1 (end-binding protein), a member of a conserved family of proteins that localise to the plus-ends of microtubules []. Ras GTPase-activating-like protein rng2, an IQGAP protein that is essential for the assembly of an actomyosin ring during cytokinesis []. Transgelin, which suppresses androgen receptor transactivation []. ; GO: 0005515 protein binding; PDB: 2DK9_A 1WYL_A 1WKU_B 1TJT_A 3FER_A 2WA7_A 2WA5_A 2WA6_A 2R0O_A 1PXY_A ....
Probab=21.61 E-value=1.6e+02 Score=16.17 Aligned_cols=43 Identities=19% Similarity=0.204 Sum_probs=26.9
Q ss_pred CChhHHHHHHHhcCCCCcccCCCCC---------HHHHHHHHHHHHHcCCCCC
Q 040579 5 SDGEVFEHMIEDDCAVDRIPLPNVT---------IKIFYKAIKYCNKHDEASM 48 (72)
Q Consensus 5 sDg~~f~~~i~~~~~~~~IplpnV~---------~~~L~kViewc~~H~~~~~ 48 (72)
+||..+-.+|..+.. ..|+...++ -.-+.+++++|+.+.+-+.
T Consensus 29 ~dG~~L~~Li~~l~p-~~i~~~~~~~~~~~~~~~~~Ni~~~l~~~~~~lg~~~ 80 (108)
T PF00307_consen 29 RDGVVLCKLINKLFP-GTIDLKKINPNLKSPFDKLENIELALEAAEKKLGIPP 80 (108)
T ss_dssp TTSHHHHHHHHHHST-TSSSGGGSSTSSSSHHHHHHHHHHHHHHHHHHTTSSC
T ss_pred cCHHHHHHHHHHHhh-ccchhhhccccchhhhHHHHHHHHHHHHHHHHcCCCC
Confidence 477777777776532 234444441 2347888999998766543
No 78
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=21.45 E-value=78 Score=16.63 Aligned_cols=20 Identities=20% Similarity=0.330 Sum_probs=10.9
Q ss_pred CCCCHHHHHHHHHHHHHcCC
Q 040579 26 PNVTIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 26 pnV~~~~L~kViewc~~H~~ 45 (72)
|-++..-.++=++||..|.+
T Consensus 53 P~Ls~~~~~~Rl~fA~~h~~ 72 (72)
T PF01498_consen 53 PFLSPKHKKKRLEFAKEHLD 72 (72)
T ss_dssp ES--HHHHHHHHHHH-----
T ss_pred CCCCHHHHHHHHHHhhhccC
Confidence 34888888899999998863
No 79
>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid [].; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.
Probab=21.20 E-value=76 Score=21.72 Aligned_cols=21 Identities=19% Similarity=0.260 Sum_probs=15.8
Q ss_pred cCCCCCHHHHHHHHHHHHHcCCC
Q 040579 24 PLPNVTIKIFYKAIKYCNKHDEA 46 (72)
Q Consensus 24 plpnV~~~~L~kViewc~~H~~~ 46 (72)
.|..|+|- ..+|+||.+|.-.
T Consensus 168 ~ledIdGy--r~~i~~a~~~~v~ 188 (233)
T PF01745_consen 168 ILEDIDGY--RYIIRFARKHQVT 188 (233)
T ss_dssp HHTTSTTH--HHHHHHHHHTT--
T ss_pred hHhhhccH--HHHHHHHHHhCCC
Confidence 35678874 9999999999764
No 80
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=20.10 E-value=1.2e+02 Score=16.35 Aligned_cols=19 Identities=21% Similarity=0.450 Sum_probs=13.5
Q ss_pred CHHHHHHHHHHHHHcCCCCC
Q 040579 29 TIKIFYKAIKYCNKHDEASM 48 (72)
Q Consensus 29 ~~~~L~kViewc~~H~~~~~ 48 (72)
....|.+||+|+..+ +.|.
T Consensus 3 ~~tql~~~VeymK~r-~~Pl 21 (65)
T PF02186_consen 3 KFTQLAKAVEYMKKR-DHPL 21 (65)
T ss_dssp THHHHHHHHHHHHHH--S-B
T ss_pred hhhHHHHHHHHHHhc-CCCc
Confidence 467899999999988 3343
No 81
>PF05321 HHA: Haemolysin expression modulating protein; InterPro: IPR007985 This family consists of haemolysin expression modulating protein (Hha) from Escherichia coli and its enterobacterial homologues, such as YmoA from Yersinia enterocolitica, and RmoA encoded on the R100 plasmid. These proteins act as modulators of bacterial gene expression. Members of the Hha/YmoA/RmoA family act in conjunction with members of the H-NS family, participating in the thermoregulation of different virulence factors and in plasmid transfer []. Hha, along with the chromatin-associated protein H-NS, is involved in the regulation of expression of the toxin alpha-haemolysin in response to osmolarity and temperature []. YmoA modulates the expression of various virulence factors, such as Yop proteins and YadA adhesin, in response to temperature. RmoA is a plasmid R100 modulator involved in plasmid transfer []. The HHA family of proteins display striking similarity to the oligomerization domain of the H-NS proteins.; PDB: 1JW2_A 2K5S_A 2JQT_A.
Probab=20.06 E-value=1.3e+02 Score=16.19 Aligned_cols=17 Identities=12% Similarity=0.055 Sum_probs=12.3
Q ss_pred CHHHHHHHHHHHHHcCC
Q 040579 29 TIKIFYKAIKYCNKHDE 45 (72)
Q Consensus 29 ~~~~L~kViewc~~H~~ 45 (72)
+..||.|||+-..+--.
T Consensus 8 s~dtLEkv~e~~~~~L~ 24 (57)
T PF05321_consen 8 SLDTLEKVIEHNRYKLT 24 (57)
T ss_dssp -HHHHHHHHHHHHHHS-
T ss_pred CHhhHHHHHHHhhCcCC
Confidence 35799999998877643
No 82
>PF05367 Phage_endo_I: Phage endonuclease I; InterPro: IPR008029 Endonuclease I (3.1.21.2 from EC) is a junction-resolving enzyme encoded by bacteriophage T7, that selectively binds and cleaves four-way Holliday DNA junctions []. The structure of the enzyme shows that it forms a symmetric homodimer arranged in two well-separated domains. Each domain, however, is composed of elements from both subunits, and amino acid side chains from both protomers contribute to the active site []. ; GO: 0008833 deoxyribonuclease IV (phage-T4-induced) activity, 0015074 DNA integration, 0016032 viral reproduction; PDB: 3CAE_A 1M0D_A 1M0I_C 1FZR_B 2PFJ_B.
Probab=20.06 E-value=54 Score=20.93 Aligned_cols=9 Identities=33% Similarity=0.826 Sum_probs=6.6
Q ss_pred HHHHHHcCC
Q 040579 37 IKYCNKHDE 45 (72)
Q Consensus 37 iewc~~H~~ 45 (72)
-+||+.|--
T Consensus 110 a~Wc~K~Gf 118 (149)
T PF05367_consen 110 AEWCEKHGF 118 (149)
T ss_dssp HHHHHHCT-
T ss_pred HHHHHHcCC
Confidence 389999943
No 83
>COG5478 Predicted small integral membrane protein [Function unknown]
Probab=20.01 E-value=1.6e+02 Score=18.64 Aligned_cols=28 Identities=4% Similarity=-0.015 Sum_probs=24.1
Q ss_pred CCcccCCCCCHHHHHHHHHHHHHcCCCC
Q 040579 20 VDRIPLPNVTIKIFYKAIKYCNKHDEAS 47 (72)
Q Consensus 20 ~~~IplpnV~~~~L~kViewc~~H~~~~ 47 (72)
.+.|=|..-+.+.++++++||+++....
T Consensus 92 n~~VgIEh~~~~~i~~~~~~~e~~a~~~ 119 (141)
T COG5478 92 NDVVGIEHLKPEEIEEIRDRLEDEAGTG 119 (141)
T ss_pred CceeeeccCCHHHHHHHHHHHHHHhcCC
Confidence 3568888999999999999999998753
Done!