Query 031315
Match_columns 161
No_of_seqs 122 out of 600
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 12:22:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031315.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031315hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2659 LisH motif-containing 100.0 8.8E-37 1.9E-41 240.9 14.1 158 2-159 70-228 (228)
2 PF10607 CLTH: CTLH/CRA C-term 100.0 6.1E-35 1.3E-39 217.0 11.6 135 2-139 7-144 (145)
3 KOG0396 Uncharacterized conser 99.9 1.5E-22 3.2E-27 168.4 9.4 131 2-135 158-289 (389)
4 smart00757 CRA CT11-RanBPM. pr 99.9 2.2E-21 4.7E-26 135.3 9.5 93 50-142 2-96 (99)
5 KOG2817 Predicted E3 ubiquitin 99.8 3E-18 6.5E-23 143.9 10.8 133 2-137 161-308 (394)
6 smart00668 CTLH C-terminal to 99.4 2.9E-13 6.3E-18 85.4 3.6 50 2-51 7-56 (58)
7 KOG1477 SPRY domain-containing 98.7 4E-09 8.7E-14 92.3 2.4 112 29-140 338-451 (469)
8 KOG0293 WD40 repeat-containing 94.3 0.32 6.9E-06 42.4 8.5 126 4-136 57-186 (519)
9 COG5109 Uncharacterized conser 92.9 0.74 1.6E-05 38.8 8.2 122 3-129 145-291 (396)
10 cd08044 TAF5_NTD2 TAF5_NTD2 is 84.2 1.1 2.4E-05 32.7 2.9 111 16-130 12-124 (133)
11 PF14559 TPR_19: Tetratricopep 75.7 11 0.00023 23.0 5.2 56 6-66 1-56 (68)
12 PF04494 TFIID_90kDa: WD40 ass 74.9 2.4 5.2E-05 31.3 2.2 98 16-117 23-122 (142)
13 smart00668 CTLH C-terminal to 68.7 6.6 0.00014 23.6 2.8 28 38-65 4-31 (58)
14 PF10827 DUF2552: Protein of u 64.0 4.7 0.0001 26.7 1.5 17 11-27 60-76 (79)
15 PF10607 CLTH: CTLH/CRA C-term 63.2 30 0.00064 24.9 5.9 27 39-65 5-31 (145)
16 PF13838 Clathrin_H_link: Clat 62.8 11 0.00025 24.4 3.1 41 36-77 7-47 (66)
17 PRK02289 4-oxalocrotonate taut 54.0 15 0.00032 22.8 2.5 26 98-123 13-38 (60)
18 PF15391 DUF4614: Domain of un 45.5 25 0.00054 27.4 3.0 49 13-61 113-178 (181)
19 PF07208 DUF1414: Protein of u 43.7 26 0.00056 21.0 2.2 20 97-116 24-43 (44)
20 PF07035 Mic1: Colon cancer-as 42.1 46 0.00099 25.5 4.0 41 21-61 72-115 (167)
21 PF05971 Methyltransf_10: Prot 40.6 46 0.001 27.9 4.2 52 104-155 49-113 (299)
22 PF00627 UBA: UBA/TS-N domain; 40.1 22 0.00048 19.7 1.6 11 9-19 27-37 (37)
23 PF07721 TPR_4: Tetratricopept 39.9 31 0.00067 17.5 2.0 16 5-20 10-25 (26)
24 PF12895 Apc3: Anaphase-promot 37.7 44 0.00095 21.4 3.0 12 48-59 38-49 (84)
25 PF12931 Sec16_C: Sec23-bindin 37.2 25 0.00053 28.9 2.0 21 2-22 1-21 (284)
26 PF14691 Fer4_20: Dihydroprymi 37.1 47 0.001 23.5 3.2 25 36-60 39-63 (111)
27 PF14973 TINF2_N: TERF1-intera 36.5 1.1E+02 0.0024 22.9 5.2 76 3-83 47-130 (145)
28 COG3492 Uncharacterized protei 35.2 81 0.0018 21.9 4.0 46 96-141 5-50 (104)
29 PRK07143 hypothetical protein; 34.5 29 0.00063 28.7 2.0 22 2-23 154-175 (279)
30 PRK01271 4-oxalocrotonate taut 33.4 46 0.001 22.0 2.5 27 97-123 13-39 (76)
31 COG3071 HemY Uncharacterized e 32.8 1.6E+02 0.0036 25.7 6.3 72 3-87 270-341 (400)
32 PF12854 PPR_1: PPR repeat 32.7 44 0.00095 18.1 2.0 19 3-21 14-32 (34)
33 PF03398 Ist1: Regulator of Vp 30.3 2.4E+02 0.0052 21.2 7.3 20 2-21 28-47 (165)
34 PF01361 Tautomerase: Tautomer 30.2 51 0.0011 20.0 2.2 25 98-122 12-36 (60)
35 PF00547 Urease_gamma: Urease, 30.0 1.1E+02 0.0023 21.5 3.9 26 39-64 40-66 (99)
36 PTZ00196 60S ribosomal protein 29.9 1.4E+02 0.0031 20.9 4.5 30 37-66 50-79 (98)
37 PRK13689 hypothetical protein; 29.3 27 0.00058 23.2 0.8 22 97-118 49-70 (75)
38 cd00390 Urease_gamma Urease ga 29.2 1.2E+02 0.0026 21.2 4.1 28 37-64 35-63 (96)
39 KOG2235 Uncharacterized conser 29.1 1.2E+02 0.0025 28.4 5.0 45 73-118 87-132 (776)
40 PF13934 ELYS: Nuclear pore co 29.0 1.5E+02 0.0032 23.5 5.2 36 47-87 120-155 (226)
41 cd00491 4Oxalocrotonate_Tautom 29.0 69 0.0015 19.0 2.7 25 98-122 12-36 (58)
42 PF01158 Ribosomal_L36e: Ribos 28.9 1.3E+02 0.0029 21.0 4.3 45 36-84 49-93 (98)
43 TIGR00193 urease_gam urease, g 27.8 1.3E+02 0.0029 21.1 4.1 28 37-64 38-66 (102)
44 TIGR00083 ribF riboflavin kina 27.8 43 0.00093 27.8 2.0 22 2-23 148-169 (288)
45 PRK05627 bifunctional riboflav 27.7 45 0.00099 27.8 2.1 23 2-24 165-187 (305)
46 KOG2659 LisH motif-containing 27.5 3.3E+02 0.0072 22.0 6.9 60 8-69 39-98 (228)
47 PRK13241 ureA urease subunit g 27.2 1.4E+02 0.0029 21.1 4.1 28 37-64 38-66 (100)
48 cd00194 UBA Ubiquitin Associat 27.1 47 0.001 18.2 1.5 13 8-20 25-37 (38)
49 TIGR00013 taut 4-oxalocrotonat 27.1 77 0.0017 19.2 2.7 27 97-123 12-38 (63)
50 PRK02220 4-oxalocrotonate taut 26.7 69 0.0015 19.3 2.4 26 97-122 12-37 (61)
51 PRK01964 4-oxalocrotonate taut 26.7 69 0.0015 19.7 2.4 26 98-123 13-38 (64)
52 smart00165 UBA Ubiquitin assoc 26.7 47 0.001 18.1 1.5 12 8-19 25-36 (37)
53 PF08283 Gemini_AL1_M: Geminiv 26.6 84 0.0018 22.3 3.0 22 4-25 10-31 (106)
54 PRK13242 ureA urease subunit g 26.1 1.5E+02 0.0032 20.8 4.1 28 37-64 38-66 (100)
55 PRK00745 4-oxalocrotonate taut 25.9 74 0.0016 19.3 2.4 25 98-122 13-37 (62)
56 PF12169 DNA_pol3_gamma3: DNA 25.3 61 0.0013 23.1 2.2 25 40-64 19-43 (143)
57 KOG0989 Replication factor C, 25.1 2.8E+02 0.006 23.8 6.2 73 7-80 219-299 (346)
58 PRK09377 tsf elongation factor 25.0 52 0.0011 27.5 2.0 40 9-48 31-95 (290)
59 COG5051 RPL36A Ribosomal prote 24.7 2E+02 0.0043 19.8 4.4 42 38-83 53-94 (97)
60 PRK13986 urease subunit alpha; 24.5 1.2E+02 0.0027 24.3 3.9 28 37-64 38-67 (225)
61 COG0264 Tsf Translation elonga 24.2 52 0.0011 27.6 1.8 40 9-48 31-97 (296)
62 TIGR00756 PPR pentatricopeptid 23.8 75 0.0016 15.9 1.9 19 3-21 7-25 (35)
63 PHA02608 67 prohead core prote 23.7 64 0.0014 21.6 1.8 14 41-54 3-16 (80)
64 PF12862 Apc5: Anaphase-promot 23.2 1.8E+02 0.0038 19.4 4.1 27 4-30 6-32 (94)
65 PF11251 DUF3050: Protein of u 22.9 3.4E+02 0.0074 22.0 6.2 68 40-118 100-168 (232)
66 PF04121 Nup84_Nup100: Nuclear 22.9 56 0.0012 30.3 2.0 21 2-22 139-159 (697)
67 PF13371 TPR_9: Tetratricopept 22.1 1.9E+02 0.0042 17.4 4.5 54 6-64 5-58 (73)
68 PF04699 P16-Arc: ARP2/3 compl 22.0 76 0.0017 23.9 2.2 23 2-24 42-64 (152)
69 TIGR03362 VI_chp_7 type VI sec 21.1 1E+02 0.0022 25.8 2.9 54 3-58 220-273 (301)
70 PRK11727 23S rRNA mA1618 methy 20.8 1.4E+02 0.003 25.2 3.8 51 105-155 59-125 (321)
71 PF07729 FCD: FCD domain; Int 20.6 1.4E+02 0.003 19.6 3.2 24 39-62 100-123 (125)
72 PF12793 SgrR_N: Sugar transpo 20.4 73 0.0016 22.7 1.7 19 2-20 76-94 (115)
73 TIGR00116 tsf translation elon 20.1 59 0.0013 27.1 1.4 40 9-48 30-94 (290)
74 KOG3452 60S ribosomal protein 20.0 2.6E+02 0.0057 19.6 4.4 42 38-83 53-94 (102)
No 1
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=100.00 E-value=8.8e-37 Score=240.86 Aligned_cols=158 Identities=59% Similarity=0.872 Sum_probs=153.3
Q ss_pred hhhhhhhcCCHHHHHHHhhcCCccccccCcchhhhhhHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHHHhH
Q 031315 2 AVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVA 81 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~l~F~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~ 81 (161)
+|+.+|.+|+|++||+.+++++|++|++|.+|.|+|++|+||||||.|..++||+|||+++++++..+++++.+++++|+
T Consensus 70 ~Ir~~I~~G~Ie~Aie~in~l~PeiLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA~~a~e~~~~~~elE~~l~ 149 (228)
T KOG2659|consen 70 QIRRAIEEGQIEEAIEKVNQLNPEILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKLAPFAEENPKKMEELERTLA 149 (228)
T ss_pred HHHHHHHhccHHHHHHHHHHhChHHHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHccccccccHHHHHHHHHHHH
Confidence 69999999999999999999999999999999999999999999999999999999999999999988999999999999
Q ss_pred HHhccccCCCcchhhhhHHHHhhhHHHHHHHHhhhccccCCCChhHHHHHHHHHHhhhhh-hcccccccccccccccCC
Q 031315 82 LLAFEDVSNCPVGDLLDISQRLKTASEVNAAILTSQSHEKDPKLPSLLKMLLWAQNQLDE-KAAYPRINDLATATLEDP 159 (161)
Q Consensus 82 LLay~~~~~sp~~~Ll~~~~r~~la~~vn~aiL~~~~~~~~~~L~~l~k~~~~~~~~l~~-~~~~p~~~~~~~~~~~~~ 159 (161)
+|+|++|+.||++++++.++|.++|+.||++||.+++....|.|+.++|...|++.++.. +.++|+++++.+|.+++|
T Consensus 150 lLvf~~~~~sp~~~l~~~s~R~kvA~~vN~aiL~~~~~~~~~~l~~llk~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 228 (228)
T KOG2659|consen 150 LLVFELSQESPSAELLSQSLRQKVASEVNSAILASQEHESEPKLPFLLKLISWAQEELDREKFSEPHFKDLTKIKSEEP 228 (228)
T ss_pred HHHcCCcccCcHHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHhHhhccccccCCccccccCCC
Confidence 999999999999999999999999999999999999999999999999999999999875 589999999999998764
No 2
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=100.00 E-value=6.1e-35 Score=217.03 Aligned_cols=135 Identities=39% Similarity=0.590 Sum_probs=128.3
Q ss_pred hhhhhhhcCCHHHHHHHhhcCCccccccCcchhhhhhHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHHHhH
Q 031315 2 AVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVA 81 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~l~F~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~ 81 (161)
+|+++|++||+++|++|+++++|.+++.++.++|.|++|+|||||++|++.+||+|||+++.++.. .+.++++++|+
T Consensus 7 ~I~~~I~~g~i~~Ai~w~~~~~~~l~~~~~~L~f~L~~q~fiell~~~~~~~Ai~y~r~~l~~~~~---~~~~~l~~~~~ 83 (145)
T PF10607_consen 7 KIRQAILNGDIDPAIEWLNENFPELLKRNSSLEFELRCQQFIELLREGDIMEAIEYARKHLSPFND---EFLEELKKLMS 83 (145)
T ss_pred HHHHHHHcCCHHHHHHHHHHcCHHHHhcCCchhHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhhHH---HHHHHHHHHHH
Confidence 699999999999999999999999999999999999999999999999999999999999966543 58899999999
Q ss_pred HHhccccCC---CcchhhhhHHHHhhhHHHHHHHHhhhccccCCCChhHHHHHHHHHHhhh
Q 031315 82 LLAFEDVSN---CPVGDLLDISQRLKTASEVNAAILTSQSHEKDPKLPSLLKMLLWAQNQL 139 (161)
Q Consensus 82 LLay~~~~~---sp~~~Ll~~~~r~~la~~vn~aiL~~~~~~~~~~L~~l~k~~~~~~~~l 139 (161)
+|||++|++ +||++++++++|+.||+.||+++|..+|.+.+|+|+.++++..|+...+
T Consensus 84 lL~~~~~~~~~~s~~~~l~~~~~~~~la~~~~~~~l~~~~~~~~s~L~~~~~~g~~~l~~l 144 (145)
T PF10607_consen 84 LLAYPDPEEPLPSPYKELLSPERREELAEEFNSAILKSYGLPKESPLEVILKAGLSALKTL 144 (145)
T ss_pred HHHcCCcccccchHHHHHhChHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHhhhc
Confidence 999999987 8999999999999999999999999999999999999999999997654
No 3
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.88 E-value=1.5e-22 Score=168.39 Aligned_cols=131 Identities=25% Similarity=0.329 Sum_probs=122.4
Q ss_pred hhhhhhhcCCHHHHHHHhhcCCccccccCcchhhhhhHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHHHhH
Q 031315 2 AVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVA 81 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~l~F~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~ 81 (161)
.|+++|+.|++.+|++||++|.-.|-+.+|.|+|.++.|+|||||+.++..+||+||++||++++. ++.++++.+||
T Consensus 158 ~I~~sll~~~l~~~Lswc~ehk~~LkK~~S~lEf~lRlQefIELi~~~~~~~Ai~~akk~f~~~~~---~~~~~Lk~a~g 234 (389)
T KOG0396|consen 158 GIRDSLLAGELEPALSWCKEHKVELKKEESSLEFQLRLQEFIELIKVDNYDKAIAFAKKHFAPWAK---SHKSDLKLAMG 234 (389)
T ss_pred HHHHHHHhcchHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhhhhh---hhHHHHHHHHH
Confidence 589999999999999999999999999999999999999999999999999999999999999985 68899999999
Q ss_pred HHhcc-ccCCCcchhhhhHHHHhhhHHHHHHHHhhhccccCCCChhHHHHHHHHH
Q 031315 82 LLAFE-DVSNCPVGDLLDISQRLKTASEVNAAILTSQSHEKDPKLPSLLKMLLWA 135 (161)
Q Consensus 82 LLay~-~~~~sp~~~Ll~~~~r~~la~~vn~aiL~~~~~~~~~~L~~l~k~~~~~ 135 (161)
+|||+ .++.++|..+++..||+.+++.|-+..+..+|.+..|+|...+.+=..+
T Consensus 235 ~laF~~~t~~sky~~l~~~~rw~~l~~lF~s~a~~l~~i~~~~~L~~~l~~GLsa 289 (389)
T KOG0396|consen 235 LLAFPKYTSSSKYLNLLTADRWSVLADLFLSEALKLFGIPINPALTIYLQAGLSA 289 (389)
T ss_pred hhcCccccCcccccCcccHHHHHHHHHHhhHHHHHHhCCCCCcHHHHHHHhhhhh
Confidence 99999 4677889999999999999999999999999999999998887754433
No 4
>smart00757 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)
Probab=99.86 E-value=2.2e-21 Score=135.30 Aligned_cols=93 Identities=46% Similarity=0.568 Sum_probs=87.7
Q ss_pred chHHHHHHHHHhcCCCCccchHHHHHHHHHhHHHhcccc-CCCcchhhhhHHHHhhhHHHHHHHHhhhc-cccCCCChhH
Q 031315 50 KVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDV-SNCPVGDLLDISQRLKTASEVNAAILTSQ-SHEKDPKLPS 127 (161)
Q Consensus 50 ~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~LLay~~~-~~sp~~~Ll~~~~r~~la~~vn~aiL~~~-~~~~~~~L~~ 127 (161)
++.+||+|||+++++|..+++..+++|+++||||||++| +.+||++++++++|+.||+.||++||..+ |.+.+|.|+.
T Consensus 2 ~~~eAi~yar~~l~~~~~~~~~~~~el~~~m~llaf~~~~~~sp~~~ll~~~~~~~la~~~n~~~l~~~~~~~~~s~L~~ 81 (99)
T smart00757 2 KIEEALAYARELLAPFAKEHEKFLKELEKTMALLAYPDPTEPSPYKELLSPSQREKLAEELNSAILELLHGKSSESPLEI 81 (99)
T ss_pred cHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHHHhcCCCCCCccHHHHCCHHHHHHHHHHHHHHHHHHccCCCCCChHHH
Confidence 578999999999999998877778999999999999999 89999999999999999999999999998 9999999999
Q ss_pred HHHHHHHHHhhhhhh
Q 031315 128 LLKMLLWAQNQLDEK 142 (161)
Q Consensus 128 l~k~~~~~~~~l~~~ 142 (161)
++++..|+..++.+.
T Consensus 82 ~~~~~~~~~~~l~~~ 96 (99)
T smart00757 82 LLSAGLAALKTLLEK 96 (99)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999888654
No 5
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.76 E-value=3e-18 Score=143.92 Aligned_cols=133 Identities=22% Similarity=0.336 Sum_probs=120.1
Q ss_pred hhhhhhhcCCHHHHHHHhhcCCccccccCcchhhhhhHHHHHHHHHccchH--HHHHHHHHhcCCCCccchHHHHHHHHH
Q 031315 2 AVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVE--EALEFAQEELAPRGEENQSFLEELERT 79 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~l~F~L~~q~fIElir~~~~~--eAl~yar~~l~~~~~~~~~~~~~l~~~ 79 (161)
+|.++|+.||+++|++|+..+.-.|.+.++.|+|+|+.++|+++++.|.-. +||.|||++++||+.. +..+||++
T Consensus 161 ~Iv~~lke~Dl~~aLeWa~~~~~~L~~~~s~LE~~Lh~l~fl~l~~~g~~~~~eAl~Yar~~~~~F~~~---~~~eIQkl 237 (394)
T KOG2817|consen 161 QIVEALKERDLEPALEWAESNRQKLKEKSSSLEFKLHSLHFLSLIRGGKSDQREALRYARTHFAPFVAD---HLREIQKL 237 (394)
T ss_pred HHHHHHHhccchhHHHHHHHhhhhhccccccHHHHHHHHHHHHHHhcCCcCcHHHHHHHHHhcCccccc---hHHHHHHH
Confidence 689999999999999999999999999999999999999999999998655 9999999999999854 58999999
Q ss_pred hHHHhccc--cCCCcchhhhhHHHHhhhHHHHHHHHhhhccccCCCCh-----------hHHHHHHHHHHh
Q 031315 80 VALLAFED--VSNCPVGDLLDISQRLKTASEVNAAILTSQSHEKDPKL-----------PSLLKMLLWAQN 137 (161)
Q Consensus 80 ~~LLay~~--~~~sp~~~Ll~~~~r~~la~~vn~aiL~~~~~~~~~~L-----------~~l~k~~~~~~~ 137 (161)
|++|.|-. .+.|||.+++++..|..+...|-+.-+...|.+.+|+| +.++++......
T Consensus 238 m~sl~~l~~gl~~spy~~~ls~~~w~~~~~~f~r~ycallg~s~eSPL~v~v~aG~~Alp~Llk~~~v~~~ 308 (394)
T KOG2817|consen 238 MGSLLYLRNGLEKSPYSEILSPKLWKELTEEFTREYCALLGISVESPLSVLVNAGCIALPQLLKYKSVMEL 308 (394)
T ss_pred HHHHHHHHcCCCCCChHHHhCHHHHHHHHHHHHHHHHHHcCCCccCcHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 99999984 47999999999999999999999999999999999855 456666655544
No 6
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=99.39 E-value=2.9e-13 Score=85.44 Aligned_cols=50 Identities=32% Similarity=0.689 Sum_probs=48.0
Q ss_pred hhhhhhhcCCHHHHHHHhhcCCccccccCcchhhhhhHHHHHHHHHccch
Q 031315 2 AVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKV 51 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~l~F~L~~q~fIElir~~~~ 51 (161)
.|+++|+.|++++|++|+++++|.+.+.++.+.|.|++|+||||++.|+.
T Consensus 7 ~i~~~i~~g~~~~a~~~~~~~~~~l~~~~~~l~f~L~~q~~lell~~~~~ 56 (58)
T smart00668 7 RIRELILKGDWDEALEWLSSLKPPLLERNSKLEFELRKQKFLELVRQGKL 56 (58)
T ss_pred HHHHHHHcCCHHHHHHHHHHcCHHHhccCCCchhHHHHHHHHHHHHcCCc
Confidence 68999999999999999999999999999999999999999999998864
No 7
>KOG1477 consensus SPRY domain-containing proteins [General function prediction only]
Probab=98.74 E-value=4e-09 Score=92.26 Aligned_cols=112 Identities=29% Similarity=0.266 Sum_probs=102.6
Q ss_pred cCcchhhhhhHHHHHHHHHccchHHHHHHHHHhcCCCCc--cchHHHHHHHHHhHHHhccccCCCcchhhhhHHHHhhhH
Q 031315 29 TNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGE--ENQSFLEELERTVALLAFEDVSNCPVGDLLDISQRLKTA 106 (161)
Q Consensus 29 ~~~~l~F~L~~q~fIElir~~~~~eAl~yar~~l~~~~~--~~~~~~~~l~~~~~LLay~~~~~sp~~~Ll~~~~r~~la 106 (161)
..+...+.+.|+.+|.+.|-+.+...+++-+..+++... .+.....+++++++||+|.+|+.||...++++.+|+-++
T Consensus 338 ~~~~~~~~~~~~~~v~~~~~g~v~~e~~~~k~~l~~~~g~~~~~~~~~~~~~s~~Llays~p~~s~~g~~~~~~~~e~v~ 417 (469)
T KOG1477|consen 338 DYPQRGAKDPCGLHVNLGRAGFVFIEANAKKWELAKDYGIKKNSAAVGMLSDSSSLLAYSDPEESPVGYLLDPIQREPVA 417 (469)
T ss_pred cccchhhccchhhhhhHHHHHHHHHHHHHHHHhhhhhhCcCccccccccccchHHHHHhcCcccCccccccCcccchhHH
Confidence 358899999999999999999999999999999998765 455678899999999999999999999999999999999
Q ss_pred HHHHHHHhhhccccCCCChhHHHHHHHHHHhhhh
Q 031315 107 SEVNAAILTSQSHEKDPKLPSLLKMLLWAQNQLD 140 (161)
Q Consensus 107 ~~vn~aiL~~~~~~~~~~L~~l~k~~~~~~~~l~ 140 (161)
+.+|.+||...+.++++.|+.++.+...+...+.
T Consensus 418 ~~~n~~il~t~~~~~~~~l~~~l~~~~~~~~~~~ 451 (469)
T KOG1477|consen 418 EALNSAILETDNNSKDPDLERVLSQTPAELSLYA 451 (469)
T ss_pred hhhcccccccCCCCccchhhhhhccchhhHhhhh
Confidence 9999999999999999999999999988876654
No 8
>KOG0293 consensus WD40 repeat-containing protein [Function unknown]
Probab=94.32 E-value=0.32 Score=42.44 Aligned_cols=126 Identities=14% Similarity=0.156 Sum_probs=83.1
Q ss_pred hhhhhcCCHHHHHHHhhcC-CccccccCcchhhhhhHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHHHhHH
Q 031315 4 KKAVQCGNVEDAIEKVNDL-NPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVAL 82 (161)
Q Consensus 4 ~~~I~~G~i~~Ai~~i~~~-~p~ll~~~~~l~F~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~L 82 (161)
.+.++.|+.+.++.-.... +|. ...-....|.+..|.|+|+.+.|++..|+..-|..+.+.- .-.+.+.++.+-
T Consensus 57 ~q~vlqg~w~q~v~~~~~i~~~d-e~~~~ea~fLv~kQ~fLEf~k~~~is~al~~l~~~~~~lr----~~~kk~~el~~s 131 (519)
T KOG0293|consen 57 DQQVLQGQWDQQVMSLVRISFED-ERNRKEAMFLVNKQIFLEFLKTGSISHALPVLRNPVLYLR----KNKKKFHELASS 131 (519)
T ss_pred HHHHHcccHHHHHHHHhhccCcc-hhhhHHHHHHHHHHHHHHHHhhccHhhhhHhhhcchhhhh----hhHHHHHHHHHH
Confidence 5788999998887766555 666 4444688999999999999999999999998886555542 235667788888
Q ss_pred HhccccCCC-c--chhhhhHHHHhhhHHHHHHHHhhhccccCCCChhHHHHHHHHHH
Q 031315 83 LAFEDVSNC-P--VGDLLDISQRLKTASEVNAAILTSQSHEKDPKLPSLLKMLLWAQ 136 (161)
Q Consensus 83 Lay~~~~~s-p--~~~Ll~~~~r~~la~~vn~aiL~~~~~~~~~~L~~l~k~~~~~~ 136 (161)
|.+++...+ . -...+..+ |..|-+++..-|=-. -+-++-.|+.|++++.--|
T Consensus 132 ll~sn~~~~ne~~~~~~~~n~-R~~ll~elskyi~p~-illP~rRLehLl~qAv~~Q 186 (519)
T KOG0293|consen 132 LLVSNDQFSNEENTTAQLNNE-RDKLLDELSKYIPPN-ILLPKRRLEHLLEQAVKYQ 186 (519)
T ss_pred Hhccccccccccchhhhhchh-HHHHHHHHHhhCCHh-hcCChHHHHHHHHHHHHHH
Confidence 888853221 1 22333333 455555544322111 1123448889999887554
No 9
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.90 E-value=0.74 Score=38.84 Aligned_cols=122 Identities=14% Similarity=0.142 Sum_probs=83.4
Q ss_pred hhhhhhcCCHHHHHHHhhcCCccccccCcchhh--hhhHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHHHh
Q 031315 3 VKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFF--HLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTV 80 (161)
Q Consensus 3 I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~l~F--~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~ 80 (161)
|.+.|.+.+...-|+|.+ ...-+-..++.+++ .+....+.-++-. ++++|+.|-++.++.|. +.|...++..|
T Consensus 145 v~~gI~~k~~~l~iE~~Q-i~gyl~kgdtesel~l~~~~~esl~l~hk-~~~~a~r~c~t~~a~f~---~kh~~dv~~~~ 219 (396)
T COG5109 145 VISGISEKSTFLLIEFLQ-IEGYLSKGDTESELELYLVSHESLLLIHK-RYDEALRLCFTKLASFV---PKHIQDVKPLL 219 (396)
T ss_pred HHHhhccchhHhHHHHHH-hcCccccCCchhhhHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH---HHhccchHHHH
Confidence 455677888888899983 33333344444444 4445555555544 79999999999999987 56778888888
Q ss_pred HHHhccccC--CC-------cchhhhh--------------HHHHhhhHHHHHHHHhhhccccCCCChhHHH
Q 031315 81 ALLAFEDVS--NC-------PVGDLLD--------------ISQRLKTASEVNAAILTSQSHEKDPKLPSLL 129 (161)
Q Consensus 81 ~LLay~~~~--~s-------p~~~Ll~--------------~~~r~~la~~vn~aiL~~~~~~~~~~L~~l~ 129 (161)
-.+.+.... -+ ...+++. ...|..+-..|-+..|...|++-+|.|.-++
T Consensus 220 ~~l~nap~dcfrhrekelmqnI~~~l~ksligqPiEdIDkvnk~~k~l~~lF~~eycaa~gm~~~spL~~~v 291 (396)
T COG5109 220 RFLVNAPTDCFRHREKELMQNIQEALKKSLIGQPIEDIDKVNKSRKKLIELFKSEYCAANGMPNRSPLRELV 291 (396)
T ss_pred HHHHcCchHHhhhcchhHHHHHHHHHHHhhcCCcHHHHHHhhhhHHHHHHHHHHHHHHhcCCCccChHHHHH
Confidence 888774221 01 1222222 1458899999999999999999999887554
No 10
>cd08044 TAF5_NTD2 TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID). The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at the N-terminal and one at the C-terminal region. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) 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 preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF5 may play a major role in forming TFIID and its related complexes. TAFs from various
Probab=84.20 E-value=1.1 Score=32.72 Aligned_cols=111 Identities=14% Similarity=0.214 Sum_probs=69.2
Q ss_pred HHHhhcCCccccccC-cchhhhhhHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHHHhHHHhccccCCCcch
Q 031315 16 IEKVNDLNPEILDTN-PQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDVSNCPVG 94 (161)
Q Consensus 16 i~~i~~~~p~ll~~~-~~l~F~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~LLay~~~~~sp~~ 94 (161)
-+|+.+. +++.+.. ..+.|=+-+-=|++||.+|...+|..|-.+.-..+. +.|.+.|+...++.--.+..+.+..
T Consensus 12 ~~wv~~~-ld~~k~EL~~lLyPiFvh~yL~lv~~~~~~~A~~F~~~f~~~~~---~~~~~~i~~L~~i~~p~~l~~n~~~ 87 (133)
T cd08044 12 RKWIESS-LDIYKYELSQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFE---DSHSEDIKKLSSITTPEHLKENELA 87 (133)
T ss_pred HHHHHhC-cHhhHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhHhhH---HHHHHHHHHHHccCCHHHHhhhHHH
Confidence 3455544 3333221 468888899999999999999999999887655553 4677788887666555555555544
Q ss_pred hhh-hHHHHhhhHHHHHHHHhhhccccCCCChhHHHH
Q 031315 95 DLL-DISQRLKTASEVNAAILTSQSHEKDPKLPSLLK 130 (161)
Q Consensus 95 ~Ll-~~~~r~~la~~vn~aiL~~~~~~~~~~L~~l~k 130 (161)
..+ +.+-+-.+....-..++.++.....+.+..+++
T Consensus 88 ~~~r~~Ky~i~ms~~s~~lL~~~L~~~~~~~~~~il~ 124 (133)
T cd08044 88 KLFRSNKYVIRMSRDAYSLLLRFLESWGGSLLLKILN 124 (133)
T ss_pred HHHHhCCEEEEECHHHHHHHHHHHHHCCcHHHHHHHH
Confidence 433 445555666666555655554333334444443
No 11
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=75.70 E-value=11 Score=23.03 Aligned_cols=56 Identities=21% Similarity=0.272 Sum_probs=34.0
Q ss_pred hhhcCCHHHHHHHhhcCCccccccCcchhhhhhHHHHHHHHHccchHHHHHHHHHhcCCCC
Q 031315 6 AVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRG 66 (161)
Q Consensus 6 ~I~~G~i~~Ai~~i~~~~p~ll~~~~~l~F~L~~q~fIElir~~~~~eAl~yar~~l~~~~ 66 (161)
++..|+.++|++..++... ....+..+.+.|- .=+++.|+.++|...-.+......
T Consensus 1 ll~~~~~~~A~~~~~~~l~-~~p~~~~~~~~la----~~~~~~g~~~~A~~~l~~~~~~~~ 56 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQ-RNPDNPEARLLLA----QCYLKQGQYDEAEELLERLLKQDP 56 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHH-HTTTSHHHHHHHH----HHHHHTT-HHHHHHHHHCCHGGGT
T ss_pred ChhccCHHHHHHHHHHHHH-HCCCCHHHHHHHH----HHHHHcCCHHHHHHHHHHHHHHCc
Confidence 4778999999998865421 1111344444322 224678999999888876655543
No 12
>PF04494 TFIID_90kDa: WD40 associated region in TFIID subunit; InterPro: IPR007582 This region, possibly a domain is found in subunits of transcription factor TFIID. The function of this region is unknown.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2J4B_D 2J49_A 2NXP_F.
Probab=74.91 E-value=2.4 Score=31.29 Aligned_cols=98 Identities=15% Similarity=0.230 Sum_probs=57.4
Q ss_pred HHHhhcCCcccccc-CcchhhhhhHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHHHhHHHhccccCCCcch
Q 031315 16 IEKVNDLNPEILDT-NPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDVSNCPVG 94 (161)
Q Consensus 16 i~~i~~~~p~ll~~-~~~l~F~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~LLay~~~~~sp~~ 94 (161)
.+|+... +++.+. =..+.|=+-+.=|++||.+|..++|-.|-.++-..+.. .+..+|+++.++-.=.+..+.+..
T Consensus 23 ~~wv~~s-ld~yK~EL~~lLyPvFvh~YL~Lv~~~~~~~A~~F~~kf~~~~~~---~~~~~i~~L~~i~~~~~l~~~~~~ 98 (142)
T PF04494_consen 23 RNWVDNS-LDIYKPELSRLLYPVFVHSYLDLVSKGHPEEAKSFLEKFSPDFED---SHQEDIEKLSSITSPEHLEENELA 98 (142)
T ss_dssp HHHHHTS--HHHHHHHGGGHHHHHHHHHHHHHHTT-HHHHHHHHHHHGGGGHG---HGHHHHHHHTT--SHHHHHHSHHH
T ss_pred HHHHHhC-cHhhHHHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHhH---HHHHHHHHHHhhCcHHHHhccHHH
Confidence 4566553 333322 15689999999999999999999999999987766643 466667777654333343444444
Q ss_pred hhhhH-HHHhhhHHHHHHHHhhhc
Q 031315 95 DLLDI-SQRLKTASEVNAAILTSQ 117 (161)
Q Consensus 95 ~Ll~~-~~r~~la~~vn~aiL~~~ 117 (161)
.++.. .-+-.+...--..++.+.
T Consensus 99 ~~~r~~Ky~I~ls~~s~~lL~~fL 122 (142)
T PF04494_consen 99 RLFRSNKYVIRLSRDSFSLLLQFL 122 (142)
T ss_dssp HHHHCSGEEEEEEHHHHHHHHHHH
T ss_pred HHHHhCCeeEEECHHHHHHHHHHH
Confidence 44422 223344444443444433
No 13
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=68.74 E-value=6.6 Score=23.63 Aligned_cols=28 Identities=36% Similarity=0.529 Sum_probs=23.2
Q ss_pred hHHHHHHHHHccchHHHHHHHHHhcCCC
Q 031315 38 QQQRLIELIRNGKVEEALEFAQEELAPR 65 (161)
Q Consensus 38 ~~q~fIElir~~~~~eAl~yar~~l~~~ 65 (161)
...++.+.|..|++++|+++..++-...
T Consensus 4 ~~~~i~~~i~~g~~~~a~~~~~~~~~~l 31 (58)
T smart00668 4 ERKRIRELILKGDWDEALEWLSSLKPPL 31 (58)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHcCHHH
Confidence 3567889999999999999999776543
No 14
>PF10827 DUF2552: Protein of unknown function (DUF2552) ; InterPro: IPR020157 This entry contains proteins with no known function.
Probab=64.03 E-value=4.7 Score=26.66 Aligned_cols=17 Identities=24% Similarity=0.329 Sum_probs=14.7
Q ss_pred CHHHHHHHhhcCCcccc
Q 031315 11 NVEDAIEKVNDLNPEIL 27 (161)
Q Consensus 11 ~i~~Ai~~i~~~~p~ll 27 (161)
.+|.||+||.+|-|++-
T Consensus 60 tld~Ai~Wi~e~M~~iT 76 (79)
T PF10827_consen 60 TLDLAIAWIGEHMPHIT 76 (79)
T ss_pred cHHHHHHHHHhcccchh
Confidence 48999999999998863
No 15
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=63.17 E-value=30 Score=24.88 Aligned_cols=27 Identities=22% Similarity=0.502 Sum_probs=23.1
Q ss_pred HHHHHHHHHccchHHHHHHHHHhcCCC
Q 031315 39 QQRLIELIRNGKVEEALEFAQEELAPR 65 (161)
Q Consensus 39 ~q~fIElir~~~~~eAl~yar~~l~~~ 65 (161)
+.+.++.|++|++++|++|.+++....
T Consensus 5 r~~I~~~I~~g~i~~Ai~w~~~~~~~l 31 (145)
T PF10607_consen 5 RKKIRQAILNGDIDPAIEWLNENFPEL 31 (145)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHcCHHH
Confidence 566788899999999999999987654
No 16
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=62.78 E-value=11 Score=24.41 Aligned_cols=41 Identities=22% Similarity=0.233 Sum_probs=27.3
Q ss_pred hhhHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHH
Q 031315 36 HLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELE 77 (161)
Q Consensus 36 ~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~ 77 (161)
.|.+++|-+++..|+..+|...|-+.=.-.- .+++-+..++
T Consensus 7 ~l~~~~F~~l~~~g~y~eAA~~AA~sP~giL-Rt~~Ti~rFk 47 (66)
T PF13838_consen 7 DLYVQQFNELFSQGQYEEAAKVAANSPRGIL-RTPETINRFK 47 (66)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHSGGGTT--SHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhCccchh-cCHHHHHHHH
Confidence 4678999999999999999988874322122 2355555555
No 17
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=54.03 E-value=15 Score=22.75 Aligned_cols=26 Identities=19% Similarity=0.170 Sum_probs=23.5
Q ss_pred hHHHHhhhHHHHHHHHhhhccccCCC
Q 031315 98 DISQRLKTASEVNAAILTSQSHEKDP 123 (161)
Q Consensus 98 ~~~~r~~la~~vn~aiL~~~~~~~~~ 123 (161)
+.+++.++++.|..++.+..|.|.++
T Consensus 13 s~EqK~~L~~~it~a~~~~~~~p~~~ 38 (60)
T PRK02289 13 SQEQKNALAREVTEVVSRIAKAPKEA 38 (60)
T ss_pred CHHHHHHHHHHHHHHHHHHhCcCcce
Confidence 78999999999999999999987654
No 18
>PF15391 DUF4614: Domain of unknown function (DUF4614)
Probab=45.52 E-value=25 Score=27.38 Aligned_cols=49 Identities=31% Similarity=0.432 Sum_probs=37.1
Q ss_pred HHHHHHhhcCCccccccCcchhhhh-hHHHHHHHHHcc----------------chHHHHHHHHHh
Q 031315 13 EDAIEKVNDLNPEILDTNPQLFFHL-QQQRLIELIRNG----------------KVEEALEFAQEE 61 (161)
Q Consensus 13 ~~Ai~~i~~~~p~ll~~~~~l~F~L-~~q~fIElir~~----------------~~~eAl~yar~~ 61 (161)
.+||+-+....|.+|.-|..|-=.| ..|+|||.-|.= .++++-+|-|.|
T Consensus 113 ~dAiEALTaYSPA~lALnDMLkQQL~LTqqFve~sr~LH~Sll~SL~~~~~hY~TLEetKeyIr~h 178 (181)
T PF15391_consen 113 ADAIEALTAYSPAVLALNDMLKQQLSLTQQFVEASRHLHQSLLQSLDADSFHYHTLEETKEYIRRH 178 (181)
T ss_pred HHHHHHHhccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcceeeHHHHHHHHHHc
Confidence 4789999999999999887666554 468999976641 267777777765
No 19
>PF07208 DUF1414: Protein of unknown function (DUF1414); InterPro: IPR009857 This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown.; PDB: 2JPQ_A 2JUZ_B 2JUW_B 2QTI_A 2OTA_A 2JR2_A 2JRX_A.
Probab=43.69 E-value=26 Score=20.96 Aligned_cols=20 Identities=25% Similarity=0.245 Sum_probs=16.2
Q ss_pred hhHHHHhhhHHHHHHHHhhh
Q 031315 97 LDISQRLKTASEVNAAILTS 116 (161)
Q Consensus 97 l~~~~r~~la~~vn~aiL~~ 116 (161)
+.+++|+.+|+.|..++...
T Consensus 24 V~~~qR~~iAe~Fa~AL~~S 43 (44)
T PF07208_consen 24 VPPAQRQAIAEKFAQALKSS 43 (44)
T ss_dssp S-HHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHhc
Confidence 35899999999999988753
No 20
>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Probab=42.12 E-value=46 Score=25.47 Aligned_cols=41 Identities=27% Similarity=0.456 Sum_probs=30.6
Q ss_pred cCCccccccCcchhhhhh-H-HHHHH-HHHccchHHHHHHHHHh
Q 031315 21 DLNPEILDTNPQLFFHLQ-Q-QRLIE-LIRNGKVEEALEFAQEE 61 (161)
Q Consensus 21 ~~~p~ll~~~~~l~F~L~-~-q~fIE-lir~~~~~eAl~yar~~ 61 (161)
..+|.+.+-.-++..+|. . -..+| |+..|++-+|+.|+|+.
T Consensus 72 ~~~~~~~Ql~lDMLkRL~~~~~~iievLL~~g~vl~ALr~ar~~ 115 (167)
T PF07035_consen 72 NQYPPAYQLGLDMLKRLGTAYEEIIEVLLSKGQVLEALRYARQY 115 (167)
T ss_pred ccChHHHHHHHHHHHHhhhhHHHHHHHHHhCCCHHHHHHHHHHc
Confidence 466777776667777766 3 34456 77899999999999974
No 21
>PF05971 Methyltransf_10: Protein of unknown function (DUF890); InterPro: IPR010286 This family consists of several conserved hypothetical proteins from both eukaryotes and prokaryotes. The function of members of this family are unknown but are predicted to be SAM-dependent methyltransferases.; GO: 0008168 methyltransferase activity; PDB: 2H00_A.
Probab=40.62 E-value=46 Score=27.87 Aligned_cols=52 Identities=25% Similarity=0.449 Sum_probs=31.9
Q ss_pred hhHHHHHHHHhhh-ccccC--------CCChhHHHHHHHHHHhhhhh-hcccc---ccccccccc
Q 031315 104 KTASEVNAAILTS-QSHEK--------DPKLPSLLKMLLWAQNQLDE-KAAYP---RINDLATAT 155 (161)
Q Consensus 104 ~la~~vn~aiL~~-~~~~~--------~~~L~~l~k~~~~~~~~l~~-~~~~p---~~~~~~~~~ 155 (161)
+-..++|+++|.+ +|..- .|.++.-+.++.|..+.|.. +...| .-+|++||.
T Consensus 49 ~Av~~Ln~aLLk~dfgl~~wdiP~~~LcP~iP~R~nYi~~i~DlL~~~~~~~~~~v~glDIGTGA 113 (299)
T PF05971_consen 49 EAVRELNKALLKHDFGLDVWDIPEGRLCPPIPNRLNYIHWIADLLASSNPGIPEKVRGLDIGTGA 113 (299)
T ss_dssp HHHHHHHHHHHHHHH--------TTS----HHHHHHHHHHHHHHHT--TCGCS---EEEEES-TT
T ss_pred HHHHHHHHHHHHHhcCCccccCCCCCcCCCCchhHHHHHHHHHHhhccccccccceEeecCCccH
Confidence 3456788898854 45543 58999999999999999975 34443 567777774
No 22
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=40.14 E-value=22 Score=19.74 Aligned_cols=11 Identities=45% Similarity=0.661 Sum_probs=9.1
Q ss_pred cCCHHHHHHHh
Q 031315 9 CGNVEDAIEKV 19 (161)
Q Consensus 9 ~G~i~~Ai~~i 19 (161)
.||++.|+.|+
T Consensus 27 ~~nve~A~~~L 37 (37)
T PF00627_consen 27 NGNVERAVDWL 37 (37)
T ss_dssp TTSHHHHHHHH
T ss_pred CCCHHHHHHhC
Confidence 56899999985
No 23
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=39.86 E-value=31 Score=17.45 Aligned_cols=16 Identities=13% Similarity=0.212 Sum_probs=12.2
Q ss_pred hhhhcCCHHHHHHHhh
Q 031315 5 KAVQCGNVEDAIEKVN 20 (161)
Q Consensus 5 ~~I~~G~i~~Ai~~i~ 20 (161)
-+...|+.++|..++.
T Consensus 10 ~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 10 ALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHcCCHHHHHHHHh
Confidence 4567888888888765
No 24
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=37.69 E-value=44 Score=21.44 Aligned_cols=12 Identities=58% Similarity=0.803 Sum_probs=5.4
Q ss_pred ccchHHHHHHHH
Q 031315 48 NGKVEEALEFAQ 59 (161)
Q Consensus 48 ~~~~~eAl~yar 59 (161)
.|+..+|+.+.+
T Consensus 38 ~~~y~~A~~~~~ 49 (84)
T PF12895_consen 38 QGKYEEAIELLQ 49 (84)
T ss_dssp TTHHHHHHHHHH
T ss_pred CCCHHHHHHHHH
Confidence 344444444443
No 25
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=37.17 E-value=25 Score=28.89 Aligned_cols=21 Identities=29% Similarity=0.401 Sum_probs=17.3
Q ss_pred hhhhhhhcCCHHHHHHHhhcC
Q 031315 2 AVKKAVQCGNVEDAIEKVNDL 22 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~~ 22 (161)
+|+++++.|+.++|++++-++
T Consensus 1 ~I~~~Ll~G~~~~Av~~al~~ 21 (284)
T PF12931_consen 1 KIQQLLLVGNREEAVELALDN 21 (284)
T ss_dssp HHHHHHHTT-HHHHHHHHHHT
T ss_pred CHHHHHhCCCHHHHHHHHHHC
Confidence 589999999999999988554
No 26
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=37.11 E-value=47 Score=23.52 Aligned_cols=25 Identities=40% Similarity=0.675 Sum_probs=19.5
Q ss_pred hhhHHHHHHHHHccchHHHHHHHHH
Q 031315 36 HLQQQRLIELIRNGKVEEALEFAQE 60 (161)
Q Consensus 36 ~L~~q~fIElir~~~~~eAl~yar~ 60 (161)
.+....||.+|+.|+..+|++..++
T Consensus 39 ~~dip~~i~~i~~g~~~~A~~~i~~ 63 (111)
T PF14691_consen 39 HIDIPEYIRLIREGNFKEAYELIRE 63 (111)
T ss_dssp ---HHHHHHHHHCT-HHHHHHHHHH
T ss_pred CCcHHHHHHHHHCCCHHHHHHHHHH
Confidence 4567999999999999999998885
No 27
>PF14973 TINF2_N: TERF1-interacting nuclear factor 2 N-terminus
Probab=36.53 E-value=1.1e+02 Score=22.87 Aligned_cols=76 Identities=18% Similarity=0.247 Sum_probs=45.2
Q ss_pred hhhhhhcCCHHHHHHHhhcCCccccccC-----cchhhhhhHHHHHHHHHc--cchHHHHHHHHHhcCC-CCccchHHHH
Q 031315 3 VKKAVQCGNVEDAIEKVNDLNPEILDTN-----PQLFFHLQQQRLIELIRN--GKVEEALEFAQEELAP-RGEENQSFLE 74 (161)
Q Consensus 3 I~~~I~~G~i~~Ai~~i~~~~p~ll~~~-----~~l~F~L~~q~fIElir~--~~~~eAl~yar~~l~~-~~~~~~~~~~ 74 (161)
|-++++.|.... +..|+.|+|.+ ..+ ++..-.=-...|..+|++ .+-.+--.|-|+.|.. |+ +.+..
T Consensus 47 ILELc~~~~~~d-l~~I~~Hl~~~-~~~~~~~~~D~~~~~~~~~F~~LV~~Ll~dp~~r~~f~qe~f~~eYG---~~f~~ 121 (145)
T PF14973_consen 47 ILELCRQERPWD-LKAIQPHLPRI-PQDPNATSKDHKMEEAHENFCQLVQNLLEDPEERENFFQEVFPQEYG---EPFDA 121 (145)
T ss_pred HHHHHhCCCCch-HHHHHHhcccc-cccccccccHHHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHC---hHHHH
Confidence 567777776544 99999999999 222 333334445667777764 2344445566655543 32 34566
Q ss_pred HHHHHhHHH
Q 031315 75 ELERTVALL 83 (161)
Q Consensus 75 ~l~~~~~LL 83 (161)
.+++.+.=.
T Consensus 122 ~Le~L~~ef 130 (145)
T PF14973_consen 122 ALEKLLWEF 130 (145)
T ss_pred HHHHHHHHH
Confidence 666665443
No 28
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.16 E-value=81 Score=21.91 Aligned_cols=46 Identities=15% Similarity=0.156 Sum_probs=36.9
Q ss_pred hhhHHHHhhhHHHHHHHHhhhccccCCCChhHHHHHHHHHHhhhhh
Q 031315 96 LLDISQRLKTASEVNAAILTSQSHEKDPKLPSLLKMLLWAQNQLDE 141 (161)
Q Consensus 96 Ll~~~~r~~la~~vn~aiL~~~~~~~~~~L~~l~k~~~~~~~~l~~ 141 (161)
-+++++|.++....-+.++.++...++-.=-.|+.++..|.|.|+.
T Consensus 5 ~ls~~q~~~leAAaFRrLv~HL~~rsdvQNIDLMnLAgFCRNCLs~ 50 (104)
T COG3492 5 ELSEEQRDRLEAAAFRRLVEHLQERSDVQNIDLMNLAGFCRNCLSN 50 (104)
T ss_pred hcCHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHH
Confidence 3678889999999999999998877776666677788888888753
No 29
>PRK07143 hypothetical protein; Provisional
Probab=34.46 E-value=29 Score=28.69 Aligned_cols=22 Identities=14% Similarity=0.061 Sum_probs=19.9
Q ss_pred hhhhhhhcCCHHHHHHHhhcCC
Q 031315 2 AVKKAVQCGNVEDAIEKVNDLN 23 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~~~ 23 (161)
.||++|.+|+++.|=+++-..|
T Consensus 154 ~IR~~l~~G~i~~A~~lLGr~y 175 (279)
T PRK07143 154 LLKEFIEFGDIELLNSLLLYNY 175 (279)
T ss_pred HHHHHHHcCCHHHHHHHcCCCc
Confidence 5999999999999999987776
No 30
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=33.41 E-value=46 Score=22.00 Aligned_cols=27 Identities=19% Similarity=0.327 Sum_probs=24.0
Q ss_pred hhHHHHhhhHHHHHHHHhhhccccCCC
Q 031315 97 LDISQRLKTASEVNAAILTSQSHEKDP 123 (161)
Q Consensus 97 l~~~~r~~la~~vn~aiL~~~~~~~~~ 123 (161)
.+.++..++|+.|.+++-+.+|.+.++
T Consensus 13 ~s~EqK~~La~~iT~a~~~~lg~~~e~ 39 (76)
T PRK01271 13 LDEEQKAALAADITDVIIRHLNSKDSS 39 (76)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcCcce
Confidence 478999999999999999999987765
No 31
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=32.83 E-value=1.6e+02 Score=25.70 Aligned_cols=72 Identities=25% Similarity=0.326 Sum_probs=51.0
Q ss_pred hhhhhhcCCHHHHHHHhhcCCccccccCcchhhhhhHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHHHhHH
Q 031315 3 VKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVAL 82 (161)
Q Consensus 3 I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~l~F~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~L 82 (161)
+..+|..|+-++|.+|+.+..+.-.+.. ...||.-++-++-..-++-+++-+..... +| .+--++|-
T Consensus 270 a~~li~l~~~~~A~~~i~~~Lk~~~D~~--------L~~~~~~l~~~d~~~l~k~~e~~l~~h~~-~p----~L~~tLG~ 336 (400)
T COG3071 270 AERLIRLGDHDEAQEIIEDALKRQWDPR--------LCRLIPRLRPGDPEPLIKAAEKWLKQHPE-DP----LLLSTLGR 336 (400)
T ss_pred HHHHHHcCChHHHHHHHHHHHHhccChh--------HHHHHhhcCCCCchHHHHHHHHHHHhCCC-Ch----hHHHHHHH
Confidence 5678999999999999999888776653 55677777777766666666655555432 23 46667777
Q ss_pred Hhccc
Q 031315 83 LAFED 87 (161)
Q Consensus 83 Lay~~ 87 (161)
|||.+
T Consensus 337 L~~k~ 341 (400)
T COG3071 337 LALKN 341 (400)
T ss_pred HHHHh
Confidence 77764
No 32
>PF12854 PPR_1: PPR repeat
Probab=32.73 E-value=44 Score=18.08 Aligned_cols=19 Identities=21% Similarity=0.490 Sum_probs=13.5
Q ss_pred hhhhhhcCCHHHHHHHhhc
Q 031315 3 VKKAVQCGNVEDAIEKVND 21 (161)
Q Consensus 3 I~~~I~~G~i~~Ai~~i~~ 21 (161)
|.-.-++|++++|++...+
T Consensus 14 I~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 14 IDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred HHHHHHCCCHHHHHHHHHh
Confidence 4445578888888887654
No 33
>PF03398 Ist1: Regulator of Vps4 activity in the MVB pathway; InterPro: IPR005061 This is a eukaryotic protein family of unknown function.; PDB: 3GGZ_B 3GGY_B 3FRR_A 3FRS_A.
Probab=30.33 E-value=2.4e+02 Score=21.24 Aligned_cols=20 Identities=20% Similarity=0.318 Sum_probs=15.5
Q ss_pred hhhhhhhcCCHHHHHHHhhc
Q 031315 2 AVKKAVQCGNVEDAIEKVND 21 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~ 21 (161)
+|-++|..|+.+.|.-.+..
T Consensus 28 dIa~LL~~g~~~~Ar~rvE~ 47 (165)
T PF03398_consen 28 DIAQLLKNGKEESARIRVEQ 47 (165)
T ss_dssp HHHHHHCCT-HHHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHHH
Confidence 57788999999999888744
No 34
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=30.23 E-value=51 Score=19.96 Aligned_cols=25 Identities=12% Similarity=0.173 Sum_probs=20.7
Q ss_pred hHHHHhhhHHHHHHHHhhhccccCC
Q 031315 98 DISQRLKTASEVNAAILTSQSHEKD 122 (161)
Q Consensus 98 ~~~~r~~la~~vn~aiL~~~~~~~~ 122 (161)
+.+++.++++.+..++.+.+|.+.+
T Consensus 12 ~~e~K~~l~~~it~~~~~~lg~~~~ 36 (60)
T PF01361_consen 12 TAEQKRELAEAITDAVVEVLGIPPE 36 (60)
T ss_dssp -HHHHHHHHHHHHHHHHHHHTS-GG
T ss_pred CHHHHHHHHHHHHHHHHHHhCcCCC
Confidence 6888999999999999999987654
No 35
>PF00547 Urease_gamma: Urease, gamma subunit enzyme!; InterPro: IPR002026 Urease 3.5.1.5 from EC is a nickel-binding enzyme that catalyzes the hydrolysis of urea to carbon dioxide and ammonia []: Urea + H2O = CO2 + 2 NH3 Historically, it was the first enzyme to be crystallized (in 1926). It is mainly found in plantseeds and microorganisms. In plants, urease is a hexamer of identical chains. In bacteria [], it consists of either two or three different subunits (alpha IPR005847 from INTERPRO, beta IPR002019 from INTERPRO and gamma, described in this entry). The structure of the urease complex is known []. This subunit does not appear to take part in the catalytic mechanism.; GO: 0009039 urease activity, 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process; PDB: 3QGA_G 3QGK_M 1E9Y_A 1E9Z_A 1FWF_A 1A5L_A 1EJW_A 1EJR_A 1FWH_A 1EJS_A ....
Probab=30.03 E-value=1.1e+02 Score=21.52 Aligned_cols=26 Identities=23% Similarity=0.419 Sum_probs=19.7
Q ss_pred HHHHHHHHHcc-chHHHHHHHHHhcCC
Q 031315 39 QQRLIELIRNG-KVEEALEFAQEELAP 64 (161)
Q Consensus 39 ~q~fIElir~~-~~~eAl~yar~~l~~ 64 (161)
+-+.+|..|.| ++.+.+++|++-+..
T Consensus 40 ~~~v~E~aRdG~svaelm~~g~~~L~~ 66 (99)
T PF00547_consen 40 SDEVLEGARDGKSVAELMSLGRTVLTR 66 (99)
T ss_dssp HHHHHHHHHHTS-HHHHHHHGGGSS-G
T ss_pred HHHHHHHhhCCCcHHHHHHHHHhhcCH
Confidence 66788888887 688999999877764
No 36
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=29.88 E-value=1.4e+02 Score=20.89 Aligned_cols=30 Identities=33% Similarity=0.583 Sum_probs=25.3
Q ss_pred hhHHHHHHHHHccchHHHHHHHHHhcCCCC
Q 031315 37 LQQQRLIELIRNGKVEEALEFAQEELAPRG 66 (161)
Q Consensus 37 L~~q~fIElir~~~~~eAl~yar~~l~~~~ 66 (161)
=+-...+||++.|.---|+.|+...+..+.
T Consensus 50 PYErr~mELLkv~kdKrAlKfaKkRlGth~ 79 (98)
T PTZ00196 50 PYERRMIELLKVGKDKRALKYAKKRLGTHK 79 (98)
T ss_pred HHHHHHHHHHHhcchHHHHHHHHHHhhhHH
Confidence 345678999999988999999999988764
No 37
>PRK13689 hypothetical protein; Provisional
Probab=29.25 E-value=27 Score=23.24 Aligned_cols=22 Identities=23% Similarity=0.194 Sum_probs=18.6
Q ss_pred hhHHHHhhhHHHHHHHHhhhcc
Q 031315 97 LDISQRLKTASEVNAAILTSQS 118 (161)
Q Consensus 97 l~~~~r~~la~~vn~aiL~~~~ 118 (161)
+.+++|..+|+.|-.|+.....
T Consensus 49 V~~~qR~~iAe~Fa~AL~~Sv~ 70 (75)
T PRK13689 49 VAPAQRQAIAESFARALQSSVK 70 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHHhh
Confidence 3589999999999999987654
No 38
>cd00390 Urease_gamma Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of external and internally-generated urea as a nitrogen source. The enzyme consists of three subunits, alpha, beta and gamma, which can exist as separate proteins or can be fused on a single protein chain. The alpha-beta-gamma heterotrimer forms multimers, mainly trimers. The large alpha subunit is the catalytic domain containing an active site with a bi-nickel center complexed by a carbamylated lysine. The beta and gamma subunits play a role in subunit association to form the higher order trimers.
Probab=29.18 E-value=1.2e+02 Score=21.16 Aligned_cols=28 Identities=25% Similarity=0.421 Sum_probs=22.4
Q ss_pred hhHHHHHHHHHcc-chHHHHHHHHHhcCC
Q 031315 37 LQQQRLIELIRNG-KVEEALEFAQEELAP 64 (161)
Q Consensus 37 L~~q~fIElir~~-~~~eAl~yar~~l~~ 64 (161)
|.+-+.+|..|.| ++.+.+..|++.+..
T Consensus 35 lIs~~v~E~aRdG~svaelm~~g~~~L~~ 63 (96)
T cd00390 35 LIADEILEGARDGKSVAELMSLGKTVLTR 63 (96)
T ss_pred HHHHHHHHHhhcCCCHHHHHHHHhhhCCH
Confidence 4467788899987 688999999987774
No 39
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.08 E-value=1.2e+02 Score=28.39 Aligned_cols=45 Identities=22% Similarity=0.305 Sum_probs=36.7
Q ss_pred HHHHHHHhHHHhccccCC-CcchhhhhHHHHhhhHHHHHHHHhhhcc
Q 031315 73 LEELERTVALLAFEDVSN-CPVGDLLDISQRLKTASEVNAAILTSQS 118 (161)
Q Consensus 73 ~~~l~~~~~LLay~~~~~-sp~~~Ll~~~~r~~la~~vn~aiL~~~~ 118 (161)
...|++....+.-.|++- -..+++++.+.|.++|+++|.-+-+ +|
T Consensus 87 l~hIEk~a~dIv~~d~~v~Lv~geiide~Y~d~iaeEinekLqE-~g 132 (776)
T KOG2235|consen 87 LDHIEKTARDIVSTDDEVTLVLGEIIDEEYVDRIAEEINEKLQE-QG 132 (776)
T ss_pred HHHHHHHHHHHhhcCCceEEehhhhhhHHHHHHHHHHHHHHHHH-hc
Confidence 567899999999888764 4578999999999999999975544 44
No 40
>PF13934 ELYS: Nuclear pore complex assembly
Probab=29.02 E-value=1.5e+02 Score=23.48 Aligned_cols=36 Identities=25% Similarity=0.199 Sum_probs=18.7
Q ss_pred HccchHHHHHHHHHhcCCCCccchHHHHHHHHHhHHHhccc
Q 031315 47 RNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAFED 87 (161)
Q Consensus 47 r~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~LLay~~ 87 (161)
++|+-.-|+.|.|..-.+.... +.+.-.+.+||...
T Consensus 120 ~~~~~~lAL~y~~~~~p~l~s~-----~~~~~~~~~La~~~ 155 (226)
T PF13934_consen 120 RRGDPKLALRYLRAVGPPLSSP-----EALTLYFVALANGL 155 (226)
T ss_pred HCCChhHHHHHHHhcCCCCCCH-----HHHHHHHHHHHcCC
Confidence 3566666777766555554433 23444444455443
No 41
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=28.96 E-value=69 Score=18.99 Aligned_cols=25 Identities=12% Similarity=0.044 Sum_probs=21.9
Q ss_pred hHHHHhhhHHHHHHHHhhhccccCC
Q 031315 98 DISQRLKTASEVNAAILTSQSHEKD 122 (161)
Q Consensus 98 ~~~~r~~la~~vn~aiL~~~~~~~~ 122 (161)
+++++.++++.+.+++-...|.+.+
T Consensus 12 t~eqk~~l~~~i~~~l~~~~g~~~~ 36 (58)
T cd00491 12 TDEQKRELIERVTEAVSEILGAPEA 36 (58)
T ss_pred CHHHHHHHHHHHHHHHHHHhCcCcc
Confidence 6889999999999999999987754
No 42
>PF01158 Ribosomal_L36e: Ribosomal protein L36e; InterPro: IPR000509 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. The L36E ribosomal family consists of mammalian, Caenorhabditis elegans and Drosophila L36, Candida albicans L39, and yeast YL39 ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1B_Q 4A1D_Q 4A19_Q 4A18_Q 3IZS_k 3IZR_k.
Probab=28.91 E-value=1.3e+02 Score=20.99 Aligned_cols=45 Identities=27% Similarity=0.318 Sum_probs=31.9
Q ss_pred hhhHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHHHhHHHh
Q 031315 36 HLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLA 84 (161)
Q Consensus 36 ~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~LLa 84 (161)
-=+-.+-+||++.+.---|+.|+++.+..+. +-....+++..+|+
T Consensus 49 aPYEkr~mELlkv~kdKrAlKf~KKRlGth~----RAKrKrEel~~vl~ 93 (98)
T PF01158_consen 49 APYEKRAMELLKVSKDKRALKFAKKRLGTHI----RAKRKREELSNVLA 93 (98)
T ss_dssp CHHHHHHHHHHHHCCHHHHHHHHHHHHCHHH----HHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHhcchhHHHHHHHHHHhhhhH----HHHHHHHHHHHHHH
Confidence 3445678999999988999999999988664 23444555544443
No 43
>TIGR00193 urease_gam urease, gamma subunit. Nomenclature for the various subunits of urease in Helicobacter differs from nomenclature in most other species.
Probab=27.83 E-value=1.3e+02 Score=21.14 Aligned_cols=28 Identities=29% Similarity=0.546 Sum_probs=23.0
Q ss_pred hhHHHHHHHHHcc-chHHHHHHHHHhcCC
Q 031315 37 LQQQRLIELIRNG-KVEEALEFAQEELAP 64 (161)
Q Consensus 37 L~~q~fIElir~~-~~~eAl~yar~~l~~ 64 (161)
|.+-+.+|..|.| .+.+.+..|++-+..
T Consensus 38 lIs~~v~E~aRdG~svaelm~~g~~~L~~ 66 (102)
T TIGR00193 38 YISAHIMEGARDGKKVAELMQYGRTLLTP 66 (102)
T ss_pred HHHHHHHHHhhcCCcHHHHHHHHHhhCCH
Confidence 4477888999988 589999999988775
No 44
>TIGR00083 ribF riboflavin kinase/FMN adenylyltransferase. multifunctional enzyme: riboflavin kinase (EC 2.7.1.26) (flavokinase) / FMN adenylyltransferase (EC 2.7.7.2) (FAD pyrophosphorylase) (FAD synthetase).
Probab=27.78 E-value=43 Score=27.75 Aligned_cols=22 Identities=23% Similarity=0.315 Sum_probs=19.7
Q ss_pred hhhhhhhcCCHHHHHHHhhcCC
Q 031315 2 AVKKAVQCGNVEDAIEKVNDLN 23 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~~~ 23 (161)
.||++|.+|+++.|-+++-..|
T Consensus 148 ~IR~~l~~G~i~~A~~lLGr~y 169 (288)
T TIGR00083 148 AIRQALKNGDLELANKLLGRPY 169 (288)
T ss_pred HHHHHHHcCCHHHHHHhhhhhh
Confidence 5999999999999999997665
No 45
>PRK05627 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed
Probab=27.67 E-value=45 Score=27.81 Aligned_cols=23 Identities=22% Similarity=0.265 Sum_probs=20.4
Q ss_pred hhhhhhhcCCHHHHHHHhhcCCc
Q 031315 2 AVKKAVQCGNVEDAIEKVNDLNP 24 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~~~p 24 (161)
.||++|.+|+++.|-+++...|.
T Consensus 165 ~IR~~I~~G~i~~A~~lLg~~y~ 187 (305)
T PRK05627 165 AIRQALAEGDLELANKLLGRPYS 187 (305)
T ss_pred HHHHHHHcCCHHHHHhhhcCCCc
Confidence 59999999999999999977763
No 46
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=27.54 E-value=3.3e+02 Score=21.98 Aligned_cols=60 Identities=22% Similarity=0.159 Sum_probs=39.2
Q ss_pred hcCCHHHHHHHhhcCCccccccCcchhhhhhHHHHHHHHHccchHHHHHHHHHhcCCCCccc
Q 031315 8 QCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEEN 69 (161)
Q Consensus 8 ~~G~i~~Ai~~i~~~~p~ll~~~~~l~F~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~ 69 (161)
-.|-.+.|-.-..+. ++-....++.+.=.+.+..++|..|++++||+...+.....-+++
T Consensus 39 ~eg~~EaA~~Fa~e~--~i~~~~~d~~~~~eR~~Ir~~I~~G~Ie~Aie~in~l~PeiLd~n 98 (228)
T KOG2659|consen 39 HEGYVEAAEKFAKES--GIKPPSIDLDSMDERLQIRRAIEEGQIEEAIEKVNQLNPEILDTN 98 (228)
T ss_pred hccHHHHHHHhcccc--CCCCccCchhhHhHHHHHHHHHHhccHHHHHHHHHHhChHHHccc
Confidence 345555444443332 111113567777778888889999999999999998776655444
No 47
>PRK13241 ureA urease subunit gamma; Provisional
Probab=27.18 E-value=1.4e+02 Score=21.05 Aligned_cols=28 Identities=29% Similarity=0.465 Sum_probs=22.3
Q ss_pred hhHHHHHHHHHcc-chHHHHHHHHHhcCC
Q 031315 37 LQQQRLIELIRNG-KVEEALEFAQEELAP 64 (161)
Q Consensus 37 L~~q~fIElir~~-~~~eAl~yar~~l~~ 64 (161)
|.+-+.+|..|.| .+.+.++.|++.+..
T Consensus 38 lI~~~v~E~aRdG~svaelm~~g~~~L~~ 66 (100)
T PRK13241 38 LISDALLEGARDGKTVAELMSYGRTVLTR 66 (100)
T ss_pred HHHHHHHHHhhCCCCHHHHHHHhhhhCCH
Confidence 3467788899987 588999999987774
No 48
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=27.10 E-value=47 Score=18.17 Aligned_cols=13 Identities=38% Similarity=0.348 Sum_probs=10.3
Q ss_pred hcCCHHHHHHHhh
Q 031315 8 QCGNVEDAIEKVN 20 (161)
Q Consensus 8 ~~G~i~~Ai~~i~ 20 (161)
..||++.|+.|+-
T Consensus 25 ~~~d~~~A~~~L~ 37 (38)
T cd00194 25 TNNNVERAVEWLL 37 (38)
T ss_pred hCCCHHHHHHHHh
Confidence 4688999999873
No 49
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=27.07 E-value=77 Score=19.22 Aligned_cols=27 Identities=11% Similarity=0.065 Sum_probs=23.3
Q ss_pred hhHHHHhhhHHHHHHHHhhhccccCCC
Q 031315 97 LDISQRLKTASEVNAAILTSQSHEKDP 123 (161)
Q Consensus 97 l~~~~r~~la~~vn~aiL~~~~~~~~~ 123 (161)
.+.+++.+++..+..++-...|.+.+.
T Consensus 12 rt~eqK~~l~~~it~~l~~~lg~~~~~ 38 (63)
T TIGR00013 12 RTDEQKRQLIEGVTEAMAETLGANLES 38 (63)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCccc
Confidence 378999999999999999999987653
No 50
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=26.75 E-value=69 Score=19.35 Aligned_cols=26 Identities=15% Similarity=0.092 Sum_probs=22.6
Q ss_pred hhHHHHhhhHHHHHHHHhhhccccCC
Q 031315 97 LDISQRLKTASEVNAAILTSQSHEKD 122 (161)
Q Consensus 97 l~~~~r~~la~~vn~aiL~~~~~~~~ 122 (161)
.+.+++.+++..+..++....|.|.+
T Consensus 12 rs~eqk~~l~~~it~~l~~~~~~p~~ 37 (61)
T PRK02220 12 RTEEQLKALVKDVTAAVSKNTGAPAE 37 (61)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcChh
Confidence 37899999999999999999998654
No 51
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=26.68 E-value=69 Score=19.71 Aligned_cols=26 Identities=19% Similarity=0.100 Sum_probs=22.8
Q ss_pred hHHHHhhhHHHHHHHHhhhccccCCC
Q 031315 98 DISQRLKTASEVNAAILTSQSHEKDP 123 (161)
Q Consensus 98 ~~~~r~~la~~vn~aiL~~~~~~~~~ 123 (161)
+.+++.++++.+..++-...|.|.+.
T Consensus 13 t~eqk~~l~~~it~~l~~~lg~p~~~ 38 (64)
T PRK01964 13 PEEKIKNLIREVTEAISATLDVPKER 38 (64)
T ss_pred CHHHHHHHHHHHHHHHHHHhCcChhh
Confidence 68899999999999999999987653
No 52
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=26.66 E-value=47 Score=18.06 Aligned_cols=12 Identities=50% Similarity=0.556 Sum_probs=9.7
Q ss_pred hcCCHHHHHHHh
Q 031315 8 QCGNVEDAIEKV 19 (161)
Q Consensus 8 ~~G~i~~Ai~~i 19 (161)
..||++.|++|+
T Consensus 25 ~~~d~~~A~~~L 36 (37)
T smart00165 25 ANGNVERAAEYL 36 (37)
T ss_pred hCCCHHHHHHHH
Confidence 368899999886
No 53
>PF08283 Gemini_AL1_M: Geminivirus rep protein central domain; InterPro: IPR022692 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. This is the central region of the geminivirus rep proteins []. It is found C-terminal to PF00799 from PFAM and is thought to be responsible for oligomerisation.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters
Probab=26.62 E-value=84 Score=22.26 Aligned_cols=22 Identities=27% Similarity=0.659 Sum_probs=17.9
Q ss_pred hhhhhcCCHHHHHHHhhcCCcc
Q 031315 4 KKAVQCGNVEDAIEKVNDLNPE 25 (161)
Q Consensus 4 ~~~I~~G~i~~Ai~~i~~~~p~ 25 (161)
-.+|-+|.-++|++.|++.+|.
T Consensus 10 a~aina~sk~EaL~iike~~P~ 31 (106)
T PF08283_consen 10 ARAINAGSKEEALSIIKELAPK 31 (106)
T ss_pred HHHHhcCCHHHHHHHHHhcCch
Confidence 3567888889999999888885
No 54
>PRK13242 ureA urease subunit gamma; Provisional
Probab=26.12 E-value=1.5e+02 Score=20.84 Aligned_cols=28 Identities=25% Similarity=0.357 Sum_probs=22.7
Q ss_pred hhHHHHHHHHHcc-chHHHHHHHHHhcCC
Q 031315 37 LQQQRLIELIRNG-KVEEALEFAQEELAP 64 (161)
Q Consensus 37 L~~q~fIElir~~-~~~eAl~yar~~l~~ 64 (161)
|.+-+.+|..|.| .+.+.+..|++.+..
T Consensus 38 lIs~~i~E~aRdG~svaelm~~g~~vL~~ 66 (100)
T PRK13242 38 VLSAYVLDGAREGKTVEEVMDGARSVLKA 66 (100)
T ss_pred HHHHHHHHHhhcCCcHHHHHHHHHhhCCH
Confidence 4477888999988 589999999988775
No 55
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=25.91 E-value=74 Score=19.28 Aligned_cols=25 Identities=12% Similarity=0.230 Sum_probs=22.2
Q ss_pred hHHHHhhhHHHHHHHHhhhccccCC
Q 031315 98 DISQRLKTASEVNAAILTSQSHEKD 122 (161)
Q Consensus 98 ~~~~r~~la~~vn~aiL~~~~~~~~ 122 (161)
+.+++.++++.+..++.+..|.+.+
T Consensus 13 s~eqk~~l~~~it~~l~~~~~~p~~ 37 (62)
T PRK00745 13 TVEQKRKLVEEITRVTVETLGCPPE 37 (62)
T ss_pred CHHHHHHHHHHHHHHHHHHcCCChh
Confidence 7899999999999999999997654
No 56
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=25.28 E-value=61 Score=23.13 Aligned_cols=25 Identities=36% Similarity=0.477 Sum_probs=14.0
Q ss_pred HHHHHHHHccchHHHHHHHHHhcCC
Q 031315 40 QRLIELIRNGKVEEALEFAQEELAP 64 (161)
Q Consensus 40 q~fIElir~~~~~eAl~yar~~l~~ 64 (161)
.++++.|-+|+..+++...++.+..
T Consensus 19 ~~l~~ai~~~d~~~~l~~~~~l~~~ 43 (143)
T PF12169_consen 19 FELLDAILEGDAAEALELLNELLEQ 43 (143)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHC
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 3455556666666666666655544
No 57
>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]
Probab=25.06 E-value=2.8e+02 Score=23.80 Aligned_cols=73 Identities=12% Similarity=0.135 Sum_probs=48.9
Q ss_pred hhcCCHHHHHHHhhcCCccccccC-cchh-------hhhhHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHH
Q 031315 7 VQCGNVEDAIEKVNDLNPEILDTN-PQLF-------FHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELER 78 (161)
Q Consensus 7 I~~G~i~~Ai~~i~~~~p~ll~~~-~~l~-------F~L~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~ 78 (161)
+-.|+.-.|+-.+++..|.--.-. +... -.-....++|+.++++....++|+|+....-... ...+.++.+
T Consensus 219 ~S~GdLR~Ait~Lqsls~~gk~It~~~~~e~~~GvVp~~~l~~lle~a~S~d~~~~v~~~Rei~~sg~~~-~~lmsQLa~ 297 (346)
T KOG0989|consen 219 ISDGDLRRAITTLQSLSLLGKRITTSLVNEELAGVVPDEKLLDLLELALSADTPNTVKRVREIMRSGYSP-LQLMSQLAE 297 (346)
T ss_pred HcCCcHHHHHHHHHHhhccCcccchHHHHHHHhccCCHHHHHHHHHHHHccChHHHHHHHHHHHHhccCH-HHHHHHHHH
Confidence 457999999999999988211111 2222 2344678999999999999999999877654332 234455544
Q ss_pred Hh
Q 031315 79 TV 80 (161)
Q Consensus 79 ~~ 80 (161)
++
T Consensus 298 vi 299 (346)
T KOG0989|consen 298 VI 299 (346)
T ss_pred HH
Confidence 43
No 58
>PRK09377 tsf elongation factor Ts; Provisional
Probab=25.01 E-value=52 Score=27.46 Aligned_cols=40 Identities=20% Similarity=0.302 Sum_probs=29.6
Q ss_pred cCCHHHHHHHhhcCC-------------------------ccccccCcchhhhhhHHHHHHHHHc
Q 031315 9 CGNVEDAIEKVNDLN-------------------------PEILDTNPQLFFHLQQQRLIELIRN 48 (161)
Q Consensus 9 ~G~i~~Ai~~i~~~~-------------------------p~ll~~~~~l~F~L~~q~fIElir~ 48 (161)
+||++.|++|+++.- ..+++-|..-.|.-+-..|+.++..
T Consensus 31 ~gD~ekAi~~Lrk~G~akA~Kk~~R~a~EG~I~~~~~~~~~~~vElncETDFVArne~F~~l~~~ 95 (290)
T PRK09377 31 DGDIEKAIEWLRKKGLAKAAKKAGRVAAEGLVAAKVDGNKGVLVEVNSETDFVAKNEDFQALANE 95 (290)
T ss_pred CCCHHHHHHHHHHhchhhHHHhcCccccceEEEEEeCCCEEEEEEEecCCccccCChHHHHHHHH
Confidence 699999999998752 2223335777888888888887653
No 59
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=24.69 E-value=2e+02 Score=19.84 Aligned_cols=42 Identities=26% Similarity=0.398 Sum_probs=31.2
Q ss_pred hHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHHHhHHH
Q 031315 38 QQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALL 83 (161)
Q Consensus 38 ~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~LL 83 (161)
+-.+.|+||++.+-..|=..+++.+..+. +....+++....|
T Consensus 53 yErr~i~Lirns~~krArKlakKRLGs~k----RAkaKvEel~~~i 94 (97)
T COG5051 53 YERRVIELIRNSQDKRARKLAKKRLGSLK----RAKAKVEELTSVI 94 (97)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHHhhhHH----HHHHHHHHHHHHH
Confidence 35678999998888888889999888874 3455666665554
No 60
>PRK13986 urease subunit alpha; Provisional
Probab=24.45 E-value=1.2e+02 Score=24.33 Aligned_cols=28 Identities=32% Similarity=0.464 Sum_probs=24.1
Q ss_pred hhHHHHHHHHHccc--hHHHHHHHHHhcCC
Q 031315 37 LQQQRLIELIRNGK--VEEALEFAQEELAP 64 (161)
Q Consensus 37 L~~q~fIElir~~~--~~eAl~yar~~l~~ 64 (161)
|.+-+.+|.+|.|+ +.+.+..|++.+..
T Consensus 38 lI~~~i~E~aRdG~~svaelm~~g~~~L~~ 67 (225)
T PRK13986 38 LISAHIMEEARAGKKTVAELMQEGRTLLKP 67 (225)
T ss_pred HHHHHHHHHHhcCCCcHHHHHHHhhhhCCH
Confidence 44788999999984 99999999988875
No 61
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=24.18 E-value=52 Score=27.59 Aligned_cols=40 Identities=23% Similarity=0.341 Sum_probs=32.6
Q ss_pred cCCHHHHHHHhhcC---------------------------CccccccCcchhhhhhHHHHHHHHHc
Q 031315 9 CGNVEDAIEKVNDL---------------------------NPEILDTNPQLFFHLQQQRLIELIRN 48 (161)
Q Consensus 9 ~G~i~~Ai~~i~~~---------------------------~p~ll~~~~~l~F~L~~q~fIElir~ 48 (161)
+||++.|++|+++. ..-+.+-|+.-.|.=+-..|.++++.
T Consensus 31 ~Gd~EkAie~LR~kG~akA~KKa~R~AaEGli~~~~~~~~~~av~vEvN~ETDFVAkN~~F~~l~~~ 97 (296)
T COG0264 31 NGDIEKAIEWLREKGIAKAAKKAGRIAAEGLIAAKVDGDGKKAVLVEVNCETDFVAKNAEFQELANK 97 (296)
T ss_pred CCCHHHHHHHHHHhchHhhhhhcCcchhcceEEEEEcCCCcEEEEEEEeccccceeCChhHHHHHHH
Confidence 79999999999775 23455667888999999999999874
No 62
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=23.80 E-value=75 Score=15.89 Aligned_cols=19 Identities=26% Similarity=0.531 Sum_probs=12.7
Q ss_pred hhhhhhcCCHHHHHHHhhc
Q 031315 3 VKKAVQCGNVEDAIEKVND 21 (161)
Q Consensus 3 I~~~I~~G~i~~Ai~~i~~ 21 (161)
|....+.|++++|++..++
T Consensus 7 i~~~~~~~~~~~a~~~~~~ 25 (35)
T TIGR00756 7 IDGLCKAGRVEEALELFKE 25 (35)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4456677778887776654
No 63
>PHA02608 67 prohead core protein; Provisional
Probab=23.71 E-value=64 Score=21.65 Aligned_cols=14 Identities=50% Similarity=0.731 Sum_probs=12.2
Q ss_pred HHHHHHHccchHHH
Q 031315 41 RLIELIRNGKVEEA 54 (161)
Q Consensus 41 ~fIElir~~~~~eA 54 (161)
+|||.|++|++-+|
T Consensus 3 ~lIeAIKS~DLV~a 16 (80)
T PHA02608 3 DLIEAIKSGDLVEA 16 (80)
T ss_pred HHHHHHhcCcHHHH
Confidence 69999999998765
No 64
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=23.24 E-value=1.8e+02 Score=19.37 Aligned_cols=27 Identities=15% Similarity=0.275 Sum_probs=20.8
Q ss_pred hhhhhcCCHHHHHHHhhcCCccccccC
Q 031315 4 KKAVQCGNVEDAIEKVNDLNPEILDTN 30 (161)
Q Consensus 4 ~~~I~~G~i~~Ai~~i~~~~p~ll~~~ 30 (161)
-.++..||+..|++-+...|---..++
T Consensus 6 ~~~~~~~dy~~A~d~L~~~fD~~~~~~ 32 (94)
T PF12862_consen 6 LNALRSGDYSEALDALHRYFDYAKQSN 32 (94)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHhhcc
Confidence 367899999999999988775544444
No 65
>PF11251 DUF3050: Protein of unknown function (DUF3050); InterPro: IPR024423 This family of proteins has no known function.
Probab=22.89 E-value=3.4e+02 Score=21.97 Aligned_cols=68 Identities=21% Similarity=0.240 Sum_probs=40.1
Q ss_pred HHHHHHHHcc-chHHHHHHHHHhcCCCCccchHHHHHHHHHhHHHhccccCCCcchhhhhHHHHhhhHHHHHHHHhhhcc
Q 031315 40 QRLIELIRNG-KVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDVSNCPVGDLLDISQRLKTASEVNAAILTSQS 118 (161)
Q Consensus 40 q~fIElir~~-~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~LLay~~~~~sp~~~Ll~~~~r~~la~~vn~aiL~~~~ 118 (161)
..||.++++| ++.+|+..+. .. +....-++.++.++.-..|..-.-+..+. |+.|.=..-+.|+...+
T Consensus 100 ~~fl~~~~~g~~v~~Al~~~~--~p------~~~~~Fv~~Tf~~i~~~~~H~iAAaFtfG---REdlIP~MF~~il~~~~ 168 (232)
T PF11251_consen 100 DRFLSLLREGTSVFEALQQAD--VP------EPAKRFVRFTFEIIAEGKPHEIAAAFTFG---REDLIPDMFRSILKDLN 168 (232)
T ss_pred HHHHHHHHcCCCHHHHHHhcC--CC------HHHHHHHHHHHHHHhcCCHHHHHHHHHhc---cccchHHHHHHHHHHhc
Confidence 5789999988 7888876543 11 12344466666666655554433333334 66666666666666553
No 66
>PF04121 Nup84_Nup100: Nuclear pore protein 84 / 107 ; InterPro: IPR007252 Nup84p forms a complex with five proteins, including Nup120p, Nup85p, Sec13p, and a Sec13p homolog. This Nup84p complex in conjunction with Sec13-type proteins is required for correct nuclear pore biogenesis [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 3CQC_A 3CQG_A 3I4R_A 3IKO_I 3JRO_C.
Probab=22.87 E-value=56 Score=30.34 Aligned_cols=21 Identities=19% Similarity=0.327 Sum_probs=17.2
Q ss_pred hhhhhhhcCCHHHHHHHhhcC
Q 031315 2 AVKKAVQCGNVEDAIEKVNDL 22 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~~ 22 (161)
.|-.+|++|++++|++||++.
T Consensus 139 ~i~~llR~G~~~eA~~lc~~~ 159 (697)
T PF04121_consen 139 YIFELLRAGRIEEAQELCRER 159 (697)
T ss_dssp HHHHHHHTT-HHHHHHHHHHT
T ss_pred HHHHHHHCCCHHHHHHHHHHC
Confidence 356789999999999999775
No 67
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=22.09 E-value=1.9e+02 Score=17.39 Aligned_cols=54 Identities=31% Similarity=0.313 Sum_probs=33.0
Q ss_pred hhhcCCHHHHHHHhhcCCccccccCcchhhhhhHHHHHHHHHccchHHHHHHHHHhcCC
Q 031315 6 AVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAP 64 (161)
Q Consensus 6 ~I~~G~i~~Ai~~i~~~~p~ll~~~~~l~F~L~~q~fIElir~~~~~eAl~yar~~l~~ 64 (161)
++..|+.+.|++.++.. +..+++ ...++...=.=+.+.|+..+|++.-+.-+..
T Consensus 5 ~~~~~~~~~A~~~~~~~----l~~~p~-~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~ 58 (73)
T PF13371_consen 5 YLQQEDYEEALEVLERA----LELDPD-DPELWLQRARCLFQLGRYEEALEDLERALEL 58 (73)
T ss_pred HHhCCCHHHHHHHHHHH----HHhCcc-cchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence 56788899988877433 222222 3333444444455678888888877766543
No 68
>PF04699 P16-Arc: ARP2/3 complex 16 kDa subunit (p16-Arc); InterPro: IPR006789 The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices [, ].; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_G 1TYQ_G 1U2V_G 2P9U_G 2P9L_G 1K8K_G 3DXM_G 2P9N_G 3DXK_G 2P9I_G ....
Probab=22.02 E-value=76 Score=23.90 Aligned_cols=23 Identities=22% Similarity=0.446 Sum_probs=16.9
Q ss_pred hhhhhhhcCCHHHHHHHhhcCCc
Q 031315 2 AVKKAVQCGNVEDAIEKVNDLNP 24 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~~~~p 24 (161)
+|+.++..|+..+|++.+=++-|
T Consensus 42 qvr~ll~~g~~~~ALk~aL~npP 64 (152)
T PF04699_consen 42 QVRQLLSSGDNEEALKAALENPP 64 (152)
T ss_dssp HHHHHHHCT-HHHHHHHHTSS--
T ss_pred HHHHHHhCCCHHHHHHHhccCCC
Confidence 57888889999999988877755
No 69
>TIGR03362 VI_chp_7 type VI secretion-associated protein, VC_A0119 family. This protein family is one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (pfam06812).
Probab=21.11 E-value=1e+02 Score=25.80 Aligned_cols=54 Identities=20% Similarity=0.335 Sum_probs=30.1
Q ss_pred hhhhhhcCCHHHHHHHhhcCCccccccCcchhhhhhHHHHHHHHHccchHHHHHHH
Q 031315 3 VKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFA 58 (161)
Q Consensus 3 I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~l~F~L~~q~fIElir~~~~~eAl~ya 58 (161)
.+..+.+|.+++|+.|+++..|..-.....++.+|..-+..+- .|..+-|+.+-
T Consensus 220 A~~l~~~~gl~~Al~~L~~~~~~~~s~R~rf~~rL~~A~l~~~--~g~~~lA~~ll 273 (301)
T TIGR03362 220 ARALAAEGGLEAALQRLQQRLAQAREPRERFHWRLLLARLLEQ--AGKAELAQQLY 273 (301)
T ss_pred HHHHHHcCCHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHH--cCCHHHHHHHH
Confidence 4556777888888888887666555443444444444444332 34434343333
No 70
>PRK11727 23S rRNA mA1618 methyltransferase; Provisional
Probab=20.75 E-value=1.4e+02 Score=25.17 Aligned_cols=51 Identities=20% Similarity=0.296 Sum_probs=35.9
Q ss_pred hHHHHHHHHhhh-ccccC--------CCChhHHHHHHHHHHhhhhhh--c-----cccccccccccc
Q 031315 105 TASEVNAAILTS-QSHEK--------DPKLPSLLKMLLWAQNQLDEK--A-----AYPRINDLATAT 155 (161)
Q Consensus 105 la~~vn~aiL~~-~~~~~--------~~~L~~l~k~~~~~~~~l~~~--~-----~~p~~~~~~~~~ 155 (161)
-...+|.+||.+ +|..- .|.++.=+.++.|..+.|.+. . .--..+|+++|+
T Consensus 59 Av~~LnkalL~~~ygl~~wdip~~~LcPpiP~R~~Yi~~l~dll~~~~~~~~p~~~~~~vLDIGtGa 125 (321)
T PRK11727 59 AVKALNKALLAHFYGVAHWDIPAGYLCPPIPGRADYIHHLADLLAEDNGGVIPRGANVRVLDIGVGA 125 (321)
T ss_pred HHHHHHHHHHHHhcCCCcccCCCCCcCCCCCcHHHHHHHHHHHhcccccccCCCCCCceEEEecCCc
Confidence 345788999854 45442 478899999999999988542 1 123678899884
No 71
>PF07729 FCD: FCD domain; InterPro: IPR011711 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (IPR000524 from INTERPRO), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (IPR008920 from INTERPRO), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA []. This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in P45427 from SWISSPROT and P31460 from SWISSPROT that are regulators of sugar biosynthesis operons.; PDB: 3SXK_A 3SXY_A 3SXM_B 3SXZ_A 3FMS_A 2DI3_B 2HS5_A 3IHU_B 3C7J_A.
Probab=20.55 E-value=1.4e+02 Score=19.63 Aligned_cols=24 Identities=29% Similarity=0.493 Sum_probs=16.7
Q ss_pred HHHHHHHHHccchHHHHHHHHHhc
Q 031315 39 QQRLIELIRNGKVEEALEFAQEEL 62 (161)
Q Consensus 39 ~q~fIElir~~~~~eAl~yar~~l 62 (161)
..+.++.|++|+.+.|-+..+.|+
T Consensus 100 h~~i~~ai~~~d~~~a~~~~~~h~ 123 (125)
T PF07729_consen 100 HREIIDAIRAGDPEAAREALRQHI 123 (125)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHh
Confidence 456677777888888877777665
No 72
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=20.43 E-value=73 Score=22.67 Aligned_cols=19 Identities=16% Similarity=0.384 Sum_probs=16.1
Q ss_pred hhhhhhhcCCHHHHHHHhh
Q 031315 2 AVKKAVQCGNVEDAIEKVN 20 (161)
Q Consensus 2 ~I~~~I~~G~i~~Ai~~i~ 20 (161)
.+++.|..|+++.|++++.
T Consensus 76 ~~~~~l~~g~~~~a~~ll~ 94 (115)
T PF12793_consen 76 QAEELLEQGKYEQALQLLD 94 (115)
T ss_pred HHHHHHHcCCHHHHHHHHH
Confidence 3577889999999999997
No 73
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=20.09 E-value=59 Score=27.11 Aligned_cols=40 Identities=20% Similarity=0.337 Sum_probs=29.5
Q ss_pred cCCHHHHHHHhhcCC-------------------------ccccccCcchhhhhhHHHHHHHHHc
Q 031315 9 CGNVEDAIEKVNDLN-------------------------PEILDTNPQLFFHLQQQRLIELIRN 48 (161)
Q Consensus 9 ~G~i~~Ai~~i~~~~-------------------------p~ll~~~~~l~F~L~~q~fIElir~ 48 (161)
+||++.|++|+++.- ..+++-|..-.|.-+-..|++++..
T Consensus 30 ~gDiekAi~~LRkkG~akA~Kk~~R~a~EG~V~~~~~~~~~~ivElncETDFVArne~F~~l~~~ 94 (290)
T TIGR00116 30 NGDFEKAIKNLRESGIAKAAKKADRVAAEGVIVLKSDGNKAVIVEVNSETDFVAKNAGFKEFANK 94 (290)
T ss_pred CCCHHHHHHHHHHhchhHHHHhcccccCCcEEEEEEcCCEEEEEEEecCCccccCChHHHHHHHH
Confidence 699999999998762 2233345777888888888888653
No 74
>KOG3452 consensus 60S ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=20.03 E-value=2.6e+02 Score=19.58 Aligned_cols=42 Identities=21% Similarity=0.310 Sum_probs=29.8
Q ss_pred hHHHHHHHHHccchHHHHHHHHHhcCCCCccchHHHHHHHHHhHHH
Q 031315 38 QQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALL 83 (161)
Q Consensus 38 ~~q~fIElir~~~~~eAl~yar~~l~~~~~~~~~~~~~l~~~~~LL 83 (161)
+-.+-+||++.++-..|+.++++.+..+.. -....+++...|
T Consensus 53 yErr~meLlkvskdkrA~K~lKkRlGth~R----Ak~KrEELsnvl 94 (102)
T KOG3452|consen 53 YERRAMELLKVSKDKRALKLLKKRLGTHKR----AKRKREELSNVL 94 (102)
T ss_pred HHHHHHHHHHHcccHHHHHHHHHHhhHHHH----HHHHHHHHHHHH
Confidence 345778999988888999999999987743 233444444444
Done!