Query 038964
Match_columns 111
No_of_seqs 120 out of 587
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 05:02:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038964.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038964hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 6.4E-44 1.4E-48 298.1 12.3 110 2-111 264-373 (846)
2 PF10551 MULE: MULE transposas 99.9 1.1E-24 2.4E-29 138.7 7.6 79 31-111 1-82 (93)
3 PF00872 Transposase_mut: Tran 98.7 3.5E-09 7.6E-14 83.1 0.6 85 25-110 163-252 (381)
4 COG3328 Transposase and inacti 97.4 0.00031 6.7E-09 55.6 5.2 84 25-110 146-231 (379)
5 PF13610 DDE_Tnp_IS240: DDE do 96.9 0.00036 7.8E-09 47.5 0.7 80 24-107 1-80 (140)
6 PF00665 rve: Integrase core d 96.4 0.04 8.7E-07 35.2 8.2 74 24-98 6-80 (120)
7 COG3316 Transposase and inacti 93.4 0.24 5.1E-06 36.5 5.3 84 23-111 69-152 (215)
8 PF01610 DDE_Tnp_ISL3: Transpo 90.9 0.45 9.8E-06 34.6 4.4 49 61-110 32-81 (249)
9 PHA02517 putative transposase 77.5 9.3 0.0002 28.2 5.9 72 22-98 108-182 (277)
10 PF02171 Piwi: Piwi domain; I 68.3 46 0.00099 24.8 7.8 70 26-95 79-157 (302)
11 cd04657 Piwi_ago-like Piwi_ago 64.7 70 0.0015 25.5 8.6 80 26-106 201-305 (426)
12 PF04937 DUF659: Protein of un 59.4 56 0.0012 22.5 7.3 84 15-102 24-110 (153)
13 PRK14702 insertion element IS2 58.5 66 0.0014 24.0 7.1 73 24-97 87-164 (262)
14 PF12762 DDE_Tnp_IS1595: ISXO2 53.7 64 0.0014 21.4 6.3 69 25-98 4-87 (151)
15 PRK09409 IS2 transposase TnpB; 52.4 1E+02 0.0022 23.4 7.4 73 24-97 126-203 (301)
16 TIGR00334 5S_RNA_mat_M5 ribonu 52.4 23 0.00049 25.4 3.5 30 82-111 45-77 (174)
17 cd01085 APP X-Prolyl Aminopept 45.8 26 0.00057 25.4 3.1 75 22-107 80-155 (224)
18 KOG1378 Purple acid phosphatas 43.3 60 0.0013 26.7 5.0 30 62-91 269-298 (452)
19 COG3915 Uncharacterized protei 41.1 35 0.00077 23.7 2.9 39 15-53 95-135 (155)
20 TIGR00500 met_pdase_I methioni 39.3 18 0.00039 26.2 1.4 50 53-104 107-156 (247)
21 cd04659 Piwi_piwi-like_ProArk 38.5 2E+02 0.0042 22.7 8.2 70 26-95 192-269 (404)
22 TIGR00824 EIIA-man PTS system, 37.0 88 0.0019 20.3 4.3 38 56-93 30-67 (116)
23 PF00076 RRM_1: RNA recognitio 35.5 50 0.0011 18.1 2.7 48 14-78 13-60 (70)
24 KOG1041 Translation initiation 33.9 2.6E+02 0.0057 24.9 7.8 69 26-95 608-687 (876)
25 PRK12897 methionine aminopepti 33.9 44 0.00095 24.4 2.7 50 53-104 108-157 (248)
26 cd01091 CDC68-like Related to 33.9 42 0.0009 24.7 2.6 51 53-106 111-161 (243)
27 KOG4027 Uncharacterized conser 33.1 57 0.0012 23.3 3.0 47 20-66 57-110 (187)
28 COG0006 PepP Xaa-Pro aminopept 32.3 56 0.0012 25.4 3.2 71 22-103 231-301 (384)
29 cd02826 Piwi-like Piwi-like: P 31.7 2.6E+02 0.0056 22.0 7.3 67 26-94 174-251 (393)
30 PF05902 4_1_CTD: 4.1 protein 31.1 30 0.00066 23.1 1.3 18 91-108 81-101 (114)
31 KOG2703 C4-type Zn-finger prot 28.5 61 0.0013 26.4 2.8 40 53-93 370-409 (460)
32 COG1658 Small primase-like pro 28.2 62 0.0013 21.9 2.5 28 84-111 55-85 (127)
33 PF05221 AdoHcyase: S-adenosyl 28.0 53 0.0011 25.1 2.3 37 62-98 98-134 (268)
34 PF13535 ATP-grasp_4: ATP-gras 27.5 1.4E+02 0.0031 19.7 4.3 36 71-106 5-41 (184)
35 PF03610 EIIA-man: PTS system 27.5 1.5E+02 0.0033 18.8 4.2 39 56-94 29-67 (116)
36 cd00758 MoCF_BD MoCF_BD: molyb 26.8 1.3E+02 0.0027 19.8 3.8 45 61-105 11-56 (133)
37 PF11775 CobT_C: Cobalamin bio 26.1 44 0.00096 24.8 1.5 32 65-96 117-148 (219)
38 PRK14575 putative peptidase; P 26.0 59 0.0013 25.8 2.4 53 53-107 276-329 (406)
39 TIGR02993 ectoine_eutD ectoine 25.0 98 0.0021 24.3 3.4 50 53-104 261-310 (391)
40 PF03400 DDE_Tnp_IS1: IS1 tran 24.8 1.6E+02 0.0036 19.8 4.1 68 32-110 12-79 (131)
41 PF03367 zf-ZPR1: ZPR1 zinc-fi 24.8 74 0.0016 22.2 2.4 30 63-92 122-151 (161)
42 KOG1616 Protein involved in Sn 24.7 1.3E+02 0.0027 23.1 3.9 95 4-110 79-183 (289)
43 PF02845 CUE: CUE domain; Int 24.4 77 0.0017 16.6 2.0 13 96-108 3-15 (42)
44 PF12367 PFO_beta_C: Pyruvate 24.2 41 0.00088 20.2 0.9 32 67-102 7-38 (67)
45 KOG3368 Transport protein part 23.7 64 0.0014 22.2 1.9 40 32-79 63-102 (140)
46 cd00885 cinA Competence-damage 23.7 1.7E+02 0.0037 20.4 4.1 49 57-105 7-56 (170)
47 TIGR00340 zpr1_rel ZPR1-relate 23.6 88 0.0019 22.0 2.6 28 65-92 118-145 (163)
48 PRK15173 peptidase; Provisiona 23.5 85 0.0018 24.1 2.8 52 53-106 193-245 (323)
49 PRK14576 putative endopeptidas 23.1 58 0.0013 25.8 1.8 52 53-106 275-327 (405)
50 PF00994 MoCF_biosynth: Probab 22.9 1.3E+02 0.0028 19.9 3.3 48 57-104 5-53 (144)
51 COG4873 Uncharacterized protei 22.0 1.3E+02 0.0029 18.3 2.8 33 24-56 45-77 (81)
52 PRK13293 F420-0--gamma-glutamy 21.1 1.7E+02 0.0037 22.0 3.9 60 33-95 94-153 (245)
53 PF14386 DUF4417: Domain of un 20.7 1.7E+02 0.0036 21.2 3.7 47 45-93 129-175 (200)
54 COG0552 FtsY Signal recognitio 20.7 47 0.001 26.3 0.8 39 19-57 117-156 (340)
55 cd01089 PA2G4-like Related to 20.5 94 0.002 22.3 2.4 37 68-104 124-160 (228)
56 cd08787 CARD_NOD2_1_CARD15 Cas 20.5 64 0.0014 20.4 1.3 19 91-109 65-83 (87)
57 KOG1522 RNA polymerase II, sub 20.5 93 0.002 23.7 2.3 22 84-105 16-37 (285)
58 smart00546 CUE Domain that may 20.4 98 0.0021 16.2 1.9 15 95-109 3-17 (43)
59 PLN02494 adenosylhomocysteinas 20.4 1.5E+02 0.0032 24.6 3.7 40 62-101 101-140 (477)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=6.4e-44 Score=298.14 Aligned_cols=110 Identities=29% Similarity=0.490 Sum_probs=108.5
Q ss_pred ccceeeEEEEechhchhhhhhCCCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHh
Q 038964 2 KRIDWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAM 81 (111)
Q Consensus 2 ~~~~l~~ifw~~~~~~~~~~~f~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~ 81 (111)
.+++|++|||+|++|+.+|.+|||||+||+||+||+|+|||+.|+|+|||+|+++||||||.||+.|||.|||++|+++|
T Consensus 264 e~~~l~niFWaD~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM 343 (846)
T PLN03097 264 EDQRLKNLFWVDAKSRHDYGNFSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAM 343 (846)
T ss_pred cCCCeeeEEeccHHHHHHHHhcCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHh
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCceEEEeeCcHHHHHHHHHhCCCCCCC
Q 038964 82 NRKNSLRVIINGDQIMSKAMATTFLDSTHK 111 (111)
Q Consensus 82 ~~~~p~~iiTD~d~a~~~Ai~~vfP~~~Hr 111 (111)
+|+.|++||||+|.+|++||++|||+|.||
T Consensus 344 ~gk~P~tIiTDqd~am~~AI~~VfP~t~Hr 373 (846)
T PLN03097 344 GGQAPKVIITDQDKAMKSVISEVFPNAHHC 373 (846)
T ss_pred CCCCCceEEecCCHHHHHHHHHHCCCceeh
Confidence 999999999999999999999999999998
No 2
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.91 E-value=1.1e-24 Score=138.69 Aligned_cols=79 Identities=30% Similarity=0.497 Sum_probs=75.8
Q ss_pred cccccCCCCCceeE---EEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHhCCC
Q 038964 31 TTYQTNAYSKPFVV---IVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLD 107 (111)
Q Consensus 31 ~Ty~tn~y~~pl~~---~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~vfP~ 107 (111)
+||+||+| +|++. ++|+|++++.+++|++++.+|+.++|.|+|+.+++.+..+ |.+|+||+|.++.+||+++||+
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~-p~~ii~D~~~~~~~Ai~~vfP~ 78 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK-PKVIISDFDKALINAIKEVFPD 78 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC-ceeeeccccHHHHHHHHHHCCC
Confidence 69999999 88885 9999999999999999999999999999999999999887 9999999999999999999999
Q ss_pred CCCC
Q 038964 108 STHK 111 (111)
Q Consensus 108 ~~Hr 111 (111)
+.|+
T Consensus 79 ~~~~ 82 (93)
T PF10551_consen 79 ARHQ 82 (93)
T ss_pred ceEe
Confidence 9985
No 3
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. 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
Probab=98.70 E-value=3.5e-09 Score=83.06 Aligned_cols=85 Identities=19% Similarity=0.181 Sum_probs=75.0
Q ss_pred CeEEEecccccCCC-----CCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHH
Q 038964 25 DIPTFDTTYQTNAY-----SKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSK 99 (111)
Q Consensus 25 dvv~~D~Ty~tn~y-----~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~ 99 (111)
++|.+|++|.+-+. +.+++.++|+|..|+-.++|+.+-..|+.++|.=+|+.+++. |-+.|..|++|..+++.+
T Consensus 163 ~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~~~~lvv~Dg~~gl~~ 241 (381)
T PF00872_consen 163 PYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLKDILLVVSDGHKGLKE 241 (381)
T ss_pred cceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-cccccceeeccccccccc
Confidence 57889999987553 467899999999999999999999999999999888888765 335699999999999999
Q ss_pred HHHHhCCCCCC
Q 038964 100 AMATTFLDSTH 110 (111)
Q Consensus 100 Ai~~vfP~~~H 110 (111)
||+++||++.|
T Consensus 242 ai~~~fp~a~~ 252 (381)
T PF00872_consen 242 AIREVFPGAKW 252 (381)
T ss_pred cccccccchhh
Confidence 99999999875
No 4
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=97.40 E-value=0.00031 Score=55.55 Aligned_cols=84 Identities=13% Similarity=0.137 Sum_probs=65.6
Q ss_pred CeEEEecccccCC--CCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHH
Q 038964 25 DIPTFDTTYQTNA--YSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMA 102 (111)
Q Consensus 25 dvv~~D~Ty~tn~--y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~ 102 (111)
.++.+|++|.+=+ -+..++..+|++.+|+-.+.|.-+=..|. ..|.-++..|... +-..-..+++|..+++.+||.
T Consensus 146 ~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-gl~~v~l~v~Dg~~gl~~aI~ 223 (379)
T COG3328 146 PYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-GLSDVLLVVVDGLKGLPEAIS 223 (379)
T ss_pred eEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-cccceeEEecchhhhhHHHHH
Confidence 4678999999988 35688899999999999999988888888 6665333334332 223445667799999999999
Q ss_pred HhCCCCCC
Q 038964 103 TTFLDSTH 110 (111)
Q Consensus 103 ~vfP~~~H 110 (111)
.+||.+.|
T Consensus 224 ~v~p~a~~ 231 (379)
T COG3328 224 AVFPQAAV 231 (379)
T ss_pred HhccHhhh
Confidence 99998765
No 5
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=96.86 E-value=0.00036 Score=47.53 Aligned_cols=80 Identities=15% Similarity=0.079 Sum_probs=61.7
Q ss_pred CCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHH
Q 038964 24 GDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMAT 103 (111)
Q Consensus 24 ~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~ 103 (111)
|+.+.+|=||-+=+ |--...+-.+|.+++ ++.+=|-...+...=..+|+..++... ..|.+|+||+.++...|+++
T Consensus 1 ~~~w~~DEt~iki~-G~~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-~~p~~ivtDk~~aY~~A~~~ 76 (140)
T PF13610_consen 1 GDSWHVDETYIKIK-GKWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKE 76 (140)
T ss_pred CCEEEEeeEEEEEC-CEEEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhh
Confidence 68899999997643 345667888899988 555556666666666666666666544 78999999999999999999
Q ss_pred hCCC
Q 038964 104 TFLD 107 (111)
Q Consensus 104 vfP~ 107 (111)
+.|+
T Consensus 77 l~~~ 80 (140)
T PF13610_consen 77 LNPE 80 (140)
T ss_pred cccc
Confidence 9997
No 6
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=96.43 E-value=0.04 Score=35.23 Aligned_cols=74 Identities=14% Similarity=0.062 Sum_probs=51.0
Q ss_pred CCeEEEeccccc-CCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHH
Q 038964 24 GDIPTFDTTYQT-NAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMS 98 (111)
Q Consensus 24 ~dvv~~D~Ty~t-n~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~ 98 (111)
++.+.+|.+... ...+.....++.+|...+-.. +..+-..++.+.+.-+++...+..++..|++|+||+..+..
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~ 80 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRFIY-AFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFT 80 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTEEE-EEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHH
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCcEE-EEEeecccccccccccccccccccccccceecccccccccc
Confidence 578889998444 445557888888888877544 55555555766776666666665555559999999999886
No 7
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.37 E-value=0.24 Score=36.54 Aligned_cols=84 Identities=14% Similarity=0.111 Sum_probs=54.6
Q ss_pred CCCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHH
Q 038964 23 FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMA 102 (111)
Q Consensus 23 f~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~ 102 (111)
=++..-+|=||-+-+=+- ....-.||..|++.-+- |-..-+...=.=++..+++.. ..|.+|+||+.+....|++
T Consensus 69 ~~~~w~vDEt~ikv~gkw-~ylyrAid~~g~~Ld~~--L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~ 143 (215)
T COG3316 69 AGDSWRVDETYIKVNGKW-HYLYRAIDADGLTLDVW--LSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALR 143 (215)
T ss_pred cccceeeeeeEEeeccEe-eehhhhhccCCCeEEEE--EEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHH
Confidence 357788899987655333 23344556667765542 222222222233445555543 6789999999999999999
Q ss_pred HhCCCCCCC
Q 038964 103 TTFLDSTHK 111 (111)
Q Consensus 103 ~vfP~~~Hr 111 (111)
++-++..||
T Consensus 144 ~l~~~~ehr 152 (215)
T COG3316 144 KLGSEVEHR 152 (215)
T ss_pred hcCcchhee
Confidence 999988886
No 8
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. 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
Probab=90.95 E-value=0.45 Score=34.63 Aligned_cols=49 Identities=18% Similarity=0.184 Sum_probs=37.2
Q ss_pred eccccccchhhHHHHHH-HHHhcCCCceEEEeeCcHHHHHHHHHhCCCCCC
Q 038964 61 LLTSETKYTNTYLLETF-LRAMNRKNSLRVIINGDQIMSKAMATTFLDSTH 110 (111)
Q Consensus 61 ll~~E~~es~~W~l~~f-~~~~~~~~p~~iiTD~d~a~~~Ai~~vfP~~~H 110 (111)
++.+-+.+++.=.|..+ -.. .....++|.+|-..+..+|+++.||+|.+
T Consensus 32 i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~~~P~A~i 81 (249)
T PF01610_consen 32 ILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIREYFPNAQI 81 (249)
T ss_pred EcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCcccccccccccccccc
Confidence 67787877774444433 222 34678899999999999999999999874
No 9
>PHA02517 putative transposase OrfB; Reviewed
Probab=77.50 E-value=9.3 Score=28.21 Aligned_cols=72 Identities=15% Similarity=0.064 Sum_probs=44.0
Q ss_pred hCCCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhc---CCCceEEEeeCcHHHH
Q 038964 22 VFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN---RKNSLRVIINGDQIMS 98 (111)
Q Consensus 22 ~f~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~---~~~p~~iiTD~d~a~~ 98 (111)
.=++++..|.||....-+. ....+-+|...+-+ +|+.+-..++.+ ++.+.+..++. ...+..+.||+.....
T Consensus 108 ~pn~~w~~D~t~~~~~~g~-~yl~~iiD~~sr~i-~~~~~~~~~~~~---~~~~~l~~a~~~~~~~~~~i~~sD~G~~y~ 182 (277)
T PHA02517 108 RPNQLWVADFTYVSTWQGW-VYVAFIIDVFARRI-VGWRVSSSMDTD---FVLDALEQALWARGRPGGLIHHSDKGSQYV 182 (277)
T ss_pred CCCCeEEeceeEEEeCCCC-EEEEEecccCCCee-eecccCCCCChH---HHHHHHHHHHHhcCCCcCcEeecccccccc
Confidence 3457899999997655443 45666677776644 466666555555 34455554443 2233466799987653
No 10
>PF02171 Piwi: Piwi domain; InterPro: IPR003165 This domain is found in the stem cell self-renewal protein Piwi and its relatives in Drosophila melanogaster []. It has been found in the C-terminal of a number of proteins which also contain the PAZ domain (IPR003100 from INTERPRO) in their central region, for example the Argonaute proteins. Several of these proteins have been implicated in the development and maintenance of stem cells through the RNA-mediated gene-quelling mechanisms associated with the protein DICER. ; GO: 0005515 protein binding; PDB: 4F1N_B 3LUH_B 4EI1_A 3QX8_A 3LUC_C 3LUJ_B 3LUD_B 3QX9_A 3LUG_B 3LUK_B ....
Probab=68.25 E-value=46 Score=24.81 Aligned_cols=70 Identities=19% Similarity=0.099 Sum_probs=40.4
Q ss_pred eEEEecccccCCC-CCcee-EEEE-EccCCceEEEEeeeccc--ccc----chhhHHHHHHHHHhcCCCceEEEeeCcH
Q 038964 26 IPTFDTTYQTNAY-SKPFV-VIVG-INQHIETISFLFGLLTS--ETK----YTNTYLLETFLRAMNRKNSLRVIINGDQ 95 (111)
Q Consensus 26 vv~~D~Ty~tn~y-~~pl~-~~~g-~n~~~~~~~~~~~ll~~--E~~----es~~W~l~~f~~~~~~~~p~~iiTD~d~ 95 (111)
+|.+|.++..... +.|-+ -+++ +|.++..+.-.+.+... |.. +.+..+++.|.+..+...|..||--||-
T Consensus 79 iIGidv~h~~~~~~~~~sv~g~~~s~~~~~~~~~~~~~~~~~~~e~~~~l~~~~~~~L~~~~~~~~~~~P~~IiiyRdG 157 (302)
T PF02171_consen 79 IIGIDVSHPSPGSDKNPSVVGFVASFDSDGSKYFSSVRFQDSGQEIIDNLEEIIKEALKEFKKNNGKWLPERIIIYRDG 157 (302)
T ss_dssp EEEEEEEEESSTCTCSCEEEEEEEEESTTTCEEEEEEEEECTTCCCHHHHHHHHHHHHHHHHHTTTT-TTSEEEEEEES
T ss_pred EEEEEEEecCcccCCcceeeEEEEeccCccccccceeEEeccchhhhcchhhHHHHHHHHHHHHcCCCCCceEEEEEcc
Confidence 6779999988887 45533 2333 34444444433333322 222 2356666777666555488888887764
No 11
>cd04657 Piwi_ago-like Piwi_ago-like: PIWI domain, Argonaute-like subfamily. Argonaute is the central component of the RNA-induced silencing complex (RISC) and related complexes. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing.
Probab=64.73 E-value=70 Score=25.55 Aligned_cols=80 Identities=21% Similarity=0.224 Sum_probs=43.9
Q ss_pred eEEEecccccCC--CCCcee--EEEEEccCCceEEEEeeecccc--cc----chhhHHHHHHHHHhcCCCceEEEeeCcH
Q 038964 26 IPTFDTTYQTNA--YSKPFV--VIVGINQHIETISFLFGLLTSE--TK----YTNTYLLETFLRAMNRKNSLRVIINGDQ 95 (111)
Q Consensus 26 vv~~D~Ty~tn~--y~~pl~--~~~g~n~~~~~~~~~~~ll~~E--~~----es~~W~l~~f~~~~~~~~p~~iiTD~d~ 95 (111)
+|.+|.|+.+.. -+.|-. .+.-+|.+...+.-.+.+-... .. +.+.-+|+.|.+.. +..|.-||--||-
T Consensus 201 iiG~Dv~H~~~~~~~~~pSiaa~Vas~d~~~~~y~~~~~~q~~~~e~i~~l~~~~~~~l~~~~~~~-~~~P~~IiiyRDG 279 (426)
T cd04657 201 VLGADVTHPSPGDPAGAPSIAAVVASVDWHLAQYPASVRLQSHRQEIIDDLESMVRELLRAFKKAT-GKLPERIIYYRDG 279 (426)
T ss_pred EEEEeeecCCCCCCCCCCcEEEEEEecCCcccccceEEEEeCCCcchHHHHHHHHHHHHHHHHHHh-CCCCceEEEEEcC
Confidence 556899998876 355532 2233455555444333333322 22 22355555665543 4589888877653
Q ss_pred ---------------HHHHHHHHhCC
Q 038964 96 ---------------IMSKAMATTFL 106 (111)
Q Consensus 96 ---------------a~~~Ai~~vfP 106 (111)
++++|+++..|
T Consensus 280 vsegq~~~v~~~E~~~i~~a~~~~~~ 305 (426)
T cd04657 280 VSEGQFAQVLNEELPAIRKACAKLYP 305 (426)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 55666666654
No 12
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=59.35 E-value=56 Score=22.53 Aligned_cols=84 Identities=15% Similarity=0.025 Sum_probs=53.1
Q ss_pred hchhhhhhCCCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHH---HhcCCCceEEEe
Q 038964 15 GSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLR---AMNRKNSLRVII 91 (111)
Q Consensus 15 ~~~~~~~~f~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~---~~~~~~p~~iiT 91 (111)
..+..+..+|=-+..|+= ++..+.++..|.-..+.|..|.-. .-..++. .+=..+++.+.+ -.|...=--|||
T Consensus 24 ~~k~~w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flks-vd~s~~~-~~a~~l~~ll~~vIeeVG~~nVvqVVT 99 (153)
T PF04937_consen 24 EHKKSWKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKS-VDASSII-KTAEYLFELLDEVIEEVGEENVVQVVT 99 (153)
T ss_pred HHHHHHHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEE-Eeccccc-ccHHHHHHHHHHHHHHhhhhhhhHHhc
Confidence 346778899988999985 666777888887766665554332 2233332 222444444444 445444445899
Q ss_pred eCcHHHHHHHH
Q 038964 92 NGDQIMSKAMA 102 (111)
Q Consensus 92 D~d~a~~~Ai~ 102 (111)
|....+++|-+
T Consensus 100 Dn~~~~~~a~~ 110 (153)
T PF04937_consen 100 DNASNMKKAGK 110 (153)
T ss_pred cCchhHHHHHH
Confidence 99999998844
No 13
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=58.46 E-value=66 Score=23.95 Aligned_cols=73 Identities=5% Similarity=-0.067 Sum_probs=44.5
Q ss_pred CCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccc-cccchhhHHHHHHHHHh-c---CCCceEEEeeCcHHH
Q 038964 24 GDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTS-ETKYTNTYLLETFLRAM-N---RKNSLRVIINGDQIM 97 (111)
Q Consensus 24 ~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~-E~~es~~W~l~~f~~~~-~---~~~p~~iiTD~d~a~ 97 (111)
..+.+.|-||.....+.-+...+-+|.+.+ .++|+++-.. .+.+.-.=+|+..++.. + ...|..|.||+....
T Consensus 87 n~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsqy 164 (262)
T PRK14702 87 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCY 164 (262)
T ss_pred CCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCccc
Confidence 467889999976655555777777888777 4557776553 33333323333323222 2 235788999987653
No 14
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=53.68 E-value=64 Score=21.44 Aligned_cols=69 Identities=13% Similarity=0.140 Sum_probs=36.5
Q ss_pred CeEEEecccccCCC--------------CCceeEEEEEccC-CceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEE
Q 038964 25 DIPTFDTTYQTNAY--------------SKPFVVIVGINQH-IETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRV 89 (111)
Q Consensus 25 dvv~~D~Ty~tn~y--------------~~pl~~~~g~n~~-~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~i 89 (111)
.+|-+|-||...+- .-....+++++.. +.+--+-...+.+.+.++..=+++...+ +..+|
T Consensus 4 G~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~~i~-----~gs~i 78 (151)
T PF12762_consen 4 GIVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQEHIE-----PGSTI 78 (151)
T ss_pred CEEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHHhhh-----cccee
Confidence 36777777765332 1122234444443 3222233345677887777444332222 34678
Q ss_pred EeeCcHHHH
Q 038964 90 IINGDQIMS 98 (111)
Q Consensus 90 iTD~d~a~~ 98 (111)
+||.-.+-.
T Consensus 79 ~TD~~~aY~ 87 (151)
T PF12762_consen 79 ITDGWRAYN 87 (151)
T ss_pred eecchhhcC
Confidence 999988764
No 15
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=52.45 E-value=1e+02 Score=23.44 Aligned_cols=73 Identities=7% Similarity=-0.032 Sum_probs=44.8
Q ss_pred CCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccc-cccchhhHHHHHHH-HHhc---CCCceEEEeeCcHHH
Q 038964 24 GDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTS-ETKYTNTYLLETFL-RAMN---RKNSLRVIINGDQIM 97 (111)
Q Consensus 24 ~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~-E~~es~~W~l~~f~-~~~~---~~~p~~iiTD~d~a~ 97 (111)
..+.+-|-||....-+.-+...+-+|-..+ .++|+++-.. .+.+.-.=+|+.-+ ...+ ...|..+.||+-...
T Consensus 126 N~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGsqy 203 (301)
T PRK09409 126 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCY 203 (301)
T ss_pred CCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCccc
Confidence 478889999976544544666677787776 4568887654 34444333443322 2222 235778999987544
No 16
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=52.36 E-value=23 Score=25.37 Aligned_cols=30 Identities=10% Similarity=0.185 Sum_probs=25.7
Q ss_pred cCCCceEEEeeCcH---HHHHHHHHhCCCCCCC
Q 038964 82 NRKNSLRVIINGDQ---IMSKAMATTFLDSTHK 111 (111)
Q Consensus 82 ~~~~p~~iiTD~d~---a~~~Ai~~vfP~~~Hr 111 (111)
..+.+-.|+||.|- -+++-|.+.+|++.|.
T Consensus 45 ~~~rgVIIfTDpD~~GekIRk~i~~~vp~~kha 77 (174)
T TIGR00334 45 QKKQGVIILTDPDFPGEKIRKKIEQHLPGYENC 77 (174)
T ss_pred hhcCCEEEEeCCCCchHHHHHHHHHHCCCCeEE
Confidence 45788899999996 5899999999999883
No 17
>cd01085 APP X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline, even from a dipeptide or tripeptide.
Probab=45.84 E-value=26 Score=25.42 Aligned_cols=75 Identities=15% Similarity=-0.011 Sum_probs=41.2
Q ss_pred hCCCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcC-CCceEEEeeCcHHHHHH
Q 038964 22 VFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNR-KNSLRVIINGDQIMSKA 100 (111)
Q Consensus 22 ~f~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~-~~p~~iiTD~d~a~~~A 100 (111)
.=||+|.+|..-..+.|--.+. +++++|- ..+|..+-|.-.++....++.. .+|...-.+-+.+.+++
T Consensus 80 ~~GD~V~iD~g~~~~gY~aD~~---------RT~~vG~--~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~v~~~~~~~ 148 (224)
T cd01085 80 SPDGLYLIDSGGQYLDGTTDIT---------RTVHLGE--PTAEQKRDYTLVLKGHIALARAKFPKGTTGSQLDALARQP 148 (224)
T ss_pred CCCCEEEEEeCccCCCcccccE---------EeecCCC--CCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence 3478888888776666644332 4554442 3444444455444444444433 34666666666666666
Q ss_pred HHHhCCC
Q 038964 101 MATTFLD 107 (111)
Q Consensus 101 i~~vfP~ 107 (111)
+.+...+
T Consensus 149 ~~~~g~~ 155 (224)
T cd01085 149 LWKAGLD 155 (224)
T ss_pred HHHhCCC
Confidence 6655443
No 18
>KOG1378 consensus Purple acid phosphatase [Carbohydrate transport and metabolism]
Probab=43.33 E-value=60 Score=26.68 Aligned_cols=30 Identities=7% Similarity=0.016 Sum_probs=23.3
Q ss_pred ccccccchhhHHHHHHHHHhcCCCceEEEe
Q 038964 62 LTSETKYTNTYLLETFLRAMNRKNSLRVII 91 (111)
Q Consensus 62 l~~E~~es~~W~l~~f~~~~~~~~p~~iiT 91 (111)
...|..+-|.||-+.|.++-..+.|..|+.
T Consensus 269 ~~~~~~~QY~WL~~dL~~v~r~~tPWlIv~ 298 (452)
T KOG1378|consen 269 NFLKGTAQYQWLERDLASVDRKKTPWLIVQ 298 (452)
T ss_pred cccccchHHHHHHHHHHHhcccCCCeEEEE
Confidence 455778899999999998855557888864
No 19
>COG3915 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.12 E-value=35 Score=23.70 Aligned_cols=39 Identities=15% Similarity=0.118 Sum_probs=32.8
Q ss_pred hchhhhhhCCCeEE--EecccccCCCCCceeEEEEEccCCc
Q 038964 15 GSLVNDEVFGDIPT--FDTTYQTNAYSKPFVVIVGINQHIE 53 (111)
Q Consensus 15 ~~~~~~~~f~dvv~--~D~Ty~tn~y~~pl~~~~g~n~~~~ 53 (111)
-...+.++|.+++. .|+.|.+=+.++|+..+.-.++..+
T Consensus 95 Ip~sDi~kynpIlA~~~nGn~M~IRerGPl~~IYplds~pe 135 (155)
T COG3915 95 IPYSDIEKYNPILAIQNNGNYMQIRERGPLWSIYPLDSSPE 135 (155)
T ss_pred CcHHHhhhcccEEEEEeCCcEEEEeccCceEEEeecCCChh
Confidence 35678899999887 5999999999999999988777653
No 20
>TIGR00500 met_pdase_I methionine aminopeptidase, type I. Methionine aminopeptidase is a cobalt-binding enzyme. Bacterial and organellar examples (type I) differ from eukaroytic and archaeal (type II) examples in lacking a region of approximately 60 amino acids between the 4th and 5th cobalt-binding ligands. This model describes type I. The role of this protein in general is to produce the mature form of cytosolic proteins by removing the N-terminal methionine.
Probab=39.32 E-value=18 Score=26.25 Aligned_cols=50 Identities=12% Similarity=0.025 Sum_probs=33.7
Q ss_pred ceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHh
Q 038964 53 ETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATT 104 (111)
Q Consensus 53 ~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~v 104 (111)
+++++|- ..+|..+.|.-+.+.....+..-.|-+-..|-+.++.+.+++-
T Consensus 107 RT~~vG~--~~~~~~~~~~~~~~a~~~~~~~~kpG~~~~~v~~~~~~~~~~~ 156 (247)
T TIGR00500 107 KTFLVGK--ISPEAEKLLECTEESLYKAIEEAKPGNRIGEIGAAIQKYAEAK 156 (247)
T ss_pred EEEEcCC--CCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHc
Confidence 4555542 4566677777777777666666667777778888777776653
No 21
>cd04659 Piwi_piwi-like_ProArk Piwi_piwi-like_ProArk: PIWI domain, Piwi-like subfamily found in Archaea and Bacteria. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism.
Probab=38.48 E-value=2e+02 Score=22.67 Aligned_cols=70 Identities=9% Similarity=0.006 Sum_probs=33.1
Q ss_pred eEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccc--------cchhhHHHHHHHHHhcCCCceEEEeeCcH
Q 038964 26 IPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSET--------KYTNTYLLETFLRAMNRKNSLRVIINGDQ 95 (111)
Q Consensus 26 vv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~--------~es~~W~l~~f~~~~~~~~p~~iiTD~d~ 95 (111)
+|.+|.++..+....-.....-++..+....+.-.-...+. .+.+.=.++.+.+..+...|.-||--+|.
T Consensus 192 iIGidv~~~~~~~~~~~~~a~vf~~~g~g~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~y~~~~~~~~P~rIiihrdg 269 (404)
T cd04659 192 YIGIGFARSRDGEVRVTGCAQVFDSDGLGLILRGAPIEEPTEDRSPADLKDLLKRVLEGYRESHRGRDPKRLVLHKDG 269 (404)
T ss_pred EEEEEEEEcCCCCEEEEEEEEEEcCCCCEEEEecCccCCcccccCHHHHHHHHHHHHHHHHHHcCCCCCeEEEEECCC
Confidence 44578887776522212223335666533333221122211 12233344555555544488888876643
No 22
>TIGR00824 EIIA-man PTS system, mannose/fructose/sorbose family, IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIA components.
Probab=36.98 E-value=88 Score=20.27 Aligned_cols=38 Identities=8% Similarity=0.036 Sum_probs=29.1
Q ss_pred EEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeC
Q 038964 56 SFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIING 93 (111)
Q Consensus 56 ~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~ 93 (111)
+..+++..+++.+.|.=-++..++..+...+-.|+||-
T Consensus 30 i~~i~~~~~~~~~~~~~~l~~~i~~~~~~~~vivltDl 67 (116)
T TIGR00824 30 VGAVPFVPGENAETLQEKYNAALADLDTEEEVLFLVDI 67 (116)
T ss_pred eEEEEcCCCcCHHHHHHHHHHHHHhcCCCCCEEEEEeC
Confidence 44566888898888877777777766666777899996
No 23
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=35.55 E-value=50 Score=18.14 Aligned_cols=48 Identities=13% Similarity=0.043 Sum_probs=29.4
Q ss_pred hhchhhhhhCCCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHH
Q 038964 14 RGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFL 78 (111)
Q Consensus 14 ~~~~~~~~~f~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~ 78 (111)
...+..+..||++..+.-... ..++. -|+|++.=++.++-..+++.+-
T Consensus 13 ~~l~~~f~~~g~i~~~~~~~~---------------~~~~~--~~~a~V~F~~~~~a~~a~~~l~ 60 (70)
T PF00076_consen 13 EELRDFFSQFGKIESIKVMRN---------------SSGKS--KGYAFVEFESEEDAEKALEELN 60 (70)
T ss_dssp HHHHHHHHTTSTEEEEEEEEE---------------TTSSE--EEEEEEEESSHHHHHHHHHHHT
T ss_pred HHHHHHHHHhhhccccccccc---------------ccccc--cceEEEEEcCHHHHHHHHHHcC
Confidence 445677888998865444332 12222 3667888788777777666543
No 24
>KOG1041 consensus Translation initiation factor 2C (eIF-2C) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=33.90 E-value=2.6e+02 Score=24.89 Aligned_cols=69 Identities=20% Similarity=0.115 Sum_probs=40.7
Q ss_pred eEEEecccccCCCCC---ceeEEEEEccC-CceEEEEeeecccc-------ccchhhHHHHHHHHHhcCCCceEEEeeCc
Q 038964 26 IPTFDTTYQTNAYSK---PFVVIVGINQH-IETISFLFGLLTSE-------TKYTNTYLLETFLRAMNRKNSLRVIINGD 94 (111)
Q Consensus 26 vv~~D~Ty~tn~y~~---pl~~~~g~n~~-~~~~~~~~~ll~~E-------~~es~~W~l~~f~~~~~~~~p~~iiTD~d 94 (111)
+|.+|.|+-....+. |-...+.-|-. .-+-..|+..+... ..+-+.+++..|.++-+. .|.-||.-||
T Consensus 608 ~IG~dVsHp~~~~~~~~~PSiagvv~s~~~~~~~y~g~~~~Q~~r~e~i~~~~~~~~~~l~~f~~~t~~-~P~~IIiyRd 686 (876)
T KOG1041|consen 608 FIGFDVSHPAAGTSFDGNPSIVGVVYNLDWHPQKFAGFVRFQKSRQEVIQDLGEMIRELLRSFRKSTRK-LPDRIVIYRD 686 (876)
T ss_pred EEEEeeeCCCcCCCcCCCccEEEEEecccccchhhcceEEEecCChhhhcchHHHHHHHHHHHHHhccC-CCceEEEEec
Confidence 345799998888755 55544333333 22222343333333 344557777777777554 8998888776
Q ss_pred H
Q 038964 95 Q 95 (111)
Q Consensus 95 ~ 95 (111)
-
T Consensus 687 G 687 (876)
T KOG1041|consen 687 G 687 (876)
T ss_pred C
Confidence 4
No 25
>PRK12897 methionine aminopeptidase; Reviewed
Probab=33.90 E-value=44 Score=24.38 Aligned_cols=50 Identities=6% Similarity=-0.073 Sum_probs=32.5
Q ss_pred ceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHh
Q 038964 53 ETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATT 104 (111)
Q Consensus 53 ~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~v 104 (111)
+|+++| =.+++..+-|.-+++....++..-.|-+-..|-+.++.+.+++-
T Consensus 108 RT~~vG--~~s~~~~~~~~~~~~a~~~~i~~~kpG~~~~dv~~a~~~~~~~~ 157 (248)
T PRK12897 108 WTYRVG--KVSDEAEKLLLVAENALYKGIDQAVIGNRVGDIGYAIESYVANE 157 (248)
T ss_pred EEEEcC--CCCHHHHHHHHHHHHHHHHHHHhhcCCCccchHHHHHHHHHHHc
Confidence 445444 24445556666666666566666677777889998888877654
No 26
>cd01091 CDC68-like Related to aminopeptidase P and aminopeptidase M, a member of this domain family is present in cell division control protein 68, a transcription factor.
Probab=33.87 E-value=42 Score=24.73 Aligned_cols=51 Identities=14% Similarity=-0.022 Sum_probs=36.5
Q ss_pred ceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHhCC
Q 038964 53 ETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFL 106 (111)
Q Consensus 53 ~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~vfP 106 (111)
+|++++ -..|-.+.|.-+++....++..-.|-+-+.|-+.+..+.+++-.|
T Consensus 111 RT~~v~---p~~~~~~~y~~~~~a~~~~i~~lkpG~~~~dv~~~a~~~i~~~~~ 161 (243)
T cd01091 111 RTFLID---PTSEQQKNYNFLLALQEEILKELKPGAKLSDVYQKTLDYIKKKKP 161 (243)
T ss_pred EEEEcC---CCHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHhCh
Confidence 556554 255666788888877777777777888888888888877776543
No 27
>KOG4027 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.09 E-value=57 Score=23.29 Aligned_cols=47 Identities=17% Similarity=0.196 Sum_probs=33.7
Q ss_pred hhhCCCeEE----Eecccc-cCCCCCcee--EEEEEccCCceEEEEeeeccccc
Q 038964 20 DEVFGDIPT----FDTTYQ-TNAYSKPFV--VIVGINQHIETISFLFGLLTSET 66 (111)
Q Consensus 20 ~~~f~dvv~----~D~Ty~-tn~y~~pl~--~~~g~n~~~~~~~~~~~ll~~E~ 66 (111)
++.+.+.|+ +|+||| ||-|+-|-+ ..-|-++.|+-.+.|+|.+.--.
T Consensus 57 ~r~~~~~iv~n~Pievt~KstsPygWPqivl~vfg~d~~G~d~v~GYg~~hiP~ 110 (187)
T KOG4027|consen 57 FRGADNQIVINLPIEVTLKSTSPYGWPQIVLNVFGKDHSGKDCVTGYGMLHIPT 110 (187)
T ss_pred cccCCCceEEecceEEEeccCCCCCCceEEEEEecCCcCCcceeeeeeeEecCc
Confidence 345555555 578998 566888755 55677999999999999776544
No 28
>COG0006 PepP Xaa-Pro aminopeptidase [Amino acid transport and metabolism]
Probab=32.31 E-value=56 Score=25.43 Aligned_cols=71 Identities=15% Similarity=0.035 Sum_probs=53.3
Q ss_pred hCCCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHH
Q 038964 22 VFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAM 101 (111)
Q Consensus 22 ~f~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai 101 (111)
+=||.|++|.--..+.|.-.+- +|+.+| =..+|-.+-|.=.++....++....|.+-..|-|.+..+.+
T Consensus 231 ~~gd~vliD~G~~~~gY~sDiT---------RT~~~G--~~~~~~~~iy~~V~~aq~aa~~~~rpG~~~~~vd~~ar~~i 299 (384)
T COG0006 231 RDGDLVLIDLGGVYNGYCSDIT---------RTFPIG--KPSDEQREIYEAVLEAQEAAIAAIRPGVTGGEVDAAARQVL 299 (384)
T ss_pred cCCCEEEEEeeeEECCccccce---------eEEecC--CCCHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHH
Confidence 4578888887666555544332 555655 66777778888888888888888888888888888888888
Q ss_pred HH
Q 038964 102 AT 103 (111)
Q Consensus 102 ~~ 103 (111)
.+
T Consensus 300 ~~ 301 (384)
T COG0006 300 EK 301 (384)
T ss_pred Hh
Confidence 77
No 29
>cd02826 Piwi-like Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism.
Probab=31.68 E-value=2.6e+02 Score=22.01 Aligned_cols=67 Identities=15% Similarity=0.119 Sum_probs=33.3
Q ss_pred eEEEecccccCC--CCCcee-EEEEE-ccCCceEEEEeeeccccc-------cchhhHHHHHHHHHhcCCCceEEEeeCc
Q 038964 26 IPTFDTTYQTNA--YSKPFV-VIVGI-NQHIETISFLFGLLTSET-------KYTNTYLLETFLRAMNRKNSLRVIINGD 94 (111)
Q Consensus 26 vv~~D~Ty~tn~--y~~pl~-~~~g~-n~~~~~~~~~~~ll~~E~-------~es~~W~l~~f~~~~~~~~p~~iiTD~d 94 (111)
+|.+|.++.... .+.|.. .+++- |++ ++.-++....... .+.+.-+|+.|++..+...|+.||--+|
T Consensus 174 iiGiDv~h~~~~~~~~~~si~~~vas~~~~--~~~g~~~~~~~~~~~~~~~l~~~~~~~L~~y~~~~~~~~P~~IiiyRD 251 (393)
T cd02826 174 FIGFDVSHPDRRTVNGGPSAVGFAANLSNH--TFLGGFLYVQPSREVKLQDLGEVIKKCLDGFKKSTGEGLPEKIVIYRD 251 (393)
T ss_pred EEEEEeeCCCCCCCCCCCcEEEEEeecCCc--cccceEEEEecCccchHHHHHHHHHHHHHHHHHHcCCCCcceeEEEec
Confidence 455888888764 444533 22221 222 2222222222222 2334555666665543228998888664
No 30
>PF05902 4_1_CTD: 4.1 protein C-terminal domain (CTD); InterPro: IPR008379 There is a unique sequence domain at the C terminus of all known 4.1 proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24 kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates [].; GO: 0003779 actin binding, 0005198 structural molecule activity, 0005856 cytoskeleton
Probab=31.08 E-value=30 Score=23.07 Aligned_cols=18 Identities=28% Similarity=0.421 Sum_probs=13.2
Q ss_pred eeCcHHHHHHHHHh---CCCC
Q 038964 91 INGDQIMSKAMATT---FLDS 108 (111)
Q Consensus 91 TD~d~a~~~Ai~~v---fP~~ 108 (111)
.|+|+||..||++- .|+.
T Consensus 81 IDhDqaLa~aI~eAk~q~Pdm 101 (114)
T PF05902_consen 81 IDHDQALAQAIKEAKEQHPDM 101 (114)
T ss_pred cchHHHHHHHHHHHHHhCCCc
Confidence 37899999999853 4553
No 31
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=28.54 E-value=61 Score=26.40 Aligned_cols=40 Identities=13% Similarity=0.135 Sum_probs=31.9
Q ss_pred ceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeC
Q 038964 53 ETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIING 93 (111)
Q Consensus 53 ~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~ 93 (111)
+++.|+ -=+..++.+.|.-++..+.+++.++.|.++|-|-
T Consensus 370 ~~f~~~-DS~~~~~~~~~~~F~~~l~~~i~~~~~~tlIldD 409 (460)
T KOG2703|consen 370 RSFTFG-DSMDEGQKARWQEFLAKLDDIIAGKLPATLILDD 409 (460)
T ss_pred Cceecc-ccCCHHHHHHHHHHHHHHHHHHhcccceEEEeec
Confidence 345666 4566677888888999999999999999998874
No 32
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=28.23 E-value=62 Score=21.90 Aligned_cols=28 Identities=7% Similarity=0.156 Sum_probs=23.6
Q ss_pred CCceEEEeeCcH---HHHHHHHHhCCCCCCC
Q 038964 84 KNSLRVIINGDQ---IMSKAMATTFLDSTHK 111 (111)
Q Consensus 84 ~~p~~iiTD~d~---a~~~Ai~~vfP~~~Hr 111 (111)
..+--|+||.|. -+++.+.+.||++.|.
T Consensus 55 ~k~VIILTD~D~~Ge~Irk~l~~~l~~~~~~ 85 (127)
T COG1658 55 YKGVIILTDPDRKGERIRKKLKEYLPGAKGA 85 (127)
T ss_pred cCCEEEEeCCCcchHHHHHHHHHHhcccccc
Confidence 567778999986 5899999999998884
No 33
>PF05221 AdoHcyase: S-adenosyl-L-homocysteine hydrolase; InterPro: IPR000043 Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase, 3.3.1.1 from EC) (AdoHcyase) is an enzyme of the activated methyl cycle, responsible for the reversible hydration of S-adenosyl-L-homocysteine into adenosine and homocysteine. This enzyme is ubiquitous, highly conserved, and may play a key role in the regulation of the intracellular concentration of adenosylhomocysteine. AdoHcyase requires NAD+ as a cofactor and contains a central glycine-rich region which is thought to be involved in NAD-binding.; GO: 0004013 adenosylhomocysteinase activity, 0006730 one-carbon metabolic process; PDB: 3N58_B 3H9U_C 2ZJ1_C 3DHY_B 2ZIZ_C 2ZJ0_D 3CE6_B 1K0U_F 1B3R_A 1XWF_D ....
Probab=28.02 E-value=53 Score=25.12 Aligned_cols=37 Identities=16% Similarity=0.184 Sum_probs=27.0
Q ss_pred ccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHH
Q 038964 62 LTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMS 98 (111)
Q Consensus 62 l~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~ 98 (111)
-.+|+.+.|.|.++.-+..-++..|..||-|......
T Consensus 98 ~~get~eey~~~i~~~L~~~~~~~P~~iiDDG~Dl~~ 134 (268)
T PF05221_consen 98 WKGETDEEYWWCIEKALSWEDDHGPNLIIDDGGDLVN 134 (268)
T ss_dssp -TT--HHHHHHHHHHCHSESTTCE-SEEEESSSHHHH
T ss_pred eCCCCHHHHHHHHHHHhcCCCCCCcceeecchHHHHH
Confidence 5789999999999988876667789999999876543
No 34
>PF13535 ATP-grasp_4: ATP-grasp domain; PDB: 3VMM_A 3LN6_A 3LN7_B 2PN1_A 4DIM_A.
Probab=27.50 E-value=1.4e+02 Score=19.72 Aligned_cols=36 Identities=11% Similarity=0.206 Sum_probs=23.1
Q ss_pred hHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHh-CC
Q 038964 71 TYLLETFLRAMNRKNSLRVIINGDQIMSKAMATT-FL 106 (111)
Q Consensus 71 ~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~v-fP 106 (111)
++.+..+++..+-+.|+..+-+....+.++++.+ ||
T Consensus 5 K~~~~~~~~~~gv~~P~~~~~~~~~~~~~~~~~~~~p 41 (184)
T PF13535_consen 5 KYRMRELLKKAGVPVPKTRIVDSEEELRAFAEDLGFP 41 (184)
T ss_dssp HHHHHHHHHHHTS----EEEECSHHHHHHHHHHSSSS
T ss_pred HHHHHHHHHHcCcCCCCEEEECCHHHHHHHHHHcCCC
Confidence 4556667776676788888888888888887765 55
No 35
>PF03610 EIIA-man: PTS system fructose IIA component; InterPro: IPR004701 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for IIA and IIB components.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane; PDB: 3GDW_B 2JZN_A 1VSQ_A 2JZO_B 1VRC_A 1PDO_A 3GX1_A 3B48_B 3BED_B 3IPR_C ....
Probab=27.47 E-value=1.5e+02 Score=18.82 Aligned_cols=39 Identities=10% Similarity=0.073 Sum_probs=28.8
Q ss_pred EEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCc
Q 038964 56 SFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGD 94 (111)
Q Consensus 56 ~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d 94 (111)
+-+.++..+++.+.+.=-++...+......+..|+||--
T Consensus 29 i~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~vlil~Dl~ 67 (116)
T PF03610_consen 29 IEAVDLYPDESIEDFEEKLEEAIEELDEGDGVLILTDLG 67 (116)
T ss_dssp EEEEEETTTSCHHHHHHHHHHHHHHCCTTSEEEEEESST
T ss_pred EEEEECcCCCCHHHHHHHHHHHHHhccCCCcEEEEeeCC
Confidence 345678888888888766666666666678888999954
No 36
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=26.79 E-value=1.3e+02 Score=19.80 Aligned_cols=45 Identities=18% Similarity=0.164 Sum_probs=30.2
Q ss_pred eccccccchhhHHHHHHHHHhcCCC-ceEEEeeCcHHHHHHHHHhC
Q 038964 61 LLTSETKYTNTYLLETFLRAMNRKN-SLRVIINGDQIMSKAMATTF 105 (111)
Q Consensus 61 ll~~E~~es~~W~l~~f~~~~~~~~-p~~iiTD~d~a~~~Ai~~vf 105 (111)
++..+..++-..++..+++..+... ...++.|...++.+++++..
T Consensus 11 l~~g~i~d~n~~~l~~~l~~~G~~v~~~~~v~Dd~~~i~~~i~~~~ 56 (133)
T cd00758 11 LSQGQIEDTNGPALEALLEDLGCEVIYAGVVPDDADSIRAALIEAS 56 (133)
T ss_pred ccCCceEEchHHHHHHHHHHCCCEEEEeeecCCCHHHHHHHHHHHH
Confidence 4445666777777777777666432 33577888888888887653
No 37
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=26.08 E-value=44 Score=24.77 Aligned_cols=32 Identities=19% Similarity=0.181 Sum_probs=26.7
Q ss_pred cccchhhHHHHHHHHHhcCCCceEEEeeCcHH
Q 038964 65 ETKYTNTYLLETFLRAMNRKNSLRVIINGDQI 96 (111)
Q Consensus 65 E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a 96 (111)
=.-|+..|+-+.++.....++-..||||..++
T Consensus 117 iDGeAl~~a~~rL~~r~e~rkiLiViSDG~P~ 148 (219)
T PF11775_consen 117 IDGEALRWAAERLLARPEQRKILIVISDGAPA 148 (219)
T ss_pred CcHHHHHHHHHHHHcCCccceEEEEEeCCCcC
Confidence 34567899999999988888888999999875
No 38
>PRK14575 putative peptidase; Provisional
Probab=25.97 E-value=59 Score=25.76 Aligned_cols=53 Identities=4% Similarity=-0.137 Sum_probs=37.2
Q ss_pred ceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHh-CCC
Q 038964 53 ETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATT-FLD 107 (111)
Q Consensus 53 ~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~v-fP~ 107 (111)
+|+.+| =..+|..+-|.-+++....++..-+|-+-..|-+.+..+.+++. +|+
T Consensus 276 RT~~vG--~~~~~~~~~~~~~~~a~~~~~~~~rpG~~~~dv~~a~~~~~~~~G~~~ 329 (406)
T PRK14575 276 RTFVVG--EPPEITRKIYQTIRTGHEHMLSMVAPGVKMKDVFDSTMEVIKKSGLPN 329 (406)
T ss_pred EEEECC--CCCHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHcCCcc
Confidence 455554 23455566677777777777777788888899999988888876 553
No 39
>TIGR02993 ectoine_eutD ectoine utilization protein EutD. Members of this family are putative peptidases or hydrolases similar to Xaa-Pro aminopeptidase (pfam00557). They belong to ectoine utilization operons, as found in Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti, Silicibacter pomeroyi, Agrobacterium tumefaciens, and Pseudomonas putida. The exact function is unknown.
Probab=25.03 E-value=98 Score=24.31 Aligned_cols=50 Identities=8% Similarity=-0.059 Sum_probs=34.2
Q ss_pred ceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHh
Q 038964 53 ETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATT 104 (111)
Q Consensus 53 ~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~v 104 (111)
+|+.+| =..+|..+-|.-.++....++..-.|-+-..|-+.+....+++.
T Consensus 261 RT~~vG--~p~~~~~~~~~~~~~a~~~~i~~ikpG~~~~dv~~~~~~~~~~~ 310 (391)
T TIGR02993 261 RTVFLG--KPTQAFLDAEKAVLEGMEAGLEAAKPGNTCEDIANAFFAVLKKY 310 (391)
T ss_pred EEEEcC--CCCHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHc
Confidence 455555 24455566676667766667777788888888888887777653
No 40
>PF03400 DDE_Tnp_IS1: IS1 transposase; InterPro: IPR005063 Transposase proteins are necessary for efficient DNA transposition. This family represents bacterial IS1 transposases []. 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
Probab=24.80 E-value=1.6e+02 Score=19.79 Aligned_cols=68 Identities=13% Similarity=0.104 Sum_probs=40.2
Q ss_pred ccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHhCCCCCC
Q 038964 32 TYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTH 110 (111)
Q Consensus 32 Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~vfP~~~H 110 (111)
||-.+|-+ +.-.+..+|.....++ ++ .+-+-+.+++.=|++.+ ..-....+.||.=. |-+.++|+..|
T Consensus 12 tfVg~K~n-~~Wiw~A~dr~t~~Iv-a~-v~G~Rs~~T~~~L~~~L----~~~~i~~~~TD~w~----~Y~~~ip~~~H 79 (131)
T PF03400_consen 12 TFVGNKKN-KRWIWYAIDRKTGGIV-AF-VFGDRSDKTFRKLWALL----KPFNIGFIYTDDWE----SYERVIPEEKH 79 (131)
T ss_pred hhhccCCC-ceEEEEEEeccCCcce-eE-EEecchhhHHHHHhhhh----ccccceEEecCCCc----cccccCccchh
Confidence 55555544 4555666666654443 32 34666777776555544 33356679999887 44556676665
No 41
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=24.76 E-value=74 Score=22.19 Aligned_cols=30 Identities=20% Similarity=0.276 Sum_probs=22.4
Q ss_pred cccccchhhHHHHHHHHHhcCCCceEEEee
Q 038964 63 TSETKYTNTYLLETFLRAMNRKNSLRVIIN 92 (111)
Q Consensus 63 ~~E~~es~~W~l~~f~~~~~~~~p~~iiTD 92 (111)
..|..+.+..+++.+.+...+..|-++|-|
T Consensus 122 ~~e~~~~~~~~i~~L~~~~~g~~pfTlIid 151 (161)
T PF03367_consen 122 DPEEKEKIEEFIEKLDELIEGKRPFTLIID 151 (161)
T ss_dssp -HHHHHHHHHHHHHHHHHHCTSS-EEEEEE
T ss_pred CHHHHHHHHHHHHHHHHHHcCCCCEEEEEE
Confidence 355667778888999998888889887765
No 42
>KOG1616 consensus Protein involved in Snf1 protein kinase complex assembly [Carbohydrate transport and metabolism]
Probab=24.68 E-value=1.3e+02 Score=23.10 Aligned_cols=95 Identities=15% Similarity=0.084 Sum_probs=60.4
Q ss_pred ceeeEEEEechhchhhhhhCCCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchh----hHHHHH---
Q 038964 4 IDWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTN----TYLLET--- 76 (111)
Q Consensus 4 ~~l~~ifw~~~~~~~~~~~f~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~----~W~l~~--- 76 (111)
++..-|=|... |..+.+++++..-++++++....+ |.-+ +..-..|...+-...| .|....
T Consensus 79 ~~pvvi~W~~g---------g~~v~v~gS~~nWk~~~~l~~~~~-~~~~--f~~~~dL~~g~~~~kf~vdge~~~s~~~p 146 (289)
T KOG1616|consen 79 GRPTVIRWSQG---------GKEVYVDGSFGNWKTKIPLVRSGK-NVGG--FSTILDLPPGEHEYKFIVDGEWRHDPDLP 146 (289)
T ss_pred CCceEEEecCC---------CceEEEecccccccccccceecCC-Cccc--ceeeEecCCceEEEEEecCCceecCCCCc
Confidence 45555666666 899999999999999998875533 2111 1111223333322222 555433
Q ss_pred -HHHHhcCCCceEEEeeCc--HHHHHHHHHhCCCCCC
Q 038964 77 -FLRAMNRKNSLRVIINGD--QIMSKAMATTFLDSTH 110 (111)
Q Consensus 77 -f~~~~~~~~p~~iiTD~d--~a~~~Ai~~vfP~~~H 110 (111)
....+++......+-|.+ .....|+++..|.+.|
T Consensus 147 ta~d~~Gn~~N~i~v~~~~~v~~~~~~l~~~~~~~~~ 183 (289)
T KOG1616|consen 147 TAEDSLGNLNNILEVQDPDEVFEVFQALEEDLPSSNH 183 (289)
T ss_pred ccccccCCcccceEecCccccchhhhhhhhhcccccc
Confidence 334566667777777777 8889999999888776
No 43
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=24.42 E-value=77 Score=16.62 Aligned_cols=13 Identities=23% Similarity=0.286 Sum_probs=10.4
Q ss_pred HHHHHHHHhCCCC
Q 038964 96 IMSKAMATTFLDS 108 (111)
Q Consensus 96 a~~~Ai~~vfP~~ 108 (111)
++...++++||+-
T Consensus 3 ~~v~~L~~mFP~~ 15 (42)
T PF02845_consen 3 EMVQQLQEMFPDL 15 (42)
T ss_dssp HHHHHHHHHSSSS
T ss_pred HHHHHHHHHCCCC
Confidence 5677899999974
No 44
>PF12367 PFO_beta_C: Pyruvate ferredoxin oxidoreductase beta subunit C terminal
Probab=24.19 E-value=41 Score=20.20 Aligned_cols=32 Identities=16% Similarity=0.157 Sum_probs=19.9
Q ss_pred cchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHH
Q 038964 67 KYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMA 102 (111)
Q Consensus 67 ~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~ 102 (111)
..+|.|.-+..-..-.+..| +|+..||..|.+
T Consensus 7 ~nT~~wY~~rvy~l~e~~Dp----~d~~~A~~~a~e 38 (67)
T PF12367_consen 7 INTYDWYKERVYKLDEDHDP----SDREAAMEKARE 38 (67)
T ss_pred cchHHHHHHheEECCCCCCc----hhHHHHHHHHHh
Confidence 45777776655444223344 778888877775
No 45
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.75 E-value=64 Score=22.23 Aligned_cols=40 Identities=20% Similarity=0.193 Sum_probs=31.3
Q ss_pred ccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHH
Q 038964 32 TYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLR 79 (111)
Q Consensus 32 Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~ 79 (111)
.|+||+|++.++. ++.| +-+-|..|-+..+++=+|++.-.
T Consensus 63 sy~Ts~Yklhfye----Tptg----lk~vl~Tdpk~~~ir~vLq~IYs 102 (140)
T KOG3368|consen 63 SYKTSKYKLHFYE----TPTG----LKFVLNTDPKAGSIRDVLQYIYS 102 (140)
T ss_pred EEeeceeEEEEEE----cCCC----cEEEEecCCCcccHHHHHHHHHH
Confidence 5899999997763 2333 45668999999999999988765
No 46
>cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
Probab=23.75 E-value=1.7e+02 Score=20.35 Aligned_cols=49 Identities=16% Similarity=0.156 Sum_probs=35.2
Q ss_pred EEeeeccccccchhhHHHHHHHHHhcCC-CceEEEeeCcHHHHHHHHHhC
Q 038964 57 FLFGLLTSETKYTNTYLLETFLRAMNRK-NSLRVIINGDQIMSKAMATTF 105 (111)
Q Consensus 57 ~~~~ll~~E~~es~~W~l~~f~~~~~~~-~p~~iiTD~d~a~~~Ai~~vf 105 (111)
.|--++..+..++-...+...++..+.. ....++.|....+.+++++..
T Consensus 7 ~GdEl~~G~i~d~n~~~l~~~L~~~G~~v~~~~~v~Dd~~~I~~~l~~~~ 56 (170)
T cd00885 7 IGDELLSGQIVDTNAAFLAKELAELGIEVYRVTVVGDDEDRIAEALRRAS 56 (170)
T ss_pred ECccccCCeEEEhHHHHHHHHHHHCCCEEEEEEEeCCCHHHHHHHHHHHH
Confidence 3444566777788887777777776654 334688899999999988754
No 47
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=23.65 E-value=88 Score=22.00 Aligned_cols=28 Identities=18% Similarity=0.217 Sum_probs=20.2
Q ss_pred cccchhhHHHHHHHHHhcCCCceEEEee
Q 038964 65 ETKYTNTYLLETFLRAMNRKNSLRVIIN 92 (111)
Q Consensus 65 E~~es~~W~l~~f~~~~~~~~p~~iiTD 92 (111)
|..+.+..+++.+.+++.|..|-++|-|
T Consensus 118 e~~~k~~~~l~kL~~~~~g~~pfTlIld 145 (163)
T TIGR00340 118 EAVKKCEEILKRIREVIEGKFKFTLIIE 145 (163)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCeEEEEE
Confidence 3445567777888888888778877665
No 48
>PRK15173 peptidase; Provisional
Probab=23.54 E-value=85 Score=24.07 Aligned_cols=52 Identities=4% Similarity=-0.153 Sum_probs=36.4
Q ss_pred ceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHh-CC
Q 038964 53 ETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATT-FL 106 (111)
Q Consensus 53 ~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~v-fP 106 (111)
+|+.+| =...|..+-|.-+++....++..-.|-+-..|-+.+..+++++. +|
T Consensus 193 RT~~vG--~p~~~~~~~y~~v~ea~~~~~~~irPG~~~~dv~~a~~~~~~~~G~~ 245 (323)
T PRK15173 193 RTFVVG--EPPEITRKIYQTIRTGHEHMLSMVAPGVKMKDVFDSTMEVIKKSGLP 245 (323)
T ss_pred EEEEcC--CCCHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHcCCc
Confidence 455554 23444556677777777777777788888888888888888876 55
No 49
>PRK14576 putative endopeptidase; Provisional
Probab=23.10 E-value=58 Score=25.80 Aligned_cols=52 Identities=6% Similarity=-0.164 Sum_probs=36.0
Q ss_pred ceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHh-CC
Q 038964 53 ETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATT-FL 106 (111)
Q Consensus 53 ~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~v-fP 106 (111)
+|+.+|- ..++..+.|.-+.+....++..-+|-+-..|-+.+..+++++. +|
T Consensus 275 RT~~~G~--p~~~~~~~~~~~~~a~~a~~~~~rPG~~~~dv~~a~~~~~~~~G~~ 327 (405)
T PRK14576 275 RTFVLGE--PDKLTQQIYDTIRTGHEHMLSMVAPGVKLKAVFDSTMAVIKTSGLP 327 (405)
T ss_pred EEEECCC--CCHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHcCCc
Confidence 4444442 3455556677777777777777788888888888888888875 44
No 50
>PF00994 MoCF_biosynth: Probable molybdopterin binding domain; InterPro: IPR001453 Eukaryotic and prokaryotic molybdoenzymes require a molybdopterin cofactor (MoCF) for their activity. The biosynthesis of this cofactor involves a complex multistep enzymatic pathway. One of the eukaryotic proteins involved in this pathway is the Drosophila protein cinnamon [] which is highly similar to gephyrin, a rat microtubule-associated protein which was thought to anchor the glycine receptor to subsynaptic microtubules. Cinnamon and gephyrin are evolutionary related, in their N-terminal half, to the Escherichia coli MoCF biosynthesis proteins mog/chlG and moaB/chlA2 and, in their C-terminal half, to E. coli moeA/chlE.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 3TCR_B 1O8O_B 1O8Q_G 1EAV_D 1O8N_C 1UUX_A 1UUY_A 2G2C_A 2G4R_C 3K6A_F ....
Probab=22.95 E-value=1.3e+02 Score=19.87 Aligned_cols=48 Identities=13% Similarity=0.177 Sum_probs=36.2
Q ss_pred EEeeeccccccchhhHHHHHHHHHhcCC-CceEEEeeCcHHHHHHHHHh
Q 038964 57 FLFGLLTSETKYTNTYLLETFLRAMNRK-NSLRVIINGDQIMSKAMATT 104 (111)
Q Consensus 57 ~~~~ll~~E~~es~~W~l~~f~~~~~~~-~p~~iiTD~d~a~~~Ai~~v 104 (111)
.|--++..+..++-..++..+++..+.. ....++-|.-.++.+++++.
T Consensus 5 ~GdEl~~g~~~d~n~~~l~~~l~~~G~~v~~~~~v~Dd~~~i~~~l~~~ 53 (144)
T PF00994_consen 5 TGDELLSGQIRDSNGPFLAALLEELGIEVIRYGIVPDDPDAIKEALRRA 53 (144)
T ss_dssp ECHHHHTTSSEBHHHHHHHHHHHHTTEEEEEEEEEESSHHHHHHHHHHH
T ss_pred ECccCcCCceEEhHHHHHHHHHHHcCCeeeEEEEECCCHHHHHHHHHhh
Confidence 4444667778888888889888887654 34568889989998888654
No 51
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.99 E-value=1.3e+02 Score=18.28 Aligned_cols=33 Identities=15% Similarity=-0.035 Sum_probs=25.9
Q ss_pred CCeEEEecccccCCCCCceeEEEEEccCCceEE
Q 038964 24 GDIPTFDTTYQTNAYSKPFVVIVGINQHIETIS 56 (111)
Q Consensus 24 ~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~ 56 (111)
-+-|.+|-||..|...+-+-.=+-+||.+...+
T Consensus 45 ensvivdlt~menf~dl~l~ektvvnhk~ykii 77 (81)
T COG4873 45 ENSVIVDLTIMENFRDLELDEKTVVNHKNYKII 77 (81)
T ss_pred CCcEEEEEEeeccccccCCcceeeEcccceEEe
Confidence 356788999999998888888888888775543
No 52
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=21.05 E-value=1.7e+02 Score=22.05 Aligned_cols=60 Identities=13% Similarity=0.020 Sum_probs=38.2
Q ss_pred cccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcH
Q 038964 33 YQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQ 95 (111)
Q Consensus 33 y~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~ 95 (111)
..++++++ +..-.|+|..|-.- |+.++-.|+-+.-.-.++.-++...+...-+||||-+-
T Consensus 94 i~~~~~G~-v~anAGID~SNv~~--g~~~LLP~DPd~SA~~ir~~l~~~~g~~v~VIItDt~g 153 (245)
T PRK13293 94 LTETKHGH-VCANAGIDESNVPD--GDLLLLPENPDESAERIREGLEELTGKKVGVIITDTNG 153 (245)
T ss_pred EEEeccce-EEeccccccccCCC--CeEEecCCCHHHHHHHHHHHHHHHHCCCEEEEEEcCCC
Confidence 44555665 45567998777532 66666666665554444444444455788899999753
No 53
>PF14386 DUF4417: Domain of unknown function (DUF4417)
Probab=20.73 E-value=1.7e+02 Score=21.16 Aligned_cols=47 Identities=13% Similarity=0.203 Sum_probs=28.5
Q ss_pred EEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeC
Q 038964 45 IVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIING 93 (111)
Q Consensus 45 ~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~ 93 (111)
+.|+ .++.++.++.-. ...+.+..++++..+.+....-.|+.||--.
T Consensus 129 ~~gi-~~~~ivaist~g-~~~~~~~~~~f~~Gl~em~~rl~P~~ilvyG 175 (200)
T PF14386_consen 129 FDGI-PKGSIVAISTNG-CINNKEDKKLFLDGLREMLKRLRPKHILVYG 175 (200)
T ss_pred Hhhc-ccCCEEEEEEec-ccCCHHHHHHHHHHHHHHHhccCCCeEEEEC
Confidence 3455 455555555433 4556677888888887776665666554433
No 54
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=20.69 E-value=47 Score=26.27 Aligned_cols=39 Identities=26% Similarity=0.365 Sum_probs=24.9
Q ss_pred hhhhCCCeEEEecccccCCCCCcee-EEEEEccCCceEEE
Q 038964 19 NDEVFGDIPTFDTTYQTNAYSKPFV-VIVGINQHIETISF 57 (111)
Q Consensus 19 ~~~~f~dvv~~D~Ty~tn~y~~pl~-~~~g~n~~~~~~~~ 57 (111)
....+.++-.+|......+-+.|.+ .|+|+|..|+|..+
T Consensus 117 l~~il~~~~~~~~~~~~~~~~~p~Vil~vGVNG~GKTTTI 156 (340)
T COG0552 117 LIEILRPVDKVDLPLEIPKEKKPFVILFVGVNGVGKTTTI 156 (340)
T ss_pred HHHHhcccccccchhhhccCCCcEEEEEEecCCCchHhHH
Confidence 3455565555555555555555655 78999999997443
No 55
>cd01089 PA2G4-like Related to aminopepdidase M, this family contains proliferation-associated protein 2G4. Family members have been implicated in cell cycle control.
Probab=20.54 E-value=94 Score=22.30 Aligned_cols=37 Identities=5% Similarity=-0.148 Sum_probs=24.3
Q ss_pred chhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHh
Q 038964 68 YTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATT 104 (111)
Q Consensus 68 es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~v 104 (111)
+-+.-+.+....++..-.|-+-..|=+.++.+.+++-
T Consensus 124 ~~~~~~~ea~~~~~~~~kpG~~~~dv~~a~~~~~~~~ 160 (228)
T cd01089 124 DVIAAAHYALEAALRLLRPGNQNSDITEAIQKVIVDY 160 (228)
T ss_pred HHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHc
Confidence 4444444444555555678888888888888777763
No 56
>cd08787 CARD_NOD2_1_CARD15 Caspase activation and recruitment domain of NOD2, repeat 1. Caspase activation and recruitment domain (CARD) similar to that found in human NOD2 (CARD15), repeat 1. NOD2 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD2, as well as NOD1, the N-terminal effector domain is a CARD. NOD2 contains two N-terminal CARD repeats. Mutations in NOD2 have been associated with Crohns disease and Blau syndrome. Nod2-CARDs have been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are pr
Probab=20.50 E-value=64 Score=20.38 Aligned_cols=19 Identities=11% Similarity=-0.059 Sum_probs=15.8
Q ss_pred eeCcHHHHHHHHHhCCCCC
Q 038964 91 INGDQIMSKAMATTFLDST 109 (111)
Q Consensus 91 TD~d~a~~~Ai~~vfP~~~ 109 (111)
+|.|.-+.+|+++++|++.
T Consensus 65 e~~C~~fl~a~~ea~~esq 83 (87)
T cd08787 65 EWACQKFLAAAQQALAEEQ 83 (87)
T ss_pred hhHHHHHHHHHHHhccccc
Confidence 4667788999999999875
No 57
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=20.46 E-value=93 Score=23.73 Aligned_cols=22 Identities=18% Similarity=0.223 Sum_probs=19.5
Q ss_pred CCceEEEeeCcHHHHHHHHHhC
Q 038964 84 KNSLRVIINGDQIMSKAMATTF 105 (111)
Q Consensus 84 ~~p~~iiTD~d~a~~~Ai~~vf 105 (111)
..-+-+++|-|.+|.+|+++||
T Consensus 16 d~vkF~L~nTdlsvANsLRRV~ 37 (285)
T KOG1522|consen 16 DNVKFVLSNTDLSVANSLRRVM 37 (285)
T ss_pred CceEEEEecChHHHHHHHHHHH
Confidence 4567899999999999999997
No 58
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=20.42 E-value=98 Score=16.21 Aligned_cols=15 Identities=7% Similarity=0.053 Sum_probs=11.4
Q ss_pred HHHHHHHHHhCCCCC
Q 038964 95 QIMSKAMATTFLDST 109 (111)
Q Consensus 95 ~a~~~Ai~~vfP~~~ 109 (111)
..+...+++.||+-.
T Consensus 3 ~~~v~~L~~mFP~l~ 17 (43)
T smart00546 3 DEALHDLKDMFPNLD 17 (43)
T ss_pred HHHHHHHHHHCCCCC
Confidence 356788999999753
No 59
>PLN02494 adenosylhomocysteinase
Probab=20.38 E-value=1.5e+02 Score=24.57 Aligned_cols=40 Identities=13% Similarity=-0.062 Sum_probs=32.0
Q ss_pred ccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHH
Q 038964 62 LTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAM 101 (111)
Q Consensus 62 l~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai 101 (111)
-.+|+.+.|-|.++..++.-++..|..||=|......-..
T Consensus 101 ~~g~~~~ey~~~~~~~l~~~~~~~p~~i~DDG~dl~~~~h 140 (477)
T PLN02494 101 WKGETLQEYWWCTERALDWGPGGGPDLIVDDGGDATLLIH 140 (477)
T ss_pred ecCCCHHHHHHHHHHHHcCCCCCCCCEEEeCCchHHHHHH
Confidence 6788999999999998887666789999988877654443
Done!