Query 033513
Match_columns 117
No_of_seqs 4 out of 6
Neff 1.2
Searched_HMMs 46136
Date Fri Mar 29 03:09:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033513.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033513hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00266 NIMA-related protein 89.9 3.2 7E-05 38.9 9.9 7 73-79 516-522 (1021)
2 PF06637 PV-1: PV-1 protein (P 83.1 17 0.00037 32.2 10.1 75 6-80 276-364 (442)
3 PTZ00266 NIMA-related protein 81.6 12 0.00027 35.1 9.2 60 16-78 467-526 (1021)
4 PRK00153 hypothetical protein; 74.8 5.6 0.00012 26.9 3.7 41 62-105 7-47 (104)
5 KOG0155 Transcription factor C 74.0 20 0.00042 33.0 7.9 38 8-47 421-458 (617)
6 TIGR00570 cdk7 CDK-activating 71.0 21 0.00045 29.7 6.9 30 14-43 64-104 (309)
7 PF03980 Nnf1: Nnf1 ; InterPr 67.8 33 0.00071 22.7 7.6 82 5-87 4-102 (109)
8 COG4741 Predicted secreted end 64.4 32 0.0007 27.3 6.4 54 29-91 33-94 (175)
9 KOG2391 Vacuolar sorting prote 59.3 33 0.00071 29.8 6.1 34 47-80 228-261 (365)
10 PF10262 Rdx: Rdx family; Int 58.8 4.2 9.1E-05 25.7 0.6 19 93-115 40-58 (76)
11 PF11351 DUF3154: Protein of u 56.8 33 0.0007 24.1 4.8 54 5-61 3-56 (123)
12 smart00302 GED Dynamin GTPase 52.6 65 0.0014 21.2 5.6 49 6-54 30-78 (92)
13 PF00235 Profilin: Profilin; 52.2 5.5 0.00012 26.2 0.3 14 99-112 60-73 (121)
14 PF09720 Unstab_antitox: Putat 51.4 13 0.00028 22.2 1.8 19 47-65 24-42 (54)
15 PF02212 GED: Dynamin GTPase e 50.3 27 0.00058 22.6 3.4 46 6-51 30-75 (92)
16 PF13573 SprB: SprB repeat 49.4 14 0.0003 21.2 1.7 15 91-105 10-24 (37)
17 cd00148 PROF Profilin binds ac 47.9 7.6 0.00016 26.8 0.5 14 100-113 62-75 (127)
18 PF12072 DUF3552: Domain of un 46.0 1.2E+02 0.0026 22.4 9.8 22 56-77 101-122 (201)
19 KOG4661 Hsp27-ERE-TATA-binding 45.4 1.1E+02 0.0025 29.1 7.7 48 37-85 629-683 (940)
20 KOG4326 Mitochondrial F1F0-ATP 44.5 79 0.0017 22.6 5.2 16 64-79 64-79 (81)
21 smart00392 PROF Profilin. Bind 44.4 9.1 0.0002 26.3 0.5 13 100-112 64-76 (129)
22 PF12072 DUF3552: Domain of un 43.5 1.3E+02 0.0029 22.2 6.5 43 34-80 62-104 (201)
23 KOG3054 Uncharacterized conser 42.7 61 0.0013 27.6 5.1 11 48-58 138-148 (299)
24 KOG0612 Rho-associated, coiled 40.1 1.7E+02 0.0037 29.3 8.2 44 28-74 670-713 (1317)
25 PF14048 MBD_C: C-terminal dom 38.7 34 0.00075 23.8 2.6 21 59-79 74-94 (96)
26 TIGR02574 stabl_TIGR02574 puta 36.5 32 0.00069 21.4 2.0 17 49-65 29-45 (63)
27 PF15236 CCDC66: Coiled-coil d 33.8 1.7E+02 0.0037 22.3 5.9 64 11-77 32-99 (157)
28 PF08367 M16C_assoc: Peptidase 33.3 1.2E+02 0.0026 22.5 5.0 46 36-82 6-52 (248)
29 cd01106 HTH_TipAL-Mta Helix-Tu 33.3 1E+02 0.0022 20.0 4.1 40 33-79 62-101 (103)
30 PF08112 ATP-synt_E_2: ATP syn 33.2 1.5E+02 0.0033 19.9 5.9 43 1-45 1-46 (56)
31 PF03154 Atrophin-1: Atrophin- 33.1 41 0.00089 32.3 2.9 7 42-48 725-731 (982)
32 PF06742 DUF1214: Protein of u 32.6 38 0.00082 21.6 1.9 15 92-106 63-77 (103)
33 KOG3088 Secretory carrier memb 32.4 42 0.00091 28.6 2.7 20 51-70 71-90 (313)
34 PF00456 Transketolase_N: Tran 32.2 1.1E+02 0.0024 24.8 4.9 52 10-62 264-315 (332)
35 PRK00106 hypothetical protein; 31.0 3.8E+02 0.0081 23.7 9.3 69 16-84 59-127 (535)
36 PF13892 DBINO: DNA-binding do 30.8 1.7E+02 0.0038 21.9 5.5 15 32-46 71-85 (139)
37 TIGR03689 pup_AAA proteasome A 30.6 1.1E+02 0.0025 26.5 5.0 27 84-110 47-73 (512)
38 PF02575 YbaB_DNA_bd: YbaB/Ebf 30.4 79 0.0017 20.0 3.1 25 78-105 15-39 (93)
39 PF06476 DUF1090: Protein of u 30.1 2E+02 0.0044 20.3 6.0 44 35-78 69-113 (115)
40 KOG4691 Uncharacterized conser 29.8 1.5E+02 0.0033 24.4 5.4 73 29-109 133-207 (227)
41 TIGR02174 CXXU_selWTH selT/sel 29.3 39 0.00084 21.4 1.5 15 91-105 36-50 (72)
42 PF10107 Endonuc_Holl: Endonuc 29.2 1.8E+02 0.0039 22.5 5.4 17 74-90 64-80 (156)
43 PF13698 DUF4156: Domain of un 29.0 54 0.0012 22.0 2.3 17 93-109 77-93 (93)
44 PRK06228 F0F1 ATP synthase sub 28.9 2E+02 0.0044 20.5 5.3 25 47-71 105-129 (131)
45 PRK00199 ihfB integration host 28.1 60 0.0013 20.9 2.3 19 5-23 22-40 (94)
46 PF00649 Copper-fist: Copper f 27.8 27 0.00059 21.9 0.6 12 100-111 2-13 (40)
47 TIGR02588 conserved hypothetic 27.4 45 0.00098 24.7 1.8 17 90-106 104-120 (122)
48 TIGR00988 hip integration host 27.3 63 0.0014 20.7 2.3 19 5-23 22-40 (94)
49 TIGR00103 DNA_YbaB_EbfC DNA-bi 27.0 1.2E+02 0.0026 20.7 3.7 39 64-105 11-49 (102)
50 PF05300 DUF737: Protein of un 26.6 3E+02 0.0066 21.2 7.2 18 52-69 135-152 (187)
51 PF00216 Bac_DNA_binding: Bact 26.4 76 0.0016 19.5 2.5 18 5-22 21-38 (90)
52 KOG4661 Hsp27-ERE-TATA-binding 25.3 1.7E+02 0.0037 28.0 5.5 40 41-81 628-669 (940)
53 PTZ00316 profilin; Provisional 25.2 29 0.00062 26.3 0.4 12 100-111 62-73 (150)
54 PF10252 PP28: Casein kinase s 24.6 64 0.0014 22.6 2.1 19 53-71 22-41 (82)
55 PF06391 MAT1: CDK-activating 24.4 25 0.00054 27.5 0.0 24 20-43 18-52 (200)
56 PF09058 L27_1: L27_1; InterP 24.0 56 0.0012 22.0 1.6 21 5-26 34-54 (64)
57 smart00099 btg1 tob/btg1 famil 23.9 24 0.00052 25.4 -0.2 11 103-113 53-63 (108)
58 TIGR01932 hflC HflC protein. H 23.7 3.6E+02 0.0078 21.1 6.8 9 25-33 214-222 (317)
59 PRK00285 ihfA integration host 23.2 83 0.0018 20.4 2.3 19 5-23 23-41 (99)
60 KOG0245 Kinesin-like protein [ 23.2 2.5E+02 0.0054 28.0 6.3 27 35-61 404-430 (1221)
61 smart00412 Cu_FIST Copper-Fist 22.3 37 0.0008 21.2 0.4 12 100-111 1-12 (39)
62 PRK14626 hypothetical protein; 22.2 1.7E+02 0.0036 20.6 3.8 12 95-106 39-50 (110)
63 smart00411 BHL bacterial (prok 22.2 93 0.002 19.2 2.3 19 5-23 21-39 (90)
64 TIGR03166 alt_F1F0_F1_eps alte 22.0 2.6E+02 0.0056 19.6 4.7 27 40-66 95-121 (122)
65 PRK10753 transcriptional regul 21.9 90 0.002 20.4 2.3 19 5-23 21-39 (90)
66 TIGR03543 divI1A_rptt_fam DivI 21.4 3.4E+02 0.0075 21.0 5.7 59 7-65 14-97 (178)
67 PRK05641 putative acetyl-CoA c 21.4 58 0.0013 23.9 1.4 16 94-109 21-36 (153)
68 PF06698 DUF1192: Protein of u 21.4 2E+02 0.0043 18.8 3.8 25 44-68 25-49 (59)
69 PF14703 DUF4463: Domain of un 21.2 1.7E+02 0.0037 17.8 3.3 26 32-57 6-31 (85)
70 PF01813 ATP-synt_D: ATP synth 20.8 82 0.0018 22.9 2.1 14 32-45 173-186 (196)
71 COG5019 CDC3 Septin family pro 20.7 4.6E+02 0.01 22.7 6.8 52 31-82 315-370 (373)
72 PF03154 Atrophin-1: Atrophin- 20.4 82 0.0018 30.4 2.5 10 40-49 718-727 (982)
73 TIGR00987 himA integration hos 20.3 1.2E+02 0.0026 19.7 2.6 18 5-22 22-39 (96)
74 PRK14435 acylphosphatase; Prov 20.1 54 0.0012 21.7 0.9 28 84-113 30-57 (90)
75 PF06825 HSBP1: Heat shock fac 20.0 2.6E+02 0.0056 18.0 4.7 43 5-47 4-46 (54)
No 1
>PTZ00266 NIMA-related protein kinase; Provisional
Probab=89.93 E-value=3.2 Score=38.87 Aligned_cols=7 Identities=57% Similarity=0.957 Sum_probs=2.7
Q ss_pred hhhhhhh
Q 033513 73 EKENLEK 79 (117)
Q Consensus 73 er~nlek 79 (117)
|++.+|+
T Consensus 516 e~e~~e~ 522 (1021)
T PTZ00266 516 ERDRLEK 522 (1021)
T ss_pred HHHHHHH
Confidence 3333333
No 2
>PF06637 PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 This family consists of several PV-1 (PLVAP) proteins, which seem to be specific to mammals. PV-1 is a novel protein component of the endothelial fenestral and stomatal diaphragms []. The function of this family is unknown.
Probab=83.07 E-value=17 Score=32.17 Aligned_cols=75 Identities=31% Similarity=0.432 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHHHhchHHHHH-----------HHhHHHHhHHHHHHH---HHHHHHHHHHHHHhhhHHHHHHHHHHHhh
Q 033513 6 KTVVDKFVQELKEALDADIQDR-----------IMKEREMQSYIEERE---REVAEREAAWKAELSRREAEIARQEARLK 71 (117)
Q Consensus 6 kavv~~fv~~lkeal~adiqdr-----------imkeremqsy~eere---revaereaawkaelsrreaei~~qearl~ 71 (117)
-.+|.+=|++|-.-|.+||..- .--|+.++.-.+..| .|.+.|++--.++-+|.-.-.....+.|+
T Consensus 276 P~~m~tKveelar~Lr~~I~~VarENs~LqrQKle~e~~l~a~qeakek~~KEAqareaklqaec~rQ~qlaLEEKaaLr 355 (442)
T PF06637_consen 276 PKIMTTKVEELARSLRAGIERVARENSDLQRQKLEAEQGLQASQEAKEKAGKEAQAREAKLQAECARQTQLALEEKAALR 355 (442)
T ss_pred hHHHHHHHHHHHHHHhhhHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567788888888888888532 222333444444443 45666777777777766554445568999
Q ss_pred hhhhhhhhh
Q 033513 72 MEKENLEKE 80 (117)
Q Consensus 72 mer~nleke 80 (117)
-|||+|+||
T Consensus 356 kerd~L~ke 364 (442)
T PF06637_consen 356 KERDSLAKE 364 (442)
T ss_pred HHHHHHHHH
Confidence 999999886
No 3
>PTZ00266 NIMA-related protein kinase; Provisional
Probab=81.57 E-value=12 Score=35.13 Aligned_cols=60 Identities=32% Similarity=0.364 Sum_probs=27.5
Q ss_pred HHHHhchHHHHHHHhHHHHhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhhhhhhh
Q 033513 16 LKEALDADIQDRIMKEREMQSYIEEREREVAEREAAWKAELSRREAEIARQEARLKMEKENLE 78 (117)
Q Consensus 16 lkeal~adiqdrimkeremqsy~eererevaereaawkaelsrreaei~~qearl~mer~nle 78 (117)
.+|.++..-+.|+.+||+=. |.+|||-.|||..=+..+-|.|.|-++...|-++|++..+
T Consensus 467 ~~er~Erer~er~erer~Er---er~erEr~erer~erer~~r~e~er~~r~e~e~~e~~rr~ 526 (1021)
T PTZ00266 467 ERERLERERMERIERERLER---ERLERERLERDRLERDRLDRLERERVDRLERDRLEKARRN 526 (1021)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 33444444444444444321 2233344444444444455555555555455555555433
No 4
>PRK00153 hypothetical protein; Validated
Probab=74.77 E-value=5.6 Score=26.86 Aligned_cols=41 Identities=12% Similarity=0.350 Sum_probs=30.2
Q ss_pred HHHHHHHHhhhhhhhhhhhhhhhhccccCCCCCCCceEEEEecc
Q 033513 62 EIARQEARLKMEKENLEKEKSVLMGTASNQDNQDGALEITVSGE 105 (117)
Q Consensus 62 ei~~qearl~mer~nlekeksvlmgtas~~dnqdgaleitvsge 105 (117)
++.+|-.+++-+-+++.++-.-.-.|+++. ||.++|||+|.
T Consensus 7 ~m~~qaq~~q~~~~~~q~~l~~~~~~~~s~---~G~V~V~v~G~ 47 (104)
T PRK00153 7 NLMKQAQQMQEKMQKMQEELAQMEVEGEAG---GGLVKVTMTGK 47 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccEEEEEEC---CCeEEEEEecC
Confidence 455666666666677777777777777775 78999999996
No 5
>KOG0155 consensus Transcription factor CA150 [Transcription]
Probab=74.01 E-value=20 Score=32.96 Aligned_cols=38 Identities=26% Similarity=0.556 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhchHHHHHHHhHHHHhHHHHHHHHHHHH
Q 033513 8 VVDKFVQELKEALDADIQDRIMKEREMQSYIEEREREVAE 47 (117)
Q Consensus 8 vv~~fv~~lkeal~adiqdrimkeremqsy~eererevae 47 (117)
+.-.||..|+.++.-|+ -.|+++....-|.+|||||.-
T Consensus 421 lf~eyia~l~~~~~sd~--e~er~~r~ea~lrererev~k 458 (617)
T KOG0155|consen 421 LFREYIANLGDETASDI--EQEREKRLEAQLREREREVEK 458 (617)
T ss_pred HHHHHHHHHHhhhcccH--HHHHHHHHHHHHHHHHHHHHH
Confidence 45679999999999998 678888887779999999853
No 6
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=70.99 E-value=21 Score=29.75 Aligned_cols=30 Identities=33% Similarity=0.570 Sum_probs=21.8
Q ss_pred HHHHHHhchHHHHHHHhH-----------HHHhHHHHHHHH
Q 033513 14 QELKEALDADIQDRIMKE-----------REMQSYIEERER 43 (117)
Q Consensus 14 ~~lkeal~adiqdrimke-----------remqsy~eerer 43 (117)
.++.--=+.||+.|+++- ++.+.|||++|-
T Consensus 64 ~D~~vekEV~iRkrv~~i~Nk~e~dF~~l~~yNdYLE~vEd 104 (309)
T TIGR00570 64 EDPTVEKEVDIRKRVLKIYNKREEDFPSLREYNDYLEEVED 104 (309)
T ss_pred ccHHHHHHHHHHHHHHHHHccchhccCCHHHHHHHHHHHHH
Confidence 344444578888888863 678899998874
No 7
>PF03980 Nnf1: Nnf1 ; InterPro: IPR007128 NNF1 is an essential yeast gene required for proper spindle orientation, nucleolar and nuclear envelope structure and mRNA export [].
Probab=67.76 E-value=33 Score=22.72 Aligned_cols=82 Identities=21% Similarity=0.445 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHHHHhchHHHHHHHhHHHHhHHHHHHHHHHHH---HH-------HHHHHHhhhHHHH-------HHHHH
Q 033513 5 IKTVVDKFVQELKEALDADIQDRIMKEREMQSYIEEREREVAE---RE-------AAWKAELSRREAE-------IARQE 67 (117)
Q Consensus 5 ikavv~~fv~~lkeal~adiqdrimkeremqsy~eererevae---re-------aawkaelsrreae-------i~~qe 67 (117)
+..|...|+..|.+....+++ -|++||.+..-|.+=+.=+.+ |. .+|.-.|+-.+.= ..++-
T Consensus 4 L~~~~~Q~~~~l~~~~~~Ef~-~I~~Er~v~~kLneLd~Li~eA~~r~~~~~~~~~~~~~~l~P~~~i~a~l~~~~~~~~ 82 (109)
T PF03980_consen 4 LESVHQQMIEFLEENCKKEFE-EILEERDVVEKLNELDKLIEEAKERKNSGEREKPVWRHSLTPEEDIRAHLAPYKKKER 82 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHHhhHHHHHHHHHHHHHHHHHhHhccccCCCCCCCCCChHHHHHHHhHHHHHHHH
Confidence 456777788888777777764 599999999988877655543 22 4787777765532 23345
Q ss_pred HHhhhhhhhhhhhhhhhhcc
Q 033513 68 ARLKMEKENLEKEKSVLMGT 87 (117)
Q Consensus 68 arl~mer~nlekeksvlmgt 87 (117)
.+|....++++++-.-|+++
T Consensus 83 ~~L~~~l~~l~~eN~~L~~~ 102 (109)
T PF03980_consen 83 EQLNARLQELEEENEALAEE 102 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 56666667777766666543
No 8
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=64.37 E-value=32 Score=27.33 Aligned_cols=54 Identities=30% Similarity=0.578 Sum_probs=33.2
Q ss_pred HhHHHHhHHHHHH--HHHH----HHHHHHHHHHh--hhHHHHHHHHHHHhhhhhhhhhhhhhhhhccccCC
Q 033513 29 MKEREMQSYIEER--EREV----AEREAAWKAEL--SRREAEIARQEARLKMEKENLEKEKSVLMGTASNQ 91 (117)
Q Consensus 29 mkeremqsy~eer--erev----aereaawkael--srreaei~~qearl~mer~nlekeksvlmgtas~~ 91 (117)
|+.|+|+.-++.+ ||-| +-++++||-+= ..+.. |+ -+|...|-++|+||-.|-|
T Consensus 33 ~k~~~l~e~l~~~e~~r~v~ea~~~ke~~~Kl~E~iekkie-----ea----R~dav~kS~~Vi~GrVtEq 94 (175)
T COG4741 33 SKARELEETLQKAERERLVNEAQARKEEEWKLKEWIEKKIE-----EA----REDAVRKSRAVILGRVTEQ 94 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HH----HHHHHHHhHHHHhhhhHhh
Confidence 6778887777765 4433 44667776431 22221 12 2467788999999987654
No 9
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=59.29 E-value=33 Score=29.77 Aligned_cols=34 Identities=35% Similarity=0.407 Sum_probs=16.2
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHhhhhhhhhhhh
Q 033513 47 EREAAWKAELSRREAEIARQEARLKMEKENLEKE 80 (117)
Q Consensus 47 ereaawkaelsrreaei~~qearl~mer~nleke 80 (117)
+|-.+-.+.|-|++-|+..--+.|+.+++.||.+
T Consensus 228 e~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq 261 (365)
T KOG2391|consen 228 ERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQ 261 (365)
T ss_pred HHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHH
Confidence 3333334455555555554444444444444444
No 10
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=58.81 E-value=4.2 Score=25.70 Aligned_cols=19 Identities=53% Similarity=0.824 Sum_probs=14.5
Q ss_pred CCCCceEEEEecceehhhhhhhc
Q 033513 93 NQDGALEITVSGEKYRCLRFAKA 115 (117)
Q Consensus 93 nqdgaleitvsgekyrclrf~ka 115 (117)
..+|+.||+|.|+ |=|||.
T Consensus 40 ~~~G~FEV~v~g~----lI~SK~ 58 (76)
T PF10262_consen 40 GSTGAFEVTVNGE----LIFSKL 58 (76)
T ss_dssp ESTT-EEEEETTE----EEEEHH
T ss_pred ccCCEEEEEEccE----EEEEeh
Confidence 5699999999998 566664
No 11
>PF11351 DUF3154: Protein of unknown function (DUF3154); InterPro: IPR021497 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=56.78 E-value=33 Score=24.13 Aligned_cols=54 Identities=22% Similarity=0.351 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHhchHHHHHHHhHHHHhHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 033513 5 IKTVVDKFVQELKEALDADIQDRIMKEREMQSYIEEREREVAEREAAWKAELSRREA 61 (117)
Q Consensus 5 ikavv~~fv~~lkeal~adiqdrimkeremqsy~eererevaereaawkaelsrrea 61 (117)
|..++|+|..+=.++..++.+ +...+++.+.+|-+.....+-..-.+++++.++
T Consensus 3 v~~~~d~~~~~~e~~~~~~~~---l~~~~~~~~~~e~~~~~~~~~~~~~~eln~~~a 56 (123)
T PF11351_consen 3 VGETIDVFRPDPEERAQAKAE---LQQAALEQFAAEFEAARRARFDRMQAELNRADA 56 (123)
T ss_pred HHHHHHHhcCCHHHHHHHHHH---HHHHHHHHHHHHHHHHHHhHHHHHHHHHhcCcc
Confidence 566788887766666555443 233566777777666556666666777777664
No 12
>smart00302 GED Dynamin GTPase effector domain.
Probab=52.64 E-value=65 Score=21.21 Aligned_cols=49 Identities=22% Similarity=0.329 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHhchHHHHHHHhHHHHhHHHHHHHHHHHHHHHHHHH
Q 033513 6 KTVVDKFVQELKEALDADIQDRIMKEREMQSYIEEREREVAEREAAWKA 54 (117)
Q Consensus 6 kavv~~fv~~lkeal~adiqdrimkeremqsy~eererevaereaawka 54 (117)
|+++--.|...++-|...+...+++...+.+.++|-.--.+.|+..++-
T Consensus 30 KaI~~~lv~~~~~~lq~~L~~~L~~~~~~~~LL~E~~~i~~kR~~~~~~ 78 (92)
T smart00302 30 KAIMYLLVNESKDSLQNELLALLYKEELLDELLEEDPEIASKRKELKKR 78 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCcccHHHHHcCCHHHHHHHHHHHHH
Confidence 6677777888899999999999999888888899888777777766653
No 13
>PF00235 Profilin: Profilin; InterPro: IPR002097 Profilin is a small eukaryotic protein that binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). It can also in certain circumstance promote actin polymerisation. Profilin also binds to polyphosphoinositides such as PIP2. Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. That region is thought to be involved in the binding to actin. A protein structurally similar to profilin is present in the genome of Variola virus and Vaccinia virus (gene A42R). Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ara t 8, Bet v 2, Cyn d 12, Hel a 2, Mer a 1 and Phl p 11.; GO: 0003779 actin binding, 0007010 cytoskeleton organization, 0015629 actin cytoskeleton; PDB: 1ACF_A 3NEC_C 2V8F_B 2V8C_A 2VK3_A 2JKF_A 2JKG_A 1F2K_B 2ACG_A 1YPR_B ....
Probab=52.19 E-value=5.5 Score=26.16 Aligned_cols=14 Identities=50% Similarity=0.731 Sum_probs=12.0
Q ss_pred EEEEecceehhhhh
Q 033513 99 EITVSGEKYRCLRF 112 (117)
Q Consensus 99 eitvsgekyrclrf 112 (117)
-|++.|.||.|+|-
T Consensus 60 gi~l~G~kY~~~~~ 73 (121)
T PF00235_consen 60 GITLGGKKYIVLRA 73 (121)
T ss_dssp -EEETTEEEEEEEE
T ss_pred CeEEcCcEeEEEec
Confidence 49999999999983
No 14
>PF09720 Unstab_antitox: Putative addiction module component; InterPro: IPR013406 This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (IPR007712 from INTERPRO). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death [] - although these gene pairs are usually found on the bacterial main chromosome.
Probab=51.42 E-value=13 Score=22.23 Aligned_cols=19 Identities=58% Similarity=0.718 Sum_probs=16.4
Q ss_pred HHHHHHHHHhhhHHHHHHH
Q 033513 47 EREAAWKAELSRREAEIAR 65 (117)
Q Consensus 47 ereaawkaelsrreaei~~ 65 (117)
+-+++|.+++.||.+++..
T Consensus 24 ~~~~~w~~el~rR~~~~~~ 42 (54)
T PF09720_consen 24 EVEAWWKEELERRLAEYES 42 (54)
T ss_pred cCcHHHHHHHHHHHHHHHc
Confidence 6788999999999988754
No 15
>PF02212 GED: Dynamin GTPase effector domain; InterPro: IPR003130 Dynamin GTPase effector domain found in proteins related to dynamin. Dynamin is a GTP-hydrolysing protein that is an essential participant in clathrin-mediated endocytosis by cells. It self-assembles into 'collars' in vivo at the necks of invaginated coated pits; the self-assembly of dynamin being coordinated by the GTPase domain. Mutation studies indicate that dynamin functions as a molecular regulator of receptor-mediated endocytosis [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 3ZYS_B 3SZR_A 3LJB_B 3T35_C 3T34_A 2X2F_D 2X2E_D 3SNH_A 3ZYC_D 3ZVR_A.
Probab=50.33 E-value=27 Score=22.64 Aligned_cols=46 Identities=20% Similarity=0.420 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHhchHHHHHHHhHHHHhHHHHHHHHHHHHHHHH
Q 033513 6 KTVVDKFVQELKEALDADIQDRIMKEREMQSYIEEREREVAEREAA 51 (117)
Q Consensus 6 kavv~~fv~~lkeal~adiqdrimkeremqsy~eererevaereaa 51 (117)
|+|+..+|+.+.+.|...+..-+..+-.+...+.|-..-+++|+..
T Consensus 30 k~I~~~lv~~~~~~L~~~l~~~l~~~~~~~~Ll~Ed~~i~~kR~~l 75 (92)
T PF02212_consen 30 KAIMHFLVNKSKEQLQSELLNELYDEEDLEELLQEDPEIAEKREEL 75 (92)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHCGGCCCCT--GHHHHHHHHHH
T ss_pred HHHHHHHHHhHHhHHHHHHHHhccchHHHHHHHCCCHHHHHHHHHH
Confidence 6777778888888888888877777777777888777666666544
No 16
>PF13573 SprB: SprB repeat
Probab=49.40 E-value=14 Score=21.25 Aligned_cols=15 Identities=33% Similarity=0.667 Sum_probs=12.6
Q ss_pred CCCCCCceEEEEecc
Q 033513 91 QDNQDGALEITVSGE 105 (117)
Q Consensus 91 ~dnqdgaleitvsge 105 (117)
..+.||.+.|+++|-
T Consensus 10 ~g~~dG~i~v~~tGG 24 (37)
T PF13573_consen 10 FGGNDGSITVTVTGG 24 (37)
T ss_pred CCCCCeEEEEEEeCC
Confidence 347899999999985
No 17
>cd00148 PROF Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway.
Probab=47.87 E-value=7.6 Score=26.79 Aligned_cols=14 Identities=36% Similarity=0.714 Sum_probs=12.4
Q ss_pred EEEecceehhhhhh
Q 033513 100 ITVSGEKYRCLRFA 113 (117)
Q Consensus 100 itvsgekyrclrf~ 113 (117)
|++.|+||.|+|-.
T Consensus 62 i~l~G~KY~~l~~d 75 (127)
T cd00148 62 LTLGGQKYMVIRAD 75 (127)
T ss_pred EEECCeEEEEEecC
Confidence 99999999999843
No 18
>PF12072 DUF3552: Domain of unknown function (DUF3552); InterPro: IPR022711 This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with PF00013 from PFAM, PF01966 from PFAM. This domain has a single completely conserved residue A that may be functionally important. ; GO: 0008663 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity
Probab=45.95 E-value=1.2e+02 Score=22.38 Aligned_cols=22 Identities=41% Similarity=0.699 Sum_probs=9.8
Q ss_pred hhhHHHHHHHHHHHhhhhhhhh
Q 033513 56 LSRREAEIARQEARLKMEKENL 77 (117)
Q Consensus 56 lsrreaei~~qearl~mer~nl 77 (117)
|..++.++..++..|.-..++|
T Consensus 101 L~~~e~~l~~~~~~l~~~~~~l 122 (201)
T PF12072_consen 101 LEKREEELEKKEEELEQRKEEL 122 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444444444333333
No 19
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=45.41 E-value=1.1e+02 Score=29.10 Aligned_cols=48 Identities=48% Similarity=0.576 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHH-HHhhhHHHHHHH---HHH---Hhhhhhhhhhhhhhhhh
Q 033513 37 YIEEREREVAEREAAWK-AELSRREAEIAR---QEA---RLKMEKENLEKEKSVLM 85 (117)
Q Consensus 37 y~eererevaereaawk-aelsrreaei~~---qea---rl~mer~nlekeksvlm 85 (117)
.-|+||||. -|+++|. .+|-|-++|..+ |.. |-+||++.||.|.--+|
T Consensus 629 irE~rerEq-R~~a~~ERee~eRl~~erlrle~qRQrLERErmErERLEreRM~ve 683 (940)
T KOG4661|consen 629 IREEREREQ-RRKAAVEREELERLKAERLRLERQRQRLERERMERERLERERMKVE 683 (940)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444442 3456663 345555555433 222 45788888888874443
No 20
>KOG4326 consensus Mitochondrial F1F0-ATP synthase, subunit e [Energy production and conversion]
Probab=44.54 E-value=79 Score=22.56 Aligned_cols=16 Identities=38% Similarity=0.349 Sum_probs=11.0
Q ss_pred HHHHHHhhhhhhhhhh
Q 033513 64 ARQEARLKMEKENLEK 79 (117)
Q Consensus 64 ~~qearl~mer~nlek 79 (117)
++.|+|--+|-.|.-.
T Consensus 64 a~~eaR~Lae~~~i~~ 79 (81)
T KOG4326|consen 64 AKDEARYLAEVVNIPF 79 (81)
T ss_pred HHHHHHHHHHhccCCC
Confidence 4558888888777543
No 21
>smart00392 PROF Profilin. Binds actin monomers, membrane polyphosphoinositides and poly-L-proline.
Probab=44.45 E-value=9.1 Score=26.28 Aligned_cols=13 Identities=38% Similarity=0.777 Sum_probs=11.9
Q ss_pred EEEecceehhhhh
Q 033513 100 ITVSGEKYRCLRF 112 (117)
Q Consensus 100 itvsgekyrclrf 112 (117)
|++.|+||.|+|-
T Consensus 64 i~l~G~Ky~~~~~ 76 (129)
T smart00392 64 LTLGGQKYMVIRA 76 (129)
T ss_pred eEECCeEEEEEEe
Confidence 8999999999984
No 22
>PF12072 DUF3552: Domain of unknown function (DUF3552); InterPro: IPR022711 This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with PF00013 from PFAM, PF01966 from PFAM. This domain has a single completely conserved residue A that may be functionally important. ; GO: 0008663 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity
Probab=43.54 E-value=1.3e+02 Score=22.17 Aligned_cols=43 Identities=40% Similarity=0.527 Sum_probs=20.4
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhhhhhhhhh
Q 033513 34 MQSYIEEREREVAEREAAWKAELSRREAEIARQEARLKMEKENLEKE 80 (117)
Q Consensus 34 mqsy~eererevaereaawkaelsrreaei~~qearl~mer~nleke 80 (117)
.+.+-.+-|+++.++ +.+|.++|..+...|..|.-..+.|++.
T Consensus 62 ~~~~r~~~E~E~~~~----~~el~~~E~rl~~rE~~L~~~~~~L~~~ 104 (201)
T PF12072_consen 62 AQKLRQELERELKER----RKELQRLEKRLQQREEQLDRRLEQLEKR 104 (201)
T ss_pred HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444433 3345555555555555555544444443
No 23
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=42.70 E-value=61 Score=27.58 Aligned_cols=11 Identities=36% Similarity=0.377 Sum_probs=5.5
Q ss_pred HHHHHHHHhhh
Q 033513 48 REAAWKAELSR 58 (117)
Q Consensus 48 reaawkaelsr 58 (117)
+|+-||.+=.|
T Consensus 138 eE~erKkdEeR 148 (299)
T KOG3054|consen 138 EEAERKKDEER 148 (299)
T ss_pred HHHHHhhhHHH
Confidence 45555554443
No 24
>KOG0612 consensus Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms]
Probab=40.06 E-value=1.7e+02 Score=29.27 Aligned_cols=44 Identities=34% Similarity=0.430 Sum_probs=34.8
Q ss_pred HHhHHHHhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhhh
Q 033513 28 IMKEREMQSYIEEREREVAEREAAWKAELSRREAEIARQEARLKMEK 74 (117)
Q Consensus 28 imkeremqsy~eererevaereaawkaelsrreaei~~qearl~mer 74 (117)
|--+|+++++..+-|++++|...- +|+-+|+++..-+.-|.-|+
T Consensus 670 ~~~e~~lk~~q~~~eq~~~E~~~~---~L~~~e~~~~e~~~~lseek 713 (1317)
T KOG0612|consen 670 IKLERKLKMLQNELEQENAEHHRL---RLQDKEAQMKEIESKLSEEK 713 (1317)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---HHhhHHHHHHHHHHHhcccc
Confidence 334899999999999999999887 88888888877666554444
No 25
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=38.74 E-value=34 Score=23.80 Aligned_cols=21 Identities=38% Similarity=0.597 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHhhhhhhhhhh
Q 033513 59 REAEIARQEARLKMEKENLEK 79 (117)
Q Consensus 59 reaei~~qearl~mer~nlek 79 (117)
-|+.|.+||.|.+.-|+.|+.
T Consensus 74 T~eDIr~QE~rVk~aR~RLae 94 (96)
T PF14048_consen 74 TEEDIRRQERRVKKARKRLAE 94 (96)
T ss_dssp -HHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999988864
No 26
>TIGR02574 stabl_TIGR02574 putative addiction module component, TIGR02574 family. Members of this family are bacterial proteins, typically are about 75 amino acids long, always found as part of a pair (at least) of two small genes. The other in the pair always belongs to a subfamily of the larger family pfam05016 (although not necessarily scoring above the designated cutoff), which contains plasmid stabilization proteins. It is likely that this protein and its pfam05016 member partner comprise some form of addiction module, although these gene pairs usually are found on the bacterial main chromosome.
Probab=36.52 E-value=32 Score=21.45 Aligned_cols=17 Identities=47% Similarity=0.458 Sum_probs=14.1
Q ss_pred HHHHHHHhhhHHHHHHH
Q 033513 49 EAAWKAELSRREAEIAR 65 (117)
Q Consensus 49 eaawkaelsrreaei~~ 65 (117)
.++|+++|.+|.+++..
T Consensus 29 ~~~~~~el~~R~~~~~~ 45 (63)
T TIGR02574 29 TEAQKAELDRRLADYKA 45 (63)
T ss_pred CHHHHHHHHHHHHHHHc
Confidence 47899999999987754
No 27
>PF15236 CCDC66: Coiled-coil domain-containing protein 66
Probab=33.77 E-value=1.7e+02 Score=22.31 Aligned_cols=64 Identities=30% Similarity=0.416 Sum_probs=34.5
Q ss_pred HHHHHHHHHhchHH----HHHHHhHHHHhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhhhhhh
Q 033513 11 KFVQELKEALDADI----QDRIMKEREMQSYIEEREREVAEREAAWKAELSRREAEIARQEARLKMEKENL 77 (117)
Q Consensus 11 ~fv~~lkeal~adi----qdrimkeremqsy~eererevaereaawkaelsrreaei~~qearl~mer~nl 77 (117)
+|++-.-..||... -+|-+|.-|.|.+|. ..|.|+...=..+..++-.|-...|-||..|++-+
T Consensus 32 s~LR~~tallDpa~~eEre~rR~kq~E~q~ai~---~QieEk~r~k~~E~err~~EE~~EE~Rl~rere~~ 99 (157)
T PF15236_consen 32 SFLRGMTALLDPAQIEERERRRQKQLEHQRAIK---QQIEEKRRQKQEEEERRRREEEEEEERLAREREEL 99 (157)
T ss_pred CccccccccCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 34444444455444 345566667777764 24445544444555555555555566666665544
No 28
>PF08367 M16C_assoc: Peptidase M16C associated; InterPro: IPR013578 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain appears in eukaryotes as well as bacteria and tends to be found near the C terminus of metalloproteases and related sequences belonging to MEROPS peptidase family M16 (subfamily M16C, clan ME). These include: eupitrilysin, falcilysin, PreP peptidase, CYM1 peptidase and subfamily M16C non-peptidase homologues.; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 2FGE_B 3S5I_A 3S5H_A 3S5M_A 3S5K_A.
Probab=33.33 E-value=1.2e+02 Score=22.50 Aligned_cols=46 Identities=37% Similarity=0.458 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhHHHHHH-HHHHHhhhhhhhhhhhhh
Q 033513 36 SYIEEREREVAEREAAWKAELSRREAEIA-RQEARLKMEKENLEKEKS 82 (117)
Q Consensus 36 sy~eererevaereaawkaelsrreaei~-~qearl~mer~nlekeks 82 (117)
.|.++++.+.+++-++-++.||..|.+-+ ++-.+|+ ++.+-+...+
T Consensus 6 ~~~~~~~~~e~~~L~~~k~~Ls~~e~~~i~~~~~~L~-~~Q~~~d~~~ 52 (248)
T PF08367_consen 6 GLSEKQEEEEKEKLAAYKASLSEEEKEKIIEQTKELK-ERQEAEDDLA 52 (248)
T ss_dssp THHHHHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHH-HHHCS--HHT
T ss_pred hHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHH-HHhCChhhHH
Confidence 46788899999999999999998886544 4444443 3333333333
No 29
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=33.25 E-value=1e+02 Score=19.99 Aligned_cols=40 Identities=10% Similarity=0.281 Sum_probs=28.4
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhhhhhhhh
Q 033513 33 EMQSYIEEREREVAEREAAWKAELSRREAEIARQEARLKMEKENLEK 79 (117)
Q Consensus 33 emqsy~eererevaereaawkaelsrreaei~~qearl~mer~nlek 79 (117)
+++.++.... ..|.+-|..+-+++..|-++|..-.+.|++
T Consensus 62 ~i~~~~~~~~-------~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~ 101 (103)
T cd01106 62 EIKELLKDPS-------EDLLEALREQKELLEEKKERLDKLIKTIDR 101 (103)
T ss_pred HHHHHHHcCc-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555433 668888888888888888888777776653
No 30
>PF08112 ATP-synt_E_2: ATP synthase epsilon subunit; InterPro: IPR012508 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. A-ATPases (or A1A0-ATPase) (3.6.3.14 from EC) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases []. A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore []. The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C []. A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species. The epsilon subunit is the smallest (7 kDa) of those found in the A1 complex. Unlike the A, B and C subunits, the epsilon subunit does not have a homologous counterpart in F- or V-ATPases []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain
Probab=33.22 E-value=1.5e+02 Score=19.91 Aligned_cols=43 Identities=30% Similarity=0.490 Sum_probs=29.9
Q ss_pred CchhHHHHHHHHHHHHHHHhch---HHHHHHHhHHHHhHHHHHHHHHH
Q 033513 1 MSLRIKTVVDKFVQELKEALDA---DIQDRIMKEREMQSYIEEREREV 45 (117)
Q Consensus 1 mslrikavv~~fv~~lkeal~a---diqdrimkeremqsy~eererev 45 (117)
||--=|..+|+|+..||.-||. .|+++|-+| .++.|..|-.+.
T Consensus 1 m~~~~~~~~d~yI~~Lk~kLd~Kk~Eil~~ln~E--Y~kiLk~r~~~l 46 (56)
T PF08112_consen 1 MSEIDKSTIDKYISILKSKLDEKKSEILSNLNME--YEKILKQRRKEL 46 (56)
T ss_pred CcchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
Confidence 3333467889999999999986 578888764 455566554433
No 31
>PF03154 Atrophin-1: Atrophin-1 family; InterPro: IPR002951 Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA (OMIM:125370) is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins [, ]. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity [].. This entry includes Atrophin-1 and related proteins.
Probab=33.12 E-value=41 Score=32.33 Aligned_cols=7 Identities=71% Similarity=1.080 Sum_probs=2.6
Q ss_pred HHHHHHH
Q 033513 42 EREVAER 48 (117)
Q Consensus 42 erevaer 48 (117)
|||.-||
T Consensus 725 ERE~Rer 731 (982)
T PF03154_consen 725 EREIRER 731 (982)
T ss_pred hhhhhhH
Confidence 3333333
No 32
>PF06742 DUF1214: Protein of unknown function (DUF1214); InterPro: IPR010621 This entry represents the C-terminal domain of several hypothetical proteins of unknown function. ; PDB: 3U07_A 3VB9_D 2P3Y_A.
Probab=32.59 E-value=38 Score=21.63 Aligned_cols=15 Identities=40% Similarity=0.638 Sum_probs=12.5
Q ss_pred CCCCCceEEEEecce
Q 033513 92 DNQDGALEITVSGEK 106 (117)
Q Consensus 92 dnqdgaleitvsgek 106 (117)
.|.||.++|++|.+.
T Consensus 63 ~~~DGsf~i~ls~~~ 77 (103)
T PF06742_consen 63 SDADGSFTITLSPEP 77 (103)
T ss_dssp TTTTSEEEEEEESS-
T ss_pred cCCCccEEEEEeCCC
Confidence 489999999999853
No 33
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.44 E-value=42 Score=28.60 Aligned_cols=20 Identities=40% Similarity=0.576 Sum_probs=0.0
Q ss_pred HHHHHhhhHHHHHHHHHHHh
Q 033513 51 AWKAELSRREAEIARQEARL 70 (117)
Q Consensus 51 awkaelsrreaei~~qearl 70 (117)
.|.+||.|+|+|+.|.|..+
T Consensus 71 ~rqeEL~Rke~ELdRREr~~ 90 (313)
T KOG3088|consen 71 KKQEELRRKEQELDRRERAL 90 (313)
T ss_pred HHHHHHHHHHHHHhHHHHHH
No 34
>PF00456 Transketolase_N: Transketolase, thiamine diphosphate binding domain; InterPro: IPR005474 Transketolase 2.2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [, ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) [] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis []. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding []. This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; PDB: 3M49_B 1NGS_B 1TKA_A 1TRK_B 1TKB_A 1GPU_B 1AY0_B 1TKC_B 3HYL_A 3RIM_A ....
Probab=32.17 E-value=1.1e+02 Score=24.77 Aligned_cols=52 Identities=27% Similarity=0.333 Sum_probs=41.1
Q ss_pred HHHHHHHHHHhchHHHHHHHhHHHHhHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 033513 10 DKFVQELKEALDADIQDRIMKEREMQSYIEEREREVAEREAAWKAELSRREAE 62 (117)
Q Consensus 10 ~~fv~~lkeal~adiqdrimkeremqsy~eererevaereaawkaelsrreae 62 (117)
+.=+.++|+.|..+ ++-..=.-|...|.+++-.+-+.-++.|+..+..-..+
T Consensus 264 ~ee~~~~k~~lg~~-~~~F~V~~eV~~~f~~~~~~g~~~~~~W~~~~~~y~~~ 315 (332)
T PF00456_consen 264 EEEVEQAKKELGWD-QEPFEVPEEVYDHFRERIAEGAKAEAEWKELFAAYKKK 315 (332)
T ss_dssp HHHHHHHHHHTTSS-TSTTCGCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCC-CCCcccCHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 34477889999888 66666677888889888888889999999988776443
No 35
>PRK00106 hypothetical protein; Provisional
Probab=30.98 E-value=3.8e+02 Score=23.71 Aligned_cols=69 Identities=17% Similarity=0.159 Sum_probs=0.0
Q ss_pred HHHHhchHHHHHHHhHHHHhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhhhhhhhhhhhhh
Q 033513 16 LKEALDADIQDRIMKEREMQSYIEEREREVAEREAAWKAELSRREAEIARQEARLKMEKENLEKEKSVL 84 (117)
Q Consensus 16 lkeal~adiqdrimkeremqsy~eererevaereaawkaelsrreaei~~qearl~mer~nlekeksvl 84 (117)
+++|...--........+...-++++..+....-...+.+|.++|..+.+.+..|.-..+.|++...-|
T Consensus 59 ~keA~~EAke~~ke~~lEaeeEi~~~R~ElEkel~eEr~rL~qrE~rL~qREE~LekRee~LekrE~eL 127 (535)
T PRK00106 59 KKTAKRESKALKKELLLEAKEEARKYREEIEQEFKSERQELKQIESRLTERATSLDRKDENLSSKEKTL 127 (535)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 36
>PF13892 DBINO: DNA-binding domain
Probab=30.83 E-value=1.7e+02 Score=21.92 Aligned_cols=15 Identities=40% Similarity=0.592 Sum_probs=11.9
Q ss_pred HHHhHHHHHHHHHHH
Q 033513 32 REMQSYIEEREREVA 46 (117)
Q Consensus 32 remqsy~eerereva 46 (117)
|||.+|....|++..
T Consensus 71 rEm~~fwkk~eke~~ 85 (139)
T PF13892_consen 71 REMLSFWKKNEKEER 85 (139)
T ss_pred HHHHHHHHHHHHHHH
Confidence 789999988877643
No 37
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=30.59 E-value=1.1e+02 Score=26.47 Aligned_cols=27 Identities=22% Similarity=0.292 Sum_probs=21.0
Q ss_pred hhccccCCCCCCCceEEEEecceehhh
Q 033513 84 LMGTASNQDNQDGALEITVSGEKYRCL 110 (117)
Q Consensus 84 lmgtas~~dnqdgaleitvsgekyrcl 110 (117)
-.||--...+.+|..+|-++|.+|||-
T Consensus 47 ~~~~~~~~~~~~~~~~v~~~g~~~~~~ 73 (512)
T TIGR03689 47 TYGTFLQTAIDDETAEVFTAGRRMRVT 73 (512)
T ss_pred ceEEEEEeccCCCeEEEEeCCceEEEE
Confidence 456655555678889999999999983
No 38
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=30.39 E-value=79 Score=20.00 Aligned_cols=25 Identities=28% Similarity=0.464 Sum_probs=16.2
Q ss_pred hhhhhhhhccccCCCCCCCceEEEEecc
Q 033513 78 EKEKSVLMGTASNQDNQDGALEITVSGE 105 (117)
Q Consensus 78 ekeksvlmgtas~~dnqdgaleitvsge 105 (117)
.++-.-+-+|+++. ||.+.+||+|.
T Consensus 15 ~~~l~~~~~~~~s~---~g~V~V~v~g~ 39 (93)
T PF02575_consen 15 QEELAEIEVTGTSG---DGLVTVTVNGN 39 (93)
T ss_dssp HHHHHHSEEEEEET---CCTEEEEEETT
T ss_pred HHHHhcCEEEEEEC---CCEEEEEEecC
Confidence 33334455666664 57899999885
No 39
>PF06476 DUF1090: Protein of unknown function (DUF1090); InterPro: IPR009468 This family consists of several bacterial proteins of unknown function and is known as YqjC in Escherichia coli.
Probab=30.10 E-value=2e+02 Score=20.33 Aligned_cols=44 Identities=36% Similarity=0.504 Sum_probs=27.3
Q ss_pred hHHHHHHHHHHHHHHHHHH-HHhhhHHHHHHHHHHHhhhhhhhhh
Q 033513 35 QSYIEEREREVAEREAAWK-AELSRREAEIARQEARLKMEKENLE 78 (117)
Q Consensus 35 qsy~eererevaereaawk-aelsrreaei~~qearl~mer~nle 78 (117)
+..|.+.+.+|+||++.-+ |.-+-..-.|.+.+..|.-.+..|.
T Consensus 69 q~ki~~~~~kV~ere~eL~eA~~~G~~~KI~K~~~KL~ea~~eL~ 113 (115)
T PF06476_consen 69 QQKIAEKQQKVAEREAELKEAQAKGDSDKIAKRQKKLAEAKAELK 113 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHh
Confidence 4567777888888876543 2233344567777777766665554
No 40
>KOG4691 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.80 E-value=1.5e+02 Score=24.37 Aligned_cols=73 Identities=32% Similarity=0.434 Sum_probs=45.6
Q ss_pred HhHHHHhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHh--hhhhhhhhhhhhhhhccccCCCCCCCceEEEEecce
Q 033513 29 MKEREMQSYIEEREREVAEREAAWKAELSRREAEIARQEARL--KMEKENLEKEKSVLMGTASNQDNQDGALEITVSGEK 106 (117)
Q Consensus 29 mkeremqsy~eererevaereaawkaelsrreaei~~qearl--~mer~nlekeksvlmgtas~~dnqdgaleitvsgek 106 (117)
-+++|-.+||.|+-+--+|++.|||..-.+ |+...-.|- -.-|+|||.- |+-.-+| .-|- ..-|+--|.|
T Consensus 133 ~~~~E~~~~i~ee~~~~~e~~~a~k~qae~---eVl~~iersknfITReNLea~--Ie~AL~~-p~~y--nfAIdraGNk 204 (227)
T KOG4691|consen 133 QEEREQEQRIAEEQARKAEEVQAWKQQAER---EVLQLIERSKNFITRENLEAR--IEAALDS-PKNY--NFAIDRAGNK 204 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHhhhhhHHhHHHH--HHHHHcC-cccc--chhhcccCCe
Confidence 356788899999999999999999975433 332222222 2467888753 3322222 2222 3457788888
Q ss_pred ehh
Q 033513 107 YRC 109 (117)
Q Consensus 107 yrc 109 (117)
|..
T Consensus 205 y~v 207 (227)
T KOG4691|consen 205 YVV 207 (227)
T ss_pred eec
Confidence 853
No 41
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=29.26 E-value=39 Score=21.42 Aligned_cols=15 Identities=40% Similarity=0.694 Sum_probs=12.7
Q ss_pred CCCCCCceEEEEecc
Q 033513 91 QDNQDGALEITVSGE 105 (117)
Q Consensus 91 ~dnqdgaleitvsge 105 (117)
.....|+.||+|.|+
T Consensus 36 ~~~~~G~Fev~~~g~ 50 (72)
T TIGR02174 36 TPPTTGAFEVTVNGQ 50 (72)
T ss_pred ecCCCcEEEEEECCE
Confidence 455799999999996
No 42
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase; InterPro: IPR019287 This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=29.19 E-value=1.8e+02 Score=22.51 Aligned_cols=17 Identities=29% Similarity=0.612 Sum_probs=12.6
Q ss_pred hhhhhhhhhhhhccccC
Q 033513 74 KENLEKEKSVLMGTASN 90 (117)
Q Consensus 74 r~nlekeksvlmgtas~ 90 (117)
+|...+-.+||+|--|-
T Consensus 64 kdav~rSravl~Gkv~E 80 (156)
T PF10107_consen 64 KDAVKRSRAVLKGKVSE 80 (156)
T ss_pred HHHHHHHHHHHcchhHH
Confidence 45667778999997654
No 43
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=29.00 E-value=54 Score=22.04 Aligned_cols=17 Identities=29% Similarity=0.602 Sum_probs=14.6
Q ss_pred CCCCceEEEEecceehh
Q 033513 93 NQDGALEITVSGEKYRC 109 (117)
Q Consensus 93 nqdgaleitvsgekyrc 109 (117)
.++.....|+.|.-|+|
T Consensus 77 ~~~~~~~~~~~g~aY~C 93 (93)
T PF13698_consen 77 PSGFPTSVTMVGNAYRC 93 (93)
T ss_pred CCCcccceEEEEEEEeC
Confidence 46677789999999999
No 44
>PRK06228 F0F1 ATP synthase subunit epsilon; Validated
Probab=28.86 E-value=2e+02 Score=20.52 Aligned_cols=25 Identities=32% Similarity=0.434 Sum_probs=16.8
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHhh
Q 033513 47 EREAAWKAELSRREAEIARQEARLK 71 (117)
Q Consensus 47 ereaawkaelsrreaei~~qearl~ 71 (117)
+++..-++.|++-|++..||=..|+
T Consensus 105 ~~~~~~r~~~~~le~~~~~~~~~~~ 129 (131)
T PRK06228 105 ERERSVRSALAKLESGFIRRFMELK 129 (131)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3344444578888999888866553
No 45
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=28.12 E-value=60 Score=20.93 Aligned_cols=19 Identities=21% Similarity=0.515 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHhchH
Q 033513 5 IKTVVDKFVQELKEALDAD 23 (117)
Q Consensus 5 ikavv~~fv~~lkeal~ad 23 (117)
++.+|+.|++.+.++|..+
T Consensus 22 ~~~vv~~~~~~i~~~L~~g 40 (94)
T PRK00199 22 VENAVKEILEEMSDALARG 40 (94)
T ss_pred HHHHHHHHHHHHHHHHHcC
Confidence 6778888888888888543
No 46
>PF00649 Copper-fist: Copper fist DNA binding domain; InterPro: IPR001083 Some fungal transcription factors contain an N-terminal domain, the copper fist, which seems to be involved in copper-dependent DNA-binding [, ]. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast [, ]. The copper fist domain, which is similar in structure to metallothionein itself, undergoes a large conformational change on copper-binding that allows DNA-binding. The domain contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet []. Conserved residues form a basic patch that may be important for DNA binding. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0005507 copper ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1CO4_A.
Probab=27.82 E-value=27 Score=21.95 Aligned_cols=12 Identities=50% Similarity=0.982 Sum_probs=9.7
Q ss_pred EEEecceehhhh
Q 033513 100 ITVSGEKYRCLR 111 (117)
Q Consensus 100 itvsgekyrclr 111 (117)
|-++|+||-|-.
T Consensus 2 ili~g~KyAC~~ 13 (40)
T PF00649_consen 2 ILIDGEKYACES 13 (40)
T ss_dssp EEETTEEEEETT
T ss_pred eeECCeEEEhhh
Confidence 568999998864
No 47
>TIGR02588 conserved hypothetical protein TIGR02588. The function of this protein is unknown. It is always found as part of a two-gene operon with TIGR02587, a protein that appears to span the membrane seven times. It is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Sinorhizobium meliloti, and Gloeobacter violaceus, so far, all of which are bacterial.
Probab=27.43 E-value=45 Score=24.72 Aligned_cols=17 Identities=35% Similarity=0.647 Sum_probs=15.0
Q ss_pred CCCCCCCceEEEEecce
Q 033513 90 NQDNQDGALEITVSGEK 106 (117)
Q Consensus 90 ~~dnqdgaleitvsgek 106 (117)
..|.++|.|.|.|+|-|
T Consensus 104 ~~dP~~g~L~irv~gY~ 120 (122)
T TIGR02588 104 RSDPRNGQLRLRVAGYK 120 (122)
T ss_pred ccCcccCeEEEEEEecc
Confidence 57899999999999954
No 48
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=27.34 E-value=63 Score=20.66 Aligned_cols=19 Identities=16% Similarity=0.396 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHhchH
Q 033513 5 IKTVVDKFVQELKEALDAD 23 (117)
Q Consensus 5 ikavv~~fv~~lkeal~ad 23 (117)
++++++.|++.+.++|..+
T Consensus 22 v~~vv~~~~~~i~~~L~~g 40 (94)
T TIGR00988 22 VEDAVKTMLEHMASALAQG 40 (94)
T ss_pred HHHHHHHHHHHHHHHHHcC
Confidence 5778888888888887643
No 49
>TIGR00103 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium.
Probab=26.97 E-value=1.2e+02 Score=20.68 Aligned_cols=39 Identities=18% Similarity=0.358 Sum_probs=21.3
Q ss_pred HHHHHHhhhhhhhhhhhhhhhhccccCCCCCCCceEEEEecc
Q 033513 64 ARQEARLKMEKENLEKEKSVLMGTASNQDNQDGALEITVSGE 105 (117)
Q Consensus 64 ~~qearl~mer~nlekeksvlmgtas~~dnqdgaleitvsge 105 (117)
.+|-.++.-+-+++.+|-.-.--|+++ .+|.+.||++|.
T Consensus 11 ~kqaq~mQ~k~~~~q~eL~~~~v~g~s---ggGlV~V~~~G~ 49 (102)
T TIGR00103 11 MKQAQQMQEKMKKLQEEIAQFEVTGKS---GAGLVTVTINGN 49 (102)
T ss_pred HHHHHHHHHHHHHHHHHHhccEEEEEE---CCCEEEEEEEcC
Confidence 334334444444444444333334433 468999999996
No 50
>PF05300 DUF737: Protein of unknown function (DUF737); InterPro: IPR007964 This family consists of several uncharacterised mammalian proteins of unknown function.
Probab=26.62 E-value=3e+02 Score=21.23 Aligned_cols=18 Identities=33% Similarity=0.494 Sum_probs=8.0
Q ss_pred HHHHhhhHHHHHHHHHHH
Q 033513 52 WKAELSRREAEIARQEAR 69 (117)
Q Consensus 52 wkaelsrreaei~~qear 69 (117)
|--+|..+|+++.++.+=
T Consensus 135 la~qLe~ke~el~~~d~f 152 (187)
T PF05300_consen 135 LARQLEEKEAELKKQDAF 152 (187)
T ss_pred HHHHHHhhHHHHHHHHHH
Confidence 333444444444444443
No 51
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=26.41 E-value=76 Score=19.49 Aligned_cols=18 Identities=33% Similarity=0.593 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHhch
Q 033513 5 IKTVVDKFVQELKEALDA 22 (117)
Q Consensus 5 ikavv~~fv~~lkeal~a 22 (117)
+++|++.|+..+.++|..
T Consensus 21 v~~vl~~~~~~i~~~L~~ 38 (90)
T PF00216_consen 21 VEAVLDALFDVIKEALKE 38 (90)
T ss_dssp HHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 577888888888888754
No 52
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=25.35 E-value=1.7e+02 Score=27.98 Aligned_cols=40 Identities=43% Similarity=0.631 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhh--hhhhhhhhh
Q 033513 41 REREVAEREAAWKAELSRREAEIARQEARLKM--EKENLEKEK 81 (117)
Q Consensus 41 rerevaereaawkaelsrreaei~~qearl~m--er~nlekek 81 (117)
|.||-.|||.--+|..-|.|.|-.+.| ||+| +|..||.|+
T Consensus 628 RirE~rerEqR~~a~~ERee~eRl~~e-rlrle~qRQrLEREr 669 (940)
T KOG4661|consen 628 RIREEREREQRRKAAVEREELERLKAE-RLRLERQRQRLERER 669 (940)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 445555566666666655555544332 3333 344555554
No 53
>PTZ00316 profilin; Provisional
Probab=25.23 E-value=29 Score=26.32 Aligned_cols=12 Identities=33% Similarity=0.559 Sum_probs=11.3
Q ss_pred EEEecceehhhh
Q 033513 100 ITVSGEKYRCLR 111 (117)
Q Consensus 100 itvsgekyrclr 111 (117)
|++.|+||-|+|
T Consensus 62 i~l~G~KY~~lr 73 (150)
T PTZ00316 62 VTIYGVKFFGLQ 73 (150)
T ss_pred EEEcceEEEEEE
Confidence 899999999997
No 54
>PF10252 PP28: Casein kinase substrate phosphoprotein PP28; InterPro: IPR019380 This domain is a region of 70 residues conserved in proteins from plants to humans and contains a serine/arginine rich motif. In rats the full protein is a casein kinase substrate, and this region contains phosphorylation sites for both cAMP-dependent protein kinase and casein kinase II [].
Probab=24.60 E-value=64 Score=22.58 Aligned_cols=19 Identities=58% Similarity=0.742 Sum_probs=10.3
Q ss_pred HHHhhhHHHH-HHHHHHHhh
Q 033513 53 KAELSRREAE-IARQEARLK 71 (117)
Q Consensus 53 kaelsrreae-i~~qearl~ 71 (117)
..+|||||.| |.+|.++-+
T Consensus 22 ~~~lSRRERE~iekq~A~er 41 (82)
T PF10252_consen 22 PPELSRREREEIEKQRARER 41 (82)
T ss_pred ccccchhHHHHHHHHHHHHH
Confidence 4566776665 445554443
No 55
>PF06391 MAT1: CDK-activating kinase assembly factor MAT1; InterPro: IPR015877 MAT1 (menage a trois 1) is a RING finger protein with a characteristic C3HC4 motif located in the N-terminal domain. This entry represents the central region of MAT1. MAT1 stabilises the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex which then goes on to activate many of the CDK enzymes intimately involved in the cell cycle []. CDK7 forms a stable complex with cyclin H and MAT1 in vivo only when phosphorylated on either one of two residues (Ser164 or Thr170) in its T-loop. The requirement for MAT1 for the activation of CAK can be by-passed by the phosphorylation of CDK7 on the T-loop. The two mechanisms for CDK7 complex stabilisation and activation (MAT1 addition and T-loop phosphorylation), which can operate independently in vitro, actually cooperate under physiological conditions to maintain complex integrity. With prolonged exposure to elevated temperature, dissociation to monomeric subunits occurs in vivo when CDK7 is dephosphorylated, even in the presence of MAT1 []. The Cyclin H-MAT1-CDK7 complex also forms part of TFIIH, a multiprotein complex required for both transcription and DNA repair.; GO: 0007049 cell cycle, 0005634 nucleus; PDB: 1G25_A.
Probab=24.42 E-value=25 Score=27.45 Aligned_cols=24 Identities=42% Similarity=0.706 Sum_probs=0.0
Q ss_pred hchHHHHHHHh-----------HHHHhHHHHHHHH
Q 033513 20 LDADIQDRIMK-----------EREMQSYIEERER 43 (117)
Q Consensus 20 l~adiqdrimk-----------eremqsy~eerer 43 (117)
=+.||+.|+++ -++.+.|||++|-
T Consensus 18 kEv~iRkrV~~ifNk~eeDF~~l~~YNdYLE~vE~ 52 (200)
T PF06391_consen 18 KEVDIRKRVLKIFNKREEDFESLREYNDYLEEVED 52 (200)
T ss_dssp -----------------------------------
T ss_pred HHHHHHHHHHHHHccChhhcCCHHHHHHHHHHHHH
Confidence 35677777776 3677888888774
No 56
>PF09058 L27_1: L27_1; InterPro: IPR015143 The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices []. ; PDB: 3LRA_A 1RSO_A.
Probab=23.95 E-value=56 Score=22.03 Aligned_cols=21 Identities=38% Similarity=0.597 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHhchHHHH
Q 033513 5 IKTVVDKFVQELKEALDADIQD 26 (117)
Q Consensus 5 ikavv~~fv~~lkeal~adiqd 26 (117)
|..|+..|-..|-.|| .||||
T Consensus 34 ierli~ifkS~LF~AL-LDIqe 54 (64)
T PF09058_consen 34 IERLINIFKSRLFQAL-LDIQE 54 (64)
T ss_dssp HHHHHHHHHSHHHHHH-HHHCC
T ss_pred HHHHHHHHHHHHHHHH-HHHHH
Confidence 4556666666666666 55554
No 57
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=23.87 E-value=24 Score=25.42 Aligned_cols=11 Identities=36% Similarity=1.069 Sum_probs=8.6
Q ss_pred ecceehhhhhh
Q 033513 103 SGEKYRCLRFA 113 (117)
Q Consensus 103 sgekyrclrf~ 113 (117)
.|+.|||+|-.
T Consensus 53 kGqayRCIrIn 63 (108)
T smart00099 53 KGSGFRCIRIN 63 (108)
T ss_pred CCcceEEEEEC
Confidence 58889999853
No 58
>TIGR01932 hflC HflC protein. HflK and HflC are paralogs encoded by tandem genes in Proteobacteria, spirochetes, and some other bacterial lineages. The HflKC complex is anchored in the membrane and exposed to the periplasm. The complex is not active as a protease, but rather binds to and appears to modulate the ATP-dependent protease FtsH. The overall function of HflKC is not fully described.//Regulation of FtsH protease appears to be negative (PubMed:8947034, PubMed:96367)
Probab=23.74 E-value=3.6e+02 Score=21.13 Aligned_cols=9 Identities=44% Similarity=0.667 Sum_probs=4.3
Q ss_pred HHHHHhHHH
Q 033513 25 QDRIMKERE 33 (117)
Q Consensus 25 qdrimkere 33 (117)
.+++..+||
T Consensus 214 ~~~~~aere 222 (317)
T TIGR01932 214 YNRMRSERE 222 (317)
T ss_pred HHHHHHHHH
Confidence 344445554
No 59
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=23.19 E-value=83 Score=20.44 Aligned_cols=19 Identities=32% Similarity=0.660 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHhchH
Q 033513 5 IKTVVDKFVQELKEALDAD 23 (117)
Q Consensus 5 ikavv~~fv~~lkeal~ad 23 (117)
++++++.|+..+.++|..+
T Consensus 23 v~~vl~~~~~~i~~~L~~g 41 (99)
T PRK00285 23 AKELVELFFEEIRDALENG 41 (99)
T ss_pred HHHHHHHHHHHHHHHHHcC
Confidence 5778888888888887644
No 60
>KOG0245 consensus Kinesin-like protein [Cytoskeleton]
Probab=23.16 E-value=2.5e+02 Score=27.98 Aligned_cols=27 Identities=30% Similarity=0.550 Sum_probs=21.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 033513 35 QSYIEEREREVAEREAAWKAELSRREA 61 (117)
Q Consensus 35 qsy~eererevaereaawkaelsrrea 61 (117)
-.-|+|+|++.||-...|...|-.-|+
T Consensus 404 ~~~L~E~Ek~mael~etW~EKl~~aEa 430 (1221)
T KOG0245|consen 404 RERLQETEKIMAELNETWEEKLREAEA 430 (1221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345899999999999999987754443
No 61
>smart00412 Cu_FIST Copper-Fist. binds DNA only in present of copper or silver
Probab=22.33 E-value=37 Score=21.22 Aligned_cols=12 Identities=33% Similarity=0.852 Sum_probs=9.4
Q ss_pred EEEecceehhhh
Q 033513 100 ITVSGEKYRCLR 111 (117)
Q Consensus 100 itvsgekyrclr 111 (117)
|-|.|+||-|-.
T Consensus 1 v~i~g~K~aC~~ 12 (39)
T smart00412 1 VVINGVKYACES 12 (39)
T ss_pred CeECCceecCHH
Confidence 458999998854
No 62
>PRK14626 hypothetical protein; Provisional
Probab=22.19 E-value=1.7e+02 Score=20.59 Aligned_cols=12 Identities=17% Similarity=0.410 Sum_probs=10.2
Q ss_pred CCceEEEEecce
Q 033513 95 DGALEITVSGEK 106 (117)
Q Consensus 95 dgaleitvsgek 106 (117)
+|.++||++|..
T Consensus 39 gG~VkV~~nG~~ 50 (110)
T PRK14626 39 GGMVKVVSNGLG 50 (110)
T ss_pred CcEEEEEEECCc
Confidence 589999999963
No 63
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=22.18 E-value=93 Score=19.24 Aligned_cols=19 Identities=37% Similarity=0.557 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHhchH
Q 033513 5 IKTVVDKFVQELKEALDAD 23 (117)
Q Consensus 5 ikavv~~fv~~lkeal~ad 23 (117)
+++|++.|...+.++|..+
T Consensus 21 v~~vl~~l~~~i~~~L~~g 39 (90)
T smart00411 21 AKAAVDAFLEIITEALKKG 39 (90)
T ss_pred HHHHHHHHHHHHHHHHhCC
Confidence 5678888888888877653
No 64
>TIGR03166 alt_F1F0_F1_eps alternate F1F0 ATPase, F1 subunit epsilon. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 epsilon subunit of this apparent second ATP synthase.
Probab=22.00 E-value=2.6e+02 Score=19.62 Aligned_cols=27 Identities=19% Similarity=0.335 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 033513 40 EREREVAEREAAWKAELSRREAEIARQ 66 (117)
Q Consensus 40 ererevaereaawkaelsrreaei~~q 66 (117)
+..++..|.+..-+..++|-|++..||
T Consensus 95 ~~~~~~~~~~~~~r~~~~~l~~~~~r~ 121 (122)
T TIGR03166 95 QEFLTLDEQERSARSAMARLESDFIRR 121 (122)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 333344555566677788888887765
No 65
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=21.92 E-value=90 Score=20.43 Aligned_cols=19 Identities=16% Similarity=0.340 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHhchH
Q 033513 5 IKTVVDKFVQELKEALDAD 23 (117)
Q Consensus 5 ikavv~~fv~~lkeal~ad 23 (117)
++++|+.|++.+.++|..+
T Consensus 21 ~~~~v~~~~~~i~~~L~~g 39 (90)
T PRK10753 21 AKAALESTLAAITESLKEG 39 (90)
T ss_pred HHHHHHHHHHHHHHHHHcC
Confidence 6788889988888888543
No 66
>TIGR03543 divI1A_rptt_fam DivIVA domain repeat protein. Members of this protein family contain two full and two partial repeats of a domain found at the N-terminus of Bacillus subtilis cell-division initiation protein DivIVA. The portion repeated four times in these proteins includes the motif GYxxxxVD.
Probab=21.44 E-value=3.4e+02 Score=21.03 Aligned_cols=59 Identities=27% Similarity=0.489 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHhchH--------HHHHH-------HhHHHHhHHHHHHHH---------HHHHH-HHHHHHHhhhHHH
Q 033513 7 TVVDKFVQELKEALDAD--------IQDRI-------MKEREMQSYIEERER---------EVAER-EAAWKAELSRREA 61 (117)
Q Consensus 7 avv~~fv~~lkeal~ad--------iqdri-------mkeremqsy~eerer---------evaer-eaawkaelsrrea 61 (117)
.=||.|+..+.++++-. |+.-- -.+-....||..=|. .+|+. +.+|++.+..+-.
T Consensus 14 ~~VD~fl~r~~~~~e~~~~~lt~~~VR~~~F~~~rgGY~~~~VDa~LdRlE~a~~~rer~~~ia~~G~~aW~a~~~~~~~ 93 (178)
T TIGR03543 14 AQVDAFLERARAAYDNEGGNLTSHDIRNVAFDLRKGGYSPAQVDAALDRLERAFADKERTWEIAQHGRVAWKAKTEKLYQ 93 (178)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHhhcCccCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHH
Confidence 34677777777777632 22211 123344445554444 44443 4688888776665
Q ss_pred HHHH
Q 033513 62 EIAR 65 (117)
Q Consensus 62 ei~~ 65 (117)
.+.-
T Consensus 94 ~l~~ 97 (178)
T TIGR03543 94 EIQD 97 (178)
T ss_pred HHHH
Confidence 5543
No 67
>PRK05641 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=21.42 E-value=58 Score=23.94 Aligned_cols=16 Identities=19% Similarity=0.582 Sum_probs=13.6
Q ss_pred CCCceEEEEecceehh
Q 033513 94 QDGALEITVSGEKYRC 109 (117)
Q Consensus 94 qdgaleitvsgekyrc 109 (117)
+++.+.|||+|..|.+
T Consensus 21 ~~~~~~itvnG~~y~V 36 (153)
T PRK05641 21 GPGKFRVSFEGKTYEV 36 (153)
T ss_pred cCccEEEEECCEEEEE
Confidence 4778999999999964
No 68
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=21.39 E-value=2e+02 Score=18.82 Aligned_cols=25 Identities=48% Similarity=0.591 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHH
Q 033513 44 EVAEREAAWKAELSRREAEIARQEA 68 (117)
Q Consensus 44 evaereaawkaelsrreaei~~qea 68 (117)
|..+|-+.-++|+-|-++++.+..+
T Consensus 25 EL~~RIa~L~aEI~R~~~~~~~K~a 49 (59)
T PF06698_consen 25 ELEERIALLEAEIARLEAAIAKKSA 49 (59)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666777777777777765544
No 69
>PF14703 DUF4463: Domain of unknown function (DUF4463)
Probab=21.18 E-value=1.7e+02 Score=17.82 Aligned_cols=26 Identities=31% Similarity=0.419 Sum_probs=20.2
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHhh
Q 033513 32 REMQSYIEEREREVAEREAAWKAELS 57 (117)
Q Consensus 32 remqsy~eererevaereaawkaels 57 (117)
..++.-+++|+.-+...|.||-.-+.
T Consensus 6 ~~L~~Lv~~R~~~~~kLE~a~~~~~~ 31 (85)
T PF14703_consen 6 SKLEKLVEEREKAVRKLESAESKYLK 31 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35677888999999999999865543
No 70
>PF01813 ATP-synt_D: ATP synthase subunit D ; InterPro: IPR002699 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents the D subunit found in V1 and A1 complexes of V- and A-ATPases, respectively. Subunit D appears to be located in the central stalk, whereas subunits E and G form part of the peripheral stalk connecting V1 and V0. This subunit is the most likely homologue to the gamma subunit of the F1 complex in F-ATPases, which undergoes rotation during ATP hydrolysis and serves an essential function in rotary catalysis [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0042626 ATPase activity, coupled to transmembrane movement of substances, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 3A5C_G 3A5D_G 3J0J_G 3AON_A.
Probab=20.85 E-value=82 Score=22.87 Aligned_cols=14 Identities=50% Similarity=0.672 Sum_probs=11.0
Q ss_pred HHHhHHHHHHHHHH
Q 033513 32 REMQSYIEEREREV 45 (117)
Q Consensus 32 remqsy~eererev 45 (117)
+-++++|+|+|||-
T Consensus 173 k~I~~~LeE~EREe 186 (196)
T PF01813_consen 173 KYIRSELEEREREE 186 (196)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 55788999998874
No 71
>COG5019 CDC3 Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]
Probab=20.72 E-value=4.6e+02 Score=22.70 Aligned_cols=52 Identities=27% Similarity=0.348 Sum_probs=29.5
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHhh----hHHHHHHHHHHHhhhhhhhhhhhhh
Q 033513 31 EREMQSYIEEREREVAEREAAWKAELS----RREAEIARQEARLKMEKENLEKEKS 82 (117)
Q Consensus 31 eremqsy~eererevaereaawkaels----rreaei~~qearl~mer~nlekeks 82 (117)
+|+|+...+++=++-..+..+|...|. ....++.++...++-...+|+++|+
T Consensus 315 ~~~~k~~~~~ki~~~e~~l~~~E~~l~~e~~~~n~~Le~~~~~l~~~e~~l~~~~~ 370 (373)
T COG5019 315 ERELKKKFTEKIREKEKRLEELEQNLIEERKELNSKLEEIQKKLEDLEKRLEKLKS 370 (373)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 456666666655555555555555443 3344555566666666666666554
No 72
>PF03154 Atrophin-1: Atrophin-1 family; InterPro: IPR002951 Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA (OMIM:125370) is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins [, ]. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity [].. This entry includes Atrophin-1 and related proteins.
Probab=20.39 E-value=82 Score=30.39 Aligned_cols=10 Identities=70% Similarity=0.989 Sum_probs=4.5
Q ss_pred HHHHHHHHHH
Q 033513 40 EREREVAERE 49 (117)
Q Consensus 40 ererevaere 49 (117)
.||||.-|||
T Consensus 718 ~rErelrERE 727 (982)
T PF03154_consen 718 ARERELRERE 727 (982)
T ss_pred hhhhhhhhhh
Confidence 3444444444
No 73
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=20.31 E-value=1.2e+02 Score=19.73 Aligned_cols=18 Identities=33% Similarity=0.652 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHhch
Q 033513 5 IKTVVDKFVQELKEALDA 22 (117)
Q Consensus 5 ikavv~~fv~~lkeal~a 22 (117)
++++++.|+..|.++|..
T Consensus 22 v~~vv~~~~~~i~~~L~~ 39 (96)
T TIGR00987 22 AKELVELFFEEIRRALEN 39 (96)
T ss_pred HHHHHHHHHHHHHHHHHc
Confidence 677888888888888754
No 74
>PRK14435 acylphosphatase; Provisional
Probab=20.08 E-value=54 Score=21.72 Aligned_cols=28 Identities=32% Similarity=0.488 Sum_probs=20.0
Q ss_pred hhccccCCCCCCCceEEEEecceehhhhhh
Q 033513 84 LMGTASNQDNQDGALEITVSGEKYRCLRFA 113 (117)
Q Consensus 84 lmgtas~~dnqdgaleitvsgekyrclrf~ 113 (117)
|-|.+.|.+ ||.+||.+.|+.-..-.|-
T Consensus 30 l~G~V~N~~--dG~Vei~~~G~~~~i~~f~ 57 (90)
T PRK14435 30 VKGYVMNMD--DGSVFIHAEGDENALRRFL 57 (90)
T ss_pred CEEEEEECC--CCCEEEEEEECHHHHHHHH
Confidence 567776654 5999999999875544443
No 75
>PF06825 HSBP1: Heat shock factor binding protein 1; InterPro: IPR009643 Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response [].; PDB: 3CI9_A.
Probab=20.02 E-value=2.6e+02 Score=18.00 Aligned_cols=43 Identities=19% Similarity=0.397 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHhchHHHHHHHhHHHHhHHHHHHHHHHHH
Q 033513 5 IKTVVDKFVQELKEALDADIQDRIMKEREMQSYIEEREREVAE 47 (117)
Q Consensus 5 ikavv~~fv~~lkeal~adiqdrimkeremqsy~eererevae 47 (117)
+-++|++.++++..-...=-..=+-|=-+|-+.|.+-|+.+++
T Consensus 4 lt~~v~~lL~qmq~kFq~mS~~I~~riDeM~~RIDdLE~si~d 46 (54)
T PF06825_consen 4 LTAFVQNLLQQMQDKFQTMSDQILGRIDEMSSRIDDLEKSIAD 46 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 4567788877777655432222233446777777777666543
Done!