Query 034131
Match_columns 103
No_of_seqs 101 out of 125
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 10:06:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034131.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034131hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3465 Signal recognition par 100.0 4.2E-40 9.1E-45 222.0 9.5 85 1-85 1-85 (86)
2 PF05486 SRP9-21: Signal recog 100.0 6.2E-34 1.3E-38 189.6 9.2 72 3-74 1-79 (79)
3 cd07268 Glo_EDI_BRP_like_4 Thi 87.1 1 2.2E-05 33.6 3.9 52 8-59 85-144 (149)
4 cd05992 PB1 The PB1 domain is 80.8 3.8 8.2E-05 25.5 4.1 35 4-40 20-54 (81)
5 smart00666 PB1 PB1 domain. Pho 79.6 4.5 9.7E-05 25.4 4.1 33 5-39 21-53 (81)
6 PF12392 DUF3656: Collagenase 78.4 15 0.00032 25.1 6.8 53 2-54 1-55 (122)
7 cd06410 PB1_UP2 Uncharacterize 76.5 4.6 9.9E-05 27.7 3.7 39 5-46 33-73 (97)
8 PF00564 PB1: PB1 domain; Int 75.0 7.1 0.00015 24.4 4.1 36 5-42 22-57 (84)
9 PRK11700 hypothetical protein; 71.5 8.7 0.00019 29.6 4.5 52 8-59 123-181 (187)
10 cd06402 PB1_p62 The PB1 domain 69.3 10 0.00023 25.7 4.1 36 5-41 27-62 (87)
11 PF04471 Mrr_cat: Restriction 66.3 8 0.00017 24.7 3.0 65 6-71 5-75 (115)
12 cd06398 PB1_Joka2 The PB1 doma 65.0 15 0.00034 24.7 4.3 39 6-45 26-64 (91)
13 PF09981 DUF2218: Uncharacteri 60.7 47 0.001 22.1 6.4 48 34-81 39-86 (89)
14 cd06903 lectin_EMP46_EMP47 EMP 58.5 20 0.00043 27.5 4.3 33 18-51 147-179 (215)
15 PF06185 YecM: YecM protein; 56.7 14 0.00031 28.3 3.2 53 6-58 116-180 (185)
16 cd06396 PB1_NBR1 The PB1 domai 52.0 36 0.00077 22.8 4.2 37 5-45 22-58 (81)
17 PRK13516 gamma-glutamyl:cystei 49.5 35 0.00076 28.2 4.7 66 2-74 196-265 (373)
18 PF13180 PDZ_2: PDZ domain; PD 48.4 65 0.0014 20.0 5.0 36 4-43 46-81 (82)
19 PHA02745 hypothetical protein; 43.9 14 0.00031 29.8 1.5 43 20-62 132-179 (265)
20 PF04502 DUF572: Family of unk 42.3 22 0.00048 28.8 2.4 21 25-46 74-94 (324)
21 cd06409 PB1_MUG70 The MUG70 pr 42.3 70 0.0015 21.5 4.5 41 6-46 22-63 (86)
22 cd06401 PB1_TFG The PB1 domain 41.5 68 0.0015 21.6 4.3 34 6-39 22-56 (81)
23 cd06896 PX_PI3K_C2_gamma The p 41.5 46 0.00099 23.4 3.6 60 4-80 30-89 (101)
24 cd01231 PH_Lnk LNK-family Plec 41.4 44 0.00096 23.8 3.5 27 34-61 73-99 (107)
25 PF12988 DUF3872: Domain of un 40.3 35 0.00075 25.2 3.0 26 23-48 63-88 (137)
26 cd06404 PB1_aPKC PB1 domain is 39.5 65 0.0014 21.8 4.0 34 5-39 20-53 (83)
27 PF02290 SRP14: Signal recogni 37.4 58 0.0013 21.9 3.5 57 6-63 2-79 (93)
28 PF12021 DUF3509: Protein of u 37.3 1.4E+02 0.0029 20.5 6.1 60 14-74 4-66 (94)
29 cd06403 PB1_Par6 The PB1 domai 36.9 81 0.0018 21.3 4.1 39 4-45 21-59 (80)
30 PF10298 WhiA_N: WhiA N-termin 36.6 14 0.0003 24.0 0.4 28 44-71 22-49 (86)
31 PRK10721 hypothetical protein; 34.3 18 0.00039 23.6 0.6 26 6-31 4-29 (66)
32 cd06407 PB1_NLP A PB1 domain i 34.0 1.3E+02 0.0027 19.8 4.7 39 6-45 21-59 (82)
33 KOG1604 Predicted mutarotase [ 32.1 81 0.0018 26.6 4.2 35 20-54 260-294 (353)
34 COG3102 Uncharacterized protei 31.3 54 0.0012 25.3 2.9 29 27-55 143-177 (185)
35 PF10480 ICAP-1_inte_bdg: Beta 30.0 2.5E+02 0.0055 22.0 6.4 37 37-73 154-194 (200)
36 PF01547 SBP_bac_1: Bacterial 28.7 61 0.0013 23.5 2.7 21 4-24 132-152 (315)
37 TIGR02664 nitr_red_assoc conse 27.8 1.2E+02 0.0026 22.5 4.1 39 47-85 45-83 (145)
38 PF07302 AroM: AroM protein; 27.5 87 0.0019 24.5 3.5 42 2-62 159-200 (221)
39 PF02120 Flg_hook: Flagellar h 26.5 1.6E+02 0.0036 18.1 5.0 54 24-77 12-68 (85)
40 PF08796 DUF1797: Protein of u 26.1 1.9E+02 0.0042 18.8 4.6 36 25-63 27-62 (67)
41 PF02375 JmjN: jmjN domain; I 25.8 19 0.00041 20.4 -0.3 13 1-13 1-13 (34)
42 CHL00191 ycf61 DNA-directed RN 24.9 54 0.0012 22.0 1.7 25 6-30 9-33 (76)
43 PF05430 Methyltransf_30: S-ad 24.8 1.2E+02 0.0026 21.3 3.5 35 9-43 2-36 (124)
44 COG2879 Uncharacterized small 24.6 1.1E+02 0.0024 20.0 3.0 22 58-79 4-25 (65)
45 PF14508 GH97_N: Glycosyl-hydr 24.2 1.3E+02 0.0028 23.3 4.0 30 28-57 83-115 (259)
46 cd06397 PB1_UP1 Uncharacterize 24.1 1.7E+02 0.0036 19.9 3.9 34 3-38 18-51 (82)
47 PF07906 Toxin_15: ShET2 enter 23.3 1.7E+02 0.0038 23.9 4.6 42 21-62 146-191 (284)
48 COG2975 Uncharacterized protei 23.3 71 0.0015 20.7 1.9 19 6-24 2-20 (64)
49 KOG2826 Actin-related protein 22.7 1.2E+02 0.0026 24.9 3.5 32 25-57 140-171 (301)
50 COG2443 Sss1 Preprotein transl 22.6 64 0.0014 20.9 1.6 11 5-15 28-38 (65)
51 COG3114 CcmD Heme exporter pro 22.2 46 0.00099 21.8 0.9 11 2-12 1-11 (67)
52 COG3144 FliK Flagellar hook-le 22.1 5E+02 0.011 22.2 7.8 69 6-75 281-352 (417)
53 PF03646 FlaG: FlaG protein; 21.6 2.5E+02 0.0055 18.5 8.0 63 8-70 37-104 (107)
54 TIGR02048 gshA_cyano glutamate 21.3 2E+02 0.0042 24.0 4.7 63 1-70 175-246 (376)
55 PF03421 YopJ: YopJ Serine/Thr 21.0 2.6E+02 0.0057 20.8 4.9 47 2-49 50-109 (177)
56 PF09655 Nitr_red_assoc: Conse 20.4 2E+02 0.0044 21.3 4.1 39 47-85 45-83 (144)
57 COG1580 FliL Flagellar basal b 20.4 2.9E+02 0.0063 20.4 5.0 45 47-91 83-131 (159)
58 PF04384 Fe-S_assembly: Iron-s 20.3 85 0.0018 20.3 1.9 18 6-23 2-19 (64)
No 1
>KOG3465 consensus Signal recognition particle, subunit Srp9 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.2e-40 Score=221.96 Aligned_cols=85 Identities=56% Similarity=0.886 Sum_probs=83.1
Q ss_pred CccccCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEEEEecCCceEEEeccchHHHHHHHHHHHHHHHHHhCCCCCC
Q 034131 1 MVYVTSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVTDNKECLKFKTDQAQDAKKMEKLNNIFFALMARGPDVD 80 (103)
Q Consensus 1 Mvy~~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLKvTDd~~cLkYkT~ka~dv~rle~l~~~l~~~Ma~~p~~~ 80 (103)
|||++||+||..||+.||.|||.+||++|||||++|.|+||+|||.+||||+||++||++|||+|++.|+++|++.|+.+
T Consensus 1 Mvy~qtwdEF~~ase~L~~A~P~~~RlvmKYrh~~g~l~lkvtd~~~CLkYkTdqaqdlkKleki~s~L~~~m~~~~~~~ 80 (86)
T KOG3465|consen 1 MVYLQTWDEFFTASESLYLANPEKTRLVMKYRHSKGSLVLKVTDNVECLKYKTDQAQDLKKLEKIASKLSRLMAGKPEQE 80 (86)
T ss_pred CceeeeHHHHHHHHHHHHhcCccceEEEEEEecCCCcEEEEeecceeeeeechhhhHHHHHHHHHHHHHHHHhccCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Ccccc
Q 034131 81 LSEVT 85 (103)
Q Consensus 81 l~~~~ 85 (103)
+...+
T Consensus 81 v~~~t 85 (86)
T KOG3465|consen 81 VVAST 85 (86)
T ss_pred eeecC
Confidence 88665
No 2
>PF05486 SRP9-21: Signal recognition particle 9 kDa protein (SRP9); InterPro: IPR008832 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the 9 kDa SRP9 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0045900 negative regulation of translational elongation, 0048500 signal recognition particle; PDB: 1E8O_A 1RY1_C.
Probab=100.00 E-value=6.2e-34 Score=189.57 Aligned_cols=72 Identities=53% Similarity=0.900 Sum_probs=64.5
Q ss_pred cccCHHHHHHHHHHHHhhCCCcceEEEeeec-----CCCeEEEEEecCCc--eEEEeccchHHHHHHHHHHHHHHHHHh
Q 034131 3 YVTSWDEFVGRSVQLYKADPQSTRYCMKYRH-----CDGKLVLKVTDNKE--CLKFKTDQAQDAKKMEKLNNIFFALMA 74 (103)
Q Consensus 3 y~~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~-----~~g~LvLKvTDd~~--cLkYkT~ka~dv~rle~l~~~l~~~Ma 74 (103)
|+++||||+++|++||+++|.+|||+|||+| ++|.|+||+|||.. ||||+|++++||+||+++++.||++||
T Consensus 1 Y~~~~deF~~~s~~L~~a~P~~TR~~~kY~~~~~~~~~~~l~lK~td~~~g~clKykT~k~~dv~Rl~~~~g~l~~~ma 79 (79)
T PF05486_consen 1 YVKSWDEFIEQSEKLYEANPSTTRYSIKYRHPSKKPPTGKLVLKTTDPHSGVCLKYKTDKAKDVSRLESFLGPLGRSMA 79 (79)
T ss_dssp -ESHHHHHHHHHHHHHHH-TTT-EEEEEBBT-----TTTBEEEEEE-SS---EEEEEE-SGGGHHHHHHHHHHHHHHH-
T ss_pred CCCCHHHHHHHHHHHHHhCCCceEEEEEEecccccCCCceEEEEEeCCCceeEEEEEeCHHHHHHHHHHHHHHHHHhcC
Confidence 8999999999999999999999999999999 99999999999987 999999999999999999999999997
No 3
>cd07268 Glo_EDI_BRP_like_4 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=87.13 E-value=1 Score=33.58 Aligned_cols=52 Identities=13% Similarity=0.238 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHhhCCCc--ceEEEeeecCCC------eEEEEEecCCceEEEeccchHHH
Q 034131 8 DEFVGRSVQLYKADPQS--TRYCMKYRHCDG------KLVLKVTDNKECLKFKTDQAQDA 59 (103)
Q Consensus 8 ~eF~~~s~~Ly~a~P~k--TRy~~KYr~~~g------~LvLKvTDd~~cLkYkT~ka~dv 59 (103)
++..+.+..|+...+.- .-+.+|.+.|.| .-+|-++++.+|+||---...++
T Consensus 85 ~~~~~~~~~ll~~~~~~~~~gikvK~SsPkge~ERL~NPTvAv~~~~i~IK~HP~slk~I 144 (149)
T cd07268 85 QESIELRAPLLLKSPPLLNAGLKVKFSSPKGEGERLPNPTIAFSFGGICIKLHPHSLEEI 144 (149)
T ss_pred chHHHHHHHhhhcccccccCCcEEEecCCCcccccCCCCcEEEEECCEEEEEcCcCHHHH
Confidence 34555666777765443 469999999988 88999999999999976665543
No 4
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=80.78 E-value=3.8 Score=25.50 Aligned_cols=35 Identities=23% Similarity=0.465 Sum_probs=29.4
Q ss_pred ccCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEE
Q 034131 4 VTSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVL 40 (103)
Q Consensus 4 ~~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvL 40 (103)
-.||+++.......|...+ ..+.+||...+|.+|.
T Consensus 20 ~~s~~~L~~~i~~~~~~~~--~~~~l~y~D~e~d~v~ 54 (81)
T cd05992 20 SISFEDLRSKIAEKFGLDA--VSFKLKYPDEDGDLVT 54 (81)
T ss_pred CCCHHHHHHHHHHHhCCCC--CcEEEEeeCCCCCEEE
Confidence 3589999999999998765 8999999999986644
No 5
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=79.55 E-value=4.5 Score=25.35 Aligned_cols=33 Identities=24% Similarity=0.556 Sum_probs=27.0
Q ss_pred cCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEE
Q 034131 5 TSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLV 39 (103)
Q Consensus 5 ~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~Lv 39 (103)
.+|++|..+....|.-.+ ..+.+||...+|.+|
T Consensus 21 ~s~~dL~~~i~~~~~~~~--~~~~l~Y~Dedgd~v 53 (81)
T smart00666 21 ISFEDLRSKVAKRFGLDN--QSFTLKYQDEDGDLV 53 (81)
T ss_pred CCHHHHHHHHHHHhCCCC--CCeEEEEECCCCCEE
Confidence 479999999999998655 568899998888654
No 6
>PF12392 DUF3656: Collagenase ; InterPro: IPR020988 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This domain is found in a number of proteins belonging to the MEROPS peptidase family U32. Peptidase family U32 contains endopeptidases, including collagenase, from bacteria.
Probab=78.42 E-value=15 Score=25.13 Aligned_cols=53 Identities=17% Similarity=0.227 Sum_probs=43.9
Q ss_pred ccccCHHHHHHHHHHHHhhCCCcceEEEeeec-CCCeEEEEEe-cCCceEEEecc
Q 034131 2 VYVTSWDEFVGRSVQLYKADPQSTRYCMKYRH-CDGKLVLKVT-DNKECLKFKTD 54 (103)
Q Consensus 2 vy~~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~-~~g~LvLKvT-Dd~~cLkYkT~ 54 (103)
||..+-.+|.+..+.-|.....+..+.+++.- ....+.|.++ ++..++.+.++
T Consensus 1 vyrt~d~~l~~~l~~~~~~~~~k~~v~~~~~~~~g~p~~l~~~d~~~~~v~~~~~ 55 (122)
T PF12392_consen 1 VYRTSDKKLEKELRKSYKSSERKIPVDLKLSAKKGEPLKLTLSDEDGNSVEVTSE 55 (122)
T ss_pred CcCccHHHHHHHHHHhhhcccceEeEEEEEEEecCCCEEEEEEECCCcEEEEEec
Confidence 68888999999999999988889999999994 5567999999 55677776654
No 7
>cd06410 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=76.53 E-value=4.6 Score=27.66 Aligned_cols=39 Identities=26% Similarity=0.479 Sum_probs=30.0
Q ss_pred cCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeE--EEEEecCC
Q 034131 5 TSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKL--VLKVTDNK 46 (103)
Q Consensus 5 ~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~L--vLKvTDd~ 46 (103)
-||.||.....+++..... +++||.-|...| .+.|+||.
T Consensus 33 ~s~~el~~kl~~~~~~~~~---~~lky~Lp~edld~Lisv~~De 73 (97)
T cd06410 33 ISFKELVSKLSELFGAGVV---VTLKYQLPDEDLDALISVSNDE 73 (97)
T ss_pred CCHHHHHHHHHHHhCCCCc---eEEEEEcCCCCcceeEEecCcH
Confidence 3799999999999977765 999998876543 45666664
No 8
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=74.96 E-value=7.1 Score=24.39 Aligned_cols=36 Identities=22% Similarity=0.394 Sum_probs=29.6
Q ss_pred cCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEEEE
Q 034131 5 TSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKV 42 (103)
Q Consensus 5 ~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLKv 42 (103)
.+|++|....+..|... ..-+.++|...+|.+|.=.
T Consensus 22 ~s~~~L~~~i~~~~~~~--~~~~~l~Y~D~dgD~V~i~ 57 (84)
T PF00564_consen 22 VSFDDLRSKIREKFGLL--DEDFQLKYKDEDGDLVTIS 57 (84)
T ss_dssp SHHHHHHHHHHHHHTTS--TSSEEEEEEETTSSEEEES
T ss_pred CCHHHHHHHHHHHhCCC--CccEEEEeeCCCCCEEEeC
Confidence 37999999999999887 5789999999998666543
No 9
>PRK11700 hypothetical protein; Provisional
Probab=71.53 E-value=8.7 Score=29.62 Aligned_cols=52 Identities=21% Similarity=0.326 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHhhCCC-cceEEEeeecCCC------eEEEEEecCCceEEEeccchHHH
Q 034131 8 DEFVGRSVQLYKADPQ-STRYCMKYRHCDG------KLVLKVTDNKECLKFKTDQAQDA 59 (103)
Q Consensus 8 ~eF~~~s~~Ly~a~P~-kTRy~~KYr~~~g------~LvLKvTDd~~cLkYkT~ka~dv 59 (103)
+...+.+..|+...|. .--+.+|.+.|.| .-+|-|+|+.+|+||---...++
T Consensus 123 ~t~~~~~~all~~~~l~~~gikvK~SsPkge~ERL~NPTlAv~~~~vcIK~HP~slk~I 181 (187)
T PRK11700 123 ETLDARALALLSDEGLSLPGIKVKTSSPKGEGERLPNPTLAVTDGGICIKFHPHSIKEI 181 (187)
T ss_pred chHHHHHHHhccccccccCCcEEEecCCCccCccCCCCcEEEeeCCEEEEEcCccHHHH
Confidence 4556677788888774 2348999999876 45788889999999977665544
No 10
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=69.26 E-value=10 Score=25.65 Aligned_cols=36 Identities=17% Similarity=0.348 Sum_probs=29.0
Q ss_pred cCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEEE
Q 034131 5 TSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLK 41 (103)
Q Consensus 5 ~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLK 41 (103)
.++++|.+....+|.... ..-|++||+..+|-+|-=
T Consensus 27 ~s~~~L~~~V~~~f~~l~-~~~ftlky~DeeGDlvtI 62 (87)
T cd06402 27 TSYEYLVEKVAAVFPSLR-GKNFQLFWKDEEGDLVAF 62 (87)
T ss_pred cCHHHHHHHHHHHccccC-CCcEEEEEECCCCCEEee
Confidence 478999999999995443 378999999999977643
No 11
>PF04471 Mrr_cat: Restriction endonuclease; InterPro: IPR007560 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents Mrr, a type IV restriction endonuclease involved in the acceptance of modified foreign DNA, restricting both adenine- and cytosine-methylated DNA. Plasmids carrying HincII, HpaI, and TaqI R and M genes are severely restricted in Escherichia coli strains that are Mrr+ []. Mrr appears to be the final effector of the bacterial SOS response, which is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations []. Mrr possesses a cleavage domain that is similar to that found in type II restriction enzymes, however it has an unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0009307 DNA restriction-modification system; PDB: 1Y88_A.
Probab=66.27 E-value=8 Score=24.72 Aligned_cols=65 Identities=15% Similarity=0.074 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEEEEec-C----CceEEEecc-chHHHHHHHHHHHHHHH
Q 034131 6 SWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVTD-N----KECLKFKTD-QAQDAKKMEKLNNIFFA 71 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLKvTD-d----~~cLkYkT~-ka~dv~rle~l~~~l~~ 71 (103)
+|.+|++.+..||++..-+ .+.......++.+=+-++. + ..+++.+.. +..+...+.+|....-.
T Consensus 5 ~~~~FE~l~~~ll~~~g~~-~v~~~~~~~d~giDi~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~~~ 75 (115)
T PF04471_consen 5 SGREFEELVAELLRKLGYT-DVEVTGGSGDGGIDIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKAKK 75 (115)
T ss_dssp ---------HHHHHTTT-E-EEEEE-SSSEEEEEEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHHGG
T ss_pred ccchHHHHHHHHHHHcCCc-cEEEeccCCCCCEEEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhhhc
Confidence 7999999999999998766 2322222333333333432 2 356666654 45666666666554443
No 12
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=64.99 E-value=15 Score=24.71 Aligned_cols=39 Identities=26% Similarity=0.470 Sum_probs=33.1
Q ss_pred CHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEEEEecC
Q 034131 6 SWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVTDN 45 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLKvTDd 45 (103)
+++++.+....+|.-.| .+.|+++|+..+|.+|.=..|+
T Consensus 26 ~~~~L~~kI~~~f~l~~-~~~~~l~Y~Dedgd~V~l~~D~ 64 (91)
T cd06398 26 NMDGLREKVEELFSLSP-DADLSLTYTDEDGDVVTLVDDN 64 (91)
T ss_pred CHHHHHHHHHHHhCCCC-CCcEEEEEECCCCCEEEEccHH
Confidence 67899999999997654 5999999999999888776666
No 13
>PF09981 DUF2218: Uncharacterized protein conserved in bacteria (DUF2218); InterPro: IPR014543 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2JPI_A.
Probab=60.71 E-value=47 Score=22.09 Aligned_cols=48 Identities=13% Similarity=0.176 Sum_probs=40.3
Q ss_pred CCCeEEEEEecCCceEEEeccchHHHHHHHHHHHHHHHHHhCCCCCCC
Q 034131 34 CDGKLVLKVTDNKECLKFKTDQAQDAKKMEKLNNIFFALMARGPDVDL 81 (103)
Q Consensus 34 ~~g~LvLKvTDd~~cLkYkT~ka~dv~rle~l~~~l~~~Ma~~p~~~l 81 (103)
+.|...|-..++.-.|.-...++..+.+++.....-+..||..+..++
T Consensus 39 ~~G~~~l~a~~~~L~l~vea~~~~~L~~~~~vv~~HL~rFa~re~l~v 86 (89)
T PF09981_consen 39 PFGTCTLSAEPDALTLRVEAPDAEALARLEDVVARHLERFAFREELEV 86 (89)
T ss_dssp SSS-EEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHTSTTSS---
T ss_pred CCEEEEEEeCCCeEEEEEEeCCHHHHHHHHHHHHHHHHHHhccCCccc
Confidence 588999999999999999999999999999999999999998765443
No 14
>cd06903 lectin_EMP46_EMP47 EMP46 and EMP47 type 1 transmembrane proteins, N-terminal lectin domain. EMP46 and EMP47, N-terminal carbohydrate recognition domain. EMP46 and EMP47 are fungal type-I transmembrane proteins that cycle between the endoplasmic reticulum and the golgi apparatus and are thought to function as cargo receptors that transport newly synthesized glycoproteins. EMP47 is a receptor for EMP46 responsible for the selective transport of EMP46 by forming hetero-oligomerization between the two proteins. EMP46 and EMP47 have an N-terminal lectin-like carbohydrate recognition domain (represented by this alignment model) as well as a C-terminal transmembrane domain. EMP46 and EMP47 are 45% sequence-identical to one another and have sequence homology to a class of intracellular lectins defined by ERGIC-53 and VIP36. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat s
Probab=58.45 E-value=20 Score=27.52 Aligned_cols=33 Identities=18% Similarity=0.425 Sum_probs=25.0
Q ss_pred HhhCCCcceEEEeeecCCCeEEEEEecCCceEEE
Q 034131 18 YKADPQSTRYCMKYRHCDGKLVLKVTDNKECLKF 51 (103)
Q Consensus 18 y~a~P~kTRy~~KYr~~~g~LvLKvTDd~~cLkY 51 (103)
|+..+..+|+.++|...++.|.|-| |+..|.+-
T Consensus 147 ~rn~~~p~~iri~Y~~~~~~l~v~v-d~~~Cf~~ 179 (215)
T cd06903 147 YQDSGVPSTIRLSYDALNSLFKVQV-DNRLCFQT 179 (215)
T ss_pred ccCCCCCEEEEEEEECCCCEEEEEE-CCCEEEec
Confidence 5556667999999999877777665 77888754
No 15
>PF06185 YecM: YecM protein; InterPro: IPR010393 This family consists of several bacterial YecM proteins of unknown function.; PDB: 1K4N_A.
Probab=56.70 E-value=14 Score=28.33 Aligned_cols=53 Identities=15% Similarity=0.253 Sum_probs=27.4
Q ss_pred CHHHHHHHHHHHHhhC------CCcceEEEeeecCCC------eEEEEEecCCceEEEeccchHH
Q 034131 6 SWDEFVGRSVQLYKAD------PQSTRYCMKYRHCDG------KLVLKVTDNKECLKFKTDQAQD 58 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~------P~kTRy~~KYr~~~g------~LvLKvTDd~~cLkYkT~ka~d 58 (103)
+.++|.+++..++.+- .....+.+|.+.|+| .-++-++++.+|+||---+..+
T Consensus 116 ~~~~~~~~~~~~~p~~~~~~~~~~~~~ikvK~S~Pkge~ErL~NPTiA~~~~~icIK~HP~slk~ 180 (185)
T PF06185_consen 116 DAQTLLEQALQLLPRLAASFDWLANPGIKVKMSSPKGEGERLPNPTIAFKDGGICIKFHPHSLKE 180 (185)
T ss_dssp -GGGHHHHHHHTS------HHHHHSTT-EEEE--------------EEEESSS-EEEEESS-HHH
T ss_pred CHHHHHHHHHHHHhhhhcccccccCCCcEEEEeCCccccCcCCCCeeEeccCCEEEEEcCcCHHH
Confidence 3455666655554221 245789999999876 5689999999999997665543
No 16
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=51.99 E-value=36 Score=22.83 Aligned_cols=37 Identities=14% Similarity=0.191 Sum_probs=31.0
Q ss_pred cCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEEEEecC
Q 034131 5 TSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVTDN 45 (103)
Q Consensus 5 ~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLKvTDd 45 (103)
.+|+++.+.....|.-+ .|++||-..+|.-|+=..|.
T Consensus 22 ~~~~~L~~ev~~rf~l~----~f~lKYlDde~e~v~lssd~ 58 (81)
T cd06396 22 TTWASVEAMVKVSFGLN----DIQIKYVDEENEEVSVNSQG 58 (81)
T ss_pred CCHHHHHHHHHHHhCCC----cceeEEEcCCCCEEEEEchh
Confidence 47999999999999877 89999999998877765544
No 17
>PRK13516 gamma-glutamyl:cysteine ligase; Provisional
Probab=49.52 E-value=35 Score=28.23 Aligned_cols=66 Identities=14% Similarity=0.201 Sum_probs=47.3
Q ss_pred ccccCHHHHHHHHHHHHhh----CCCcceEEEeeecCCCeEEEEEecCCceEEEeccchHHHHHHHHHHHHHHHHHh
Q 034131 2 VYVTSWDEFVGRSVQLYKA----DPQSTRYCMKYRHCDGKLVLKVTDNKECLKFKTDQAQDAKKMEKLNNIFFALMA 74 (103)
Q Consensus 2 vy~~tw~eF~~~s~~Ly~a----~P~kTRy~~KYr~~~g~LvLKvTDd~~cLkYkT~ka~dv~rle~l~~~l~~~Ma 74 (103)
+||.||++|.+-...|+.. ++...-+-+.=++.-|+|-|.|-|-..|+ .+.--|-.|...|.....
T Consensus 196 p~~~~~~~y~~~~~~l~~~G~i~d~~~~~WdvRp~~~~~TvEiRv~D~~~~~-------~~~~~iaal~~alv~~~~ 265 (373)
T PRK13516 196 PFVLNWQEFEAYFRKMSYTGVIDSMKDFYWDIRPKPEFGTVEVRVMDTPLTL-------ERAAAIAAYIQALARWLL 265 (373)
T ss_pred CCcCCHHHHHHHHHHHHHcCCcCCCCeeEEEeccCCCCCCeEEecCCCCCCH-------HHHHHHHHHHHHHHHHHH
Confidence 6899999999999999987 66667777776777799999998865443 333344444544544443
No 18
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=48.41 E-value=65 Score=19.98 Aligned_cols=36 Identities=17% Similarity=0.231 Sum_probs=26.0
Q ss_pred ccCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEEEEe
Q 034131 4 VTSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVT 43 (103)
Q Consensus 4 ~~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLKvT 43 (103)
+.+|++|.. ++...+....+.+++.+....+.+.++
T Consensus 46 v~~~~~~~~----~l~~~~~g~~v~l~v~R~g~~~~~~v~ 81 (82)
T PF13180_consen 46 VNSSEDLVN----ILSKGKPGDTVTLTVLRDGEELTVEVT 81 (82)
T ss_dssp SSSHHHHHH----HHHCSSTTSEEEEEEEETTEEEEEEEE
T ss_pred cCCHHHHHH----HHHhCCCCCEEEEEEEECCEEEEEEEE
Confidence 467888873 343556668899999888877777764
No 19
>PHA02745 hypothetical protein; Provisional
Probab=43.87 E-value=14 Score=29.83 Aligned_cols=43 Identities=23% Similarity=0.289 Sum_probs=25.8
Q ss_pred hCCCcceEEEeeecCCCeEEEEEecCC-----ceEEEeccchHHHHHH
Q 034131 20 ADPQSTRYCMKYRHCDGKLVLKVTDNK-----ECLKFKTDQAQDAKKM 62 (103)
Q Consensus 20 a~P~kTRy~~KYr~~~g~LvLKvTDd~-----~cLkYkT~ka~dv~rl 62 (103)
=||..||.|+|||.+.-.||==+-.-+ .=|+|...-+-|-+-|
T Consensus 132 YDpnDsRWTLKyR~~~pGLVEL~P~SgVYV~~~~L~~C~~~SKDCksL 179 (265)
T PHA02745 132 YDPNDSRWTLKHRYPGSGLVELLPHSGVYINAINLSNCKELSKDCKSL 179 (265)
T ss_pred CCCCCCcceeeccCCCCCcEEeecCCceEEeHHHHHHHHHHhhhHHHH
Confidence 389999999999997754443332222 3344544444444444
No 20
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=42.28 E-value=22 Score=28.75 Aligned_cols=21 Identities=33% Similarity=0.659 Sum_probs=18.6
Q ss_pred ceEEEeeecCCCeEEEEEecCC
Q 034131 25 TRYCMKYRHCDGKLVLKVTDNK 46 (103)
Q Consensus 25 TRy~~KYr~~~g~LvLKvTDd~ 46 (103)
-||.||-.+|.+.|++| |||.
T Consensus 74 ~rF~~kC~~C~~~i~~k-TDPk 94 (324)
T PF04502_consen 74 YRFYIKCPRCSNEIEFK-TDPK 94 (324)
T ss_pred EEEEEEcCCCCCEEeee-cCCC
Confidence 68999999999999999 6775
No 21
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=42.28 E-value=70 Score=21.54 Aligned_cols=41 Identities=24% Similarity=0.334 Sum_probs=31.4
Q ss_pred CHHHHHHHHHHHHhhCCC-cceEEEeeecCCCeEEEEEecCC
Q 034131 6 SWDEFVGRSVQLYKADPQ-STRYCMKYRHCDGKLVLKVTDNK 46 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~P~-kTRy~~KYr~~~g~LvLKvTDd~ 46 (103)
++.+..+....=+..+.. +++|.+||-..+|..||=++|..
T Consensus 22 ~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~VllT~D~D 63 (86)
T cd06409 22 SLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVLITSDSD 63 (86)
T ss_pred CHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEEEeccch
Confidence 456666665555555554 68999999999999999999874
No 22
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=41.50 E-value=68 Score=21.63 Aligned_cols=34 Identities=24% Similarity=0.503 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHHhhC-CCcceEEEeeecCCCeEE
Q 034131 6 SWDEFVGRSVQLYKAD-PQSTRYCMKYRHCDGKLV 39 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~-P~kTRy~~KYr~~~g~Lv 39 (103)
+..+-......+|... |..-=+.+||+.++|-||
T Consensus 22 t~~~L~~~v~~~F~~~~~~~~~flIKYkD~dGDlV 56 (81)
T cd06401 22 TYDELLLMMQRVFRGKLGSSDDVLIKYKDEDGDLI 56 (81)
T ss_pred cHHHHHHHHHHHhccccCCcccEEEEEECCCCCEE
Confidence 4455556666666643 777889999999999775
No 23
>cd06896 PX_PI3K_C2_gamma The phosphoinositide binding Phox Homology Domain of the Gamma Isoform of Class II Phosphoinositide 3-Kinases. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The Phosphoinositide 3-Kinase (PI3K) family of enzymes catalyzes the phosphorylation of the 3-hydroxyl group of the inositol ring of phosphatidylinositol. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI3Ks are divided into three main classes (I, II, and III) based on their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PI as a substrate to produce PI3P, but can also phosphorylate PI4P to produce PI(3,4)P2. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 dom
Probab=41.45 E-value=46 Score=23.41 Aligned_cols=60 Identities=25% Similarity=0.314 Sum_probs=43.4
Q ss_pred ccCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEEEEecCCceEEEeccchHHHHHHHHHHHHHHHHHhCCCCCC
Q 034131 4 VTSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVTDNKECLKFKTDQAQDAKKMEKLNNIFFALMARGPDVD 80 (103)
Q Consensus 4 ~~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLKvTDd~~cLkYkT~ka~dv~rle~l~~~l~~~Ma~~p~~~ 80 (103)
..||+||.+==..|-..-| -|..-++.+ ..+|..+ ..+.+|+..|+.-+-.+|++.|+..
T Consensus 30 ~Rs~eeF~eLH~~L~~~FP--~~~LP~fP~---~~~~~~~------------~~~~~R~~~L~~Yl~~Ll~~~~eVa 89 (101)
T cd06896 30 EKSFEQFSELHSQLQKQFP--SLALPEFPH---WWHLPFT------------DSDHKRVRDLNHYLEQLLSGSREVA 89 (101)
T ss_pred eecHHHHHHHHHHHHHHCc--cccccCCCC---ccccCcc------------cHHHHHHHHHHHHHHHHHccCHHHh
Confidence 5799999999999999999 344444433 3334333 2367899999998888888877543
No 24
>cd01231 PH_Lnk LNK-family Pleckstrin homology (PH) domain. LNK-family Pleckstrin homology (PH) domain. The Lnk family of proteins consists of Lnk, APS and SH2B. They are adaptor proteins consisting of a PH domain and an SH2 domain, which mediates signaling through growth factor receptors. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. The lnk family PH domain is likely involved in targeting of the adaptor proteins to the plasma membrane.
Probab=41.40 E-value=44 Score=23.75 Aligned_cols=27 Identities=30% Similarity=0.309 Sum_probs=22.2
Q ss_pred CCCeEEEEEecCCceEEEeccchHHHHH
Q 034131 34 CDGKLVLKVTDNKECLKFKTDQAQDAKK 61 (103)
Q Consensus 34 ~~g~LvLKvTDd~~cLkYkT~ka~dv~r 61 (103)
...++|||+.|+. =+-|.+.++++++-
T Consensus 73 ~~nTFvLK~~~~~-eyI~Ea~d~~q~~S 99 (107)
T cd01231 73 NLYTFVLKVDDNT-DIIFEVGDEQQLNS 99 (107)
T ss_pred cccEEEEEecCCc-eEEEEcCCHHHHHH
Confidence 5689999999876 67789999887764
No 25
>PF12988 DUF3872: Domain of unknown function, B. Theta Gene description (DUF3872); InterPro: IPR024355 This entry represents proteins of unknown function found primarily in Bacteroides species. The Bacteroides thetaiotaomicron gene coding for this protein is located in a conjugate transposon and appears to be upregulated in the presence of host or other bacterial species compared to growth in pure culture [, ].; PDB: 2L3B_A 2L7Q_A.
Probab=40.32 E-value=35 Score=25.21 Aligned_cols=26 Identities=35% Similarity=0.551 Sum_probs=16.4
Q ss_pred CcceEEEeeecCCCeEEEEEecCCce
Q 034131 23 QSTRYCMKYRHCDGKLVLKVTDNKEC 48 (103)
Q Consensus 23 ~kTRy~~KYr~~~g~LvLKvTDd~~c 48 (103)
..|||++.|=.++|+=+|+..|..+.
T Consensus 63 ~~t~Y~iRYFQ~dGkG~L~~~~g~~~ 88 (137)
T PF12988_consen 63 ADTRYTIRYFQPDGKGTLRMDDGTVL 88 (137)
T ss_dssp SS---EEEEE-SSS-EEEEETTS-EE
T ss_pred cccEEEEEEEeecCCEEEEecCCcEe
Confidence 46999999999999999998666543
No 26
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=39.50 E-value=65 Score=21.85 Aligned_cols=34 Identities=12% Similarity=0.269 Sum_probs=27.8
Q ss_pred cCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEE
Q 034131 5 TSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLV 39 (103)
Q Consensus 5 ~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~Lv 39 (103)
.+.+++.+...+++.-.+. -=|++||...+|-.+
T Consensus 20 ~s~e~L~~~v~~~c~~~~~-q~ft~kw~DEEGDp~ 53 (83)
T cd06404 20 ISLEELCNEVRDMCRFHND-QPFTLKWIDEEGDPC 53 (83)
T ss_pred cCHHHHHHHHHHHhCCCCC-CcEEEEEECCCCCce
Confidence 3688999999999988663 569999999888654
No 27
>PF02290 SRP14: Signal recognition particle 14kD protein; InterPro: IPR003210 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the 14 kDa SRP14 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0030942 endoplasmic reticulum signal peptide binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0005786 signal recognition particle, endoplasmic reticulum targeting; PDB: 1914_A 1RY1_D 1E8O_B 2W9J_B.
Probab=37.39 E-value=58 Score=21.91 Aligned_cols=57 Identities=19% Similarity=0.237 Sum_probs=35.2
Q ss_pred CHHHHHHHHHHHHhhCCCc---ceEEEeeecC-----------------CCeEEEEEecCCceEEEeccc-hHHHHHHH
Q 034131 6 SWDEFVGRSVQLYKADPQS---TRYCMKYRHC-----------------DGKLVLKVTDNKECLKFKTDQ-AQDAKKME 63 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~P~k---TRy~~KYr~~-----------------~g~LvLKvTDd~~cLkYkT~k-a~dv~rle 63 (103)
+-+||+.+-..||+.+-.+ .++|+|--.. .-.+.+.+||. .=+|+.|-- +.|+.+|-
T Consensus 2 ~ndeFL~~L~~lf~~~~~k~gSV~lT~KR~~~~~k~~~~~~~~~~~~~~~~~~LiRAt~G-kk~KiSTvV~~~~l~~F~ 79 (93)
T PF02290_consen 2 SNDEFLSELTKLFEKSKEKGGSVYLTQKRLDGKTKPKPKKQKPSSSEDKEYPCLIRATNG-KKIKISTVVDPDDLDKFW 79 (93)
T ss_dssp -HHHHHHHHHHHHHHCSSSSS-EEEEEEEEEE-------------------EEEEEEESS-SS-EEEEEEETTCHHHHH
T ss_pred CHHHHHHHHHHHHHHcccCCceEEEEEeecCCCCCCCCccccCCCCCCCCceEEEEEecC-CCCeEEEEECHHHHHHHH
Confidence 3489999999999999984 5888886331 22456666665 223444433 24455554
No 28
>PF12021 DUF3509: Protein of unknown function (DUF3509); InterPro: IPR021898 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 92 to 110 amino acids in length. This protein has two completely conserved residues (G and R) that may be functionally important.
Probab=37.26 E-value=1.4e+02 Score=20.50 Aligned_cols=60 Identities=18% Similarity=0.147 Sum_probs=42.8
Q ss_pred HHHHHhhCCCcceEEEeeecCCCeEEEEEecCC-ceEEEec--cchHHHHHHHHHHHHHHHHHh
Q 034131 14 SVQLYKADPQSTRYCMKYRHCDGKLVLKVTDNK-ECLKFKT--DQAQDAKKMEKLNNIFFALMA 74 (103)
Q Consensus 14 s~~Ly~a~P~kTRy~~KYr~~~g~LvLKvTDd~-~cLkYkT--~ka~dv~rle~l~~~l~~~Ma 74 (103)
.+.|-.+-|. -|.++.=..++|.+.|.+.|+. ++++=-. .+..|-..|+.++..+-+-.+
T Consensus 4 ~q~L~~AF~p-y~v~~~~~rpDG~~llTL~d~~g~~~~R~is~~Ql~d~~~L~~vI~~irrdLa 66 (94)
T PF12021_consen 4 FQLLAEAFSP-YQVNLSPPRPDGSILLTLRDEQGVVVKRAISAAQLNDQQQLEWVIDSIRRDLA 66 (94)
T ss_pred HHHHHHhcCc-ceEecccCCCCCCEEEEEEcCCceEEEEecCHHHhcCHHHHHHHHHHHHHHHH
Confidence 4566677777 8888888889999999999985 4444333 344566677777777766554
No 29
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=36.94 E-value=81 Score=21.31 Aligned_cols=39 Identities=13% Similarity=0.312 Sum_probs=30.1
Q ss_pred ccCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEEEEecC
Q 034131 4 VTSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVTDN 45 (103)
Q Consensus 4 ~~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLKvTDd 45 (103)
..+++||..--+.|..-.. .-|+++|..+.|-|. -++||
T Consensus 21 ~~~f~ef~~ll~~lH~l~~--~~f~i~Y~D~~gDLL-PInND 59 (80)
T cd06403 21 PGKFEDFYKLLEHLHHIPN--VDFLIGYTDPHGDLL-PINND 59 (80)
T ss_pred CcCHHHHHHHHHHHhCCCC--CcEEEEEeCCCCCEe-cccCc
Confidence 3689999999999987654 789999999988763 44443
No 30
>PF10298 WhiA_N: WhiA N-terminal LAGLIDADG-like domain; InterPro: IPR018478 This entry represents the N-terminal domain of sporulation factor WhiA []. This domain is related to the LAGLIDADG homing endonuclease domain while the C-terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain [].; PDB: 3HYI_A 3HYJ_D.
Probab=36.58 E-value=14 Score=23.98 Aligned_cols=28 Identities=21% Similarity=0.362 Sum_probs=20.7
Q ss_pred cCCceEEEeccchHHHHHHHHHHHHHHH
Q 034131 44 DNKECLKFKTDQAQDAKKMEKLNNIFFA 71 (103)
Q Consensus 44 Dd~~cLkYkT~ka~dv~rle~l~~~l~~ 71 (103)
++..+|.+.|+.++-.+|+-.++..++.
T Consensus 22 ~~~~~l~~~ten~~vARri~~llk~~f~ 49 (86)
T PF10298_consen 22 NGRISLEISTENAAVARRIYSLLKKLFD 49 (86)
T ss_dssp TTEEEE--EES-HHHHHHHHHHHHHTT-
T ss_pred CCEEEEEEEeCCHHHHHHHHHHHHHHhC
Confidence 6778999999999999999888776653
No 31
>PRK10721 hypothetical protein; Provisional
Probab=34.32 E-value=18 Score=23.65 Aligned_cols=26 Identities=19% Similarity=0.405 Sum_probs=19.8
Q ss_pred CHHHHHHHHHHHHhhCCCcceEEEee
Q 034131 6 SWDEFVGRSVQLYKADPQSTRYCMKY 31 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~P~kTRy~~KY 31 (103)
.|.+-.+-|+.|+.++|..-=+++.|
T Consensus 4 kW~D~~dIA~~L~e~~Pd~DP~~vrF 29 (66)
T PRK10721 4 KWTDSREIGEALYDAYPDLDPKTVRF 29 (66)
T ss_pred cccCHHHHHHHHHHHCCCCCCCEeeh
Confidence 58889999999999888754444444
No 32
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=33.99 E-value=1.3e+02 Score=19.77 Aligned_cols=39 Identities=23% Similarity=0.342 Sum_probs=29.6
Q ss_pred CHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEEEEecC
Q 034131 6 SWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVTDN 45 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLKvTDd 45 (103)
+++++.+.-...|.-++ -+-|++||...+|..|+=++|.
T Consensus 21 ~~~~L~~~i~~r~~~~~-~~~f~LkY~Ddegd~v~ltsd~ 59 (82)
T cd06407 21 GFTELKQEIAKRFKLDD-MSAFDLKYLDDDEEWVLLTCDA 59 (82)
T ss_pred CHHHHHHHHHHHhCCCC-CCeeEEEEECCCCCeEEeecHH
Confidence 56777777777776543 2889999999999888766654
No 33
>KOG1604 consensus Predicted mutarotase [Carbohydrate transport and metabolism]
Probab=32.08 E-value=81 Score=26.62 Aligned_cols=35 Identities=26% Similarity=0.286 Sum_probs=32.1
Q ss_pred hCCCcceEEEeeecCCCeEEEEEecCCceEEEecc
Q 034131 20 ADPQSTRYCMKYRHCDGKLVLKVTDNKECLKFKTD 54 (103)
Q Consensus 20 a~P~kTRy~~KYr~~~g~LvLKvTDd~~cLkYkT~ 54 (103)
..|.+.|.+.|.-|+...+.|-|+-+.-|++|-|-
T Consensus 260 ~~~~~l~~v~k~~hp~Sgr~lEv~TnqPgvqfYTg 294 (353)
T KOG1604|consen 260 VPPNKLRKVAKAVHPKSGRKLEVSTNQPGVQFYTG 294 (353)
T ss_pred CCCcccEEEEEEEcCccCcEEEEEeCCCcEEEEec
Confidence 35669999999999999999999999999999996
No 34
>COG3102 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.26 E-value=54 Score=25.32 Aligned_cols=29 Identities=31% Similarity=0.376 Sum_probs=24.0
Q ss_pred EEEeeecCCC------eEEEEEecCCceEEEeccc
Q 034131 27 YCMKYRHCDG------KLVLKVTDNKECLKFKTDQ 55 (103)
Q Consensus 27 y~~KYr~~~g------~LvLKvTDd~~cLkYkT~k 55 (103)
+.+|-+.|.| .-+|-|+|+..|+||---.
T Consensus 143 i~vk~ssp~ge~erl~nptlav~~~~~~ik~hp~~ 177 (185)
T COG3102 143 ISVKLSSPQGEHERLPNPTLAVTDGKTTIKFHPWS 177 (185)
T ss_pred eEEEecCCCCccccCCCCcEEEecCCceEEecCcc
Confidence 8899988776 4689999999999996544
No 35
>PF10480 ICAP-1_inte_bdg: Beta-1 integrin binding protein; InterPro: IPR019517 ICAP-1 is a serine/threonine-rich protein that binds to the cytoplasmic domains of beta-1 integrins in a highly specific manner, binding to a NPXY sequence motif on the beta-1 integrin. The cytoplasmic domains of integrins are essential for cell adhesion, and the fact that phosphorylation of ICAP-1 by interaction with the cell-matrix implies an important role of ICAP-1 during integrin-dependent cell adhesion []. Over expression of ICAP-1 strongly reduces the integrin-mediated cell spreading on extracellular matrix and inhibits both Cdc42 and Rac1. In addition, ICAP-1 induces release of Cdc42 from cellular membranes and prevents the dissociation of GDP from this GTPase []. An additional function of ICAP-1 is to promote differentiation of osteoprogenitors by supporting their condensation through modulating the integrin high affinity state [].
Probab=29.97 E-value=2.5e+02 Score=21.96 Aligned_cols=37 Identities=22% Similarity=0.323 Sum_probs=28.8
Q ss_pred eEEEEEecCC----ceEEEeccchHHHHHHHHHHHHHHHHH
Q 034131 37 KLVLKVTDNK----ECLKFKTDQAQDAKKMEKLNNIFFALM 73 (103)
Q Consensus 37 ~LvLKvTDd~----~cLkYkT~ka~dv~rle~l~~~l~~~M 73 (103)
.|.||+++.. .|+-|.+++...-..|=++++.-|...
T Consensus 154 llAlK~~~~~~e~y~l~v~Qcss~~qA~~ICk~l~~aF~~v 194 (200)
T PF10480_consen 154 LLALKVGDERQEEYQLWVYQCSSDEQAQEICKVLGQAFDSV 194 (200)
T ss_pred EEEEEccCCCcceEEEEEEEcCCHHHHHHHHHHHHHHHHHh
Confidence 5667999884 889999999888888877777666543
No 36
>PF01547 SBP_bac_1: Bacterial extracellular solute-binding protein; InterPro: IPR006059 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins and a high affinity periplasmic solute-binding protein. In Gram-positive bacteria, which are surrounded by a single membrane and therefore have no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute through the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped into eight family clusters [], which generally correlate with the nature of the solute bound. Family 1 includes the maltose/maltodextrin-binding proteins of Enterobacteriaceae (gene malE) [] and Streptococcus pneumoniae malX; multiple oligosaccharide binding protein of Streptococcus mutans (gene msmE); Escherichia coli glycerol-3-phosphate-binding protein; Serratia marcescens iron-binding protein (gene sfuA) and the homologous proteins (gene fbp) from Haemophilus influenzae and Neisseria; and the E. coli thiamine-binding protein (gene tbpA).; GO: 0005215 transporter activity, 0006810 transport; PDB: 3CFZ_A 2THI_A 3THI_A 4THI_A 1O7T_C 1D9Y_A 1URG_A 1URS_A 1URD_B 3OMB_A ....
Probab=28.66 E-value=61 Score=23.47 Aligned_cols=21 Identities=24% Similarity=0.596 Sum_probs=19.2
Q ss_pred ccCHHHHHHHHHHHHhhCCCc
Q 034131 4 VTSWDEFVGRSVQLYKADPQS 24 (103)
Q Consensus 4 ~~tw~eF~~~s~~Ly~a~P~k 24 (103)
-.||+||.+.++.+=.+.|..
T Consensus 132 p~Twde~~~~~~~~~~~~~~~ 152 (315)
T PF01547_consen 132 PWTWDEFLEAAKKIKEKGPDP 152 (315)
T ss_dssp TSBHHHHHHHHHHHHHTTTCE
T ss_pred CCCHHHHHHHHHHHHhcCCCC
Confidence 359999999999999999986
No 37
>TIGR02664 nitr_red_assoc conserved hypothetical protein. Most members of this protein family are found in the Cyanobacteria, and these mostly near nitrate reductase genes and molybdopterin biosynthesis genes. We note that molybdopterin guanine dinucleotide is a cofactor for nitrate reductase. This protein is sometimes annotated as nitrate reductase-associated protein. Its function is unknown.
Probab=27.75 E-value=1.2e+02 Score=22.52 Aligned_cols=39 Identities=18% Similarity=0.179 Sum_probs=31.3
Q ss_pred ceEEEeccchHHHHHHHHHHHHHHHHHhCCCCCCCcccc
Q 034131 47 ECLKFKTDQAQDAKKMEKLNNIFFALMARGPDVDLSEVT 85 (103)
Q Consensus 47 ~cLkYkT~ka~dv~rle~l~~~l~~~Ma~~p~~~l~~~~ 85 (103)
..+.+-.+...++......+..|.+.|++.|..+++++.
T Consensus 45 ~Lv~~pc~t~~e~~~yr~~L~~l~~~~a~~~~~~l~~~~ 83 (145)
T TIGR02664 45 ELVRLPCDTAEVIDPYREYLRDLLRTHADTPPSDLPPDE 83 (145)
T ss_pred HHHhCccCCHHHHHHHHHHHHHHHHHHcCCCCcCCCCCC
Confidence 334455677888999999999999999999988888544
No 38
>PF07302 AroM: AroM protein; InterPro: IPR010843 This family consists of several bacterial and archaeal AroM proteins. In Escherichia coli the aroM gene is cotranscribed with aroL []. The function of this family is unknown.
Probab=27.55 E-value=87 Score=24.54 Aligned_cols=42 Identities=14% Similarity=0.346 Sum_probs=35.2
Q ss_pred ccccCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeEEEEEecCCceEEEeccchHHHHHH
Q 034131 2 VYVTSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVTDNKECLKFKTDQAQDAKKM 62 (103)
Q Consensus 2 vy~~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLKvTDd~~cLkYkT~ka~dv~rl 62 (103)
||..+|++|.+++..|-.+..+ .+|| -|+=|.....+.+.+.
T Consensus 159 Py~~~~~~l~~Aa~~L~~~gad-------------lIvL------DCmGYt~~~r~~~~~~ 200 (221)
T PF07302_consen 159 PYEGDEEELAAAARELAEQGAD-------------LIVL------DCMGYTQEMRDIVQRA 200 (221)
T ss_pred CCCCCHHHHHHHHHHHHhcCCC-------------EEEE------ECCCCCHHHHHHHHHH
Confidence 6889999999999999999987 6666 6999988777766664
No 39
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=26.50 E-value=1.6e+02 Score=18.14 Aligned_cols=54 Identities=7% Similarity=0.136 Sum_probs=36.4
Q ss_pred cceEEEeeecCC-CeE--EEEEecCCceEEEeccchHHHHHHHHHHHHHHHHHhCCC
Q 034131 24 STRYCMKYRHCD-GKL--VLKVTDNKECLKFKTDQAQDAKKMEKLNNIFFALMARGP 77 (103)
Q Consensus 24 kTRy~~KYr~~~-g~L--vLKvTDd~~cLkYkT~ka~dv~rle~l~~~l~~~Ma~~p 77 (103)
..+++++..++. |.| .|.+.++.+.+.+.++...-...|+.-...|-..++...
T Consensus 12 ~~~~~l~L~p~~LG~v~v~l~~~~~~l~v~~~~~~~~~~~~L~~~~~~L~~~L~~~G 68 (85)
T PF02120_consen 12 SWELSLQLDPPELGSVEVKLRLQGGNLSVQFTAENPETKELLRQNLPELKERLQAQG 68 (85)
T ss_dssp --EEEE--SSGGG--EEEEEEEETTEEEEEEE--SSHHHHHHHHTHHHHHHHHHTTT
T ss_pred ceEEEEEEcccccCcEEEEEEEeCCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHCC
Confidence 456666666655 544 455557789999999999999999998888888888654
No 40
>PF08796 DUF1797: Protein of unknown function (DUF1797); InterPro: IPR014904 The function of this protein is unknown. It forms a central anti-parallel beta sheet with flanking alpha helical regions. ; PDB: 2FFG_B.
Probab=26.09 E-value=1.9e+02 Score=18.77 Aligned_cols=36 Identities=17% Similarity=0.223 Sum_probs=27.2
Q ss_pred ceEEEeeecCCCeEEEEEecCCceEEEeccchHHHHHHH
Q 034131 25 TRYCMKYRHCDGKLVLKVTDNKECLKFKTDQAQDAKKME 63 (103)
Q Consensus 25 TRy~~KYr~~~g~LvLKvTDd~~cLkYkT~ka~dv~rle 63 (103)
.+.+++|.+.++...|..+.+..-++|. ..|+-.||
T Consensus 27 ~~c~V~y~~~t~~F~l~~~~~~~~f~FD---dIDLvAIE 62 (67)
T PF08796_consen 27 EVCTVTYDQETETFELEEYRQKQKFQFD---DIDLVAIE 62 (67)
T ss_dssp EEEEEEEETTTTEEEEEEEETTCEEEES----HHHHHHH
T ss_pred EEEEEEEECCCCeEEEEEecCCCEeecc---cccchHhh
Confidence 3468999999999999999998887663 34444554
No 41
>PF02375 JmjN: jmjN domain; InterPro: IPR003349 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with JmjC (see IPR003347 from INTERPRO).; PDB: 2XML_A 2W2I_C 3DXT_A 3DXU_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=25.84 E-value=19 Score=20.39 Aligned_cols=13 Identities=23% Similarity=0.422 Sum_probs=6.3
Q ss_pred CccccCHHHHHHH
Q 034131 1 MVYVTSWDEFVGR 13 (103)
Q Consensus 1 Mvy~~tw~eF~~~ 13 (103)
+||..|++||.+=
T Consensus 1 Pvf~Pt~eEF~dp 13 (34)
T PF02375_consen 1 PVFYPTMEEFKDP 13 (34)
T ss_dssp EEE---HHHHS-H
T ss_pred CcccCCHHHHhCH
Confidence 3677888888653
No 42
>CHL00191 ycf61 DNA-directed RNA polymerase subunit omega; Provisional
Probab=24.94 E-value=54 Score=21.98 Aligned_cols=25 Identities=12% Similarity=0.231 Sum_probs=21.1
Q ss_pred CHHHHHHHHHHHHhhCCCcceEEEe
Q 034131 6 SWDEFVGRSVQLYKADPQSTRYCMK 30 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~P~kTRy~~K 30 (103)
+..|-...++.|+.+..+.-|+|++
T Consensus 9 ds~ei~~r~E~Li~~asNRY~iTvq 33 (76)
T CHL00191 9 DSNEILYKTEELLNAASNRYKITIQ 33 (76)
T ss_pred CHHHHHHHHHHHHHhhccceeehHH
Confidence 3578899999999999988777765
No 43
>PF05430 Methyltransf_30: S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR008471 This entry contains several uncharacterised bacterial proteins with no known function.; GO: 0016645 oxidoreductase activity, acting on the CH-NH group of donors, 0055114 oxidation-reduction process; PDB: 2E58_D 3SGL_A 3PVC_A 3AWI_D 3PS9_A 2QY6_A.
Probab=24.83 E-value=1.2e+02 Score=21.30 Aligned_cols=35 Identities=20% Similarity=0.153 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhhCCCcceEEEeeecCCCeEEEEEe
Q 034131 9 EFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVT 43 (103)
Q Consensus 9 eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~LvLKvT 43 (103)
||.+-+++|+.+.|.-..=+-++...+|.++|.+.
T Consensus 2 el~~~~~~l~~~~p~~~~g~hrl~~~~~~v~L~L~ 36 (124)
T PF05430_consen 2 ELAELAEQLLAQWPPLLPGFHRLEFDDGNVTLTLW 36 (124)
T ss_dssp GGHHHHHHHHHC---S-SEEEEEEETTTTEEEEEE
T ss_pred cchHHHHHHHHhCccccCCcEEEEecCCCEEEEEE
Confidence 67888999999999876665566656666666543
No 44
>COG2879 Uncharacterized small protein [Function unknown]
Probab=24.65 E-value=1.1e+02 Score=19.97 Aligned_cols=22 Identities=23% Similarity=0.101 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHhCCCCC
Q 034131 58 DAKKMEKLNNIFFALMARGPDV 79 (103)
Q Consensus 58 dv~rle~l~~~l~~~Ma~~p~~ 79 (103)
.+..+-+-++..+++|+|.||=
T Consensus 4 ~l~~~~k~l~q~~~lmvGvpdY 25 (65)
T COG2879 4 KLASAGKYLGQAAKLMVGVPDY 25 (65)
T ss_pred HHHHHHHHHHHHHHHHcCCCcH
Confidence 4555566788899999999863
No 45
>PF14508 GH97_N: Glycosyl-hydrolase 97 N-terminal; PDB: 3A24_A 2JKP_A 2JKE_A 2D73_B 2ZQ0_B 2JKA_A.
Probab=24.22 E-value=1.3e+02 Score=23.35 Aligned_cols=30 Identities=10% Similarity=0.358 Sum_probs=20.6
Q ss_pred EEeeecCCC---eEEEEEecCCceEEEeccchH
Q 034131 28 CMKYRHCDG---KLVLKVTDNKECLKFKTDQAQ 57 (103)
Q Consensus 28 ~~KYr~~~g---~LvLKvTDd~~cLkYkT~ka~ 57 (103)
++.++...| .|++.++||++.+.|.+....
T Consensus 83 ~l~~~~~~~~~l~l~fRayddGvAfRY~~p~~~ 115 (259)
T PF14508_consen 83 TLSFKNKYGRRLNLEFRAYDDGVAFRYELPEQG 115 (259)
T ss_dssp EEEECCCCCEEEEEEEEEETTEEEEEEEE--BT
T ss_pred EEEEecCCCceeEEEEEEEcCCEEEEEEECCCC
Confidence 344444443 499999999999999987644
No 46
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=24.10 E-value=1.7e+02 Score=19.91 Aligned_cols=34 Identities=15% Similarity=0.340 Sum_probs=29.0
Q ss_pred cccCHHHHHHHHHHHHhhCCCcceEEEeeecCCCeE
Q 034131 3 YVTSWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKL 38 (103)
Q Consensus 3 y~~tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~g~L 38 (103)
-..+|.+-.+.-+.||.=.|.. +.++|-..+|-+
T Consensus 18 ~~pt~~~L~~kl~~Lf~lp~~~--~~vtYiDeD~D~ 51 (82)
T cd06397 18 DIPTWEALASKLENLYNLPEIK--VGVTYIDNDNDE 51 (82)
T ss_pred CCccHHHHHHHHHHHhCCChhH--eEEEEEcCCCCE
Confidence 3578999999999999998875 999999988643
No 47
>PF07906 Toxin_15: ShET2 enterotoxin, N-terminal region; InterPro: IPR012927 This domain is present in the N-terminal region of the ShET2 enterotoxin produced by Shigella flexneri (Q47635 from SWISSPROT) and Escherichia coli (Q47634 from SWISSPROT). This protein was found to confer toxigenicity in Ussing chamber assays, and the N-terminal region was found to be important for its enterotoxic effect. It is thought to be a hydrophobic protein that forms inclusion bodies within the bacterial cell, and may be secreted by the Mxi system []. Most proteins containing this domain are annotated as putative enterotoxins, but one member (Q8X606 from SWISSPROT) is a regulator of acetyl CoA synthetase, and another two members (P76205 from SWISSPROT and P23325 from SWISSPROT) are annotated as ankyrin-like regulatory proteins and contain Ank repeats (IPR002110 from INTERPRO).
Probab=23.34 E-value=1.7e+02 Score=23.88 Aligned_cols=42 Identities=14% Similarity=0.206 Sum_probs=31.2
Q ss_pred CCCcceEEEeeecCCC-eEEEEEecCC---ceEEEeccchHHHHHH
Q 034131 21 DPQSTRYCMKYRHCDG-KLVLKVTDNK---ECLKFKTDQAQDAKKM 62 (103)
Q Consensus 21 ~P~kTRy~~KYr~~~g-~LvLKvTDd~---~cLkYkT~ka~dv~rl 62 (103)
+-+..|.-||=....+ .-|+.++||. +...+++++..+++++
T Consensus 146 HaMAvrLrIK~~~~g~~~yVv~~YDPN~T~th~R~~~~~~~~l~~l 191 (284)
T PF07906_consen 146 HAMAVRLRIKQTKEGETKYVVSFYDPNRTNTHVRCEVDDLDSLGHL 191 (284)
T ss_pred chhheEEEEEecCCCCeEEEEEEeCCCcccceeeecccCHHHHhhc
Confidence 3344566666554444 8999999995 7788899999988866
No 48
>COG2975 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.29 E-value=71 Score=20.71 Aligned_cols=19 Identities=26% Similarity=0.490 Sum_probs=16.3
Q ss_pred CHHHHHHHHHHHHhhCCCc
Q 034131 6 SWDEFVGRSVQLYKADPQS 24 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~P~k 24 (103)
.|.+=.+-|+.||.++|..
T Consensus 2 kWtD~~~Iae~Lyd~~pdv 20 (64)
T COG2975 2 KWTDSQEIAEALYDAYPDV 20 (64)
T ss_pred CcchHHHHHHHHHhcCCCC
Confidence 4888899999999998863
No 49
>KOG2826 consensus Actin-related protein Arp2/3 complex, subunit ARPC2 [Cytoskeleton]
Probab=22.66 E-value=1.2e+02 Score=24.89 Aligned_cols=32 Identities=19% Similarity=0.365 Sum_probs=25.9
Q ss_pred ceEEEeeecCCCeEEEEEecCCceEEEeccchH
Q 034131 25 TRYCMKYRHCDGKLVLKVTDNKECLKFKTDQAQ 57 (103)
Q Consensus 25 TRy~~KYr~~~g~LvLKvTDd~~cLkYkT~ka~ 57 (103)
-|.+|+||. +..+.++.-+|.+++-|.|-=..
T Consensus 140 ~r~~I~YRd-dEti~i~~k~DRVTvvFsTiF~d 171 (301)
T KOG2826|consen 140 KRAVIHYRD-DETIYIEPKNDRVTVVFSTIFRD 171 (301)
T ss_pred heeEEEecc-CceEEEecCCCeEEEEEEEeecc
Confidence 579999997 55889999999999888774333
No 50
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=22.61 E-value=64 Score=20.95 Aligned_cols=11 Identities=18% Similarity=0.640 Sum_probs=8.8
Q ss_pred cCHHHHHHHHH
Q 034131 5 TSWDEFVGRSV 15 (103)
Q Consensus 5 ~tw~eF~~~s~ 15 (103)
.||+||...|.
T Consensus 28 P~~eEy~~~aK 38 (65)
T COG2443 28 PDWEEYSKIAK 38 (65)
T ss_pred CCHHHHHHHHH
Confidence 58999988764
No 51
>COG3114 CcmD Heme exporter protein D [Intracellular trafficking and secretion]
Probab=22.18 E-value=46 Score=21.85 Aligned_cols=11 Identities=27% Similarity=0.827 Sum_probs=7.8
Q ss_pred ccccCHHHHHH
Q 034131 2 VYVTSWDEFVG 12 (103)
Q Consensus 2 vy~~tw~eF~~ 12 (103)
+.|.||.||..
T Consensus 1 m~F~Sw~dFfa 11 (67)
T COG3114 1 MAFASWSDFFA 11 (67)
T ss_pred CchhhHHHHHH
Confidence 45778888863
No 52
>COG3144 FliK Flagellar hook-length control protein [Cell motility and secretion]
Probab=22.13 E-value=5e+02 Score=22.17 Aligned_cols=69 Identities=13% Similarity=0.235 Sum_probs=45.9
Q ss_pred CHHHHHHHHHHHHhhCCCcceEEEeeecCC-CeEEEEEe--cCCceEEEeccchHHHHHHHHHHHHHHHHHhC
Q 034131 6 SWDEFVGRSVQLYKADPQSTRYCMKYRHCD-GKLVLKVT--DNKECLKFKTDQAQDAKKMEKLNNIFFALMAR 75 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~P~kTRy~~KYr~~~-g~LvLKvT--Dd~~cLkYkT~ka~dv~rle~l~~~l~~~Ma~ 75 (103)
.|.+=+.+.. +|...-.-++.+|+..+++ |.|.|++| ||..-++|.+....-=.-||.-+..|-..++.
T Consensus 281 ~w~q~l~qqv-~~~~~q~~~~a~IrL~P~eLG~l~I~Lt~e~g~~q~~f~ss~~~vr~aLEs~mp~Lr~~l~e 352 (417)
T COG3144 281 EWQQTLSQQV-NLMQRQGQKSATIRLDPEELGRLDISLTMENGQAQAKFVSSHQEVREALESAMPRLRQALAE 352 (417)
T ss_pred HHHHHHHHHH-HHHHhcCCcceEEeeCcHHhCceEEEEEeeCCEEEEEEeeCcHHHHHHHHHHHHHHHHHHHh
Confidence 4666555566 4555555688999999977 76665555 77899999988765555555555555555553
No 53
>PF03646 FlaG: FlaG protein; InterPro: IPR005186 Although these proteins are known to be important for flagellar their exact function is unknown.; PDB: 2HC5_A.
Probab=21.62 E-value=2.5e+02 Score=18.53 Aligned_cols=63 Identities=17% Similarity=0.278 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHhh-CCCcceEEEeeecCCCeEEEEEecCC---ceEEEeccchHHH-HHHHHHHHHHH
Q 034131 8 DEFVGRSVQLYKA-DPQSTRYCMKYRHCDGKLVLKVTDNK---ECLKFKTDQAQDA-KKMEKLNNIFF 70 (103)
Q Consensus 8 ~eF~~~s~~Ly~a-~P~kTRy~~KYr~~~g~LvLKvTDd~---~cLkYkT~ka~dv-~rle~l~~~l~ 70 (103)
++-.++.+.|=.. .+..+++.+.+....|.+++||.|.. +-=++-.+..-++ .+|..+.|.|+
T Consensus 37 e~l~~~v~~ln~~~~~~~~~l~F~vde~~~~~vVkViD~~T~eVIRqIP~Ee~l~l~~~l~e~~Gll~ 104 (107)
T PF03646_consen 37 EELEEAVEKLNEFLQALNTSLRFSVDEESGRVVVKVIDKETGEVIRQIPPEELLDLAKRLRELVGLLV 104 (107)
T ss_dssp HHHHHHHHHHHHHHTTSS--EEEEEEEETTEEEEEEEETTT-SEEEEE-HHHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHHHhcCCceEEEEecCCCcEEEEEEECCCCcEEEeCCcHHHHHHHHHHHHHhceee
Confidence 4444555555443 34568888888888899999999984 5556666666554 45556666554
No 54
>TIGR02048 gshA_cyano glutamate--cysteine ligase, cyanobacterial, putative. This family consists of proteins believed (see Copley SD, Dhillon JK, 2002) to be the glutamate--cysteine ligases of several cyanobacteria, which are known to make glutathione.
Probab=21.34 E-value=2e+02 Score=23.96 Aligned_cols=63 Identities=13% Similarity=0.060 Sum_probs=41.5
Q ss_pred CccccCHHHHHHHHHHHHhhCCCcceEEEee--e--c-----CCCeEEEEEecCCceEEEeccchHHHHHHHHHHHHHH
Q 034131 1 MVYVTSWDEFVGRSVQLYKADPQSTRYCMKY--R--H-----CDGKLVLKVTDNKECLKFKTDQAQDAKKMEKLNNIFF 70 (103)
Q Consensus 1 Mvy~~tw~eF~~~s~~Ly~a~P~kTRy~~KY--r--~-----~~g~LvLKvTDd~~cLkYkT~ka~dv~rle~l~~~l~ 70 (103)
.++|.||++|.+....|....+..-.=-+=| | . .-|+|-|.|-|-.. ...+.--|-.|...|.
T Consensus 175 pP~f~~~~~y~~~~~~li~~G~i~d~~~~wwdvRPs~~~~~~~~~TlEiRV~D~~~-------~~~~~~aiaalv~aLv 246 (376)
T TIGR02048 175 VPLFTSHAHFIEWTEEQLTLGTMQNVRHLWSAVRPNGDRRPYDLNRLELRICDLVT-------DPISLLAITALLEARL 246 (376)
T ss_pred CCCcCCHHHHHHHHHHHHHcCCccccCeeEEecCCCCCCCcCCCCCEEEEeccCcC-------CHHHHHHHHHHHHHHH
Confidence 3789999999999999999877654222222 2 2 37899999999733 3344334545554443
No 55
>PF03421 YopJ: YopJ Serine/Threonine acetyltransferase; InterPro: IPR005083 The infection of mammalian host cells by Yersinia sp. causes a rapid induction of the mitogen-activated protein kinase (MAPK; including the ERK, JNK and p38 pathways) and nuclear factor kappaB (NF-kappaB) signalling pathways that would typically result in cytokine production and initiation of the innate immune response. However, these pathways are rapidly inhibited promoting apoptosis. YopJ has been shown to block phosphorylation of active site residues []. It has also been shown that YopJ acetyltransferase is activated by eukaryotic host cell inositol hexakisphosphate []. Serine and threonine acetylation is yet another complication to the control of signalling pathways and may be a may be a widespread mode of biochemical regulation of endogenous processes in eukaryotic cells. It has been shown that YopJ is a serine/threonine acetyltransferase []. It acetylates the serine and threonine residues in the phosphorylation sites of MAPK kinases and nuclear factor kappaB, preventing their activation by phosphorylation and the inhibition of these signalling pathways []. This entry contains YopJ and related proteins.
Probab=20.99 E-value=2.6e+02 Score=20.79 Aligned_cols=47 Identities=26% Similarity=0.283 Sum_probs=34.4
Q ss_pred ccccCHHHHHHHHHHHHhhCCCcceEEEe------------ee-cCCCeEEEEEecCCceE
Q 034131 2 VYVTSWDEFVGRSVQLYKADPQSTRYCMK------------YR-HCDGKLVLKVTDNKECL 49 (103)
Q Consensus 2 vy~~tw~eF~~~s~~Ly~a~P~kTRy~~K------------Yr-~~~g~LvLKvTDd~~cL 49 (103)
.|+.+.++|.++-.+ -...|..-|+++. ++ ++.|...|=+.++..+.
T Consensus 50 ~~~~~~~~~~~~i~~-~~~~~~s~R~Iv~~~~~~~H~~a~Dvr~~~~~k~SlI~~Epa~~~ 109 (177)
T PF03421_consen 50 HFFDSPEDFVQAIKE-INSGPQSWRAIVNLGGDGIHHVALDVRHTPNGKPSLIVFEPASFY 109 (177)
T ss_pred EEcCCcHHHHHHHHh-hcCCCCceEEEEeCCCCCCcEEEEEEeecCCCCceEEEEcccccc
Confidence 467889999888877 7778888999999 34 45666666666665443
No 56
>PF09655 Nitr_red_assoc: Conserved nitrate reductase-associated protein (Nitr_red_assoc); InterPro: IPR013481 Proteins in this entry are found in the Cyanobacteria, and are mostly encoded near nitrate reductase and molybdopterin biosynthesis genes. Molybdopterin guanine dinucleotide is a cofactor for nitrate reductase. These proteins are sometimes annotated as nitrate reductase-associated proteins, though their function is unknown.
Probab=20.42 E-value=2e+02 Score=21.28 Aligned_cols=39 Identities=15% Similarity=0.274 Sum_probs=31.0
Q ss_pred ceEEEeccchHHHHHHHHHHHHHHHHHhCCCCCCCcccc
Q 034131 47 ECLKFKTDQAQDAKKMEKLNNIFFALMARGPDVDLSEVT 85 (103)
Q Consensus 47 ~cLkYkT~ka~dv~rle~l~~~l~~~Ma~~p~~~l~~~~ 85 (103)
..+.+-.+...++.....++..|.+.++|+|..+|+.+.
T Consensus 45 ~Lv~~pc~t~~ei~~yr~~L~~li~~~~~~~~~~l~~~~ 83 (144)
T PF09655_consen 45 QLVDLPCDTPEEIQNYREFLQELIRTHAGGPAKDLPPDP 83 (144)
T ss_pred HHHcCCCCCHHHHHHHHHHHHHHHHHHhCCCcccCCCCC
Confidence 344455577888889999999999999999988887544
No 57
>COG1580 FliL Flagellar basal body-associated protein [Cell motility and secretion]
Probab=20.39 E-value=2.9e+02 Score=20.42 Aligned_cols=45 Identities=16% Similarity=0.345 Sum_probs=38.7
Q ss_pred ceEEEeccchHHHHHHH----HHHHHHHHHHhCCCCCCCcccccccccc
Q 034131 47 ECLKFKTDQAQDAKKME----KLNNIFFALMARGPDVDLSEVTGKEQME 91 (103)
Q Consensus 47 ~cLkYkT~ka~dv~rle----~l~~~l~~~Ma~~p~~~l~~~~~~~~~~ 91 (103)
+-|.|..++.+....|+ .+.+.++.+.++....+|+...|+|+--
T Consensus 83 i~i~l~~~n~~~~~el~~~~p~vrd~li~lfsskt~~eL~t~~Gke~Lk 131 (159)
T COG1580 83 IAITLEVANKALLEELEEKKPEVRDALLMLFSSKTAAELSTPEGKEKLK 131 (159)
T ss_pred EEEEEeeCCHHHHHHHHHhhHHHHHHHHHHHHhCCHHHhcCchhHHHHH
Confidence 67899999988887776 7889999999999999999999988743
No 58
>PF04384 Fe-S_assembly: Iron-sulphur cluster assembly; InterPro: IPR007479 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents IscX proteins (also known as hypothetical protein YfhJ) that are part of the ISC system. IscX is active as a monomer. The structure of YfhJ is an orthogonal alpha-bundle []. YfhJ is a small acidic protein that binds IscS, and contains a modified winged helix motif that is usually found in DNA-binding proteins []. YfhJ/IscX can bind Fe, and may function as an Fe donor in the assembly of FeS clusters ; GO: 0016226 iron-sulfur cluster assembly; PDB: 2BZT_A 1UJ8_A.
Probab=20.29 E-value=85 Score=20.30 Aligned_cols=18 Identities=22% Similarity=0.617 Sum_probs=15.0
Q ss_pred CHHHHHHHHHHHHhhCCC
Q 034131 6 SWDEFVGRSVQLYKADPQ 23 (103)
Q Consensus 6 tw~eF~~~s~~Ly~a~P~ 23 (103)
.|.+.++-|..|+.++|.
T Consensus 2 kW~D~~eIA~~L~e~~pd 19 (64)
T PF04384_consen 2 KWTDSEEIAIELYEKYPD 19 (64)
T ss_dssp -TT-HHHHHHHHHHHSTT
T ss_pred CCcCHHHHHHHHHHHCCC
Confidence 589999999999999997
Done!