Query 032231
Match_columns 145
No_of_seqs 110 out of 617
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 11:20:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032231hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3343 Vesicle coat complex C 100.0 3.1E-40 6.7E-45 242.7 12.1 138 2-143 4-142 (175)
2 PF01217 Clat_adaptor_s: Clath 100.0 1.8E-38 3.9E-43 232.2 17.3 134 6-143 1-134 (141)
3 COG5030 APS2 Clathrin adaptor 100.0 6.3E-39 1.4E-43 231.3 12.6 134 6-143 1-134 (152)
4 KOG0936 Clathrin adaptor compl 100.0 5.5E-35 1.2E-39 213.9 13.2 133 6-142 1-139 (182)
5 KOG0934 Clathrin adaptor compl 100.0 5.2E-36 1.1E-40 215.6 7.2 132 6-141 1-132 (145)
6 KOG0935 Clathrin adaptor compl 100.0 4.3E-35 9.4E-40 207.0 10.2 135 6-143 1-135 (143)
7 COG5541 RET3 Vesicle coat comp 100.0 5.1E-29 1.1E-33 183.2 9.6 137 3-143 4-149 (187)
8 KOG0938 Adaptor complexes medi 99.9 1.2E-21 2.7E-26 159.6 11.2 129 6-141 1-129 (446)
9 KOG0937 Adaptor complexes medi 99.7 6.5E-17 1.4E-21 135.6 13.5 130 7-141 1-130 (424)
10 KOG2740 Clathrin-associated pr 99.4 7.1E-13 1.5E-17 109.2 8.3 130 6-141 1-132 (418)
11 KOG2635 Medium subunit of clat 98.3 1.1E-05 2.4E-10 68.6 11.3 126 6-139 2-129 (512)
12 PF15001 AP-5_subunit_s1: AP-5 97.6 0.0041 8.9E-08 47.9 13.8 79 61-139 102-180 (189)
13 PF08923 MAPKK1_Int: Mitogen-a 97.3 0.0038 8.2E-08 44.7 9.9 99 3-102 13-115 (119)
14 PF03164 Mon1: Trafficking pro 94.9 0.68 1.5E-05 39.6 11.9 91 8-103 12-103 (415)
15 PF13774 Longin: Regulated-SNA 87.5 5.9 0.00013 25.7 8.9 63 40-104 3-65 (83)
16 KOG0862 Synaptobrevin/VAMP-lik 85.6 16 0.00035 28.8 10.4 92 15-109 11-105 (216)
17 PF03259 Robl_LC7: Roadblock/L 75.6 16 0.00035 23.4 6.2 73 3-77 11-89 (91)
18 KOG0859 Synaptobrevin/VAMP-lik 71.3 48 0.001 26.0 10.3 86 15-106 9-94 (217)
19 COG3322 Predicted periplasmic 64.8 5.9 0.00013 32.6 2.6 24 5-28 102-125 (295)
20 KOG0997 Uncharacterized conser 62.8 95 0.0021 27.6 9.6 75 8-88 118-194 (523)
21 PF09561 RE_HpaII: HpaII restr 47.6 74 0.0016 27.0 6.4 56 7-75 292-347 (355)
22 PF05228 CHASE4: CHASE4 domain 37.3 1.5E+02 0.0032 20.9 7.1 24 5-28 48-73 (161)
23 PF13812 PPR_3: Pentatricopept 36.8 30 0.00064 17.6 1.7 17 115-131 16-32 (34)
24 TIGR03882 cyclo_dehyd_2 bacter 34.3 97 0.0021 23.5 4.8 42 96-137 32-79 (193)
25 PF01535 PPR: PPR repeat; Int 34.0 36 0.00078 16.7 1.7 18 114-131 14-31 (31)
26 PF05184 SapB_1: Saposin-like 33.7 82 0.0018 17.0 3.3 31 90-120 5-35 (39)
27 KOG1373 Transport protein Sec6 30.5 70 0.0015 27.7 3.6 46 87-133 123-177 (476)
28 PF02334 RTP: Replication term 29.2 1E+02 0.0022 22.0 3.8 37 95-135 37-73 (122)
29 PF14903 WG_beta_rep: WG conta 28.4 62 0.0013 16.8 2.1 17 12-28 3-19 (35)
30 PF04086 SRP-alpha_N: Signal r 28.0 3E+02 0.0066 21.7 7.6 51 54-104 18-70 (279)
31 PF13998 MgrB: MgrB protein 27.9 41 0.0009 18.1 1.2 14 120-133 3-16 (29)
32 PF08866 DUF1831: Putative ami 27.8 51 0.0011 23.4 2.0 22 112-133 90-111 (112)
33 COG5122 TRS23 Transport protei 26.5 2.5E+02 0.0054 20.2 9.7 96 6-104 2-107 (134)
34 PF09639 YjcQ: YjcQ protein; 25.4 1.2E+02 0.0026 20.0 3.5 17 117-133 25-41 (88)
35 PF08784 RPA_C: Replication pr 25.2 63 0.0014 21.6 2.2 30 107-136 66-99 (102)
36 cd04670 Nudix_Hydrolase_12 Mem 24.7 2.3E+02 0.0049 19.1 5.1 38 10-47 7-55 (127)
37 PF04099 Sybindin: Sybindin-li 23.5 2.9E+02 0.0062 19.9 11.9 98 7-105 1-118 (142)
38 PF04315 DUF462: Protein of un 23.4 69 0.0015 24.2 2.2 20 21-40 65-84 (164)
39 cd03016 PRX_1cys Peroxiredoxin 21.6 2.6E+02 0.0056 21.1 5.2 21 7-27 117-137 (203)
40 cd03671 Ap4A_hydrolase_plant_l 21.5 1.1E+02 0.0024 21.6 2.9 40 9-48 7-56 (147)
41 COG4001 Predicted metal-bindin 21.3 2.1E+02 0.0046 19.6 4.0 36 84-121 53-88 (102)
42 cd04685 Nudix_Hydrolase_26 Mem 20.7 1.1E+02 0.0024 21.5 2.8 40 9-48 4-57 (133)
43 TIGR00756 PPR pentatricopeptid 20.5 76 0.0016 15.6 1.5 19 114-132 14-32 (35)
44 PF05402 PqqD: Coenzyme PQQ sy 20.4 2.1E+02 0.0046 17.2 4.6 35 94-133 34-68 (68)
45 PRK00714 RNA pyrophosphohydrol 20.3 2.8E+02 0.006 19.9 4.9 40 9-48 12-61 (156)
No 1
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.1e-40 Score=242.75 Aligned_cols=138 Identities=52% Similarity=0.809 Sum_probs=133.1
Q ss_pred CCccceeEEEEEcCCCCEEEEecCCCCCCC-hHHHHHHHHHHHHHhhcCCcccccceeeecCeEEEEEEeCcEEEEEEec
Q 032231 2 DTCPSIKNILLLDSEGKRVAVKYYSNDWPT-NSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGG 80 (145)
Q Consensus 2 ~~~~~I~~i~iln~~G~~~~~kyY~~~~~~-~~~~~~fe~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~ 80 (145)
-|+|.|+|++|+|++|+|+++|||++++++ .++|++|||.+|+|+.+. +++|..++|..+|||.+-||+||++|+
T Consensus 4 ~sly~vk~iliLD~~G~Ri~aKYY~~~~~s~vkeqkaFEK~lF~KT~kt----~~eI~~ldg~~vvYk~~~Dl~fyv~G~ 79 (175)
T KOG3343|consen 4 LSLYTVKAILILDSDGKRILAKYYDDPHPSTVKEQKAFEKNLFSKTSKT----ESEILLLDGNTVVYKSVIDLHFYVVGS 79 (175)
T ss_pred cchhhhheEEEEcCCCCEeeeeecCCCcchhHHHHHHHHHHHhcccccc----cceeEEecCcEEEEEecccEEEEEecC
Confidence 479999999999999999999999999887 899999999999999975 689999999999999999999999999
Q ss_pred CCccHHHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhhhccc
Q 032231 81 EDENELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFILLINF 143 (145)
Q Consensus 81 ~~eNEl~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~il~~ 143 (145)
.+|||++|.++++++.++++..+++|++++.+++|+|.+++++||+||+|+|+||++..|..|
T Consensus 80 ~~ENEl~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~r 142 (175)
T KOG3343|consen 80 EEENELMLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQR 142 (175)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999998765
No 2
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species [, , , ]. The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly [, ]. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1W63_W 2JKR_I 2VGL_S 2JKT_I 2XA7_S 2HF6_A 3TJZ_C.
Probab=100.00 E-value=1.8e-38 Score=232.25 Aligned_cols=134 Identities=35% Similarity=0.538 Sum_probs=117.7
Q ss_pred ceeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcCCcccccceeeecCeEEEEEEeCcEEEEEEecCCccH
Q 032231 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (145)
Q Consensus 6 ~I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNE 85 (145)
||+|++|+|++|+++++|||++. ++. +++++.+++.++..++++ ..+|++.++++++||++++||||+++++.++||
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~-~~~-~~~~~~~~~~~~~~~~~~-~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNe 77 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDV-SEE-ERQKLFEKFIKKKSSRNS-KQSPIFEHDNYRIVYKRYSDLYFVVVGDENENE 77 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTS-TSH-HHHHHHHHHHHHHHTSSS-SSTSEEEETTEEEEEEEETTEEEEEEESSTSBH
T ss_pred CEEEEEEEcCCCCEEEehhcCCc-cHH-HHHHHHHHHHHHHHhccc-ccceeeecccceeeeEeeccEEEEEEeecccch
Confidence 89999999999999999999654 444 556666666666665542 248999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhhhccc
Q 032231 86 LILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFILLINF 143 (145)
Q Consensus 86 l~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~il~~ 143 (145)
++++++|++++++|+.+|| ++||+++++||+++|++|||+||+|+|+||+++.|++|
T Consensus 78 l~~~e~l~~~v~~l~~~~~-~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~ 134 (141)
T PF01217_consen 78 LLLLEFLHRLVEVLDDYFG-NVSEKDILENFDLVYLILDEIIDGGIILETDPNVILKR 134 (141)
T ss_dssp HHHHHHHHHHHHHHHHHHS-S-SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHH
T ss_pred HHHHHHHHHhhhhhhhhhc-cccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHH
Confidence 9999999999999999999 89999999999999999999999999999999999875
No 3
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=100.00 E-value=6.3e-39 Score=231.27 Aligned_cols=134 Identities=22% Similarity=0.349 Sum_probs=126.7
Q ss_pred ceeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcCCcccccceeeecCeEEEEEEeCcEEEEEEecCCccH
Q 032231 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (145)
Q Consensus 6 ~I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNE 85 (145)
||++++++|++|++|++|||+|. +..+|.+..+++++.+.+|+++ ++++..+.+.++||||||+|||+++.+.++||
T Consensus 1 ~i~~vli~nrqgk~RL~K~yt~~--~~~e~~kli~~i~~lIs~R~~k-e~N~~e~k~~kiVYrrYA~LyF~f~Vd~~dnE 77 (152)
T COG5030 1 MIKFVLIFNRQGKPRLVKWYTPV--SDPEQAKLIADIYELISARKPK-ESNFIEGKNEKIVYRRYATLYFVFGVDNDDNE 77 (152)
T ss_pred CeEEEEEEcCCCceeeeEeeccC--CcHHHHHHHHHHHHHHHcCCch-hcccccccCcEEEeeecCcEEEEEEEcCCCCc
Confidence 79999999999999999999876 4458888999999999988765 78999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhhhccc
Q 032231 86 LILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFILLINF 143 (145)
Q Consensus 86 l~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~il~~ 143 (145)
++++++||.|||+||++|| +|||+|+++||.++|.+|||++.+|.++|+|++.++++
T Consensus 78 l~iL~lIh~FVE~lDr~Fg-nVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl~~ 134 (152)
T COG5030 78 LIILELIHNFVEILDRFFG-NVCELDLIFNFQKVYAILDEMILGGEIIESSKNEVLEH 134 (152)
T ss_pred chHHHHHHHHHHHHHHHhc-cceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHHHH
Confidence 9999999999999999999 89999999999999999999999999999999999854
No 4
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5.5e-35 Score=213.92 Aligned_cols=133 Identities=22% Similarity=0.335 Sum_probs=121.5
Q ss_pred ceeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcCCcccccceee----ec--CeEEEEEEeCcEEEEEEe
Q 032231 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAM----LE--GNVIVYKFVQDLHFFVTG 79 (145)
Q Consensus 6 ~I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~~~~~~~~i~~----~~--~~~ivy~~~~dl~~~~v~ 79 (145)
||+|++|+|.+||+|++|||+|. +++.|+++.+++|....+|+. +.++++. ++ +.+++||+|+.|||+.+.
T Consensus 1 MI~AvlifNn~gkPRL~KFY~p~--~~~~Qq~lir~vf~lvs~R~~-n~~nFLe~~~l~g~~d~rlIYrhYATLYFvfvv 77 (182)
T KOG0936|consen 1 MIKAVLIFNNKGKPRLVKFYTPV--DEEKQQQLIREVFHLVSKRPD-NVCNFLEGNSLIGGSDNRLIYRHYATLYFVFVV 77 (182)
T ss_pred CeeEEEEecCCCCcceeeecCcC--ChHHHHHHHHHHHHHHHcCCc-hHhhhhccccccCCccceeehheeeeEEEEEEE
Confidence 89999999999999999999986 567999999999999998863 2344432 33 799999999999999999
Q ss_pred cCCccHHHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhhhcc
Q 032231 80 GEDENELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFILLIN 142 (145)
Q Consensus 80 ~~~eNEl~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~il~ 142 (145)
|++||||+++++|+.|||+||++|. +|||+|+++||++++.+|+|++.+|.++|||.+.|+.
T Consensus 78 D~sEsEL~iLDLIQvfVEtLDkCF~-nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~ 139 (182)
T KOG0936|consen 78 DSSESELGILDLIQVFVETLDKCFE-NVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVA 139 (182)
T ss_pred cCCcchhHHHHHHHHHHHHHHHHHH-hhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHH
Confidence 9999999999999999999999998 8999999999999999999999999999999988863
No 5
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5.2e-36 Score=215.64 Aligned_cols=132 Identities=19% Similarity=0.295 Sum_probs=124.6
Q ss_pred ceeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcCCcccccceeeecCeEEEEEEeCcEEEEEEecCCccH
Q 032231 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (145)
Q Consensus 6 ~I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNE 85 (145)
||+++++.++|||.|++|||.+. +.++|.+.++.+.+.+.+++++ .++++.++++++|||||++|+|+++.+.++||
T Consensus 1 mi~f~LlvsrQGk~rL~k~y~~~--~~~er~~i~re~i~~~Lar~pk-~csfie~kd~kvVyrryasl~f~~~v~~~dNE 77 (145)
T KOG0934|consen 1 MIKFFLLVSRQGKTRLQKWYEAL--SIKERKKIERELIKSVLARKPK-MCSFIEYKDEKVVYRRYASLFFCVGVEDNDNE 77 (145)
T ss_pred CeEEEEEEeccCceehhHHHhhh--cHHHHHHHHHHHHHHHHhCCcc-cccchhccCceehhhhhhhEEEEEEEecCCch
Confidence 79999999999999999999986 5579999999999999988765 68899999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhhhc
Q 032231 86 LILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFILLI 141 (145)
Q Consensus 86 l~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~il 141 (145)
|+++|+||.+||+||+||| +|||+|+++||+++|.+|||++.+|.++|++++..+
T Consensus 78 L~~LE~IH~~vE~lDkYFg-~VCELDiiFNfekay~ILde~~~~g~~~e~~k~~~~ 132 (145)
T KOG0934|consen 78 LAILEFIHNYVELLDKYFG-SVCELDIIFNFEKAYFILDEFLLGGEIQETSKNDVL 132 (145)
T ss_pred hhHHHHHHHHHHHHHHHhc-cceeeEEEEehHhHHHHHHHHhcCcchHhhhcccHH
Confidence 9999999999999999999 899999999999999999999999999999887654
No 6
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.3e-35 Score=206.99 Aligned_cols=135 Identities=18% Similarity=0.201 Sum_probs=123.1
Q ss_pred ceeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcCCcccccceeeecCeEEEEEEeCcEEEEEEecCCccH
Q 032231 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (145)
Q Consensus 6 ~I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNE 85 (145)
||++|++.|++|++|++|||-+. +..++++.+.++++....++++-.+.+......++++|+|++|||+++.|..+||
T Consensus 1 mi~FILiqNr~Gk~RLak~yv~~--dd~ek~~~~~~vh~lvs~Rd~K~~~~~~~~~~~~~~~rryagLyf~~~vd~tDne 78 (143)
T KOG0935|consen 1 MIRFILIQNRAGKTRLAKWYVQF--DDDEKQKLIEEVHALVTVRDAKHTNFVEFRNFKIIYRRRYAGLYFCICVDVTDNE 78 (143)
T ss_pred CeEEEEEEccccceeheeeeecc--CchHHHHHHHHHHHHHhhccchhhhheeeeeceEEEEEeeCCEEEEEEEecCCch
Confidence 79999999999999999999765 3347788999999999988877556666666677777799999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhhhccc
Q 032231 86 LILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFILLINF 143 (145)
Q Consensus 86 l~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~il~~ 143 (145)
++.++-||.|||+|+.+|+ ||||+|+++||.+||.++|||+.+|.|+|||++.+|+|
T Consensus 79 layLe~IHlFVEvLd~fF~-NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vler 135 (143)
T KOG0935|consen 79 LAYLEHIHLFVEVLDEFFH-NVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLER 135 (143)
T ss_pred HHHHHHHHHHHHHHHHHhc-cccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHH
Confidence 9999999999999999999 89999999999999999999999999999999999986
No 7
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=5.1e-29 Score=183.22 Aligned_cols=137 Identities=27% Similarity=0.407 Sum_probs=129.3
Q ss_pred CccceeEEEEEcCCCCEEEEecCCCCC---------CChHHHHHHHHHHHHHhhcCCcccccceeeecCeEEEEEEeCcE
Q 032231 3 TCPSIKNILLLDSEGKRVAVKYYSNDW---------PTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDL 73 (145)
Q Consensus 3 ~~~~I~~i~iln~~G~~~~~kyY~~~~---------~~~~~~~~fe~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl 73 (145)
|++.|+|++|+|++|+|++.|||.|++ .+.++++.||+++++|+.+. +++|+.+++..++|+++-|+
T Consensus 4 sLy~v~a~LilDsqGeriy~kyy~pph~~eg~~~vFnsvkkekefek~l~eKt~k~----~~~Il~f~d~lV~~k~~~dv 79 (187)
T COG5541 4 SLYDVEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTAKD----RESILMFYDRLVMCKRLDDV 79 (187)
T ss_pred chheeeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhhcC----ccceeeEcceeeeeeeehhE
Confidence 589999999999999999999999875 33468999999999999976 46999999999999999999
Q ss_pred EEEEEecCCccHHHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhhhccc
Q 032231 74 HFFVTGGEDENELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFILLINF 143 (145)
Q Consensus 74 ~~~~v~~~~eNEl~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~il~~ 143 (145)
.+++++.-+|||.++.+.+..+..+|..+++...+++.+.+|||.+.+++||.+|+|+|+||+++.|.+|
T Consensus 80 ~~yiv~~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ia~r 149 (187)
T COG5541 80 LLYIVSPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADR 149 (187)
T ss_pred EEEEecccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHHHHHh
Confidence 9999999999999999999999999999999888899999999999999999999999999999999876
No 8
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.87 E-value=1.2e-21 Score=159.63 Aligned_cols=129 Identities=14% Similarity=0.150 Sum_probs=119.9
Q ss_pred ceeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcCCcccccceeeecCeEEEEEEeCcEEEEEEecCCccH
Q 032231 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (145)
Q Consensus 6 ~I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNE 85 (145)
||+|++|+|..|++++.|.|+.+.... .-+.|+-++.+...- .+|+..+++++++|.+..+||+++++.+|.|-
T Consensus 1 misglfi~n~rGevlink~fr~dlkrs-~~diFRv~vi~n~d~-----r~PV~~igsttf~~~r~~nl~lvaitksN~Nv 74 (446)
T KOG0938|consen 1 MISGLFIYNLRGEVLINKTFRDDLKRS-IVDIFRVQVINNLDV-----RSPVLTIGSTTFHHIRSSNLWLVAITKSNANV 74 (446)
T ss_pred CcceEEEEeccCcEEEehhhhhhhhhh-HHHHHHHhhhhcccc-----CCCeeEecceeEEEEeeccEEEEEEecCCCch
Confidence 799999999999999999999876443 778999999887443 37999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhhhc
Q 032231 86 LILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFILLI 141 (145)
Q Consensus 86 l~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~il 141 (145)
.+++|++..+.+++.+||| ..+|+.+.+||..+|++||||+|.||||+|+++.+.
T Consensus 75 a~v~eFl~kl~avm~aYfg-k~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~ 129 (446)
T KOG0938|consen 75 AAVFEFLYKLDAVMNAYFG-KDREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALK 129 (446)
T ss_pred hhHHHHHHHHHHHHHHHhc-ccchhhhhhceEeHHHHHHHHHhcCCCccCChhHHH
Confidence 9999999999999999999 799999999999999999999999999999999864
No 9
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.73 E-value=6.5e-17 Score=135.56 Aligned_cols=130 Identities=20% Similarity=0.324 Sum_probs=116.5
Q ss_pred eeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcCCcccccceeeecCeEEEEEEeCcEEEEEEecCCccHH
Q 032231 7 IKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENEL 86 (145)
Q Consensus 7 I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNEl 86 (145)
++|++++|.+|+++++|-|+.+.+ ...-.+|-+.++.+.... ...|++.++|..++|.+++++|+++++..|.|..
T Consensus 1 ~sa~fild~~G~~lisr~yr~dv~-~s~~~~F~~~l~~~e~~~---~~~p~l~~~g~~~~~ik~s~lylv~~~~~n~~a~ 76 (424)
T KOG0937|consen 1 ASAVFILDHKGEVLISRDYRGDVP-MSSTEKFFRKLFEKEEGD---ESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAA 76 (424)
T ss_pred CceEEEEcCCCcEeEeecccccCC-hhhhhhHHHHHhhhcccC---CCCCeEEeCCceEEEEeecceEEEEEeccCCCHH
Confidence 478999999999999999998864 347788887777765222 2468999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhhhc
Q 032231 87 ILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFILLI 141 (145)
Q Consensus 87 ~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~il 141 (145)
.++++++++++++..||+ .+.|..+.+||..+|.+|||++|.|++|.|+++.+-
T Consensus 77 ~v~~~l~~~~~v~~~y~~-~l~e~si~~n~vlvyElLde~mDFGypQ~t~s~iL~ 130 (424)
T KOG0937|consen 77 LVLSFLYAVADVFGDYLS-ELEEESIRDNFVLVYELLDEVMDFGYPQTTDSEILK 130 (424)
T ss_pred HHHHHHHHHHHHHHHHhc-cCCccceecchHHHHHHHHHHhccCCcccchHHHHH
Confidence 999999999999999999 899999999999999999999999999999887753
No 10
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.41 E-value=7.1e-13 Score=109.21 Aligned_cols=130 Identities=14% Similarity=0.215 Sum_probs=95.0
Q ss_pred ceeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcCCccc-ccceeeecCeEEEEEEe-CcEEEEEEecCCc
Q 032231 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNART-EAEIAMLEGNVIVYKFV-QDLHFFVTGGEDE 83 (145)
Q Consensus 6 ~I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~~~~~-~~~i~~~~~~~ivy~~~-~dl~~~~v~~~~e 83 (145)
||+++++.|.+|+.++.|-.+... .-+..+...++.-.+.. +. .++....-.+...+--+ .+++|++++..+-
T Consensus 1 mi~siflidtsg~l~lek~~~g~t----~~rsic~~f~e~~~~~~-~~e~~ppvi~~p~hylfsv~~~~i~~~~~st~e~ 75 (418)
T KOG2740|consen 1 MILSIFLIDTSGDLLLEKHLKGST----VVRSICDYFFEDQSSDD-DLEHVPPVISTPHHYLFSVYRDLIFFCAVSTVET 75 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCce----eeeehHHHHHHhhhhcc-ccccCCceecCCceeeeeeeccCcEEEEEEeccC
Confidence 799999999999999999877421 11222333333222111 11 23333333344444444 4567777777777
Q ss_pred cHHHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhhhc
Q 032231 84 NELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFILLI 141 (145)
Q Consensus 84 NEl~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~il 141 (145)
-.|.+.|+|++++++|..||| ..++..+.+|++.||++||||+|+|++..|++++|-
T Consensus 76 pPL~~iefL~rv~dv~~eyFg-~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLk 132 (418)
T KOG2740|consen 76 PPLMVIEFLHRVVDVLLEYFG-GLSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILK 132 (418)
T ss_pred CChhHHHHHHHHHHHHHHHhc-ccCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHH
Confidence 899999999999999999999 699999999999999999999999999999997653
No 11
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.29 E-value=1.1e-05 Score=68.64 Aligned_cols=126 Identities=18% Similarity=0.221 Sum_probs=104.3
Q ss_pred ceeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHH--HHhhcCCcccccceeeecCeEEEEEEeCcEEEEEEecCCc
Q 032231 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVF--TKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDE 83 (145)
Q Consensus 6 ~I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~--~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~e 83 (145)
++-|..+.+++||.+++|-|... .|.+.|.-+- .+.-+. ..+.-++.-+..++||+..-.+|+++++..+.
T Consensus 2 vvlaa~i~t~~Gk~ivsRqf~~M-----sr~RIEgLl~aFpkLv~~--~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~S 74 (512)
T KOG2635|consen 2 VVLAASINTKTGKAIVSRQFREM-----SRSRIEGLLAAFPKLVSA--GKQHTFVETDSVRYVYQPLDNLYIVLITTKQS 74 (512)
T ss_pred eEEEEEEeecCCceeeehHhHhh-----hHHHHHHHHHHhHHhhcc--CCCccEEecccEEEEEEecccEEEEEEecccc
Confidence 45678888999999999998843 4556665443 333322 22457888999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhh
Q 032231 84 NELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFIL 139 (145)
Q Consensus 84 NEl~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~ 139 (145)
|=+==++.|+.|..+...|+. .++|+.|.+|-=.+...+||++-=||=.+.+...
T Consensus 75 NIleDl~TL~Lfskvipey~~-slde~eI~~~~FelifAFDEivsLGyre~v~laQ 129 (512)
T KOG2635|consen 75 NILEDLETLRLFSKVIPEYCS-SLDEKEILENAFELIFAFDEIVSLGYRENVNLAQ 129 (512)
T ss_pred chhhHHHHHHHHHHhchhhhh-hhhHHHHHHhhhhhhhccchhhhhcccccccHHH
Confidence 999999999999999999999 8999999999989999999999999866655443
No 12
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=97.62 E-value=0.0041 Score=47.88 Aligned_cols=79 Identities=22% Similarity=0.201 Sum_probs=69.6
Q ss_pred cCeEEEEEEeCcEEEEEEecCCccHHHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeeechhh
Q 032231 61 EGNVIVYKFVQDLHFFVTGGEDENELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCYSFIL 139 (145)
Q Consensus 61 ~~~~ivy~~~~dl~~~~v~~~~eNEl~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et~~~~ 139 (145)
....++|+..+++.|.+|-+..||=++.-.+|+.++..|...++.-..-..++.+-|.+..+|+.++-.|-.+=.|...
T Consensus 102 ~~k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~ 180 (189)
T PF15001_consen 102 TPKIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRF 180 (189)
T ss_pred CCcEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHH
Confidence 3578999999999999999999999999999999999998888633334778889999999999999999988777654
No 13
>PF08923 MAPKK1_Int: Mitogen-activated protein kinase kinase 1 interacting; InterPro: IPR015019 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry represents Mitogen-activated protein kinase kinase 1 interacting protein, which is a small subcellular adaptor protein required for MAPK signalling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer []. ; PDB: 1VEU_A 1VET_A 1SKO_A 2ZL1_A 3CPT_A.
Probab=97.34 E-value=0.0038 Score=44.69 Aligned_cols=99 Identities=12% Similarity=0.160 Sum_probs=68.4
Q ss_pred CccceeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhh---cCC-cccccceeeecCeEEEEEEeCcEEEEEE
Q 032231 3 TCPSIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQ---KTN-ARTEAEIAMLEGNVIVYKFVQDLHFFVT 78 (145)
Q Consensus 3 ~~~~I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~---~~~-~~~~~~i~~~~~~~ivy~~~~dl~~~~v 78 (145)
+...+.+|+|.|++|=+++.=..+.. +....+.+|....-..+. +-+ +++.+=+..|+++.++.-....+++.++
T Consensus 13 ~v~Gl~~I~itDrDGvpi~~v~~~~~-~~~~~~~~~~~tf~~a~~Q~~KL~lG~nk~ii~~Y~~~qvv~~~~~pl~it~i 91 (119)
T PF08923_consen 13 RVDGLQAIVITDRDGVPIAKVSSDSA-PESAMRPSLLSTFAMAIDQASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFI 91 (119)
T ss_dssp GSTTEEEEEEEETTS-EEEEEE-TTS--GGGGSHHHHCCHHHHHHHHTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEE
T ss_pred ccCCeEEEEEECCCCcEEEEecCCCC-cchhhhhHHHHHHHHHhhcccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEE
Confidence 45678999999999988777554432 444455555543222222 211 2333457789999999999999999999
Q ss_pred ecCCccHHHHHHHHHHHHHHHHhh
Q 032231 79 GGEDENELILATVLQGFFDAVGLL 102 (145)
Q Consensus 79 ~~~~eNEl~l~e~l~~~ve~L~~~ 102 (145)
++++.|--+++.+-+.+...|..+
T Consensus 92 as~~aN~G~il~l~~~L~~~l~~l 115 (119)
T PF08923_consen 92 ASSNANTGLILSLEEELAPILNEL 115 (119)
T ss_dssp EETTS-HHHHHHHHHHHHHHHHHH
T ss_pred ecCCCCHHHHHHhHHHHHHHHHHH
Confidence 999999999999888888877654
No 14
>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole [, ]. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes [, ].
Probab=94.87 E-value=0.68 Score=39.61 Aligned_cols=91 Identities=16% Similarity=0.195 Sum_probs=60.9
Q ss_pred eEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcCCccc-ccceeeecCeEEEEEEeCcEEEEEEecCCccHH
Q 032231 8 KNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNART-EAEIAMLEGNVIVYKFVQDLHFFVTGGEDENEL 86 (145)
Q Consensus 8 ~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~~~~~-~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNEl 86 (145)
+-++|+...||++++|| .. ++.-..|..-+.+..+-..... .-..+.-++.++||..-+-|+++++++.+|.+-
T Consensus 12 kh~fIlS~AGKPIysr~-G~----e~~l~~~~g~~~aiiS~~~~~~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~ 86 (415)
T PF03164_consen 12 KHFFILSSAGKPIYSRY-GD----EDKLSSLMGVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESES 86 (415)
T ss_pred CeEEEECCCCceeEEec-CC----hHHHHHHHHHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHH
Confidence 45889999999999998 22 2233444443333333111110 112345789999999999999999999999988
Q ss_pred HHHHHHHHHHHHHHhhh
Q 032231 87 ILATVLQGFFDAVGLLL 103 (145)
Q Consensus 87 ~l~e~l~~~ve~L~~~~ 103 (145)
.+..-|+.+...+-.++
T Consensus 87 ~l~~qL~~ly~qils~l 103 (415)
T PF03164_consen 87 QLRKQLDYLYSQILSIL 103 (415)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 88777776665554433
No 15
>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D ....
Probab=87.52 E-value=5.9 Score=25.69 Aligned_cols=63 Identities=5% Similarity=0.027 Sum_probs=49.5
Q ss_pred HHHHHHhhcCCcccccceeeecCeEEEEEEeCcEEEEEEecCCccHHHHHHHHHHHHHHHHhhhc
Q 032231 40 KAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENELILATVLQGFFDAVGLLLR 104 (145)
Q Consensus 40 ~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNEl~l~e~l~~~ve~L~~~~~ 104 (145)
+++.+++...+. ....+..+++.+-|..-+++.++++++.+...-..+.+|+.+.+-+..-++
T Consensus 3 ~~il~~i~~~~~--~k~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~ 65 (83)
T PF13774_consen 3 RKILKRIPPNGN--SKMSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYG 65 (83)
T ss_dssp HHHHHTS-TTSE--SEEEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCT
T ss_pred HHHHHhcCCCCC--CeEEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcC
Confidence 455555553220 125677899999999999999999999999999999999999999988887
No 16
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.57 E-value=16 Score=28.80 Aligned_cols=92 Identities=12% Similarity=0.076 Sum_probs=67.1
Q ss_pred CCCCEEEEecCCC--CCCChHHHHHHHHHHHHHhhcCCc-ccccceeeecCeEEEEEEeCcEEEEEEecCCccHHHHHHH
Q 032231 15 SEGKRVAVKYYSN--DWPTNSAKEAFEKAVFTKTQKTNA-RTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENELILATV 91 (145)
Q Consensus 15 ~~G~~~~~kyY~~--~~~~~~~~~~fe~~i~~~~~~~~~-~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNEl~l~e~ 91 (145)
++|-++.+-+=+. .-....+.++--|.++.+..+.++ | .-..-+.+.+-|...++++.+++.+.+.---+.+..
T Consensus 11 ~DGLPLa~s~d~~e~~~~s~~e~r~q~K~L~kkLs~~s~~r---~Sietg~f~fHfli~~~Vcylvicd~~yP~kLAF~Y 87 (216)
T KOG0862|consen 11 RDGLPLAASTDDNEQSGDSLLEYRQQAKSLFKKLSQQSPTR---CSIETGPFVFHFLIESGVCYLVICDKSYPRKLAFSY 87 (216)
T ss_pred cCCcccccccCcccCCCchHHHHHHHHHHHHHhccCCCCcc---cccccCCeEEEEEecCCEEEEEEecCCCcHHHHHHH
Confidence 5777766654211 111214555556788888776532 2 233456799999999999999999999999999999
Q ss_pred HHHHHHHHHhhhcCCCCH
Q 032231 92 LQGFFDAVGLLLRGNVDK 109 (145)
Q Consensus 92 l~~~ve~L~~~~~~~v~e 109 (145)
|+.+.+-+.+.++.++..
T Consensus 88 LedL~~EF~~~~~~~~~~ 105 (216)
T KOG0862|consen 88 LEDLAQEFDKSYGKNIIQ 105 (216)
T ss_pred HHHHHHHHHHhcccccCC
Confidence 999999999999865544
No 17
>PF03259 Robl_LC7: Roadblock/LC7 domain; InterPro: IPR004942 This family includes proteins that are about 100 amino acids long and have been shown to be related []. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions []. This family also includes Golgi-associated MP1 adapter protein (Q9Y2Q5 from SWISSPROT) and MglB from Myxococcus xanthus (Q50883 from SWISSPROT), a protein involved in gliding motility []. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.; PDB: 2B95_B 1Z09_A 2E8J_B 2HZ5_B 3KYE_A 2ZL1_B 1SKO_B 3CPT_B 1VEU_B 1VET_B ....
Probab=75.63 E-value=16 Score=23.36 Aligned_cols=73 Identities=19% Similarity=0.236 Sum_probs=38.6
Q ss_pred CccceeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcC----C-cccccceeeecCeEEEEEEeCc-EEEE
Q 032231 3 TCPSIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKT----N-ARTEAEIAMLEGNVIVYKFVQD-LHFF 76 (145)
Q Consensus 3 ~~~~I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~----~-~~~~~~i~~~~~~~ivy~~~~d-l~~~ 76 (145)
+.+.+++.+++|++|.++.+ ........+.-.+.-..++....+. + +....=.+..++..++..+.++ .+++
T Consensus 11 ~~~gv~~~~l~~~dG~~i~~--~~~~~~~~~~~aa~~a~~~~~~~~~~~~l~~~~~~~v~i~~~~~~i~i~~~~~~~~L~ 88 (91)
T PF03259_consen 11 SVPGVRGAVLVDKDGLVIAS--SGIDDDDAEKLAAMAASLLAAAEKLAKELGEGELEQVRIETEKGEIIITPVGDFYLLV 88 (91)
T ss_dssp HSTTEEEEEEEETTSEEEEE--TSSSHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEEEEEESSEEEEEEECSTCEEEE
T ss_pred CCCCeeEEEEEcCCCCEEEE--ecCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEEEEEECCCEEEEEEcCCCEEEE
Confidence 46789999999999999888 2221111111122223444333321 1 0001113456677777777777 4444
Q ss_pred E
Q 032231 77 V 77 (145)
Q Consensus 77 ~ 77 (145)
+
T Consensus 89 v 89 (91)
T PF03259_consen 89 V 89 (91)
T ss_dssp E
T ss_pred E
Confidence 4
No 18
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=71.30 E-value=48 Score=26.01 Aligned_cols=86 Identities=9% Similarity=0.154 Sum_probs=63.8
Q ss_pred CCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcCCcccccceeeecCeEEEEEEeCcEEEEEEecCCccHHHHHHHHHH
Q 032231 15 SEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENELILATVLQG 94 (145)
Q Consensus 15 ~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNEl~l~e~l~~ 94 (145)
..|-+++++|=.-. ..-...-+++.+|.-+.+. ..-...+|++.+-|.+-+++.++++++++..--.-+.+|..
T Consensus 9 ARGTvvLaeft~~~----gNf~sva~qiL~klp~~~n--~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFLe~ 82 (217)
T KOG0859|consen 9 ARGTVILAEFTEFS----GNFSSIAAQILQKLPSSSN--SKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFLER 82 (217)
T ss_pred ecceEEEEeeeecc----CCHHHHHHHHHHhCCCCCC--CceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHHHHH
Confidence 57999999984321 2344556777777765421 12345689999999999999999999999888888888888
Q ss_pred HHHHHHhhhcCC
Q 032231 95 FFDAVGLLLRGN 106 (145)
Q Consensus 95 ~ve~L~~~~~~~ 106 (145)
+-+-+.+-+|+.
T Consensus 83 Ik~~F~k~YG~~ 94 (217)
T KOG0859|consen 83 IKEDFKKRYGGG 94 (217)
T ss_pred HHHHHHHHhccc
Confidence 887777666644
No 19
>COG3322 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=64.81 E-value=5.9 Score=32.61 Aligned_cols=24 Identities=21% Similarity=0.412 Sum_probs=21.3
Q ss_pred cceeEEEEEcCCCCEEEEecCCCC
Q 032231 5 PSIKNILLLDSEGKRVAVKYYSND 28 (145)
Q Consensus 5 ~~I~~i~iln~~G~~~~~kyY~~~ 28 (145)
-.+.+++++|.+|+++++|.|++.
T Consensus 102 ~g~d~vf~vd~~G~~vy~~~~d~~ 125 (295)
T COG3322 102 LGLDGVFVVDPSGKLVYSKLVDQE 125 (295)
T ss_pred cCccEEEEECCCCCEEEEeeeccc
Confidence 457899999999999999999764
No 20
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown]
Probab=62.79 E-value=95 Score=27.57 Aligned_cols=75 Identities=19% Similarity=0.173 Sum_probs=47.2
Q ss_pred eEEEEEcCCCCEEEEecCCCC--CCChHHHHHHHHHHHHHhhcCCcccccceeeecCeEEEEEEeCcEEEEEEecCCccH
Q 032231 8 KNILLLDSEGKRVAVKYYSND--WPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (145)
Q Consensus 8 ~~i~iln~~G~~~~~kyY~~~--~~~~~~~~~fe~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNE 85 (145)
+-++|+.+.||++++++=... ..+....++...-+ .. + +..--.+...|+++||-+-+-++++++...+...
T Consensus 118 khifilseaGKPiyS~~gs~e~l~stmGv~~alISf~----q~-~-~~~i~si~a~g~k~vfl~kspl~LvA~s~t~~Sa 191 (523)
T KOG0997|consen 118 KHIFILSEAGKPIYSRHGSDEALSSTMGVMQALISFF----QV-S-GLAITSIHAFGNKLVFLQKSPLLLVAVSRTSQSA 191 (523)
T ss_pred ceEEEEecCCCceeeecCcHHHHHHHHHHHHHHHHHH----hh-C-CceEEEEEecCceEEEEecCcEEEEEEcccccCH
Confidence 458999999999999985432 11222233332221 11 1 1011235678999999999999999999876654
Q ss_pred HHH
Q 032231 86 LIL 88 (145)
Q Consensus 86 l~l 88 (145)
--|
T Consensus 192 ~qL 194 (523)
T KOG0997|consen 192 AQL 194 (523)
T ss_pred HHH
Confidence 333
No 21
>PF09561 RE_HpaII: HpaII restriction endonuclease; InterPro: IPR019062 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. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This family includes HpaII, which recognises the double-stranded sequence CCGG and cleaves after C-1.
Probab=47.60 E-value=74 Score=26.99 Aligned_cols=56 Identities=13% Similarity=0.290 Sum_probs=39.6
Q ss_pred eeEEEEEcCCCCEEEEecCCCCCCChHHHHHHHHHHHHHhhcCCcccccceeeecCeEEEEEEeCcEEE
Q 032231 7 IKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHF 75 (145)
Q Consensus 7 I~~i~iln~~G~~~~~kyY~~~~~~~~~~~~fe~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~ 75 (145)
.-+.++.+.+|++++-.-| .|+.||.-++..++=. .|-..-.++-.+|+.-+..||
T Consensus 292 ~gGyivV~~dGevlcYHiy--------~rn~FedYL~~NTkle-----~~SssRh~fG~iy~enG~~yf 347 (355)
T PF09561_consen 292 TGGYIVVKEDGEVLCYHIY--------NRNEFEDYLYNNTKLE-----TPSSSRHKFGFIYRENGEYYF 347 (355)
T ss_pred cceEEEEeCCCCEEEEEeh--------hHHHHHHHHHhccccc-----CCCCCcccceEEEEECCEEEE
Confidence 4588999999999876654 6789999999877632 222223456778887666655
No 22
>PF05228 CHASE4: CHASE4 domain; InterPro: IPR007892 CHASE4 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are upstream of signal transduction pathways in prokaryotes. Specifically, CHASE4 domains are found in histidine kinases in archaea and in predicted diguanylate cyclases/phosphodiesterases in bacteria. Environmental factors that are recognised by CHASE4 domains are not known at this time [].
Probab=37.29 E-value=1.5e+02 Score=20.87 Aligned_cols=24 Identities=25% Similarity=0.425 Sum_probs=19.6
Q ss_pred cceeEEEEEcCCCCEEE--EecCCCC
Q 032231 5 PSIKNILLLDSEGKRVA--VKYYSND 28 (145)
Q Consensus 5 ~~I~~i~iln~~G~~~~--~kyY~~~ 28 (145)
..+.+++++|.+|++++ ++.++..
T Consensus 48 ~~~d~~~~~d~~g~~~~~~~~~~~~~ 73 (161)
T PF05228_consen 48 FGLDLIFILDPDGRVLYSSSKGYDFE 73 (161)
T ss_pred cCccEEEEEcCCCCEEEEeccCcccC
Confidence 56889999999999999 6666543
No 23
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=36.79 E-value=30 Score=17.56 Aligned_cols=17 Identities=29% Similarity=0.429 Sum_probs=14.4
Q ss_pred cHHHHHHHHHHHhcCcE
Q 032231 115 NLDLILLCLDEIVDGGY 131 (145)
Q Consensus 115 n~~~v~lilDEiid~G~ 131 (145)
+++.+..++++|...|+
T Consensus 16 ~~~~a~~~~~~M~~~gv 32 (34)
T PF13812_consen 16 DPDAALQLFDEMKEQGV 32 (34)
T ss_pred CHHHHHHHHHHHHHhCC
Confidence 56778999999999885
No 24
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=34.32 E-value=97 Score=23.55 Aligned_cols=42 Identities=24% Similarity=0.342 Sum_probs=29.4
Q ss_pred HHHHHhhhcCCCCHHHHHHcH------HHHHHHHHHHhcCcEEeeech
Q 032231 96 FDAVGLLLRGNVDKKEALENL------DLILLCLDEIVDGGYATCYSF 137 (145)
Q Consensus 96 ve~L~~~~~~~v~e~~i~~n~------~~v~lilDEiid~G~i~et~~ 137 (145)
+..|-..+++.-+..+|+... +.+..+|+++.+.|++.+.++
T Consensus 32 ~~~L~~lLdG~rt~~eI~~~l~~~~p~~~v~~~L~~L~~~G~l~~~~~ 79 (193)
T TIGR03882 32 YCQLAPLLDGRRTLDEIIAALAGRFPAEEVLYALDRLERRGYLVEDAP 79 (193)
T ss_pred HHHHHHHHcCCCCHHHHHHHhhccCCHHHHHHHHHHHHHCCCEeccCC
Confidence 333334444566666665554 679999999999999998543
No 25
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=34.00 E-value=36 Score=16.74 Aligned_cols=18 Identities=22% Similarity=0.383 Sum_probs=14.6
Q ss_pred HcHHHHHHHHHHHhcCcE
Q 032231 114 ENLDLILLCLDEIVDGGY 131 (145)
Q Consensus 114 ~n~~~v~lilDEiid~G~ 131 (145)
.+++.+..+++||...|+
T Consensus 14 ~~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 14 GQFEEALEVFDEMRERGI 31 (31)
T ss_pred chHHHHHHHHHHHhHCcC
Confidence 467788999999998874
No 26
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=33.71 E-value=82 Score=16.96 Aligned_cols=31 Identities=16% Similarity=0.199 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHhhhcCCCCHHHHHHcHHHHH
Q 032231 90 TVLQGFFDAVGLLLRGNVDKKEALENLDLIL 120 (145)
Q Consensus 90 e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~ 120 (145)
++-+.++..++.+++.+-++..|..-.+.++
T Consensus 5 ~~C~~~v~~i~~~l~~~~t~~~I~~~l~~~C 35 (39)
T PF05184_consen 5 DICKFVVKEIEKLLKNNKTEEEIKKALEKAC 35 (39)
T ss_dssp HHHHHHHHHHHHHHHSTCHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHcCccHHHHHHHHHHHH
Confidence 4567788888999988899998888777665
No 27
>KOG1373 consensus Transport protein Sec61, alpha subunit [Intracellular trafficking, secretion, and vesicular transport; Posttranslational modification, protein turnover, chaperones]
Probab=30.50 E-value=70 Score=27.72 Aligned_cols=46 Identities=24% Similarity=0.299 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCHHHH----HHc-----HHHHHHHHHHHhcCcEEe
Q 032231 87 ILATVLQGFFDAVGLLLRGNVDKKEA----LEN-----LDLILLCLDEIVDGGYAT 133 (145)
Q Consensus 87 ~l~e~l~~~ve~L~~~~~~~v~e~~i----~~n-----~~~v~lilDEiid~G~i~ 133 (145)
++..+.++.+-++..++| ..++..+ +=+ -..+.++|||+++.||=+
T Consensus 123 iii~vgqa~~yV~tG~yG-~p~dLg~~~clLii~QL~~Agiiv~lLdEllqKGyGl 177 (476)
T KOG1373|consen 123 IIITVGQAVVYVMTGMYG-SPSDLGVGICLLIILQLFFAGIIVILLDELLQKGYGL 177 (476)
T ss_pred HHHHHHHHHHHhhhcccC-ChhhcchhHHHHHHHHHHHhhHHHHHHHHHHHhccCc
Confidence 456677778888888888 5666432 222 245678999999999843
No 28
>PF02334 RTP: Replication terminator protein; InterPro: IPR003432 The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.; GO: 0003677 DNA binding, 0006274 DNA replication termination; PDB: 2DPU_A 2DPD_A 1F4K_A 1J0R_B 2EFW_F 2DQR_B 1BM9_B.
Probab=29.18 E-value=1e+02 Score=21.98 Aligned_cols=37 Identities=19% Similarity=0.242 Sum_probs=25.3
Q ss_pred HHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEeee
Q 032231 95 FFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYATCY 135 (145)
Q Consensus 95 ~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~et 135 (145)
+.+.|..-|+ ++. -.=|-..+|-.|+|++++|++-.+
T Consensus 37 ~Ld~lr~EFk-~~G---y~P~hsEvYraLHeL~~dGilk~~ 73 (122)
T PF02334_consen 37 LLDELRSEFK-PLG---YRPNHSEVYRALHELVDDGILKQV 73 (122)
T ss_dssp HHHHHHHHHT-TTT-------HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHhh-hcC---CCCCHHHHHHHHHHHHhhhHHHHH
Confidence 4566777787 444 445667899999999999998433
No 29
>PF14903 WG_beta_rep: WG containing repeat
Probab=28.43 E-value=62 Score=16.78 Aligned_cols=17 Identities=29% Similarity=0.382 Sum_probs=13.8
Q ss_pred EEcCCCCEEEEecCCCC
Q 032231 12 LLDSEGKRVAVKYYSND 28 (145)
Q Consensus 12 iln~~G~~~~~kyY~~~ 28 (145)
++|.+|+.++.--|+..
T Consensus 3 ~id~~G~~vi~~~yd~i 19 (35)
T PF14903_consen 3 YIDKNGKIVIPPKYDEI 19 (35)
T ss_pred EEeCCCCEEEEccccCc
Confidence 57999999998887753
No 30
>PF04086 SRP-alpha_N: Signal recognition particle, alpha subunit, N-terminal; InterPro: IPR007222 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 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. This entry represents the alpha subunit of the SR receptor.; GO: 0003924 GTPase activity, 0005047 signal recognition particle binding, 0005525 GTP binding, 0006184 GTP catabolic process, 0006886 intracellular protein transport, 0005785 signal recognition particle receptor complex; PDB: 2FH5_A 2GO5_1.
Probab=28.04 E-value=3e+02 Score=21.71 Aligned_cols=51 Identities=10% Similarity=0.061 Sum_probs=25.6
Q ss_pred ccceeeecCeEEEEEEeCcE--EEEEEecCCccHHHHHHHHHHHHHHHHhhhc
Q 032231 54 EAEIAMLEGNVIVYKFVQDL--HFFVTGGEDENELILATVLQGFFDAVGLLLR 104 (145)
Q Consensus 54 ~~~i~~~~~~~ivy~~~~dl--~~~~v~~~~eNEl~l~e~l~~~ve~L~~~~~ 104 (145)
..+.+.+++|.+=|+-.+++ .|+||-..-=.=..+-++|..+...+...|+
T Consensus 18 ~~~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~ 70 (279)
T PF04086_consen 18 GNSSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYK 70 (279)
T ss_dssp ----------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTH
T ss_pred CCCceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHh
Confidence 34668999999999998875 5555544444555556666666666655555
No 31
>PF13998 MgrB: MgrB protein
Probab=27.92 E-value=41 Score=18.07 Aligned_cols=14 Identities=43% Similarity=0.522 Sum_probs=11.0
Q ss_pred HHHHHHHhcCcEEe
Q 032231 120 LLCLDEIVDGGYAT 133 (145)
Q Consensus 120 ~lilDEiid~G~i~ 133 (145)
.+.||-++|+|...
T Consensus 3 llald~~CDQg~~F 16 (29)
T PF13998_consen 3 LLALDSYCDQGEQF 16 (29)
T ss_pred HHHHHHHhcCCCCc
Confidence 46899999999543
No 32
>PF08866 DUF1831: Putative amino acid metabolism; InterPro: IPR014965 These short proteins are functionally uncharacterised. ; PDB: 2IAY_A.
Probab=27.77 E-value=51 Score=23.37 Aligned_cols=22 Identities=18% Similarity=0.365 Sum_probs=16.3
Q ss_pred HHHcHHHHHHHHHHHhcCcEEe
Q 032231 112 ALENLDLILLCLDEIVDGGYAT 133 (145)
Q Consensus 112 i~~n~~~v~lilDEiid~G~i~ 133 (145)
--..-++.+.++|++|+.|++.
T Consensus 90 ~~~~ve~~~Fi~d~lveR~Vl~ 111 (112)
T PF08866_consen 90 NAELVEKYYFIMDDLVERGVLE 111 (112)
T ss_dssp -HHHHHHHHHHHHHHHHTTSEE
T ss_pred cHHHHHHHHHHHHHHHhccccc
Confidence 3344566789999999999864
No 33
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=26.50 E-value=2.5e+02 Score=20.18 Aligned_cols=96 Identities=8% Similarity=0.150 Sum_probs=53.7
Q ss_pred ceeEEEEEcCCCCEEEEecCCCCCCChH--HHHHH---HHHHHHHhhcCCc-ccccc--eeeecC-eEEEEEEeCcEEEE
Q 032231 6 SIKNILLLDSEGKRVAVKYYSNDWPTNS--AKEAF---EKAVFTKTQKTNA-RTEAE--IAMLEG-NVIVYKFVQDLHFF 76 (145)
Q Consensus 6 ~I~~i~iln~~G~~~~~kyY~~~~~~~~--~~~~f---e~~i~~~~~~~~~-~~~~~--i~~~~~-~~ivy~~~~dl~~~ 76 (145)
.|++++|+|+.|..++.|-+........ +---+ -..++.-..+..+ ...++ .+..++ .-.+|+..-++-|+
T Consensus 2 ave~~~iINksGglifqref~~~et~lnsneyLiLastlhgV~aI~tq~~p~~gssg~~~l~~~~f~m~I~qT~TG~kFV 81 (134)
T COG5122 2 AVEQFFIINKSGGLIFQREFGEGETELNSNEYLILASTLHGVSAILTQTIPLPGSSGRLVLYFRNFVMTIFQTTTGTKFV 81 (134)
T ss_pred ceeEEEEEecCCcEEEEEeccCCccccCcccEEEEeechhhhhhhhhhcccCCCCCceEEEEeccEEEEEEEecCCcEEE
Confidence 4789999999999999999965311100 00000 0122221111111 11233 344555 44578899999999
Q ss_pred EEe-cCCccHHHHHHHHHHHHHHHHhhhc
Q 032231 77 VTG-GEDENELILATVLQGFFDAVGLLLR 104 (145)
Q Consensus 77 ~v~-~~~eNEl~l~e~l~~~ve~L~~~~~ 104 (145)
+++ +...|.++= ++.+++....|--
T Consensus 82 ~~~~k~t~na~~q---l~kiY~lYsdYV~ 107 (134)
T COG5122 82 FVAEKRTVNALFQ---LQKIYSLYSDYVT 107 (134)
T ss_pred EEecCCchhHHHH---HHHHHHHHHHHhh
Confidence 999 445565443 5566666655544
No 34
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=25.40 E-value=1.2e+02 Score=20.02 Aligned_cols=17 Identities=24% Similarity=0.239 Sum_probs=15.3
Q ss_pred HHHHHHHHHHhcCcEEe
Q 032231 117 DLILLCLDEIVDGGYAT 133 (145)
Q Consensus 117 ~~v~lilDEiid~G~i~ 133 (145)
+....+++++.++|+|.
T Consensus 25 ~~~~~il~~L~d~GyI~ 41 (88)
T PF09639_consen 25 SYWSDILRMLQDEGYIK 41 (88)
T ss_dssp HHHHHHHHHHHHHTSEE
T ss_pred HHHHHHHHHHHHCCCcc
Confidence 77889999999999995
No 35
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=25.24 E-value=63 Score=21.58 Aligned_cols=30 Identities=17% Similarity=0.098 Sum_probs=23.3
Q ss_pred CCHHHHHHc----HHHHHHHHHHHhcCcEEeeec
Q 032231 107 VDKKEALEN----LDLILLCLDEIVDGGYATCYS 136 (145)
Q Consensus 107 v~e~~i~~n----~~~v~lilDEiid~G~i~et~ 136 (145)
+....|... -+.|-.++|++++.|+|-.|-
T Consensus 66 v~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi 99 (102)
T PF08784_consen 66 VHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTI 99 (102)
T ss_dssp EEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESS
T ss_pred ccHHHHHHHhCcCHHHHHHHHHHHHhCCeEeccc
Confidence 555555544 478999999999999998874
No 36
>cd04670 Nudix_Hydrolase_12 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=24.72 E-value=2.3e+02 Score=19.09 Aligned_cols=38 Identities=18% Similarity=0.373 Sum_probs=25.7
Q ss_pred EEEEcCCCCEEEEecCCC--C-C--------CChHHHHHHHHHHHHHhh
Q 032231 10 ILLLDSEGKRVAVKYYSN--D-W--------PTNSAKEAFEKAVFTKTQ 47 (145)
Q Consensus 10 i~iln~~G~~~~~kyY~~--~-~--------~~~~~~~~fe~~i~~~~~ 47 (145)
.+++|.+|+.++.|.+.. . + +.+.-.++..+.+.+.+.
T Consensus 7 ~~v~~~~~~vLl~~r~~~~~~~w~~PGG~ve~gEt~~~aa~RE~~EE~G 55 (127)
T cd04670 7 GLVLNEKNEVLVVQERNKTPNGWKLPGGLVDPGEDIFDGAVREVLEETG 55 (127)
T ss_pred EEEEcCCCeEEEEEccCCCCCcEECCCccCCCCCCHHHHHHHHHHHHHC
Confidence 466788999999886652 1 0 223466777888887776
No 37
>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses. Syndecan-2 induces spine formation by recruiting intracellular vesicles toward postsynaptic sites through the interaction with synbindin []. ; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005801 cis-Golgi network; PDB: 3CUE_C 2J3T_C 2ZMV_B 2JSN_A.
Probab=23.54 E-value=2.9e+02 Score=19.88 Aligned_cols=98 Identities=6% Similarity=0.160 Sum_probs=52.7
Q ss_pred eeEEEEEcCCCCEEEEecCCCCC------CChHHHHHHHHHHHH------HhhcCCcc----cccce--eeecCeEEE-E
Q 032231 7 IKNILLLDSEGKRVAVKYYSNDW------PTNSAKEAFEKAVFT------KTQKTNAR----TEAEI--AMLEGNVIV-Y 67 (145)
Q Consensus 7 I~~i~iln~~G~~~~~kyY~~~~------~~~~~~~~fe~~i~~------~~~~~~~~----~~~~i--~~~~~~~iv-y 67 (145)
|.+++|+|+.|.-++.|-|.... .+..++..+-.-++. +....+.. ..+.+ +.-+.+++- |
T Consensus 1 IyslyI~nr~G~lIy~~~~~~~~~~~~~~~~~ne~~ll~g~l~sl~~i~~klsp~~~~~~~~~~~g~~~~~T~~yklh~~ 80 (142)
T PF04099_consen 1 IYSLYIFNRSGGLIYYREWNRSKNEGQPKLSSNEYKLLAGMLHSLKAIASKLSPVDSKPNEPGSSGFESFETDTYKLHCF 80 (142)
T ss_dssp EEEEEEE-TTS-EEEEEETSSSS--E-SSSCHHHHHHHHHHHHHHHHHHHHT-SSSSSS-SSS--SEEEEEESS-EEEEE
T ss_pred CeEEEEEeCCcceeeehhhCCCCccccCCCChhHHHHHHhhHHHHHHHHHHhCCCCcccccccceeEEEEEeCCEEEEEE
Confidence 67899999999999999997642 233444444443332 22221111 11223 345566654 4
Q ss_pred EEeCcEEEEEEecCCccHHHHHHHHHHHHHHHHhh-hcC
Q 032231 68 KFVQDLHFFVTGGEDENELILATVLQGFFDAVGLL-LRG 105 (145)
Q Consensus 68 ~~~~dl~~~~v~~~~eNEl~l~e~l~~~ve~L~~~-~~~ 105 (145)
..-.++-|++++|.+... ..-++++.+.+....| .++
T Consensus 81 eT~TGlKFvl~td~~~~~-~~~~l~~~~~~lY~dyV~KN 118 (142)
T PF04099_consen 81 ETPTGLKFVLITDPNVPS-LRDELLRIYYELYVDYVVKN 118 (142)
T ss_dssp E-TTS-EEEEEE-TTCCH-CHHHHHHHHHHHHHHHHHS-
T ss_pred EcCcCcEEEEEecCCCcc-HHHHHHHHHHHHHHHHHhhC
Confidence 567889999999998743 3455566677766554 443
No 38
>PF04315 DUF462: Protein of unknown function, DUF462; InterPro: IPR007411 This family consists of bacterial proteins of uncharacterised function.
Probab=23.41 E-value=69 Score=24.19 Aligned_cols=20 Identities=20% Similarity=0.277 Sum_probs=16.5
Q ss_pred EEecCCCCCCChHHHHHHHH
Q 032231 21 AVKYYSNDWPTNSAKEAFEK 40 (145)
Q Consensus 21 ~~kyY~~~~~~~~~~~~fe~ 40 (145)
+.-||.|+-.+.++|++||+
T Consensus 65 fGYWY~PDGR~~~qQ~~FE~ 84 (164)
T PF04315_consen 65 FGYWYCPDGRDAEQQAEFEQ 84 (164)
T ss_pred CCCCcCCCCCCHHHHHHHHh
Confidence 45689998778889999998
No 39
>cd03016 PRX_1cys Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides. As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its substrates. Having no resolving cysteine, the oxidized enzyme is resolved by an external small-molecule or protein reductant such as thioredoxin or glutaredoxin. Similar to typical 2-cys PRX, 1-cys PRX forms a functional dimeric unit with a B-type interface, as well as a decameric structure which is stabilized in the reduced form of the enzyme. Other oligomeric forms, tetramers and hexamers, have also been reported. Mammalian 1-cys PRX is localized cellularly in the cytosol and is expressed at high levels in brain, eye, testes an
Probab=21.59 E-value=2.6e+02 Score=21.06 Aligned_cols=21 Identities=19% Similarity=0.591 Sum_probs=17.9
Q ss_pred eeEEEEEcCCCCEEEEecCCC
Q 032231 7 IKNILLLDSEGKRVAVKYYSN 27 (145)
Q Consensus 7 I~~i~iln~~G~~~~~kyY~~ 27 (145)
+.+.+|+|.+|+++...+|..
T Consensus 117 ~r~~fiID~~G~I~~~~~~~~ 137 (203)
T cd03016 117 VRAVFIIDPDKKIRLILYYPA 137 (203)
T ss_pred eeEEEEECCCCeEEEEEecCC
Confidence 457999999999999988854
No 40
>cd03671 Ap4A_hydrolase_plant_like Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one group (represented by this subfamily) and fungi/animals/archaea enzymes fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for the inhibition of such invasive bacteria. Besides the signature nudix motif (G[X5]E[X7]REUXEEXGU where U is Ile, Leu, or Val), Ap4A hydrolase is structurally
Probab=21.52 E-value=1.1e+02 Score=21.59 Aligned_cols=40 Identities=13% Similarity=0.164 Sum_probs=27.6
Q ss_pred EEEEEcCCCCEEEEecCCCC-C---------CChHHHHHHHHHHHHHhhc
Q 032231 9 NILLLDSEGKRVAVKYYSND-W---------PTNSAKEAFEKAVFTKTQK 48 (145)
Q Consensus 9 ~i~iln~~G~~~~~kyY~~~-~---------~~~~~~~~fe~~i~~~~~~ 48 (145)
+++++|.+|+.++.|.+... . +.+.-.++-.+.+.+.+.-
T Consensus 7 ~~ii~~~~~~vLL~~r~~~~~~W~~PgG~~e~gE~~~~aA~REv~EEtGl 56 (147)
T cd03671 7 GVVLFNEDGKVFVGRRIDTPGAWQFPQGGIDEGEDPEQAALRELEEETGL 56 (147)
T ss_pred EEEEEeCCCEEEEEEEcCCCCCEECCcCCCCCCcCHHHHHHHHHHHHHCC
Confidence 56777999999998887643 1 2234566777777777663
No 41
>COG4001 Predicted metal-binding protein [General function prediction only]
Probab=21.28 E-value=2.1e+02 Score=19.58 Aligned_cols=36 Identities=14% Similarity=0.160 Sum_probs=30.1
Q ss_pred cHHHHHHHHHHHHHHHHhhhcCCCCHHHHHHcHHHHHH
Q 032231 84 NELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILL 121 (145)
Q Consensus 84 NEl~l~e~l~~~ve~L~~~~~~~v~e~~i~~n~~~v~l 121 (145)
-.-++..++..++|.=..-|+ |+|++|.+.+..-|.
T Consensus 53 kCra~a~ivkkive~garAfg--Vdee~iRE~~~d~yw 88 (102)
T COG4001 53 KCRALASIVKKIVERGARAFG--VDEEDIREQMHDQYW 88 (102)
T ss_pred HHHHHHHHHHHHHHhcchhcC--CCHHHHHHHHHHHHH
Confidence 456788888889988888886 999999999887664
No 42
>cd04685 Nudix_Hydrolase_26 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=20.73 E-value=1.1e+02 Score=21.47 Aligned_cols=40 Identities=20% Similarity=0.297 Sum_probs=28.3
Q ss_pred EEEEEcCCCCEEEEecCCCC--C------------CChHHHHHHHHHHHHHhhc
Q 032231 9 NILLLDSEGKRVAVKYYSND--W------------PTNSAKEAFEKAVFTKTQK 48 (145)
Q Consensus 9 ~i~iln~~G~~~~~kyY~~~--~------------~~~~~~~~fe~~i~~~~~~ 48 (145)
.++++|.+|+.++.|...+. . +.+...++..+.+.+.+.-
T Consensus 4 ~~~i~~~~g~vLl~r~~~~~~~~~~~w~~PgG~ve~gE~~~~a~~Re~~EE~G~ 57 (133)
T cd04685 4 RVVLLDPDDRVLLLRGDDPDSPGPDWWFTPGGGVEPGESPEQAARRELREETGI 57 (133)
T ss_pred EEEEEcCCCeEEEEEEeCCCCCCCCEEECCcCCCCCCCCHHHHHHHHHHHHHCC
Confidence 47788999999998876531 0 2335677777888877663
No 43
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=20.55 E-value=76 Score=15.64 Aligned_cols=19 Identities=16% Similarity=0.319 Sum_probs=15.4
Q ss_pred HcHHHHHHHHHHHhcCcEE
Q 032231 114 ENLDLILLCLDEIVDGGYA 132 (145)
Q Consensus 114 ~n~~~v~lilDEiid~G~i 132 (145)
.+++.+..++++|...|+.
T Consensus 14 ~~~~~a~~~~~~M~~~g~~ 32 (35)
T TIGR00756 14 GRVEEALELFKEMLERGIE 32 (35)
T ss_pred CCHHHHHHHHHHHHHcCCC
Confidence 3567889999999998864
No 44
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=20.40 E-value=2.1e+02 Score=17.19 Aligned_cols=35 Identities=23% Similarity=0.265 Sum_probs=21.2
Q ss_pred HHHHHHHhhhcCCCCHHHHHHcHHHHHHHHHHHhcCcEEe
Q 032231 94 GFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGYAT 133 (145)
Q Consensus 94 ~~ve~L~~~~~~~v~e~~i~~n~~~v~lilDEiid~G~i~ 133 (145)
.+++.|..-|+ +++..+ -..+.-.|.++...|+|+
T Consensus 34 ei~~~l~~~y~--~~~~~~---~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 34 EIVDALAEEYD--VDPEEA---EEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp HHHHHHHHHTT----HHHH---HHHHHHHHHHHHHTT---
T ss_pred HHHHHHHHHcC--CCHHHH---HHHHHHHHHHHHHCcCcC
Confidence 46666666664 666655 456777888888888874
No 45
>PRK00714 RNA pyrophosphohydrolase; Reviewed
Probab=20.26 E-value=2.8e+02 Score=19.94 Aligned_cols=40 Identities=15% Similarity=0.297 Sum_probs=27.8
Q ss_pred EEEEEcCCCCEEEEecCCCC----------CCChHHHHHHHHHHHHHhhc
Q 032231 9 NILLLDSEGKRVAVKYYSND----------WPTNSAKEAFEKAVFTKTQK 48 (145)
Q Consensus 9 ~i~iln~~G~~~~~kyY~~~----------~~~~~~~~~fe~~i~~~~~~ 48 (145)
+++++|.+|+.++.|..... -+.+...++..+.+.+.+.-
T Consensus 12 ~~~i~~~~g~vLL~~r~~~~~~w~~P~G~~~~gE~~~~aa~REl~EEtG~ 61 (156)
T PRK00714 12 GIILLNRQGQVFWGRRIGQGHSWQFPQGGIDPGETPEQAMYRELYEEVGL 61 (156)
T ss_pred EEEEEecCCEEEEEEEcCCCCeEECCcccCCCCcCHHHHHHHHHHHHhCC
Confidence 46788999999999987641 12334567777777777653
Done!