Query 030448
Match_columns 177
No_of_seqs 107 out of 841
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 13:53:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030448.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030448hhsearch_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 3.3E-40 7.1E-45 247.4 16.0 170 2-177 4-175 (175)
2 PF01217 Clat_adaptor_s: Clath 100.0 1.1E-36 2.3E-41 229.6 18.7 139 6-148 1-139 (141)
3 COG5541 RET3 Vesicle coat comp 100.0 2.6E-31 5.6E-36 199.0 13.4 170 3-177 4-185 (187)
4 COG5030 APS2 Clathrin adaptor 100.0 2.3E-31 5E-36 195.7 12.6 141 6-150 1-141 (152)
5 KOG0936 Clathrin adaptor compl 100.0 6.2E-29 1.3E-33 185.5 14.4 139 6-148 1-145 (182)
6 KOG0935 Clathrin adaptor compl 100.0 1.4E-28 2.9E-33 177.0 11.3 138 6-146 1-138 (143)
7 KOG0934 Clathrin adaptor compl 100.0 1.7E-28 3.7E-33 180.2 7.2 139 6-148 1-139 (145)
8 KOG0938 Adaptor complexes medi 99.9 9.9E-26 2.2E-30 187.5 12.0 138 6-150 1-138 (446)
9 KOG0937 Adaptor complexes medi 99.9 1.8E-21 3.8E-26 167.1 14.5 137 7-148 1-137 (424)
10 KOG2740 Clathrin-associated pr 99.8 1E-20 2.2E-25 158.6 8.1 140 6-150 1-141 (418)
11 KOG2635 Medium subunit of clat 98.5 5.9E-06 1.3E-10 71.9 13.8 139 6-150 2-140 (512)
12 PF15001 AP-5_subunit_s1: AP-5 97.6 0.0046 9.9E-08 48.8 13.6 82 61-142 102-183 (189)
13 PF03164 Mon1: Trafficking pro 97.1 0.017 3.7E-07 50.9 13.4 90 8-102 12-102 (415)
14 PF08923 MAPKK1_Int: Mitogen-a 97.0 0.015 3.2E-07 42.7 10.4 97 5-102 15-115 (119)
15 PF13774 Longin: Regulated-SNA 92.2 2.4 5.2E-05 28.4 8.9 49 56-104 17-65 (83)
16 KOG0997 Uncharacterized conser 91.0 4.5 9.8E-05 36.4 11.4 76 8-89 118-195 (523)
17 KOG0859 Synaptobrevin/VAMP-lik 87.3 6.9 0.00015 31.3 8.8 85 15-105 9-93 (217)
18 KOG0862 Synaptobrevin/VAMP-lik 84.4 20 0.00043 29.0 10.7 74 34-109 32-105 (216)
19 PF04099 Sybindin: Sybindin-li 82.1 19 0.00041 26.9 11.9 98 7-105 1-118 (142)
20 COG5122 TRS23 Transport protei 68.1 45 0.00097 24.4 10.0 94 6-105 2-108 (134)
21 PF03690 UPF0160: Uncharacteri 62.5 63 0.0014 27.7 8.5 78 98-175 94-184 (318)
22 KOG3368 Transport protein part 62.4 64 0.0014 24.2 10.6 90 6-97 2-102 (140)
23 PF09561 RE_HpaII: HpaII restr 60.0 24 0.00053 30.6 5.6 56 7-75 292-347 (355)
24 PF05228 CHASE4: CHASE4 domain 52.4 51 0.0011 24.1 5.7 23 6-28 49-73 (161)
25 PF09201 SRX: SRX; InterPro: 51.0 1.1E+02 0.0023 23.2 7.3 76 6-81 1-86 (148)
26 PF04086 SRP-alpha_N: Signal r 48.3 1.3E+02 0.0028 24.6 8.0 52 55-106 19-72 (279)
27 PF03259 Robl_LC7: Roadblock/L 45.1 86 0.0019 20.4 6.7 69 4-77 12-89 (91)
28 PF08784 RPA_C: Replication pr 40.8 26 0.00057 24.2 2.4 49 88-136 45-99 (102)
29 KOG2948 Predicted metal-bindin 38.1 2.2E+02 0.0048 24.3 7.7 79 97-175 97-188 (327)
30 COG3322 Predicted periplasmic 36.6 30 0.00066 29.3 2.5 23 6-28 103-125 (295)
31 PF01535 PPR: PPR repeat; Int 35.2 33 0.00073 17.3 1.8 18 114-131 14-31 (31)
32 PF13812 PPR_3: Pentatricopept 33.6 34 0.00074 17.8 1.6 18 114-131 15-32 (34)
33 PF02001 DUF134: Protein of un 32.8 65 0.0014 23.1 3.4 24 153-176 67-90 (106)
34 PF15349 DCA16: DDB1- and CUL4 31.5 47 0.001 25.4 2.6 20 156-175 137-156 (216)
35 PF02268 TFIIA_gamma_N: Transc 30.0 49 0.0011 20.4 2.0 13 121-133 17-29 (49)
36 KOG3369 Transport protein part 27.6 3.1E+02 0.0067 21.7 9.2 45 57-103 125-170 (199)
37 PRK15360 pathogenicity island 26.7 2E+02 0.0044 21.6 5.2 38 57-94 30-71 (137)
38 COG1500 Predicted exosome subu 25.1 1.5E+02 0.0033 24.2 4.6 63 106-168 57-133 (234)
39 TIGR03882 cyclo_dehyd_2 bacter 24.7 1.6E+02 0.0036 22.9 4.7 35 102-136 38-78 (193)
40 PF06694 Plant_NMP1: Plant nuc 24.0 4.6E+02 0.01 22.5 7.6 79 88-172 102-185 (325)
41 KOG1766 Enhancer of rudimentar 23.6 1.1E+02 0.0024 21.5 3.1 43 87-129 24-67 (104)
42 cd00894 PI3Kc_IB_gamma Phospho 22.9 3.5E+02 0.0076 23.7 6.7 93 52-146 219-329 (365)
43 TIGR00756 PPR pentatricopeptid 22.5 70 0.0015 16.2 1.6 20 114-133 14-33 (35)
44 KOG0861 SNARE protein YKT6, sy 22.1 4E+02 0.0087 21.1 9.3 65 35-99 36-101 (198)
45 cd05174 PI3Kc_IA_delta Phospho 20.5 4.6E+02 0.01 22.9 7.0 93 52-146 215-325 (361)
No 1
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.3e-40 Score=247.38 Aligned_cols=170 Identities=56% Similarity=0.882 Sum_probs=161.5
Q ss_pred CCccceeeEEEEcCCCCEeEEecCCCCCCC-hhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEEEEEec
Q 030448 2 DTCPSIKNILLLDSEGKRVAVKYYSNDWPT-NSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGG 80 (177)
Q Consensus 2 ~~~~mI~~i~iln~~G~~il~k~Y~~~~~~-~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~ 80 (177)
-|++.+++++|+|++|+|+++|||.+++++ .++|++||+.+|.|+.+. +++|..++|..+||+..-||+|+++|.
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 478899999999999999999999998887 789999999999997763 479999999999999999999999999
Q ss_pred CCccHHHHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcCCCcCCCCCCChhhH
Q 030448 81 EDENELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVASHSVDVGAPLSEQTI 160 (177)
Q Consensus 81 ~~eNel~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~~~~~~~~~~~~~~~ 160 (177)
.+|||+++.++|+++++++...++++.+++.+++|+|.+++++||+||+|+|+||||+.|..|+..++.+. ++++|..
T Consensus 80 ~~ENEl~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~~~~~--~~~eq~~ 157 (175)
T KOG3343|consen 80 EEENELMLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALRPTDE--PLSEQSV 157 (175)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccCCCCc--chHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999986 7889999
Q ss_pred HHH-HHHHHHHHHHHhhC
Q 030448 161 SQA-LATAREHLTRSLLK 177 (177)
Q Consensus 161 ~~a-~~~a~~~~~~~l~~ 177 (177)
.+. +.+||+++..++++
T Consensus 158 ~~~~~q~A~eq~k~~llk 175 (175)
T KOG3343|consen 158 AQGFLQSAKEQIKWSLLK 175 (175)
T ss_pred HHHHHHHHHHHHHHHhhC
Confidence 999 99999999999875
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=1.1e-36 Score=229.64 Aligned_cols=139 Identities=40% Similarity=0.635 Sum_probs=123.1
Q ss_pred ceeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEEEEEecCCccH
Q 030448 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNe 85 (177)
||+|++|+|++|+++++|||++. +.++++.+.+++.+++..++.. .+|++.++++.++|++++||||+++++.++||
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~--~~~~~~~~~~~~~~~~~~~~~~-~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNe 77 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDV--SEEERQKLFEKFIKKKSSRNSK-QSPIFEHDNYRIVYKRYSDLYFVVVGDENENE 77 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTS--TSHHHHHHHHHHHHHHHTSSSS-STSEEEETTEEEEEEEETTEEEEEEESSTSBH
T ss_pred CEEEEEEEcCCCCEEEehhcCCc--cHHHHHHHHHHHHHHHHhcccc-cceeeecccceeeeEeeccEEEEEEeecccch
Confidence 89999999999999999999764 4566677777777777666533 37999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcCCC
Q 030448 86 LILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVASHS 148 (177)
Q Consensus 86 l~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~~~ 148 (177)
++++++|++++++|+.||++ +++.++++||+.+|++||||+|+|+|++||++.|++|+.+++
T Consensus 78 l~~~e~l~~~v~~l~~~~~~-v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~v~~~~ 139 (141)
T PF01217_consen 78 LLLLEFLHRLVEVLDDYFGN-VSEKDILENFDLVYLILDEIIDGGIILETDPNVILKRVTMQD 139 (141)
T ss_dssp HHHHHHHHHHHHHHHHHHSS--SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHHHHHCC
T ss_pred HHHHHHHHHhhhhhhhhhcc-ccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHHHHHhh
Confidence 99999999999999999995 677789999999999999999999999999999999998875
No 3
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=2.6e-31 Score=198.97 Aligned_cols=170 Identities=29% Similarity=0.464 Sum_probs=154.4
Q ss_pred CccceeeEEEEcCCCCEeEEecCCCC---------CCChhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcE
Q 030448 3 TCPSIKNILLLDSEGKRVAVKYYSND---------WPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDL 73 (177)
Q Consensus 3 ~~~mI~~i~iln~~G~~il~k~Y~~~---------~~~~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl 73 (177)
|+..|.|++|+|++|++|+.|||.|. +.+.++++.||..+++|+.+.. .+|..+++..++|+++.|+
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 SLYDVEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTAKDR----ESILMFYDRLVMCKRLDDV 79 (187)
T ss_pred chheeeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhhcCc----cceeeEcceeeeeeeehhE
Confidence 47789999999999999999999874 2334578999999999876654 5899999999999999999
Q ss_pred EEEEEecCCccHHHHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcCCC-cCC-
Q 030448 74 HFFVTGGEDENELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVASHS-VDV- 151 (177)
Q Consensus 74 ~~~~v~~~~eNel~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~~~-~~~- 151 (177)
.+++++.-++||.++.+.++.|..+|..+++.+.+++.+.+|||.+.+++||.+|+|+|++|+++.|++|+..++ .++
T Consensus 80 ~~yiv~~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ia~rv~K~p~~E~q 159 (187)
T COG5541 80 LLYIVSPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRVPKPPNFEGQ 159 (187)
T ss_pred EEEEecccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHHHHHhCCCCCCcchh
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999855 454
Q ss_pred -CCCCChhhHHHHHHHHHHHHHHHhhC
Q 030448 152 -GAPLSEQTISQALATAREHLTRSLLK 177 (177)
Q Consensus 152 -~~~~~~~~~~~a~~~a~~~~~~~l~~ 177 (177)
.++. |+||.++|.+||+++..++++
T Consensus 160 ~~~~~-~~GF~~~~~kA~~k~ser~~k 185 (187)
T COG5541 160 DGMKV-PRGFASFLHKATKKLSERSNK 185 (187)
T ss_pred hhhcc-chhHHHHHHHHHHHHHHHHhc
Confidence 3444 889999999999999998764
No 4
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=99.97 E-value=2.3e-31 Score=195.70 Aligned_cols=141 Identities=21% Similarity=0.380 Sum_probs=131.6
Q ss_pred ceeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEEEEEecCCccH
Q 030448 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNe 85 (177)
||++++|.|++|++++.|||.+. +..+|.++..++++.+..++.+ +++++...+..+|||+|++|||+++++.++||
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 79999999999999999999886 6778888999999999888765 58999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcCCCcC
Q 030448 86 LILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVASHSVD 150 (177)
Q Consensus 86 l~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~~~~~ 150 (177)
+++++++|.|+++|++||+++|+.+ +++||.++|.+||||+-+|.++||+++.+.+++..-..+
T Consensus 78 l~iL~lIh~FVE~lDr~FgnVCELd-lIFNF~kv~~ILdE~i~gG~i~Es~~~~vl~~v~~lda~ 141 (152)
T COG5030 78 LIILELIHNFVEILDRFFGNVCELD-LIFNFQKVYAILDEMILGGEIIESSKNEVLEHVYALDAE 141 (152)
T ss_pred chHHHHHHHHHHHHHHHhccceeeE-eEeeHHHHHHHHHHHHhCCeeeecCHHHHHHHHHHHHhh
Confidence 9999999999999999999999996 999999999999999999999999999999998765433
No 5
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=6.2e-29 Score=185.49 Aligned_cols=139 Identities=24% Similarity=0.385 Sum_probs=127.5
Q ss_pred ceeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCcccCceEE----e--cCeEEEEEEeCcEEEEEEe
Q 030448 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAM----L--EGNVIVYKFVQDLHFFVTG 79 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~~~~~i~~----~--~~~~ivy~~~~dl~~~~v~ 79 (177)
||+|++|+|.+|++++.|||++. +.+.|+.+.+++|+.+.+++.. .|+++. . .+..++||+|+.|||+.|.
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--DEEKQQQLIREVFHLVSKRPDN-VCNFLEGNSLIGGSDNRLIYRHYATLYFVFVV 77 (182)
T ss_pred CeeEEEEecCCCCcceeeecCcC--ChHHHHHHHHHHHHHHHcCCch-HhhhhccccccCCccceeehheeeeEEEEEEE
Confidence 89999999999999999999996 6889999999999999998743 244433 2 4789999999999999999
Q ss_pred cCCccHHHHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcCCC
Q 030448 80 GEDENELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVASHS 148 (177)
Q Consensus 80 ~~~eNel~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~~~ 148 (177)
|++|+||+++++++.|+++|+++|.++|+.+ +++|+++++.+|+|++.+|.++||+.+.|...+..+.
T Consensus 78 D~sEsEL~iLDLIQvfVEtLDkCF~nVcELD-liF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~~n 145 (182)
T KOG0936|consen 78 DSSESELGILDLIQVFVETLDKCFENVCELD-LIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDEQN 145 (182)
T ss_pred cCCcchhHHHHHHHHHHHHHHHHHHhhhhhh-heeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHHhc
Confidence 9999999999999999999999999999996 9999999999999999999999999999999997665
No 6
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=1.4e-28 Score=177.04 Aligned_cols=138 Identities=17% Similarity=0.222 Sum_probs=126.0
Q ss_pred ceeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEEEEEecCCccH
Q 030448 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNe 85 (177)
||++|+|+|++|+++++|||-+. +..+++..+.++++.+..++.+.+..+......++++|++++|||++|++.-.||
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 89999999999999999999775 4566788899999999999887655666666667777799999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcC
Q 030448 86 LILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVAS 146 (177)
Q Consensus 86 l~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~ 146 (177)
++.++-+|.++++|+.+|+++|+.+ +..||.+||.++|||+-+|.++||++..+.+|+.+
T Consensus 79 layLe~IHlFVEvLd~fF~NVCELD-lvFNFyKVy~i~DEm~l~GEi~Etsk~~vlerl~~ 138 (143)
T KOG0935|consen 79 LAYLEHIHLFVEVLDEFFHNVCELD-LVFNFYKVYTIVDEMFLAGEIRETSKTKVLERLLM 138 (143)
T ss_pred HHHHHHHHHHHHHHHHHhcccccee-eeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHHHHH
Confidence 9999999999999999999999996 99999999999999999999999999999999865
No 7
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.95 E-value=1.7e-28 Score=180.20 Aligned_cols=139 Identities=20% Similarity=0.333 Sum_probs=129.7
Q ss_pred ceeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEEEEEecCCccH
Q 030448 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNe 85 (177)
||+++++.+++|+++++|||.+. +.++|+..++++.+.+..++++. |+++.++++.+|||+++++||+++...++||
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--SIKERKKIERELIKSVLARKPKM-CSFIEYKDEKVVYRRYASLFFCVGVEDNDNE 77 (145)
T ss_pred CeEEEEEEeccCceehhHHHhhh--cHHHHHHHHHHHHHHHHhCCccc-ccchhccCceehhhhhhhEEEEEEEecCCch
Confidence 79999999999999999999986 68899999999999999887664 8999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcCCC
Q 030448 86 LILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVASHS 148 (177)
Q Consensus 86 l~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~~~ 148 (177)
|+++|++|+++++|++|||++|+.+ |++||.++|.+|||++-.|-++||..+....-+...+
T Consensus 78 L~~LE~IH~~vE~lDkYFg~VCELD-iiFNfekay~ILde~~~~g~~~e~~k~~~~~~i~~ad 139 (145)
T KOG0934|consen 78 LAILEFIHNYVELLDKYFGSVCELD-IIFNFEKAYFILDEFLLGGEIQETSKNDVLKAIAQAD 139 (145)
T ss_pred hhHHHHHHHHHHHHHHHhccceeeE-EEEehHhHHHHHHHHhcCcchHhhhcccHHHHHHHhh
Confidence 9999999999999999999999996 9999999999999999999999999888777765543
No 8
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.93 E-value=9.9e-26 Score=187.47 Aligned_cols=138 Identities=17% Similarity=0.227 Sum_probs=120.4
Q ss_pred ceeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEEEEEecCCccH
Q 030448 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNe 85 (177)
||++++|+|.+|++++.|.|+++.. ...-..|+-++. .+...++|+..+++++++|.+..+||+++++++|.|.
T Consensus 1 misglfi~n~rGevlink~fr~dlk-rs~~diFRv~vi-----~n~d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nv 74 (446)
T KOG0938|consen 1 MISGLFIYNLRGEVLINKTFRDDLK-RSIVDIFRVQVI-----NNLDVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANV 74 (446)
T ss_pred CcceEEEEeccCcEEEehhhhhhhh-hhHHHHHHHhhh-----hccccCCCeeEecceeEEEEeeccEEEEEEecCCCch
Confidence 8999999999999999999998721 222333443333 3333458999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcCCCcC
Q 030448 86 LILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVASHSVD 150 (177)
Q Consensus 86 l~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~~~~~ 150 (177)
.+++|||..+..++..||++ ..++.|++||..||++||||+|+||||+|+|+.++..+..++..
T Consensus 75 a~v~eFl~kl~avm~aYfgk-~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~~~Vr 138 (446)
T KOG0938|consen 75 AAVFEFLYKLDAVMNAYFGK-DREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQKGVR 138 (446)
T ss_pred hhHHHHHHHHHHHHHHHhcc-cchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhhhhhh
Confidence 99999999999999999995 66778999999999999999999999999999999999988754
No 9
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.87 E-value=1.8e-21 Score=167.07 Aligned_cols=137 Identities=19% Similarity=0.329 Sum_probs=118.9
Q ss_pred eeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEEEEEecCCccHH
Q 030448 7 IKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENEL 86 (177)
Q Consensus 7 I~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNel 86 (177)
+++++++|.+|+++++|.|+.+++ ...-..|-..++.+. ......|++.++|..++|.++.++|+++++..|.|..
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-MSSTEKFFRKLFEKE---EGDESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAA 76 (424)
T ss_pred CceEEEEcCCCcEeEeecccccCC-hhhhhhHHHHHhhhc---ccCCCCCeEEeCCceEEEEeecceEEEEEeccCCCHH
Confidence 579999999999999999999854 333344443333322 2222369999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcCCC
Q 030448 87 ILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVASHS 148 (177)
Q Consensus 87 ~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~~~ 148 (177)
.++++|+++++++++||+ .+++.++++||+.+|++|||++|+||||+|+++.+++++.+++
T Consensus 77 ~v~~~l~~~~~v~~~y~~-~l~e~si~~n~vlvyElLde~mDFGypQ~t~s~iL~~yi~~~~ 137 (424)
T KOG0937|consen 77 LVLSFLYAVADVFGDYLS-ELEEESIRDNFVLVYELLDEVMDFGYPQTTDSEILKNYITQKA 137 (424)
T ss_pred HHHHHHHHHHHHHHHHhc-cCCccceecchHHHHHHHHHHhccCCcccchHHHHHHHhcccc
Confidence 999999999999999999 5888899999999999999999999999999999999999885
No 10
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.83 E-value=1e-20 Score=158.65 Aligned_cols=140 Identities=16% Similarity=0.242 Sum_probs=117.9
Q ss_pred ceeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCccc-CceEEecCeEEEEEEeCcEEEEEEecCCcc
Q 030448 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTE-AEIAMLEGNVIVYKFVQDLHFFVTGGEDEN 84 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~~~-~~i~~~~~~~ivy~~~~dl~~~~v~~~~eN 84 (177)
||.++++.|.+|+.++.+.+++.. ..+..+..++..........+ .|++....+++.-.-..+++|+++...+.-
T Consensus 1 mi~siflidtsg~l~lek~~~g~t----~~rsic~~f~e~~~~~~~~e~~ppvi~~p~hylfsv~~~~i~~~~~st~e~p 76 (418)
T KOG2740|consen 1 MILSIFLIDTSGDLLLEKHLKGST----VVRSICDYFFEDQSSDDDLEHVPPVISTPHHYLFSVYRDLIFFCAVSTVETP 76 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCce----eeeehHHHHHHhhhhccccccCCceecCCceeeeeeeccCcEEEEEEeccCC
Confidence 899999999999999999999631 134566667765544432222 356666777777777788999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcCCCcC
Q 030448 85 ELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVASHSVD 150 (177)
Q Consensus 85 el~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~~~~~ 150 (177)
||.+.|||+++++++.+|||+ +++..|.+|++.||++||||+|+|+|..|||++|++.|.+++..
T Consensus 77 PL~~iefL~rv~dv~~eyFg~-~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i~pps~l 141 (418)
T KOG2740|consen 77 PLMVIEFLHRVVDVLLEYFGG-LSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELIPPPSFL 141 (418)
T ss_pred ChhHHHHHHHHHHHHHHHhcc-cCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhcCChHHH
Confidence 999999999999999999996 88888999999999999999999999999999999999998754
No 11
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.45 E-value=5.9e-06 Score=71.91 Aligned_cols=139 Identities=17% Similarity=0.182 Sum_probs=113.1
Q ss_pred ceeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEEEEEecCCccH
Q 030448 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNe 85 (177)
++-+..+.+.+|+.+++|-|+.. + +.++|.-+..=-+--....+.-++..+.+.+||+...++|+++++....|-
T Consensus 2 vvlaa~i~t~~Gk~ivsRqf~~M--s---r~RIEgLl~aFpkLv~~~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~SNI 76 (512)
T KOG2635|consen 2 VVLAASINTKTGKAIVSRQFREM--S---RSRIEGLLAAFPKLVSAGKQHTFVETDSVRYVYQPLDNLYIVLITTKQSNI 76 (512)
T ss_pred eEEEEEEeecCCceeeehHhHhh--h---HHHHHHHHHHhHHhhccCCCccEEecccEEEEEEecccEEEEEEeccccch
Confidence 56678889999999999999853 3 345555443211111222235788899999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcCCCcC
Q 030448 86 LILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVASHSVD 150 (177)
Q Consensus 86 l~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~~~~~ 150 (177)
+-=++-|+.|..+.-.|+.. ++++.|.+|-=-+...+||++--||=...+-.-|+.+..|.+.+
T Consensus 77 leDl~TL~Lfskvipey~~s-lde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eMdSHE 140 (512)
T KOG2635|consen 77 LEDLETLRLFSKVIPEYCSS-LDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEMDSHE 140 (512)
T ss_pred hhHHHHHHHHHHhchhhhhh-hhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhccccHH
Confidence 99999999999999999876 67767999988888999999999999999999999999887654
No 12
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=97.56 E-value=0.0046 Score=48.82 Aligned_cols=82 Identities=22% Similarity=0.226 Sum_probs=71.1
Q ss_pred cCeEEEEEEeCcEEEEEEecCCccHHHHHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHH
Q 030448 61 EGNVIVYKFVQDLHFFVTGGEDENELILATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVI 140 (177)
Q Consensus 61 ~~~~ivy~~~~dl~~~~v~~~~eNel~l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i 140 (177)
+...++|...+++.|..|.+..||-++.-.+|..++..|.+.++....-..+..+-|.|..+|+..+-+|-.+=-+...+
T Consensus 102 ~~k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~~ 181 (189)
T PF15001_consen 102 TPKIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRFV 181 (189)
T ss_pred CCcEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHHH
Confidence 34589999999999999999999999999999999999988886533334588899999999999999999888887766
Q ss_pred HH
Q 030448 141 AG 142 (177)
Q Consensus 141 ~~ 142 (177)
+.
T Consensus 182 k~ 183 (189)
T PF15001_consen 182 KQ 183 (189)
T ss_pred HH
Confidence 54
No 13
>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=97.08 E-value=0.017 Score=50.86 Aligned_cols=90 Identities=16% Similarity=0.186 Sum_probs=62.0
Q ss_pred eeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCc-ccCceEEecCeEEEEEEeCcEEEEEEecCCccHH
Q 030448 8 KNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNAR-TEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENEL 86 (177)
Q Consensus 8 ~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~-~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNel 86 (177)
+-+||+...|++|++|| .+ ++.-..+...+...+..-... .+---+..++..+||...+-|+++++++..|++-
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 46899999999999999 22 233334444333333222111 1123466799999999999999999999999988
Q ss_pred HHHHHHHHHHHHHHhh
Q 030448 87 ILATVLQGFFDAVGLL 102 (177)
Q Consensus 87 ~l~e~L~~i~~~l~~~ 102 (177)
.+..-|+.++.-+-.+
T Consensus 87 ~l~~qL~~ly~qils~ 102 (415)
T PF03164_consen 87 QLRKQLDYLYSQILSI 102 (415)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 8777777766655444
No 14
>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=97.02 E-value=0.015 Score=42.69 Aligned_cols=97 Identities=12% Similarity=0.166 Sum_probs=66.4
Q ss_pred cceeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHH---hhhcC-CcccCceEEecCeEEEEEEeCcEEEEEEec
Q 030448 5 PSIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTK---TQKTN-ARTEAEIAMLEGNVIVYKFVQDLHFFVTGG 80 (177)
Q Consensus 5 ~mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~---~~~~~-~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~ 80 (177)
.-+.+|+|.|++|=+++.=..... +....+..|...+-.. +.+.+ +++..=+..++++.+++.....+++.++++
T Consensus 15 ~Gl~~I~itDrDGvpi~~v~~~~~-~~~~~~~~~~~tf~~a~~Q~~KL~lG~nk~ii~~Y~~~qvv~~~~~pl~it~ias 93 (119)
T PF08923_consen 15 DGLQAIVITDRDGVPIAKVSSDSA-PESAMRPSLLSTFAMAIDQASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFIAS 93 (119)
T ss_dssp TTEEEEEEEETTS-EEEEEE-TTS--GGGGSHHHHCCHHHHHHHHTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEEEE
T ss_pred CCeEEEEEECCCCcEEEEecCCCC-cchhhhhHHHHHHHHHhhcccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEEec
Confidence 347899999999999888555443 3333334444332221 22222 333335678999999999999999999999
Q ss_pred CCccHHHHHHHHHHHHHHHHhh
Q 030448 81 EDENELILATVLQGFFDAVGLL 102 (177)
Q Consensus 81 ~~eNel~l~e~L~~i~~~l~~~ 102 (177)
++.|--+++.+-+.+...+...
T Consensus 94 ~~aN~G~il~l~~~L~~~l~~l 115 (119)
T PF08923_consen 94 SNANTGLILSLEEELAPILNEL 115 (119)
T ss_dssp TTS-HHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHhHHHHHHHHHHH
Confidence 9999999999888888877665
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=92.25 E-value=2.4 Score=28.39 Aligned_cols=49 Identities=6% Similarity=-0.028 Sum_probs=44.0
Q ss_pred ceEEecCeEEEEEEeCcEEEEEEecCCccHHHHHHHHHHHHHHHHhhcc
Q 030448 56 EIAMLEGNVIVYKFVQDLHFFVTGGEDENELILATVLQGFFDAVGLLLR 104 (177)
Q Consensus 56 ~i~~~~~~~ivy~~~~dl~~~~v~~~~eNel~l~e~L~~i~~~l~~~~~ 104 (177)
-.+..+++.+-|...+++.++++++.+...-..+.+|+.+..-+..-++
T Consensus 17 ~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~ 65 (83)
T PF13774_consen 17 MSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYG 65 (83)
T ss_dssp EEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCT
T ss_pred EEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcC
Confidence 4677899999999999999999999999999999999999998888777
No 16
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown]
Probab=91.05 E-value=4.5 Score=36.43 Aligned_cols=76 Identities=17% Similarity=0.129 Sum_probs=49.7
Q ss_pred eeEEEEcCCCCEeEEecCCCCCC--ChhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEEEEEecCCccH
Q 030448 8 KNILLLDSEGKRVAVKYYSNDWP--TNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENE 85 (177)
Q Consensus 8 ~~i~iln~~G~~il~k~Y~~~~~--~~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNe 85 (177)
+-+||+.+.|++++++|=..+.. +-...++....+. . + +..--.+..+|+.++|-..+-++++++...+.+.
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 KHIFILSEAGKPIYSRHGSDEALSSTMGVMQALISFFQ-V----S-GLAITSIHAFGNKLVFLQKSPLLLVAVSRTSQSA 191 (523)
T ss_pred ceEEEEecCCCceeeecCcHHHHHHHHHHHHHHHHHHh-h----C-CceEEEEEecCceEEEEecCcEEEEEEcccccCH
Confidence 35899999999999999654310 0122333332221 1 1 1111335679999999999999999999988766
Q ss_pred HHHH
Q 030448 86 LILA 89 (177)
Q Consensus 86 l~l~ 89 (177)
--+.
T Consensus 192 ~qL~ 195 (523)
T KOG0997|consen 192 AQLL 195 (523)
T ss_pred HHHH
Confidence 5444
No 17
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.35 E-value=6.9 Score=31.30 Aligned_cols=85 Identities=9% Similarity=0.154 Sum_probs=58.5
Q ss_pred CCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEEEEEecCCccHHHHHHHHHH
Q 030448 15 SEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENELILATVLQG 94 (177)
Q Consensus 15 ~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNel~l~e~L~~ 94 (177)
.+|-++|++|=.-. ..-...-.++.+|....++ ..--..+|+|.|-|.+.+++.++++++.+..--.-+.||++
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 58999999985311 1122455666666544421 01235689999999999999999999988776666777777
Q ss_pred HHHHHHhhccC
Q 030448 95 FFDAVGLLLRG 105 (177)
Q Consensus 95 i~~~l~~~~~~ 105 (177)
+-+-+.+-+|+
T Consensus 83 Ik~~F~k~YG~ 93 (217)
T KOG0859|consen 83 IKEDFKKRYGG 93 (217)
T ss_pred HHHHHHHHhcc
Confidence 77666555554
No 18
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.45 E-value=20 Score=28.97 Aligned_cols=74 Identities=11% Similarity=0.071 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEEEEEecCCccHHHHHHHHHHHHHHHHhhccCCCCH
Q 030448 34 AKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHFFVTGGEDENELILATVLQGFFDAVGLLLRGNVDK 109 (177)
Q Consensus 34 ~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNel~l~e~L~~i~~~l~~~~~~~~~~ 109 (177)
+.++-.+.++++...... . ---+..|.+.|-|...++++.++.++.+..--+.+.+|+.+.+-+.+.+++.+..
T Consensus 32 e~r~q~K~L~kkLs~~s~-~-r~Sietg~f~fHfli~~~Vcylvicd~~yP~kLAF~YLedL~~EF~~~~~~~~~~ 105 (216)
T KOG0862|consen 32 EYRQQAKSLFKKLSQQSP-T-RCSIETGPFVFHFLIESGVCYLVICDKSYPRKLAFSYLEDLAQEFDKSYGKNIIQ 105 (216)
T ss_pred HHHHHHHHHHHhccCCCC-c-ccccccCCeEEEEEecCCEEEEEEecCCCcHHHHHHHHHHHHHHHHHhcccccCC
Confidence 344444556655444321 0 1234568899999999999999999999999999999999999998888864443
No 19
>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=82.08 E-value=19 Score=26.92 Aligned_cols=98 Identities=7% Similarity=0.154 Sum_probs=57.4
Q ss_pred eeeEEEEcCCCCEeEEecCCCCC------CChhHHHHHHHHHHHHh---hhcCC---c----ccC--ceEEecCeEEE-E
Q 030448 7 IKNILLLDSEGKRVAVKYYSNDW------PTNSAKEAFEKAVFTKT---QKTNA---R----TEA--EIAMLEGNVIV-Y 67 (177)
Q Consensus 7 I~~i~iln~~G~~il~k~Y~~~~------~~~~~~~~~e~~i~~~~---~~~~~---~----~~~--~i~~~~~~~iv-y 67 (177)
|..++|+|++|..|+.|-|.... ...+++..+-.-++... .+-.. . ..+ ..+..+.+.+- |
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 57899999999999999997531 22455666655555331 11111 0 011 23456776554 4
Q ss_pred EEeCcEEEEEEecCCccHHHHHHHHHHHHHHHHhhc-cC
Q 030448 68 KFVQDLHFFVTGGEDENELILATVLQGFFDAVGLLL-RG 105 (177)
Q Consensus 68 ~~~~dl~~~~v~~~~eNel~l~e~L~~i~~~l~~~~-~~ 105 (177)
..-.++-|+++++.+... ..-++++.+++...+|. ++
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 567889999999998853 34556788888887774 44
No 20
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=68.09 E-value=45 Score=24.40 Aligned_cols=94 Identities=10% Similarity=0.199 Sum_probs=55.2
Q ss_pred ceeeEEEEcCCCCEeEEecCCCCCCChhHHH------HHHHHHHH---HhhhcCCcccCc--eEEecC-eEEEEEEeCcE
Q 030448 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKE------AFEKAVFT---KTQKTNARTEAE--IAMLEG-NVIVYKFVQDL 73 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~------~~e~~i~~---~~~~~~~~~~~~--i~~~~~-~~ivy~~~~dl 73 (177)
.+.+++|+|+.|..++.|-+..+ ++.-... .-...++. ++....+. ++ ++..+. ...+|+...++
T Consensus 2 ave~~~iINksGglifqref~~~-et~lnsneyLiLastlhgV~aI~tq~~p~~gs--sg~~~l~~~~f~m~I~qT~TG~ 78 (134)
T COG5122 2 AVEQFFIINKSGGLIFQREFGEG-ETELNSNEYLILASTLHGVSAILTQTIPLPGS--SGRLVLYFRNFVMTIFQTTTGT 78 (134)
T ss_pred ceeEEEEEecCCcEEEEEeccCC-ccccCcccEEEEeechhhhhhhhhhcccCCCC--CceEEEEeccEEEEEEEecCCc
Confidence 47899999999999999999653 1110000 01111111 11111111 23 344555 35688899999
Q ss_pred EEEEEec-CCccHHHHHHHHHHHHHHHHhhccC
Q 030448 74 HFFVTGG-EDENELILATVLQGFFDAVGLLLRG 105 (177)
Q Consensus 74 ~~~~v~~-~~eNel~l~e~L~~i~~~l~~~~~~ 105 (177)
-|++++. .-.|.++= ++.+++..++|.-+
T Consensus 79 kFV~~~~k~t~na~~q---l~kiY~lYsdYV~k 108 (134)
T COG5122 79 KFVFVAEKRTVNALFQ---LQKIYSLYSDYVTK 108 (134)
T ss_pred EEEEEecCCchhHHHH---HHHHHHHHHHHhhc
Confidence 9999994 34454433 77788888888543
No 21
>PF03690 UPF0160: Uncharacterised protein family (UPF0160); InterPro: IPR003226 The function of this domain is not known, but it is found in several uncharacterised proteins and a probable metal dependent protein hydrolase.
Probab=62.54 E-value=63 Score=27.66 Aligned_cols=78 Identities=15% Similarity=0.183 Sum_probs=45.1
Q ss_pred HHHhhccCCCCHHHHHHhHHHHHHHHHHHh---hCcEEee---------cCHHHHHHhhcCCCcCCC-CCCChhhHHHHH
Q 030448 98 AVGLLLRGNVDKKEALENLDLILLCLDEIV---DGGIILE---------TDANVIAGKVASHSVDVG-APLSEQTISQAL 164 (177)
Q Consensus 98 ~l~~~~~~~~~~~~i~~nf~~v~~lLDE~i---d~G~i~e---------Td~~~i~~~i~~~~~~~~-~~~~~~~~~~a~ 164 (177)
++..+++...+.+.+..=|.++|.-+=|-| |+|+.+. |+-..+..+..+.-.+.. ....+..|.+|+
T Consensus 94 ii~~~~~~~~~~~~~~~l~~~iy~~fv~~iDaiDNGv~~~~~~~~y~~~~~ls~~V~~~Np~w~~~~~~~~~~~~F~~A~ 173 (318)
T PF03690_consen 94 IIRNLLGDPVDEEDIELLYEKIYESFVESIDAIDNGVSIYDGEPKYKINTSLSSRVSRLNPSWNEPDDDEDEDERFEKAM 173 (318)
T ss_pred HHHHhcCcCCChHHHHHHHHHHHHHHHHHhhhhhcCCcccCccccccCCCCHHHHHHHhCCCCCCCCcchhHHHHHHHHH
Confidence 444555544555545555555555544444 6887765 444444444444323221 123467999999
Q ss_pred HHHHHHHHHHh
Q 030448 165 ATAREHLTRSL 175 (177)
Q Consensus 165 ~~a~~~~~~~l 175 (177)
+.|++-|.+.+
T Consensus 174 ~l~~~~f~~~v 184 (318)
T PF03690_consen 174 ELAGEEFENRV 184 (318)
T ss_pred HHHHHHHHHHH
Confidence 99999988765
No 22
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=62.45 E-value=64 Score=24.18 Aligned_cols=90 Identities=13% Similarity=0.211 Sum_probs=53.3
Q ss_pred ceeeEEEEcCCCCEeEEecCCCC----CCChhHHHHHHHHHH------HHhhhcCCcccCceEEecCeEEEEE-EeCcEE
Q 030448 6 SIKNILLLDSEGKRVAVKYYSND----WPTNSAKEAFEKAVF------TKTQKTNARTEAEIAMLEGNVIVYK-FVQDLH 74 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~----~~~~~~~~~~e~~i~------~~~~~~~~~~~~~i~~~~~~~ivy~-~~~dl~ 74 (177)
.|.++.|.|++|.-++.+-|... .+.+++.+-.-.-+| +|....+.+..---+....|.+-|- .-.++.
T Consensus 2 tiy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d~k~~f~sy~Ts~YklhfyeTptglk 81 (140)
T KOG3368|consen 2 TIYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGDVKDGFLSYKTSKYKLHFYETPTGLK 81 (140)
T ss_pred eEEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCCcccCeeEEeeceeEEEEEEcCCCcE
Confidence 57899999999999998888532 222222333333333 2322222221112233455555443 457899
Q ss_pred EEEEecCCccHHHHHHHHHHHHH
Q 030448 75 FFVTGGEDENELILATVLQGFFD 97 (177)
Q Consensus 75 ~~~v~~~~eNel~l~e~L~~i~~ 97 (177)
|+..++..... +-++|+.|+.
T Consensus 82 ~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 82 FVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred EEEecCCCccc--HHHHHHHHHH
Confidence 99999987755 4577888877
No 23
>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=60.02 E-value=24 Score=30.64 Aligned_cols=56 Identities=14% Similarity=0.323 Sum_probs=41.6
Q ss_pred eeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcCCcccCceEEecCeEEEEEEeCcEEE
Q 030448 7 IKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTNARTEAEIAMLEGNVIVYKFVQDLHF 75 (177)
Q Consensus 7 I~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~ 75 (177)
.-+.+|.+.+|+++.-+-|. |..||+-+++.++ .+.|--.-.++-.+|+..+..||
T Consensus 292 ~gGyivV~~dGevlcYHiy~--------rn~FedYL~~NTk-----le~~SssRh~fG~iy~enG~~yf 347 (355)
T PF09561_consen 292 TGGYIVVKEDGEVLCYHIYN--------RNEFEDYLYNNTK-----LETPSSSRHKFGFIYRENGEYYF 347 (355)
T ss_pred cceEEEEeCCCCEEEEEehh--------HHHHHHHHHhccc-----ccCCCCCcccceEEEEECCEEEE
Confidence 45889999999999887764 4479999997543 33454555678888887776665
No 24
>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=52.41 E-value=51 Score=24.12 Aligned_cols=23 Identities=26% Similarity=0.498 Sum_probs=18.9
Q ss_pred ceeeEEEEcCCCCEeE--EecCCCC
Q 030448 6 SIKNILLLDSEGKRVA--VKYYSND 28 (177)
Q Consensus 6 mI~~i~iln~~G~~il--~k~Y~~~ 28 (177)
-+.+++++|.+|++++ ++.+...
T Consensus 49 ~~d~~~~~d~~g~~~~~~~~~~~~~ 73 (161)
T PF05228_consen 49 GLDLIFILDPDGRVLYSSSKGYDFE 73 (161)
T ss_pred CccEEEEEcCCCCEEEEeccCcccC
Confidence 5789999999999999 6666543
No 25
>PF09201 SRX: SRX; InterPro: IPR015284 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 a homologue of the alpha subunit of the SR receptor. Members of this entry consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta) []. ; PDB: 1NRJ_A.
Probab=51.05 E-value=1.1e+02 Score=23.23 Aligned_cols=76 Identities=11% Similarity=0.134 Sum_probs=35.0
Q ss_pred ceeeEEEEcCCCCEeEEecCCCCCCChhHHHHHHHHHHHHhhhcC-CcccCceEE-------ecCeEEEEE--EeCcEEE
Q 030448 6 SIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFEKAVFTKTQKTN-ARTEAEIAM-------LEGNVIVYK--FVQDLHF 75 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e~~i~~~~~~~~-~~~~~~i~~-------~~~~~ivy~--~~~dl~~ 75 (177)
|+..+.|...+|++++.-..-+--.++..-.+|.+.+...=...+ ......+.. .+++...|. +...||+
T Consensus 1 MfdQlaIFTpqGqvLyqyN~~gKKFsE~QiN~FIs~lItsP~~~~e~~~~~k~~~i~s~~~~~~~f~~mfh~sKQPeLy~ 80 (148)
T PF09201_consen 1 MFDQLAIFTPQGQVLYQYNCLGKKFSETQINAFISHLITSPVTKKEDSSKSKFLTISSEKKNSRSFSAMFHISKQPELYY 80 (148)
T ss_dssp ---EEEEE-TT-BEEEEEETTS----HHHHHHHHHHHHHS---GGGTT--EEEEE-----------EEEEEEETTTTEEE
T ss_pred CcceeEEeccCceEEEEecccchHHHHHHHHHHHHHHhcCCCcccCCCcceeeEEecccccCCCChheeeeecCCCcEEE
Confidence 788999999999998864443321234444566655553211111 111123333 447777666 4578888
Q ss_pred EEEecC
Q 030448 76 FVTGGE 81 (177)
Q Consensus 76 ~~v~~~ 81 (177)
++.-.+
T Consensus 81 VvTyae 86 (148)
T PF09201_consen 81 VVTYAE 86 (148)
T ss_dssp EEEESS
T ss_pred EEEecc
Confidence 887665
No 26
>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=48.29 E-value=1.3e+02 Score=24.64 Aligned_cols=52 Identities=10% Similarity=0.072 Sum_probs=29.5
Q ss_pred CceEEecCeEEEEEEeCcE--EEEEEecCCccHHHHHHHHHHHHHHHHhhccCC
Q 030448 55 AEIAMLEGNVIVYKFVQDL--HFFVTGGEDENELILATVLQGFFDAVGLLLRGN 106 (177)
Q Consensus 55 ~~i~~~~~~~ivy~~~~dl--~~~~v~~~~eNel~l~e~L~~i~~~l~~~~~~~ 106 (177)
.+.+.+++|.+=|+..+++ .|+||=..=-.-..+-++|..+...+...++..
T Consensus 19 ~~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~~~ 72 (279)
T PF04086_consen 19 NSSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYKNQ 72 (279)
T ss_dssp ---------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTHHH
T ss_pred CCceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHhHH
Confidence 4568999999999999876 444444433455666778888888777777754
No 27
>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=45.06 E-value=86 Score=20.44 Aligned_cols=69 Identities=20% Similarity=0.298 Sum_probs=37.7
Q ss_pred ccceeeEEEEcCCCCEeEEecCCCCCCChhHHHHHH---HHHHHHhhhc----C-CcccCceEEecCeEEEEEEeCc-EE
Q 030448 4 CPSIKNILLLDSEGKRVAVKYYSNDWPTNSAKEAFE---KAVFTKTQKT----N-ARTEAEIAMLEGNVIVYKFVQD-LH 74 (177)
Q Consensus 4 ~~mI~~i~iln~~G~~il~k~Y~~~~~~~~~~~~~e---~~i~~~~~~~----~-~~~~~~i~~~~~~~ivy~~~~d-l~ 74 (177)
.+-+.+.+++|++|.++-+ +..+ ....+.+- ..++....+. + +..+.-.+..++..++..+.++ .+
T Consensus 12 ~~gv~~~~l~~~dG~~i~~--~~~~---~~~~~~~aa~~a~~~~~~~~~~~~l~~~~~~~v~i~~~~~~i~i~~~~~~~~ 86 (91)
T PF03259_consen 12 VPGVRGAVLVDKDGLVIAS--SGID---DDDAEKLAAMAASLLAAAEKLAKELGEGELEQVRIETEKGEIIITPVGDFYL 86 (91)
T ss_dssp STTEEEEEEEETTSEEEEE--TSSS---HHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEEEEEESSEEEEEEECSTCEE
T ss_pred CCCeeEEEEEcCCCCEEEE--ecCC---cccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEEEEEECCCEEEEEEcCCCEE
Confidence 3568899999999999998 3221 22222222 2333222111 1 1111134557777777788888 44
Q ss_pred EEE
Q 030448 75 FFV 77 (177)
Q Consensus 75 ~~~ 77 (177)
+++
T Consensus 87 L~v 89 (91)
T PF03259_consen 87 LVV 89 (91)
T ss_dssp EEE
T ss_pred EEE
Confidence 444
No 28
>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=40.76 E-value=26 Score=24.20 Aligned_cols=49 Identities=18% Similarity=0.194 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhhc--cCCCCHHHHHHhH----HHHHHHHHHHhhCcEEeecC
Q 030448 88 LATVLQGFFDAVGLLL--RGNVDKKEALENL----DLILLCLDEIVDGGIILETD 136 (177)
Q Consensus 88 l~e~L~~i~~~l~~~~--~~~~~~~~i~~nf----~~v~~lLDE~id~G~i~eTd 136 (177)
+-..-.+++++++.-. ...+..+.|...+ ..|..++|++++.|.|..|-
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi 99 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTI 99 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESS
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEeccc
Confidence 3344455555555411 1235555555544 78999999999999999883
No 29
>KOG2948 consensus Predicted metal-binding protein [General function prediction only]
Probab=38.06 E-value=2.2e+02 Score=24.30 Aligned_cols=79 Identities=14% Similarity=0.208 Sum_probs=47.4
Q ss_pred HHHHhhccCCCCHHHHHHhHHHHHHHHHHHh---hCcEEeecC--HH-----HHHHhhcCCCcCC---CCCCChhhHHHH
Q 030448 97 DAVGLLLRGNVDKKEALENLDLILLCLDEIV---DGGIILETD--AN-----VIAGKVASHSVDV---GAPLSEQTISQA 163 (177)
Q Consensus 97 ~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~i---d~G~i~eTd--~~-----~i~~~i~~~~~~~---~~~~~~~~~~~a 163 (177)
+++..++....+...+.-=|++||.-.=|-+ |+|+.+=++ |. .|-.||.....+- +..-.+.+|.+|
T Consensus 97 ~vi~~~l~~~~s~~~~~~l~~kvY~~Fve~~DAiDNGi~~y~~~~Pry~~~~~l~~rv~~~N~~w~e~~~~~~~e~F~~A 176 (327)
T KOG2948|consen 97 EVISKILQNKVSSSDLDLLYDKVYKNFVEALDAIDNGISQYGEIEPRYKSSTSLSHRVGRFNPDWNEDSDDDEDERFQRA 176 (327)
T ss_pred HHHHHHhcccCChhHHHHHHHHHHHHHHHHhhccccchhhhcCCCCccccccchHHHHhhcCCCcccCcchhHHHHHHHH
Confidence 4556666665555567666777776655544 788877654 22 2224554433221 112235699999
Q ss_pred HHHHHHHHHHHh
Q 030448 164 LATAREHLTRSL 175 (177)
Q Consensus 164 ~~~a~~~~~~~l 175 (177)
+..|-+.+.++.
T Consensus 177 m~~vg~ef~~~v 188 (327)
T KOG2948|consen 177 MDLVGKEFVNSV 188 (327)
T ss_pred HHHHHHHHHHHH
Confidence 999988887654
No 30
>COG3322 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=36.58 E-value=30 Score=29.27 Aligned_cols=23 Identities=22% Similarity=0.463 Sum_probs=20.6
Q ss_pred ceeeEEEEcCCCCEeEEecCCCC
Q 030448 6 SIKNILLLDSEGKRVAVKYYSND 28 (177)
Q Consensus 6 mI~~i~iln~~G~~il~k~Y~~~ 28 (177)
-+.++|++|.+|+++++|.+++.
T Consensus 103 g~d~vf~vd~~G~~vy~~~~d~~ 125 (295)
T COG3322 103 GLDGVFVVDPSGKLVYSKLVDQE 125 (295)
T ss_pred CccEEEEECCCCCEEEEeeeccc
Confidence 46799999999999999999764
No 31
>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=35.19 E-value=33 Score=17.31 Aligned_cols=18 Identities=28% Similarity=0.470 Sum_probs=14.9
Q ss_pred HhHHHHHHHHHHHhhCcE
Q 030448 114 ENLDLILLCLDEIVDGGI 131 (177)
Q Consensus 114 ~nf~~v~~lLDE~id~G~ 131 (177)
.+++.+..+++||.+.|+
T Consensus 14 ~~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 14 GQFEEALEVFDEMRERGI 31 (31)
T ss_pred chHHHHHHHHHHHhHCcC
Confidence 567888999999998884
No 32
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=33.58 E-value=34 Score=17.78 Aligned_cols=18 Identities=28% Similarity=0.468 Sum_probs=14.7
Q ss_pred HhHHHHHHHHHHHhhCcE
Q 030448 114 ENLDLILLCLDEIVDGGI 131 (177)
Q Consensus 114 ~nf~~v~~lLDE~id~G~ 131 (177)
.+++.+..++++|...|+
T Consensus 15 g~~~~a~~~~~~M~~~gv 32 (34)
T PF13812_consen 15 GDPDAALQLFDEMKEQGV 32 (34)
T ss_pred CCHHHHHHHHHHHHHhCC
Confidence 356778999999999885
No 33
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=32.84 E-value=65 Score=23.07 Aligned_cols=24 Identities=25% Similarity=0.427 Sum_probs=21.4
Q ss_pred CCCChhhHHHHHHHHHHHHHHHhh
Q 030448 153 APLSEQTISQALATAREHLTRSLL 176 (177)
Q Consensus 153 ~~~~~~~~~~a~~~a~~~~~~~l~ 176 (177)
|..|-++|...+.+|++++++.|.
T Consensus 67 MgVSR~T~~ril~~ARkKiA~ALv 90 (106)
T PF02001_consen 67 MGVSRPTFQRILESARKKIADALV 90 (106)
T ss_pred cCCcHHHHHHHHHHHHHHHHHHHH
Confidence 567888999999999999999884
No 34
>PF15349 DCA16: DDB1- and CUL4-associated factor 16
Probab=31.52 E-value=47 Score=25.41 Aligned_cols=20 Identities=35% Similarity=0.504 Sum_probs=17.6
Q ss_pred ChhhHHHHHHHHHHHHHHHh
Q 030448 156 SEQTISQALATAREHLTRSL 175 (177)
Q Consensus 156 ~~~~~~~a~~~a~~~~~~~l 175 (177)
++.+++.|+++|.+++.|-|
T Consensus 137 dhatlngalqfatkqlsrtl 156 (216)
T PF15349_consen 137 DHATLNGALQFATKQLSRTL 156 (216)
T ss_pred hhhhhhhHHHHHHHHHHHHH
Confidence 36699999999999999876
No 35
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=30.02 E-value=49 Score=20.35 Aligned_cols=13 Identities=38% Similarity=0.539 Sum_probs=6.9
Q ss_pred HHHHHHhhCcEEe
Q 030448 121 LCLDEIVDGGIIL 133 (177)
Q Consensus 121 ~lLDE~id~G~i~ 133 (177)
..|||++..|.|.
T Consensus 17 dtLDeli~~~~I~ 29 (49)
T PF02268_consen 17 DTLDELIQEGKIT 29 (49)
T ss_dssp HHHHHHHHTTSS-
T ss_pred HHHHHHHHcCCCC
Confidence 4566666665543
No 36
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.57 E-value=3.1e+02 Score=21.66 Aligned_cols=45 Identities=7% Similarity=0.145 Sum_probs=33.7
Q ss_pred eEEecCe-EEEEEEeCcEEEEEEecCCccHHHHHHHHHHHHHHHHhhc
Q 030448 57 IAMLEGN-VIVYKFVQDLHFFVTGGEDENELILATVLQGFFDAVGLLL 103 (177)
Q Consensus 57 i~~~~~~-~ivy~~~~dl~~~~v~~~~eNel~l~e~L~~i~~~l~~~~ 103 (177)
++..+.. ...|+...++-|+++++.-. -..-.+|..+++.-++|-
T Consensus 125 ~LetdtF~l~~~QTlTG~KFVvis~~~~--~~aD~lLrKiYelYsDyv 170 (199)
T KOG3369|consen 125 VLETDTFTLHIFQTLTGTKFVVIAEPGT--QGADSLLRKIYELYSDYV 170 (199)
T ss_pred EEEeccEEEEEEEccCCcEEEEEecCCc--hhHHHHHHHHHHHHHHHh
Confidence 4445553 56788889999999998766 455677888898888884
No 37
>PRK15360 pathogenicity island 2 effector protein SseE; Provisional
Probab=26.70 E-value=2e+02 Score=21.55 Aligned_cols=38 Identities=11% Similarity=0.072 Sum_probs=22.7
Q ss_pred eEEecCeEEEEEEeCcEEEEEE-ecCC---ccHHHHHHHHHH
Q 030448 57 IAMLEGNVIVYKFVQDLHFFVT-GGED---ENELILATVLQG 94 (177)
Q Consensus 57 i~~~~~~~ivy~~~~dl~~~~v-~~~~---eNel~l~e~L~~ 94 (177)
-+.+.++.++||-.++=.++|- -..+ ..+..++.+++.
T Consensus 30 ~~~~~g~~lvyRvE~~eliIc~lrR~~~~~~~p~~~~~L~~~ 71 (137)
T PRK15360 30 QFILSPYLVIYRIEAKEMIICEFRRLTPGQPRPQQLFHLLGL 71 (137)
T ss_pred EEEEcCEEEEEEecCCEEEEEEEEeccCCCCCHHHHHHHHHH
Confidence 3668999999998876554444 3322 235554444333
No 38
>COG1500 Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=25.14 E-value=1.5e+02 Score=24.25 Aligned_cols=63 Identities=19% Similarity=0.241 Sum_probs=43.2
Q ss_pred CCCHHHHHHhHHH--HHHHHHHHhhCcEEeecCHHH----------HHHhhcCCCcCC--CCCCChhhHHHHHHHHH
Q 030448 106 NVDKKEALENLDL--ILLCLDEIVDGGIILETDANV----------IAGKVASHSVDV--GAPLSEQTISQALATAR 168 (177)
Q Consensus 106 ~~~~~~i~~nf~~--v~~lLDE~id~G~i~eTd~~~----------i~~~i~~~~~~~--~~~~~~~~~~~a~~~a~ 168 (177)
.-+++++..=|.. +.++.-|++..|.+|-|..+- |...|.....+- +.+..|..+.+|+.-||
T Consensus 57 ~Ase~dL~k~FgTtd~~eI~~eIl~kGeiQlTaeqR~~m~e~k~rqIi~~IsRn~IdP~t~~P~Pp~rIe~Ameeak 133 (234)
T COG1500 57 KASEEDLKKAFGTTDPDEIAEEILKKGEIQLTAEQRREMLEEKKRQIINIISRNAIDPQTKAPHPPARIEKAMEEAK 133 (234)
T ss_pred cCCHHHHHHHhCCCCHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHhcC
Confidence 4566668777765 899999999999999998642 333333332221 24677888888888554
No 39
>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=24.68 E-value=1.6e+02 Score=22.93 Aligned_cols=35 Identities=29% Similarity=0.480 Sum_probs=24.9
Q ss_pred hccCCCCHHHHHHhH------HHHHHHHHHHhhCcEEeecC
Q 030448 102 LLRGNVDKKEALENL------DLILLCLDEIVDGGIILETD 136 (177)
Q Consensus 102 ~~~~~~~~~~i~~nf------~~v~~lLDE~id~G~i~eTd 136 (177)
.+.+.-+.+.|.+.. ..+..+|+++.+.|++.+..
T Consensus 38 lLdG~rt~~eI~~~l~~~~p~~~v~~~L~~L~~~G~l~~~~ 78 (193)
T TIGR03882 38 LLDGRRTLDEIIAALAGRFPAEEVLYALDRLERRGYLVEDA 78 (193)
T ss_pred HHcCCCCHHHHHHHhhccCCHHHHHHHHHHHHHCCCEeccC
Confidence 444445555555444 56999999999999998754
No 40
>PF06694 Plant_NMP1: Plant nuclear matrix protein 1 (NMP1); InterPro: IPR010604 This family consists of several plant specific nuclear matrix protein 1 (NMP1) sequences. Nuclear Matrix Protein 1 is a ubiquitously expressed 36 kDa protein, which has no homologues in animals and fungi, but is highly conserved among flowering and non-flowering plants. NMP1 is located both in the cytoplasm and nucleus and that the nuclear fraction is associated with the nuclear matrix. NMP1 is a candidate for a plant-specific structural protein with a function both in the nucleus and cytoplasm [].
Probab=24.00 E-value=4.6e+02 Score=22.48 Aligned_cols=79 Identities=18% Similarity=0.161 Sum_probs=50.7
Q ss_pred HHHHHHHHHHHHHhhccCCCCHHHHHHhHHHHHHHHHHHhhCcEEeecCHHHHHHhhcCCCcCC----CCCC-ChhhHHH
Q 030448 88 LATVLQGFFDAVGLLLRGNVDKKEALENLDLILLCLDEIVDGGIILETDANVIAGKVASHSVDV----GAPL-SEQTISQ 162 (177)
Q Consensus 88 l~e~L~~i~~~l~~~~~~~~~~~~i~~nf~~v~~lLDE~id~G~i~eTd~~~i~~~i~~~~~~~----~~~~-~~~~~~~ 162 (177)
-.+||+.|++.++.-....-.+-++.+.|.+=+.++|-+. |-.+......++..|-+. .-+. +-+.|..
T Consensus 102 ~~~~l~~IVDlVeas~~~~n~e~Sl~eQ~~kD~~LiD~Ia------E~~~QvFs~~ckLFP~DVqi~S~~~lPD~seLe~ 175 (325)
T PF06694_consen 102 RAEFLRLIVDLVEASMYADNPEWSLDEQFAKDIQLIDAIA------EKQQQVFSEECKLFPPDVQIQSIYPLPDVSELEK 175 (325)
T ss_pred HHHHHHHHHHHHHHHHhhcCchhhHHHHHHHHHHHHHHHH------HhHHHHHhhhcCcCCHHHhhccCCCCCCHHHHHH
Confidence 4578888999887766544455579999999999999998 344456666666554331 1111 2235666
Q ss_pred HHHHHHHHHH
Q 030448 163 ALATAREHLT 172 (177)
Q Consensus 163 a~~~a~~~~~ 172 (177)
+++...+++.
T Consensus 176 ~~s~~sk~Lq 185 (325)
T PF06694_consen 176 KASELSKQLQ 185 (325)
T ss_pred HHHHHHHHHH
Confidence 6666555543
No 41
>KOG1766 consensus Enhancer of rudimentary [General function prediction only]
Probab=23.64 E-value=1.1e+02 Score=21.55 Aligned_cols=43 Identities=12% Similarity=0.198 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHhhccC-CCCHHHHHHhHHHHHHHHHHHhhC
Q 030448 87 ILATVLQGFFDAVGLLLRG-NVDKKEALENLDLILLCLDEIVDG 129 (177)
Q Consensus 87 ~l~e~L~~i~~~l~~~~~~-~~~~~~i~~nf~~v~~lLDE~id~ 129 (177)
.+-|.++++.....+++++ +.+...|-.-...+|+.||.+.|-
T Consensus 24 sv~e~megiCk~yEe~Lkk~nPs~~~ITYDIsqlfeFiD~L~Dl 67 (104)
T KOG1766|consen 24 SVTECMEGICKMYEEHLKKKNPSAPPITYDISQLFEFIDDLADL 67 (104)
T ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCCcceeHHHHHHHHHHHhhh
Confidence 3567888888888888875 344455778888999999998873
No 42
>cd00894 PI3Kc_IB_gamma Phosphoinositide 3-kinase (PI3K), class IB, gamma isoform, catalytic domain; The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. They are further classified into class IA (alpha, beta and
Probab=22.94 E-value=3.5e+02 Score=23.66 Aligned_cols=93 Identities=11% Similarity=0.065 Sum_probs=50.8
Q ss_pred cccCceEEecCeEEEEEEeCcEEEEE----EecCCccHHHH-HHHHHHH----------HHHHHhhccCCCCHHHHHHhH
Q 030448 52 RTEAEIAMLEGNVIVYKFVQDLHFFV----TGGEDENELIL-ATVLQGF----------FDAVGLLLRGNVDKKEALENL 116 (177)
Q Consensus 52 ~~~~~i~~~~~~~ivy~~~~dl~~~~----v~~~~eNel~l-~e~L~~i----------~~~l~~~~~~~~~~~~i~~nf 116 (177)
+...+|+...+-.++|+-+|-++=-. ....+--|.-+ -++++.+ ++.+.+++.... ..++.|-
T Consensus 219 RHndNImi~~~G~lfHIDFG~ilg~~~~~~gi~~E~~PFkLT~e~v~vmg~~gg~~s~~f~~F~~~c~~a~--~~LRk~~ 296 (365)
T cd00894 219 RHNDNIMITETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSLHFQKFQDVCVKAY--LALRHHT 296 (365)
T ss_pred ccccceeEcCCCCEEEEeeHHhhCCCCccCCCCCCCCCeeecHHHHHHhCccCCcCChhHHHHHHHHHHHH--HHHHhhH
Confidence 44467877777788899887554110 00111222211 1222222 112222222111 2588999
Q ss_pred HHHHHHHHHHhhCcEEeecC---HHHHHHhhcC
Q 030448 117 DLILLCLDEIVDGGIILETD---ANVIAGKVAS 146 (177)
Q Consensus 117 ~~v~~lLDE~id~G~i~eTd---~~~i~~~i~~ 146 (177)
..+..++.=|++.|+|+-+. ...++++...
T Consensus 297 ~lil~L~~lM~~sgip~l~~~~~i~~l~~~~~l 329 (365)
T cd00894 297 NLLIILFSMMLMTGMPQLTSKEDIEYIRDALTV 329 (365)
T ss_pred HHHHHHHHHHhcCCCcccCcchHHHHHHHHhCC
Confidence 99999999999999998774 4445555544
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=22.52 E-value=70 Score=16.24 Aligned_cols=20 Identities=20% Similarity=0.298 Sum_probs=15.9
Q ss_pred HhHHHHHHHHHHHhhCcEEe
Q 030448 114 ENLDLILLCLDEIVDGGIIL 133 (177)
Q Consensus 114 ~nf~~v~~lLDE~id~G~i~ 133 (177)
.+++.+..++++|...|+..
T Consensus 14 ~~~~~a~~~~~~M~~~g~~p 33 (35)
T TIGR00756 14 GRVEEALELFKEMLERGIEP 33 (35)
T ss_pred CCHHHHHHHHHHHHHcCCCC
Confidence 45678899999999988653
No 44
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.14 E-value=4e+02 Score=21.06 Aligned_cols=65 Identities=14% Similarity=0.105 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHhhhcCCcccCceEEecCe-EEEEEEeCcEEEEEEecCCccHHHHHHHHHHHHHHH
Q 030448 35 KEAFEKAVFTKTQKTNARTEAEIAMLEGN-VIVYKFVQDLHFFVTGGEDENELILATVLQGFFDAV 99 (177)
Q Consensus 35 ~~~~e~~i~~~~~~~~~~~~~~i~~~~~~-~ivy~~~~dl~~~~v~~~~eNel~l~e~L~~i~~~l 99 (177)
-++|-..+-+.+..+.+..+-.-+.++.| ..+|.+..+|.-++++|.++.--..+.+|+.+.+-.
T Consensus 36 V~Efm~F~sktvaeRt~~g~rqsvk~~~Y~~h~yvrndgL~~V~~~D~eYP~rvA~tLL~kvld~~ 101 (198)
T KOG0861|consen 36 VQEFMTFISKTVAERTGPGQRQSVKHEEYLVHVYVRNDGLCGVLIADDEYPVRVAFTLLNKVLDEF 101 (198)
T ss_pred HHHHHHHHHHHHHHhcCcccccccccceeEEEEEEecCCeeEEEEecCcCchhHHHHHHHHHHHHH
Confidence 34566555555566653322234556666 446677779999999998888888888877766544
No 45
>cd05174 PI3Kc_IA_delta Phosphoinositide 3-kinase (PI3K), class IA, delta isoform, catalytic domain; The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. They are further classified into class IA (alpha, beta and
Probab=20.54 E-value=4.6e+02 Score=22.89 Aligned_cols=93 Identities=12% Similarity=0.048 Sum_probs=52.9
Q ss_pred cccCceEEecCeEEEEEEeCcEEEEEEe----cCCccHHHHH-HHHHHH----------HHHHHhhccCCCCHHHHHHhH
Q 030448 52 RTEAEIAMLEGNVIVYKFVQDLHFFVTG----GEDENELILA-TVLQGF----------FDAVGLLLRGNVDKKEALENL 116 (177)
Q Consensus 52 ~~~~~i~~~~~~~ivy~~~~dl~~~~v~----~~~eNel~l~-e~L~~i----------~~~l~~~~~~~~~~~~i~~nf 116 (177)
+...+|+...+-.++|+-+|.+.=-.-+ ..+.-|.-+. ++++.+ +..++.++.... ..++.|-
T Consensus 215 RHn~NILi~~~G~l~HIDFG~ilg~~~~~~~~~~E~vPFkLT~e~v~vmg~G~~~~s~~f~~F~~~c~~a~--~~LRk~~ 292 (361)
T cd05174 215 RHSDNIMIRESGQLFHIDFGHFLGNFKTKFGINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCEQAY--KILRRHG 292 (361)
T ss_pred cCccceeEcCCCCEEEEehHHhhcCCcccCCCCCCCCCeeccHHHHHHHccCCCCCCchhhHHHHHHHHHH--HHHHhhH
Confidence 4446787777778999988874311111 1123333221 233222 112222322111 2588999
Q ss_pred HHHHHHHHHHhhCcEEeecCH---HHHHHhhcC
Q 030448 117 DLILLCLDEIVDGGIILETDA---NVIAGKVAS 146 (177)
Q Consensus 117 ~~v~~lLDE~id~G~i~eTd~---~~i~~~i~~ 146 (177)
+.+..++.=|++.|+|.-+.. ..++++...
T Consensus 293 ~~il~l~~lM~~sgip~~~~~~~i~~l~~~~~l 325 (361)
T cd05174 293 TLFLHLFALMKAAGLPELNCSKDIQYLKDSLAL 325 (361)
T ss_pred HHHHHHHHHHhcCCCCccCchhHHHHHHHHhCC
Confidence 999999999999999997653 444455443
Done!