Query psy3409
Match_columns 139
No_of_seqs 125 out of 629
Neff 7.2
Searched_HMMs 46136
Date Sat Aug 17 00:16:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3409.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3409hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04628 Sedlin_N: Sedlin, N-t 100.0 8.6E-43 1.9E-47 250.4 13.3 126 9-134 1-132 (132)
2 KOG3487|consensus 100.0 2.2E-41 4.7E-46 237.4 11.9 135 1-137 1-138 (139)
3 COG5603 TRS20 Subunit of TRAPP 100.0 2.5E-41 5.4E-46 234.3 11.8 131 6-136 4-136 (136)
4 PF04099 Sybindin: Sybindin-li 100.0 1.1E-30 2.3E-35 189.8 16.4 130 4-134 1-142 (142)
5 KOG3444|consensus 100.0 1.9E-29 4.1E-34 172.7 10.9 107 5-116 3-120 (121)
6 KOG3368|consensus 100.0 8E-28 1.7E-32 170.0 14.5 131 2-134 1-138 (140)
7 KOG3369|consensus 99.9 5.1E-25 1.1E-29 162.5 13.1 95 38-134 101-197 (199)
8 COG5122 TRS23 Transport protei 99.9 9.6E-22 2.1E-26 136.1 10.8 127 3-134 2-133 (134)
9 PF01217 Clat_adaptor_s: Clath 87.7 7.8 0.00017 27.3 12.1 93 4-108 2-95 (141)
10 PF13774 Longin: Regulated-SNA 69.5 26 0.00057 22.2 7.1 48 60-108 16-64 (83)
11 PF03164 Mon1: Trafficking pro 65.8 82 0.0018 26.6 11.4 91 6-109 13-104 (415)
12 KOG0861|consensus 63.1 46 0.00099 25.3 6.8 66 37-107 38-104 (198)
13 PF08800 VirE_N: VirE N-termin 59.4 28 0.0006 24.7 5.0 22 66-87 56-79 (136)
14 KOG4497|consensus 56.5 7.6 0.00016 32.5 1.8 49 38-86 170-220 (447)
15 PF13388 DUF4106: Protein of u 50.9 26 0.00056 28.9 4.0 40 92-135 52-92 (422)
16 PF04370 DUF508: Domain of unk 39.6 1E+02 0.0022 22.5 5.2 63 72-134 48-137 (156)
17 PF10436 BCDHK_Adom3: Mitochon 35.4 58 0.0013 23.9 3.6 40 97-136 55-96 (164)
18 PF15001 AP-5_subunit_s1: AP-5 34.1 2.1E+02 0.0046 21.8 7.0 68 63-138 98-171 (189)
19 COG4472 Uncharacterized protei 33.7 87 0.0019 20.7 3.7 51 89-139 16-84 (88)
20 PHA01632 hypothetical protein 33.6 1E+02 0.0022 19.0 3.8 33 78-110 14-50 (64)
21 PHA00743 helix-turn-helix prot 33.0 58 0.0013 19.5 2.6 33 90-124 5-37 (51)
22 COG4918 Uncharacterized protei 32.6 29 0.00062 24.0 1.4 17 8-24 55-71 (114)
23 PF15205 PLAC9: Placenta-speci 30.8 37 0.00081 21.7 1.6 21 34-54 17-37 (74)
24 cd04516 TBP_eukaryotes eukaryo 30.5 2.3E+02 0.0049 21.1 6.6 49 55-105 124-172 (174)
25 KOG2583|consensus 29.2 1.2E+02 0.0025 26.1 4.7 44 92-136 153-197 (429)
26 PF14026 DUF4242: Protein of u 29.1 1.6E+02 0.0034 18.8 4.8 30 70-99 37-66 (77)
27 PF09441 Abp2: ARS binding pro 28.6 59 0.0013 24.3 2.6 24 91-114 101-128 (175)
28 cd04517 TLF TBP-like factors ( 28.5 2.5E+02 0.0054 20.8 7.3 48 55-104 125-172 (174)
29 cd04920 ACT_AKiii-DAPDC_2 ACT 26.7 1.5E+02 0.0032 17.7 4.0 29 74-105 34-62 (63)
30 COG4092 Predicted glycosyltran 26.6 27 0.0006 28.5 0.6 27 89-115 50-78 (346)
31 PRK14449 acylphosphatase; Prov 26.4 1.4E+02 0.003 19.5 3.9 35 67-102 28-63 (90)
32 COG1507 Uncharacterized conser 25.4 2.1E+02 0.0045 21.2 4.9 19 89-107 81-99 (167)
33 KOG1299|consensus 24.7 62 0.0013 28.4 2.4 24 90-113 112-136 (549)
34 PF13198 DUF4014: Protein of u 24.7 50 0.0011 21.2 1.4 25 96-120 43-67 (72)
35 COG1618 Predicted nucleotide k 24.5 98 0.0021 23.4 3.1 18 117-134 112-129 (179)
36 cd04915 ACT_AK-Ectoine_2 ACT d 23.9 1.7E+02 0.0037 17.6 3.8 28 75-105 38-65 (66)
37 PF03288 Pox_D5: Poxvirus D5 p 22.9 1.3E+02 0.0028 19.0 3.2 34 98-134 25-59 (86)
38 PF05729 NACHT: NACHT domain 22.3 1.3E+02 0.0029 20.5 3.4 48 76-138 118-165 (166)
39 COG3016 PhuW Uncharacterized i 21.2 3E+02 0.0065 22.3 5.4 68 57-127 27-114 (295)
40 PF01541 GIY-YIG: GIY-YIG cata 21.0 90 0.0019 18.9 2.1 21 1-23 1-21 (80)
41 PF01152 Bac_globin: Bacterial 20.8 2.2E+02 0.0048 19.0 4.2 46 90-138 9-55 (120)
42 PF10100 DUF2338: Uncharacteri 20.4 1.3E+02 0.0029 25.8 3.5 29 89-117 293-329 (429)
43 PF09843 DUF2070: Predicted me 20.1 3.7E+02 0.0079 19.8 8.3 72 65-136 58-147 (179)
No 1
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=100.00 E-value=8.6e-43 Score=250.35 Aligned_cols=126 Identities=45% Similarity=0.865 Sum_probs=107.0
Q ss_pred EEcCCCCeeEEEecCCCCCCC-chhhHHHHHHHHHhHHHHHHhhcc-cccCCceeeeeeCCeeEEEEEcCCCcEEEEEec
Q psy3409 9 MVGREDNPLYQRGFSCKEAND-NENKYYYEFIAHASLDLLDEQVWQ-TDHMYLKTIDKFNDMMVSAFVTPTGVKFLMVHD 86 (139)
Q Consensus 9 Ii~~~~~ply~~~~~~~~~~~-~~~~~~~~f~~~~SLD~i~~~~~~-~~~~yL~~l~~~~~~~v~~y~T~t~~Kfvl~~~ 86 (139)
|||++|+|||++++++..... +..++++||++|+|||+||+++|. ++++|||.|+++++|+||||+|+||+||||+++
T Consensus 1 IIg~~n~PLy~~~~~~~~~~~~~~~~~l~~~~~h~sLD~iee~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~ 80 (132)
T PF04628_consen 1 IIGPNNNPLYIRSFPSEKESSSSDARHLYQFIAHSSLDVIEEKLWKSSSDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHD 80 (132)
T ss_dssp EE-TTS-EEEEEEE--ST-CGHHHHHHHHHHHHHHHHHHHHHCCHCSSSCSEEEEEEEETTEEEEEEETTT--EEEEEEC
T ss_pred CCCCCCcceEEEecCCCcccccchHHHHHHHHHHHHHHHHHHHHhhcccccccCceehhhhHHHHhhhccCceeEEEEEe
Confidence 899999999999999543211 113455999999999999999999 889999999999999999999999999999999
Q ss_pred ----cCChHHHHHHHHHHHHHHHHhhhCCCCCCCCCCcChhHHHHHHHHHHh
Q psy3409 87 ----SKNEEGIKKFFTSVYELFIKYSLNPFYKINTPINSTYFDSKVNFLGRK 134 (139)
Q Consensus 87 ----~~~~~~i~~~f~~i~~~Yv~~v~NPf~~~~~~I~s~~F~~~v~~~~~~ 134 (139)
..++++||+||++||++|++++|||||+++++|+|+.|+++|+++++|
T Consensus 81 ~~~~~~~d~~ik~fF~~vh~~Y~~~~~NPF~~~~~~I~S~~Fd~~v~~l~~k 132 (132)
T PF04628_consen 81 MSDNSIRDEDIKQFFKEVHELYVKALCNPFYQPGTPIKSPKFDSRVRALAKK 132 (132)
T ss_dssp GGG-S--HHHHHHHHHHHHHHHHHHHTSTTCGCT-HHHHHHHHHHHHHHHHH
T ss_pred cccCCcchHHHHHHHHHHHHHHHHHccCCCCCCCCCcCCHHHHHHHHHHhcC
Confidence 458999999999999999999999999999999999999999999986
No 2
>KOG3487|consensus
Probab=100.00 E-value=2.2e-41 Score=237.44 Aligned_cols=135 Identities=48% Similarity=0.897 Sum_probs=126.5
Q ss_pred CCceEEEEEEcCCCCeeEEEecCC---CCCCCchhhHHHHHHHHHhHHHHHHhhcccccCCceeeeeeCCeeEEEEEcCC
Q psy3409 1 MANRYYFVMVGREDNPLYQRGFSC---KEANDNENKYYYEFIAHASLDLLDEQVWQTDHMYLKTIDKFNDMMVSAFVTPT 77 (139)
Q Consensus 1 m~~~~~~~Ii~~~~~ply~~~~~~---~~~~~~~~~~~~~f~~~~SLD~i~~~~~~~~~~yL~~l~~~~~~~v~~y~T~t 77 (139)
|++ ||+|||++|+|+|+.+|+. +.+.+++.+++.||++|+|||+|||.+|.++.+|||.+|+++++-|++|+|++
T Consensus 1 m~~--yfaIig~~d~Pvye~e~~~~~~~~~~~~~~~~LN~FI~HAaLdiVde~~W~~snmYLktVDkfne~~VSAyvTas 78 (139)
T KOG3487|consen 1 MTA--YFAIIGHCDNPVYEMEFGCPENSKAARDDNRHLNQFIVHAALDIVDELQWTTSNMYLKTVDKFNELFVSAYVTAS 78 (139)
T ss_pred Cce--EEEEEecCCCceEEeecCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHhhcceeEEEEEccC
Confidence 555 9999999999999999982 22345677888999999999999999999999999999999999999999999
Q ss_pred CcEEEEEeccCChHHHHHHHHHHHHHHHHhhhCCCCCCCCCCcChhHHHHHHHHHHhhcc
Q psy3409 78 GVKFLMVHDSKNEEGIKKFFTSVYELFIKYSLNPFYKINTPINSTYFDSKVNFLGRKFLT 137 (139)
Q Consensus 78 ~~Kfvl~~~~~~~~~i~~~f~~i~~~Yv~~v~NPf~~~~~~I~s~~F~~~v~~~~~~~~~ 137 (139)
++||++++..+.+++++.||+++|++|++.+|||||.+++||+|+.||.+++-+.++||.
T Consensus 79 ~i~f~mlh~~~~~~~ik~Ffqev~elyik~lmnpFy~~~dpirs~afd~kv~~~~rkhl~ 138 (139)
T KOG3487|consen 79 HIRFIMLHINRADDNIKLFFQEVHELYIKTLMNPFYEINDPIRSPAFDHKVRGLARKHLS 138 (139)
T ss_pred cEEEEEEeeccccccHHHHHHHHHHHHHHHHhCcccccCCccccHHHHHHHHHHHHHHhc
Confidence 999999999988999999999999999999999999999999999999999999999985
No 3
>COG5603 TRS20 Subunit of TRAPP, an ER-Golgi tethering complex [Cell motility and secretion]
Probab=100.00 E-value=2.5e-41 Score=234.35 Aligned_cols=131 Identities=34% Similarity=0.700 Sum_probs=123.6
Q ss_pred EEEEEcCCCCeeEEEecCC--CCCCCchhhHHHHHHHHHhHHHHHHhhcccccCCceeeeeeCCeeEEEEEcCCCcEEEE
Q psy3409 6 YFVMVGREDNPLYQRGFSC--KEANDNENKYYYEFIAHASLDLLDEQVWQTDHMYLKTIDKFNDMMVSAFVTPTGVKFLM 83 (139)
Q Consensus 6 ~~~Ii~~~~~ply~~~~~~--~~~~~~~~~~~~~f~~~~SLD~i~~~~~~~~~~yL~~l~~~~~~~v~~y~T~t~~Kfvl 83 (139)
+++|||++|+|+|+++++. +++..+..+++.||++|+|||++++++|+.+.+|+++++.+++.+++||+||+|+||++
T Consensus 4 y~aIIg~KdnpVYe~e~~~~n~~~d~~~~~~ln~fiihaSlDiv~~lqwsvN~~Y~~~~d~f~~l~IsAYi~pSgmkf~~ 83 (136)
T COG5603 4 YLAIIGEKDNPVYEREYDPINKTSDGEYCRLLNQFIIHASLDIVVWLQWSVNTSYFDCLDSFGDLRISAYIMPSGMKFLF 83 (136)
T ss_pred eEEEEecCCCceeeeeecCcCcccCHHHHHHHhHHhhhhhHHHHHHHHHHhhhHHHHHHHhhCCeEEEEEEccCCceEEE
Confidence 8999999999999999993 34455667888999999999999999999999999999999999999999999999999
Q ss_pred EeccCChHHHHHHHHHHHHHHHHhhhCCCCCCCCCCcChhHHHHHHHHHHhhc
Q psy3409 84 VHDSKNEEGIKKFFTSVYELFIKYSLNPFYKINTPINSTYFDSKVNFLGRKFL 136 (139)
Q Consensus 84 ~~~~~~~~~i~~~f~~i~~~Yv~~v~NPf~~~~~~I~s~~F~~~v~~~~~~~~ 136 (139)
+|.....+++|.||+++|++|++.+|||||++++||+|++||.+||+++|++|
T Consensus 84 iH~n~s~~N~rsF~qevHely~ktLmspfy~~~~pirsqafd~~Vr~~ar~~L 136 (136)
T COG5603 84 IHQNQSRKNARSFLQEVHELYAKTLMSPFYEPDEPIRSQAFDDGVREAARVCL 136 (136)
T ss_pred EeccchhhhHHHHHHHHHHHHHHHhhCcccCCCccccchhhhhhHHHHHHhhC
Confidence 99887788999999999999999999999999999999999999999999986
No 4
>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=99.97 E-value=1.1e-30 Score=189.80 Aligned_cols=130 Identities=22% Similarity=0.415 Sum_probs=96.4
Q ss_pred eEEEEEEcCCCCeeEEEecCCCC----CCCchhhHHHHHHHHHhHHHHHHhhccc-------ccCCceeeeeeCCeeEEE
Q psy3409 4 RYYFVMVGREDNPLYQRGFSCKE----ANDNENKYYYEFIAHASLDLLDEQVWQT-------DHMYLKTIDKFNDMMVSA 72 (139)
Q Consensus 4 ~~~~~Ii~~~~~ply~~~~~~~~----~~~~~~~~~~~f~~~~SLD~i~~~~~~~-------~~~yL~~l~~~~~~~v~~ 72 (139)
+|+|+||||+|++||.++|.... +...+++.+..+++..||..|..++++. +...+.. ..++.|++|+
T Consensus 1 IyslyI~nr~G~lIy~~~~~~~~~~~~~~~~~ne~~ll~g~l~sl~~i~~klsp~~~~~~~~~~~g~~~-~~T~~yklh~ 79 (142)
T PF04099_consen 1 IYSLYIFNRSGGLIYYREWNRSKNEGQPKLSSNEYKLLAGMLHSLKAIASKLSPVDSKPNEPGSSGFES-FETDTYKLHC 79 (142)
T ss_dssp EEEEEEE-TTS-EEEEEETSSSS--E-SSSCHHHHHHHHHHHHHHHHHHHHT-SSSSSS-SSS--SEEE-EEESS-EEEE
T ss_pred CeEEEEEeCCcceeeehhhCCCCccccCCCChhHHHHHHhhHHHHHHHHHHhCCCCcccccccceeEEE-EEeCCEEEEE
Confidence 68999999999999999998432 2234556667899999999999999972 2346645 5589999999
Q ss_pred EEcCCCcEEEEEeccCChHHHHHHHHHHHHHHHHhhh-CCCCCCCCCCcChhHHHHHHHHHHh
Q psy3409 73 FVTPTGVKFLMVHDSKNEEGIKKFFTSVYELFIKYSL-NPFYKINTPINSTYFDSKVNFLGRK 134 (139)
Q Consensus 73 y~T~t~~Kfvl~~~~~~~~~i~~~f~~i~~~Yv~~v~-NPf~~~~~~I~s~~F~~~v~~~~~~ 134 (139)
|+|+||+|||+++|+........+++.+|++|++||+ ||||++++||+|+.||++|++++++
T Consensus 80 ~eT~TGlKFvl~td~~~~~~~~~l~~~~~~lY~dyV~KNPfy~~~~pI~~~lF~~~l~~~~~~ 142 (142)
T PF04099_consen 80 FETPTGLKFVLITDPNVPSLRDELLRIYYELYVDYVVKNPFYSLEMPIRCELFDTKLDQYVKS 142 (142)
T ss_dssp EE-TTS-EEEEEE-TTCCHCHHHHHHHHHHHHHHHHHS-TTS-TTS----HHHHHHHHHHHHC
T ss_pred EEcCcCcEEEEEecCCCccHHHHHHHHHHHHHHHHHhhCCCCCCCCcEehHHHHHHHHHHHhC
Confidence 9999999999999994435566677888899999999 9999999999999999999999874
No 5
>KOG3444|consensus
Probab=99.96 E-value=1.9e-29 Score=172.68 Aligned_cols=107 Identities=31% Similarity=0.523 Sum_probs=98.3
Q ss_pred EEEEEEcCCCCeeEEEecCCCCCCCchhhHHHHHHHHHhHHHHHHhhcc-------cccCCceeeeeeCCeeEEEEEcCC
Q psy3409 5 YYFVMVGREDNPLYQRGFSCKEANDNENKYYYEFIAHASLDLLDEQVWQ-------TDHMYLKTIDKFNDMMVSAFVTPT 77 (139)
Q Consensus 5 ~~~~Ii~~~~~ply~~~~~~~~~~~~~~~~~~~f~~~~SLD~i~~~~~~-------~~~~yL~~l~~~~~~~v~~y~T~t 77 (139)
.|++++|++|+|+|++.+++ .++++++|+..|+|||+|||+... ++++|||.++++++|++|||+|+|
T Consensus 3 v~~av~g~kn~~lyi~s~t~-----~e~~L~~~y~v~~sLDVieekvn~~gkg~~tsne~fLGLLy~ted~kvYgfvtNT 77 (121)
T KOG3444|consen 3 VCLAVAGPKNEPLYIESITP-----KEKELKLHYQVHLSLDVIEEKVNDPGKGERTSNELFLGLLYPTEDYKVYGFVTNT 77 (121)
T ss_pred EEEEEEcCCCCccEEEecCc-----HHHHHHhHhhhhhhHHHHHHHhcCcccCccchhhhhhcccccccceeEEEEEecc
Confidence 59999999999999999985 456788999999999999999952 468999999999999999999999
Q ss_pred CcEEEEEeccC----ChHHHHHHHHHHHHHHHHhhhCCCCCCC
Q psy3409 78 GVKFLMVHDSK----NEEGIKKFFTSVYELFIKYSLNPFYKIN 116 (139)
Q Consensus 78 ~~Kfvl~~~~~----~~~~i~~~f~~i~~~Yv~~v~NPf~~~~ 116 (139)
.+|||+++|.. ++.+||++||.+|-+|.+..|||||-++
T Consensus 78 kVKFIlvvdssd~avreteiRsv~r~~h~l~td~~~npfy~pg 120 (121)
T KOG3444|consen 78 KVKFILVVDSSDYAVRETEIRSVFRILHLLYTDLSCNPFYLPG 120 (121)
T ss_pred EEEEEEEEcCCcceehhHHHHHHHHHHHHHHHHheecceeccC
Confidence 99999999864 5889999999999999999999999876
No 6
>KOG3368|consensus
Probab=99.96 E-value=8e-28 Score=169.97 Aligned_cols=131 Identities=23% Similarity=0.376 Sum_probs=114.9
Q ss_pred CceEEEEEEcCCCCeeEEEecCC--CCCCCchhhHHHHHHHHHhHHHHHHhhcccc-cCCceeeeeeCCeeEEEEEcCCC
Q psy3409 2 ANRYYFVMVGREDNPLYQRGFSC--KEANDNENKYYYEFIAHASLDLLDEQVWQTD-HMYLKTIDKFNDMMVSAFVTPTG 78 (139)
Q Consensus 2 ~~~~~~~Ii~~~~~ply~~~~~~--~~~~~~~~~~~~~f~~~~SLD~i~~~~~~~~-~~yL~~l~~~~~~~v~~y~T~t~ 78 (139)
+++|.++|++|+|+|||.++|.. .++..++++.++-|++..||..+-+|+++.+ +..+ .-++++.|++|.|+||||
T Consensus 1 Mtiy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d~k~~f-~sy~Ts~YklhfyeTptg 79 (140)
T KOG3368|consen 1 MTIYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGDVKDGF-LSYKTSKYKLHFYETPTG 79 (140)
T ss_pred CeEEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCCcccCe-eEEeeceeEEEEEEcCCC
Confidence 47899999999999999999983 2333455667888999999999999998763 2233 347799999999999999
Q ss_pred cEEEEEeccCChHHHHHHHHHHHH-HHHHhhh-CCCCC--CCCCCcChhHHHHHHHHHHh
Q psy3409 79 VKFLMVHDSKNEEGIKKFFTSVYE-LFIKYSL-NPFYK--INTPINSTYFDSKVNFLGRK 134 (139)
Q Consensus 79 ~Kfvl~~~~~~~~~i~~~f~~i~~-~Yv~~v~-NPf~~--~~~~I~s~~F~~~v~~~~~~ 134 (139)
+||||++|+ +..++|++++.||. +||++|. ||+++ +++||+|+.|.+.+++.++.
T Consensus 80 lk~vl~Tdp-k~~~ir~vLq~IYs~lyVE~Vvknpl~~~~~~~~i~~E~fr~~ld~~vrs 138 (140)
T KOG3368|consen 80 LKFVLNTDP-KAGSIRDVLQYIYSHLYVEYVVKNPLYTYDPGSPIRSELFRKILDRFVRS 138 (140)
T ss_pred cEEEEecCC-CcccHHHHHHHHHHHHHHHHHHcCcccccCCCCccchHHHHHHHHhhhcc
Confidence 999999999 88899999999995 9999999 99999 99999999999999999873
No 7
>KOG3369|consensus
Probab=99.93 E-value=5.1e-25 Score=162.52 Aligned_cols=95 Identities=27% Similarity=0.533 Sum_probs=85.0
Q ss_pred HHHHHhHHHHHHhhccccc-CCceeeeeeCCeeEEEEEcCCCcEEEEEeccCChHHHHHHHHHHHHHHHHhhh-CCCCCC
Q psy3409 38 FIAHASLDLLDEQVWQTDH-MYLKTIDKFNDMMVSAFVTPTGVKFLMVHDSKNEEGIKKFFTSVYELFIKYSL-NPFYKI 115 (139)
Q Consensus 38 f~~~~SLD~i~~~~~~~~~-~yL~~l~~~~~~~v~~y~T~t~~Kfvl~~~~~~~~~i~~~f~~i~~~Yv~~v~-NPf~~~ 115 (139)
-.++.||+.|.+++++-+. +.+..++ ++.+++|+|+|-||+|||+++++ ....+..+|++||++|.+|++ ||||++
T Consensus 101 as~fhsl~aI~~qlsp~~ksSGie~Le-tdtF~l~~~QTlTG~KFVvis~~-~~~~aD~lLrKiYelYsDyvlKNPfYSl 178 (199)
T KOG3369|consen 101 ASSFHSLFAISTQLSPEPKSSGIEVLE-TDTFTLHIFQTLTGTKFVVIAEP-GTQGADSLLRKIYELYSDYVLKNPFYSL 178 (199)
T ss_pred hhhhcchhheeeccCCCCCCCceEEEE-eccEEEEEEEccCCcEEEEEecC-CchhHHHHHHHHHHHHHHHhhcCCccCc
Confidence 4467889999999987554 6675555 88999999999999999999998 567899999999999999999 999999
Q ss_pred CCCCcChhHHHHHHHHHHh
Q psy3409 116 NTPINSTYFDSKVNFLGRK 134 (139)
Q Consensus 116 ~~~I~s~~F~~~v~~~~~~ 134 (139)
++||+|++||.+++.++..
T Consensus 179 EMPIRc~lFDe~lk~~le~ 197 (199)
T KOG3369|consen 179 EMPIRCELFDEKLKFLLES 197 (199)
T ss_pred ccceeHHHhhHHHHHHHhh
Confidence 9999999999999998865
No 8
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=99.87 E-value=9.6e-22 Score=136.13 Aligned_cols=127 Identities=24% Similarity=0.407 Sum_probs=92.5
Q ss_pred ceEEEEEEcCCCCeeEEEecCCCCCCCchhhHHHHHHHHHhHHH---HHHhhcc-cccCCceeeeeeCCeeEEEEEcCCC
Q psy3409 3 NRYYFVMVGREDNPLYQRGFSCKEANDNENKYYYEFIAHASLDL---LDEQVWQ-TDHMYLKTIDKFNDMMVSAFVTPTG 78 (139)
Q Consensus 3 ~~~~~~Ii~~~~~ply~~~~~~~~~~~~~~~~~~~f~~~~SLD~---i~~~~~~-~~~~yL~~l~~~~~~~v~~y~T~t~ 78 (139)
++.-|.|||+.|..||.|+|++.+..-..++++ ++-++|.- |..+..+ .+...+..++ ++.+.++-|+|-||
T Consensus 2 ave~~~iINksGglifqref~~~et~lnsneyL---iLastlhgV~aI~tq~~p~~gssg~~~l~-~~~f~m~I~qT~TG 77 (134)
T COG5122 2 AVEQFFIINKSGGLIFQREFGEGETELNSNEYL---ILASTLHGVSAILTQTIPLPGSSGRLVLY-FRNFVMTIFQTTTG 77 (134)
T ss_pred ceeEEEEEecCCcEEEEEeccCCccccCcccEE---EEeechhhhhhhhhhcccCCCCCceEEEE-eccEEEEEEEecCC
Confidence 457789999999999999997432211222222 22233333 3333332 1223443444 78999999999999
Q ss_pred cEEEEEeccCChHHHHHHHHHHHHHHHHhhh-CCCCCCCCCCcChhHHHHHHHHHHh
Q psy3409 79 VKFLMVHDSKNEEGIKKFFTSVYELFIKYSL-NPFYKINTPINSTYFDSKVNFLGRK 134 (139)
Q Consensus 79 ~Kfvl~~~~~~~~~i~~~f~~i~~~Yv~~v~-NPf~~~~~~I~s~~F~~~v~~~~~~ 134 (139)
+|||++++.+. .+.+--++++|++|.+||+ ||||++++||+|.+||.++++.+..
T Consensus 78 ~kFV~~~~k~t-~na~~ql~kiY~lYsdYV~knPfys~EMPI~c~lFde~lkrm~e~ 133 (134)
T COG5122 78 TKFVFVAEKRT-VNALFQLQKIYSLYSDYVTKNPFYSPEMPIQCSLFDEHLKRMFEG 133 (134)
T ss_pred cEEEEEecCCc-hhHHHHHHHHHHHHHHHhhcCCCCCcccceehhhhhHHHHHHhcC
Confidence 99999998743 3455558999999999999 9999999999999999999988754
No 9
>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=87.70 E-value=7.8 Score=27.34 Aligned_cols=93 Identities=11% Similarity=0.219 Sum_probs=55.3
Q ss_pred eEEEEEEcCCCCeeEEEecCCCCCCCchhhHHHHHHHHHhHHHHHHhhcccccCCceeeeeeCCeeEEEEEcCCCcEEEE
Q psy3409 4 RYYFVMVGREDNPLYQRGFSCKEANDNENKYYYEFIAHASLDLLDEQVWQTDHMYLKTIDKFNDMMVSAFVTPTGVKFLM 83 (139)
Q Consensus 4 ~~~~~Ii~~~~~ply~~~~~~~~~~~~~~~~~~~f~~~~SLD~i~~~~~~~~~~yL~~l~~~~~~~v~~y~T~t~~Kfvl 83 (139)
+.++.|+|++|++++.|-|...+. ... +-.... ....+..+.++. ..+...+++++ .|.--+++-|++
T Consensus 2 I~~i~i~n~~G~~i~~k~y~~~~~--~~~----~~~~~~---~~~~~~~~~~~~--~~i~~~~~~~~-vy~~~~dl~~~~ 69 (141)
T PF01217_consen 2 IKAILILNSQGKRILSKYYRDVSE--EER----QKLFEK---FIKKKSSRNSKQ--SPIFEHDNYRI-VYKRYSDLYFVV 69 (141)
T ss_dssp EEEEEEEETTSEEEEEEESSTSTS--HHH----HHHHHH---HHHHHHTSSSSS--TSEEEETTEEE-EEEEETTEEEEE
T ss_pred EEEEEEEcCCCCEEEehhcCCccH--HHH----HHHHHH---HHHHHHhccccc--ceeeeccccee-eeEeeccEEEEE
Confidence 568999999999999999963211 111 111111 011112222211 23344566554 777888999999
Q ss_pred Eecc-CChHHHHHHHHHHHHHHHHhh
Q psy3409 84 VHDS-KNEEGIKKFFTSVYELFIKYS 108 (139)
Q Consensus 84 ~~~~-~~~~~i~~~f~~i~~~Yv~~v 108 (139)
+++. .++-.+-.+++.+.+++-++.
T Consensus 70 v~~~~eNel~~~e~l~~~v~~l~~~~ 95 (141)
T PF01217_consen 70 VGDENENELLLLEFLHRLVEVLDDYF 95 (141)
T ss_dssp EESSTSBHHHHHHHHHHHHHHHHHHH
T ss_pred EeecccchHHHHHHHHHhhhhhhhhh
Confidence 9986 244455777777777776664
No 10
>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=69.47 E-value=26 Score=22.24 Aligned_cols=48 Identities=17% Similarity=0.268 Sum_probs=36.2
Q ss_pred eeeeeeCCeeEEEEEcCCCcEEEEEeccCC-hHHHHHHHHHHHHHHHHhh
Q psy3409 60 KTIDKFNDMMVSAFVTPTGVKFLMVHDSKN-EEGIKKFFTSVYELFIKYS 108 (139)
Q Consensus 60 ~~l~~~~~~~v~~y~T~t~~Kfvl~~~~~~-~~~i~~~f~~i~~~Yv~~v 108 (139)
+.....++|.+|.++ ..|+-++.+++..- ..-.=.|+++|.+.|.+..
T Consensus 16 k~s~~~~~~~fh~~~-~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~ 64 (83)
T PF13774_consen 16 KMSYESGNYVFHYLV-EDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTY 64 (83)
T ss_dssp EEEEEETTEEEEEEE-ETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHC
T ss_pred eEEEEECCEEEEEEE-cCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHc
Confidence 355667888888888 99999999999742 3334567888888887753
No 11
>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=65.84 E-value=82 Score=26.63 Aligned_cols=91 Identities=15% Similarity=0.235 Sum_probs=52.9
Q ss_pred EEEEEcCCCCeeEEEecCCCCCCCchhhHHHHHHHHHhHHHHHHhhcccccCCceeeeeeCCeeEEEEEcCCCcEEEEEe
Q psy3409 6 YFVMVGREDNPLYQRGFSCKEANDNENKYYYEFIAHASLDLLDEQVWQTDHMYLKTIDKFNDMMVSAFVTPTGVKFLMVH 85 (139)
Q Consensus 6 ~~~Ii~~~~~ply~~~~~~~~~~~~~~~~~~~f~~~~SLD~i~~~~~~~~~~yL~~l~~~~~~~v~~y~T~t~~Kfvl~~ 85 (139)
-+.|++..|+|||.+. + +++.+...+++..|| -......+ .-|+.+. .++.++. |..-+.+-+|.++
T Consensus 13 h~fIlS~AGKPIysr~-G------~e~~l~~~~g~~~ai---iS~~~~~~-d~l~~i~-~~~~~iv-fl~r~pl~lv~vS 79 (415)
T PF03164_consen 13 HFFILSSAGKPIYSRY-G------DEDKLSSLMGVIQAI---ISFFQSNG-DELRSIR-AGDHRIV-FLNRGPLILVAVS 79 (415)
T ss_pred eEEEECCCCceeEEec-C------ChHHHHHHHHHHHHH---HHHHHhCC-CcEEEEE-eCCEEEE-EEecCCEEEEEEc
Confidence 4789999999999985 4 233333334443333 22222222 2344443 3555554 5567777777777
Q ss_pred ccC-ChHHHHHHHHHHHHHHHHhhh
Q psy3409 86 DSK-NEEGIKKFFTSVYELFIKYSL 109 (139)
Q Consensus 86 ~~~-~~~~i~~~f~~i~~~Yv~~v~ 109 (139)
... .+..++.-++-+|..-+..+.
T Consensus 80 ~~~e~~~~l~~qL~~ly~qils~lt 104 (415)
T PF03164_consen 80 KTGESESQLRKQLDYLYSQILSILT 104 (415)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHhcc
Confidence 652 356678888888866555544
No 12
>KOG0861|consensus
Probab=63.14 E-value=46 Score=25.33 Aligned_cols=66 Identities=17% Similarity=0.223 Sum_probs=43.6
Q ss_pred HHHHHHhHHHHHHhhcccccCCceeeeeeCCeeEEEEEcCCCcEEEEEeccCC-hHHHHHHHHHHHHHHHHh
Q psy3409 37 EFIAHASLDLLDEQVWQTDHMYLKTIDKFNDMMVSAFVTPTGVKFLMVHDSKN-EEGIKKFFTSVYELFIKY 107 (139)
Q Consensus 37 ~f~~~~SLD~i~~~~~~~~~~yL~~l~~~~~~~v~~y~T~t~~Kfvl~~~~~~-~~~i~~~f~~i~~~Yv~~ 107 (139)
+|..+.|=- +.++. ..+.++-.+.++|.+|+|+-+.|+.-|++.|..- ..-.-.++++|-+-|..-
T Consensus 38 Efm~F~skt-vaeRt----~~g~rqsvk~~~Y~~h~yvrndgL~~V~~~D~eYP~rvA~tLL~kvld~~~~k 104 (198)
T KOG0861|consen 38 EFMTFISKT-VAERT----GPGQRQSVKHEEYLVHVYVRNDGLCGVLIADDEYPVRVAFTLLNKVLDEFTTK 104 (198)
T ss_pred HHHHHHHHH-HHHhc----CcccccccccceeEEEEEEecCCeeEEEEecCcCchhHHHHHHHHHHHHHhhc
Confidence 466665433 33333 2344555667899999999999999999999732 223355677877777433
No 13
>PF08800 VirE_N: VirE N-terminal domain; InterPro: IPR014907 This domain is associated with the N terminus of Virulence E proteins. The function of the domain is unknown.
Probab=59.39 E-value=28 Score=24.73 Aligned_cols=22 Identities=36% Similarity=0.705 Sum_probs=17.4
Q ss_pred CCeeEEEEEcCCC--cEEEEEecc
Q psy3409 66 NDMMVSAFVTPTG--VKFLMVHDS 87 (139)
Q Consensus 66 ~~~~v~~y~T~t~--~Kfvl~~~~ 87 (139)
+.+.+.+|+||+| +|+++-.+.
T Consensus 56 ~p~t~~~f~SpSG~GvKi~v~~~~ 79 (136)
T PF08800_consen 56 DPYTLAAFVSPSGRGVKIIVPFDY 79 (136)
T ss_pred CCcEEEEEEcCCCCeEEEEEEecC
Confidence 4566899999875 898888765
No 14
>KOG4497|consensus
Probab=56.51 E-value=7.6 Score=32.51 Aligned_cols=49 Identities=24% Similarity=0.379 Sum_probs=36.2
Q ss_pred HHHHHhHHHHHHhh--cccccCCceeeeeeCCeeEEEEEcCCCcEEEEEec
Q psy3409 38 FIAHASLDLLDEQV--WQTDHMYLKTIDKFNDMMVSAFVTPTGVKFLMVHD 86 (139)
Q Consensus 38 f~~~~SLD~i~~~~--~~~~~~yL~~l~~~~~~~v~~y~T~t~~Kfvl~~~ 86 (139)
.+-++.+|.+|-.- |+.+.+.|-..+..-+|+||+|+-.+|+|||--..
T Consensus 170 ll~~f~~dT~DltgieWsPdg~~laVwd~~Leykv~aYe~~lG~k~v~wsP 220 (447)
T KOG4497|consen 170 LLKEFKLDTIDLTGIEWSPDGNWLAVWDNVLEYKVYAYERGLGLKFVEWSP 220 (447)
T ss_pred HHHhcCCCcccccCceECCCCcEEEEecchhhheeeeeeeccceeEEEecc
Confidence 34466666666332 44556778777877899999999999999997654
No 15
>PF13388 DUF4106: Protein of unknown function (DUF4106)
Probab=50.89 E-value=26 Score=28.91 Aligned_cols=40 Identities=23% Similarity=0.352 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHhhh-CCCCCCCCCCcChhHHHHHHHHHHhh
Q psy3409 92 GIKKFFTSVYELFIKYSL-NPFYKINTPINSTYFDSKVNFLGRKF 135 (139)
Q Consensus 92 ~i~~~f~~i~~~Yv~~v~-NPf~~~~~~I~s~~F~~~v~~~~~~~ 135 (139)
+.++-|+.+| .+..+ |-|.+ +..++|+.||+.+++.++.-
T Consensus 52 dfknafealh---skvklvndfss-gkklksegfdkelrevaqnm 92 (422)
T PF13388_consen 52 DFKNAFEALH---SKVKLVNDFSS-GKKLKSEGFDKELREVAQNM 92 (422)
T ss_pred hHHHHHHHHH---hhhhhhccccc-ccccccchhhHHHHHHHHHH
Confidence 3444455444 34444 88854 78999999999999988753
No 16
>PF04370 DUF508: Domain of unknown function (DUF508) ; InterPro: IPR007465 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=39.62 E-value=1e+02 Score=22.50 Aligned_cols=63 Identities=16% Similarity=0.255 Sum_probs=43.4
Q ss_pred EEEcCCCcEEEEEeccC--------------ChHHHHHHHHHHHHHHHHhhh-CCCCCC------------CCCCcChhH
Q psy3409 72 AFVTPTGVKFLMVHDSK--------------NEEGIKKFFTSVYELFIKYSL-NPFYKI------------NTPINSTYF 124 (139)
Q Consensus 72 ~y~T~t~~Kfvl~~~~~--------------~~~~i~~~f~~i~~~Yv~~v~-NPf~~~------------~~~I~s~~F 124 (139)
-|+|.-++||||+|-.. .|--+..+.-.-|+++.+.+- +-|.+- ..|+.....
T Consensus 48 K~V~MVhVKFilLh~Dv~kRrvQS~F~DEF~SDc~LqdVi~nF~qlc~RqLr~~~f~PRlsYCIGeln~~nSKPv~~~Dl 127 (156)
T PF04370_consen 48 KYVTMVHVKFILLHRDVFKRRVQSCFTDEFPSDCLLQDVIINFHQLCSRQLRNQEFNPRLSYCIGELNYKNSKPVLKSDL 127 (156)
T ss_pred cEEEEEEEEEEEEehHHHHHHHHHhhcccCcccCcHHHHHHHHHHHHHHHHhccccCcceeeeeccccccCCCcchHHHH
Confidence 46788899999998651 233455666667788888777 444331 247877888
Q ss_pred HHHHHHHHHh
Q psy3409 125 DSKVNFLGRK 134 (139)
Q Consensus 125 ~~~v~~~~~~ 134 (139)
.+.+.++++.
T Consensus 128 ~KtLAqLA~t 137 (156)
T PF04370_consen 128 GKTLAQLAAT 137 (156)
T ss_pred HHHHHHHhcc
Confidence 8888888765
No 17
>PF10436 BCDHK_Adom3: Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase; InterPro: IPR018955 Catabolism and synthesis of leucine, isoleucine and valine are finely balanced, allowing the body to make the most of dietary input but removing excesses to prevent toxic build-up of their corresponding keto-acids. Regulating the activity of the branched-chain alpha-ketoacid dehydrogenase (BCDH) complex is the primary means by which these processes are coordinated. BCDH kinase regulates BCDH by phosphorylation, thereby inactivating it when synthesis is required. Pyruvate dehydrogenase kinase inhibits the pyruvate dehydrogenase complex by phosphorylation of the E1 alpha subunit, thus contributing to the regulation of glucose metabolism. It is also involved in telomere maintenance. This entry is associated with IPR003594 from INTERPRO which is found towards the C terminus. ; PDB: 1GKX_A 1GJV_A 1GKZ_A 1JM6_B 3CRL_B 3CRK_B 1Y8O_A 2PNR_A 1Y8P_A 1Y8N_A ....
Probab=35.40 E-value=58 Score=23.88 Aligned_cols=40 Identities=15% Similarity=0.177 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhhh--CCCCCCCCCCcChhHHHHHHHHHHhhc
Q psy3409 97 FTSVYELFIKYSL--NPFYKINTPINSTYFDSKVNFLGRKFL 136 (139)
Q Consensus 97 f~~i~~~Yv~~v~--NPf~~~~~~I~s~~F~~~v~~~~~~~~ 136 (139)
.++||+.|.+... -.|-.+.+.=++..|.+.++++.+++-
T Consensus 55 i~~V~~~Y~~sF~~L~~~~~~~~~~~~~~F~~~l~~i~~~H~ 96 (164)
T PF10436_consen 55 IQQVYEWYLQSFEELRSFPPPKTLEDNEKFTELLERILDRHS 96 (164)
T ss_dssp HHHHHHHHHHHHHHHHTTSTTTSCCHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhc
Confidence 6677777777766 455445555568899999999988763
No 18
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=34.10 E-value=2.1e+02 Score=21.79 Aligned_cols=68 Identities=18% Similarity=0.336 Sum_probs=40.5
Q ss_pred eeeCCeeEEEEEcCCCcEEEEEeccCC-----hHHHHHHHHHHHHHHHHhhhCCCCCCCCCCcChhHHHHHHHHHHhhcc
Q psy3409 63 DKFNDMMVSAFVTPTGVKFLMVHDSKN-----EEGIKKFFTSVYELFIKYSLNPFYKINTPINSTYFDSKVNFLGRKFLT 137 (139)
Q Consensus 63 ~~~~~~~v~~y~T~t~~Kfvl~~~~~~-----~~~i~~~f~~i~~~Yv~~v~NPf~~~~~~I~s~~F~~~v~~~~~~~~~ 137 (139)
+++.+=++--|..-.++-|+|+++++. +.-++.+.+.+.+.+ +.+..| ... -.=-.+|+.++..||+
T Consensus 98 d~f~~~k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~-~~l~~~----~e~---l~k~d~i~aiL~~fLP 169 (189)
T PF15001_consen 98 DPFSTPKIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHL-KILSQP----SEV---LLKSDRILAILHRFLP 169 (189)
T ss_pred CCCCCCcEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHH-HHhCcH----HHh---hhhHHHHHHHHHHhCC
Confidence 334445566778889999999999832 334455556665555 222121 111 1123467888888888
Q ss_pred -C
Q psy3409 138 -G 138 (139)
Q Consensus 138 -~ 138 (139)
|
T Consensus 170 ~G 171 (189)
T PF15001_consen 170 HG 171 (189)
T ss_pred CC
Confidence 6
No 19
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.70 E-value=87 Score=20.73 Aligned_cols=51 Identities=27% Similarity=0.415 Sum_probs=32.7
Q ss_pred ChHHHHHHHHHHHHHHHH-----------hhh--CCCCCCCC-----CCcChhHHHHHHHHHHhhccCC
Q psy3409 89 NEEGIKKFFTSVYELFIK-----------YSL--NPFYKINT-----PINSTYFDSKVNFLGRKFLTGN 139 (139)
Q Consensus 89 ~~~~i~~~f~~i~~~Yv~-----------~v~--NPf~~~~~-----~I~s~~F~~~v~~~~~~~~~~~ 139 (139)
..++++..+.++|..-=+ |+. .|=|-|.. .|+---=|.-|+++++.||.||
T Consensus 16 ~~~~v~e~L~~VY~sL~ekGYNpiNQiVGYllSGDPaYIpr~ndARn~IRk~eRDeIvEElvk~YLk~~ 84 (88)
T COG4472 16 DKKDVKETLNDVYNSLEEKGYNPINQIVGYLLSGDPAYIPRYNDARNQIRKLERDEIVEELVKYYLKGN 84 (88)
T ss_pred hHHHHHHHHHHHHHHHHHcCCChHHHHHhhhccCCccccCccccHHHHHHHHhHHHHHHHHHHHHHhhc
Confidence 678999999999976433 333 44444321 2433334567889999998853
No 20
>PHA01632 hypothetical protein
Probab=33.60 E-value=1e+02 Score=18.98 Aligned_cols=33 Identities=15% Similarity=0.331 Sum_probs=26.3
Q ss_pred CcEEEEEecc----CChHHHHHHHHHHHHHHHHhhhC
Q psy3409 78 GVKFLMVHDS----KNEEGIKKFFTSVYELFIKYSLN 110 (139)
Q Consensus 78 ~~Kfvl~~~~----~~~~~i~~~f~~i~~~Yv~~v~N 110 (139)
.+|+-++.++ ..++++|..+-+|-.-|.+.+-|
T Consensus 14 hikiyilieqvp~kpteeelrkvlpkilkdyanmie~ 50 (64)
T PHA01632 14 HIKIYILIEQVPQKPTEEELRKVLPKILKDYANMIEN 50 (64)
T ss_pred EEEEEEehhhcCCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 4677677664 36899999999999999998754
No 21
>PHA00743 helix-turn-helix protein
Probab=33.02 E-value=58 Score=19.50 Aligned_cols=33 Identities=18% Similarity=0.394 Sum_probs=24.2
Q ss_pred hHHHHHHHHHHHHHHHHhhhCCCCCCCCCCcChhH
Q psy3409 90 EEGIKKFFTSVYELFIKYSLNPFYKINTPINSTYF 124 (139)
Q Consensus 90 ~~~i~~~f~~i~~~Yv~~v~NPf~~~~~~I~s~~F 124 (139)
++++|.++.-||++=++.+.+- + +.+.++-..|
T Consensus 5 D~~iReLLs~iheIKID~i~~~-~-~k~kvekAl~ 37 (51)
T PHA00743 5 DEDVRELLSIIHEIKIDIITQS-Y-DKEKIEKAIF 37 (51)
T ss_pred HHHHHHHHHHHHHHhhhhhccc-C-CHHHHHHHHH
Confidence 6799999999999999999944 3 3344444444
No 22
>COG4918 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.65 E-value=29 Score=24.02 Aligned_cols=17 Identities=12% Similarity=0.456 Sum_probs=14.9
Q ss_pred EEEcCCCCeeEEEecCC
Q psy3409 8 VMVGREDNPLYQRGFSC 24 (139)
Q Consensus 8 ~Ii~~~~~ply~~~~~~ 24 (139)
.+|+.+..|||+++|++
T Consensus 55 ~~idsn~gPiyik~~~~ 71 (114)
T COG4918 55 ASIDSNFGPIYIKDYGS 71 (114)
T ss_pred cccccCCCcEEEEecce
Confidence 47899999999999983
No 23
>PF15205 PLAC9: Placenta-specific protein 9
Probab=30.80 E-value=37 Score=21.70 Aligned_cols=21 Identities=29% Similarity=0.411 Sum_probs=17.3
Q ss_pred HHHHHHHHHhHHHHHHhhccc
Q psy3409 34 YYYEFIAHASLDLLDEQVWQT 54 (139)
Q Consensus 34 ~~~~f~~~~SLD~i~~~~~~~ 54 (139)
-..++.+|.-||+||+++-++
T Consensus 17 Cdrhmav~~RLdviEe~veKT 37 (74)
T PF15205_consen 17 CDRHMAVHSRLDVIEETVEKT 37 (74)
T ss_pred hHHHHHHHHHHHHHHHHHHHH
Confidence 335789999999999999754
No 24
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=30.54 E-value=2.3e+02 Score=21.08 Aligned_cols=49 Identities=16% Similarity=0.392 Sum_probs=35.0
Q ss_pred ccCCceeeeeeCCeeEEEEEcCCCcEEEEEeccCChHHHHHHHHHHHHHHH
Q psy3409 55 DHMYLKTIDKFNDMMVSAFVTPTGVKFLMVHDSKNEEGIKKFFTSVYELFI 105 (139)
Q Consensus 55 ~~~yL~~l~~~~~~~v~~y~T~t~~Kfvl~~~~~~~~~i~~~f~~i~~~Yv 105 (139)
++.|=|.+++..+-++-.-+=+|| | |+++..++.++++.-++.|+..-.
T Consensus 124 PE~fPgliyr~~~pk~~~liF~sG-k-vvitGaks~~~~~~a~~~i~p~L~ 172 (174)
T cd04516 124 PELFPGLIYRMVKPKIVLLIFVSG-K-IVLTGAKSREEIYQAFENIYPILL 172 (174)
T ss_pred CccCceEEEEecCCcEEEEEeCCC-E-EEEEecCCHHHHHHHHHHHHHHHh
Confidence 356777888888877777777777 3 344444477899999999986543
No 25
>KOG2583|consensus
Probab=29.20 E-value=1.2e+02 Score=26.10 Aligned_cols=44 Identities=11% Similarity=0.036 Sum_probs=30.0
Q ss_pred HHHHHHHHHH-HHHHHhhhCCCCCCCCCCcChhHHHHHHHHHHhhc
Q psy3409 92 GIKKFFTSVY-ELFIKYSLNPFYKINTPINSTYFDSKVNFLGRKFL 136 (139)
Q Consensus 92 ~i~~~f~~i~-~~Yv~~v~NPf~~~~~~I~s~~F~~~v~~~~~~~~ 136 (139)
..+..+++|| -+|-+-+-||.|.|+-.|.+..-.+ +...+++++
T Consensus 153 ~~~~a~e~lH~aAfRngLgnslY~p~~~vg~vss~e-L~~Fa~k~f 197 (429)
T KOG2583|consen 153 PYTIAIEQLHAAAFRNGLGNSLYSPGYQVGSVSSSE-LKDFAAKHF 197 (429)
T ss_pred hHHHHHHHHHHHHHhcccCCcccCCcccccCccHHH-HHHHHHHHh
Confidence 4567799999 6688877799999987766554333 333444443
No 26
>PF14026 DUF4242: Protein of unknown function (DUF4242)
Probab=29.14 E-value=1.6e+02 Score=18.79 Aligned_cols=30 Identities=13% Similarity=0.348 Sum_probs=24.4
Q ss_pred EEEEEcCCCcEEEEEeccCChHHHHHHHHH
Q psy3409 70 VSAFVTPTGVKFLMVHDSKNEEGIKKFFTS 99 (139)
Q Consensus 70 v~~y~T~t~~Kfvl~~~~~~~~~i~~~f~~ 99 (139)
+..|+++.+-|...+.+..+++.|+...++
T Consensus 37 ~~s~v~~d~~k~~Cly~Ap~~eaV~~~~~~ 66 (77)
T PF14026_consen 37 LRSYVSEDDGKIFCLYEAPDEEAVREHARR 66 (77)
T ss_pred EEEEEecCCCeEEEEEECCCHHHHHHHHHH
Confidence 467888888899999988788888887665
No 27
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=28.58 E-value=59 Score=24.33 Aligned_cols=24 Identities=25% Similarity=0.743 Sum_probs=20.9
Q ss_pred HHHHHHHHHHH-HHHHHhhh---CCCCC
Q psy3409 91 EGIKKFFTSVY-ELFIKYSL---NPFYK 114 (139)
Q Consensus 91 ~~i~~~f~~i~-~~Yv~~v~---NPf~~ 114 (139)
-.++..++..| ++|.+|++ ||.|.
T Consensus 101 VRLKRWM~aMHVDAFFeYllg~~~~Y~t 128 (175)
T PF09441_consen 101 VRLKRWMRAMHVDAFFEYLLGKPHPYYT 128 (175)
T ss_pred HHHHHHHHHhhHHHHHHHHhCCCCcccc
Confidence 45788999999 99999999 77776
No 28
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=28.48 E-value=2.5e+02 Score=20.83 Aligned_cols=48 Identities=10% Similarity=0.233 Sum_probs=36.3
Q ss_pred ccCCceeeeeeCCeeEEEEEcCCCcEEEEEeccCChHHHHHHHHHHHHHH
Q psy3409 55 DHMYLKTIDKFNDMMVSAFVTPTGVKFLMVHDSKNEEGIKKFFTSVYELF 104 (139)
Q Consensus 55 ~~~yL~~l~~~~~~~v~~y~T~t~~Kfvl~~~~~~~~~i~~~f~~i~~~Y 104 (139)
++.|=|.+++..+-++.+.+=+||- |.++..++.++++..++.++..-
T Consensus 125 PE~fPgliyr~~~p~~t~lIF~sGk--ivitGaks~~~~~~a~~~i~pil 172 (174)
T cd04517 125 PELHPGVVYRITGPRATLSIFSTGS--VTVTGARSMEDVREAVEKIYPIV 172 (174)
T ss_pred CccCCEEEEEECCCcEEEEEeCCCE--EEEEecCCHHHHHHHHHHHHHHH
Confidence 4567788888888888888888884 44455447789999999988653
No 29
>cd04920 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.68 E-value=1.5e+02 Score=17.69 Aligned_cols=29 Identities=10% Similarity=0.154 Sum_probs=20.7
Q ss_pred EcCCCcEEEEEeccCChHHHHHHHHHHHHHHH
Q psy3409 74 VTPTGVKFLMVHDSKNEEGIKKFFTSVYELFI 105 (139)
Q Consensus 74 ~T~t~~Kfvl~~~~~~~~~i~~~f~~i~~~Yv 105 (139)
.+.+..++=++.+. ++.+...+.+|+.++
T Consensus 34 ~~~s~~~is~vv~~---~d~~~av~~LH~~f~ 62 (63)
T cd04920 34 QAANDLNLTFVVDE---DQADGLCARLHFQLI 62 (63)
T ss_pred EeCCCCeEEEEEeH---HHHHHHHHHHHHHHh
Confidence 34567777555554 588899999998765
No 30
>COG4092 Predicted glycosyltransferase involved in capsule biosynthesis [Cell envelope biogenesis, outer membrane]
Probab=26.56 E-value=27 Score=28.46 Aligned_cols=27 Identities=15% Similarity=0.436 Sum_probs=23.8
Q ss_pred ChHHHHHHHHHHHH-HHHHhhh-CCCCCC
Q psy3409 89 NEEGIKKFFTSVYE-LFIKYSL-NPFYKI 115 (139)
Q Consensus 89 ~~~~i~~~f~~i~~-~Yv~~v~-NPf~~~ 115 (139)
.+..|+++.+..|. +|++.-. |||+++
T Consensus 50 ~d~~i~~~i~~~~~~~yl~~~s~~~F~s~ 78 (346)
T COG4092 50 MDRLIRSYIDPMPRVLYLDFGSPEPFASE 78 (346)
T ss_pred HHHHHHHHhccccceEEEecCCCccccch
Confidence 46789999999997 8999999 999995
No 31
>PRK14449 acylphosphatase; Provisional
Probab=26.36 E-value=1.4e+02 Score=19.51 Aligned_cols=35 Identities=14% Similarity=0.244 Sum_probs=23.0
Q ss_pred CeeEEEEEcCCCc-EEEEEeccCChHHHHHHHHHHHH
Q psy3409 67 DMMVSAFVTPTGV-KFLMVHDSKNEEGIKKFFTSVYE 102 (139)
Q Consensus 67 ~~~v~~y~T~t~~-Kfvl~~~~~~~~~i~~~f~~i~~ 102 (139)
.+.+.||+.+..= ..-+..+. +++.+.+|++.+.+
T Consensus 28 ~lgl~G~V~N~~dG~Vei~~~G-~~~~v~~f~~~l~~ 63 (90)
T PRK14449 28 SLGITGYAENLYDGSVEVVAEG-DEENIKELINFIKT 63 (90)
T ss_pred HcCCEEEEEECCCCeEEEEEEe-CHHHHHHHHHHHhh
Confidence 4567888775442 34444444 66789999988874
No 32
>COG1507 Uncharacterized conserved protein [Function unknown]
Probab=25.41 E-value=2.1e+02 Score=21.21 Aligned_cols=19 Identities=21% Similarity=0.551 Sum_probs=16.4
Q ss_pred ChHHHHHHHHHHHHHHHHh
Q psy3409 89 NEEGIKKFFTSVYELFIKY 107 (139)
Q Consensus 89 ~~~~i~~~f~~i~~~Yv~~ 107 (139)
.++.+++++++.|+-|++-
T Consensus 81 ~d~eL~~~~~raHe~~lkk 99 (167)
T COG1507 81 QDEELRAFYRRAHESYLKK 99 (167)
T ss_pred ccHHHHHHHHHHHHHHHHH
Confidence 4789999999999999864
No 33
>KOG1299|consensus
Probab=24.69 E-value=62 Score=28.36 Aligned_cols=24 Identities=21% Similarity=0.386 Sum_probs=19.5
Q ss_pred hHHHHHHHHHHHHHHHHhhh-CCCC
Q psy3409 90 EEGIKKFFTSVYELFIKYSL-NPFY 113 (139)
Q Consensus 90 ~~~i~~~f~~i~~~Yv~~v~-NPf~ 113 (139)
+.|-...-++|+|.|.++++ ||+.
T Consensus 112 esD~~E~V~eVqE~y~Df~~~n~~L 136 (549)
T KOG1299|consen 112 ESDEQEVVREVQEIYLDFFKVNPDL 136 (549)
T ss_pred hcchHHHHHHHHHHHHhhhccCCce
Confidence 34556678899999999999 9974
No 34
>PF13198 DUF4014: Protein of unknown function (DUF4014)
Probab=24.68 E-value=50 Score=21.24 Aligned_cols=25 Identities=28% Similarity=0.656 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHhhhCCCCCCCCCCc
Q psy3409 96 FFTSVYELFIKYSLNPFYKINTPIN 120 (139)
Q Consensus 96 ~f~~i~~~Yv~~v~NPf~~~~~~I~ 120 (139)
.++.+.+.|.+.+.|||-..+..|.
T Consensus 43 ~~E~l~e~Y~~~~w~~F~~Lhnkin 67 (72)
T PF13198_consen 43 IIEPLFELYKDWFWNPFNALHNKIN 67 (72)
T ss_pred HHHHHHHHHHHHHHHhHHHHhcccc
Confidence 5788889999999999987666653
No 35
>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=24.49 E-value=98 Score=23.40 Aligned_cols=18 Identities=17% Similarity=0.183 Sum_probs=15.5
Q ss_pred CCCcChhHHHHHHHHHHh
Q psy3409 117 TPINSTYFDSKVNFLGRK 134 (139)
Q Consensus 117 ~~I~s~~F~~~v~~~~~~ 134 (139)
+..+|+.|.+.|+++++.
T Consensus 112 MElks~~f~~~ve~vl~~ 129 (179)
T COG1618 112 MELKSKKFREAVEEVLKS 129 (179)
T ss_pred hhhccHHHHHHHHHHhcC
Confidence 578999999999998853
No 36
>cd04915 ACT_AK-Ectoine_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinas
Probab=23.88 E-value=1.7e+02 Score=17.63 Aligned_cols=28 Identities=11% Similarity=0.192 Sum_probs=19.5
Q ss_pred cCCCcEEEEEeccCChHHHHHHHHHHHHHHH
Q psy3409 75 TPTGVKFLMVHDSKNEEGIKKFFTSVYELFI 105 (139)
Q Consensus 75 T~t~~Kfvl~~~~~~~~~i~~~f~~i~~~Yv 105 (139)
++++..+-++.+. ++.+...+.+|+.+.
T Consensus 38 ~~s~~~is~~V~~---~~~~~av~~Lh~~f~ 65 (66)
T cd04915 38 SMRNVDVQFVVDR---DDYDNAIKALHAALV 65 (66)
T ss_pred cCCeeEEEEEEEH---HHHHHHHHHHHHHHh
Confidence 4556777555554 578888999997664
No 37
>PF03288 Pox_D5: Poxvirus D5 protein-like; InterPro: IPR004968 This domain is found at the C terminus of phage P4 alpha protein and related proteins. Phage P4 DNA replication depends on the product of the alpha gene, which has origin recognition ability, DNA helicase activity, and DNA primase activity. The structure of the protein can be summarised as follows: The N terminus provides the primase activity, the central region is the helicase/nucleoside triphosphatase domain and the ori DNA recognition resides in the C-terminal 1/3 of the protein []. The domain is also found at the C terminus of a number of proteins from orthopox viruses including vaccinia virus D5. D5 encodes a 90kDa protein that is transiently expressed at early times after infection. It has an nucleoside triphosphatase activity which is independent of common nucleic acid cofactors and it can hydrolyse all the common ribo- and deoxyribonucleoside triphosphates to diphosphates in the presence of a divalent cation [].; PDB: 1KA8_E.
Probab=22.88 E-value=1.3e+02 Score=18.96 Aligned_cols=34 Identities=12% Similarity=0.340 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhh-CCCCCCCCCCcChhHHHHHHHHHHh
Q psy3409 98 TSVYELFIKYSL-NPFYKINTPINSTYFDSKVNFLGRK 134 (139)
Q Consensus 98 ~~i~~~Yv~~v~-NPf~~~~~~I~s~~F~~~v~~~~~~ 134 (139)
..+|++|..+.- |=... ++....|.+++++.+..
T Consensus 25 ~~lY~~Y~~wc~~ng~~~---~ls~~~F~~~L~~~~~~ 59 (86)
T PF03288_consen 25 KDLYDAYKEWCEENGYKP---PLSKRKFGKELKQYFPE 59 (86)
T ss_dssp TBHHHHHHHHHHHTT-S-------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCc---ccCHHHHHHHHHHHhhh
Confidence 578888888877 65422 58999999999998865
No 38
>PF05729 NACHT: NACHT domain
Probab=22.31 E-value=1.3e+02 Score=20.46 Aligned_cols=48 Identities=19% Similarity=0.450 Sum_probs=28.0
Q ss_pred CCCcEEEEEeccCChHHHHHHHHHHHHHHHHhhhCCCCCCCCCCcChhHHHHHHHHHHhhccC
Q psy3409 76 PTGVKFLMVHDSKNEEGIKKFFTSVYELFIKYSLNPFYKINTPINSTYFDSKVNFLGRKFLTG 138 (139)
Q Consensus 76 ~t~~Kfvl~~~~~~~~~i~~~f~~i~~~Yv~~v~NPf~~~~~~I~s~~F~~~v~~~~~~~~~~ 138 (139)
+.++|+++.+.+....+++..+..- ..+-++||- +..+++++++|+.+
T Consensus 118 ~~~~~liit~r~~~~~~~~~~~~~~----~~~~l~~~~-----------~~~~~~~~~~~f~~ 165 (166)
T PF05729_consen 118 PPGVKLIITSRPRAFPDLRRRLKQA----QILELEPFS-----------EEDIKQYLRKYFSN 165 (166)
T ss_pred CCCCeEEEEEcCChHHHHHHhcCCC----cEEEECCCC-----------HHHHHHHHHHHhhc
Confidence 5789988888774433333333322 122226662 46777888888753
No 39
>COG3016 PhuW Uncharacterized iron-regulated protein [Function unknown]
Probab=21.22 E-value=3e+02 Score=22.31 Aligned_cols=68 Identities=25% Similarity=0.448 Sum_probs=40.0
Q ss_pred CCceeeeeeCCeeEEEEEcCCCcEE--------------EEEeccCChHHHHH----HHHHHHHHHHHhhh--CCCCCCC
Q psy3409 57 MYLKTIDKFNDMMVSAFVTPTGVKF--------------LMVHDSKNEEGIKK----FFTSVYELFIKYSL--NPFYKIN 116 (139)
Q Consensus 57 ~yL~~l~~~~~~~v~~y~T~t~~Kf--------------vl~~~~~~~~~i~~----~f~~i~~~Yv~~v~--NPf~~~~ 116 (139)
+-+|+-+++.+ |-..|+||.++ |++-+.++.++++. +|+.++|.|...+. --|-++.
T Consensus 27 sl~g~~d~~~~---yil~t~tg~~iS~q~LiaeL~nadvIlvGEkHdn~~~h~~Ql~l~kal~e~~~q~iLamEmf~~~~ 103 (295)
T COG3016 27 SLLGCSDTFYD---YILATPTGEEISFQALIAELLNADVILVGEKHDNEEIHELQLKLFKALHERYRQVILAMEMFQQPY 103 (295)
T ss_pred CcccCCccccc---eeeecCcCceecHHHHHHHHhcCCEEEEecccCchhHHHHHHHHHHHHHHhcccceehHHhhCccc
Confidence 45666665544 55689999986 33433344455544 48899988876654 4555555
Q ss_pred CCCcChhHHHH
Q psy3409 117 TPINSTYFDSK 127 (139)
Q Consensus 117 ~~I~s~~F~~~ 127 (139)
+|.-.+.|..+
T Consensus 104 Qp~lD~~~~gk 114 (295)
T COG3016 104 QPFLDEFVEGK 114 (295)
T ss_pred chhHHHHHhcc
Confidence 55443444333
No 40
>PF01541 GIY-YIG: GIY-YIG catalytic domain; InterPro: IPR000305 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. It is found in the amino terminal region of excinuclease abc subunit c (uvrC), Bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage.; GO: 0004518 nuclease activity, 0006281 DNA repair, 0005622 intracellular; PDB: 1YWL_A 1YD6_D 1YD5_A 1YD1_A 1YCZ_A 1YD0_A 1YD3_A 1YD4_A 1YD2_A 1LN0_A ....
Probab=21.00 E-value=90 Score=18.88 Aligned_cols=21 Identities=10% Similarity=0.249 Sum_probs=14.2
Q ss_pred CCceEEEEEEcCCCCeeEEEecC
Q psy3409 1 MANRYYFVMVGREDNPLYQRGFS 23 (139)
Q Consensus 1 m~~~~~~~Ii~~~~~ply~~~~~ 23 (139)
|.++|++ .+.++..+|+-.-.
T Consensus 1 k~gIY~i--~~~~~~~~YIG~t~ 21 (80)
T PF01541_consen 1 KYGIYII--YNKDNKKIYIGSTK 21 (80)
T ss_dssp -EEEEEE--EETTTEEEEEEEES
T ss_pred CcEEEEE--EECCCCEEEEEEEC
Confidence 3455544 47899999998664
No 41
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=20.79 E-value=2.2e+02 Score=18.97 Aligned_cols=46 Identities=26% Similarity=0.481 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHH-HHHHHhhhCCCCCCCCCCcChhHHHHHHHHHHhhccC
Q psy3409 90 EEGIKKFFTSVY-ELFIKYSLNPFYKINTPINSTYFDSKVNFLGRKFLTG 138 (139)
Q Consensus 90 ~~~i~~~f~~i~-~~Yv~~v~NPf~~~~~~I~s~~F~~~v~~~~~~~~~~ 138 (139)
++.|+.+....| .++.+-...||+. .++-+....++.+....+++|
T Consensus 9 ~~~I~~lv~~fY~rv~~d~~l~~~F~---~~d~~~~~~~~~~fl~~~~GG 55 (120)
T PF01152_consen 9 EEGIRALVDAFYDRVLADPRLKPFFE---GIDLEKHKEKQAEFLSQLLGG 55 (120)
T ss_dssp HHHHHHHHHHHHHHHHT-TTTGGGGT---TSCHHHHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHHHHHHcCHHHHhhcC---CCCHHHHHHHHHHHHHHHhCC
Confidence 457888887777 5555555544444 445566667777777777665
No 42
>PF10100 DUF2338: Uncharacterized protein conserved in bacteria (DUF2338); InterPro: IPR016935 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.39 E-value=1.3e+02 Score=25.81 Aligned_cols=29 Identities=24% Similarity=0.668 Sum_probs=21.7
Q ss_pred ChHHHHHH-----HHHHHHHHHHhhh---CCCCCCCC
Q psy3409 89 NEEGIKKF-----FTSVYELFIKYSL---NPFYKINT 117 (139)
Q Consensus 89 ~~~~i~~~-----f~~i~~~Yv~~v~---NPf~~~~~ 117 (139)
+.++|.+| .++-|-+||+|-+ .||.+|+.
T Consensus 293 sr~~Ie~F~~l~~i~QEYLLYVRYtsiLIDPFS~PD~ 329 (429)
T PF10100_consen 293 SRDDIESFEELPAIHQEYLLYVRYTSILIDPFSEPDE 329 (429)
T ss_pred CHHHHhhhhcCChHHhhHHHHHHhhhheeCCCCCCCC
Confidence 45678887 4566677888765 99999975
No 43
>PF09843 DUF2070: Predicted membrane protein (DUF2070); InterPro: IPR019204 This domain of unknown function is found in various bacterial and archael hypothetical proteins, as well as in prokaryotic polyketide synthase.
Probab=20.06 E-value=3.7e+02 Score=19.79 Aligned_cols=72 Identities=18% Similarity=0.105 Sum_probs=43.4
Q ss_pred eCCeeEEEE--EcCCCcEEEEEeccCC-h----HHHHHHHHHH---------HHHHHHhhh--CCCCCCCCCCcChhHHH
Q psy3409 65 FNDMMVSAF--VTPTGVKFLMVHDSKN-E----EGIKKFFTSV---------YELFIKYSL--NPFYKINTPINSTYFDS 126 (139)
Q Consensus 65 ~~~~~v~~y--~T~t~~Kfvl~~~~~~-~----~~i~~~f~~i---------~~~Yv~~v~--NPf~~~~~~I~s~~F~~ 126 (139)
...-.+.++ ++..+-.++++.|.-| + +.|++.+.++ -..++..++ |+-++.+..+..+.+++
T Consensus 58 lg~~gi~~~~v~~~g~~~~lv~~DsNNm~~~lr~~i~~~~~~~~d~~ev~TTDtH~~~~~~~g~~y~~vG~~~~~~~i~~ 137 (179)
T PF09843_consen 58 LGIGGISALVVEVGGQRSALVLADSNNMEPGLREKIREALGDVVDEVEVMTTDTHFVNGESGGNGYWPVGPLIPPREIIE 137 (179)
T ss_pred cCccccEEEEEEeCCcEEEEEEEECCCCCHHHHHHHHHHHhhhcceeEEecCcccEEccEECCccceeccccCCHHHHHH
Confidence 333444444 4445555555566522 2 3445555555 445667776 75555677778889998
Q ss_pred HHHHHHHhhc
Q psy3409 127 KVNFLGRKFL 136 (139)
Q Consensus 127 ~v~~~~~~~~ 136 (139)
.+++.++...
T Consensus 138 ~~~~~~~~A~ 147 (179)
T PF09843_consen 138 SRREAVSEAE 147 (179)
T ss_pred HHHHHHHHHH
Confidence 8888887653
Done!