Query 040695
Match_columns 169
No_of_seqs 90 out of 92
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 10:51:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040695.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040695hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02245 HAD_IIID1 HAD-superf 99.7 1.3E-17 2.7E-22 137.9 5.9 95 5-109 96-190 (195)
2 PF03031 NIF: NLI interacting 99.1 3.8E-11 8.3E-16 92.2 0.9 64 24-104 96-159 (159)
3 KOG1605 TFIIF-interacting CTD 98.9 6.1E-10 1.3E-14 96.4 4.2 79 19-109 180-258 (262)
4 TIGR02251 HIF-SF_euk Dullard-l 98.9 1.5E-09 3.2E-14 85.8 3.3 74 2-102 89-162 (162)
5 smart00577 CPDc catalytic doma 97.4 0.00019 4.2E-09 55.4 3.7 47 18-78 99-145 (148)
6 TIGR02250 FCP1_euk FCP1-like p 96.2 0.0032 6.9E-08 50.1 2.4 41 23-76 115-155 (156)
7 COG5190 FCP1 TFIIF-interacting 91.6 0.12 2.5E-06 47.7 2.2 66 23-106 310-377 (390)
8 KOG2832 TFIIF-interacting CTD 86.1 1.2 2.6E-05 41.4 4.6 68 24-109 273-342 (393)
9 cd03210 GST_C_Pi GST_C family, 42.5 32 0.00069 25.3 3.1 35 85-119 88-122 (126)
10 cd03209 GST_C_Mu GST_C family, 39.3 33 0.00072 24.8 2.8 31 85-115 85-115 (121)
11 PF08325 WLM: WLM domain; Int 25.1 64 0.0014 26.7 2.5 33 89-123 17-49 (186)
12 COG0774 LpxC UDP-3-O-acyl-N-ac 24.8 51 0.0011 29.9 2.0 47 21-77 192-238 (300)
13 PF03991 Prion_octapep: Copper 22.0 41 0.00089 15.2 0.4 6 156-161 1-6 (8)
14 KOG3441 Mitochondrial ribosoma 20.6 59 0.0013 26.5 1.4 24 44-72 101-124 (149)
15 PF10929 DUF2811: Protein of u 20.5 44 0.00096 23.4 0.6 20 120-139 20-39 (57)
No 1
>TIGR02245 HAD_IIID1 HAD-superfamily subfamily IIID hydrolase, TIGR02245. This family of sequences appears to belong to the Haloacid Dehalogenase (HAD) superfamily of enzymes by virtue of the presence of three catalytic domains, in this case: LLVLD(ILV)D(YH)T, I(VMG)IWS, and (DN)(VC)K(PA)Lx{15-17}T(IL)(MH)(FV)DD(IL)(GRS)(RK)N. Since this family has no large "cap" domain between motifs 1 and 2 or between 2 and 3, it is formally a "class III" HAD.
Probab=99.70 E-value=1.3e-17 Score=137.86 Aligned_cols=95 Identities=21% Similarity=0.334 Sum_probs=72.8
Q ss_pred CCccccCcccccCCCCceEeeehHHhhcccCCCCCcCCCCCCCCceEEecCCchhhccCCCCcccccCCCCCCCCCCCcC
Q 040695 5 SQCSETGLHSLENKRKPLVLKELKKLWEKIDPNLPWKKGEYNETNTLLLDDSPYKALCNPAHTAIFPYPYDYRNAEDSSL 84 (169)
Q Consensus 5 ~~CT~~g~~t~e~~~Kp~~~K~L~kVW~~~~~~~pw~~g~~~~sNTLLIDDSPyKA~~NP~~naI~P~ef~~~~~~D~~L 84 (169)
++|...++.+ .+.++.++|+|+.||++.. +.|+++|||||||+|+|+++|| .|+|.+++|.++..++...
T Consensus 96 d~~~~~~~~~--~~~g~~~vKdL~~lw~~l~-------~~~~~~ntiiVDd~p~~~~~~P-~N~i~I~~f~~~~~~~~~D 165 (195)
T TIGR02245 96 DSTAMITVHT--PRRGKFDVKPLGVIWALLP-------EFYSMKNTIMFDDLRRNFLMNP-QNGLKIRPFKKAHANRGTD 165 (195)
T ss_pred ccccceeeEe--eccCcEEEeecHHhhhhcc-------cCCCcccEEEEeCCHHHHhcCC-CCccccCCccccCCCCccc
Confidence 3454333333 2345678999999998543 3589999999999999999999 8899999999864222222
Q ss_pred CCcchHHHHHHHhhcCcChHHHHhh
Q 040695 85 GHGGNLRVYLEGLADAENVQEYVRQ 109 (169)
Q Consensus 85 ~~~g~Lr~YLe~La~a~dV~~yVr~ 109 (169)
.++.+|..||++||.++||+.+...
T Consensus 166 ~eL~~L~~yL~~la~~~Dvr~~~~~ 190 (195)
T TIGR02245 166 QELLKLTQYLKTIAELEDFSSLDHK 190 (195)
T ss_pred HHHHHHHHHHHHHhcCcccchhhhc
Confidence 2336999999999999999998764
No 2
>PF03031 NIF: NLI interacting factor-like phosphatase; InterPro: IPR004274 The function of this domain is unclear. It is found in proteins of diverse function including phosphatases some of which may be active in active in ternary elongation complexes and a number of NLI interacting factors. In the phospatases this domain is often present N-terminal to the BRCT domain (IPR001357 from INTERPRO).; GO: 0005515 protein binding; PDB: 3L0Y_A 2GHQ_A 3PGL_A 3L0C_B 1TA0_A 2GHT_A 3L0B_B 1T9Z_A 3QLE_A 2Q5E_E ....
Probab=99.06 E-value=3.8e-11 Score=92.17 Aligned_cols=64 Identities=33% Similarity=0.444 Sum_probs=45.9
Q ss_pred eeehHHhhcccCCCCCcCCCCCCCCceEEecCCchhhccCCCCcccccCCCCCCCCCCCcCCCcchHHHHHHHhhcCcCh
Q 040695 24 LKELKKLWEKIDPNLPWKKGEYNETNTLLLDDSPYKALCNPAHTAIFPYPYDYRNAEDSSLGHGGNLRVYLEGLADAENV 103 (169)
Q Consensus 24 ~K~L~kVW~~~~~~~pw~~g~~~~sNTLLIDDSPyKA~~NP~~naI~P~ef~~~~~~D~~L~~~g~Lr~YLe~La~a~dV 103 (169)
.|+|++| +.+.+|||||||+|.+...+| .|+|.+++|.++..+|..| ..|..||++|+.++||
T Consensus 96 ~KdL~~l-------------~~~~~~vvivDD~~~~~~~~~-~N~i~v~~f~~~~~~D~~L---~~l~~~L~~l~~~~Dv 158 (159)
T PF03031_consen 96 IKDLSKL-------------GRDLDNVVIVDDSPRKWALQP-DNGIPVPPFFGDTPNDREL---LRLLPFLEELAKEDDV 158 (159)
T ss_dssp E--GGGS-------------SS-GGGEEEEES-GGGGTTSG-GGEEE----SSCHTT--HH---HHHHHHHHHHHTHS-C
T ss_pred ccchHHH-------------hhccccEEEEeCCHHHeeccC-CceEEeccccCCCcchhHH---HHHHHHHHHhCcccCC
Confidence 5999999 248999999999999999997 9999999999984345444 3899999999999998
Q ss_pred H
Q 040695 104 Q 104 (169)
Q Consensus 104 ~ 104 (169)
+
T Consensus 159 r 159 (159)
T PF03031_consen 159 R 159 (159)
T ss_dssp H
T ss_pred C
Confidence 6
No 3
>KOG1605 consensus TFIIF-interacting CTD phosphatase, including NLI-interacting factor (involved in RNA polymerase II regulation) [Transcription]
Probab=98.95 E-value=6.1e-10 Score=96.35 Aligned_cols=79 Identities=20% Similarity=0.252 Sum_probs=63.0
Q ss_pred CCceEeeehHHhhcccCCCCCcCCCCCCCCceEEecCCchhhccCCCCcccccCCCCCCCCCCCcCCCcchHHHHHHHhh
Q 040695 19 RKPLVLKELKKLWEKIDPNLPWKKGEYNETNTLLLDDSPYKALCNPAHTAIFPYPYDYRNAEDSSLGHGGNLRVYLEGLA 98 (169)
Q Consensus 19 ~Kp~~~K~L~kVW~~~~~~~pw~~g~~~~sNTLLIDDSPyKA~~NP~~naI~P~ef~~~~~~D~~L~~~g~Lr~YLe~La 98 (169)
+..+++++..-||+.-.. |+ +++|||||||||...++|| .|||-+.+|..+..++++| .|..||++|+
T Consensus 180 R~~C~~~~g~yvKdls~~------~~-dL~~viIiDNsP~sy~~~p-~NgIpI~sw~~d~~D~eLL----~LlpfLe~L~ 247 (262)
T KOG1605|consen 180 RDSCTLKDGNYVKDLSVL------GR-DLSKVIIVDNSPQSYRLQP-ENGIPIKSWFDDPTDTELL----KLLPFLEALA 247 (262)
T ss_pred ccceEeECCcEEEEccee------cc-CcccEEEEcCChHHhccCc-cCCCcccccccCCChHHHH----HHHHHHHHhc
Confidence 334444555555443221 45 9999999999999999999 9999999999988777766 8999999999
Q ss_pred cCcChHHHHhh
Q 040695 99 DAENVQEYVRQ 109 (169)
Q Consensus 99 ~a~dV~~yVr~ 109 (169)
.++||+..++.
T Consensus 248 ~~~Dvr~~l~~ 258 (262)
T KOG1605|consen 248 FVDDVRPILAR 258 (262)
T ss_pred ccccHHHHHHH
Confidence 99999887764
No 4
>TIGR02251 HIF-SF_euk Dullard-like phosphatase domain. This domain is related to domains found in FCP1-like phosphatases (TIGR02250), and together both are detected by the Pfam model pfam03031.
Probab=98.86 E-value=1.5e-09 Score=85.80 Aligned_cols=74 Identities=26% Similarity=0.318 Sum_probs=60.0
Q ss_pred CCCCCccccCcccccCCCCceEeeehHHhhcccCCCCCcCCCCCCCCceEEecCCchhhccCCCCcccccCCCCCCCCCC
Q 040695 2 QDASQCSETGLHSLENKRKPLVLKELKKLWEKIDPNLPWKKGEYNETNTLLLDDSPYKALCNPAHTAIFPYPYDYRNAED 81 (169)
Q Consensus 2 W~q~~CT~~g~~t~e~~~Kp~~~K~L~kVW~~~~~~~pw~~g~~~~sNTLLIDDSPyKA~~NP~~naI~P~ef~~~~~~D 81 (169)
|.+++|+.. ++.++|+|+++| .+.+++|+|||+|++...+| .|+|.+..|.|+. +|
T Consensus 89 l~r~~~~~~---------~~~~~K~L~~l~-------------~~~~~vIiVDD~~~~~~~~~-~NgI~i~~f~~~~-~D 144 (162)
T TIGR02251 89 LYRESCVFT---------NGKYVKDLSLVG-------------KDLSKVIIIDNSPYSYSLQP-DNAIPIKSWFGDP-ND 144 (162)
T ss_pred EEccccEEe---------CCCEEeEchhcC-------------CChhhEEEEeCChhhhccCc-cCEeecCCCCCCC-CH
Confidence 456666642 333899999993 46789999999999999999 8899999999864 55
Q ss_pred CcCCCcchHHHHHHHhhcCcC
Q 040695 82 SSLGHGGNLRVYLEGLADAEN 102 (169)
Q Consensus 82 ~~L~~~g~Lr~YLe~La~a~d 102 (169)
+.| ..|..||+.|+..+|
T Consensus 145 ~~L---~~l~~~L~~l~~~~~ 162 (162)
T TIGR02251 145 TEL---LNLIPFLEGLRFEDD 162 (162)
T ss_pred HHH---HHHHHHHHHHhccCC
Confidence 555 489999999998865
No 5
>smart00577 CPDc catalytic domain of ctd-like phosphatases.
Probab=97.37 E-value=0.00019 Score=55.40 Aligned_cols=47 Identities=26% Similarity=0.214 Sum_probs=41.2
Q ss_pred CCCceEeeehHHhhcccCCCCCcCCCCCCCCceEEecCCchhhccCCCCcccccCCCCCCC
Q 040695 18 KRKPLVLKELKKLWEKIDPNLPWKKGEYNETNTLLLDDSPYKALCNPAHTAIFPYPYDYRN 78 (169)
Q Consensus 18 ~~Kp~~~K~L~kVW~~~~~~~pw~~g~~~~sNTLLIDDSPyKA~~NP~~naI~P~ef~~~~ 78 (169)
..||.++|.|++++ .+++++|+||||+.....+| .|+|...+|.++.
T Consensus 99 ~~KP~~~k~l~~l~-------------~~p~~~i~i~Ds~~~~~aa~-~ngI~i~~f~~~~ 145 (148)
T smart00577 99 FVKGKYVKDLSLLG-------------RDLSNVIIIDDSPDSWPFHP-ENLIPIKPWFGDP 145 (148)
T ss_pred ccCCeEeecHHHcC-------------CChhcEEEEECCHHHhhcCc-cCEEEecCcCCCC
Confidence 36788999999992 46789999999999999998 8999999999965
No 6
>TIGR02250 FCP1_euk FCP1-like phosphatase, phosphatase domain. This domain is related to domains found in the human NLI interacting factor-like phosphatases, and together both are detected by the Pfam model pfam03031.
Probab=96.20 E-value=0.0032 Score=50.06 Aligned_cols=41 Identities=24% Similarity=0.338 Sum_probs=34.5
Q ss_pred EeeehHHhhcccCCCCCcCCCCCCCCceEEecCCchhhccCCCCcccccCCCCC
Q 040695 23 VLKELKKLWEKIDPNLPWKKGEYNETNTLLLDDSPYKALCNPAHTAIFPYPYDY 76 (169)
Q Consensus 23 ~~K~L~kVW~~~~~~~pw~~g~~~~sNTLLIDDSPyKA~~NP~~naI~P~ef~~ 76 (169)
..|+|.+|+. .+.+++|+|||+|.--..+| .|+|.+.+|.+
T Consensus 115 ~~KdL~~i~~------------~d~~~vvivDd~~~~~~~~~-~N~i~i~~~~~ 155 (156)
T TIGR02250 115 HTKSLLRLFP------------ADESMVVIIDDREDVWPWHK-RNLIQIEPYNY 155 (156)
T ss_pred ccccHHHHcC------------CCcccEEEEeCCHHHhhcCc-cCEEEeCCccc
Confidence 5789988832 36788999999999999999 89999998864
No 7
>COG5190 FCP1 TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=91.63 E-value=0.12 Score=47.72 Aligned_cols=66 Identities=26% Similarity=0.380 Sum_probs=55.6
Q ss_pred EeeehHHhhcccCCCCCcCCCCCCCCceEEecCCchhhccCCCCcccccCCCCCCCCCCCcCCCcchHHHHHHHhhc--C
Q 040695 23 VLKELKKLWEKIDPNLPWKKGEYNETNTLLLDDSPYKALCNPAHTAIFPYPYDYRNAEDSSLGHGGNLRVYLEGLAD--A 100 (169)
Q Consensus 23 ~~K~L~kVW~~~~~~~pw~~g~~~~sNTLLIDDSPyKA~~NP~~naI~P~ef~~~~~~D~~L~~~g~Lr~YLe~La~--a 100 (169)
+.|+|.++ ..+.+-|+|||.+|+=-..+| .++|-.+++..+..+++.+ .|.-+|+.|++ .
T Consensus 310 ~ikDis~i-------------~r~l~~viiId~~p~SY~~~p-~~~i~i~~W~~d~~d~el~----~ll~~le~L~~~~~ 371 (390)
T COG5190 310 YIKDISKI-------------GRSLDKVIIIDNSPASYEFHP-ENAIPIEKWISDEHDDELL----NLLPFLEDLPDRDL 371 (390)
T ss_pred hhhhHHhh-------------ccCCCceEEeeCChhhhhhCc-cceeccCcccccccchhhh----hhcccccccccccc
Confidence 78889888 367889999999999999999 8899999999987677666 88889999998 4
Q ss_pred cChHHH
Q 040695 101 ENVQEY 106 (169)
Q Consensus 101 ~dV~~y 106 (169)
.||+..
T Consensus 372 ~d~~~~ 377 (390)
T COG5190 372 KDVSSI 377 (390)
T ss_pred hhhhhh
Confidence 577654
No 8
>KOG2832 consensus TFIIF-interacting CTD phosphatase, including NLI-interacting factor (involved in RNA polymerase II regulation) [Transcription]
Probab=86.09 E-value=1.2 Score=41.36 Aligned_cols=68 Identities=24% Similarity=0.359 Sum_probs=54.3
Q ss_pred eeehHHhhcccCCCCCcCCCCCCCCceEEecCCchhhccCCCCcccccCCCCCCCCCCCcCCCcchHHHHHHHhhcC--c
Q 040695 24 LKELKKLWEKIDPNLPWKKGEYNETNTLLLDDSPYKALCNPAHTAIFPYPYDYRNAEDSSLGHGGNLRVYLEGLADA--E 101 (169)
Q Consensus 24 ~K~L~kVW~~~~~~~pw~~g~~~~sNTLLIDDSPyKA~~NP~~naI~P~ef~~~~~~D~~L~~~g~Lr~YLe~La~a--~ 101 (169)
+|+|.+| .=+.+..|.||=.++=..++| .|.|-.+++.|+. +|..|- +|..+|+.||.+ +
T Consensus 273 vKdls~L-------------NRdl~kVivVd~d~~~~~l~P-~N~l~l~~W~Gn~-dDt~L~---dL~~FL~~ia~~~~e 334 (393)
T KOG2832|consen 273 VKDLSKL-------------NRDLQKVIVVDFDANSYKLQP-ENMLPLEPWSGND-DDTSLF---DLLAFLEYIAQQQVE 334 (393)
T ss_pred hhhhhhh-------------ccccceeEEEEccccccccCc-ccccccCcCCCCc-ccchhh---hHHHHHHHHHHccHH
Confidence 7899888 236788999999999999999 6688888899954 444443 999999999877 5
Q ss_pred ChHHHHhh
Q 040695 102 NVQEYVRQ 109 (169)
Q Consensus 102 dV~~yVr~ 109 (169)
||+..++.
T Consensus 335 DvR~vL~~ 342 (393)
T KOG2832|consen 335 DVRPVLQS 342 (393)
T ss_pred HHHHHHHH
Confidence 88876663
No 9
>cd03210 GST_C_Pi GST_C family, Class Pi subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Class Pi GST is a homodimeric eukaryotic protein. The human GSTP1 is mainly found in erythrocytes, kidney, placenta and fetal liver. It is involved in stress responses and in cellular proliferation pathways as an inhibitor of JNK (c-Jun N-terminal kinase). Following oxidative stress, monomeric GSTP1 dissociates from JNK and dimerizes, losing its ability to bind JNK and causing an incre
Probab=42.46 E-value=32 Score=25.28 Aligned_cols=35 Identities=17% Similarity=0.357 Sum_probs=29.8
Q ss_pred CCcchHHHHHHHhhcCcChHHHHhhCCCCCCCCCC
Q 040695 85 GHGGNLRVYLEGLADAENVQEYVRQNPFGQEAITE 119 (169)
Q Consensus 85 ~~~g~Lr~YLe~La~a~dV~~yVr~~PFgq~~i~~ 119 (169)
..-+.|..|.+++...+.|++|+...++....|++
T Consensus 88 ~~~P~l~~~~~rv~~~p~v~~~~~~~~~~~~~~~~ 122 (126)
T cd03210 88 DAFPLLKAFVERLSARPKLKAYLESDAFKNRPING 122 (126)
T ss_pred hcChHHHHHHHHHHhCcHHHHHHhCcCCCCCCCCC
Confidence 34579999999999999999999998887766654
No 10
>cd03209 GST_C_Mu GST_C family, Class Mu subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. The class Mu subfamily is composed of eukaryotic GSTs. In rats, at least six distinct class Mu subunits have been identified, with homologous genes in humans for five of these subunits. Class Mu GSTs can form homodimers and heterodimers, giving a large number of possible isoenzymes that can be formed, all with overlapping activities but different substrate specificities. They are the m
Probab=39.28 E-value=33 Score=24.83 Aligned_cols=31 Identities=19% Similarity=0.315 Sum_probs=26.7
Q ss_pred CCcchHHHHHHHhhcCcChHHHHhhCCCCCC
Q 040695 85 GHGGNLRVYLEGLADAENVQEYVRQNPFGQE 115 (169)
Q Consensus 85 ~~~g~Lr~YLe~La~a~dV~~yVr~~PFgq~ 115 (169)
..-|.|..|.+++...+.|++|++..|+-..
T Consensus 85 ~~~P~l~~~~~rv~~~p~vk~~~~~~~~~~~ 115 (121)
T cd03209 85 DAFPNLKDFLERFEALPKISAYMKSDRFIKW 115 (121)
T ss_pred ccChHHHHHHHHHHHCHHHHHHHhcccCcCC
Confidence 3457999999999999999999999887553
No 11
>PF08325 WLM: WLM domain; InterPro: IPR013536 The WLM (WSS1-like metalloprotease) domain is a globular domain related to the zincin-like superfamily of Zn-dependent peptidase. Since the WLM domain contains all known active site residues of zincins, it is predicted to be a catalytically active peptidase domain. The WLM domain is a eukaryotic domain represented in plants, fungi, Plasmodium, and kinetoplastids. By contrast, it is absent in animals, Cryptosporidium, and Microsporidia, suggesting that it has been lost on multiple occasions during the evolution of eukaryotes. The WLM domain is found either in stand-alone form or in association with other domains such as the RanBP2 zinc finger , the ubiquitin domain, or the PUB/PUG domain. This domain could function as a specific de-SUMOylating domain of distinct protein complexes in the nucleus and the cytoplasm []. It has been suggested to form a segregated alpha/beta structure with eight helices and five strands. Proteins containign this domain include yeast WSS1 (a weak suppressor of the Ub-related protein SMT3), and various putative metalloproteases from plant and fungal species.
Probab=25.08 E-value=64 Score=26.75 Aligned_cols=33 Identities=24% Similarity=0.312 Sum_probs=29.8
Q ss_pred hHHHHHHHhhcCcChHHHHhhCCCCCCCCCCCCCC
Q 040695 89 NLRVYLEGLADAENVQEYVRQNPFGQEAITERNPS 123 (169)
Q Consensus 89 ~Lr~YLe~La~a~dV~~yVr~~PFgq~~i~~~~~~ 123 (169)
.-+.+|+.||.+ |+-.|++|-|....+.|..|.
T Consensus 17 ~A~~lL~rlA~~--v~pIM~~~~~~V~~L~E~~P~ 49 (186)
T PF08325_consen 17 EALELLERLAAD--VKPIMRKHGWRVGSLEEFYPN 49 (186)
T ss_pred HHHHHHHHHHHH--HHHHHHHcCcccCeeeccCCC
Confidence 567899999988 999999999999999998875
No 12
>COG0774 LpxC UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]
Probab=24.76 E-value=51 Score=29.89 Aligned_cols=47 Identities=17% Similarity=0.145 Sum_probs=33.8
Q ss_pred ceEeeehHHhhcccCCCCCcCCCCCCCCceEEecCCchhhccCCCCcccccCCCCCC
Q 040695 21 PLVLKELKKLWEKIDPNLPWKKGEYNETNTLLLDDSPYKALCNPAHTAIFPYPYDYR 77 (169)
Q Consensus 21 p~~~K~L~kVW~~~~~~~pw~~g~~~~sNTLLIDDSPyKA~~NP~~naI~P~ef~~~ 77 (169)
--|++++..||+.-= . .+=+..|+|+||| ++ .+|| .-+-|+.||.-.
T Consensus 192 FGF~~dvE~L~~~gL---a---lGGSleNaiVidd--~~-vlN~-~gLRf~dEfVRH 238 (300)
T COG0774 192 FGFMRDVEYLRSKGL---A---LGGSLENAIVIDD--DR-VLNP-EGLRFEDEFVRH 238 (300)
T ss_pred hhhHHHHHHHHHcCc---c---ccccccceEEECC--Cc-eeCC-ccccCCCcchhh
Confidence 347789999988542 1 2348999999999 44 5676 457788888763
No 13
>PF03991 Prion_octapep: Copper binding octapeptide repeat; InterPro: IPR020949 Prion protein (PrP-c) [, , ] is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown. Several results, mainly obtained in transgenic animals, indicate that PrP-c might play a role in long-term potentiation, in sleep physiology, in oxidative burst compensation (PrP can fix four Cu2+ through its octarepeat domain), in interactions with the extracellular matrix (PrP-c can bind to the precursor of the laminin receptor, LRP), in apoptosis and in signal transduction (costimulation of PrP-c induces a modulation of Fyn kinase phosphorylation) []. The normal isoform, PrP-c, is anchored at the cell membrane, in rafts, through a glycosyl phosphatidyl inositol (GPI); its half-life at the cell surface is 5 h, after which the protein is internalised through a caveolae-dependent mechanism and degraded in the endolysosome compartment. Conversion between PrP-c and PrP-sc occurs likely during the internalisation process. This repeat is found at the amino terminus of mammalian prion proteins. It has been shown to bind to copper [].
Probab=21.97 E-value=41 Score=15.22 Aligned_cols=6 Identities=67% Similarity=1.105 Sum_probs=4.2
Q ss_pred cccCCC
Q 040695 156 PHVGGN 161 (169)
Q Consensus 156 ~~~~~~ 161 (169)
||.||-
T Consensus 1 phgG~W 6 (8)
T PF03991_consen 1 PHGGGW 6 (8)
T ss_pred CCCCcC
Confidence 788763
No 14
>KOG3441 consensus Mitochondrial ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=20.64 E-value=59 Score=26.45 Aligned_cols=24 Identities=33% Similarity=0.499 Sum_probs=19.8
Q ss_pred CCCCCceEEecCCchhhccCCCCcccccC
Q 040695 44 EYNETNTLLLDDSPYKALCNPAHTAIFPY 72 (169)
Q Consensus 44 ~~~~sNTLLIDDSPyKA~~NP~~naI~P~ 72 (169)
.||+.|.|||||. -||-.|-|..|
T Consensus 101 ~fDsNniVLiddn-----GnPlGtRI~~P 124 (149)
T KOG3441|consen 101 VFDSNNIVLIDDN-----GNPLGTRITAP 124 (149)
T ss_pred ccCCCcEEEECCC-----CCcccceEecc
Confidence 6999999999996 58888877643
No 15
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=20.48 E-value=44 Score=23.38 Aligned_cols=20 Identities=15% Similarity=0.275 Sum_probs=15.0
Q ss_pred CCCCchhHHHHhhhcCCCCC
Q 040695 120 RNPSWGFYSKIFSTKSQPPP 139 (169)
Q Consensus 120 ~~~~W~fY~~v~~~~~~~~~ 139 (169)
+||+|+=|+-+...++-=+.
T Consensus 20 ~hP~WDQ~Rl~~aALa~FL~ 39 (57)
T PF10929_consen 20 THPNWDQYRLFQAALAGFLL 39 (57)
T ss_pred cCCCchHHHHHHHHHHHHHH
Confidence 45699999998887764443
Done!