Query psy17633
Match_columns 99
No_of_seqs 104 out of 362
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 19:02:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17633.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17633hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00182 TBOX T-box DNA binding 100.0 2.2E-42 4.8E-47 243.2 9.3 96 1-98 22-117 (188)
2 KOG3586|consensus 100.0 1.7E-42 3.6E-47 262.0 9.0 99 1-99 100-198 (437)
3 smart00425 TBOX Domain first f 100.0 5.3E-42 1.1E-46 241.7 10.0 96 1-98 21-116 (190)
4 KOG3585|consensus 100.0 6.6E-39 1.4E-43 241.3 8.7 96 1-98 45-140 (328)
5 PF00907 T-box: T-box; InterP 100.0 4.7E-37 1E-41 214.8 7.2 96 1-98 20-115 (184)
6 PF00041 fn3: Fibronectin type 88.2 1.1 2.3E-05 25.8 3.8 23 15-37 57-79 (85)
7 PF04775 Bile_Hydr_Trans: Acyl 87.1 1.1 2.3E-05 29.5 3.7 29 14-42 5-33 (126)
8 smart00060 FN3 Fibronectin typ 73.1 6.5 0.00014 21.0 3.2 23 13-35 56-78 (83)
9 cd00063 FN3 Fibronectin type 3 70.1 7.5 0.00016 21.5 3.1 25 12-36 55-79 (93)
10 PF09294 Interfer-bind: Interf 69.5 8.7 0.00019 23.5 3.5 23 15-37 68-90 (106)
11 PF10179 DUF2369: Uncharacteri 68.7 9.5 0.00021 29.0 4.1 39 14-55 260-298 (300)
12 KOG0179|consensus 59.2 6.2 0.00013 28.8 1.5 20 7-26 118-138 (235)
13 cd02861 E_set_proteins_like E 46.8 39 0.00084 20.0 3.5 26 25-52 36-61 (82)
14 COG2706 3-carboxymuconate cycl 44.9 29 0.00062 27.0 3.2 52 18-71 149-203 (346)
15 PF01687 Flavokinase: Riboflav 42.2 75 0.0016 20.9 4.6 38 3-42 15-55 (125)
16 PF12929 Mid1: Stretch-activat 40.0 33 0.00072 27.4 3.0 30 3-32 176-205 (427)
17 cd02859 AMPKbeta_GBD_like AMP- 36.6 58 0.0013 19.2 3.1 25 27-53 37-61 (79)
18 PF07351 DUF1480: Protein of u 34.8 35 0.00075 21.0 1.9 41 12-52 37-77 (80)
19 KOG1948|consensus 32.3 40 0.00087 29.7 2.5 20 15-34 947-966 (1165)
20 PF04170 NlpE: NlpE N-terminal 32.2 78 0.0017 19.2 3.3 41 12-54 11-51 (87)
21 PF08234 Spindle_Spc25: Chromo 27.7 1.1E+02 0.0023 18.0 3.2 26 14-42 9-37 (74)
22 PF10419 TFIIIC_sub6: TFIIIC s 27.3 45 0.00097 17.1 1.3 21 16-42 1-21 (35)
23 PF14109 GldH_lipo: GldH lipop 26.9 1.7E+02 0.0038 19.1 4.4 57 13-74 21-83 (131)
24 COG4875 Uncharacterized protei 26.7 80 0.0017 21.4 2.7 18 43-60 135-152 (156)
25 PF14352 DUF4402: Domain of un 26.2 73 0.0016 20.5 2.5 19 13-32 46-64 (130)
26 PF00080 Sod_Cu: Copper/zinc s 26.1 65 0.0014 21.0 2.3 24 13-37 28-51 (142)
27 PF09423 PhoD: PhoD-like phosp 25.8 68 0.0015 25.1 2.6 20 14-33 64-83 (453)
28 KOG1887|consensus 25.7 52 0.0011 28.4 2.1 40 14-54 715-756 (806)
29 PF08294 TIM21: TIM21; InterP 25.1 1.6E+02 0.0035 19.8 4.1 30 13-44 97-127 (145)
30 COG2366 Protein related to pen 24.4 1.2E+02 0.0026 26.1 4.0 41 13-56 312-352 (768)
31 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 24.0 1E+02 0.0022 23.0 3.1 33 7-39 160-192 (251)
32 PF04326 AAA_4: Divergent AAA 23.9 1.3E+02 0.0029 18.4 3.3 48 8-55 69-116 (122)
33 PF13620 CarboxypepD_reg: Carb 22.2 63 0.0014 18.5 1.5 16 15-31 39-54 (82)
34 TIGR03511 GldH_lipo gliding mo 22.0 1.7E+02 0.0036 20.1 3.7 37 13-54 43-79 (156)
35 PF08547 CIA30: Complex I inte 21.5 1.2E+02 0.0027 20.0 3.0 65 17-92 59-123 (157)
36 KOG1230|consensus 21.3 1.2E+02 0.0027 24.6 3.2 59 40-98 100-180 (521)
37 PF15513 DUF4651: Domain of un 20.9 1.1E+02 0.0024 17.9 2.3 19 31-49 38-56 (62)
No 1
>cd00182 TBOX T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors.
Probab=100.00 E-value=2.2e-42 Score=243.20 Aligned_cols=96 Identities=55% Similarity=0.950 Sum_probs=92.7
Q ss_pred CccccCCCCCCCcceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEcccCCCCCCCceEEcCCCCCchHHHhhC
Q psy17633 1 MTGLSHFLRMFPTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPPAPLRLYMHPDSPFTGDQLRKQ 80 (99)
Q Consensus 1 ~~~~~~gRrmFP~l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~~~e~~~~~~~~~Hp~~~~tG~~WM~~ 80 (99)
|+|||.||||||.|+|+|+||||++.|.|.|+|+++|++||||. +|+|++++++|+..+.++|+|||||++|++||++
T Consensus 22 MIITk~GRrmFP~l~~~vsGLdp~~~Y~v~l~~~~~D~~Rykf~--~~~W~~~g~~e~~~~~~~~~HPdsp~tG~~wM~~ 99 (188)
T cd00182 22 MIITKSGRRMFPTLKVKVSGLDPNALYSVLMDLVPVDDHRYKFS--GGKWVVAGKAEPHLPPRVYVHPDSPATGAHWMKQ 99 (188)
T ss_pred EEEecCCcccccceEEEEeCCCcccceEEEEEEEEcCCcEEEec--CCcEeEcCCCCCCCCCceEECCCCCcCHHHHhhC
Confidence 89999999999999999999999999999999999999999994 8999999999999999999999999999999999
Q ss_pred CceeeeEeeecccccCCC
Q psy17633 81 VVSFEKVKLTNNEMDKNG 98 (99)
Q Consensus 81 ~v~F~~lklTN~~~~~~~ 98 (99)
+|+|++|||||+..++.|
T Consensus 100 ~isF~kvKlTN~~~~~~~ 117 (188)
T cd00182 100 PVSFDKLKLTNNTLDNNG 117 (188)
T ss_pred ccccchhhcccCCCCCCC
Confidence 999999999999977765
No 2
>KOG3586|consensus
Probab=100.00 E-value=1.7e-42 Score=262.01 Aligned_cols=99 Identities=66% Similarity=1.077 Sum_probs=97.9
Q ss_pred CccccCCCCCCCcceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEcccCCCCCCCceEEcCCCCCchHHHhhC
Q psy17633 1 MTGLSHFLRMFPTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPPAPLRLYMHPDSPFTGDQLRKQ 80 (99)
Q Consensus 1 ~~~~~~gRrmFP~l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~~~e~~~~~~~~~Hp~~~~tG~~WM~~ 80 (99)
|+|||.||||||+++++|+||||.+.|.|.||++++|++||||.|+...|.++|++|+..+.|+|+|||||++|+.||++
T Consensus 100 MIITKsGRRMFPTvrV~~~GldP~a~Y~vlmDvVPvD~KRYRYayH~S~WlvAGkADp~~p~R~yvHPDSP~sGe~wmkq 179 (437)
T KOG3586|consen 100 MIITKSGRRMFPTVRVKFSGLDPMADYYVLMDVVPVDSKRYRYAYHSSSWLVAGKADPAPPPRVYVHPDSPASGEQWMKQ 179 (437)
T ss_pred EEEecccccccceEEEEEecCCcccceEEEEeEEecccceeeeeecccceeeecCCCCCCCCceeeCCCCCCCHHHHHHh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeeeEeeecccccCCCC
Q psy17633 81 VVSFEKVKLTNNEMDKNGQ 99 (99)
Q Consensus 81 ~v~F~~lklTN~~~~~~~~ 99 (99)
.|||+|+|||||+.|++||
T Consensus 180 iVSFdK~KLTNNelD~nGH 198 (437)
T KOG3586|consen 180 IVSFDKLKLTNNELDDNGH 198 (437)
T ss_pred hhchheeeccccccccCCc
Confidence 9999999999999999995
No 3
>smart00425 TBOX Domain first found in the mice T locus (Brachyury) protein.
Probab=100.00 E-value=5.3e-42 Score=241.72 Aligned_cols=96 Identities=57% Similarity=0.960 Sum_probs=93.2
Q ss_pred CccccCCCCCCCcceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEcccCCCCCCCceEEcCCCCCchHHHhhC
Q psy17633 1 MTGLSHFLRMFPTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPPAPLRLYMHPDSPFTGDQLRKQ 80 (99)
Q Consensus 1 ~~~~~~gRrmFP~l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~~~e~~~~~~~~~Hp~~~~tG~~WM~~ 80 (99)
|+|||.||||||.|+|+|+||||++.|.|.|+|+++|++|||| ++|+|+++|++|+..+.++|+|||||++|++||++
T Consensus 21 MIVTk~GRrmFP~l~~~vsGLdp~~~Y~v~l~~~~~d~~rykf--~~~~W~~~g~~e~~~~~~~~~Hpdsp~tG~~wM~~ 98 (190)
T smart00425 21 MIVTKSGRRMFPTLKYKVSGLDPNALYSVLMDLVPVDDKRYKF--NNGKWVVAGKAEPHMPSRVYVHPDSPATGAHWMKQ 98 (190)
T ss_pred EEEecCCceeCCeeEEEEeCCCccCcEEEEEEEEEccCcEEEe--cCCcEEEcCCCCCCCCCceEECCCCccCHHHHhhC
Confidence 8999999999999999999999999999999999999999998 58999999999999999999999999999999999
Q ss_pred CceeeeEeeecccccCCC
Q psy17633 81 VVSFEKVKLTNNEMDKNG 98 (99)
Q Consensus 81 ~v~F~~lklTN~~~~~~~ 98 (99)
+|+|++|||||+..+++|
T Consensus 99 ~v~F~kvKlTN~~~~~~~ 116 (190)
T smart00425 99 PVSFDKVKLTNNQSDKNG 116 (190)
T ss_pred cccccccceeccccccCC
Confidence 999999999999988876
No 4
>KOG3585|consensus
Probab=100.00 E-value=6.6e-39 Score=241.31 Aligned_cols=96 Identities=44% Similarity=0.885 Sum_probs=93.4
Q ss_pred CccccCCCCCCCcceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEcccCCCCCCCceEEcCCCCCchHHHhhC
Q psy17633 1 MTGLSHFLRMFPTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPPAPLRLYMHPDSPFTGDQLRKQ 80 (99)
Q Consensus 1 ~~~~~~gRrmFP~l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~~~e~~~~~~~~~Hp~~~~tG~~WM~~ 80 (99)
|+|||.||||||.|+|+|+||||+++|+|.|+|+++|++||+| .+|+|++++++|+..+.++++||||++||++||++
T Consensus 45 miitK~GRrmFP~l~~~VsGLdp~s~Y~i~l~~~~~D~~rykf--~ng~W~p~gk~e~~~~~~~~~Hpd~p~TG~~WM~~ 122 (328)
T KOG3585|consen 45 MIVTKRGRRMFPALKFKVSGLDPNSLYSILLELVPIDDKRYKF--NNGKWVPSGKAEPHVPSKVYVHPDGPATGAHWMSE 122 (328)
T ss_pred EEEecCCceeccccceeeccCCcccceEEEEEEEEccCceeee--cCCeeccCCCCCCCCCceEEEecCCccchHHHhcC
Confidence 8999999999999999999999999999999999999999998 59999999999998899999999999999999999
Q ss_pred CceeeeEeeecccccCCC
Q psy17633 81 VVSFEKVKLTNNEMDKNG 98 (99)
Q Consensus 81 ~v~F~~lklTN~~~~~~~ 98 (99)
+|+|++|||||+..+.+|
T Consensus 123 ~V~F~kvKITN~~~~~~~ 140 (328)
T KOG3585|consen 123 PVSFDKVKITNNKSDKKG 140 (328)
T ss_pred CcccceeEeeccccccCC
Confidence 999999999999999876
No 5
>PF00907 T-box: T-box; InterPro: IPR001699 Transcription factors of the T-box family are required both for early cell-fate decisions, such as those necessary for formation of the basic vertebrate body plan, and for differentiation and organogenesis []. The T-box is defined as the minimal region within the T-box protein that is both necessary and sufficient for sequence-specific DNA binding, all members of the family so far examined bind to the DNA consensus sequence TCACACCT. The T-box is a relatively large DNA-binding domain, generally comprising about a third of the entire protein (17-26 kDa). These genes were uncovered on the basis of similarity to the DNA binding domain [] of Mus musculus (Mouse) Brachyury (T) gene product, which similarity is the defining feature of the family. The Brachyury gene is named for its phenotype, which was identified 70 years ago as a mutant mouse strain with a short blunted tail. The gene, and its paralogues, have become a well-studied model for the family, and hence much of what is known about the T-box family is derived from the murine Brachyury gene. Consistent with its nuclear location, Brachyury protein has a sequence-specific DNA-binding activity and can act as a transcriptional regulator []. Homozygous mutants for the gene undergo extensive developmental anomalies, thus rendering the mutation lethal []. The postulated role of Brachyury is as a transcription factor, regulating the specification and differentiation of posterior mesoderm during gastrulation in a dose-dependent manner []. T-box proteins tend to be expressed in specific organs or cell types, especially during development, and they are generally required for the development of those tissues, for example, Brachyury is expressed in posterior mesoderm and in the developing notochord, and it is required for the formation of these cells in mice []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1H6F_B 4A04_A 1XBR_B 2X6V_B 2X6U_A.
Probab=100.00 E-value=4.7e-37 Score=214.76 Aligned_cols=96 Identities=48% Similarity=0.825 Sum_probs=74.7
Q ss_pred CccccCCCCCCCcceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEcccCCCCCCCceEEcCCCCCchHHHhhC
Q psy17633 1 MTGLSHFLRMFPTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPPAPLRLYMHPDSPFTGDQLRKQ 80 (99)
Q Consensus 1 ~~~~~~gRrmFP~l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~~~e~~~~~~~~~Hp~~~~tG~~WM~~ 80 (99)
|+||+.||+|||.|+|+|+||||++.|+|+|+|+++|+++|+| .+|+|.+++++++..+.++++||+|+++|++||++
T Consensus 20 Mivt~~GR~~FP~l~y~vsGL~p~~~Y~i~l~~~~~d~~~~k~--~~~~W~~~~~~~~~~~~~~~~h~~~~~~G~~WM~~ 97 (184)
T PF00907_consen 20 MIVTKNGRRMFPTLEYSVSGLDPDSLYSISLHFERVDNKRYKF--SNGKWVPSGKAEPPMPPRVVIHPDGPQTGSEWMKN 97 (184)
T ss_dssp EE-BTT-EE-SS-EEEEEESS-TTSEEEEEEEEEESCSEEEEE--ETTEEEEEEE---B-----EE-TT-SEEHHHHHHS
T ss_pred EEEeecccccccccEEEecCCCCCcceEEEEEEEEecCceeec--ccccccccccccccccceEEEEecCcCCHHHhCcc
Confidence 8999999999999999999999999999999999999999998 58999999999988888999999999999999999
Q ss_pred CceeeeEeeecccccCCC
Q psy17633 81 VVSFEKVKLTNNEMDKNG 98 (99)
Q Consensus 81 ~v~F~~lklTN~~~~~~~ 98 (99)
+|+|+++||||+..++.|
T Consensus 98 ~v~F~~vkitn~~~~~~~ 115 (184)
T PF00907_consen 98 GVSFDKVKITNNKEDKKG 115 (184)
T ss_dssp -EEETT-EEESSTT-TST
T ss_pred cEEeehhhhhCCCCCccc
Confidence 999999999999876655
No 6
>PF00041 fn3: Fibronectin type III domain; InterPro: IPR003961 Fibronectins are multi-domain glycoproteins found in a soluble form in plasma, and in an insoluble form in loose connective tissue and basement membranes []. They contain multiple copies of 3 repeat regions (types I, II and III), which bind to a variety of substances including heparin, collagen, DNA, actin, fibrin and fibronectin receptors on cell surfaces. The wide variety of these substances means that fibronectins are involved in a number of important functions: e.g., wound healing; cell adhesion; blood coagulation; cell differentiation and migration; maintenance of the cellular cytoskeleton; and tumour metastasis []. The role of fibronectin in cell differentiation is demonstrated by the marked reduction in the expression of its gene when neoplastic transformation occurs. Cell attachment has been found to be mediated by the binding of the tetrapeptide RGDS to integrins on the cell surface [], although related sequences can also display cell adhesion activity. Plasma fibronectin occurs as a dimer of 2 different subunits, linked together by 2 disulphide bonds near the C terminus. The difference in the 2 chains occurs in the type III repeat region and is caused by alternative splicing of the mRNA from one gene []. The observation that, in a given protein, an individual repeat of one of the 3 types (e.g., the first FnIII repeat) shows much less similarity to its subsequent tandem repeats within that protein than to its equivalent repeat between fibronectins from other species, has suggested that the repeating structure of fibronectin arose at an early stage of evolution. It also seems to suggest that the structure is subject to high selective pressure []. The fibronectin type III repeat region is an approximately 100 amino acid domain, different tandem repeats of which contain binding sites for DNA, heparin and the cell surface []. The superfamily of sequences believed to contain FnIII repeats represents 45 different families, the majority of which are involved in cell surface binding in some manner, or are receptor protein tyrosine kinases, or cytokine receptors.; GO: 0005515 protein binding; PDB: 1UEM_A 1TDQ_A 1X5I_A 2IC2_B 2IBG_C 2IBB_A 3R8Q_A 2FNB_A 1FNH_A 2EDB_A ....
Probab=88.22 E-value=1.1 Score=25.78 Aligned_cols=23 Identities=30% Similarity=0.518 Sum_probs=20.3
Q ss_pred eEEEecCCCCCCeeEEEEEEEcc
Q psy17633 15 RVSFTGLRPDQRYAVLMDIVPVD 37 (99)
Q Consensus 15 ~~~vsGLdp~~~Y~i~l~~~~~d 37 (99)
.+.|.||+|...|.+.|.....+
T Consensus 57 ~~~i~~L~p~t~Y~~~v~a~~~~ 79 (85)
T PF00041_consen 57 SYTITGLQPGTTYEFRVRAVNSD 79 (85)
T ss_dssp EEEEESCCTTSEEEEEEEEEETT
T ss_pred eeeeccCCCCCEEEEEEEEEeCC
Confidence 79999999999999999876654
No 7
>PF04775 Bile_Hydr_Trans: Acyl-CoA thioester hydrolase/BAAT N-terminal region; InterPro: IPR006862 This entry presents the N-termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT) []. This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism []. For example, in peroxisomes, the hydrolase acts on bile-CoA esters [].; GO: 0016290 palmitoyl-CoA hydrolase activity, 0006629 lipid metabolic process; PDB: 3HLK_B 3K2I_B.
Probab=87.15 E-value=1.1 Score=29.53 Aligned_cols=29 Identities=14% Similarity=0.367 Sum_probs=18.4
Q ss_pred ceEEEecCCCCCCeeEEEEEEEccCcceE
Q psy17633 14 LRVSFTGLRPDQRYAVLMDIVPVDNKRYR 42 (99)
Q Consensus 14 l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr 42 (99)
+.++|+||.|.+.|.|.+.+.--....|+
T Consensus 5 ~~I~v~GL~p~~~vtl~a~~~~~~g~~w~ 33 (126)
T PF04775_consen 5 VDIRVSGLPPGQEVTLRARLTDDNGVQWQ 33 (126)
T ss_dssp -EEEEES--TT-EEEEEEEEE-TTS-EEE
T ss_pred eEEEEeCCCCCCEEEEEEEEEeCCCCEEE
Confidence 68999999999999999988854343443
No 8
>smart00060 FN3 Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
Probab=73.06 E-value=6.5 Score=21.01 Aligned_cols=23 Identities=26% Similarity=0.508 Sum_probs=19.4
Q ss_pred cceEEEecCCCCCCeeEEEEEEE
Q psy17633 13 TLRVSFTGLRPDQRYAVLMDIVP 35 (99)
Q Consensus 13 ~l~~~vsGLdp~~~Y~i~l~~~~ 35 (99)
...+.|.+|.|...|.+.|....
T Consensus 56 ~~~~~i~~L~~~~~Y~v~v~a~~ 78 (83)
T smart00060 56 STSYTLTGLKPGTEYEFRVRAVN 78 (83)
T ss_pred ccEEEEeCcCCCCEEEEEEEEEc
Confidence 46789999999999999887654
No 9
>cd00063 FN3 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
Probab=70.12 E-value=7.5 Score=21.49 Aligned_cols=25 Identities=24% Similarity=0.408 Sum_probs=19.7
Q ss_pred CcceEEEecCCCCCCeeEEEEEEEc
Q psy17633 12 PTLRVSFTGLRPDQRYAVLMDIVPV 36 (99)
Q Consensus 12 P~l~~~vsGLdp~~~Y~i~l~~~~~ 36 (99)
....+.|.||.|...|.+.|.....
T Consensus 55 ~~~~~~i~~l~p~~~Y~~~v~a~~~ 79 (93)
T cd00063 55 SETSYTLTGLKPGTEYEFRVRAVNG 79 (93)
T ss_pred cccEEEEccccCCCEEEEEEEEECC
Confidence 4568889999999999988765443
No 10
>PF09294 Interfer-bind: Interferon-alpha/beta receptor, fibronectin type III; InterPro: IPR015373 Members of this family adopt a secondary structure consisting of seven beta-strands arranged in an immunoglobulin-like beta-sandwich, in a Greek-key topology. They are required for binding to interferon-alpha []. ; PDB: 1A21_A 3LQM_B 3ELA_T 1AHW_C 2A2Q_T 1TFH_B 1FAK_T 1WSS_T 1W2K_T 2FIR_T ....
Probab=69.49 E-value=8.7 Score=23.50 Aligned_cols=23 Identities=22% Similarity=0.486 Sum_probs=17.1
Q ss_pred eEEEecCCCCCCeeEEEEEEEcc
Q psy17633 15 RVSFTGLRPDQRYAVLMDIVPVD 37 (99)
Q Consensus 15 ~~~vsGLdp~~~Y~i~l~~~~~d 37 (99)
.+.|.+|+|...|.+.+......
T Consensus 68 ~~~l~~L~p~t~YCv~V~~~~~~ 90 (106)
T PF09294_consen 68 SVTLSDLKPGTNYCVSVQAFSPS 90 (106)
T ss_dssp EEEEES--TTSEEEEEEEEEECS
T ss_pred EEEEeCCCCCCCEEEEEEEEecc
Confidence 46799999999999999994433
No 11
>PF10179 DUF2369: Uncharacterised conserved protein (DUF2369); InterPro: IPR019326 This is a proline-rich region of a group of proteins found from plants to fungi. The function is largely unknown, although the entry contains Fibronectin type-III domain-containing protein C4orf31, which promotes matrix assembly and cell adhesiveness.
Probab=68.71 E-value=9.5 Score=29.00 Aligned_cols=39 Identities=21% Similarity=0.443 Sum_probs=31.3
Q ss_pred ceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEccc
Q psy17633 14 LRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGK 55 (99)
Q Consensus 14 l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~~ 55 (99)
+...|.||+|...|.+-|-+.+....-.+| ...|+...+
T Consensus 260 ~tetI~~L~PG~~Yl~dV~~~~~~G~sl~Y---~s~~VkTr~ 298 (300)
T PF10179_consen 260 TTETIKGLKPGTTYLFDVYVNGPSGQSLPY---RSKWVKTRR 298 (300)
T ss_pred ceeecccCCCCcEEEEEEEEecCCCceeec---ceEEEEecC
Confidence 345799999999999999999888887887 466776544
No 12
>KOG0179|consensus
Probab=59.23 E-value=6.2 Score=28.79 Aligned_cols=20 Identities=20% Similarity=0.463 Sum_probs=16.6
Q ss_pred CCCCCCcceEEE-ecCCCCCC
Q psy17633 7 FLRMFPTLRVSF-TGLRPDQR 26 (99)
Q Consensus 7 gRrmFP~l~~~v-sGLdp~~~ 26 (99)
+||.||...|.| .|||.+.+
T Consensus 118 ~kRFFPYYv~~ilaGiDeeGK 138 (235)
T KOG0179|consen 118 SKRFFPYYVFNILAGIDEEGK 138 (235)
T ss_pred hcccccceeeeeeecccccCc
Confidence 799999999985 67999554
No 13
>cd02861 E_set_proteins_like E or "early" set-like proteins. These alpha amylase-like sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies are associated with different types of catalytic domains at either the N-terminal or C-terminal end. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=46.77 E-value=39 Score=19.97 Aligned_cols=26 Identities=15% Similarity=0.611 Sum_probs=18.1
Q ss_pred CCeeEEEEEEEccCcceEEeeeCCcEEE
Q psy17633 25 QRYAVLMDIVPVDNKRYRYAYHRSSWLV 52 (99)
Q Consensus 25 ~~Y~i~l~~~~~d~~ryr~~~~~~~W~~ 52 (99)
..|++.+.+.+ ..++|||. .+|.|..
T Consensus 36 G~w~~~~~l~~-G~y~Ykf~-vdg~~~~ 61 (82)
T cd02861 36 GLWVVTVELRP-GRYEYKFV-VDGEWVI 61 (82)
T ss_pred CcEEEEEeCCC-CcEEEEEE-ECCEEee
Confidence 57888887554 34678885 7888873
No 14
>COG2706 3-carboxymuconate cyclase [Carbohydrate transport and metabolism]
Probab=44.92 E-value=29 Score=27.02 Aligned_cols=52 Identities=23% Similarity=0.338 Sum_probs=37.1
Q ss_pred EecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEcccCCCC---CCCceEEcCCCC
Q psy17633 18 FTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPP---APLRLYMHPDSP 71 (99)
Q Consensus 18 vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~~~e~~---~~~~~~~Hp~~~ 71 (99)
-.+++|+.+|.+..++-.---.-|++ .+|+-.++..++.. .|..+..||++.
T Consensus 149 ~a~~tP~~~~l~v~DLG~Dri~~y~~--~dg~L~~~~~~~v~~G~GPRHi~FHpn~k 203 (346)
T COG2706 149 SANFTPDGRYLVVPDLGTDRIFLYDL--DDGKLTPADPAEVKPGAGPRHIVFHPNGK 203 (346)
T ss_pred eeeeCCCCCEEEEeecCCceEEEEEc--ccCccccccccccCCCCCcceEEEcCCCc
Confidence 46789999999998875432234554 58888887665533 477899999875
No 15
>PF01687 Flavokinase: Riboflavin kinase; InterPro: IPR015865 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents the riboflavin kinase domains from bacteria and eukaryotes.; GO: 0008531 riboflavin kinase activity, 0009231 riboflavin biosynthetic process; PDB: 1Q9S_A 1NB9_A 1P4M_A 1NB0_A 3OP1_B 1T6Z_A 2I1L_A 1T6Y_B 1T6X_B 1S4M_A ....
Probab=42.19 E-value=75 Score=20.86 Aligned_cols=38 Identities=32% Similarity=0.501 Sum_probs=22.4
Q ss_pred cccCCCCC-CCcceEEEe-c-CCCCCCeeEEEEEEEccCcceE
Q psy17633 3 GLSHFLRM-FPTLRVSFT-G-LRPDQRYAVLMDIVPVDNKRYR 42 (99)
Q Consensus 3 ~~~~gRrm-FP~l~~~vs-G-Ldp~~~Y~i~l~~~~~d~~ryr 42 (99)
..+.||.+ ||+.+..+. . +.|.. -|....+.+++..|.
T Consensus 15 G~~~Gr~lGfPTANl~~~~~~~~p~~--GVYa~~v~~~~~~~~ 55 (125)
T PF01687_consen 15 GFGRGRKLGFPTANLDIPDDKLLPKE--GVYAVWVRVDGKWYP 55 (125)
T ss_dssp -SSCCCCTTS-EEEEEEHCCCTCCCT--EEEEEEEEETSEEEE
T ss_pred CCccccccCCccccccCCcccccccC--EEEEEEEEECCEEEE
Confidence 34678887 999999993 3 33322 444455555666555
No 16
>PF12929 Mid1: Stretch-activated Ca2+-permeable channel component; InterPro: IPR024338 Mid1 is a yeast plasma membrane protein required for Ca2+ influx induced by the mating pheromone alpha-factor during the mating process [, , ]. The protein is composed of 548-amino-acid residues, contains four hydrophobic regions (H1, H2, H3 and H4) and two cysteine-rich regions (C1 and C2) at the C terminus. H1 appears to be a signal sequence necessary for the alpha-factor-induced delivery to the plasma membrane. The region from H1 to H3 is required for the localisation of Mid1 in the plasma and ER membranes. C1 and C2 are thought to be involved in oligomerisation via the formation of disulphide bonds. Trafficking of Mid1-GFP to the plasma membrane is dependent on the N-glycosylation of Mid1 and the transporter protein Sec12. This suggests that the trafficking of Mid1-GFP to the plasma membrane requires a Sec12-dependent pathway from the ER to the Golgi, and that Mid1 is recruited via a Sec6- and Sec7-independent pathway from the Golgi to the plasma membrane.
Probab=40.03 E-value=33 Score=27.36 Aligned_cols=30 Identities=17% Similarity=0.122 Sum_probs=25.5
Q ss_pred cccCCCCCCCcceEEEecCCCCCCeeEEEE
Q psy17633 3 GLSHFLRMFPTLRVSFTGLRPDQRYAVLMD 32 (99)
Q Consensus 3 ~~~~gRrmFP~l~~~vsGLdp~~~Y~i~l~ 32 (99)
+|++|---.|.-+|-|+||++...|.-.|-
T Consensus 176 mt~Rg~g~~~k~QFyv~GLn~ST~Y~a~L~ 205 (427)
T PF12929_consen 176 MTTRGGGNGPKQQFYVTGLNSSTNYTAYLA 205 (427)
T ss_pred EEEECCCCCceeeEEecCCCCCCeEEEEEE
Confidence 455666668999999999999999998877
No 17
>cd02859 AMPKbeta_GBD_like AMP-activated protein kinase (AMPK) beta subunit glycogen binding domain (GBD). AMPK is a metabolic stress sensing protein that senses AMP/ATP and has recently been found to act as a glycogen sensor as well. The protein functions as a alpha-beta-gamma heterotrimer. This domain is the glycogen binding domain of the beta subunit.
Probab=36.55 E-value=58 Score=19.25 Aligned_cols=25 Identities=12% Similarity=0.542 Sum_probs=17.9
Q ss_pred eeEEEEEEEccCcceEEeeeCCcEEEc
Q psy17633 27 YAVLMDIVPVDNKRYRYAYHRSSWLVA 53 (99)
Q Consensus 27 Y~i~l~~~~~d~~ryr~~~~~~~W~~~ 53 (99)
|.+.+.+.+ ..+.|||. .+|.|...
T Consensus 37 ~~~~~~L~~-g~y~YkF~-Vdg~w~~d 61 (79)
T cd02859 37 FSATLRLPP-GKYQYKFI-VDGEWRHS 61 (79)
T ss_pred cEEEEEcCC-CCEEEEEE-ECCEEEeC
Confidence 677777655 45677775 78999765
No 18
>PF07351 DUF1480: Protein of unknown function (DUF1480); InterPro: IPR009950 This family consists of several hypothetical Enterobacterial proteins of around 80 residues in length. The function of this family is unknown.
Probab=34.75 E-value=35 Score=20.97 Aligned_cols=41 Identities=20% Similarity=0.413 Sum_probs=28.4
Q ss_pred CcceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEE
Q psy17633 12 PTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLV 52 (99)
Q Consensus 12 P~l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~ 52 (99)
|.|..++-|-|.+..---.|+=..+.-+|-.|..++-.|+-
T Consensus 37 pdlcmQLDgWDe~TSiPA~ldgk~~lLyr~hYD~q~d~Wvm 77 (80)
T PF07351_consen 37 PDLCMQLDGWDEHTSIPAILDGKPSLLYRQHYDKQQDAWVM 77 (80)
T ss_pred hhheeEecccccCCccceEECCceeeeeehhccccCceeEE
Confidence 67777777877777776666666666666666656666753
No 19
>KOG1948|consensus
Probab=32.31 E-value=40 Score=29.74 Aligned_cols=20 Identities=30% Similarity=0.439 Sum_probs=17.5
Q ss_pred eEEEecCCCCCCeeEEEEEE
Q psy17633 15 RVSFTGLRPDQRYAVLMDIV 34 (99)
Q Consensus 15 ~~~vsGLdp~~~Y~i~l~~~ 34 (99)
+|+|.||-|+..|++.+.-.
T Consensus 947 ~yRiRGL~Pdc~Y~V~vk~~ 966 (1165)
T KOG1948|consen 947 TYRIRGLLPDCEYQVHVKSY 966 (1165)
T ss_pred cEEEeccCCCceEEEEEeec
Confidence 69999999999999887644
No 20
>PF04170 NlpE: NlpE N-terminal domain; InterPro: IPR007298 This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway []. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. NlpE from Escherichia coli and Salmonella typhi is also known to confer copper tolerance in copper-sensitive strains of E. coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes [].; PDB: 3LHN_A 2Z4I_B 2Z4H_A.
Probab=32.20 E-value=78 Score=19.18 Aligned_cols=41 Identities=20% Similarity=0.462 Sum_probs=26.2
Q ss_pred CcceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEcc
Q psy17633 12 PTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAG 54 (99)
Q Consensus 12 P~l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~ 54 (99)
|.++..|+ |+++..|.+.-...-.++..+.+. ..++|...+
T Consensus 11 ~GI~t~L~-L~~D~ty~l~~~Yl~~~~~~~~~~-g~g~w~~~~ 51 (87)
T PF04170_consen 11 PGIKTTLT-LNADGTYTLTETYLGKEDGPFTEK-GSGTWNVDG 51 (87)
T ss_dssp SEEEEEEE-E-TTSEEEEEEEEETTTSCCCEEE-EEEEEECTS
T ss_pred CCeEEEEE-ECCCCcEEEEEEECCCCCCCceEE-EEEEEEccC
Confidence 45667777 888888887777666665455543 456786543
No 21
>PF08234 Spindle_Spc25: Chromosome segregation protein Spc25; InterPro: IPR013255 This is a family of chromosome segregation proteins. It contains Spc25, which is a conserved eukaryotic kinetochore protein involved in cell division. In fungi the Spc25 protein is a subunit of the Nuf2-Ndc80 complex [], and in vertebrates it forms part of the Ndc80 complex []. ; PDB: 2VE7_B.
Probab=27.71 E-value=1.1e+02 Score=17.98 Aligned_cols=26 Identities=31% Similarity=0.791 Sum_probs=13.8
Q ss_pred ceEEEecC---CCCCCeeEEEEEEEccCcceE
Q psy17633 14 LRVSFTGL---RPDQRYAVLMDIVPVDNKRYR 42 (99)
Q Consensus 14 l~~~vsGL---dp~~~Y~i~l~~~~~d~~ryr 42 (99)
|+|..+.+ ||+..|++.|++ ++..|+
T Consensus 9 lkf~F~~id~~d~~re~s~~l~i---~~~~Y~ 37 (74)
T PF08234_consen 9 LKFVFTNIDPNDPDREFSFTLDI---SSDKYE 37 (74)
T ss_dssp EEEEE-S-BTTBSSS-EEEEEE----SSS-EE
T ss_pred EEEEEeEcCCCCCCceEEEEEEE---CCCeEE
Confidence 67888888 556677777774 334454
No 22
>PF10419 TFIIIC_sub6: TFIIIC subunit; InterPro: IPR019481 This conserved domain is found in a family of proteins that function as subunits of transcription factor IIIC (TFIIIC) []. TFIIIC in yeast and humans is required for transcription of tRNA and 5 S RNA genes by RNA polymerase III. The yeast proteins in this entry are fused to phosphoglycerate mutase domain.
Probab=27.33 E-value=45 Score=17.14 Aligned_cols=21 Identities=14% Similarity=0.411 Sum_probs=14.2
Q ss_pred EEEecCCCCCCeeEEEEEEEccCcceE
Q psy17633 16 VSFTGLRPDQRYAVLMDIVPVDNKRYR 42 (99)
Q Consensus 16 ~~vsGLdp~~~Y~i~l~~~~~d~~ryr 42 (99)
++|.|||.+.-.. ++++.-|+
T Consensus 1 ~qi~gLdt~~Pil------~i~~~vf~ 21 (35)
T PF10419_consen 1 IQILGLDTENPIL------QIGNQVFE 21 (35)
T ss_pred CEEeccCCCCCEE------EECCEEEE
Confidence 4688888776554 67776653
No 23
>PF14109 GldH_lipo: GldH lipoprotein
Probab=26.93 E-value=1.7e+02 Score=19.10 Aligned_cols=57 Identities=21% Similarity=0.395 Sum_probs=38.9
Q ss_pred cceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEcccCCCCC------CCceEEcCCCCCch
Q psy17633 13 TLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPPA------PLRLYMHPDSPFTG 74 (99)
Q Consensus 13 ~l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~~~e~~~------~~~~~~Hp~~~~tG 74 (99)
.+.|.|.=.|....|.+.|.+.-.++..| .+=|.......+.. -......|+|--.|
T Consensus 21 ~~~F~~~~~dt~~~Y~l~l~lR~~~~Ypy-----~NL~l~v~~~~p~~~~~~dtl~~~Lad~~G~w~G 83 (131)
T PF14109_consen 21 TLSFDFPIQDTTGPYNLYLNLRNNNDYPY-----SNLWLIVELTDPDGKKVTDTLECELADPDGKWLG 83 (131)
T ss_pred cEEEEccccccCCeeEEEEEEEcCCCCCc-----CCEEEEEEEEcCCCCEEeeeEEEEEECCCCcEee
Confidence 47888888999999999999999887555 45677655444422 23445556655444
No 24
>COG4875 Uncharacterized protein conserved in bacteria with a cystatin-like fold [Function unknown]
Probab=26.69 E-value=80 Score=21.37 Aligned_cols=18 Identities=17% Similarity=0.639 Sum_probs=11.2
Q ss_pred EeeeCCcEEEcccCCCCC
Q psy17633 43 YAYHRSSWLVAGKADPPA 60 (99)
Q Consensus 43 ~~~~~~~W~~~~~~e~~~ 60 (99)
|.+++|+|.....-...+
T Consensus 135 Y~w~~g~WlI~~HHSSAM 152 (156)
T COG4875 135 YSWIDGTWLIVNHHSSAM 152 (156)
T ss_pred EEecCCeEEEEecccccC
Confidence 445799998865443333
No 25
>PF14352 DUF4402: Domain of unknown function (DUF4402)
Probab=26.24 E-value=73 Score=20.47 Aligned_cols=19 Identities=11% Similarity=0.380 Sum_probs=17.0
Q ss_pred cceEEEecCCCCCCeeEEEE
Q psy17633 13 TLRVSFTGLRPDQRYAVLMD 32 (99)
Q Consensus 13 ~l~~~vsGLdp~~~Y~i~l~ 32 (99)
.-+|.|+| +|...|.|.+.
T Consensus 46 ~a~f~V~G-~~~~~v~it~p 64 (130)
T PF14352_consen 46 PAEFTVSG-EPGSNVSITLP 64 (130)
T ss_pred CEEEEEEc-CCCCEEEEEec
Confidence 67899999 99999998886
No 26
>PF00080 Sod_Cu: Copper/zinc superoxide dismutase (SODC); InterPro: IPR001424 Superoxide dismutases are ubiquitous metalloproteins that prevent damage by oxygen-mediated free radicals by catalysing the dismutation of superoxide into molecular oxygen and hydrogen peroxide []. Superoxide is a normal by-product of aerobic respiration and is produced by a number of reactions, including oxidative phosphorylation and photosynthesis. The dismutase enzymes have a very high catalytic efficiency due to the attraction of superoxide to the ions bound at the active site [, ]. There are three forms of superoxide dismutase, depending on the metal cofactor: Cu/Zn (which binds both copper and zinc), Fe and Mn types. The Fe and Mn forms are similar in their primary, secondary and tertiary structures, but are distinct from the Cu/Zn form []. Prokaryotes and protists contain Mn, Fe or both types, while most eukaryotic organisms utilise the Cu/Zn type.; GO: 0046872 metal ion binding, 0006801 superoxide metabolic process, 0055114 oxidation-reduction process; PDB: 2K4W_A 2APS_B 2WWN_B 2WWO_B 1ESO_A 2AQM_A 3F7L_A 3F7K_A 2E47_A 2E46_A ....
Probab=26.08 E-value=65 Score=21.00 Aligned_cols=24 Identities=21% Similarity=0.199 Sum_probs=17.9
Q ss_pred cceEEEecCCCCCCeeEEEEEEEcc
Q psy17633 13 TLRVSFTGLRPDQRYAVLMDIVPVD 37 (99)
Q Consensus 13 ~l~~~vsGLdp~~~Y~i~l~~~~~d 37 (99)
.+.+.|+||.|. .|.+.||-.+..
T Consensus 28 ~v~~~~~GL~~g-~~~~hIH~~g~~ 51 (142)
T PF00080_consen 28 QVTVSLNGLPPG-QHGYHIHENGDC 51 (142)
T ss_dssp EEEEEEESSSSE-EEEEEEESSSTC
T ss_pred EEEEEEECCCCC-CceEEEEecccc
Confidence 457789999775 888888876653
No 27
>PF09423 PhoD: PhoD-like phosphatase; InterPro: IPR018946 This entry contains a number of putative proteins as well as Alkaline phosphatase D which catalyses the reaction: A phosphate monoester + H(2)O = an alcohol + phosphate ; PDB: 2YEQ_B.
Probab=25.81 E-value=68 Score=25.08 Aligned_cols=20 Identities=35% Similarity=0.660 Sum_probs=13.0
Q ss_pred ceEEEecCCCCCCeeEEEEE
Q psy17633 14 LRVSFTGLRPDQRYAVLMDI 33 (99)
Q Consensus 14 l~~~vsGLdp~~~Y~i~l~~ 33 (99)
.++.|+||.|...|...+..
T Consensus 64 ~~v~v~gL~p~t~Y~Y~~~~ 83 (453)
T PF09423_consen 64 VKVDVTGLQPGTRYYYRFVV 83 (453)
T ss_dssp EEEEE-S--TT-EEEEEEEE
T ss_pred eecccCCCCCCceEEEEEEE
Confidence 57899999999999866666
No 28
>KOG1887|consensus
Probab=25.72 E-value=52 Score=28.41 Aligned_cols=40 Identities=18% Similarity=0.391 Sum_probs=28.7
Q ss_pred ceEEEecCCCCCCeeEEEEEEEc--cCcceEEeeeCCcEEEcc
Q psy17633 14 LRVSFTGLRPDQRYAVLMDIVPV--DNKRYRYAYHRSSWLVAG 54 (99)
Q Consensus 14 l~~~vsGLdp~~~Y~i~l~~~~~--d~~ryr~~~~~~~W~~~~ 54 (99)
.-|+ .|++|..+|+++--...- .+..-.++|.++.|+-..
T Consensus 715 ~~y~-~g~ep~t~yrLVSmv~~~e~~~~~~C~Aye~Nrwvs~r 756 (806)
T KOG1887|consen 715 RLYR-EGLEPNTKYRLVSMVGNHEEGEEYICFAYEPNRWVSLR 756 (806)
T ss_pred HHhh-hccCcCceeEEEEEeeeccccceEEEeeccCCcchhhH
Confidence 3455 799999999977666665 444555678899998543
No 29
>PF08294 TIM21: TIM21; InterPro: IPR013261 TIM21 interacts with the outer mitochondrial TOM complex and promotes the insertion of proteins into the inner mitochondrial membrane [].; PDB: 2CIU_A.
Probab=25.05 E-value=1.6e+02 Score=19.79 Aligned_cols=30 Identities=23% Similarity=0.494 Sum_probs=19.7
Q ss_pred cceEEEecCCCCCCeeEEEEEEEccC-cceEEe
Q psy17633 13 TLRVSFTGLRPDQRYAVLMDIVPVDN-KRYRYA 44 (99)
Q Consensus 13 ~l~~~vsGLdp~~~Y~i~l~~~~~d~-~ryr~~ 44 (99)
.++|.|.| |...=.+.+++...+. ..|+|.
T Consensus 97 ~m~F~V~G--~~~~G~V~~e~~k~~~~~~~e~~ 127 (145)
T PF08294_consen 97 RMKFYVEG--PRGKGVVHLEMVKDDGSGEYEYR 127 (145)
T ss_dssp EEEEEEE---SS-EEEEEEEEE--SS-SS-EEE
T ss_pred EEEEEEEe--CCCeEEEEEEEEECCCCCCeeEE
Confidence 47899999 8888889999998884 556654
No 30
>COG2366 Protein related to penicillin acylase [General function prediction only]
Probab=24.38 E-value=1.2e+02 Score=26.07 Aligned_cols=41 Identities=22% Similarity=0.344 Sum_probs=32.1
Q ss_pred cceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEcccC
Q psy17633 13 TLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKA 56 (99)
Q Consensus 13 ~l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~~~ 56 (99)
.+.--+++...+..+.....+.+.+..+|+| +|+|......
T Consensus 312 ~vaWg~T~~~~d~~d~Y~e~~~~~n~~~Y~~---~g~W~~~~~~ 352 (768)
T COG2366 312 YVAWGLTNTGADSQDAYAERDNPANPNQYRY---NGQWLPFEQR 352 (768)
T ss_pred ceeecccCCCCceeeEEEEEecCCCCCeeEE---CCEEeecccc
Confidence 3444566777888888888888889999998 8999986544
No 31
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=24.02 E-value=1e+02 Score=22.97 Aligned_cols=33 Identities=15% Similarity=0.168 Sum_probs=30.0
Q ss_pred CCCCCCcceEEEecCCCCCCeeEEEEEEEccCc
Q psy17633 7 FLRMFPTLRVSFTGLRPDQRYAVLMDIVPVDNK 39 (99)
Q Consensus 7 gRrmFP~l~~~vsGLdp~~~Y~i~l~~~~~d~~ 39 (99)
.|..-|.+.++|.|+-|.......|.|.+.++.
T Consensus 160 ~RdVtp~~klRV~d~~~~~~~~~~LTIWrPted 192 (251)
T cd04494 160 KRDVTPVWKLRVTDYRSKPEKSGLLSIWRPTED 192 (251)
T ss_pred CCcceeEEEEEEeecccCCCceEEEEEeCCCHH
Confidence 488999999999999999999999999988764
No 32
>PF04326 AAA_4: Divergent AAA domain; InterPro: IPR007421 AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate. This entry is related to IPR003959 from INTERPRO, and presumably has the same function (ATP-binding). A number of the archaeal members of this group are annotated as ATP-dependent DNA helicases 3.6.1 from EC.; GO: 0005524 ATP binding; PDB: 2KYY_A 3LMM_D.
Probab=23.93 E-value=1.3e+02 Score=18.44 Aligned_cols=48 Identities=13% Similarity=0.380 Sum_probs=27.8
Q ss_pred CCCCCcceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEccc
Q psy17633 8 LRMFPTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGK 55 (99)
Q Consensus 8 RrmFP~l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~~ 55 (99)
+.+.|.+.+.+.-+.=+..|.+.|++.+.+...+.......-|.+.+.
T Consensus 69 ~~~~p~~~~~~~~~~~~~~~v~~I~V~~~~~~~~~~~~~~~~y~R~g~ 116 (122)
T PF04326_consen 69 DYISPPINPDIEEVEVEGKYVLVIEVPPSSRKPYYFNNDGRIYIRVGS 116 (122)
T ss_dssp HCCSS--EEEEEEEECTTEEEEEEEE---SSTT--BSTTS-SEEESSS
T ss_pred HhCCCCceeEEEEEEECCCEEEEEEECCCCCCCceEccCCEEEEEeCC
Confidence 457788888888887788899999999988776322212334555443
No 33
>PF13620 CarboxypepD_reg: Carboxypeptidase regulatory-like domain; PDB: 3MN8_D 3P0D_I 3KCP_A 2B59_B 1UWY_A 1H8L_A 1QMU_A 2NSM_A.
Probab=22.19 E-value=63 Score=18.45 Aligned_cols=16 Identities=44% Similarity=0.825 Sum_probs=9.6
Q ss_pred eEEEecCCCCCCeeEEE
Q psy17633 15 RVSFTGLRPDQRYAVLM 31 (99)
Q Consensus 15 ~~~vsGLdp~~~Y~i~l 31 (99)
.|.+.+|.| ..|.|.+
T Consensus 39 ~f~~~~l~~-g~Y~l~v 54 (82)
T PF13620_consen 39 RFSFEGLPP-GTYTLRV 54 (82)
T ss_dssp EEEEEEE-S-EEEEEEE
T ss_pred eEEEEccCC-EeEEEEE
Confidence 466777777 5566554
No 34
>TIGR03511 GldH_lipo gliding motility-associated lipoprotein GldH. Members of this protein family are predicted lipoproteins, exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). Members include GldH, a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family may have gliding motility.
Probab=22.02 E-value=1.7e+02 Score=20.06 Aligned_cols=37 Identities=19% Similarity=0.266 Sum_probs=28.5
Q ss_pred cceEEEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEcc
Q psy17633 13 TLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAG 54 (99)
Q Consensus 13 ~l~~~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~ 54 (99)
.|.|.|.=.|+...|.+.+.+.-..+..| .+=|....
T Consensus 43 ~l~F~~~~~d~~~~y~l~l~lR~n~~Ypy-----~nl~l~~~ 79 (156)
T TIGR03511 43 TLDFEIPITDYTASYRLFLLIRNDNRYPY-----RNLWALIH 79 (156)
T ss_pred cEEEEEeecCCCCcEEEEEEEEcCCCCcc-----cCeEEEEE
Confidence 47899999999999999999988776444 34565543
No 35
>PF08547 CIA30: Complex I intermediate-associated protein 30 (CIA30); InterPro: IPR013857 Mitochondrial complex I intermediate-associated protein 30 (CIA30) is present in human and mouse, and also in Schizosaccharomyces pombe (Fission yeast) which does not contain the NADH dehydrogenase component of complex I, or many of the other essential subunits. This means it is possible that it is not directly involved in oxidative phosphorylation [, ].
Probab=21.46 E-value=1.2e+02 Score=20.04 Aligned_cols=65 Identities=12% Similarity=0.088 Sum_probs=35.9
Q ss_pred EEecCCCCCCeeEEEEEEEccCcceEEeeeCCcEEEcccCCCCCCCceEEcCCCCCchHHHhhCCceeeeEeeecc
Q psy17633 17 SFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPPAPLRLYMHPDSPFTGDQLRKQVVSFEKVKLTNN 92 (99)
Q Consensus 17 ~vsGLdp~~~Y~i~l~~~~~d~~ryr~~~~~~~W~~~~~~e~~~~~~~~~Hp~~~~tG~~WM~~~v~F~~lklTN~ 92 (99)
...++|-...-.|.|++. .|..+|+.......+ .+...|.+.=-...|+ |..--|-|+++..|..
T Consensus 59 ~~~~~dls~y~~l~l~vr-gdGr~Y~~~l~~~~~---------~~~~~y~~~f~t~~~~-w~~v~iPFs~F~~~~r 123 (157)
T PF08547_consen 59 FPSPLDLSGYDGLELRVR-GDGRTYKVNLRTDND---------EPSDSYQARFQTPPGE-WQTVRIPFSDFVPTFR 123 (157)
T ss_pred CCCcCCCCCCcEEEEEEE-cCCceEEEEEEeCCC---------CCCceEEEEEeccCCc-cEEEEEEHHHCceeeC
Confidence 345677666667777776 777777765333322 2222333322222333 7777777777776644
No 36
>KOG1230|consensus
Probab=21.28 E-value=1.2e+02 Score=24.63 Aligned_cols=59 Identities=15% Similarity=0.342 Sum_probs=35.8
Q ss_pred ceEEeeeCCcEEEcccCCCCC---CCceEEcCCCCC--c-h--------------HHHhhCCc--eeeeEeeecccccCC
Q psy17633 40 RYRYAYHRSSWLVAGKADPPA---PLRLYMHPDSPF--T-G--------------DQLRKQVV--SFEKVKLTNNEMDKN 97 (99)
Q Consensus 40 ryr~~~~~~~W~~~~~~e~~~---~~~~~~Hp~~~~--t-G--------------~~WM~~~v--~F~~lklTN~~~~~~ 97 (99)
-|.|+-.+..|.......++. ..++++||++.. . | -.||-.-+ .|.+|.+++.+....
T Consensus 100 Ly~Yn~k~~eWkk~~spn~P~pRsshq~va~~s~~l~~fGGEfaSPnq~qF~HYkD~W~fd~~trkweql~~~g~PS~RS 179 (521)
T KOG1230|consen 100 LYSYNTKKNEWKKVVSPNAPPPRSSHQAVAVPSNILWLFGGEFASPNQEQFHHYKDLWLFDLKTRKWEQLEFGGGPSPRS 179 (521)
T ss_pred eeEEeccccceeEeccCCCcCCCccceeEEeccCeEEEeccccCCcchhhhhhhhheeeeeeccchheeeccCCCCCCCc
Confidence 367766788998765444433 346888886521 1 1 23554433 277788888777766
Q ss_pred C
Q psy17633 98 G 98 (99)
Q Consensus 98 ~ 98 (99)
|
T Consensus 180 G 180 (521)
T KOG1230|consen 180 G 180 (521)
T ss_pred c
Confidence 6
No 37
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=20.90 E-value=1.1e+02 Score=17.89 Aligned_cols=19 Identities=21% Similarity=0.511 Sum_probs=14.9
Q ss_pred EEEEEccCcceEEeeeCCc
Q psy17633 31 MDIVPVDNKRYRYAYHRSS 49 (99)
Q Consensus 31 l~~~~~d~~ryr~~~~~~~ 49 (99)
=-++..|...|.|.|.+|+
T Consensus 38 GGvV~eDgR~y~F~Y~~G~ 56 (62)
T PF15513_consen 38 GGVVMEDGRHYTFVYENGQ 56 (62)
T ss_pred ccEEEeCCCEEEEEEeCCc
Confidence 3467788889999888885
Done!