Query psy16369
Match_columns 101
No_of_seqs 108 out of 181
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 19:32:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16369.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16369hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1233|consensus 99.5 1.8E-15 3.9E-20 128.2 1.9 72 28-100 404-475 (613)
2 PF02913 FAD-oxidase_C: FAD li 95.6 0.0075 1.6E-07 43.4 2.0 62 37-98 53-121 (248)
3 TIGR00387 glcD glycolate oxida 95.3 0.012 2.5E-07 48.2 2.4 59 38-96 226-289 (413)
4 PRK11230 glycolate oxidase sub 89.6 0.31 6.6E-06 41.5 2.8 59 38-96 283-346 (499)
5 PLN02805 D-lactate dehydrogena 74.0 5.6 0.00012 34.7 4.5 32 43-74 363-394 (555)
6 PF12738 PTCB-BRCT: twin BRCT 51.4 10 0.00023 22.6 1.5 29 44-78 2-30 (63)
7 smart00120 HX Hemopexin-like r 48.3 31 0.00067 18.9 3.0 14 8-21 13-26 (45)
8 PF05152 DUF705: Protein of un 47.2 15 0.00032 30.4 2.2 53 24-82 144-201 (297)
9 PF00045 Hemopexin: Hemopexin; 45.8 31 0.00067 19.6 2.8 15 7-21 12-26 (45)
10 PF11308 GHL1-3: Glycosyl hydr 39.7 42 0.00092 27.4 3.7 79 9-87 88-178 (307)
11 PF08496 Peptidase_S49_N: Pept 36.5 67 0.0014 23.8 4.0 30 41-70 96-127 (155)
12 PF10986 DUF2796: Protein of u 36.2 72 0.0016 23.9 4.2 29 5-54 10-38 (168)
13 CHL00123 rps6 ribosomal protei 35.6 80 0.0017 21.3 4.0 34 43-76 9-42 (97)
14 PF04832 SOUL: SOUL heme-bindi 33.7 43 0.00093 24.2 2.6 51 41-96 112-164 (176)
15 PF06230 DUF1009: Protein of u 31.5 31 0.00066 27.0 1.6 46 43-94 124-170 (214)
16 PF01250 Ribosomal_S6: Ribosom 31.2 92 0.002 20.1 3.6 36 44-79 5-40 (92)
17 PRK04804 minC septum formation 30.6 52 0.0011 25.2 2.7 70 8-78 6-79 (221)
18 PF05939 Phage_min_tail: Phage 29.9 1.1E+02 0.0023 21.0 4.0 42 30-76 29-70 (109)
19 TIGR01752 flav_long flavodoxin 29.6 2.1E+02 0.0045 20.3 5.6 70 13-83 46-122 (167)
20 PF01766 Birna_VP2: Birnavirus 29.3 8.7 0.00019 33.4 -1.9 63 33-95 106-173 (441)
21 PF07045 DUF1330: Protein of u 28.3 67 0.0015 19.7 2.5 23 55-77 2-24 (65)
22 PF13368 Toprim_C_rpt: Topoiso 27.4 21 0.00045 22.2 0.0 12 85-97 10-21 (61)
23 PRK10569 NAD(P)H-dependent FMN 26.7 1.1E+02 0.0023 22.8 3.7 56 20-76 78-133 (191)
24 PRK00339 minC septum formation 26.4 82 0.0018 24.8 3.2 69 6-76 11-86 (249)
25 PRK00453 rpsF 30S ribosomal pr 26.1 1.5E+02 0.0033 19.9 4.1 35 44-78 6-40 (108)
26 PRK07308 flavodoxin; Validated 26.0 2E+02 0.0043 19.7 4.8 53 25-78 66-119 (146)
27 PF03358 FMN_red: NADPH-depend 24.1 92 0.002 21.1 2.8 57 21-78 83-142 (152)
28 cd06522 GH25_AtlA-like AtlA is 24.0 1.3E+02 0.0027 22.1 3.7 62 27-89 76-139 (192)
29 PF13691 Lactamase_B_4: tRNase 23.9 1E+02 0.0022 19.7 2.7 32 4-35 13-56 (63)
30 PF08804 gp32: gp32 DNA bindin 23.6 98 0.0021 21.7 2.8 18 5-22 35-53 (94)
31 TIGR01753 flav_short flavodoxi 22.6 1.6E+02 0.0034 19.4 3.7 52 26-78 65-116 (140)
32 cd07262 Glo_EDI_BRP_like_19 Th 22.6 1.3E+02 0.0028 19.1 3.1 51 43-97 63-114 (123)
33 COG1647 Esterase/lipase [Gener 22.3 1.1E+02 0.0023 24.9 3.2 24 42-65 16-39 (243)
34 PF13740 ACT_6: ACT domain; PD 22.0 1.5E+02 0.0032 18.5 3.2 31 42-72 40-70 (76)
35 PF05651 Diacid_rec: Putative 21.9 2.1E+02 0.0045 20.5 4.4 26 42-67 81-106 (135)
36 TIGR00166 S6 ribosomal protein 20.8 1.7E+02 0.0036 19.1 3.4 33 44-77 5-37 (93)
37 PRK02551 flavoprotein NrdI; Pr 20.7 1.8E+02 0.0038 21.5 3.9 20 52-71 134-153 (154)
38 PF14740 DUF4471: Domain of un 20.2 81 0.0018 25.7 2.1 22 54-75 263-284 (289)
39 PF00533 BRCT: BRCA1 C Terminu 20.0 1.1E+02 0.0024 17.9 2.3 17 60-76 20-36 (78)
No 1
>KOG1233|consensus
Probab=99.54 E-value=1.8e-15 Score=128.24 Aligned_cols=72 Identities=36% Similarity=0.523 Sum_probs=68.0
Q ss_pred ccchhccccCCCCCCceEEEEeecCChHHHHHHHHHHHHHHHhcCCccCCcccccccccccccccccCCCCCC
Q psy16369 28 HYPLTDMRENEKPGIDSFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPAGETNGMRGYMLTFVIAYIRIVPML 100 (101)
Q Consensus 28 ~~~l~~~~~~~~~~~~CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~lG~~~G~~W~~~RF~~PYLRD~lL~ 100 (101)
|.|+|..++ |++++.|.+++.|||+.++|+++++++++|+.+++|+++|+++|+++|.++|+++||||+.|.
T Consensus 404 k~YiTswKG-fd~nqicaATllfEGdre~V~qhE~~~y~iAekF~G~~aG~~NGqrGY~LTfvIAYiRDlgl~ 475 (613)
T KOG1233|consen 404 KMYITSWKG-FDVNQICAATLLFEGDREEVDQHEERLYKIAEKFHGVVAGAENGQRGYRLTFVIAYIRDLGLN 475 (613)
T ss_pred hheeecccC-cCHhhhhhhhheecccHHHHHHHHHHHHHHHHHhCCccccccccccceEEEEeHHHHHhhccc
Confidence 457777666 999999999999999999999999999999999999999999999999999999999999885
No 2
>PF02913 FAD-oxidase_C: FAD linked oxidases, C-terminal domain; InterPro: IPR004113 Some oxygen-dependent oxidoreductases are flavoproteins that contain a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. The region around the histidine that binds the FAD group is conserved in these enzymes (see IPR006093 from INTERPRO).; GO: 0003824 catalytic activity, 0050660 flavin adenine dinucleotide binding; PDB: 1WVE_B 1DII_B 1WVF_A 1DIQ_A 2UUU_B 2UUV_A 1W1M_A 1E8H_B 1E0Y_B 1DZN_B ....
Probab=95.64 E-value=0.0075 Score=43.39 Aligned_cols=62 Identities=18% Similarity=0.212 Sum_probs=45.8
Q ss_pred CCCCCCceEEEEeecCChHH-HHHHHH-HHHHHHHhcCCcc-----CCcccccccccccccccccCCCC
Q psy16369 37 NEKPGIDSFGKPDSHGDPED-VKKNQA-KIYSVALKFGGIP-----AGETNGMRGYMLTFVIAYIRIVP 98 (101)
Q Consensus 37 ~~~~~~~CL~vlgFEGt~~~-V~~r~~-~~~~I~~~~GG~~-----lG~~~G~~W~~~RF~~PYLRD~l 98 (101)
++.....|++++.|||++++ ++.+.+ .+.++++++++.. -.++..+-|..-++..|++++..
T Consensus 53 ~~~~~~~~~llv~~~g~~~~~~~~~~~~~i~~~~~~~~~~~~~~a~~~~~~~~~W~~R~~~~~~~~~~~ 121 (248)
T PF02913_consen 53 PLPPEGGAVLLVEFEGSDEEAVEEQLEAEIEEICKKYGGEDVVIADDEEEQERLWAIRRAIMPYLRDAA 121 (248)
T ss_dssp TSSTTTSEEEEEECCCHHHCCHHHHHHHHHHHHHCTCTCCEEEEEHCHHCTSTHHHHHHHHCCGGGCSH
T ss_pred CccCCcccEEEEEECCCcHHHHHHHHHHHHHHHHhhcCCceeEEeCCHHHHHhhhhhhhhhcccccccc
Confidence 46777899999999999854 555555 6778888888775 12344677888888888888764
No 3
>TIGR00387 glcD glycolate oxidase, subunit GlcD. This protein, the glycolate oxidase GlcD subunit, is similar in sequence to that of several D-lactate dehydrogenases, including that of E. coli. The glycolate oxidase has been found to have some D-lactate dehydrogenase activity.
Probab=95.34 E-value=0.012 Score=48.18 Aligned_cols=59 Identities=14% Similarity=0.051 Sum_probs=47.0
Q ss_pred CCCCCceEEEEeecCChHHHHHHHHHHHHHHHhcCCccC----C-cccccccccccccccccCC
Q psy16369 38 EKPGIDSFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPA----G-ETNGMRGYMLTFVIAYIRI 96 (101)
Q Consensus 38 ~~~~~~CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~l----G-~~~G~~W~~~RF~~PYLRD 96 (101)
++....|++++.|||.+++++.+.+++.++++++|+... + ++..+-|...++..|++++
T Consensus 226 ~p~~~~~~l~v~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~r~~~~~~~~~ 289 (413)
T TIGR00387 226 LPKDAGAILLVEIDGVHEAVERDEEKIEQICRKNGAVDVQIAQDEEERALLWAGRRNAFKAASK 289 (413)
T ss_pred CCCCCceEEEEEecCCcHHHHHHHHHHHHHHHhCCCceEEEeCCHHHHHHHHHHHHHhHHHHHh
Confidence 444567999999999999999999999999999988643 1 2455668887888888875
No 4
>PRK11230 glycolate oxidase subunit GlcD; Provisional
Probab=89.55 E-value=0.31 Score=41.46 Aligned_cols=59 Identities=10% Similarity=-0.030 Sum_probs=42.1
Q ss_pred CCCCCceEEEEeecCChHHHHHHHHHHHHHHHhcCCccCCc-----ccccccccccccccccCC
Q psy16369 38 EKPGIDSFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPAGE-----TNGMRGYMLTFVIAYIRI 96 (101)
Q Consensus 38 ~~~~~~CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~lG~-----~~G~~W~~~RF~~PYLRD 96 (101)
+..+..+++++.++|++++|+.+.+++.++++++|+....- +..+.|..-+...|+++.
T Consensus 283 ~p~~~~~~ll~e~~g~~~~v~~~~~~l~~~~~~~g~~~~~~a~~~~~~~~~W~~R~~~~~~~~~ 346 (499)
T PRK11230 283 YPVDAEAILLCELDGVESDVQEDCERVNDILLKAGATDVRLAQDEAERVRFWAGRKNAFPAVGR 346 (499)
T ss_pred CCCCcceEEEEEecCCchHHHHHHHHHHHHHHhcCCceEEEeCCHHHHHHHHHHHHhhHHHHHh
Confidence 44455689999999999999999999999999999754421 223456553344566654
No 5
>PLN02805 D-lactate dehydrogenase [cytochrome]
Probab=73.99 E-value=5.6 Score=34.65 Aligned_cols=32 Identities=13% Similarity=0.043 Sum_probs=29.4
Q ss_pred ceEEEEeecCChHHHHHHHHHHHHHHHhcCCc
Q psy16369 43 DSFGKPDSHGDPEDVKKNQAKIYSVALKFGGI 74 (101)
Q Consensus 43 ~CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~ 74 (101)
.|++++.|+|++++++.+.+.+.+|++++|+.
T Consensus 363 ~~~Ll~e~~g~~~~~~~~~~~~~~i~~~~g~~ 394 (555)
T PLN02805 363 APTLMFEFIGTEAYAREQTLIVQKIASKHNGS 394 (555)
T ss_pred ceEEEEEEecCcHHHHHHHHHHHHHHHhCCCc
Confidence 59999999999999999999999999999985
No 6
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=51.45 E-value=10 Score=22.65 Aligned_cols=29 Identities=10% Similarity=0.169 Sum_probs=20.8
Q ss_pred eEEEEeecCChHHHHHHHHHHHHHHHhcCCccCCc
Q psy16369 44 SFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPAGE 78 (101)
Q Consensus 44 CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~lG~ 78 (101)
++++.||++.+ +..+.+++..+||.....
T Consensus 2 ~i~~sg~~~~~------~~~l~~~i~~~Gg~~~~~ 30 (63)
T PF12738_consen 2 VICFSGFSGKE------RSQLRKLIEALGGKYSKD 30 (63)
T ss_dssp EEEEEEB-TTT------CCHHHHHHHCTT-EEESS
T ss_pred EEEECCCCHHH------HHHHHHHHHHCCCEEecc
Confidence 56788898754 677888999999987643
No 7
>smart00120 HX Hemopexin-like repeats. Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metalloproteinases (TIMPs).
Probab=48.29 E-value=31 Score=18.93 Aligned_cols=14 Identities=36% Similarity=0.698 Sum_probs=11.1
Q ss_pred EEEecceEEEEecc
Q psy16369 8 VFFKGNRYLVETST 21 (101)
Q Consensus 8 ~~~~~~~~~~~~~~ 21 (101)
.|||||+|..=...
T Consensus 13 yfFkg~~yw~~~~~ 26 (45)
T smart00120 13 YFFKGDKYWRFDPK 26 (45)
T ss_pred EEEeCCEEEEEcCC
Confidence 79999999876544
No 8
>PF05152 DUF705: Protein of unknown function (DUF705); InterPro: IPR007827 This family contains uncharacterised baculoviral proteins.
Probab=47.23 E-value=15 Score=30.42 Aligned_cols=53 Identities=23% Similarity=0.194 Sum_probs=39.0
Q ss_pred ccccccchhccccCCCCCCceEEEEeecCChHHHHHHHHHHHHHHHh-----cCCccCCccccc
Q psy16369 24 SRPRHYPLTDMRENEKPGIDSFGKPDSHGDPEDVKKNQAKIYSVALK-----FGGIPAGETNGM 82 (101)
Q Consensus 24 ~~~~~~~l~~~~~~~~~~~~CL~vlgFEGt~~~V~~r~~~~~~I~~~-----~GG~~lG~~~G~ 82 (101)
...+...|.++++ .+|+++++--|.+++|.+..+++. |..- .||..+|+.+..
T Consensus 144 ~~~v~~sL~~Lk~-----~g~vLvLWSyG~~eHV~~sl~~~~-L~~~Fd~ii~~G~~~~~~~~~ 201 (297)
T PF05152_consen 144 DPAVYDSLRELKE-----QGCVLVLWSYGNREHVRHSLKELK-LEGYFDIIICGGNKAGEYNSR 201 (297)
T ss_pred ChHHHHHHHHHHH-----cCCEEEEecCCCHHHHHHHHHHhC-CccccEEEEeCCccCCcCCcc
Confidence 3456788999999 999999999999999999888763 2221 255555555544
No 9
>PF00045 Hemopexin: Hemopexin; InterPro: IPR018487 Hemopexin (3.2.1.35 from EC) is a serum glycoprotein that binds haem and transports it to the liver for breakdown and iron recovery, after which the free hemopexin returns to the circulation []. Hemopexin prevents haem-mediated oxidative stress. Structurally hemopexin consists of two similar halves of approximately two hundred amino acid residues connected by a histidine-rich hinge region. Each half is itself formed by the repetition of a basic unit of some 35 to 45 residues. Hemopexin-like domains have been found in two other types of proteins, vitronectin [], a cell adhesion and spreading factor found in plasma and tissues, and matrixins MMP-1, MMP-2, MMP-3, MMP-9, MMP-10, MMP-11, MMP-12, MMP-14, MMP-15 and MMP-16, members of the matrix metalloproteinase family that cleave extracellular matrix constituents []. These zinc endopeptidases, which belong to MEROPS peptidase subfamily M10A, have a single hemopexin-like domain in their C-terminal section. It is suggested that the hemopexin domain facilitates binding to a variety of molecules and proteins, for example the HX repeats of some matrixins bind tissue inhibitor of metallopeptidases (TIMPs). This entry represents the repeat found in hempoxein and related domains.; PDB: 1SU3_B 2CLT_B 3V6N_B 3C7X_A 1GXD_A 1RTG_A 1CK7_A 1GEN_A 1ITV_A 2JXY_A ....
Probab=45.80 E-value=31 Score=19.55 Aligned_cols=15 Identities=40% Similarity=0.698 Sum_probs=11.4
Q ss_pred eEEEecceEEEEecc
Q psy16369 7 NVFFKGNRYLVETST 21 (101)
Q Consensus 7 ~~~~~~~~~~~~~~~ 21 (101)
-.|||||+|..=...
T Consensus 12 ~yfFkg~~ywr~~~~ 26 (45)
T PF00045_consen 12 TYFFKGNQYWRFDES 26 (45)
T ss_dssp EEEEETTEEEEEETT
T ss_pred EEEEECCEEEEEcCc
Confidence 368999999875555
No 10
>PF11308 GHL1-3: Glycosyl hydrolases related to GH101 family, GHL1-GHL3; InterPro: IPR021459 Some members in this family of proteins with unknown function are annotated as lipoproteins however this cannot be confirmed. Currently no function is known.
Probab=39.68 E-value=42 Score=27.38 Aligned_cols=79 Identities=11% Similarity=-0.055 Sum_probs=49.5
Q ss_pred EE-ecceEEEEeccccccccccchhccccCCCCCCceEEEEe----ec-------CChHHHHHHHHHHHHHHHhcCCccC
Q psy16369 9 FF-KGNRYLVETSTSYSRPRHYPLTDMRENEKPGIDSFGKPD----SH-------GDPEDVKKNQAKIYSVALKFGGIPA 76 (101)
Q Consensus 9 ~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~CL~vlg----FE-------Gt~~~V~~r~~~~~~I~~~~GG~~l 76 (101)
|. .+++|+.-+.+-...-+|.=++.|.++...+..-|-+.+ || -++++..+.+.+..+.+++..|+++
T Consensus 88 f~w~~g~~~~~~p~~~~~~v~~r~~~i~~~~~~ns~FlDv~~~~~~~~dy~~~h~~t~~~~~~~r~~~~~~l~~~~~~v~ 167 (307)
T PF11308_consen 88 FRWGGGRYLNVCPTCALPYVKRRVEEILKGIGFNSWFLDVDAAGEPYEDYNPEHPMTRAQDLAARLARMQYLREELGLVL 167 (307)
T ss_pred eecCCcceeccCcccccHHHHHHHHHHHHhCCCCeEEEeccccccccccCCCCCCCCHHHHHHHHHHHHHHHHhcCceee
Confidence 44 677887755555555566667777775555542222222 22 2344545555555667777889999
Q ss_pred Ccccccccccc
Q psy16369 77 GETNGMRGYML 87 (101)
Q Consensus 77 G~~~G~~W~~~ 87 (101)
|++.|..|...
T Consensus 168 GSE~Gnd~a~~ 178 (307)
T PF11308_consen 168 GSEDGNDWAAP 178 (307)
T ss_pred ccCchhhhhcc
Confidence 99999999764
No 11
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=36.51 E-value=67 Score=23.83 Aligned_cols=30 Identities=17% Similarity=0.091 Sum_probs=26.5
Q ss_pred CCceEEEEeecCCh--HHHHHHHHHHHHHHHh
Q psy16369 41 GIDSFGKPDSHGDP--EDVKKNQAKIYSVALK 70 (101)
Q Consensus 41 ~~~CL~vlgFEGt~--~~V~~r~~~~~~I~~~ 70 (101)
..+|+-|+-|.|+- .+|+.-|++|.+|+.-
T Consensus 96 ~~~r~~VldF~Gdi~A~~v~~LReeisail~~ 127 (155)
T PF08496_consen 96 PKPRLFVLDFKGDIKASEVESLREEISAILSV 127 (155)
T ss_pred CCCeEEEEecCCCccHHHHHHHHHHHHHHHHh
Confidence 57999999999984 8899999999999864
No 12
>PF10986 DUF2796: Protein of unknown function (DUF2796); InterPro: IPR021253 This bacterial family of proteins has no known function.
Probab=36.25 E-value=72 Score=23.87 Aligned_cols=29 Identities=21% Similarity=0.204 Sum_probs=22.7
Q ss_pred eeeEEEecceEEEEeccccccccccchhccccCCCCCCceEEEEeecCCh
Q psy16369 5 VVNVFFKGNRYLVETSTSYSRPRHYPLTDMRENEKPGIDSFGKPDSHGDP 54 (101)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~CL~vlgFEGt~ 54 (101)
-+||-+.||..++|-. .+..-|+|||-.+
T Consensus 10 el~ia~dg~~l~iel~---------------------sP~~dlvGFEhap 38 (168)
T PF10986_consen 10 ELNIAQDGNTLLIELE---------------------SPGADLVGFEHAP 38 (168)
T ss_pred EEEEEEcCCEEEEEEE---------------------CCcccccccccCC
Confidence 3689999999999853 3456788999876
No 13
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=35.61 E-value=80 Score=21.27 Aligned_cols=34 Identities=12% Similarity=-0.002 Sum_probs=29.3
Q ss_pred ceEEEEeecCChHHHHHHHHHHHHHHHhcCCccC
Q psy16369 43 DSFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPA 76 (101)
Q Consensus 43 ~CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~l 76 (101)
.|+.|+-=+-++++++.-.+.+.++++++||...
T Consensus 9 E~~~Il~p~l~e~~~~~~~~~~~~~i~~~gg~i~ 42 (97)
T CHL00123 9 ETMYLLKPDLNEEELLKWIENYKKLLRKRGAKNI 42 (97)
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEE
Confidence 4677777777789999999999999999999865
No 14
>PF04832 SOUL: SOUL heme-binding protein; InterPro: IPR006917 This family represents a group of putative haem-binding proteins []. It includes archaeal and bacterial homologues.; PDB: 2HVA_A 2GOV_A 4A1M_A 3R85_E 2YC9_A 3R8K_B 3R8J_B.
Probab=33.72 E-value=43 Score=24.19 Aligned_cols=51 Identities=12% Similarity=0.062 Sum_probs=34.8
Q ss_pred CCceEEEEeecCCh--HHHHHHHHHHHHHHHhcCCccCCcccccccccccccccccCC
Q psy16369 41 GIDSFGKPDSHGDP--EDVKKNQAKIYSVALKFGGIPAGETNGMRGYMLTFVIAYIRI 96 (101)
Q Consensus 41 ~~~CL~vlgFEGt~--~~V~~r~~~~~~I~~~~GG~~lG~~~G~~W~~~RF~~PYLRD 96 (101)
...+++++.|.|.. +.+..+.+++.+.|.+.| +. ....++-..|+.|+.+.
T Consensus 112 p~~~~~v~~F~G~~~~~~~~~~~~~L~~~L~~~g-~~----~~~~~~~a~Yd~P~~~~ 164 (176)
T PF04832_consen 112 PERTVYVRRFSGFATDEKIQEEAKKLRAALKKDG-LK----DKGYYYVAGYDPPFTPP 164 (176)
T ss_dssp -SEEEEEEEECS--SHHHHHHHHHHHHHHCCCTT-HH----CCCEEEEEESSSS-SSS
T ss_pred cCcEEEEEEECCcCCHHHHHHHHHHHHHHHHHcC-CC----cCCCeEEEEcCCCCCCc
Confidence 34889999999975 557777777777777666 22 45568888999985443
No 15
>PF06230 DUF1009: Protein of unknown function (DUF1009); InterPro: IPR010415 This is a family of uncharacterised bacterial proteins.
Probab=31.47 E-value=31 Score=27.02 Aligned_cols=46 Identities=15% Similarity=0.144 Sum_probs=26.6
Q ss_pred ceEEEEeecCChHHHHHHHHHHHHHHH-hcCCccCCccccccccccccccccc
Q psy16369 43 DSFGKPDSHGDPEDVKKNQAKIYSVAL-KFGGIPAGETNGMRGYMLTFVIAYI 94 (101)
Q Consensus 43 ~CL~vlgFEGt~~~V~~r~~~~~~I~~-~~GG~~lG~~~G~~W~~~RF~~PYL 94 (101)
.|++|=+.|||++-.+ ++.++.. ..||+.. +..+..++.||+.|=+
T Consensus 124 ~VlAVEa~EGTD~~i~----R~~~l~~~~~~~Vlv--K~~Kp~QD~R~DlPtI 170 (214)
T PF06230_consen 124 RVLAVEAIEGTDAMIR----RAGELRGKGKGGVLV--KVPKPGQDLRFDLPTI 170 (214)
T ss_pred EEEEEeccccHHHHHH----HHHHhcCCCCCEEEE--EccCCCCccccccccc
Confidence 5677778888765533 2333333 3445443 2333446899999953
No 16
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=31.22 E-value=92 Score=20.08 Aligned_cols=36 Identities=17% Similarity=0.119 Sum_probs=27.7
Q ss_pred eEEEEeecCChHHHHHHHHHHHHHHHhcCCccCCcc
Q psy16369 44 SFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPAGET 79 (101)
Q Consensus 44 CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~lG~~ 79 (101)
++.|+-=+-++++++...+.+.+++.++||.....+
T Consensus 5 ~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~ 40 (92)
T PF01250_consen 5 LMFILRPDLSEEEIKKLIERVKKIIEKNGGVVRSVE 40 (92)
T ss_dssp EEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEE
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEE
Confidence 445555556678999999999999999999986543
No 17
>PRK04804 minC septum formation inhibitor; Reviewed
Probab=30.58 E-value=52 Score=25.21 Aligned_cols=70 Identities=9% Similarity=-0.061 Sum_probs=42.7
Q ss_pred EEEecceEEEEeccccccccccchhccccCCCCCC----ceEEEEeecCChHHHHHHHHHHHHHHHhcCCccCCc
Q psy16369 8 VFFKGNRYLVETSTSYSRPRHYPLTDMRENEKPGI----DSFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPAGE 78 (101)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~----~CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~lG~ 78 (101)
+-|||+++-+-.-...+.++...++.+++-+.... +.-+++-+++-.. .......+.++++.+|-...|-
T Consensus 6 v~iKg~~~~l~~l~~~~~~~~~l~~~L~~kl~~a~~Ff~~~~vvld~~~~~~-~~~~~~~L~~~l~~~gl~~~~v 79 (221)
T PRK04804 6 LELKGSSFTLSVLHLNSSDLAAVAAELDEKLAQAPQFFAGAPLVVNLSAIQD-GDIDFVALKELLESRQLIIVGI 79 (221)
T ss_pred EEEEcCcccEEEEEcCCCCHHHHHHHHHHHHHhChhhhCCCEEEEEecCcCC-CHHHHHHHHHHHHHCCCEEEEE
Confidence 56899988655544444455555555444333332 4456777776442 2245677889999999887643
No 18
>PF05939 Phage_min_tail: Phage minor tail protein; InterPro: IPR010265 This entry is represented by Bacteriophage lambda, GpM, the minor tail protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of a series of phage minor tail proteins and related sequences from several bacterial species.
Probab=29.90 E-value=1.1e+02 Score=21.04 Aligned_cols=42 Identities=12% Similarity=0.207 Sum_probs=28.4
Q ss_pred chhccccCCCCCCceEEEEeecCChHHHHHHHHHHHHHHHhcCCccC
Q psy16369 30 PLTDMRENEKPGIDSFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPA 76 (101)
Q Consensus 30 ~l~~~~~~~~~~~~CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~l 76 (101)
|=++...|++.......+. |.|..+++.. |.+-|.+|+|+..
T Consensus 29 YeQr~~~GiN~~~~~~~lt-f~~~~~~~~~----I~~FL~~h~G~~s 70 (109)
T PF05939_consen 29 YEQRAPDGINNKLRSWSLT-FTGTEAEIRA----IEAFLDRHGGVKS 70 (109)
T ss_pred hhhhhhhhccccccEEEEE-EEECHHHHHH----HHHHHHHCCCceE
Confidence 3455566677766555544 8887755443 8999999999643
No 19
>TIGR01752 flav_long flavodoxin, long chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in E. coli.
Probab=29.59 E-value=2.1e+02 Score=20.34 Aligned_cols=70 Identities=11% Similarity=-0.044 Sum_probs=43.1
Q ss_pred ceEEEEeccccc----cccccchhccccCCCCCCceEEEEeecCC---hHHHHHHHHHHHHHHHhcCCccCCcccccc
Q psy16369 13 NRYLVETSTSYS----RPRHYPLTDMRENEKPGIDSFGKPDSHGD---PEDVKKNQAKIYSVALKFGGIPAGETNGMR 83 (101)
Q Consensus 13 ~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~CL~vlgFEGt---~~~V~~r~~~~~~I~~~~GG~~lG~~~G~~ 83 (101)
...++=++|-.. ..++.|++.+.+ -+.....++++|.=+. .+.--.-.+.+.+++++.|+..+|+-+-+-
T Consensus 46 d~ii~gspty~~g~~p~~~~~fl~~l~~-~~l~gk~v~~fg~g~~~~y~~~f~~a~~~l~~~l~~~G~~~ig~~~~~g 122 (167)
T TIGR01752 46 DKLILGTPTWGVGELQEDWEDFLPTLEE-LDFTGKTVALFGLGDQEGYSETFCDGMGILYDKIKARGAKVVGFWPTDG 122 (167)
T ss_pred CEEEEEecCCCCCcCcHHHHHHHHHhhc-CCCCCCEEEEEecCCCCcccHHHHHHHHHHHHHHHHcCCeEEceecCCC
Confidence 344555555322 335568887765 4555667778886332 122223356788889999999999866653
No 20
>PF01766 Birna_VP2: Birnavirus VP2 protein; InterPro: IPR002662 Infectious pancreatic necrosis virus (IPNV), a birnavirus, is an important pathogen in fish farms. Analyses of viral proteins showed that VP2 is the major structural and immunogenic polypeptide of the virus [, ]. All neutralizing monoclonal antibodies are specific to VP2 and bind to continuous or discontinuous epitopes. The variable domain of VP2 and the 20 adjacent amino acids of the conserved C-terminal are probably the most important in inducing an immune response for the protection of animals []. The large RNA segment of the Birnaviridae codes for a polyprotein (N-VP2-VP4-VP3-C), most of which is then processed to generate the constituent polypeptides. VP4 protein is involved in generating VP2 and VP3 []. Recombinant VP3 is more immunogenic than recombinant VP2 [].; GO: 0005198 structural molecule activity; PDB: 2DF7_T 3IDE_D 3FBM_A 2GSY_J 2IMU_A 1WCD_J.
Probab=29.29 E-value=8.7 Score=33.36 Aligned_cols=63 Identities=14% Similarity=0.144 Sum_probs=36.4
Q ss_pred ccccCCCCCCceEEEEeecCChHHHHHH-----HHHHHHHHHhcCCccCCcccccccccccccccccC
Q psy16369 33 DMRENEKPGIDSFGKPDSHGDPEDVKKN-----QAKIYSVALKFGGIPAGETNGMRGYMLTFVIAYIR 95 (101)
Q Consensus 33 ~~~~~~~~~~~CL~vlgFEGt~~~V~~r-----~~~~~~I~~~~GG~~lG~~~G~~W~~~RF~~PYLR 95 (101)
.+..|-=.-.+-+=-+.|||+..||..- ......+.-|-|.+.+|++.+--=--.+|+.||.|
T Consensus 106 tLPaGvYalnGT~Navt~~G~lSEv~~~~Y~~llS~tsn~~DKvgnvlV~dGv~VLSLPt~fD~pYVR 173 (441)
T PF01766_consen 106 TLPAGVYALNGTFNAVTFQGSLSEVEDLSYNSLLSATSNPLDKVGNVLVGDGVAVLSLPTGFDNPYVR 173 (441)
T ss_dssp BECTTC-CEB-EEEEEEESS-GGG-S--STTGGGGS-S-GGGEEEEEETTT-EEEE---S-SS---EE
T ss_pred cCCceeeEecceeeeEEeccCHHHcccccccceeeeccChhhhhcCEEecCceEEEecCcccCCCcee
Confidence 3444444445666778999999888743 45556788899999999999888888899999998
No 21
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=28.30 E-value=67 Score=19.71 Aligned_cols=23 Identities=17% Similarity=0.302 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHhcCCccCC
Q psy16369 55 EDVKKNQAKIYSVALKFGGIPAG 77 (101)
Q Consensus 55 ~~V~~r~~~~~~I~~~~GG~~lG 77 (101)
+..+.-.+.+..++++|||..+-
T Consensus 2 ~~~~~Y~~~~~~~l~~~GG~~l~ 24 (65)
T PF07045_consen 2 EAYQEYREAVPPILEKYGGRVLA 24 (65)
T ss_dssp HHHHHHHHHHHHHHHHTT-EEEE
T ss_pred hHHHHHHHHHHHHHHHcCCEEEE
Confidence 34556678899999999999883
No 22
>PF13368 Toprim_C_rpt: Topoisomerase C-terminal repeat
Probab=27.37 E-value=21 Score=22.20 Aligned_cols=12 Identities=17% Similarity=0.058 Sum_probs=9.6
Q ss_pred ccccccccccCCC
Q psy16369 85 YMLTFVIAYIRIV 97 (101)
Q Consensus 85 ~~~RF~~PYLRD~ 97 (101)
..+|| +||+.+-
T Consensus 10 ~~GRf-GPYv~~g 21 (61)
T PF13368_consen 10 KNGRF-GPYVKHG 21 (61)
T ss_pred eECCC-CceEEEC
Confidence 67899 9998754
No 23
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=26.68 E-value=1.1e+02 Score=22.80 Aligned_cols=56 Identities=11% Similarity=-0.020 Sum_probs=40.4
Q ss_pred ccccccccccchhccccCCCCCCceEEEEeecCChHHHHHHHHHHHHHHHhcCCccC
Q psy16369 20 STSYSRPRHYPLTDMRENEKPGIDSFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPA 76 (101)
Q Consensus 20 ~~~~~~~~~~~l~~~~~~~~~~~~CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~l 76 (101)
.-||+..+|.||..+..+. .....+++++.-|+..+.......+..++...|+..+
T Consensus 78 ~~s~pg~LKn~iD~l~~~~-l~~K~v~iiat~G~~~~~~~~~~~lr~~l~~l~a~~~ 133 (191)
T PRK10569 78 KASFSGALKTLLDLLPERA-LEHKVVLPLATGGSVAHMLAVDYALKPVLSALKAQEI 133 (191)
T ss_pred CCCCCHHHHHHHHhCChhh-hCCCEEEEEEecCCchhHHHHHHHHHHHHHHcCCeec
Confidence 3578899999998886432 2223445555558888877777788889999998765
No 24
>PRK00339 minC septum formation inhibitor; Reviewed
Probab=26.39 E-value=82 Score=24.76 Aligned_cols=69 Identities=9% Similarity=-0.054 Sum_probs=41.1
Q ss_pred eeEEEecceEEEEeccccccccccchhcccc------CCCCCCceEEEEeecCChH-HHHHHHHHHHHHHHhcCCccC
Q psy16369 6 VNVFFKGNRYLVETSTSYSRPRHYPLTDMRE------NEKPGIDSFGKPDSHGDPE-DVKKNQAKIYSVALKFGGIPA 76 (101)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~------~~~~~~~CL~vlgFEGt~~-~V~~r~~~~~~I~~~~GG~~l 76 (101)
-.+-|||+++-+-.-......+....+.+.+ +|=. +.-+++-++.-.+ ........+.++++.+|-.++
T Consensus 11 ~~i~iKg~~~~l~~l~~~~~d~~~l~~~L~~kl~~a~~FF~--~~pvvld~~~~~~~~~~~dl~~L~~~l~~~gl~~v 86 (249)
T PRK00339 11 PVFQLKGSMLAITVLELARNDLDRLDRQLAAKVAQAPNFFS--NTPLVLALDKLPEGEGELDLPGLMRICRRHGLRTL 86 (249)
T ss_pred CeEEEEcCcceEEEEEcCCCCHHHHHHHHHHHHHhChhhhC--CCeEEEEecccccccchHHHHHHHHHHHHCCCEEE
Confidence 3467899998665555555555544444333 2332 3445677765432 223457779999999987753
No 25
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=26.09 E-value=1.5e+02 Score=19.86 Aligned_cols=35 Identities=17% Similarity=-0.011 Sum_probs=28.4
Q ss_pred eEEEEeecCChHHHHHHHHHHHHHHHhcCCccCCc
Q psy16369 44 SFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPAGE 78 (101)
Q Consensus 44 CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~lG~ 78 (101)
|+.++-=+-++++++.-.+.+.+++.+.||.....
T Consensus 6 ~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~i~~~ 40 (108)
T PRK00453 6 IVFILRPDLSEEQVKALVERFKGVITENGGTIHKV 40 (108)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEE
Confidence 56666556678999999999999999999997643
No 26
>PRK07308 flavodoxin; Validated
Probab=26.00 E-value=2e+02 Score=19.69 Aligned_cols=53 Identities=11% Similarity=-0.033 Sum_probs=35.4
Q ss_pred cccccchhccccCCCCCCceEEEEeecCC-hHHHHHHHHHHHHHHHhcCCccCCc
Q psy16369 25 RPRHYPLTDMRENEKPGIDSFGKPDSHGD-PEDVKKNQAKIYSVALKFGGIPAGE 78 (101)
Q Consensus 25 ~~~~~~l~~~~~~~~~~~~CL~vlgFEGt-~~~V~~r~~~~~~I~~~~GG~~lG~ 78 (101)
..++.|++.++. -+....+.+++|.=.. -+.--...+.+.+.+.+.|+..+++
T Consensus 66 ~~~~~fl~~l~~-~~l~~k~~~vfG~Gd~~y~~~~~a~~~~~~~l~~~g~~~~~~ 119 (146)
T PRK07308 66 DEIVDFYEDLAD-LDLSGKIYGVVGSGDTFYDYFCKSVDDFEAQFALTGATKGAE 119 (146)
T ss_pred HHHHHHHHHHhc-CCCCCCEEEEEeeCCCCHHHHHHHHHHHHHHHHHcCCeEccC
Confidence 357889998877 5556678888887221 1233334455667888999888765
No 27
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=24.14 E-value=92 Score=21.12 Aligned_cols=57 Identities=11% Similarity=-0.032 Sum_probs=32.7
Q ss_pred cccccccccchhccc---cCCCCCCceEEEEeecCChHHHHHHHHHHHHHHHhcCCccCCc
Q psy16369 21 TSYSRPRHYPLTDMR---ENEKPGIDSFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPAGE 78 (101)
Q Consensus 21 ~~~~~~~~~~l~~~~---~~~~~~~~CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~lG~ 78 (101)
-+++..+|.|+.++- .+.-. ...++++..-|....-..-...+..++..+|...+++
T Consensus 83 ~~~s~~lK~~lD~~~~~~~~~~~-~K~~~~i~~~g~~~g~~~~~~~l~~~~~~~~~~~~~~ 142 (152)
T PF03358_consen 83 GSVSGQLKNFLDRLSCWFRRALR-GKPVAIIAVGGGRRGGLRALEQLRQILDYLGMIVVPS 142 (152)
T ss_dssp TBE-HHHHHHHHTHHHTHTTTTT-TSEEEEEEEESSSSTTHHHHHHHHHHHHHTTBEEECC
T ss_pred CcCChhhhHHHHHhccccccccC-CCEEEEEEEecCCcHHHHHHHHHHHHHHHCCCEEcCC
Confidence 356888999999995 31222 3344444444443333334455556777788877766
No 28
>cd06522 GH25_AtlA-like AtlA is an autolysin found in Gram-positive lactic acid bacteria that degrades bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues. This family includes the AtlA and Aml autolysins from Streptococcus mutans which have a C-terminal glycosyl hydrolase family 25 (GH25) catalytic domain as well as six tandem N-terminal repeats of the GBS (group B Streptococcus) Bsp-like peptidoglycan-binding domain. Other members of this family have one or more C-terminal peptidoglycan-binding domain(s) (SH3 or LysM) in addition to the GH25 domain.
Probab=24.05 E-value=1.3e+02 Score=22.11 Aligned_cols=62 Identities=6% Similarity=-0.054 Sum_probs=40.0
Q ss_pred cccchhccccCCCCCCceEEEEeecCCh--HHHHHHHHHHHHHHHhcCCccCCcccccccccccc
Q psy16369 27 RHYPLTDMRENEKPGIDSFGKPDSHGDP--EDVKKNQAKIYSVALKFGGIPAGETNGMRGYMLTF 89 (101)
Q Consensus 27 ~~~~l~~~~~~~~~~~~CL~vlgFEGt~--~~V~~r~~~~~~I~~~~GG~~lG~~~G~~W~~~RF 89 (101)
.+.|+..+++ ......+..++-+|... +.+...-++-.+.++++|+...+=-.+..|.....
T Consensus 76 A~~f~~~~~~-~~~~~~~~~~lD~E~~~~~~~~~~~~~~F~~~v~~~g~~~~~iY~~~~~~~~~~ 139 (192)
T cd06522 76 ARYFANTAKS-LGLSKNTVMVADMEDSSSSGNATANVNAFWQTMKAAGYKNTDVYTSASWLNSRA 139 (192)
T ss_pred HHHHHHHHHH-cCCCCCCceEEEeecCCCcchHHHHHHHHHHHHHHcCCCCcEEEccHHHHhcCC
Confidence 5678888876 33334567788999754 34555556666777888986555555556655443
No 29
>PF13691 Lactamase_B_4: tRNase Z endonuclease
Probab=23.94 E-value=1e+02 Score=19.71 Aligned_cols=32 Identities=25% Similarity=0.416 Sum_probs=21.1
Q ss_pred ceeeEEEecceEEE-Ee-----------ccccccccccchhccc
Q psy16369 4 SVVNVFFKGNRYLV-ET-----------STSYSRPRHYPLTDMR 35 (101)
Q Consensus 4 ~~~~~~~~~~~~~~-~~-----------~~~~~~~~~~~l~~~~ 35 (101)
..+-++|..+|||. .. ....+|--+=|||...
T Consensus 13 p~l~l~~d~~rYlFGn~gEGtQR~~~e~~ikl~kl~~IFlT~~~ 56 (63)
T PF13691_consen 13 PSLLLFFDSRRYLFGNCGEGTQRACNEHKIKLSKLNDIFLTGLS 56 (63)
T ss_pred CEEEEEeCCceEEeccCCcHHHHHHHHcCCCccccceEEECCCC
Confidence 45778999999999 33 3344555555565555
No 30
>PF08804 gp32: gp32 DNA binding protein like; InterPro: IPR012339 This entry is represented by the Bacteriophage T4, Gp32, single-stranded DNA-binding protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Gp32 is essential for T4 DNA replication, recombination and repair, acting to stimulate replisome processing and accuracy through its binding to ssDNA as the replication fork advances. The crystal structure of Gp32 shows an ssDNA binding cleft comprised of regions from three structural subdomains, through which ssDNA can slide freely []. The structure of Gp32 is similar to other phage ssDNA-binding proteins such as Gp2.5 from bacteriophage T4, and gene V protein, both of which have a nucleic acid-binding OB-type fold. However, Gp32 contains a zinc-finger subdomain at residues 63-111 that is not found in the other two phage proteins.; GO: 0003697 single-stranded DNA binding; PDB: 1GPC_A 2A1K_B 2ATQ_B.
Probab=23.62 E-value=98 Score=21.71 Aligned_cols=18 Identities=44% Similarity=0.650 Sum_probs=14.2
Q ss_pred eeeEEEecc-eEEEEeccc
Q psy16369 5 VVNVFFKGN-RYLVETSTS 22 (101)
Q Consensus 5 ~~~~~~~~~-~~~~~~~~~ 22 (101)
++|-.||+| ++.+|.|+|
T Consensus 35 l~~H~Fk~~g~WyiEN~~s 53 (94)
T PF08804_consen 35 LVNHGFKGNGGWYIENCPS 53 (94)
T ss_dssp EEEEEEEETTEEEEEEEGG
T ss_pred hhhhhccCCCcEEEecCcc
Confidence 678788765 789998876
No 31
>TIGR01753 flav_short flavodoxin, short chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the short chain type. Many of these are involved in sulfite reduction.
Probab=22.65 E-value=1.6e+02 Score=19.39 Aligned_cols=52 Identities=8% Similarity=-0.121 Sum_probs=32.1
Q ss_pred ccccchhccccCCCCCCceEEEEeecCChHHHHHHHHHHHHHHHhcCCccCCc
Q psy16369 26 PRHYPLTDMRENEKPGIDSFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPAGE 78 (101)
Q Consensus 26 ~~~~~l~~~~~~~~~~~~CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~lG~ 78 (101)
.++.|++++.+ .+....-.+++|--|...+-..-.+.+.+++++.|+..+++
T Consensus 65 ~~~~f~~~l~~-~~~~gk~~~vfgt~g~~~~f~~~~~~~~~~l~~~g~~~v~~ 116 (140)
T TIGR01753 65 DFEPFFEELED-IDLGGKKVALFGSGDWGYEFCEAVDDWEERLKEAGATIIAE 116 (140)
T ss_pred hHHHHHHHhhh-CCCCCCEEEEEecCCCCchhhHHHHHHHHHHHHCCCEEecC
Confidence 45688888776 33344445555554543312234456677888899988876
No 32
>cd07262 Glo_EDI_BRP_like_19 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=22.62 E-value=1.3e+02 Score=19.09 Aligned_cols=51 Identities=22% Similarity=0.181 Sum_probs=26.7
Q ss_pred ceEEEEeecCCh-HHHHHHHHHHHHHHHhcCCccCCcccccccccccccccccCCC
Q psy16369 43 DSFGKPDSHGDP-EDVKKNQAKIYSVALKFGGIPAGETNGMRGYMLTFVIAYIRIV 97 (101)
Q Consensus 43 ~CL~vlgFEGt~-~~V~~r~~~~~~I~~~~GG~~lG~~~G~~W~~~RF~~PYLRD~ 97 (101)
.....+.|+=.. ++++. +.+-+.+.|+....+.....|...++...|++|.
T Consensus 63 ~~~~hi~f~v~~~~~v~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~DP 114 (123)
T cd07262 63 GNGTHVAFAAPSREAVDA----FHAAALAAGGTDEGAPGLRPHYGPGYYAAYVRDP 114 (123)
T ss_pred CCceEEEEECCCHHHHHH----HHHHHHHcCCccCCCCCCCCCCCCCeEEEEEECC
Confidence 345577786433 34443 4445556777765543333343334445677764
No 33
>COG1647 Esterase/lipase [General function prediction only]
Probab=22.27 E-value=1.1e+02 Score=24.87 Aligned_cols=24 Identities=17% Similarity=0.091 Sum_probs=19.3
Q ss_pred CceEEEEeecCChHHHHHHHHHHH
Q psy16369 42 IDSFGKPDSHGDPEDVKKNQAKIY 65 (101)
Q Consensus 42 ~~CL~vlgFEGt~~~V~~r~~~~~ 65 (101)
..||++=||.|++++|+.--+.+.
T Consensus 16 ~AVLllHGFTGt~~Dvr~Lgr~L~ 39 (243)
T COG1647 16 RAVLLLHGFTGTPRDVRMLGRYLN 39 (243)
T ss_pred EEEEEEeccCCCcHHHHHHHHHHH
Confidence 479999999999999987655443
No 34
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=22.03 E-value=1.5e+02 Score=18.47 Aligned_cols=31 Identities=6% Similarity=-0.103 Sum_probs=24.2
Q ss_pred CceEEEEeecCChHHHHHHHHHHHHHHHhcC
Q psy16369 42 IDSFGKPDSHGDPEDVKKNQAKIYSVALKFG 72 (101)
Q Consensus 42 ~~CL~vlgFEGt~~~V~~r~~~~~~I~~~~G 72 (101)
....+++-.+++++..+.-++.+.+++++.|
T Consensus 40 ~~f~~~~~v~~~~~~~~~l~~~L~~l~~~~~ 70 (76)
T PF13740_consen 40 GRFTLIMLVSIPEDSLERLESALEELAEELG 70 (76)
T ss_dssp TEEEEEEEEEESHHHHHHHHHHHHHHHHHTT
T ss_pred CeEEEEEEEEeCcccHHHHHHHHHHHHHHCC
Confidence 4566777788888888888888888888765
No 35
>PF05651 Diacid_rec: Putative sugar diacid recognition; InterPro: IPR008599 This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. P36047 from SWISSPROT). An HTH DNA-binding motif is found at the C terminus of these proteins suggesting that this region includes the sugar recognition region.
Probab=21.91 E-value=2.1e+02 Score=20.47 Aligned_cols=26 Identities=19% Similarity=0.335 Sum_probs=20.9
Q ss_pred CceEEEEeecCChHHHHHHHHHHHHH
Q psy16369 42 IDSFGKPDSHGDPEDVKKNQAKIYSV 67 (101)
Q Consensus 42 ~~CL~vlgFEGt~~~V~~r~~~~~~I 67 (101)
..++.++|-.|.+++|..--..+...
T Consensus 81 g~~iGviGItG~p~eV~~~~~lvk~~ 106 (135)
T PF05651_consen 81 GEVIGVIGITGEPEEVRPYAQLVKKM 106 (135)
T ss_pred CEEEEEEEEecCHHHHHHHHHHHHHH
Confidence 47899999999999998876655543
No 36
>TIGR00166 S6 ribosomal protein S6. MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6.
Probab=20.77 E-value=1.7e+02 Score=19.14 Aligned_cols=33 Identities=15% Similarity=-0.094 Sum_probs=25.0
Q ss_pred eEEEEeecCChHHHHHHHHHHHHHHHhcCCccCC
Q psy16369 44 SFGKPDSHGDPEDVKKNQAKIYSVALKFGGIPAG 77 (101)
Q Consensus 44 CL~vlgFEGt~~~V~~r~~~~~~I~~~~GG~~lG 77 (101)
++.++-=+.+++ ++.-.+++.+++.++||....
T Consensus 5 ~~~Il~p~~~~~-~~~~~~~~~~~i~~~gg~i~~ 37 (93)
T TIGR00166 5 IIFLVRPTLSEE-VKGQIERYKKVITLNGAEIVR 37 (93)
T ss_pred EEEEECCCCcHH-HHHHHHHHHHHHHhCCCEEEE
Confidence 455555555555 888899999999999998754
No 37
>PRK02551 flavoprotein NrdI; Provisional
Probab=20.74 E-value=1.8e+02 Score=21.52 Aligned_cols=20 Identities=25% Similarity=0.326 Sum_probs=13.7
Q ss_pred CChHHHHHHHHHHHHHHHhc
Q psy16369 52 GDPEDVKKNQAKIYSVALKF 71 (101)
Q Consensus 52 Gt~~~V~~r~~~~~~I~~~~ 71 (101)
|++++|+.-++.+.+++.++
T Consensus 134 GT~~Dv~~v~~~~~~~~~~~ 153 (154)
T PRK02551 134 GTPSDIERIAAIIAELYAAE 153 (154)
T ss_pred CCHHHHHHHHHHHHHHHHhc
Confidence 77777777777776666554
No 38
>PF14740 DUF4471: Domain of unknown function (DUF4471)
Probab=20.20 E-value=81 Score=25.72 Aligned_cols=22 Identities=23% Similarity=0.215 Sum_probs=17.5
Q ss_pred hHHHHHHHHHHHHHHHhcCCcc
Q psy16369 54 PEDVKKNQAKIYSVALKFGGIP 75 (101)
Q Consensus 54 ~~~V~~r~~~~~~I~~~~GG~~ 75 (101)
+++++.-.+++.++|+++|=.+
T Consensus 263 KEq~~~F~~kv~eLA~~aG~~p 284 (289)
T PF14740_consen 263 KEQLQEFVKKVKELAKAAGFKP 284 (289)
T ss_pred HHHHHHHHHHHHHHHHHCCCcc
Confidence 4778888889999999887544
No 39
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=20.02 E-value=1.1e+02 Score=17.88 Aligned_cols=17 Identities=18% Similarity=0.350 Sum_probs=13.4
Q ss_pred HHHHHHHHHHhcCCccC
Q psy16369 60 NQAKIYSVALKFGGIPA 76 (101)
Q Consensus 60 r~~~~~~I~~~~GG~~l 76 (101)
.+..+.++++++||...
T Consensus 20 ~~~~l~~~i~~~GG~v~ 36 (78)
T PF00533_consen 20 EREELEQLIKKHGGTVS 36 (78)
T ss_dssp HHHHHHHHHHHTTEEEE
T ss_pred CHHHHHHHHHHcCCEEE
Confidence 45566889999999983
Done!