Query 043767
Match_columns 105
No_of_seqs 112 out of 225
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 08:09:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043767.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043767hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00198 60S ribosomal protein 100.0 6.6E-45 1.4E-49 264.5 7.2 86 18-103 8-95 (122)
2 PF01776 Ribosomal_L22e: Ribos 100.0 3.8E-43 8.3E-48 251.9 4.5 80 24-103 1-82 (112)
3 KOG3434 60S ribosomal protein 100.0 3.2E-41 6.9E-46 246.0 5.1 84 20-103 9-94 (125)
4 PF02576 DUF150: Uncharacteris 69.2 28 0.00061 24.8 6.5 32 29-60 61-93 (141)
5 PF02747 PCNA_C: Proliferating 59.0 17 0.00036 25.5 3.7 34 44-84 13-46 (128)
6 PF14728 PHTB1_C: PTHB1 C-term 49.9 38 0.00081 28.7 5.0 26 25-54 98-124 (377)
7 PF13202 EF-hand_5: EF hand; P 46.9 13 0.00029 19.5 1.3 14 40-53 12-25 (25)
8 PF12970 DUF3858: Domain of Un 43.5 27 0.00059 25.7 2.8 36 55-92 56-91 (116)
9 cd01734 YlxS_C YxlS is a Bacil 37.3 45 0.00098 21.8 2.9 29 31-59 1-30 (83)
10 smart00054 EFh EF-hand, calciu 36.4 28 0.00062 15.8 1.4 17 39-55 12-28 (29)
11 PRK14638 hypothetical protein; 36.4 1.2E+02 0.0026 22.4 5.3 31 29-59 74-105 (150)
12 PRK15084 formate hydrogenlyase 35.5 25 0.00054 26.5 1.6 21 32-54 41-61 (133)
13 PF07450 HycH: Formate hydroge 35.1 26 0.00057 26.2 1.7 22 32-55 39-60 (131)
14 PRK14640 hypothetical protein; 34.1 62 0.0013 23.8 3.5 31 30-60 72-103 (152)
15 COG1018 Hmp Flavodoxin reducta 33.9 30 0.00066 27.5 2.0 45 26-78 51-102 (266)
16 PRK14646 hypothetical protein; 33.8 1.9E+02 0.0042 21.4 6.1 31 30-60 75-106 (155)
17 PF15547 DUF4654: Domain of un 33.1 26 0.00056 26.6 1.4 11 28-38 11-21 (138)
18 PRK14633 hypothetical protein; 32.0 73 0.0016 23.5 3.6 31 29-59 68-99 (150)
19 PRK14639 hypothetical protein; 31.5 1.7E+02 0.0038 21.2 5.5 31 30-60 63-94 (140)
20 KOG1354 Serine/threonine prote 30.9 17 0.00036 31.9 0.0 18 82-99 275-294 (433)
21 PRK14631 hypothetical protein; 29.5 1.1E+02 0.0025 23.2 4.4 30 30-59 92-122 (174)
22 PRK14630 hypothetical protein; 29.4 2.3E+02 0.005 20.7 6.2 30 30-59 72-102 (143)
23 PRK14636 hypothetical protein; 28.8 82 0.0018 24.0 3.5 31 29-59 72-103 (176)
24 PF13833 EF-hand_8: EF-hand do 28.3 38 0.00082 19.5 1.3 21 36-56 34-54 (54)
25 PF10986 DUF2796: Protein of u 28.2 63 0.0014 24.5 2.8 48 28-75 116-164 (168)
26 PF08980 DUF1883: Domain of un 27.3 35 0.00075 24.1 1.1 25 30-54 16-40 (94)
27 KOG2775 Metallopeptidase [Gene 26.1 14 0.00031 31.9 -1.2 17 83-100 330-350 (397)
28 PF10698 DUF2505: Protein of u 26.0 62 0.0014 23.3 2.3 67 30-100 2-71 (159)
29 cd07675 F-BAR_FNBP1L The F-BAR 25.9 11 0.00024 30.3 -1.7 40 39-102 14-54 (252)
30 PRK10811 rne ribonuclease E; R 25.5 44 0.00096 32.5 1.8 28 67-94 97-130 (1068)
31 PRK14632 hypothetical protein; 25.3 1.1E+02 0.0023 23.2 3.5 30 30-59 73-103 (172)
32 PRK14645 hypothetical protein; 25.2 2E+02 0.0043 21.4 4.9 32 29-60 76-108 (154)
33 PHA03383 PCNA-like protein; Pr 25.1 70 0.0015 25.5 2.6 32 44-82 146-177 (262)
34 cd00559 Cyanase_C Cyanase C-te 24.6 60 0.0013 22.0 1.8 31 40-76 31-61 (69)
35 PRK14637 hypothetical protein; 24.3 1.8E+02 0.0039 21.5 4.6 30 30-59 73-103 (151)
36 PRK00092 ribosome maturation p 24.2 1.2E+02 0.0026 22.1 3.5 31 30-60 73-104 (154)
37 PF08845 SymE_toxin: Toxin Sym 24.0 1.3E+02 0.0027 19.2 3.2 18 66-83 40-57 (57)
38 smart00055 FCH Fes/CIP4 homolo 23.8 11 0.00024 24.0 -1.8 22 39-60 18-39 (87)
39 TIGR00673 cynS cyanate hydrata 23.5 59 0.0013 24.6 1.8 31 40-76 112-142 (150)
40 PF09279 EF-hand_like: Phospho 23.1 51 0.0011 20.8 1.3 17 40-56 12-28 (83)
41 PRK02866 cyanate hydratase; Va 23.0 63 0.0014 24.4 1.9 31 40-76 109-139 (147)
42 PF04006 Mpp10: Mpp10 protein; 23.0 49 0.0011 29.4 1.5 18 38-55 183-200 (600)
43 PF02560 Cyanate_lyase: Cyanat 22.8 31 0.00066 23.7 0.2 31 40-76 35-65 (73)
44 PF05481 Myco_19_kDa: Mycobact 22.4 1.4E+02 0.0029 22.8 3.6 33 55-87 51-83 (160)
45 PF13405 EF-hand_6: EF-hand do 22.0 64 0.0014 17.0 1.3 15 40-54 13-27 (31)
46 PF14819 QueF_N: Nitrile reduc 20.7 78 0.0017 23.1 1.9 24 29-55 55-78 (110)
47 PF09066 B2-adapt-app_C: Beta2 20.5 55 0.0012 22.0 1.1 15 39-53 2-16 (114)
48 PF09386 ParD: Antitoxin ParD; 20.5 44 0.00096 23.2 0.6 37 30-67 29-66 (79)
49 PTZ00113 proliferating cell nu 20.4 1.3E+02 0.0028 24.3 3.3 33 44-83 141-173 (275)
50 COG1855 ATPase (PilT family) [ 20.4 2.4E+02 0.0053 25.9 5.3 79 7-92 148-234 (604)
51 COG2098 Uncharacterized protei 20.3 53 0.0012 24.3 1.0 58 31-92 26-84 (116)
52 PF07683 CobW_C: Cobalamin syn 20.3 1.4E+02 0.003 18.9 2.9 21 30-55 3-23 (94)
53 PRK10598 lipoprotein; Provisio 20.3 72 0.0016 24.9 1.8 42 44-85 27-79 (186)
54 PF00611 FCH: Fes/CIP4, and EF 20.2 10 0.00022 23.8 -2.4 21 40-60 19-39 (91)
No 1
>PTZ00198 60S ribosomal protein L22; Provisional
Probab=100.00 E-value=6.6e-45 Score=264.50 Aligned_cols=86 Identities=50% Similarity=0.757 Sum_probs=80.3
Q ss_pred CCCCCCCccceeEEEEeeecccCCCccchhHHHHHhhcceeeccccCCCCCeEEEEeeCCeEEEEecccccceee--hhh
Q 043767 18 AGGGAKGKKKGATFTIDCAKPVEDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDKTKITVLSDSNFSKRYL--LLK 95 (105)
Q Consensus 18 ~~~~~k~kK~~~kF~IDCt~PveD~I~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k~kI~V~s~~pfSKRYL--LTK 95 (105)
+...+.++|..++|+||||+||||+|||+++||+||||||||||++||||+.|+|++++++|+|+|++||||||| |||
T Consensus 8 ~~~~~~~kk~~~kF~IDCt~PveD~I~d~a~fekfL~erIKV~GK~gnLg~~V~v~~~k~ki~V~s~~~FSKRYLKYLTK 87 (122)
T PTZ00198 8 RKRQKQVKKKKKKFKIDCTIPAEDGIIDLSGFEQFLQDRIKVDGKTGNLGNKVRVSREKNKITVTTTIPFSKRYLKYLTK 87 (122)
T ss_pred ccccchhcccceEEEEEcCCcccCCcccHHHHHHHHHHhEEECCCcCccCCcEEEEEECCEEEEEecccccHHHHHHHHH
Confidence 444355678889999999999999999999999999999999999999999999999999999999999999999 999
Q ss_pred hhhccccc
Q 043767 96 RLLKLPCA 103 (105)
Q Consensus 96 KyLKK~~~ 103 (105)
||||||+-
T Consensus 88 KyLKK~~L 95 (122)
T PTZ00198 88 KYLKKKQL 95 (122)
T ss_pred HHHhhhhh
Confidence 99999863
No 2
>PF01776 Ribosomal_L22e: Ribosomal L22e protein family; InterPro: IPR002671 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 L22e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes. Rattus norvegicus (Rat) L22 is related to ribosomal proteins from other eukaryotes and is identical in amino acid sequence to human EAP, the EBER 1 (Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) encoded RNA) associated protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1D_M 4A1B_M 4A19_M 4A18_M 3IZR_W 3IZS_W.
Probab=100.00 E-value=3.8e-43 Score=251.88 Aligned_cols=80 Identities=63% Similarity=0.897 Sum_probs=70.3
Q ss_pred CccceeEEEEeeecccCCCccchhHHHHHhhcceeeccccCCCCCeEEEEeeCCeEEEEecccccceee--hhhhhhccc
Q 043767 24 GKKKGATFTIDCAKPVEDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDKTKITVLSDSNFSKRYL--LLKRLLKLP 101 (105)
Q Consensus 24 ~kK~~~kF~IDCt~PveD~I~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k~kI~V~s~~pfSKRYL--LTKKyLKK~ 101 (105)
++|+.++|+||||+||||+|||+++||+||||||||||++||||+.|+|++++++|+|+|++||||||| ||||||||+
T Consensus 1 kkk~~~kF~IDCt~pveD~I~d~~~fe~fL~erIKV~gk~gnlg~~V~i~~~~~ki~V~s~v~fsKrYLKYLTKKyLKK~ 80 (112)
T PF01776_consen 1 KKKQTLKFTIDCTHPVEDGIMDPADFEKFLQERIKVNGKTGNLGNKVTISRDKNKITVTSEVPFSKRYLKYLTKKYLKKN 80 (112)
T ss_dssp --EEEEEEEEE-HHSSSTS---SHHHHHHHHHHHHHHSCSSSSTTTEEEEE-SSEEEEEESSS-SHHHHHHHHHHHHTTS
T ss_pred CCcccEEEEEEeCCcccCceecHHHHHHHHHHheEeCCcccccCCeEEEEecCCEEEEEecccccHHHHHHHHHHHHhhc
Confidence 477889999999999999999999999999999999999999999999999999999999999999999 999999998
Q ss_pred cc
Q 043767 102 CA 103 (105)
Q Consensus 102 ~~ 103 (105)
+-
T Consensus 81 ~L 82 (112)
T PF01776_consen 81 NL 82 (112)
T ss_dssp SS
T ss_pred ch
Confidence 74
No 3
>KOG3434 consensus 60S ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.2e-41 Score=246.02 Aligned_cols=84 Identities=62% Similarity=0.871 Sum_probs=79.5
Q ss_pred CCCCCccceeEEEEeeecccCCCccchhHHHHHhhcceeeccccCCCCCeEEEEeeCCeEEEEecccccceee--hhhhh
Q 043767 20 GGAKGKKKGATFTIDCAKPVEDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDKTKITVLSDSNFSKRYL--LLKRL 97 (105)
Q Consensus 20 ~~~k~kK~~~kF~IDCt~PveD~I~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k~kI~V~s~~pfSKRYL--LTKKy 97 (105)
.+.+++|..++|+|||++||||+|||+|+||+|||||||||||+||||+.|+|++.+++|+|+|+++||+||| |||||
T Consensus 9 ~~~~~kKv~~~f~iDct~p~eDgI~d~A~fe~fLqerIKv~GK~gnLg~vv~ie~~kskitV~s~~~Fs~rylKyltkkY 88 (125)
T KOG3434|consen 9 KTAKKKKVHLRFTIDCTNPVEDGILDIADLEKFLQERIKVNGKVGNLGNVVTIERSKSKITVVSTVHFSKRYLKYLTKKY 88 (125)
T ss_pred hccccceeEEEEEEEecCccccccccHHHHHHHHHHHhhhcccccccCCeEEEecCCcEEEEEecCCccHHHHHHHHHHH
Confidence 3356788899999999999999999999999999999999999999999999999999999999999999999 99999
Q ss_pred hccccc
Q 043767 98 LKLPCA 103 (105)
Q Consensus 98 LKK~~~ 103 (105)
|||++-
T Consensus 89 Lkk~~L 94 (125)
T KOG3434|consen 89 LKKNNL 94 (125)
T ss_pred HhhhhH
Confidence 999863
No 4
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=69.18 E-value=28 Score=24.78 Aligned_cols=32 Identities=19% Similarity=0.505 Sum_probs=22.0
Q ss_pred eEEEEeeeccc-CCCccchhHHHHHhhcceeec
Q 043767 29 ATFTIDCAKPV-EDKIMDIASLEKFLQERIKVG 60 (105)
Q Consensus 29 ~kF~IDCt~Pv-eD~I~d~a~FEkFL~erIKVn 60 (105)
-.|+++.|.|- +.-+....+|+.|+-+.|+|.
T Consensus 61 ~~y~LEVSSPG~~r~L~~~~~~~~~iG~~v~v~ 93 (141)
T PF02576_consen 61 EDYTLEVSSPGIDRPLKSPRDFERFIGRKVKVK 93 (141)
T ss_dssp S-EEEEEE--SSSS--SSHHHHHHH-SEEEEEE
T ss_pred cceEEEEeCCCCCCcCCCHHHHHHhcCCeEEEE
Confidence 47999999996 555556889999999999994
No 5
>PF02747 PCNA_C: Proliferating cell nuclear antigen, C-terminal domain; InterPro: IPR022649 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []. It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA replication []. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta. Homologues of PCNA have also been identified in the archaea (Euryarchaeota and Crenarchaeota) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. ; GO: 0003677 DNA binding, 0030337 DNA polymerase processivity factor activity, 0006275 regulation of DNA replication, 0043626 PCNA complex; PDB: 1IZ5_A 1IZ4_A 1GE8_A 1ISQ_A 3A2F_B 1RWZ_A 3P83_A 1RXM_A 1RXZ_A 1SXJ_F ....
Probab=58.98 E-value=17 Score=25.46 Aligned_cols=34 Identities=26% Similarity=0.504 Sum_probs=25.4
Q ss_pred cchhHHHHHhhcceeeccccCCCCCeEEEEeeCCeEEEEec
Q 043767 44 MDIASLEKFLQERIKVGGKAGALGDTVTVTRDKTKITVLSD 84 (105)
Q Consensus 44 ~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k~kI~V~s~ 84 (105)
|+.+.|.+.+++ ..++|+.|+|+.+++.|.+.++
T Consensus 13 m~S~~f~~~~kd-------l~~v~d~v~i~~~~~~~~f~~~ 46 (128)
T PF02747_consen 13 MPSSEFKKICKD-------LSSVGDTVTISADKDSVIFSAE 46 (128)
T ss_dssp EEHHHHHHHHHH-------HHTTCSEEEEEEETTEEEEEEE
T ss_pred EEHHHHHHHHHH-------HHhcCCEEEEEEeCCEEEEEEE
Confidence 677888888776 3466888888888888776554
No 6
>PF14728 PHTB1_C: PTHB1 C-terminus
Probab=49.95 E-value=38 Score=28.70 Aligned_cols=26 Identities=31% Similarity=0.525 Sum_probs=19.2
Q ss_pred ccceeEEEEeeecccCCCccchhH-HHHHhh
Q 043767 25 KKKGATFTIDCAKPVEDKIMDIAS-LEKFLQ 54 (105)
Q Consensus 25 kK~~~kF~IDCt~PveD~I~d~a~-FEkFL~ 54 (105)
|....|.|||+.+|.-+ .++ |..|+.
T Consensus 98 k~a~~KlTi~tn~~~v~----L~~lFpdf~~ 124 (377)
T PF14728_consen 98 KNAKHKLTIDTNKPPVS----LSDLFPDFLE 124 (377)
T ss_pred cccceEEEEeCCCCCcC----HHHHhhHhhc
Confidence 44568999999998643 555 778876
No 7
>PF13202 EF-hand_5: EF hand; PDB: 3DD4_A 2Q4U_A 2BE4_A 1UHJ_B 1UHI_A 1UHH_B 1EJ3_B 1UHK_A 2ZFD_A 1UHN_A ....
Probab=46.91 E-value=13 Score=19.51 Aligned_cols=14 Identities=7% Similarity=0.361 Sum_probs=12.1
Q ss_pred CCCccchhHHHHHh
Q 043767 40 EDKIMDIASLEKFL 53 (105)
Q Consensus 40 eD~I~d~a~FEkFL 53 (105)
.||.++.++|.+|+
T Consensus 12 ~DG~is~~E~~~~~ 25 (25)
T PF13202_consen 12 GDGKISFEEFQRLV 25 (25)
T ss_dssp SSSEEEHHHHHHHH
T ss_pred CCCcCCHHHHHHHC
Confidence 58999999999875
No 8
>PF12970 DUF3858: Domain of Unknown Function with PDB structure (DUF3858); InterPro: IPR024544 This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.; PDB: 3KD4_A.
Probab=43.50 E-value=27 Score=25.70 Aligned_cols=36 Identities=19% Similarity=0.367 Sum_probs=27.4
Q ss_pred cceeeccccCCCCCeEEEEeeCCeEEEEecccccceee
Q 043767 55 ERIKVGGKAGALGDTVTVTRDKTKITVLSDSNFSKRYL 92 (105)
Q Consensus 55 erIKVnGKtgnLg~~V~i~r~k~kI~V~s~~pfSKRYL 92 (105)
...++++..|.+ .|+|..+++++.|+.++.++|+-.
T Consensus 56 ~~K~I~N~~Gk~--~isv~~~~~~~~V~rsL~L~Kqli 91 (116)
T PF12970_consen 56 MEKKIDNPVGKV--SISVKPEGNKIKVTRSLELKKQLI 91 (116)
T ss_dssp S-EEEEETTEEE--EEEEEEETTEEEEEEEEEE--SEE
T ss_pred cceeccCCcceE--EEEEEecCCeEEEEEEEEEeeeee
Confidence 345677777776 688999999999999999999765
No 9
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=37.30 E-value=45 Score=21.83 Aligned_cols=29 Identities=17% Similarity=0.369 Sum_probs=22.6
Q ss_pred EEEeeeccc-CCCccchhHHHHHhhcceee
Q 043767 31 FTIDCAKPV-EDKIMDIASLEKFLQERIKV 59 (105)
Q Consensus 31 F~IDCt~Pv-eD~I~d~a~FEkFL~erIKV 59 (105)
|++.-|.|- +--+..+.+|+.|+-..|+|
T Consensus 1 Y~LEVSSPGl~RpL~~~~~~~r~~G~~v~v 30 (83)
T cd01734 1 YFLEVSSPGAERPLKKEADFERAVGKYVHV 30 (83)
T ss_pred CEEEEcCCCCCCcCCCHHHHHHhCCCEEEE
Confidence 456667774 55667789999999998988
No 10
>smart00054 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
Probab=36.41 E-value=28 Score=15.85 Aligned_cols=17 Identities=18% Similarity=0.343 Sum_probs=13.7
Q ss_pred cCCCccchhHHHHHhhc
Q 043767 39 VEDKIMDIASLEKFLQE 55 (105)
Q Consensus 39 veD~I~d~a~FEkFL~e 55 (105)
-.++.++..+|..++++
T Consensus 12 ~~~g~i~~~e~~~~~~~ 28 (29)
T smart00054 12 DGDGKIDFEEFKDLLKA 28 (29)
T ss_pred CCCCcEeHHHHHHHHHh
Confidence 35789999999998864
No 11
>PRK14638 hypothetical protein; Provisional
Probab=36.37 E-value=1.2e+02 Score=22.37 Aligned_cols=31 Identities=13% Similarity=0.322 Sum_probs=25.9
Q ss_pred eEEEEeeeccc-CCCccchhHHHHHhhcceee
Q 043767 29 ATFTIDCAKPV-EDKIMDIASLEKFLQERIKV 59 (105)
Q Consensus 29 ~kF~IDCt~Pv-eD~I~d~a~FEkFL~erIKV 59 (105)
..|++.-|.|- +--+..+.+|+.|.-..++|
T Consensus 74 ~~Y~LEVSSPGldRpL~~~~~f~r~~G~~v~V 105 (150)
T PRK14638 74 HSYTLEVSSPGLDRPLRGPKDYVRFTGKLAKI 105 (150)
T ss_pred CceEEEEeCCCCCCCCCCHHHHHHhCCCEEEE
Confidence 36999999995 55667789999999998888
No 12
>PRK15084 formate hydrogenlyase maturation protein HycH; Provisional
Probab=35.48 E-value=25 Score=26.46 Aligned_cols=21 Identities=14% Similarity=0.351 Sum_probs=18.1
Q ss_pred EEeeecccCCCccchhHHHHHhh
Q 043767 32 TIDCAKPVEDKIMDIASLEKFLQ 54 (105)
Q Consensus 32 ~IDCt~PveD~I~d~a~FEkFL~ 54 (105)
+|||..|+ -.++.++|++++.
T Consensus 41 vIDcle~~--L~~~~e~y~~wi~ 61 (133)
T PRK15084 41 VIDCLEAA--LTCPLDEYLAWIA 61 (133)
T ss_pred eEecchhh--hcCCHHHHHHHHH
Confidence 69999998 6688999999974
No 13
>PF07450 HycH: Formate hydrogenlyase maturation protein HycH; InterPro: IPR010005 This family contains the bacterial formate hydrogenlyase maturation protein HycH, which is approximately 140 residues long. This may be required for the conversion of a precursor form of the large subunit of hydrogenlyase 3 into a mature form [].
Probab=35.13 E-value=26 Score=26.21 Aligned_cols=22 Identities=23% Similarity=0.513 Sum_probs=18.8
Q ss_pred EEeeecccCCCccchhHHHHHhhc
Q 043767 32 TIDCAKPVEDKIMDIASLEKFLQE 55 (105)
Q Consensus 32 ~IDCt~PveD~I~d~a~FEkFL~e 55 (105)
+|||..|+ -.++.++|++++..
T Consensus 39 vIDcle~~--l~cp~~~y~~wi~~ 60 (131)
T PF07450_consen 39 VIDCLEKV--LECPLEEYERWIAQ 60 (131)
T ss_pred eEeechhh--ccCCHHHHHHHHHh
Confidence 69999998 67899999999854
No 14
>PRK14640 hypothetical protein; Provisional
Probab=34.06 E-value=62 Score=23.83 Aligned_cols=31 Identities=16% Similarity=0.533 Sum_probs=26.9
Q ss_pred EEEEeeecc-cCCCccchhHHHHHhhcceeec
Q 043767 30 TFTIDCAKP-VEDKIMDIASLEKFLQERIKVG 60 (105)
Q Consensus 30 kF~IDCt~P-veD~I~d~a~FEkFL~erIKVn 60 (105)
.|++.-|.| ++--+..+.+|+.|+-..++|.
T Consensus 72 ~Y~LEVSSPGl~RpL~~~~~f~r~~G~~v~V~ 103 (152)
T PRK14640 72 EYYLEVSSPGLDRPLFKVAQFEKYVGQEAAVT 103 (152)
T ss_pred CeEEEEeCCCCCCcCCCHHHHHHhCCCeEEEE
Confidence 699999999 4667788999999999999983
No 15
>COG1018 Hmp Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]
Probab=33.87 E-value=30 Score=27.48 Aligned_cols=45 Identities=24% Similarity=0.417 Sum_probs=30.7
Q ss_pred cceeEEEEeeecccCCCcc-------chhHHHHHhhcceeeccccCCCCCeEEEEeeCCe
Q 043767 26 KKGATFTIDCAKPVEDKIM-------DIASLEKFLQERIKVGGKAGALGDTVTVTRDKTK 78 (105)
Q Consensus 26 K~~~kF~IDCt~PveD~I~-------d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k~k 78 (105)
....-|+| |+.|-++... |-..+-.||+|++|+ |+.|.|+.--+.
T Consensus 51 ~~~R~YSl-~s~p~~~~~~~isVk~~~~G~~S~~Lh~~lk~-------Gd~l~v~~P~G~ 102 (266)
T COG1018 51 PLLRAYSL-SSAPDEDSLYRISVKREDGGGGSNWLHDHLKV-------GDTLEVSAPAGD 102 (266)
T ss_pred eeeEEEEe-ccCCCCCceEEEEEEEeCCCcccHHHHhcCCC-------CCEEEEecCCCC
Confidence 45566888 8888777221 224577899999998 788877554443
No 16
>PRK14646 hypothetical protein; Provisional
Probab=33.82 E-value=1.9e+02 Score=21.36 Aligned_cols=31 Identities=13% Similarity=0.327 Sum_probs=26.6
Q ss_pred EEEEeeecc-cCCCccchhHHHHHhhcceeec
Q 043767 30 TFTIDCAKP-VEDKIMDIASLEKFLQERIKVG 60 (105)
Q Consensus 30 kF~IDCt~P-veD~I~d~a~FEkFL~erIKVn 60 (105)
.|++.-|.| ++--+....+|+.|+-..++|.
T Consensus 75 ~Y~LEVSSPGldRpL~~~~df~r~~G~~v~V~ 106 (155)
T PRK14646 75 SYVLEISSQGVSDELTSERDFKTFKGFPVNVE 106 (155)
T ss_pred CeEEEEcCCCCCCcCCCHHHHHHhCCCEEEEE
Confidence 699999999 4667778999999999999983
No 17
>PF15547 DUF4654: Domain of unknown function (DUF4654)
Probab=33.14 E-value=26 Score=26.57 Aligned_cols=11 Identities=55% Similarity=0.927 Sum_probs=9.0
Q ss_pred eeEEEEeeecc
Q 043767 28 GATFTIDCAKP 38 (105)
Q Consensus 28 ~~kF~IDCt~P 38 (105)
-+.|+|||+.-
T Consensus 11 HlTFvIDCa~G 21 (138)
T PF15547_consen 11 HLTFVIDCARG 21 (138)
T ss_pred ceEEEEEcCCC
Confidence 47999999864
No 18
>PRK14633 hypothetical protein; Provisional
Probab=31.97 E-value=73 Score=23.46 Aligned_cols=31 Identities=13% Similarity=0.379 Sum_probs=26.3
Q ss_pred eEEEEeeeccc-CCCccchhHHHHHhhcceee
Q 043767 29 ATFTIDCAKPV-EDKIMDIASLEKFLQERIKV 59 (105)
Q Consensus 29 ~kF~IDCt~Pv-eD~I~d~a~FEkFL~erIKV 59 (105)
..|++.-|.|- +--+..+.+|+.|+-++++|
T Consensus 68 ~~Y~LEVSSPGldRpL~~~~~f~r~~G~~v~V 99 (150)
T PRK14633 68 GKYILEVSSPGMNRQIFNIIQAQALVGFNVKA 99 (150)
T ss_pred CCeEEEEeCCCCCCCCCCHHHHHHhCCCeEEE
Confidence 36999999994 66677899999999999888
No 19
>PRK14639 hypothetical protein; Provisional
Probab=31.47 E-value=1.7e+02 Score=21.25 Aligned_cols=31 Identities=23% Similarity=0.430 Sum_probs=26.0
Q ss_pred EEEEeeeccc-CCCccchhHHHHHhhcceeec
Q 043767 30 TFTIDCAKPV-EDKIMDIASLEKFLQERIKVG 60 (105)
Q Consensus 30 kF~IDCt~Pv-eD~I~d~a~FEkFL~erIKVn 60 (105)
.|++.-|.|- +--+..+.+|+.|+-..++|.
T Consensus 63 ~Y~LEVSSPGl~RpL~~~~~f~r~~G~~v~v~ 94 (140)
T PRK14639 63 EYFLEVSSPGLERKLSKIEHFAKSIGELVKIT 94 (140)
T ss_pred CeEEEEeCCCCCCcCCCHHHHHHhCCCEEEEE
Confidence 5899999884 666777999999999999983
No 20
>KOG1354 consensus Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms]
Probab=30.93 E-value=17 Score=31.90 Aligned_cols=18 Identities=44% Similarity=0.796 Sum_probs=14.5
Q ss_pred Eecccccc--eeehhhhhhc
Q 043767 82 LSDSNFSK--RYLLLKRLLK 99 (105)
Q Consensus 82 ~s~~pfSK--RYLLTKKyLK 99 (105)
.|++.||. ||+|++.||-
T Consensus 275 ISDvKFs~sGryilsRDylt 294 (433)
T KOG1354|consen 275 ISDVKFSHSGRYILSRDYLT 294 (433)
T ss_pred hhceEEccCCcEEEEeccce
Confidence 46778876 9999999984
No 21
>PRK14631 hypothetical protein; Provisional
Probab=29.49 E-value=1.1e+02 Score=23.21 Aligned_cols=30 Identities=7% Similarity=0.499 Sum_probs=26.7
Q ss_pred EEEEeeecc-cCCCccchhHHHHHhhcceee
Q 043767 30 TFTIDCAKP-VEDKIMDIASLEKFLQERIKV 59 (105)
Q Consensus 30 kF~IDCt~P-veD~I~d~a~FEkFL~erIKV 59 (105)
.|++.-|.| ++.-+....+|+.|+-..++|
T Consensus 92 ~Y~LEVSSPGldRpL~~~~df~r~~G~~V~V 122 (174)
T PRK14631 92 EYALEVSSPGWDRPFFQLEQLQGYIGQQVAL 122 (174)
T ss_pred CeEEEEeCCCCCCcCCCHHHHHHhCCCeEEE
Confidence 699999999 577788899999999999888
No 22
>PRK14630 hypothetical protein; Provisional
Probab=29.42 E-value=2.3e+02 Score=20.75 Aligned_cols=30 Identities=23% Similarity=0.432 Sum_probs=25.9
Q ss_pred EEEEeeeccc-CCCccchhHHHHHhhcceee
Q 043767 30 TFTIDCAKPV-EDKIMDIASLEKFLQERIKV 59 (105)
Q Consensus 30 kF~IDCt~Pv-eD~I~d~a~FEkFL~erIKV 59 (105)
.|++.-|.|- +--+....+|+.|+-+.++|
T Consensus 72 ~Y~LEVSSPGldRpL~~~~df~r~~G~~v~V 102 (143)
T PRK14630 72 NFSLEISTPGINRKIKSDREFKIFEGKKIKL 102 (143)
T ss_pred CeEEEEeCCCCCCcCCCHHHHHHhCCCEEEE
Confidence 5889999884 66677899999999999999
No 23
>PRK14636 hypothetical protein; Provisional
Probab=28.80 E-value=82 Score=23.97 Aligned_cols=31 Identities=3% Similarity=0.362 Sum_probs=25.9
Q ss_pred eEEEEeeecc-cCCCccchhHHHHHhhcceee
Q 043767 29 ATFTIDCAKP-VEDKIMDIASLEKFLQERIKV 59 (105)
Q Consensus 29 ~kF~IDCt~P-veD~I~d~a~FEkFL~erIKV 59 (105)
..|++.-|.| ++--+..+.+|+.|+-..++|
T Consensus 72 ~~Y~LEVSSPGldRpL~~~~df~r~~G~~V~V 103 (176)
T PRK14636 72 DAYRLEVSSPGIDRPLTRPKDFADWAGHEARI 103 (176)
T ss_pred CCeEEEEeCCCCCCCCCCHHHHHHhCCCeEEE
Confidence 3689999999 466677799999999998888
No 24
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=28.29 E-value=38 Score=19.49 Aligned_cols=21 Identities=14% Similarity=0.208 Sum_probs=15.6
Q ss_pred ecccCCCccchhHHHHHhhcc
Q 043767 36 AKPVEDKIMDIASLEKFLQER 56 (105)
Q Consensus 36 t~PveD~I~d~a~FEkFL~er 56 (105)
--+-.||.++..+|-.+++.|
T Consensus 34 ~D~~~~G~I~~~EF~~~~~~~ 54 (54)
T PF13833_consen 34 FDTDGDGYISFDEFISMMQRR 54 (54)
T ss_dssp HTTSSSSSEEHHHHHHHHHHH
T ss_pred cccCCCCCCCHHHHHHHHHhC
Confidence 345578888888888888764
No 25
>PF10986 DUF2796: Protein of unknown function (DUF2796); InterPro: IPR021253 This bacterial family of proteins has no known function.
Probab=28.19 E-value=63 Score=24.46 Aligned_cols=48 Identities=25% Similarity=0.324 Sum_probs=33.9
Q ss_pred eeEEEEeeecccCCCccchhHHHHHhh-cceeeccccCCCCCeEEEEee
Q 043767 28 GATFTIDCAKPVEDKIMDIASLEKFLQ-ERIKVGGKAGALGDTVTVTRD 75 (105)
Q Consensus 28 ~~kF~IDCt~PveD~I~d~a~FEkFL~-erIKVnGKtgnLg~~V~i~r~ 75 (105)
...|+..|..|..=.-||+.=|+.|=. ++|.|+--+.+=-....+++.
T Consensus 116 ~a~Y~f~C~~p~~L~~i~~~~F~~FP~~e~i~Vq~it~~gQ~a~~Lt~~ 164 (168)
T PF10986_consen 116 HAEYTFHCANPAALSSIDTQLFKAFPGTEKIDVQWITPKGQGAAELTPD 164 (168)
T ss_pred EEEEEEEcCCHHHhceehhhhHhhCCCccEEEEEEECCCCcceeEeCCC
Confidence 458999999998878899999999954 688886444432233444443
No 26
>PF08980 DUF1883: Domain of unknown function (DUF1883); InterPro: IPR015073 This family consist of hypothetical bacterial proteins. ; PDB: 2B1Y_A.
Probab=27.27 E-value=35 Score=24.14 Aligned_cols=25 Identities=12% Similarity=0.352 Sum_probs=10.6
Q ss_pred EEEEeeecccCCCccchhHHHHHhh
Q 043767 30 TFTIDCAKPVEDKIMDIASLEKFLQ 54 (105)
Q Consensus 30 kF~IDCt~PveD~I~d~a~FEkFL~ 54 (105)
.-+|.|+++..=-.||.++|+.|=.
T Consensus 16 ~V~V~ls~~~nV~LMd~~Nf~~y~~ 40 (94)
T PF08980_consen 16 TVVVRLSHQANVRLMDDSNFQRYKN 40 (94)
T ss_dssp ------SSS-------HHHHHHHHH
T ss_pred EEEEEeCCcccEEEcChhHhhhhcc
Confidence 4568999999888999999999954
No 27
>KOG2775 consensus Metallopeptidase [General function prediction only]
Probab=26.08 E-value=14 Score=31.90 Aligned_cols=17 Identities=29% Similarity=0.415 Sum_probs=13.4
Q ss_pred ecccccceee----hhhhhhcc
Q 043767 83 SDSNFSKRYL----LLKRLLKL 100 (105)
Q Consensus 83 s~~pfSKRYL----LTKKyLKK 100 (105)
+..||++||| .|| ||.-
T Consensus 330 gTLaFcrR~lDrlGetK-yLmA 350 (397)
T KOG2775|consen 330 GTLAFCRRWLDRLGETK-YLMA 350 (397)
T ss_pred ccccccHHHHHHhhhHH-HHHH
Confidence 4578999999 776 8854
No 28
>PF10698 DUF2505: Protein of unknown function (DUF2505); InterPro: IPR019639 This entry represents proteins found Actinobacteria and Proteobacteria. The function is not known.
Probab=25.99 E-value=62 Score=23.26 Aligned_cols=67 Identities=15% Similarity=0.231 Sum_probs=41.6
Q ss_pred EEEEeeecccCCCccchhHHHHHhhcceeeccccCC-CCCeEEEEeeCCeEEEEecccccceee--hhhhhhcc
Q 043767 30 TFTIDCAKPVEDKIMDIASLEKFLQERIKVGGKAGA-LGDTVTVTRDKTKITVLSDSNFSKRYL--LLKRLLKL 100 (105)
Q Consensus 30 kF~IDCt~PveD~I~d~a~FEkFL~erIKVnGKtgn-Lg~~V~i~r~k~kI~V~s~~pfSKRYL--LTKKyLKK 100 (105)
.+++++.+|+++ ++.+=.=|.|+++|..- .|. ......++.+++.+.|+..-..+...| +-+|+++.
T Consensus 2 ~~~~~~~~~~~~-v~~~~~d~~y~~~r~~~---~g~~~~~~~~~~~~~~g~~v~~~~~v~~~~lP~~~~k~v~~ 71 (159)
T PF10698_consen 2 EHSVEYPAPVER-VWAAFTDEDYWEARCAA---LGADNAEVESFEVDGDGVRVTVRQTVPADKLPSAARKFVGG 71 (159)
T ss_pred eEEEEcCCCHHH-HHHHHcCHHHHHHHHHH---cCCCCceEEEEEEcCCeEEEEEEEecChhhCCHHHHHhcCC
Confidence 467888889864 44333337888887753 233 344566777776677666555566667 66666654
No 29
>cd07675 F-BAR_FNBP1L The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Formin Binding Protein 1-Like. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FormiN Binding Protein 1-Like (FNBP1L), also known as Toca-1 (Transducer of Cdc42-dependent actin assembly), forms a complex with neural Wiskott-Aldrich syndrome protein (N-WASP). The FNBP1L/N-WASP complex induces the formation of filopodia and endocytic vesicles. FNBP1L is required for Cdc42-induced actin assembly and is essential for autophagy of intracellular pathogens. It contains an N-terminal F-BAR domain, a central Cdc42-binding HR1 domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=25.90 E-value=11 Score=30.31 Aligned_cols=40 Identities=23% Similarity=0.351 Sum_probs=30.7
Q ss_pred cCCCccchhHHHHHhhcceeeccccCCCCCeEEEEeeCCeEEEEecccccceee-hhhhhhcccc
Q 043767 39 VEDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDKTKITVLSDSNFSKRYL-LLKRLLKLPC 102 (105)
Q Consensus 39 veD~I~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k~kI~V~s~~pfSKRYL-LTKKyLKK~~ 102 (105)
|.+||-=+.++++|++||-.+. ..+|+... |+|+|.-|..
T Consensus 14 ~~~Gi~~l~~~~~F~keRa~IE------------------------~eYakkL~~L~Kky~~KK~ 54 (252)
T cd07675 14 TQWGIDFLERYAKFVKERLEIE------------------------QNYAKQLRNLVKKYCPKRS 54 (252)
T ss_pred HHhhHHHHHHHHHHHHHHHHHH------------------------HHHHHHHHHHHHHhccccC
Confidence 4677777889999999987762 34788888 8888876654
No 30
>PRK10811 rne ribonuclease E; Reviewed
Probab=25.54 E-value=44 Score=32.49 Aligned_cols=28 Identities=21% Similarity=0.462 Sum_probs=21.4
Q ss_pred CCe--EEEEee--CCe-EEEEecccccceee-hh
Q 043767 67 GDT--VTVTRD--KTK-ITVLSDSNFSKRYL-LL 94 (105)
Q Consensus 67 g~~--V~i~r~--k~k-I~V~s~~pfSKRYL-LT 94 (105)
|+. |+|.++ ++| -.||+.+-|..||| ||
T Consensus 97 GqeILVQV~KEa~gtKGp~LTt~ISLpGRYLVLt 130 (1068)
T PRK10811 97 GQEVIVQIDKEERGNKGAALTTFISLAGSYLVLM 130 (1068)
T ss_pred CCEEEEEEeecccCCCCCceeeeEEecceeEEEe
Confidence 664 566665 455 88999999999999 54
No 31
>PRK14632 hypothetical protein; Provisional
Probab=25.33 E-value=1.1e+02 Score=23.21 Aligned_cols=30 Identities=10% Similarity=0.483 Sum_probs=25.8
Q ss_pred EEEEeeecc-cCCCccchhHHHHHhhcceee
Q 043767 30 TFTIDCAKP-VEDKIMDIASLEKFLQERIKV 59 (105)
Q Consensus 30 kF~IDCt~P-veD~I~d~a~FEkFL~erIKV 59 (105)
.|++.-|.| ++.-+....+|+.|+-..++|
T Consensus 73 ~Y~LEVSSPGldRpL~~~~~f~r~iG~~V~V 103 (172)
T PRK14632 73 AYVLEVSSPGLERPFFRAEQMSPYVGRQIEL 103 (172)
T ss_pred CeEEEEeCCCCCCcCCCHHHHHHhCCCEEEE
Confidence 689999998 466677799999999999998
No 32
>PRK14645 hypothetical protein; Provisional
Probab=25.18 E-value=2e+02 Score=21.43 Aligned_cols=32 Identities=16% Similarity=0.393 Sum_probs=26.8
Q ss_pred eEEEEeeecc-cCCCccchhHHHHHhhcceeec
Q 043767 29 ATFTIDCAKP-VEDKIMDIASLEKFLQERIKVG 60 (105)
Q Consensus 29 ~kF~IDCt~P-veD~I~d~a~FEkFL~erIKVn 60 (105)
..|++.-|.| ++.-+....+|++|+-..++|.
T Consensus 76 ~~Y~LEVSSPGldRpL~~~~df~r~~G~~v~v~ 108 (154)
T PRK14645 76 GEYRLEVESPGPKRPLFTARHFERFAGLKAKVR 108 (154)
T ss_pred CceEEEEeCCCCCCCCCCHHHHHHhCCCEEEEE
Confidence 3688888888 5777778999999999999994
No 33
>PHA03383 PCNA-like protein; Provisional
Probab=25.09 E-value=70 Score=25.49 Aligned_cols=32 Identities=6% Similarity=0.295 Sum_probs=18.7
Q ss_pred cchhHHHHHhhcceeeccccCCCCCeEEEEeeCCeEEEE
Q 043767 44 MDIASLEKFLQERIKVGGKAGALGDTVTVTRDKTKITVL 82 (105)
Q Consensus 44 ~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k~kI~V~ 82 (105)
|+.+.|.+.+++ ...+|+.|.|+.+++.|.+.
T Consensus 146 m~s~~f~~i~kd-------l~~igD~v~i~~~~~~v~f~ 177 (262)
T PHA03383 146 LPSNYFQRLCRD-------MSNITDDLEITKKGKEVSFR 177 (262)
T ss_pred EEHHHHHHHHHH-------HHHcCCeEEEEEeCCEEEEE
Confidence 456667776665 22346666666666555554
No 34
>cd00559 Cyanase_C Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the toxicity of environmental cyanate and to use cyanate as a source of nitrogen for growth. This enzyme is a homodecamer, formed by five dimers. Each monomer is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain.
Probab=24.58 E-value=60 Score=22.03 Aligned_cols=31 Identities=29% Similarity=0.380 Sum_probs=19.0
Q ss_pred CCCccchhHHHHHhhcceeeccccCCCCCeEEEEeeC
Q 043767 40 EDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDK 76 (105)
Q Consensus 40 eD~I~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k 76 (105)
-||||++=+|. +.|+-..+.-|+.|.|+-++
T Consensus 31 GDGIMSAIdF~------~~v~k~~dp~gdRvvit~~G 61 (69)
T cd00559 31 GDGIMSAIDFK------LDVDKVEDPGGDRVVITLDG 61 (69)
T ss_pred CCceeeeEEee------eeEEeccCCCCCEEEEEEcc
Confidence 68999887774 34444444446666665443
No 35
>PRK14637 hypothetical protein; Provisional
Probab=24.27 E-value=1.8e+02 Score=21.51 Aligned_cols=30 Identities=27% Similarity=0.495 Sum_probs=25.4
Q ss_pred EEEEeeecc-cCCCccchhHHHHHhhcceee
Q 043767 30 TFTIDCAKP-VEDKIMDIASLEKFLQERIKV 59 (105)
Q Consensus 30 kF~IDCt~P-veD~I~d~a~FEkFL~erIKV 59 (105)
.|++.-|.| ++--+..+.+|+.|+-..++|
T Consensus 73 ~y~LEVSSPGldRpL~~~~~f~r~~G~~V~V 103 (151)
T PRK14637 73 DVFLEVSSPGIERVIKNAAEFSIFVGETVKV 103 (151)
T ss_pred CcEEEEeCCCCCCCCCCHHHHHHhCCCEEEE
Confidence 478888888 466677899999999999999
No 36
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=24.16 E-value=1.2e+02 Score=22.09 Aligned_cols=31 Identities=16% Similarity=0.488 Sum_probs=26.3
Q ss_pred EEEEeeeccc-CCCccchhHHHHHhhcceeec
Q 043767 30 TFTIDCAKPV-EDKIMDIASLEKFLQERIKVG 60 (105)
Q Consensus 30 kF~IDCt~Pv-eD~I~d~a~FEkFL~erIKVn 60 (105)
.|++.-|.|- +.-+..+.+|+.|+-..++|.
T Consensus 73 ~Y~LEVSSPGi~RpL~~~~~f~r~~G~~v~V~ 104 (154)
T PRK00092 73 AYTLEVSSPGLDRPLKKARDFRRFIGREVKVK 104 (154)
T ss_pred CeEEEEeCCCCCCcCCCHHHHHHhCCCeEEEE
Confidence 5999999994 666677899999999999984
No 37
>PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm
Probab=23.99 E-value=1.3e+02 Score=19.15 Aligned_cols=18 Identities=22% Similarity=0.305 Sum_probs=15.7
Q ss_pred CCCeEEEEeeCCeEEEEe
Q 043767 66 LGDTVTVTRDKTKITVLS 83 (105)
Q Consensus 66 Lg~~V~i~r~k~kI~V~s 83 (105)
.|+.|+|+...++|++++
T Consensus 40 ~G~~v~V~v~~g~lvIt~ 57 (57)
T PF08845_consen 40 IGDPVKVRVMPGCLVITP 57 (57)
T ss_pred CCCEEEEEEECCEEEEeC
Confidence 588999999999998874
No 38
>smart00055 FCH Fes/CIP4 homology domain. Alignment extended from original report. Highly alpha-helical. Also known as the RAEYL motif or the S. pombe Cdc15 N-terminal domain.
Probab=23.81 E-value=11 Score=23.97 Aligned_cols=22 Identities=27% Similarity=0.564 Sum_probs=18.0
Q ss_pred cCCCccchhHHHHHhhcceeec
Q 043767 39 VEDKIMDIASLEKFLQERIKVG 60 (105)
Q Consensus 39 veD~I~d~a~FEkFL~erIKVn 60 (105)
+++++-...+|.+|+++|..++
T Consensus 18 ~~~~~~~~~~~~~f~~~Ra~iE 39 (87)
T smart00055 18 LKNGLRLLEDLKKFIRERAKIE 39 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3566777889999999999884
No 39
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=23.47 E-value=59 Score=24.65 Aligned_cols=31 Identities=23% Similarity=0.312 Sum_probs=20.2
Q ss_pred CCCccchhHHHHHhhcceeeccccCCCCCeEEEEeeC
Q 043767 40 EDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDK 76 (105)
Q Consensus 40 eD~I~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k 76 (105)
-||||++=+|- +.|+-..+.-|+.|.|+-++
T Consensus 112 GDGIMSAIdF~------~~v~k~~dp~Gdrv~it~~G 142 (150)
T TIGR00673 112 GDGIMSAIDFK------LDVEKVADPGGERAVITLNG 142 (150)
T ss_pred Ccceeeeeeec------eeeeeecCCCCCEEEEEecc
Confidence 68999887763 45555555666667665543
No 40
>PF09279 EF-hand_like: Phosphoinositide-specific phospholipase C, efhand-like; InterPro: IPR015359 This domain is predominantly found in the enzyme phosphoinositol-specific phospholipase C. It adopts a structure consisting of a core of four alpha helices, in an EF like fold, and is required for functioning of the enzyme []. ; PDB: 3OHM_B 3QR0_A 2ZKM_X 2FJU_B 3QR1_D 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B ....
Probab=23.05 E-value=51 Score=20.83 Aligned_cols=17 Identities=24% Similarity=0.569 Sum_probs=14.2
Q ss_pred CCCccchhHHHHHhhcc
Q 043767 40 EDKIMDIASLEKFLQER 56 (105)
Q Consensus 40 eD~I~d~a~FEkFL~er 56 (105)
....|++.+|.+||++.
T Consensus 12 ~~~~mt~~~f~~FL~~e 28 (83)
T PF09279_consen 12 DKEYMTAEEFRRFLREE 28 (83)
T ss_dssp TSSSEEHHHHHHHHHHT
T ss_pred CCCcCCHHHHHHHHHHH
Confidence 35789999999999873
No 41
>PRK02866 cyanate hydratase; Validated
Probab=23.03 E-value=63 Score=24.41 Aligned_cols=31 Identities=29% Similarity=0.404 Sum_probs=19.7
Q ss_pred CCCccchhHHHHHhhcceeeccccCCCCCeEEEEeeC
Q 043767 40 EDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDK 76 (105)
Q Consensus 40 eD~I~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k 76 (105)
-||||++=+|- +.|+-..+.-|+.|.|+-++
T Consensus 109 GDGIMSAIdf~------~~v~k~~dp~Gdrv~it~~G 139 (147)
T PRK02866 109 GDGIMSAIDFK------LDVDKVEDPKGDRVVITLDG 139 (147)
T ss_pred CCceeeeeeec------eeeeeccCCCCCEEEEEecc
Confidence 68999887773 44554455556666665543
No 42
>PF04006 Mpp10: Mpp10 protein; InterPro: IPR007151 This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites [].
Probab=23.01 E-value=49 Score=29.36 Aligned_cols=18 Identities=28% Similarity=0.455 Sum_probs=16.1
Q ss_pred ccCCCccchhHHHHHhhc
Q 043767 38 PVEDKIMDIASLEKFLQE 55 (105)
Q Consensus 38 PveD~I~d~a~FEkFL~e 55 (105)
-|+|+.|++.+|++|+..
T Consensus 183 glnD~FFsidEfnk~~e~ 200 (600)
T PF04006_consen 183 GLNDGFFSIDEFNKQLEE 200 (600)
T ss_pred CcCCCcCCHHHHHHHHHH
Confidence 379999999999999965
No 43
>PF02560 Cyanate_lyase: Cyanate lyase C-terminal domain; InterPro: IPR003712 Some bacteria can overcome the toxicity of environmental cyanate by hydrolysis of cyanate. This reaction is catalyzed by cyanate lyase (also known as cyanase) []. Cyanate lyase is found in bacteria and plants and catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. The cyanate lyase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer []. ; GO: 0008824 cyanate hydratase activity, 0009439 cyanate metabolic process; PDB: 2IV1_B 2IUO_A 2IVQ_B 1DW9_A 1DWK_E 2IVG_G 2IU7_J 2IVB_A.
Probab=22.76 E-value=31 Score=23.65 Aligned_cols=31 Identities=26% Similarity=0.386 Sum_probs=18.8
Q ss_pred CCCccchhHHHHHhhcceeeccccCCCCCeEEEEeeC
Q 043767 40 EDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDK 76 (105)
Q Consensus 40 eD~I~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k 76 (105)
-||||++=+| ++.|+-..+.-|+.|.|+-++
T Consensus 35 GDGIMSAIdF------~~~v~k~~d~~GdRv~it~~G 65 (73)
T PF02560_consen 35 GDGIMSAIDF------KMDVEKVEDPKGDRVVITMNG 65 (73)
T ss_dssp -SEEEEEEEE------EEEEEEEE-TTSEEEEEEEEE
T ss_pred CcceEEEeeE------EEEEEEeeCCCCCEEEEEEec
Confidence 5888888776 455655566667666665543
No 44
>PF05481 Myco_19_kDa: Mycobacterium 19 kDa lipoprotein antigen; InterPro: IPR008691 Most of the antigens of Mycobacterium leprae and Mycobacterium tuberculosis that have been identified are members of stress protein families, which are highly conserved throughout many diverse species. Of the M. leprae and M. tuberculosis antigens identified by monoclonal antibodies, all except the 18 kDa M. leprae antigen and the 19 kDa M. tuberculosis antigen are strongly cross-reactive between these two species and are coded within very similar genes [, ].; GO: 0016020 membrane
Probab=22.38 E-value=1.4e+02 Score=22.77 Aligned_cols=33 Identities=21% Similarity=0.272 Sum_probs=26.0
Q ss_pred cceeeccccCCCCCeEEEEeeCCeEEEEecccc
Q 043767 55 ERIKVGGKAGALGDTVTVTRDKTKITVLSDSNF 87 (105)
Q Consensus 55 erIKVnGKtgnLg~~V~i~r~k~kI~V~s~~pf 87 (105)
.++.|||+.-+....|+++.....+.|...-..
T Consensus 51 ~~VtVdG~~~~~~~~V~C~~~~g~~~I~ig~~~ 83 (160)
T PF05481_consen 51 TKVTVDGKDQNVTGPVTCSQTGGKTTIAIGDAP 83 (160)
T ss_pred CEEEECCCccCCCcCeEEeecCCEEEEEeCCCC
Confidence 388999999888778999998888777654433
No 45
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=21.99 E-value=64 Score=16.97 Aligned_cols=15 Identities=27% Similarity=0.505 Sum_probs=13.4
Q ss_pred CCCccchhHHHHHhh
Q 043767 40 EDKIMDIASLEKFLQ 54 (105)
Q Consensus 40 eD~I~d~a~FEkFL~ 54 (105)
.||.++.++|...|.
T Consensus 13 ~dG~I~~~el~~~l~ 27 (31)
T PF13405_consen 13 GDGFIDFEELRAILR 27 (31)
T ss_dssp SSSEEEHHHHHHHHH
T ss_pred CCCcCcHHHHHHHHH
Confidence 589999999999986
No 46
>PF14819 QueF_N: Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term; PDB: 3UXV_C 3RJB_A 3BP1_D 3RZP_B 3RJ4_A 3UXJ_C 3S19_D 3RZQ_B.
Probab=20.74 E-value=78 Score=23.08 Aligned_cols=24 Identities=29% Similarity=0.600 Sum_probs=19.9
Q ss_pred eEEEEeeecccCCCccchhHHHHHhhc
Q 043767 29 ATFTIDCAKPVEDKIMDIASLEKFLQE 55 (105)
Q Consensus 29 ~kF~IDCt~PveD~I~d~a~FEkFL~e 55 (105)
.+|+|+|+.| .|+..-+|.=||..
T Consensus 55 ~~~~vpa~Sp---niIESKSfKLYLNS 78 (110)
T PF14819_consen 55 AEFTVPADSP---NIIESKSFKLYLNS 78 (110)
T ss_dssp EEEEEETTSS---EEE-HHHHHHHHHT
T ss_pred EEEEecCCCC---cceeechhhhhhcc
Confidence 4899999999 79999999988853
No 47
>PF09066 B2-adapt-app_C: Beta2-adaptin appendage, C-terminal sub-domain; InterPro: IPR015151 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents a subdomain of the appendage (ear) domain of beta-adaptin from AP clathrin adaptor complexes. This domain has a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet []. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15) []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1E42_B 2G30_A 2IV9_B 2IV8_A 3HS9_A 3H1Z_A.
Probab=20.52 E-value=55 Score=22.01 Aligned_cols=15 Identities=33% Similarity=0.472 Sum_probs=6.0
Q ss_pred cCCCccchhHHHHHh
Q 043767 39 VEDKIMDIASLEKFL 53 (105)
Q Consensus 39 veD~I~d~a~FEkFL 53 (105)
|+|+-||.++|++-=
T Consensus 2 ~~d~~~~~~~F~~~W 16 (114)
T PF09066_consen 2 VEDGSMDPEEFQEMW 16 (114)
T ss_dssp -TT----HHHHHHHH
T ss_pred CCCCccCHHHHHHHH
Confidence 456666666666543
No 48
>PF09386 ParD: Antitoxin ParD; InterPro: IPR018985 ParD is a plasmid anti-toxin than forms a ribbon-helix-helix DNA binding structure []. It stabilises plasmids by inhibiting ParE toxicity in cells that express ParD and ParE. ParD forms a dimer and also regulates its own promoter (parDE). ; PDB: 2AN7_A.
Probab=20.50 E-value=44 Score=23.21 Aligned_cols=37 Identities=27% Similarity=0.381 Sum_probs=17.5
Q ss_pred EEEEeeeccc-CCCccchhHHHHHhhcceeeccccCCCC
Q 043767 30 TFTIDCAKPV-EDKIMDIASLEKFLQERIKVGGKAGALG 67 (105)
Q Consensus 30 kF~IDCt~Pv-eD~I~d~a~FEkFL~erIKVnGKtgnLg 67 (105)
.|++.-.-|. .|.---..+++.||.+||. .|..|++.
T Consensus 29 qYalErl~p~~~d~~~Aw~eL~~lL~~Ri~-~g~~G~vs 66 (79)
T PF09386_consen 29 QYALERLFPGDADADQAWQELKALLGERIA-QGLAGKVS 66 (79)
T ss_dssp HHHHHHCS---SSHHHHHHHHCHHS-S----SS-SS--S
T ss_pred HHHHHHhCCCCcchHHHHHHHHHHHHHHHH-HHHcCCCc
Confidence 3444444453 3333336679999999996 88888864
No 49
>PTZ00113 proliferating cell nuclear antigen; Provisional
Probab=20.39 E-value=1.3e+02 Score=24.27 Aligned_cols=33 Identities=18% Similarity=0.324 Sum_probs=20.1
Q ss_pred cchhHHHHHhhcceeeccccCCCCCeEEEEeeCCeEEEEe
Q 043767 44 MDIASLEKFLQERIKVGGKAGALGDTVTVTRDKTKITVLS 83 (105)
Q Consensus 44 ~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k~kI~V~s 83 (105)
|+.+.|.+.+++ ...+|+.|+|+.+++.|.+.+
T Consensus 141 m~s~~f~~i~rd-------l~~vgd~V~i~~~~~~v~f~a 173 (275)
T PTZ00113 141 LSSKELTNICRQ-------MNEFSDTVKIEIDSNSIKFTT 173 (275)
T ss_pred EEHHHHHHHHHH-------HHHcCCEEEEEEeCCEEEEEE
Confidence 567778888776 224456666666655555443
No 50
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=20.37 E-value=2.4e+02 Score=25.93 Aligned_cols=79 Identities=25% Similarity=0.327 Sum_probs=53.3
Q ss_pred hhhccccC-CCCCCCCCCCccceeEEEEeeecccCCCccchhHHHHHhhcceeeccccCCCCCeEEEEeeCCeEE-----
Q 043767 7 ERTMSRGS-GGAAGGGAKGKKKGATFTIDCAKPVEDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDKTKIT----- 80 (105)
Q Consensus 7 ~~~m~~~~-~~~~~~~~k~kK~~~kF~IDCt~PveD~I~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k~kI~----- 80 (105)
+.||.--. .+.++..|+.+-..|+|+ +..|..|+-+++|..-.|=|+ .++..+ ..-|.|+|.+..|.
T Consensus 148 ~~TMSvHLKeg~~P~aK~GkpG~~k~v-----~l~d~pl~~~ele~ia~eIi~-~a~~~~-~sfIEi~r~GatVvQlrn~ 220 (604)
T COG1855 148 EETMSVHLKEGVPPMAKKGKPGEWKLV-----RLSDKPLTREELEEIAREIIE-RAKRDP-DSFIEIDRPGATVVQLRNY 220 (604)
T ss_pred CcceEEeeccCCCcccccCCCCcEEEE-----EcCCccCCHHHHHHHHHHHHH-HHhhCc-CceEEEccCCceEEEeccE
Confidence 44555331 122333366677788986 568888999999999988665 566665 66788888766543
Q ss_pred --EEecccccceee
Q 043767 81 --VLSDSNFSKRYL 92 (105)
Q Consensus 81 --V~s~~pfSKRYL 92 (105)
+-+.-|||-|+=
T Consensus 221 RIvIarPPfSd~~E 234 (604)
T COG1855 221 RIVIARPPFSDRWE 234 (604)
T ss_pred EEEEecCCCCCceE
Confidence 445668998764
No 51
>COG2098 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.31 E-value=53 Score=24.25 Aligned_cols=58 Identities=29% Similarity=0.327 Sum_probs=34.5
Q ss_pred EEEeeecccCCCccchhHHHHHhhcceeeccccCCCCCeEEEEeeCCeEEE-Eecccccceee
Q 043767 31 FTIDCAKPVEDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDKTKITV-LSDSNFSKRYL 92 (105)
Q Consensus 31 F~IDCt~PveD~I~d~a~FEkFL~erIKVnGKtgnLg~~V~i~r~k~kI~V-~s~~pfSKRYL 92 (105)
|+==|-.||+- =+++++|+=++|-|+|. .=-.+-.|.|.++++|... -.-...|.++|
T Consensus 26 yHqf~GtPvs~--~~a~~le~aI~esi~~Q--P~v~daeV~Id~~~~K~~~~~gYt~LsG~mL 84 (116)
T COG2098 26 YHQFVGTPVSP--GTAESLEKAIEESIKVQ--PFVEDAEVKIDRDKEKLDGEFGYTELSGEML 84 (116)
T ss_pred hhhhcCCcCCc--cchHHHHHHHHHHHhcC--CceeeEEEEecccccccccccceEEeccccE
Confidence 44447788854 45788999999999983 2222345667666555221 11123555655
No 52
>PF07683 CobW_C: Cobalamin synthesis protein cobW C-terminal domain; InterPro: IPR011629 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [].; PDB: 1NIJ_A.
Probab=20.27 E-value=1.4e+02 Score=18.90 Aligned_cols=21 Identities=38% Similarity=0.661 Sum_probs=15.5
Q ss_pred EEEEeeecccCCCccchhHHHHHhhc
Q 043767 30 TFTIDCAKPVEDKIMDIASLEKFLQE 55 (105)
Q Consensus 30 kF~IDCt~PveD~I~d~a~FEkFL~e 55 (105)
.|++....| +|.+.|+.||++
T Consensus 3 s~~~~~~~p-----~~~~~l~~~l~~ 23 (94)
T PF07683_consen 3 SVTFEFDRP-----FDPERLEAWLQE 23 (94)
T ss_dssp EEEEEESS------B-HHHHHHHHHH
T ss_pred EEEEEeCCC-----CCHHHHHHHHHh
Confidence 466666666 789999999998
No 53
>PRK10598 lipoprotein; Provisional
Probab=20.26 E-value=72 Score=24.86 Aligned_cols=42 Identities=19% Similarity=0.382 Sum_probs=29.1
Q ss_pred cchhHHHHHhhcceeeccccCCCCC----------eEEEEeeC-CeEEEEecc
Q 043767 44 MDIASLEKFLQERIKVGGKAGALGD----------TVTVTRDK-TKITVLSDS 85 (105)
Q Consensus 44 ~d~a~FEkFL~erIKVnGKtgnLg~----------~V~i~r~k-~kI~V~s~~ 85 (105)
+.-++.++||.+++.+.-+.|.-|- .|+|.|+. ++|.|+++.
T Consensus 27 ISE~Ein~yL~k~~~~~k~~G~~gl~~a~i~l~~l~~~IGr~~~~~v~l~g~a 79 (186)
T PRK10598 27 ISEQEINQYLAKHNNFEKQIGLPGVADAHIVLTNLTSQIGREEPNKVTLTGDA 79 (186)
T ss_pred ecHHHHHHHHHHhccHHHhcCCCceeeeEEEeeeceeecCCCCCCEEEEecee
Confidence 3456689999999988777772221 46677764 788888743
No 54
>PF00611 FCH: Fes/CIP4, and EFC/F-BAR homology domain; InterPro: IPR001060 The FCH domain is a short conserved region of around 60 amino acids first described as a region of homology between FER and CIP4 proteins []. Many proteins containing an FCH domain are involved in the regulation of cytoskeletal rearrangements, vesicular transport and endocytosis. In the CIP4 protein the FCH domain binds to microtubules []. The FCH domain is always found N-terminally and is followed by a coiled-coil region. Proteins containing an FCH domain can be divided in 3 classes []: A subfamily of protein kinases usually associated with an SH2 domain: Fps/fes (Fujimani poultry sarcoma/feline sarcoma) proto-oncogenes. They are non-receptor protein-tyrosine kinases preferentially expressed in myeloid lineage. The viral oncogene has an unregulated kinase activity which abrogates the need for cytokines and influences differentiation of haematopoietic progenitor cells. Fes related protein (fer). It is an ubiquitously expressed homologue of Fes. Adaptor proteins usually associated with a C-terminal SH3 domain: Schizosaccharomyces pombe CDC15 protein. It mediates cytoskeletal rearrangements required for cytokinesis. It is essential for viability. CD2 cytoplasmic domain binding protein. Mammalian Cdc42-interacting protein 4 (CIP4). It may act as a link between Cdc42 signaling and regulation of the actin cytoskeleton. Mammalian PACSIN proteins. A family of cytoplasmic phosphoproteins playing a role in vesicle formation and transport. A subfamily of Rho-GAP proteins: Mammalian RhoGAP4 proteins. They may down-regulate Rho-like GTPases in hematopoietic cells. Yeast hypothetical protein YBR260C. Caenorhabditis elegans hypothetical protein ZK669.1. ; PDB: 2EFK_A 2EFL_A 2X3W_A 2X3X_C 2X3V_C 3I2W_A 3ABH_B 3Q0K_B 3HAJ_A 3ACO_B ....
Probab=20.22 E-value=10 Score=23.85 Aligned_cols=21 Identities=24% Similarity=0.411 Sum_probs=16.9
Q ss_pred CCCccchhHHHHHhhcceeec
Q 043767 40 EDKIMDIASLEKFLQERIKVG 60 (105)
Q Consensus 40 eD~I~d~a~FEkFL~erIKVn 60 (105)
++++-...++..|+++|+.+.
T Consensus 19 ~~~~~~~~~l~~~~keRa~lE 39 (91)
T PF00611_consen 19 KQGIKLLEELASFFKERASLE 39 (91)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 456677889999999998774
Done!