Query 032134
Match_columns 146
No_of_seqs 41 out of 43
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 10:03:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032134.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032134hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12732 YtxH: YtxH-like prote 96.7 0.00048 1E-08 46.9 0.1 28 77-104 1-28 (74)
2 COG4980 GvpP Gas vesicle prote 93.0 0.035 7.6E-07 42.6 0.6 33 73-105 3-35 (115)
3 PTZ00234 variable surface prot 68.4 2.5 5.5E-05 38.3 1.2 52 76-130 362-417 (433)
4 PF07882 Fucose_iso_N2: L-fuco 62.4 4.2 9.1E-05 33.7 1.3 44 82-125 5-51 (181)
5 PF11240 DUF3042: Protein of u 59.0 8 0.00017 26.5 2.0 44 76-133 3-46 (54)
6 PF08566 Pam17: Mitochondrial 53.7 6.8 0.00015 32.1 1.1 25 83-107 82-106 (173)
7 PF01594 UPF0118: Domain of un 49.5 8.6 0.00019 30.9 1.1 28 76-103 292-319 (327)
8 PRK13818 ribosome-binding fact 46.5 7.1 0.00015 29.4 0.2 32 96-134 71-104 (121)
9 PF13664 DUF4149: Domain of un 46.1 6.8 0.00015 27.0 0.0 39 79-121 3-42 (101)
10 TIGR00082 rbfA ribosome-bindin 46.0 7.4 0.00016 28.8 0.2 33 96-135 71-105 (114)
11 PF02033 RBFA: Ribosome-bindin 45.6 7.5 0.00016 27.5 0.2 33 96-135 67-101 (104)
12 PRK00521 rbfA ribosome-binding 45.0 8.5 0.00018 28.4 0.4 32 95-133 72-105 (120)
13 PF09813 Coiled-coil_56: Coile 43.7 8.2 0.00018 29.5 0.1 20 76-95 51-70 (100)
14 PF05283 MGC-24: Multi-glycosy 42.3 8.7 0.00019 31.6 0.1 20 73-95 159-178 (186)
15 KOG2408 Peroxidase/oxygenase [ 37.4 20 0.00043 34.6 1.7 23 83-105 624-646 (719)
16 PF04971 Lysis_S: Lysis protei 36.9 15 0.00032 26.3 0.6 14 82-95 38-51 (68)
17 TIGR01089 fucI L-fucose isomer 33.4 27 0.00059 33.5 1.9 53 82-134 176-234 (587)
18 PF10779 XhlA: Haemolysin XhlA 33.2 20 0.00043 24.4 0.7 18 78-95 53-70 (71)
19 PRK13815 ribosome-binding fact 33.0 15 0.00033 27.6 0.2 31 96-133 70-102 (122)
20 cd08321 Pyrin_ASC-like Pyrin D 33.0 15 0.00032 25.9 0.1 37 97-135 32-68 (82)
21 TIGR02872 spore_ytvI sporulati 30.4 26 0.00057 28.1 1.1 29 76-104 305-333 (341)
22 PRK10983 putative inner membra 30.2 64 0.0014 28.0 3.5 29 75-103 309-337 (368)
23 cd03556 L-fucose_isomerase L-f 28.5 37 0.0008 32.7 1.9 54 82-135 173-232 (584)
24 PRK13816 ribosome-binding fact 26.6 23 0.00049 27.1 0.1 32 95-133 77-110 (131)
25 PF04505 Dispanin: Interferon- 26.5 24 0.00053 24.8 0.2 43 88-144 33-76 (82)
26 PF14034 Spore_YtrH: Sporulati 25.4 30 0.00064 26.4 0.6 17 80-96 12-28 (102)
27 PF14242 DUF4342: Domain of un 24.9 39 0.00085 24.4 1.1 18 84-101 50-67 (84)
28 PRK13817 ribosome-binding fact 23.2 29 0.00064 26.0 0.2 31 96-133 69-101 (119)
29 PF06682 DUF1183: Protein of u 21.2 51 0.0011 29.1 1.3 26 70-99 247-272 (318)
30 COG4177 LivM ABC-type branched 21.0 47 0.001 28.8 1.0 23 78-100 208-230 (314)
31 PHA03048 IMV membrane protein; 20.0 49 0.0011 25.1 0.8 19 79-97 12-30 (93)
No 1
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=96.66 E-value=0.00048 Score=46.87 Aligned_cols=28 Identities=29% Similarity=0.526 Sum_probs=24.3
Q ss_pred eeehhhhhhhhhhhhhhhhhhhhHHHHh
Q 032134 77 FVGGFVLGGIIVGTLGCVYAPQISKALA 104 (146)
Q Consensus 77 Fv~GFlLGGaVfGtLGyvfAPQIskaL~ 104 (146)
|+.||++|+++-.++|++|||+--+-+-
T Consensus 1 F~~g~l~Ga~~Ga~~glL~aP~sG~e~R 28 (74)
T PF12732_consen 1 FLLGFLAGAAAGAAAGLLFAPKSGKETR 28 (74)
T ss_pred CHHHHHHHHHHHHHHHHHhCCCCcHHHH
Confidence 8899999999999999999998555443
No 2
>COG4980 GvpP Gas vesicle protein [General function prediction only]
Probab=93.04 E-value=0.035 Score=42.61 Aligned_cols=33 Identities=30% Similarity=0.507 Sum_probs=29.3
Q ss_pred CCCceeehhhhhhhhhhhhhhhhhhhhHHHHhc
Q 032134 73 SAGFFVGGFVLGGIIVGTLGCVYAPQISKALAG 105 (146)
Q Consensus 73 ~gg~Fv~GFlLGGaVfGtLGyvfAPQIskaL~~ 105 (146)
++++|+.|.++||+|=.+.+-+|||.-.|-|-.
T Consensus 3 ~~~~~l~G~liGgiiGa~aaLL~AP~sGkelR~ 35 (115)
T COG4980 3 KGKDFLFGILIGGIIGAAAALLFAPKSGKELRK 35 (115)
T ss_pred ccchHHHHHHHHHHHHHHHHHHhCCcccHHHHH
Confidence 568999999999999999999999998877763
No 3
>PTZ00234 variable surface protein Vir12; Provisional
Probab=68.43 E-value=2.5 Score=38.32 Aligned_cols=52 Identities=23% Similarity=0.296 Sum_probs=33.8
Q ss_pred ceeehhhhhhhhhhhhhhhhhhhhHHHHhchhhchhHHHhhCCcc---cchh-hHHhhh
Q 032134 76 FFVGGFVLGGIIVGTLGCVYAPQISKALAGAAADRKDLMRKLPKF---IYDE-EKALEV 130 (146)
Q Consensus 76 ~Fv~GFlLGGaVfGtLGyvfAPQIskaL~~~~~d~~~l~rk~pk~---~yDE-ek~LEk 130 (146)
-|+==.+.|.||.||+=++|-=-.|-.|-.-.-.++ ||..+| |||| ||.||+
T Consensus 362 n~~rniim~~ailGtifFlfyyn~ss~lks~~~krk---rkk~~~ehnyyeeyEkel~~ 417 (433)
T PTZ00234 362 EYFRHSIVGASIIGVLVFLFFFFKSTPIRSQTNKGE---KKKRKPQNNYYDEYEEELPR 417 (433)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhcccchhccccchh---hcccchhhhhHHHHHHhhcc
Confidence 355567899999999999997666655554222222 233333 7777 777775
No 4
>PF07882 Fucose_iso_N2: L-fucose isomerase, second N-terminal domain; InterPro: IPR012889 Proteins containing this domain are similar to L-fucose isomerase expressed by Escherichia coli (P11552 from SWISSPROT, 5.3.1.3 from EC). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol cleavage. The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta- sheets with surrounding alpha helices. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting residues []. ; GO: 0008736 L-fucose isomerase activity, 0006004 fucose metabolic process, 0005737 cytoplasm; PDB: 3A9R_A 3A9T_C 3A9S_C 1FUI_E.
Probab=62.39 E-value=4.2 Score=33.72 Aligned_cols=44 Identities=30% Similarity=0.637 Sum_probs=29.8
Q ss_pred hhhhhhhhhhhhhhhhhhHHHHhchh---hchhHHHhhCCcccchhh
Q 032134 82 VLGGIIVGTLGCVYAPQISKALAGAA---ADRKDLMRKLPKFIYDEE 125 (146)
Q Consensus 82 lLGGaVfGtLGyvfAPQIskaL~~~~---~d~~~l~rk~pk~~yDEe 125 (146)
.+||.-.|.-|.++-|+.=..-+|.- -|...+.|+.-.-|||+|
T Consensus 5 ~iG~~sMGIagsivd~~f~~~ylGmr~E~VD~~Ei~RR~e~~iyD~~ 51 (181)
T PF07882_consen 5 SIGGVSMGIAGSIVDPDFFQEYLGMRVEYVDMSEIIRRMEEGIYDEE 51 (181)
T ss_dssp EESS-STT-GGGS--HHHHHHCT--EEEEE-THHHHHHHHCT-S-HH
T ss_pred ccCCccccccccccCHHHHHHHhCCCceeecHHHHHHHHHccCCCHH
Confidence 47899999999999999988887743 588899998888889875
No 5
>PF11240 DUF3042: Protein of unknown function (DUF3042); InterPro: IPR021402 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=58.99 E-value=8 Score=26.54 Aligned_cols=44 Identities=20% Similarity=0.281 Sum_probs=22.5
Q ss_pred ceeehhhhhhhhhhhhhhhhhhhhHHHHhchhhchhHHHhhCCcccchhhHHhhhhhc
Q 032134 76 FFVGGFVLGGIIVGTLGCVYAPQISKALAGAAADRKDLMRKLPKFIYDEEKALEVSHY 133 (146)
Q Consensus 76 ~Fv~GFlLGGaVfGtLGyvfAPQIskaL~~~~~d~~~l~rk~pk~~yDEek~LEkTR~ 133 (146)
.|.-|||+|- ++|+|.+-.- + ..+.++.-+-+.|+|.-.|..|+
T Consensus 3 kF~~G~l~G~--~~t~aa~a~a-----v-------~~~kK~vi~Pie~ke~~~eenRk 46 (54)
T PF11240_consen 3 KFGKGFLTGV--AATLAAIAGA-----V-------FTFKKTVIEPIEEKEAKIEENRK 46 (54)
T ss_pred chhhhHHHhH--HHHHHHHHHH-----H-------HHHHHHhcCcHHHHHHHHHHHHH
Confidence 4778888873 3444433211 1 12223333445566666776665
No 6
>PF08566 Pam17: Mitochondrial import protein Pam17; InterPro: IPR013875 The presequence translocase-associated motor (PAM) drives the completion of preprotein translocation into the mitochondrial matrix. The Pam17 subunit is required for formation of a stable complex between cochaperones Pam16 and Pam18 and promotes the association of Pam16-Pam18 with the presequence translocase []. Mitochondria lacking Pam17 are selectively impaired in the import of matrix proteins [].
Probab=53.71 E-value=6.8 Score=32.14 Aligned_cols=25 Identities=20% Similarity=0.416 Sum_probs=21.6
Q ss_pred hhhhhhhhhhhhhhhhhHHHHhchh
Q 032134 83 LGGIIVGTLGCVYAPQISKALAGAA 107 (146)
Q Consensus 83 LGGaVfGtLGyvfAPQIskaL~~~~ 107 (146)
++.+.+|+||||.-|-|-.+++++.
T Consensus 82 ~~t~a~g~lG~L~GP~~G~~vf~l~ 106 (173)
T PF08566_consen 82 LATLACGALGWLVGPSLGNQVFRLL 106 (173)
T ss_pred HHHHHHHHHHHHhcchHHHHHHHHH
Confidence 5667789999999999999998865
No 7
>PF01594 UPF0118: Domain of unknown function DUF20; InterPro: IPR002549 This is a family of hypothetical proteins. A number of the sequence records state they are transmembrane proteins or putative permeases. It is not clear what source suggested that these proteins might be permeases and this information should be treated with caution.
Probab=49.53 E-value=8.6 Score=30.85 Aligned_cols=28 Identities=25% Similarity=0.618 Sum_probs=23.1
Q ss_pred ceeehhhhhhhhhhhhhhhhhhhhHHHH
Q 032134 76 FFVGGFVLGGIIVGTLGCVYAPQISKAL 103 (146)
Q Consensus 76 ~Fv~GFlLGGaVfGtLGyvfAPQIskaL 103 (146)
--+-+.++|+.+||..|.++||-+--.+
T Consensus 292 ~~l~~~~~g~~~fG~~G~il~~pi~~~~ 319 (327)
T PF01594_consen 292 LILLAVIIGGYLFGFIGLILAPPILAVI 319 (327)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 3456889999999999999999875444
No 8
>PRK13818 ribosome-binding factor A; Provisional
Probab=46.48 E-value=7.1 Score=29.42 Aligned_cols=32 Identities=16% Similarity=0.258 Sum_probs=19.6
Q ss_pred hhhhHHHHhchhhchhHHHhhCCc--ccchhhHHhhhhhcc
Q 032134 96 APQISKALAGAAADRKDLMRKLPK--FIYDEEKALEVSHYF 134 (146)
Q Consensus 96 APQIskaL~~~~~d~~~l~rk~pk--~~yDEek~LEkTR~~ 134 (146)
++.|++.|..-+ . ||+.|. |+||+ ++|+..+.
T Consensus 71 ~g~iR~~la~~l--~---lR~~P~L~F~~D~--s~e~~~~I 104 (121)
T PRK13818 71 KGMMRHLLGQTL--T---VYKVPELIFKRDN--SVAYGSKI 104 (121)
T ss_pred HHHHHHHHHhhC--C---CeECCEEEEEeCC--ChHHHHHH
Confidence 455666665521 1 567776 89998 66665543
No 9
>PF13664 DUF4149: Domain of unknown function (DUF4149)
Probab=46.14 E-value=6.8 Score=26.97 Aligned_cols=39 Identities=31% Similarity=0.483 Sum_probs=26.3
Q ss_pred ehhhhhhhhhhhhhhhhhhhhHHHHhchhhchhHHHhhC-Cccc
Q 032134 79 GGFVLGGIIVGTLGCVYAPQISKALAGAAADRKDLMRKL-PKFI 121 (146)
Q Consensus 79 ~GFlLGGaVfGtLGyvfAPQIskaL~~~~~d~~~l~rk~-pk~~ 121 (146)
.++.+|+.+| .++|.||-+-|+|.. +.--.+++++ |+|+
T Consensus 3 ~~~w~G~~~~--~~fvvap~lF~~L~~--~~ag~i~~~lFp~y~ 42 (101)
T PF13664_consen 3 LALWLGSMVF--FTFVVAPVLFKALPR--QQAGKIQGKLFPKYF 42 (101)
T ss_pred HHHHHHHHHH--HHHHHHHHHHHhCCH--HHHHHHHHHHHHHHH
Confidence 4677888876 456899999999855 4344455555 5443
No 10
>TIGR00082 rbfA ribosome-binding factor A. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'terminal helix region of 16S rRNA. Mutants lacking rbfA have a cold-sensitive phenotype.
Probab=46.05 E-value=7.4 Score=28.83 Aligned_cols=33 Identities=30% Similarity=0.475 Sum_probs=20.3
Q ss_pred hhhhHHHHhchhhchhHHHhhCCc--ccchhhHHhhhhhcce
Q 032134 96 APQISKALAGAAADRKDLMRKLPK--FIYDEEKALEVSHYFD 135 (146)
Q Consensus 96 APQIskaL~~~~~d~~~l~rk~pk--~~yDEek~LEkTR~~l 135 (146)
++.|++.|..-+ . ||+.|+ |+||+ .+|+..+..
T Consensus 71 ~g~iR~~l~k~l--~---lR~~P~L~F~~D~--s~e~~~~i~ 105 (114)
T TIGR00082 71 KGFIRSLLGQAM--R---LRKTPELHFVKDN--SLDKGMRIE 105 (114)
T ss_pred HHHHHHHHHhhC--C---ceECCEEEEEecC--cHHHHHHHH
Confidence 445666665522 1 566776 89998 677765543
No 11
>PF02033 RBFA: Ribosome-binding factor A; InterPro: IPR000238 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 [, ]. Ribosome-binding factor A [] (gene rbfA) is a bacterial protein that associates with free 30S ribosomal subunits. It does not associate with 30S subunits that are part of 70S ribosomes or polysomes. It is essential for efficient processing of 16S rRNA. Ribosome-binding factor A is a protein of from 13 to 15 Kd which is found in most bacteria. A putative chloroplastic form seems to exist in plants.; GO: 0006364 rRNA processing; PDB: 2R1C_A 2DYJ_B 2KZF_A 2E7G_A 1JOS_A 1KKG_A 1PA4_A.
Probab=45.58 E-value=7.5 Score=27.49 Aligned_cols=33 Identities=30% Similarity=0.606 Sum_probs=17.6
Q ss_pred hhhhHHHHhchhhchhHHHhhCCc--ccchhhHHhhhhhcce
Q 032134 96 APQISKALAGAAADRKDLMRKLPK--FIYDEEKALEVSHYFD 135 (146)
Q Consensus 96 APQIskaL~~~~~d~~~l~rk~pk--~~yDEek~LEkTR~~l 135 (146)
+|.|++.|...+. ||+.|+ |+||+ .+|+..+..
T Consensus 67 ~~~iR~~l~~~l~-----lr~~P~L~F~~D~--~~e~~~~i~ 101 (104)
T PF02033_consen 67 AGFIRHELAKRLN-----LRRVPELRFVYDD--SIEKAARIE 101 (104)
T ss_dssp HHHHHHHHHHHTT-----SSSG-EEEEEEST--TTSSS----
T ss_pred HHHHHHHHHhhcC-----CCcCCEEEEEECC--CHHHHHHHH
Confidence 4566666666221 456676 78887 677665543
No 12
>PRK00521 rbfA ribosome-binding factor A; Validated
Probab=44.99 E-value=8.5 Score=28.41 Aligned_cols=32 Identities=34% Similarity=0.569 Sum_probs=20.9
Q ss_pred hhhhhHHHHhchhhchhHHHhhCCc--ccchhhHHhhhhhc
Q 032134 95 YAPQISKALAGAAADRKDLMRKLPK--FIYDEEKALEVSHY 133 (146)
Q Consensus 95 fAPQIskaL~~~~~d~~~l~rk~pk--~~yDEek~LEkTR~ 133 (146)
-+++|++.|..-. . ||+.|. |+||+ .+|+.-+
T Consensus 72 ~~~~iR~~la~~l--~---lr~~P~L~F~~D~--s~e~~~~ 105 (120)
T PRK00521 72 AAGFLRSELGKRL--R---LRYVPELRFVYDE--SLEYGNR 105 (120)
T ss_pred hHHHHHHHHHhhC--C---CccCCEEEEEECC--CHHHHHH
Confidence 4677888887732 1 577886 88887 4554443
No 13
>PF09813 Coiled-coil_56: Coiled-coil domain-containing protein 56; InterPro: IPR018628 Members of this family of proteins have no known function.
Probab=43.74 E-value=8.2 Score=29.46 Aligned_cols=20 Identities=25% Similarity=0.537 Sum_probs=16.9
Q ss_pred ceeehhhhhhhhhhhhhhhh
Q 032134 76 FFVGGFVLGGIIVGTLGCVY 95 (146)
Q Consensus 76 ~Fv~GFlLGGaVfGtLGyvf 95 (146)
..++|+.||++|+|.-+|-+
T Consensus 51 N~~Tgl~L~~~v~gIY~YTi 70 (100)
T PF09813_consen 51 NLLTGLALGAFVVGIYAYTI 70 (100)
T ss_pred hHHHHHHHHHHHHHHHhhee
Confidence 46899999999999988743
No 14
>PF05283 MGC-24: Multi-glycosylated core protein 24 (MGC-24); InterPro: IPR007947 CD164 is a mucin-like receptor, or sialomucin, with specificity in receptor/ ligand interactions that depends on the structural characteristics of the mucin-like receptor. Its functions include mediating, or regulating, haematopoietic progenitor cell adhesion and the negative regulation of their growth and/or-differentiation. It exists in the native state as a disulphide- linked homodimer of two 80-85kDa subunits. It is usually expressed by CD34+ and CD341o/- haematopoietic stem cells and associated microenvironmental cells. It contains, in its extracellular region, two mucin domains (I and II) linked by a non-mucin domain, which has been predicted to contain intra- disulphide bridges. This receptor may play a key role in haematopoiesis by facilitating the adhesion of human CD34+ cells to bone marrow stroma and by negatively regulating CD34+ CD341o/- haematopoietic progenitor cell proliferation. These effects involve the CD164 class I and/or II epitopes recognised by the monoclonal antibodies (mAbs) 105A5 and 103B2/9E10. These epitopes are carbohydrate-dependent and are located on the N-terminal mucin domain I [, ]. It has been found that murine MGC-24v and rat endolyn share significant sequence similarities with human CD164. However, CD164 lacks the consensus glycosaminoglycan (GAG)-attachment site found in MGC-24; it is possible that GAG-association is responsible for the high molecular weight of the epithelial-derived MGC-24 glycoprotein []. Genomic structure studies have placed CD164 within the mucin-subgroup that comprises multiple exons, and demonstrate the diverse chromosomal distribution of this family of molecules. Molecules with such multiple exons may have sophisticated regulatory mechanisms that involve not only post-translational modifications of the oligosaccharide side chains, but also differential exon usage. Although differences in the intron and exon sizes are seen between the mouse and human genes, the predicted proteins are similar in size and structure, maintaining functionally important motifs that regulate cell proliferation or subcellular distribution []. CD164 is a gene whose expression depends on differential usage of poly- adenylation sites within the 3'-UTR. The conserved distribution of the 3.2- and 1.2-kb CD164 transcripts between mouse and human suggests that (i) a mechanism may exist to regulate tissue-specific polyadenylation, and (ii) differences in polyadenylation are important for the expression and function of CD164 in different tissues. Two other aspects of the structure of CD164 are of particular interest. First, it shares one of several conserved features of a cytokine-binding pocket - in this respect, it is notable that evidence exists for a class of cell-surface sialomucin modulators that directly interact with growth factor receptors to regulate their response to physiological ligands. Second, its cytoplasmic tail contains a C-terminal YHTL motif found in many endocytic membrane proteins or receptors. These Tyr-based motifs bind to adaptor proteins, which mediate the sorting of membrane proteins into transport vesicles from the plasma membrane to the endosomes, and between intracellular compartments.
Probab=42.29 E-value=8.7 Score=31.56 Aligned_cols=20 Identities=40% Similarity=0.861 Sum_probs=13.0
Q ss_pred CCCceeehhhhhhhhhhhhhhhh
Q 032134 73 SAGFFVGGFVLGGIIVGTLGCVY 95 (146)
Q Consensus 73 ~gg~Fv~GFlLGGaVfGtLGyvf 95 (146)
-++.||||.|| ++|.|+.+|
T Consensus 159 D~~SFiGGIVL---~LGv~aI~f 178 (186)
T PF05283_consen 159 DAASFIGGIVL---TLGVLAIIF 178 (186)
T ss_pred chhhhhhHHHH---HHHHHHHHH
Confidence 34678888775 566666555
No 15
>KOG2408 consensus Peroxidase/oxygenase [General function prediction only]
Probab=37.40 E-value=20 Score=34.57 Aligned_cols=23 Identities=35% Similarity=0.608 Sum_probs=19.2
Q ss_pred hhhhhhhhhhhhhhhhhHHHHhc
Q 032134 83 LGGIIVGTLGCVYAPQISKALAG 105 (146)
Q Consensus 83 LGGaVfGtLGyvfAPQIskaL~~ 105 (146)
-||+|.=||+|++|+|+.|...+
T Consensus 624 ~g~~vGPTl~cii~~Qf~r~r~g 646 (719)
T KOG2408|consen 624 PGGLVGPTLACIIAEQFLRLRDG 646 (719)
T ss_pred CCceecccHHHHHHHHHHHHhcc
Confidence 45555559999999999999988
No 16
>PF04971 Lysis_S: Lysis protein S ; InterPro: IPR007054 The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis. The action of Lysis S is independent of the proportion of acidic phospholipids in the membrane [].
Probab=36.93 E-value=15 Score=26.34 Aligned_cols=14 Identities=43% Similarity=0.764 Sum_probs=12.4
Q ss_pred hhhhhhhhhhhhhh
Q 032134 82 VLGGIIVGTLGCVY 95 (146)
Q Consensus 82 lLGGaVfGtLGyvf 95 (146)
++||++||.|+|+-
T Consensus 38 vi~gi~~~~lt~lt 51 (68)
T PF04971_consen 38 VIGGIFFGLLTYLT 51 (68)
T ss_pred HHHHHHHHHHHHHh
Confidence 79999999999973
No 17
>TIGR01089 fucI L-fucose isomerase. This enzyme catalyzes the first step in fucose metabolism, and has been characterized in Escherichia coli and Bacteroides thetaiotaomicron.
Probab=33.40 E-value=27 Score=33.51 Aligned_cols=53 Identities=26% Similarity=0.471 Sum_probs=41.5
Q ss_pred hhhhhhhhhhhhhhhhhhHHHHhchh---hchhHHHhhCCcccchhh---HHhhhhhcc
Q 032134 82 VLGGIIVGTLGCVYAPQISKALAGAA---ADRKDLMRKLPKFIYDEE---KALEVSHYF 134 (146)
Q Consensus 82 lLGGaVfGtLGyvfAPQIskaL~~~~---~d~~~l~rk~pk~~yDEe---k~LEkTR~~ 134 (146)
++|+.-.|.-|+++-|+.=+..+|.. -|..++.|+.-.-+||+| +++|.+.++
T Consensus 176 ~IG~~smGi~gs~vd~~f~q~~lGmrvE~vD~~EivrR~~~~iyd~eE~e~Al~W~~~~ 234 (587)
T TIGR01089 176 SLGSVSMGIAGSIVNHNFFQEYLGMRNEAVDMTEIRRRIDQKIYDEEELEMALAWADKY 234 (587)
T ss_pred EECCccCcccccCCCHHHHHHHhCCeeEEecHHHHHHHHhccCCCHHHHHHHHHHHHHh
Confidence 57889999999999998888877754 688899998866667764 666666655
No 18
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=33.17 E-value=20 Score=24.36 Aligned_cols=18 Identities=17% Similarity=0.307 Sum_probs=13.6
Q ss_pred eehhhhhhhhhhhhhhhh
Q 032134 78 VGGFVLGGIIVGTLGCVY 95 (146)
Q Consensus 78 v~GFlLGGaVfGtLGyvf 95 (146)
+-|+++|++|.|.+++++
T Consensus 53 ~~r~iiGaiI~~i~~~i~ 70 (71)
T PF10779_consen 53 IWRTIIGAIITAIIYLII 70 (71)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 446888888888888765
No 19
>PRK13815 ribosome-binding factor A; Provisional
Probab=33.01 E-value=15 Score=27.64 Aligned_cols=31 Identities=39% Similarity=0.501 Sum_probs=18.2
Q ss_pred hhhhHHHHhchhhchhHHHhhCCc--ccchhhHHhhhhhc
Q 032134 96 APQISKALAGAAADRKDLMRKLPK--FIYDEEKALEVSHY 133 (146)
Q Consensus 96 APQIskaL~~~~~d~~~l~rk~pk--~~yDEek~LEkTR~ 133 (146)
++.|++.|..-+ . +|+.|. |+||+ .+|+.-+
T Consensus 70 ~g~iR~~l~~~l--~---lR~~PeL~F~~D~--s~e~~~~ 102 (122)
T PRK13815 70 RGFIRKELGKVL--R---MRYAPELIFKYDE--SQEYGNR 102 (122)
T ss_pred HHHHHHHHHHhC--C---CeECCEEEEEECC--ChHHHHH
Confidence 455666665521 1 567776 89998 5555443
No 20
>cd08321 Pyrin_ASC-like Pyrin Death Domain found in ASC. Pyrin Death Domain found in ASC (Apoptosis-associated speck-like protein containing a CARD) and similar proteins. ASC is an adaptor molecule that functions in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. ASC contains two domains from the Death Domain (DD) superfamily, an N-terminal pyrin-like domain and a C-terminal Caspase activation and recruitment domain (CARD). Through these 2 domains, ASC serves as an adaptor for inflammasome integrity and oligomerizes to form supramolecular assemblies. Other members of this subfamily are associated with ATPase domains and their function remains unknown. In general, Pyrin is a subfamily of the DD superfamily and functions in several signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=32.95 E-value=15 Score=25.95 Aligned_cols=37 Identities=41% Similarity=0.568 Sum_probs=28.4
Q ss_pred hhhHHHHhchhhchhHHHhhCCcccchhhHHhhhhhcce
Q 032134 97 PQISKALAGAAADRKDLMRKLPKFIYDEEKALEVSHYFD 135 (146)
Q Consensus 97 PQIskaL~~~~~d~~~l~rk~pk~~yDEek~LEkTR~~l 135 (146)
|+|++.=+.- +|+.++-..+-.+ |.|+.+.+.|.+.+
T Consensus 32 ~~Ip~~~le~-ad~~dla~lLv~~-y~~~~A~~vt~~il 68 (82)
T cd08321 32 PRIPRGELEN-ADRVDLVDKMVQF-YGEEYAVEVTVKIL 68 (82)
T ss_pred CCCChHhhcc-CCHHHHHHHHHHH-cChhHHHHHHHHHH
Confidence 6788876543 7888888888776 68888999887765
No 21
>TIGR02872 spore_ytvI sporulation integral membrane protein YtvI. Three lines of evidence show this protein to be involved in sporulation. First, it is under control of a sporulation-specific sigma factor, sigma-E. Second, mutation leads to a sporulation defect. Third, it if found in exactly those genomes whose bacteria are capable of sporulation, except for being absent in Clostridium acetobutylicum ATCC824. This protein has extensive hydrophobic regions and is likely an integral membrane protein.
Probab=30.38 E-value=26 Score=28.08 Aligned_cols=29 Identities=21% Similarity=0.340 Sum_probs=23.4
Q ss_pred ceeehhhhhhhhhhhhhhhhhhhhHHHHh
Q 032134 76 FFVGGFVLGGIIVGTLGCVYAPQISKALA 104 (146)
Q Consensus 76 ~Fv~GFlLGGaVfGtLGyvfAPQIskaL~ 104 (146)
--+-+.+.||.+||.+|.+.||-+--.+.
T Consensus 305 ~vl~~~l~g~~~~G~~G~~l~~~~~~~~~ 333 (341)
T TIGR02872 305 ATLISMYIGLKLFGFLGLIFGPVIVVLFK 333 (341)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999998765443
No 22
>PRK10983 putative inner membrane protein; Provisional
Probab=30.15 E-value=64 Score=28.03 Aligned_cols=29 Identities=21% Similarity=0.347 Sum_probs=23.1
Q ss_pred CceeehhhhhhhhhhhhhhhhhhhhHHHH
Q 032134 75 GFFVGGFVLGGIIVGTLGCVYAPQISKAL 103 (146)
Q Consensus 75 g~Fv~GFlLGGaVfGtLGyvfAPQIskaL 103 (146)
-..+.|.+.|+.+||.+|.+++|-+=--+
T Consensus 309 ~~il~~~~~G~~~fG~~G~~lgp~i~a~~ 337 (368)
T PRK10983 309 ILILSGVIGGLIAFGMIGLFIGPVVLAVS 337 (368)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667888888889999999999865333
No 23
>cd03556 L-fucose_isomerase L-fucose isomerase (FucIase); FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose during glycolysis). L-fucose (or 6-deoxy-L-galactose) is found in blood group determinants as well as in various oligo- and polysaccharides, and glycosides in mammals, bacteria and plants.
Probab=28.50 E-value=37 Score=32.65 Aligned_cols=54 Identities=26% Similarity=0.460 Sum_probs=41.7
Q ss_pred hhhhhhhhhhhhhhhhhhHHHHhchh---hchhHHHhhCCcccchhh---HHhhhhhcce
Q 032134 82 VLGGIIVGTLGCVYAPQISKALAGAA---ADRKDLMRKLPKFIYDEE---KALEVSHYFD 135 (146)
Q Consensus 82 lLGGaVfGtLGyvfAPQIskaL~~~~---~d~~~l~rk~pk~~yDEe---k~LEkTR~~l 135 (146)
++||.-.|.-|+++-|+.=+..+|.. -|..++.|+.-.-+||+| +++|.+.++.
T Consensus 173 ~IG~~smGi~gs~vd~~f~q~~lGmrvE~vD~~EivrR~~~~iyd~eE~e~Al~W~~~~~ 232 (584)
T cd03556 173 SIGSVSMGIAGSIVDPNFFEEYLGMRVESVDMTEIIRRMDEEIYDPEEYEKALAWTKENC 232 (584)
T ss_pred EECCccCcccccCCCHHHHHHHhCCeeEEecHHHHHHHHhccCCCHHHHHHHHHHHHHhc
Confidence 57889999999999998888887754 688899887776567764 5666666553
No 24
>PRK13816 ribosome-binding factor A; Provisional
Probab=26.62 E-value=23 Score=27.05 Aligned_cols=32 Identities=22% Similarity=0.399 Sum_probs=19.8
Q ss_pred hhhhhHHHHhchhhchhHHHhhCCc--ccchhhHHhhhhhc
Q 032134 95 YAPQISKALAGAAADRKDLMRKLPK--FIYDEEKALEVSHY 133 (146)
Q Consensus 95 fAPQIskaL~~~~~d~~~l~rk~pk--~~yDEek~LEkTR~ 133 (146)
.++.|++.|..-+ . ||+.|. |.||+ .+|+.-+
T Consensus 77 a~g~iR~~L~krl--~---lR~~PeL~F~~D~--s~e~~~~ 110 (131)
T PRK13816 77 ASGFLRTELSRRI--K---TRITPRLRFHYDK--TNAYGNY 110 (131)
T ss_pred HHHHHHHHHHhhc--C---CeECCEEEEEECC--ChhHHHH
Confidence 3566777776622 1 577786 88897 5555433
No 25
>PF04505 Dispanin: Interferon-induced transmembrane protein; InterPro: IPR007593 This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression [].; GO: 0009607 response to biotic stimulus, 0016021 integral to membrane
Probab=26.49 E-value=24 Score=24.81 Aligned_cols=43 Identities=21% Similarity=0.526 Sum_probs=28.2
Q ss_pred hhhhhhhhhhhhHHHHhchhhchhHHHhhCCcccchh-hHHhhhhhcceeeeeehhcc
Q 032134 88 VGTLGCVYAPQISKALAGAAADRKDLMRKLPKFIYDE-EKALEVSHYFDILSIFLGLI 144 (146)
Q Consensus 88 fGtLGyvfAPQIskaL~~~~~d~~~l~rk~pk~~yDE-ek~LEkTR~~l~~~~~~~~~ 144 (146)
+|.++.+||-|.++.... .|- ++ +++=+++|+--+.++.+|++
T Consensus 33 lGi~Ai~~s~kv~~~~~~--Gd~------------~~A~~aS~~Ak~~~~ia~~~g~~ 76 (82)
T PF04505_consen 33 LGIVAIVYSSKVRSRYAA--GDY------------EGARRASRKAKKWSIIAIIIGIV 76 (82)
T ss_pred HHHHHheechhhHHHHHC--CCH------------HHHHHHHHHhHHHHHHHHHHHHH
Confidence 689999999998888776 452 22 23445566666666666653
No 26
>PF14034 Spore_YtrH: Sporulation protein YtrH
Probab=25.42 E-value=30 Score=26.42 Aligned_cols=17 Identities=47% Similarity=0.954 Sum_probs=15.6
Q ss_pred hhhhhhhhhhhhhhhhh
Q 032134 80 GFVLGGIIVGTLGCVYA 96 (146)
Q Consensus 80 GFlLGGaVfGtLGyvfA 96 (146)
|.+|||.++|.+|-++.
T Consensus 12 GVvlGGsliGglga~l~ 28 (102)
T PF14034_consen 12 GVVLGGSLIGGLGAFLT 28 (102)
T ss_pred HHHHHHHHHHHHHHHHc
Confidence 88999999999999875
No 27
>PF14242 DUF4342: Domain of unknown function (DUF4342)
Probab=24.95 E-value=39 Score=24.38 Aligned_cols=18 Identities=28% Similarity=0.737 Sum_probs=14.0
Q ss_pred hhhhhhhhhhhhhhhhHH
Q 032134 84 GGIIVGTLGCVYAPQISK 101 (146)
Q Consensus 84 GGaVfGtLGyvfAPQIsk 101 (146)
-|++.|++|.++||.+.-
T Consensus 50 ~gv~~g~i~~~~aP~la~ 67 (84)
T PF14242_consen 50 AGVAAGVIGALLAPVLAA 67 (84)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 456778889999999753
No 28
>PRK13817 ribosome-binding factor A; Provisional
Probab=23.24 E-value=29 Score=25.97 Aligned_cols=31 Identities=39% Similarity=0.653 Sum_probs=17.5
Q ss_pred hhhhHHHHhchhhchhHHHhhCCc--ccchhhHHhhhhhc
Q 032134 96 APQISKALAGAAADRKDLMRKLPK--FIYDEEKALEVSHY 133 (146)
Q Consensus 96 APQIskaL~~~~~d~~~l~rk~pk--~~yDEek~LEkTR~ 133 (146)
++.|++.|..-+ . +|..|+ |+||+ .+|+.-+
T Consensus 69 ~g~iR~~l~~~l--~---lR~~PeL~F~~D~--s~e~~~~ 101 (119)
T PRK13817 69 TGYLRHLLAQAT--V---LRYVPKLEFVYDE--SIERAHR 101 (119)
T ss_pred HHHHHHHHHHhC--C---CeECCEEEEEEcC--chHHHHH
Confidence 344566555511 1 466776 88997 5555433
No 29
>PF06682 DUF1183: Protein of unknown function (DUF1183); InterPro: IPR009567 This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown.
Probab=21.24 E-value=51 Score=29.12 Aligned_cols=26 Identities=23% Similarity=0.393 Sum_probs=20.0
Q ss_pred CCCCCCceeehhhhhhhhhhhhhhhhhhhh
Q 032134 70 RANSAGFFVGGFVLGGIIVGTLGCVYAPQI 99 (146)
Q Consensus 70 r~~~gg~Fv~GFlLGGaVfGtLGyvfAPQI 99 (146)
..+.+..|++|+..|| ++||+|--+=
T Consensus 247 ~~~wgPGFWTGla~Gg----~aGYl~G~r~ 272 (318)
T PF06682_consen 247 QQNWGPGFWTGLAAGG----AAGYLFGRRR 272 (318)
T ss_pred CCCCCCCchHHHHHHH----HHHhhhccCC
Confidence 3456678999999887 7899986553
No 30
>COG4177 LivM ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]
Probab=20.99 E-value=47 Score=28.76 Aligned_cols=23 Identities=30% Similarity=0.557 Sum_probs=20.4
Q ss_pred eehhhhhhhhhhhhhhhhhhhhH
Q 032134 78 VGGFVLGGIIVGTLGCVYAPQIS 100 (146)
Q Consensus 78 v~GFlLGGaVfGtLGyvfAPQIs 100 (146)
+.-|++|+++.|..|-+||+|+.
T Consensus 208 l~aF~isa~~AGiAGaL~a~~~~ 230 (314)
T COG4177 208 LLAFVISAAIAGIAGALYALYLG 230 (314)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 45799999999999999999953
No 31
>PHA03048 IMV membrane protein; Provisional
Probab=20.01 E-value=49 Score=25.13 Aligned_cols=19 Identities=32% Similarity=0.672 Sum_probs=16.9
Q ss_pred ehhhhhhhhhhhhhhhhhh
Q 032134 79 GGFVLGGIIVGTLGCVYAP 97 (146)
Q Consensus 79 ~GFlLGGaVfGtLGyvfAP 97 (146)
.|.|++|++.=+++|+||=
T Consensus 12 S~vli~GIiLL~~aCIfAf 30 (93)
T PHA03048 12 STALIGGIILLAASCIFAF 30 (93)
T ss_pred chHHHHHHHHHHHHHHHhh
Confidence 5789999999999999993
Done!