Query gi|254780890|ref|YP_003065303.1| hypothetical protein CLIBASIA_03935 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 104
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 00:23:25 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780890.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02403 trehalose_treC alpha 49.7 8.8 0.00022 19.3 1.4 23 19-41 394-419 (555)
2 COG3294 HD supefamily hydrolas 37.5 15 0.00038 18.0 1.0 24 2-25 137-160 (269)
3 pfam07568 HisKA_2 Histidine ki 34.0 41 0.001 15.6 3.4 55 15-77 1-55 (76)
4 PRK13560 hypothetical protein; 33.3 22 0.00056 17.1 1.3 51 6-57 603-653 (807)
5 COG4840 Uncharacterized protei 27.3 41 0.001 15.6 1.9 31 65-95 41-71 (71)
6 KOG3303 consensus 24.6 60 0.0015 14.7 4.0 36 66-101 9-48 (192)
7 COG2088 SpoVG Uncharacterized 22.8 6.6 0.00017 20.0 -2.9 34 13-46 27-60 (95)
8 TIGR01171 rplB_bact ribosomal 22.5 13 0.00033 18.4 -1.4 15 55-69 92-106 (279)
9 KOG0574 consensus 19.6 67 0.0017 14.4 1.7 35 67-103 114-154 (502)
10 pfam03089 RAG2 Recombination a 11.8 92 0.0023 13.6 0.8 14 38-51 98-111 (528)
No 1
>TIGR02403 trehalose_treC alpha,alpha-phosphotrehalase; InterPro: IPR012769 Trehalose is a glucose disaccharide that serves in many biological systems as a compatible solute for protection against hyperosmotic and thermal stress. This family describes trehalose-6-phosphate hydrolase, product of the treC (or treA) gene, which is often found together with a trehalose uptake transporter and a trehalose operon repressor.; GO: 0008788 alphaalpha-phosphotrehalase activity, 0005993 trehalose catabolic process, 0005737 cytoplasm.
Probab=49.67 E-value=8.8 Score=19.28 Aligned_cols=23 Identities=52% Similarity=0.505 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHCCCC---CCCH
Q ss_conf 5677588889985100247---9642
Q gi|254780890|r 19 NIRLQIEEISAILSKKSRD---TPNQ 41 (104)
Q Consensus 19 nirlqieeisailskksrd---tpnq 41 (104)
+--.+-+|+-|||..|||| ||-|
T Consensus 394 ~~G~~~~e~~~Il~~KSRDNsRTPMQ 419 (555)
T TIGR02403 394 KKGKSEEEALAILKQKSRDNSRTPMQ 419 (555)
T ss_pred HHCCCHHHHHHHHHHHCCCCCCCCCC
T ss_conf 71578769999999741346788622
No 2
>COG3294 HD supefamily hydrolase [General function prediction only]
Probab=37.54 E-value=15 Score=18.02 Aligned_cols=24 Identities=42% Similarity=0.491 Sum_probs=16.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 726400312322553355677588
Q gi|254780890|r 2 FYDSREKEVFLESEVVHNIRLQIE 25 (104)
Q Consensus 2 fydsrekevflesevvhnirlqie 25 (104)
||++.+|.+++.|||.|.|--.-+
T Consensus 137 iy~~~~k~~~~rsevlhAI~ch~~ 160 (269)
T COG3294 137 IYPDPEKAVRVRSEVLHAIYCHDE 160 (269)
T ss_pred HCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf 369999978489988777531688
No 3
>pfam07568 HisKA_2 Histidine kinase. This is the dimerization and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with pfam00512 and pfam07536. It is usually found adjacent to a C-terminal ATPase domain (pfam02518). This domain is found in a wide range of Bacteria and also several Archaea.
Probab=33.95 E-value=41 Score=15.61 Aligned_cols=55 Identities=20% Similarity=0.448 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCHHHEEEEEEEHHHHHHHHHHHCCCHHHHHHHHHCCCC
Q ss_conf 533556775888899851002479642222010001012442464205635789999751643
Q gi|254780890|r 15 EVVHNIRLQIEEISAILSKKSRDTPNQEIRTKIYIITARIIALIVFREGEKSLIFDLLRTNQK 77 (104)
Q Consensus 15 evvhnirlqieeisailskksrdtpnqeirtkiyiitariialivfregekslifdllrtnqk 77 (104)
|+-|-++-...-|+++++-.+|..++.+.|...--+..||-|+ +++.+.|..+..
T Consensus 1 Ev~HRVKNnLq~i~sll~lq~~~~~~~~~~~~l~~~~~RI~a~--------a~vH~~Ly~~~~ 55 (76)
T pfam07568 1 EIHHRVKNNLQVISSLLRLQARRAKDEEVKEALRESQNRVLSM--------ALIHEELYKSED 55 (76)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH--------HHHHHHHHCCCC
T ss_conf 9038898579999999998734259999999999999999999--------999999976999
No 4
>PRK13560 hypothetical protein; Provisional
Probab=33.35 E-value=22 Score=17.11 Aligned_cols=51 Identities=27% Similarity=0.425 Sum_probs=40.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHEEEEEEEHHHHHHH
Q ss_conf 0031232255335567758888998510024796422220100010124424
Q gi|254780890|r 6 REKEVFLESEVVHNIRLQIEEISAILSKKSRDTPNQEIRTKIYIITARIIAL 57 (104)
Q Consensus 6 rekevflesevvhnirlqieeisailskksrdtpnqeirtkiyiitariial 57 (104)
.|||++| .|+-|-++-...-||++|+-.+|.+.+.+.+.-.--...||.++
T Consensus 603 ~EKE~LL-kEIHHRVKNNLQiIsSLL~LQar~~~d~ear~aL~esq~RI~Sm 653 (807)
T PRK13560 603 TEKEVLL-KEIHHRVKNNLQIISSLLDLQAEKLHDEEAKCAFAESQDRICAM 653 (807)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 9889999-98776752039999999998876559999999999999999999
No 5
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.25 E-value=41 Score=15.61 Aligned_cols=31 Identities=26% Similarity=0.425 Sum_probs=21.4
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 5789999751643303699999999998999
Q gi|254780890|r 65 KSLIFDLLRTNQKTNSSLTQAIIQEIDTLQH 95 (104)
Q Consensus 65 kslifdllrtnqktnssltqaiiqeidtlqh 95 (104)
-.-|+|+......-..|--|||-+|...|.|
T Consensus 41 Ltdiy~mvkkkenfSpsEmqaiA~eL~rlRk 71 (71)
T COG4840 41 LTDIYDMVKKKENFSPSEMQAIADELGRLRK 71 (71)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHC
T ss_conf 9999999998625998999999999987309
No 6
>KOG3303 consensus
Probab=24.63 E-value=60 Score=14.67 Aligned_cols=36 Identities=42% Similarity=0.575 Sum_probs=21.6
Q ss_pred HHHHHHHHCCC----CCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 78999975164----3303699999999998999755410
Q gi|254780890|r 66 SLIFDLLRTNQ----KTNSSLTQAIIQEIDTLQHQCKSIE 101 (104)
Q Consensus 66 slifdllrtnq----ktnssltqaiiqeidtlqhqcksie 101 (104)
-||-|+-|+.+ .-|+-+-.+|++|+|.|.++-.+|-
T Consensus 9 ~Li~d~kr~~~~~Lppyn~d~ir~i~~E~~~l~~~~~~i~ 48 (192)
T KOG3303 9 QLILDLKRTPLGQLPPYNEDLIRQILEEIDALDARNESIK 48 (192)
T ss_pred HHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999986181346897317999999999999999889999
No 7
>COG2088 SpoVG Uncharacterized protein, involved in the regulation of septum location [Cell envelope biogenesis, outer membrane]
Probab=22.81 E-value=6.6 Score=19.98 Aligned_cols=34 Identities=32% Similarity=0.409 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHEEE
Q ss_conf 2553355677588889985100247964222201
Q gi|254780890|r 13 ESEVVHNIRLQIEEISAILSKKSRDTPNQEIRTK 46 (104)
Q Consensus 13 esevvhnirlqieeisailskksrdtpnqeirtk 46 (104)
+.-|||+||+--.+-.-..+-.||-||+.|.|.-
T Consensus 27 ~efVvhdirVi~G~~GlfVAMPSrrt~dgEFrDI 60 (95)
T COG2088 27 NEFVVHDIRVIEGNNGLFVAMPSRRTPDGEFRDI 60 (95)
T ss_pred CEEEEECCEEEECCCCEEEECCCCCCCCCCHHHC
T ss_conf 6289822189837862599866765899631021
No 8
>TIGR01171 rplB_bact ribosomal protein L2; InterPro: IPR005880 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 of 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 , . The protein L2 is found in all ribosomes and is one of the best conserved proteins of this mega-dalton complex. L2 is elongated, exposing one end of the protein to the surface of the intersubunit interface of the 50 S subunit and is essential for the association of the ribosomal subunits and might participate in the binding and translocation of the tRNAs . This entry represents bacterial, chloroplast and mitochondrial forms.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0016740 transferase activity, 0006412 translation, 0015934 large ribosomal subunit.
Probab=22.51 E-value=13 Score=18.36 Aligned_cols=15 Identities=47% Similarity=0.835 Sum_probs=13.4
Q ss_pred HHHHHHHCCCHHHHH
Q ss_conf 424642056357899
Q gi|254780890|r 55 IALIVFREGEKSLIF 69 (104)
Q Consensus 55 ialivfregekslif 69 (104)
|||+.+..|||..|.
T Consensus 92 IALl~Y~DGEKRYIL 106 (279)
T TIGR01171 92 IALLHYADGEKRYIL 106 (279)
T ss_pred EEEEECCCCCEEEEE
T ss_conf 224432787676643
No 9
>KOG0574 consensus
Probab=19.59 E-value=67 Score=14.43 Aligned_cols=35 Identities=37% Similarity=0.536 Sum_probs=15.9
Q ss_pred HHHHHHHCCCCCHHHHHHH-HHHHHHHH-----HHHHHHHHCC
Q ss_conf 8999975164330369999-99999989-----9975541035
Q gi|254780890|r 67 LIFDLLRTNQKTNSSLTQA-IIQEIDTL-----QHQCKSIERD 103 (104)
Q Consensus 67 lifdllrtnqktnssltqa-iiqeidtl-----qhqcksierd 103 (104)
-|-|..|...|+-+.-.-+ |.+ ||| -|-.+.|.||
T Consensus 114 SiSDI~R~R~K~L~E~EIs~iL~--~TLKGL~YLH~~~KIHRD 154 (502)
T KOG0574 114 SISDIMRARRKPLSEQEISAVLR--DTLKGLQYLHDLKKIHRD 154 (502)
T ss_pred CHHHHHHHHCCCCCHHHHHHHHH--HHHHHHHHHHHHHHHHHH
T ss_conf 38999997127861889999999--988678999999998743
No 10
>pfam03089 RAG2 Recombination activating protein 2. V-D-J recombination is the combinatorial process by which the huge range of immunoglobulin and T cell binding specificity is generated from a limited amount of genetic material. This process is synergistically activated by RAG1 and RAG2 in developing lymphocytes. Defects in RAG2 in humans are a cause of severe combined immunodeficiency B cell negative and Omenn syndrome.
Probab=11.82 E-value=92 Score=13.65 Aligned_cols=14 Identities=57% Similarity=1.073 Sum_probs=0.0
Q ss_pred CCCHHHEEEEEEEH
Q ss_conf 96422220100010
Q gi|254780890|r 38 TPNQEIRTKIYIIT 51 (104)
Q Consensus 38 tpnqeirtkiyiit 51 (104)
|||.|+-.|+|+++
T Consensus 98 TPNNElS~~LYims 111 (528)
T pfam03089 98 TPNNELSSKLYIMT 111 (528)
T ss_pred CCCCHHCCCEEEEE
T ss_conf 99731020148998
Done!