Query 029970
Match_columns 184
No_of_seqs 89 out of 114
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 06:29:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029970.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029970hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03195 DUF260: Protein of un 100.0 5.9E-30 1.3E-34 194.1 5.0 85 1-90 17-101 (101)
2 PF06519 TolA: TolA C-terminal 60.7 6.8 0.00015 29.6 2.1 24 70-93 57-80 (96)
3 COG3408 GDB1 Glycogen debranch 39.8 18 0.00039 35.6 1.8 67 23-90 280-381 (641)
4 KOG1386 Nucleoside phosphatase 22.3 57 0.0012 32.0 1.9 18 69-86 283-300 (501)
5 PF15300 INT_SG_DDX_CT_C: INTS 18.0 74 0.0016 23.1 1.3 27 29-55 23-51 (65)
6 PF07208 DUF1414: Protein of u 14.8 61 0.0013 22.3 0.2 20 31-50 16-36 (44)
7 TIGR02794 tolA_full TolA prote 14.1 1.7E+02 0.0037 26.8 2.9 31 54-90 295-325 (346)
8 PF08452 DNAP_B_exo_N: DNA pol 12.3 71 0.0015 19.3 -0.0 10 4-13 4-13 (22)
9 cd03717 SOCS_SOCS_like SOCS (s 12.2 2.1E+02 0.0045 18.2 2.1 21 74-94 7-27 (39)
10 cd05562 Peptidases_S53_like Pe 11.4 2.4E+02 0.0052 24.2 2.9 40 29-69 224-267 (275)
No 1
>PF03195 DUF260: Protein of unknown function DUF260; InterPro: IPR004883 The lateral organ boundaries (LOB) gene is expressed at the adaxial base of initiating lateral organs and encodes a plant-specific protein of unknown function. The N-terminal one half of the LOB protein contains a conserved approximately 100-amino acid domain (the LOB domain) that is present in 42 other Arabidopsis thaliana proteins and in proteins from a variety of other plant species. Genes encoding LOB domain (LBD) proteins are expressed in a variety of temporal- and tissue-specific patterns, suggesting that they may function in diverse processes [] The LOB domain contains conserved blocks of amino acids that identify the LBD gene family. In particular, a conserved C-x(2)-C-x(6)-C-x(3)-C motif, which is defining feature of the LOB domain, is present in all LBD proteins. It is possible that this motif forms a new zinc finger [].
Probab=99.96 E-value=5.9e-30 Score=194.09 Aligned_cols=85 Identities=29% Similarity=0.429 Sum_probs=80.3
Q ss_pred CccccccccCCccccchhhhhhhhhccccchHHHhhhCCCCCchHHHHHHHHHHhccccCCcccccccccccchHHHHHH
Q 029970 1 MLRQSIQWIGTPQAQANATVFVAKFFGRAGLMSFISAVPETQRPSLFQSLLYEAVGRTVNPVSGAVGLLWTGNWNVCQSA 80 (184)
Q Consensus 1 ~lr~cl~wi~~pe~q~~at~fVhK~FG~snl~klL~~vP~~~R~~~f~SLlYEA~gRi~dPVyGcVGli~tg~w~~cq~a 80 (184)
+++|++ |..|.+.+.+||||||++||+|||+++|+++|+++++||+|||++|++||||||+|+||.++|++++.+
T Consensus 17 ~laPyF-----P~~~~~~F~~vhkvFG~sni~k~L~~~~~~~R~~a~~Sl~yEA~~R~~dPv~Gc~G~i~~L~~ql~~~~ 91 (101)
T PF03195_consen 17 VLAPYF-----PADQPQRFANVHKVFGVSNISKMLQELPPEQREDAMRSLVYEANARARDPVYGCVGIISQLQQQLQQLQ 91 (101)
T ss_pred cCCCCC-----ChhHHHHHHHHHHHHchhHHHHHHHhCCccchhhHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHH
Confidence 467887 888999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCCc
Q 029970 81 VERVLCGGAL 90 (184)
Q Consensus 81 ve~Vl~g~~i 90 (184)
+|.++.+..|
T Consensus 92 ~el~~~~~~l 101 (101)
T PF03195_consen 92 AELALVRAQL 101 (101)
T ss_pred HHHHHHHccC
Confidence 9999877654
No 2
>PF06519 TolA: TolA C-terminal; InterPro: IPR014161 TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cut-offs are based largely on conserved operon structure. The Tol-Pal complex is required for maintaining outer membrane integrity, and is also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins OmpC, PhoE and LamB.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2X9A_D 3QDP_A 3QDR_A 1TOL_A 1S62_A.
Probab=60.67 E-value=6.8 Score=29.64 Aligned_cols=24 Identities=17% Similarity=0.331 Sum_probs=15.5
Q ss_pred cccchHHHHHHHHHHHcCCCcccC
Q 029970 70 WTGNWNVCQSAVERVLCGGALQPL 93 (184)
Q Consensus 70 ~tg~w~~cq~ave~Vl~g~~i~~~ 93 (184)
-+|+..+|++|+.||.+-+.+-+-
T Consensus 57 ~~GD~~lC~aa~~Ai~k~~~~P~p 80 (96)
T PF06519_consen 57 ESGDPALCRAAKSAIAKAAKFPPP 80 (96)
T ss_dssp EEE-HHHHHHHHHH-HCCS-----
T ss_pred cCCCHHHHHHHHHHHHHhcCCCCC
Confidence 568999999999999998776443
No 3
>COG3408 GDB1 Glycogen debranching enzyme [Carbohydrate transport and metabolism]
Probab=39.83 E-value=18 Score=35.58 Aligned_cols=67 Identities=30% Similarity=0.453 Sum_probs=53.8
Q ss_pred hhh--ccccchHHHhhhCCCCCchHHHHHHH-----HHHhccc---------cCCcccccc------------ccccc--
Q 029970 23 AKF--FGRAGLMSFISAVPETQRPSLFQSLL-----YEAVGRT---------VNPVSGAVG------------LLWTG-- 72 (184)
Q Consensus 23 hK~--FG~snl~klL~~vP~~~R~~~f~SLl-----YEA~gRi---------~dPVyGcVG------------li~tg-- 72 (184)
|.| |||-.+++++.-++. .|+++.+..| ||.-||| .+|+||.|= +.|++
T Consensus 280 ~WF~~fGRD~lIS~lgll~~-g~~elArg~L~~~a~~~~~GkIPhe~~~~~~~~~~Y~tvD~t~~~i~~~~~y~~~t~d~ 358 (641)
T COG3408 280 HWFSPFGRDTLISALGLLLV-GRFELARGTLNTLARYSEPGKIPHEILLSIPGEPYYNTVDATPLFIYLLGAYLKYTGDT 358 (641)
T ss_pred hhccccchHHHHHHHHHHhc-CCHHHHHHHHHHHHhhccCCCCcchhhhcCCCcceeccCCCcHHHHHHHHHHHHHhccH
Confidence 788 999999999999999 8888777654 7888886 469999886 22343
Q ss_pred -----chHHHHHHHHHHHcCCCc
Q 029970 73 -----NWNVCQSAVERVLCGGAL 90 (184)
Q Consensus 73 -----~w~~cq~ave~Vl~g~~i 90 (184)
.|+.=+.|++.+++|..-
T Consensus 359 ~~i~e~~~~v~~a~d~~~~~~~~ 381 (641)
T COG3408 359 EFIRELWPSVGAALDWILKGFDF 381 (641)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCc
Confidence 588889999999999743
No 4
>KOG1386 consensus Nucleoside phosphatase [Nucleotide transport and metabolism]
Probab=22.30 E-value=57 Score=31.97 Aligned_cols=18 Identities=50% Similarity=0.781 Sum_probs=16.5
Q ss_pred ccccchHHHHHHHHHHHc
Q 029970 69 LWTGNWNVCQSAVERVLC 86 (184)
Q Consensus 69 i~tg~w~~cq~ave~Vl~ 86 (184)
--+|||++|-++|-..|.
T Consensus 283 ~GtGn~~~C~~~v~~ll~ 300 (501)
T KOG1386|consen 283 QGTGNWSQCRSAVLPLLN 300 (501)
T ss_pred ecCCCHHHHHHHHHHhcC
Confidence 368999999999999998
No 5
>PF15300 INT_SG_DDX_CT_C: INTS6/SAGE1/DDX26B/CT45 C-terminus
Probab=18.04 E-value=74 Score=23.12 Aligned_cols=27 Identities=19% Similarity=0.385 Sum_probs=23.1
Q ss_pred cchHHHhhhC--CCCCchHHHHHHHHHHh
Q 029970 29 AGLMSFISAV--PETQRPSLFQSLLYEAV 55 (184)
Q Consensus 29 snl~klL~~v--P~~~R~~~f~SLlYEA~ 55 (184)
+.+.++|+.| |...|...+..++.||.
T Consensus 23 e~iF~lL~~vqG~~~~r~~fv~~~IkEA~ 51 (65)
T PF15300_consen 23 EKIFKLLEQVQGPLEVRKQFVEMIIKEAA 51 (65)
T ss_pred HHHHHHHHHccCCHHHHHHHHHHHHHHHH
Confidence 3577888886 88899999999999995
No 6
>PF07208 DUF1414: Protein of unknown function (DUF1414); InterPro: IPR009857 This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown.; PDB: 2JPQ_A 2JUZ_B 2JUW_B 2QTI_A 2OTA_A 2JR2_A 2JRX_A.
Probab=14.78 E-value=61 Score=22.27 Aligned_cols=20 Identities=20% Similarity=0.527 Sum_probs=14.2
Q ss_pred hHHHhh-hCCCCCchHHHHHH
Q 029970 31 LMSFIS-AVPETQRPSLFQSL 50 (184)
Q Consensus 31 l~klL~-~vP~~~R~~~f~SL 50 (184)
+.++|+ +||+.||..+.++.
T Consensus 16 vTniln~~V~~~qR~~iAe~F 36 (44)
T PF07208_consen 16 VTNILNTSVPPAQRQAIAEKF 36 (44)
T ss_dssp HHHHHHHCS-HHHHHHHHHHH
T ss_pred HHHHHhhcCCHHHHHHHHHHH
Confidence 456675 69999999887654
No 7
>TIGR02794 tolA_full TolA protein. TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB.
Probab=14.06 E-value=1.7e+02 Score=26.75 Aligned_cols=31 Identities=26% Similarity=0.371 Sum_probs=23.3
Q ss_pred HhccccCCcccccccccccchHHHHHHHHHHHcCCCc
Q 029970 54 AVGRTVNPVSGAVGLLWTGNWNVCQSAVERVLCGGAL 90 (184)
Q Consensus 54 A~gRi~dPVyGcVGli~tg~w~~cq~ave~Vl~g~~i 90 (184)
..|++.+ |. .++|+=.+|++|+.+|.+-+++
T Consensus 295 pdG~V~~-I~-----~sSGd~~lD~AAl~AV~ka~p~ 325 (346)
T TIGR02794 295 PDGTLLS-VT-----KSSGDPALCQAALAAVAKAAKL 325 (346)
T ss_pred CCCCEEe-ec-----cCCCCHHHHHHHHHHHHHhCCC
Confidence 4555555 22 2568889999999999998877
No 8
>PF08452 DNAP_B_exo_N: DNA polymerase family B exonuclease domain, N-terminal; InterPro: IPR013660 This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (IPR006133 from INTERPRO). ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=12.31 E-value=71 Score=19.31 Aligned_cols=10 Identities=20% Similarity=0.677 Sum_probs=7.6
Q ss_pred ccccccCCcc
Q 029970 4 QSIQWIGTPQ 13 (184)
Q Consensus 4 ~cl~wi~~pe 13 (184)
-||.|.++--
T Consensus 4 kCiNWFE~~g 13 (22)
T PF08452_consen 4 KCINWFESRG 13 (22)
T ss_pred EEeehhhhCC
Confidence 4999998754
No 9
>cd03717 SOCS_SOCS_like SOCS (suppressors of cytokine signaling) box of SOCS-like proteins. The CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. These intracellular proteins regulate the responses of immune cells to cytokines. Identified as negative regulators of the cytokine-JAK-STAT pathway, they seem to play a role in many immunological and pathological processes. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. Related SOCS boxes are also present in Rab40-like proteins and insect proteins of unknown function that also contain a NEUZ (domain in neuralized proteins) domain.
Probab=12.22 E-value=2.1e+02 Score=18.22 Aligned_cols=21 Identities=14% Similarity=0.400 Sum_probs=15.6
Q ss_pred hHHHHHHHHHHHcCCCcccCC
Q 029970 74 WNVCQSAVERVLCGGALQPLP 94 (184)
Q Consensus 74 w~~cq~ave~Vl~g~~i~~~~ 94 (184)
.|+|..++...+....|..+|
T Consensus 7 q~LCR~~Ir~~~~~~~i~~Lp 27 (39)
T cd03717 7 QHLCRFVIRQCTRRDLIDQLP 27 (39)
T ss_pred HHHHHHHHHHHccccccccCC
Confidence 489999999998666555543
No 10
>cd05562 Peptidases_S53_like Peptidase domain in the S53 family. Members of the peptidase S53 (sedolisin) family include endopeptidases and exopeptidases. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of Asn in subtilisin. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. Characterized sedolisins include Kumamolisin, an extracellular calcium-dependent thermostable endopeptidase from Bacillus. The enzyme is synthesized with a 188 amino acid N-terminal preprotein region which is cleaved after the extraction into the extracellular space with low pH. One kumamolysin paralog, kumamolisin-As, is believed to be a collagenase. TPP1 is a serine protease that functi
Probab=11.36 E-value=2.4e+02 Score=24.18 Aligned_cols=40 Identities=20% Similarity=0.301 Sum_probs=26.7
Q ss_pred cchHHHhhhCCCCCchHHHHHHHHHHhccc----cCCcccccccc
Q 029970 29 AGLMSFISAVPETQRPSLFQSLLYEAVGRT----VNPVSGAVGLL 69 (184)
Q Consensus 29 snl~klL~~vP~~~R~~~f~SLlYEA~gRi----~dPVyGcVGli 69 (184)
+++.-||.+.-++.-++.++.+|.+.+=++ .|+.|| .|+|
T Consensus 224 aG~aALl~~~~p~lt~~~v~~~L~~tA~~~~~~g~d~~~G-~G~v 267 (275)
T cd05562 224 AGVAALVLSANPGLTPADIRDALRSTALDMGEPGYDNASG-SGLV 267 (275)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCcccCCCCCCCCcC-cCcc
Confidence 456666666666677888888888876443 456666 4554
Done!