Query 032908
Match_columns 130
No_of_seqs 118 out of 185
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 07:26:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032908.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032908hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03222 rapid alkalinization 100.0 1.8E-31 3.8E-36 200.2 1.8 75 49-130 42-119 (119)
2 PLN03221 rapid alkalinization 100.0 4.1E-30 8.8E-35 196.5 4.2 61 63-130 77-137 (137)
3 PF05498 RALF: Rapid ALkaliniz 99.9 2.8E-27 6.1E-32 160.8 2.9 65 59-130 2-66 (66)
4 PF07127 Nodulin_late: Late no 24.2 63 0.0014 20.6 1.8 19 8-26 2-20 (54)
5 PF15339 Afaf: Acrosome format 20.5 1E+02 0.0022 25.6 2.8 18 11-28 130-147 (200)
6 PRK08457 motB flagellar motor 18.7 91 0.002 25.5 2.2 15 36-50 40-54 (257)
7 PF14851 FAM176: FAM176 family 17.5 2.3E+02 0.005 22.3 4.1 13 15-27 32-44 (153)
8 PF08358 Flexi_CP_N: Carlaviru 17.4 68 0.0015 21.2 0.9 34 79-121 14-47 (52)
9 PF12729 4HB_MCP_1: Four helix 15.3 3.5E+02 0.0075 18.4 4.1 38 11-48 8-45 (181)
10 PRK06667 motB flagellar motor 14.4 1.7E+02 0.0037 23.7 2.7 30 13-49 26-55 (252)
No 1
>PLN03222 rapid alkalinization factor 23-like protein; Provisional
Probab=99.96 E-value=1.8e-31 Score=200.24 Aligned_cols=75 Identities=47% Similarity=0.772 Sum_probs=65.1
Q ss_pred cCccccccccc---ccCCCCCccccccccccccccceeccccccCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCcc
Q 032908 49 EWPMLSMSFDE---EEGEGPEGEGGRRSLFWQRMKYYISYGALSANRIPCPPRSGRSYYTPNCYKARGPVHPYTRGCSVI 125 (130)
Q Consensus 49 ~~~~~~~~~~~---~ee~~m~se~~RR~L~~~~~~kYIsYgAL~rd~vPC~pr~G~SYy~~nC~kp~~pANPYsRGCs~I 125 (130)
++-+++.+|.+ |||++||||++||+|+ +++|||||||++|++||+ ++|+||| ||+ +++|+|||+|||++|
T Consensus 42 ~C~Gsi~EC~~~~~e~e~~mdSe~sRR~L~---~~rYISYgALrrd~vPCs-rrG~SYy--nC~-~~~~ANPY~RGCs~I 114 (119)
T PLN03222 42 KCNGTIAECSLSTAEEEFEMDSEINRRILA---TTKYISYGALRRNTVPCS-RRGASYY--NCR-RGAQANPYSRGCSAI 114 (119)
T ss_pred cCCCCHHHhhcccccchhccccHHHHHHHh---hcCeecHHHhcCCCCCCC-CCCCCcc--ccC-CCCCCCCCCCCchhh
Confidence 35677878754 3445999999999998 469999999999999999 5799999 996 478999999999999
Q ss_pred cccCC
Q 032908 126 TRCRR 130 (130)
Q Consensus 126 tRCRR 130 (130)
|||||
T Consensus 115 TrCrR 119 (119)
T PLN03222 115 TRCRR 119 (119)
T ss_pred ccccC
Confidence 99997
No 2
>PLN03221 rapid alkalinization factor 23; Provisional
Probab=99.96 E-value=4.1e-30 Score=196.52 Aligned_cols=61 Identities=56% Similarity=1.012 Sum_probs=56.1
Q ss_pred CCCCccccccccccccccceeccccccCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCcccccCC
Q 032908 63 EGPEGEGGRRSLFWQRMKYYISYGALSANRIPCPPRSGRSYYTPNCYKARGPVHPYTRGCSVITRCRR 130 (130)
Q Consensus 63 ~~m~se~~RR~L~~~~~~kYIsYgAL~rd~vPC~pr~G~SYy~~nC~kp~~pANPYsRGCs~ItRCRR 130 (130)
..||||++||+|+ +++||||+||++|++||+ ++|+||| ||++ ++|+|||+|||++||||||
T Consensus 77 ~~MdSE~sRR~L~---~~rYISYgALrrd~vPCs-rrG~SYy--nC~~-~~pANPY~RGCs~ITRCrR 137 (137)
T PLN03221 77 FEMDSEINRRILA---TRRYISYGALRRNTIPCS-RRGASYY--NCRR-GAQANPYSRGCSAITRCRR 137 (137)
T ss_pred hhcccHHHHHHHh---cCCccCHHHhccCCCCCC-CCCCCcc--ccCC-CCCCCCCCCCcccccccCC
Confidence 3899999999998 468999999999999999 5699999 9964 7899999999999999997
No 3
>PF05498 RALF: Rapid ALkalinization Factor (RALF) ; InterPro: IPR008801 RALF, a 5 kDa ubiquitous polypeptide in plants, arrests root growth and development.
Probab=99.93 E-value=2.8e-27 Score=160.83 Aligned_cols=65 Identities=58% Similarity=1.035 Sum_probs=57.9
Q ss_pred cccCCCCCccccccccccccccceeccccccCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCcccccCC
Q 032908 59 EEEGEGPEGEGGRRSLFWQRMKYYISYGALSANRIPCPPRSGRSYYTPNCYKARGPVHPYTRGCSVITRCRR 130 (130)
Q Consensus 59 ~~ee~~m~se~~RR~L~~~~~~kYIsYgAL~rd~vPC~pr~G~SYy~~nC~kp~~pANPYsRGCs~ItRCRR 130 (130)
||+++.|+++++||+|++ ++|||||||++|.+||+ .+|.||| ||. +++|+|||+|||++||||||
T Consensus 2 ee~~~~~~s~~~~R~~a~---~~yIsYgaL~~~~~pc~-~~g~~~~--~c~-~~~paNpY~RGC~~~~rCrr 66 (66)
T PF05498_consen 2 EEEEVVMESEASRRILAA---RRYISYGALRRDRVPCS-PRGCSYY--NCC-PRQPANPYSRGCSKITRCRR 66 (66)
T ss_pred hhHHhhhhhHHHHHHHhc---CCeecchhccCCCCCCC-cccCCCc--ccC-CCCCCCCCCCCCCccccCCC
Confidence 345569999999999984 48999999999999999 4699999 884 58999999999999999997
No 4
>PF07127 Nodulin_late: Late nodulin protein; InterPro: IPR009810 This family consists of several plant specific late nodulin sequences which are homologous to the Pisum sativum (Garden pea) ENOD3 protein. ENOD3 is expressed in the late stages of root nodule formation and contains two pairs of cysteine residues toward the proteins C terminus which may be involved in metal-binding [].; GO: 0046872 metal ion binding, 0009878 nodule morphogenesis
Probab=24.16 E-value=63 Score=20.56 Aligned_cols=19 Identities=21% Similarity=0.520 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHhh
Q 032908 8 VKLLKFGFGLMLMHMISMN 26 (130)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~ 26 (130)
+|.+||.-++.+++.+++.
T Consensus 2 a~ilKFvY~mIiflslflv 20 (54)
T PF07127_consen 2 AKILKFVYAMIIFLSLFLV 20 (54)
T ss_pred ccchhhHHHHHHHHHHHHh
Confidence 4678887777666555443
No 5
>PF15339 Afaf: Acrosome formation-associated factor
Probab=20.49 E-value=1e+02 Score=25.60 Aligned_cols=18 Identities=33% Similarity=0.586 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHhhhH
Q 032908 11 LKFGFGLMLMHMISMNLL 28 (130)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~ 28 (130)
||+.|+++||..+++..+
T Consensus 130 lkLmLGIsLmTl~lfv~L 147 (200)
T PF15339_consen 130 LKLMLGISLMTLFLFVIL 147 (200)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 678888888877766654
No 6
>PRK08457 motB flagellar motor protein MotB; Reviewed
Probab=18.67 E-value=91 Score=25.53 Aligned_cols=15 Identities=13% Similarity=0.302 Sum_probs=8.6
Q ss_pred hhhhHHhhhhccccC
Q 032908 36 VDESRLELMSDALEW 50 (130)
Q Consensus 36 vd~~~~~~~~~~~~~ 50 (130)
||..-++.+.+.+++
T Consensus 40 vd~~K~~~~~~sl~~ 54 (257)
T PRK08457 40 VNKAKVEALKTEFIK 54 (257)
T ss_pred cCHHHHHHHHHHHHH
Confidence 465566666555544
No 7
>PF14851 FAM176: FAM176 family
Probab=17.50 E-value=2.3e+02 Score=22.34 Aligned_cols=13 Identities=23% Similarity=0.232 Sum_probs=5.4
Q ss_pred HHHHHHHHHHhhh
Q 032908 15 FGLMLMHMISMNL 27 (130)
Q Consensus 15 ~~~~~~~~~~~~~ 27 (130)
++|.|++|++...
T Consensus 32 ~GLlLtLcllV~r 44 (153)
T PF14851_consen 32 AGLLLTLCLLVIR 44 (153)
T ss_pred HHHHHHHHHHHhh
Confidence 3344444444333
No 8
>PF08358 Flexi_CP_N: Carlavirus coat; InterPro: IPR013569 This domain is found together with the viral coat protein domain (IPR000052 from INTERPRO) in coat/capsid proteins of the plant infecting Carlavirus. It is required for genome encapsidation by forming ribonucleoprotein complexes along with TGB1 helicase and viral RNA. The N- and the C terminus of this coat protein can be exposed on the surface of the virus particle. The central core sequence may be important in maintaining correct tertiary structure of the coat protein and/or play a role in the interaction with the viral RNA. Coat proteins are often used to distinguish between Carlavirus isolates. In the coat protein amino acid sequences of definitive and tentative species of carlaviruses, there is a region of seven amino acids (GLGVPTE) that are conserved []. The complete coat protein (CP) sequences of 29 Indian Chrysanthemum virus B (CVB) isolates were highly heterogeneous, sharing nucleotide sequence identities of 74-98% [, ].
Probab=17.36 E-value=68 Score=21.21 Aligned_cols=34 Identities=18% Similarity=0.387 Sum_probs=19.0
Q ss_pred ccceeccccccCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCC
Q 032908 79 MKYYISYGALSANRIPCPPRSGRSYYTPNCYKARGPVHPYTRG 121 (130)
Q Consensus 79 ~~kYIsYgAL~rd~vPC~pr~G~SYy~~nC~kp~~pANPYsRG 121 (130)
...-|..+++.-.++.=.+ +.+= | +.++|||+|-
T Consensus 14 ~~~~v~N~~fE~GRP~l~~-------~~~m-r-~d~tN~y~Rp 47 (52)
T PF08358_consen 14 TASNVTNPGFEIGRPKLEP-------SDDM-R-GDPTNPYSRP 47 (52)
T ss_pred cCCcccccccccCCcCCcC-------chhh-C-CCcCcccCCc
Confidence 4456666777665443221 1111 2 5799999983
No 9
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=15.33 E-value=3.5e+02 Score=18.40 Aligned_cols=38 Identities=18% Similarity=0.493 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHhhhHhhhhhhhhhhhHHhhhhccc
Q 032908 11 LKFGFGLMLMHMISMNLLHVEAQVAVDESRLELMSDAL 48 (130)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~aq~~vd~~~~~~~~~~~ 48 (130)
|-++|++.+++++.+..+.+..--.++...-++..+.+
T Consensus 8 L~~~f~~~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~ 45 (181)
T PF12729_consen 8 LILGFGLIILLLLIVGIVGLYSLSQINQNVEEIYENNL 45 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
No 10
>PRK06667 motB flagellar motor protein MotB; Validated
Probab=14.43 E-value=1.7e+02 Score=23.68 Aligned_cols=30 Identities=23% Similarity=0.334 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHhhhHhhhhhhhhhhhHHhhhhcccc
Q 032908 13 FGFGLMLMHMISMNLLHVEAQVAVDESRLELMSDALE 49 (130)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~aq~~vd~~~~~~~~~~~~ 49 (130)
.||+|+||+.+.... . +|...++.+.+.++
T Consensus 26 ~TLLL~FFVlL~smS-----~--~d~~k~~~~~~s~~ 55 (252)
T PRK06667 26 VTLLLCFFVMLFTTN-----D--VDENVLQIISASFT 55 (252)
T ss_pred HHHHHHHHHHHHHhh-----h--cCHHHHHHHHHHhh
Done!