Query gi|254780122|ref|YP_003064535.1| hypothetical protein CLIBASIA_00005 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 123
No_of_seqs 2 out of 4
Neff 1.5
Searched_HMMs 39220
Date Wed May 18 18:32:25 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780122.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4832 consensus 46.0 26 0.00067 16.7 4.1 31 1-31 6-36 (253)
2 cd03066 PDI_b_Calsequestrin_mi 40.9 2.4 6.2E-05 23.0 -2.6 63 32-94 2-71 (102)
3 pfam11472 DUF3206 Protein of u 37.9 18 0.00045 17.8 1.5 59 25-85 39-97 (128)
4 COG4053 Uncharacterized protei 34.8 39 0.001 15.7 4.8 72 29-119 8-101 (244)
5 PRK08178 acetolactate synthase 26.8 26 0.00065 16.8 0.8 38 21-59 42-80 (96)
6 pfam08651 DASH_Duo1 DASH compl 24.9 58 0.0015 14.6 6.2 62 41-102 3-76 (78)
7 TIGR01051 topA_bact DNA topois 24.9 57 0.0014 14.7 2.2 36 41-77 327-364 (688)
8 pfam10312 Cactin_mid Conserved 23.0 63 0.0016 14.4 4.3 30 61-96 71-100 (190)
9 PRK03659 glutathione-regulated 22.6 65 0.0016 14.3 3.6 44 49-92 542-586 (602)
10 COG1310 Predicted metal-depend 19.9 39 0.00099 15.7 0.6 13 17-29 74-86 (134)
No 1
>KOG4832 consensus
Probab=46.00 E-value=26 Score=16.73 Aligned_cols=31 Identities=19% Similarity=0.215 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEE
Q ss_conf 9327888999876213656379998766057
Q gi|254780122|r 1 MGALKNHFHDEINENFYFHSHPNADPDISIE 31 (123)
Q Consensus 1 MG~LK~~~~~EI~~N~~F~S~~N~~P~~~~E 31 (123)
|-+|--++-++|.+++...|.-|++|+.+|-
T Consensus 6 LeSLIss~ne~igEl~kl~s~rnm~~e~TI~ 36 (253)
T KOG4832 6 LESLISSVNEKIGELKKLLSLRNMGQEPTIK 36 (253)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHH
T ss_conf 9999999989888999999985689887533
No 2
>cd03066 PDI_b_Calsequestrin_middle PDIb family, Calsequestrin subfamily, Middle TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca
Probab=40.94 E-value=2.4 Score=23.00 Aligned_cols=63 Identities=24% Similarity=0.302 Sum_probs=46.4
Q ss_pred EEEECHHHHHHH--HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH----HHHHHHHHHHHHHHHHH
Q ss_conf 665000368999--999758899998755778887-9999999999999----99987888999999997
Q gi|254780122|r 32 MQISENQRYLDE--EISQCNAVVDVFKRSDSTILD-KLDAMDDLKTYIS----LLQATAKNLKSLLKEYW 94 (123)
Q Consensus 32 ~~i~E~~~~L~~--~i~~~~~~v~~~~Rs~~T~l~-~~D~~~~~~~~I~----L~~A~~k~L~~~l~E~W 94 (123)
|+||.+.+-|.. .+-.+-+||.+|+--+|.|.. -.||-++...+|. .-+..||.|.+++|||=
T Consensus 2 VeiI~~~~el~~F~~~eediklIGyFk~~~S~hy~~F~eAAe~F~P~IkFfAtf~~kvAk~L~LK~neVd 71 (102)
T cd03066 2 VEIINSERELQAFENIEDDIKLIGYFKSEDSEHYKAFEEAAEEFHPYIKFFATFDSKVAKKLGLKMNEVD 71 (102)
T ss_pred EEEECCHHHHHHHHHHHHCEEEEEEECCCCCHHHHHHHHHHHHCCCCEEEEEEECHHHHHHHCCCCCCEE
T ss_conf 5574678788887630211578887448986689999999986366235665645889988376004153
No 3
>pfam11472 DUF3206 Protein of unknown function (DUF3206). This bacterial family of proteins has no known function.
Probab=37.93 E-value=18 Score=17.76 Aligned_cols=59 Identities=27% Similarity=0.465 Sum_probs=42.5
Q ss_pred CCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8766057665000368999999758899998755778887999999999999999987888
Q gi|254780122|r 25 DPDISIEMQISENQRYLDEEISQCNAVVDVFKRSDSTILDKLDAMDDLKTYISLLQATAKN 85 (123)
Q Consensus 25 ~P~~~~E~~i~E~~~~L~~~i~~~~~~v~~~~Rs~~T~l~~~D~~~~~~~~I~L~~A~~k~ 85 (123)
+|+.--+|+ |...+|+++..-|..||-----.+...-|.+.+|+++++.|-|--|.+++
T Consensus 39 ~p~vl~~me--edpdwleea~~~cq~liv~slld~~nf~~~~el~~e~~~li~ly~~~~k~ 97 (128)
T pfam11472 39 DPEVLAEME--EDPDWLEEAAAGCQGLIVGSLLDDENFDDTEELKDEFACLINLYDAAAKD 97 (128)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHCCEEHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999998762--08208999851042111334404567674999999999999999999876
No 4
>COG4053 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.76 E-value=39 Score=15.65 Aligned_cols=72 Identities=22% Similarity=0.343 Sum_probs=42.8
Q ss_pred EEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------------HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0576650003689999997588999987557788879----------------------999999999999999878889
Q gi|254780122|r 29 SIEMQISENQRYLDEEISQCNAVVDVFKRSDSTILDK----------------------LDAMDDLKTYISLLQATAKNL 86 (123)
Q Consensus 29 ~~E~~i~E~~~~L~~~i~~~~~~v~~~~Rs~~T~l~~----------------------~D~~~~~~~~I~L~~A~~k~L 86 (123)
|+-..||+| ..+++.+|+....|++...+++ +++++++|+.|.-
T Consensus 8 sigaDiSdn------Dv~~sr~l~~~ve~~ik~ll~~~~~~a~l~nitGDDivi~~fVee~~lE~vN~aife-------- 73 (244)
T COG4053 8 SIGADISDN------DVKTSRKLNELVEKEIKKLLSKLGIKATLSNITGDDIVITSFVEENLLEKVNKAIFE-------- 73 (244)
T ss_pred EEECCCCCC------CCCCCHHHHHHHHHHHHHHHHHHCCEEEECCCCCCCEEEEEECCCCHHHHHHHHHHH--------
T ss_conf 974223466------420289899999999999997415115753655773799996150278888899999--------
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHH
Q ss_conf 999999975431388703567386756776556
Q gi|254780122|r 87 KSLLKEYWEESLDGEDDEEIYEHPDQEHREDYY 119 (123)
Q Consensus 87 ~~~l~E~WE~~~D~E~~E~~~EHPDQEHrEDYY 119 (123)
.+++| ++.++|-+-+||.||.--.---|
T Consensus 74 --vlr~y---~eg~~Dl~GiSe~pdgAGEG~SY 101 (244)
T COG4053 74 --VLRKY---AEGFDDLRGISEDPDGAGEGLSY 101 (244)
T ss_pred --HHHHH---HHCCCCCCCCCCCCCCCCCCCHH
T ss_conf --99987---53324213655797767777017
No 5
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=26.80 E-value=26 Score=16.78 Aligned_cols=38 Identities=37% Similarity=0.497 Sum_probs=26.9
Q ss_pred CCCCCCCCE-EEEEEECHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 799987660-576650003689999997588999987557
Q gi|254780122|r 21 HPNADPDIS-IEMQISENQRYLDEEISQCNAVVDVFKRSD 59 (123)
Q Consensus 21 ~~N~~P~~~-~E~~i~E~~~~L~~~i~~~~~~v~~~~Rs~ 59 (123)
+|-.+|.+| +.+-+...++ ++.-+||.+|+|+|.+-.+
T Consensus 42 ~~te~~~~SRiTivv~~d~~-leQi~kQL~KLidVi~V~~ 80 (96)
T PRK08178 42 LPIQDSDKSRIWLLVNDDQR-LEQMISQIDKLEDVLKVRR 80 (96)
T ss_pred EECCCCCCEEEEEEECCCCC-HHHHHHHHHHCCCEEEEEE
T ss_conf 51389981089999889844-8999999861507699998
No 6
>pfam08651 DASH_Duo1 DASH complex subunit Duo1. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.
Probab=24.93 E-value=58 Score=14.62 Aligned_cols=62 Identities=26% Similarity=0.380 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCC
Q ss_conf 999999758899998755778887999999-----------9999999999878889999999975-4313887
Q gi|254780122|r 41 LDEEISQCNAVVDVFKRSDSTILDKLDAMD-----------DLKTYISLLQATAKNLKSLLKEYWE-ESLDGED 102 (123)
Q Consensus 41 L~~~i~~~~~~v~~~~Rs~~T~l~~~D~~~-----------~~~~~I~L~~A~~k~L~~~l~E~WE-~~~D~E~ 102 (123)
|.+++.+-.++..++.-.+.++-.-..-|+ =++++|..+--+..+-+++.+.-|. ++.|..+
T Consensus 3 L~kEL~~L~~iN~vie~~~~sL~~a~~n~~~v~~t~~st~~LLd~W~~IlSQte~~~~Ll~n~~W~G~~~d~~~ 76 (78)
T pfam08651 3 LLKELEQLRKINEVIEGLIESLRGAKGNMEKIQETCKSTNTLLDTWIRILSQTEHTQRLMLNPTWLGSSEDGAD 76 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf 88999999989999999999999999889999999877999999999999877899988709665674233330
No 7
>TIGR01051 topA_bact DNA topoisomerase I; InterPro: IPR005733 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry describes topoisomerase I from bacteria, which is more closely related to archaeal than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. Prokaryotic topoisomerase I folds in an unusual way to give 4 distinct domains, enclosing a hole large enough to accommodate a double-stranded DNA segment. A tyrosine at the active site, which lies at the interface of 2 domains, is involved in transient breakage of a DNA strand, and the formation of a covalent protein-DNA intermediate through a 5-phosphotyrosine linkage. The structure reveals a plausible mechanism by which this and related enzymes could catalyse the passage of one DNA strand through a transient break in another strand . Topoisomerase I require Mg2+ as a cofactor for catalysis to take place. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=24.88 E-value=57 Score=14.68 Aligned_cols=36 Identities=31% Similarity=0.450 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999975889999--87557788879999999999999
Q gi|254780122|r 41 LDEEISQCNAVVDV--FKRSDSTILDKLDAMDDLKTYIS 77 (123)
Q Consensus 41 L~~~i~~~~~~v~~--~~Rs~~T~l~~~D~~~~~~~~I~ 77 (123)
|=|.+++-...|-+ .-|||||.| -.+|++++..+|.
T Consensus 327 LYEGv~~~~~~~G~ITYMRTDS~~l-S~~A~~eaR~~I~ 364 (688)
T TIGR01051 327 LYEGVSLGEGTVGLITYMRTDSTRL-SNEAVNEARNLID 364 (688)
T ss_pred HHCCEECCCCEEEEEECCCCCCHHH-HHHHHHHHHHHHH
T ss_conf 3125443895589983286330578-9999999998888
No 8
>pfam10312 Cactin_mid Conserved mid region of cactin. This is the conserved middle region of a family of proteins referred to as cactins. The region contains two of three predicted coiled-coil domains. Most members of this family have a CactinC_cactus pfam09732 domain at the C-terminal end. Upstream of Mid_cactin in Drosophila members are a serine-rich region, some non-typical RD motifs and three predicted bipartite nuclear localisation signals, none of which are well-conserved. Cactin associates with IkappaB-cactus as one of the intracellular members of the Rel (NF-kappaB) pathway which is conserved in invertebrates and vertebrates. In mammals, this pathway controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo.
Probab=22.96 E-value=63 Score=14.38 Aligned_cols=30 Identities=30% Similarity=0.644 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 888799999999999999998788899999999754
Q gi|254780122|r 61 TILDKLDAMDDLKTYISLLQATAKNLKSLLKEYWEE 96 (123)
Q Consensus 61 T~l~~~D~~~~~~~~I~L~~A~~k~L~~~l~E~WE~ 96 (123)
|.-+++++.+|+++|+.|-+..+ | .+||.+
T Consensus 71 ~~~eleeL~~dIk~y~~Le~~~~-n-----~~fW~~ 100 (190)
T pfam10312 71 TVDELEELEEDIKMYLELEKNPK-N-----REYWKA 100 (190)
T ss_pred CHHHHHHHHHHHHHHHHHHCCCH-H-----HHHHHH
T ss_conf 99999999999999999874525-8-----899999
No 9
>PRK03659 glutathione-regulated potassium-efflux system protein KefB; Provisional
Probab=22.55 E-value=65 Score=14.33 Aligned_cols=44 Identities=14% Similarity=0.223 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8899998755778-8879999999999999999878889999999
Q gi|254780122|r 49 NAVVDVFKRSDST-ILDKLDAMDDLKTYISLLQATAKNLKSLLKE 92 (123)
Q Consensus 49 ~~~v~~~~Rs~~T-~l~~~D~~~~~~~~I~L~~A~~k~L~~~l~E 92 (123)
...+..|.+-|.. .-+.-..-+|-+.+|+..+...+.|+.++..
T Consensus 542 ~~~~~~f~~~d~~~l~~~~~~~~d~~~~~~~~~~~~~el~~l~~~ 586 (602)
T PRK03659 542 QRAQLHFRRLDMRMLRELIPQHNEDTVQISRAKEARRELEEIFQR 586 (602)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999998763388799999999999999999999
No 10
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=19.89 E-value=39 Score=15.68 Aligned_cols=13 Identities=46% Similarity=0.912 Sum_probs=8.0
Q ss_pred HHHHCCCCCCCCE
Q ss_conf 6563799987660
Q gi|254780122|r 17 YFHSHPNADPDIS 29 (123)
Q Consensus 17 ~F~S~~N~~P~~~ 29 (123)
-|||||+..|..|
T Consensus 74 ~yHSHP~~~~~pS 86 (134)
T COG1310 74 WYHSHPGGPPYPS 86 (134)
T ss_pred EECCCCCCCCCCC
T ss_conf 9817989988859
Done!