254781188

254781188

hypothetical protein CLIBASIA_05475

GeneID in NCBI database:8210213Locus tag:CLIBASIA_05475
Protein GI in NCBI database:254781188Protein Accession:YP_003065601.1
Gene range:-(1186354, 1186911)Protein Length:185aa
Gene description:hypothetical protein
COG prediction:none
KEGG prediction:hypothetical protein
SEED prediction:hypothetical protein
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-----
MSNLVKKAKKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKHTIDLRPAIERLREHYKHLKPIDSERIPHKSTEKPLEIVESSIAEQSIIEHNN
cHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHccHHHHHHHHccccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHcc
cHHHHccccHHHHHHHHHHHccHHHHHHHHHHHHccccccccccccccccccEEHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHcccccHHHHHHHHHHHHHHcccccccEEEEEccccccHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHEccc
MSNLVKKAKKAVRAkkgciyyspelfaGILDQVANGKALGHVLrkvgmpkySTFYRWIKKDLKLQEAYTEALQCRLDLLAEElleepaptaeelanpvfYSKMRDRKQRMGTFLLEklsnqkygprvsveskhtidlRPAIERLREHYkhlkpidseriphkstekpleIVESSIAEQSIIEHNN
msnlvkkakkavrakkgciyYSPELFAGILDQVANGKALGHvlrkvgmpkySTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEepaptaeelanpvfYSKMRDRKQRMGTFlleklsnqkygprvsveskhtidlrpAIERLREHYKhlkpidseriphkstekpleivessiaeqsiiehnn
MSNLvkkakkavrakkGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRldllaeelleepaptaeelaNPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKHTIDLRPAIERLREHYKHLKPIDSERIPHKSTEKPLEIVESSIAEQSIIEHNN
**********************PELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRV**********************************************************
*************AKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKHTIDLRPAIERLREHYKHLKPIDSERIPHKSTEKPLEIVESSIAEQSIIEHNN
MSN*VKKAKKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKHTIDLRPAIERLREHYKHLKPIDSERIPHKSTEKPLEIVESSIAEQSIIE***
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSNLVKKAKKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKHTIDLRPAIERLREHYKHLKPIDSERIPHKSTEKPLEIVESSIAEQSIIEHNN
MSNLVKKAKKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKHTIDLRPAIERLREHYKHLKPIDSERIPHKSTEKPLEIVESSIAEQSIIEHNN
MSNLVKKAKKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKHTIDLRPAIERLREHYKHLKPIDSERIPHKSTEKPLEIVESSIAEQSIIEHNN

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target185 hypothetical protein CLIBASIA_05475 [Candidatus Liberib
254781217162 hypothetical protein CLIBASIA_05620 [Candidatus Li 3e-14
>gi|254781217|ref|YP_003065630.1| hypothetical protein CLIBASIA_05620 [Candidatus Liberibacter asiaticus str. psy62] Length = 162 Back     alignment
 Score = 69.7 bits (169), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 54/154 (35%), Positives = 83/154 (53%), Gaps = 8/154 (5%)

Query: 21  YSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLK-LQEAYTEALQCRLDLL 79
           Y+ E    IL   + G +L    +K G+   S F+ W+K+D + L++ Y +A Q  ++ L
Sbjct: 6   YTKERIDNILASFSGGLSLSQSCKKHGVTVVS-FHGWVKQDREDLEKRYEQAKQSHMEHL 64

Query: 80  AEELLEE-PAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKHTIDLR 138
           +E L     AP  EE  +     K+R+ + +   + LEK     YG  VSVE KHTIDL+
Sbjct: 65  SENLASVVEAPLTEEERDHPQAIKLRELRMKRLQWELEKRYRNVYGNHVSVEQKHTIDLK 124

Query: 139 PAIERLRE--HYKHLKPIDSERIPHKSTEKPLEI 170
           P ++R++     K LKP+   +   K TEKPLE+
Sbjct: 125 PLMDRVQHSIQSKGLKPV---KALDKQTEKPLEL 155

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target185 hypothetical protein CLIBASIA_05475 [Candidatus Liberib
315122903180 hypothetical protein CKC_05795 [Candidatus Liberibacter 1 6e-31
254781217162 hypothetical protein CLIBASIA_05620 [Candidatus Liberib 1 2e-10
317120681171 hypothetical protein SC1_gp120 [Liberibacter phage SC1] 1 2e-10
260596961164 hypothetical protein CTU_11690 [Cronobacter turicensis 1 4e-09
315121941172 hypothetical protein CKC_00955 [Candidatus Liberibacter 1 8e-09
156934896150 hypothetical protein ESA_02744 [Cronobacter sakazakii A 1 2e-08
251791567245 hypothetical protein Dd1591_4010 [Dickeya zeae Ech1591] 1 1e-06
268589861140 conserved hypothetical protein [Providencia rettgeri DS 1 2e-06
329119588135 putative phage associated protein [Neisseria bacillifor 1 1e-05
254240164188 hypothetical protein PA2G_00805 [Pseudomonas aeruginosa 1 1e-05
>gi|315122903|ref|YP_004063392.1| hypothetical protein CKC_05795 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 180 Back     alignment and organism information
 Score =  137 bits (345), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 73/177 (41%), Positives = 112/177 (63%), Gaps = 1/177 (0%)

Query: 5   VKKAKKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKL 64
           +K   K  + +K  + YS  L   I+ ++ANG+ +  VL+   MP    FY W+ +  + 
Sbjct: 1   MKANSKKRKPQKPTVKYSQSLTKEIITRIANGETMQAVLKYPNMPTADAFYDWLARYPEH 60

Query: 65  QEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYG 124
           +E+Y +A   +L+L+ EE+  EP PT  ELANPVFYSKMRDRKQ+   +L E+L+ Q YG
Sbjct: 61  RESYNQARVKKLELMVEEVTNEPEPTEHELANPVFYSKMRDRKQKSVLWLAERLNRQIYG 120

Query: 125 PRVSVESKHTIDLRPAIERLREHYKHLKPIDSERIPHKSTEKPLEIVESSIAEQSII 181
             ++VE KHTIDL+P + ++ E  KH +   + R+  ++TEKPLE+ + S A+QS +
Sbjct: 121 NHMTVEQKHTIDLKPVLAKIEERRKHQQANKAMRV-LEATEKPLELTKLSKAKQSTM 176


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|254781217|ref|YP_003065630.1| hypothetical protein CLIBASIA_05620 [Candidatus Liberibacter asiaticus str. psy62] Length = 162 Back     alignment and organism information
>gi|317120681|gb|ADV02504.1| hypothetical protein SC1_gp120 [Liberibacter phage SC1] Length = 171 Back     alignment and organism information
>gi|260596961|ref|YP_003209532.1| hypothetical protein CTU_11690 [Cronobacter turicensis z3032] Length = 164 Back     alignment and organism information
>gi|315121941|ref|YP_004062430.1| hypothetical protein CKC_00955 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 172 Back     alignment and organism information
>gi|156934896|ref|YP_001438812.1| hypothetical protein ESA_02744 [Cronobacter sakazakii ATCC BAA-894] Length = 150 Back     alignment and organism information
>gi|251791567|ref|YP_003006288.1| hypothetical protein Dd1591_4010 [Dickeya zeae Ech1591] Length = 245 Back     alignment and organism information
>gi|268589861|ref|ZP_06124082.1| conserved hypothetical protein [Providencia rettgeri DSM 1131] Length = 140 Back     alignment and organism information
>gi|329119588|ref|ZP_08248269.1| putative phage associated protein [Neisseria bacilliformis ATCC BAA-1200] Length = 135 Back     alignment and organism information
>gi|254240164|ref|ZP_04933486.1| hypothetical protein PA2G_00805 [Pseudomonas aeruginosa 2192] Length = 188 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

No hit with e-value below 0.005

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 185 hypothetical protein CLIBASIA_05475 [Candidatus Liberib
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and related 96.45
pfam0152775 Transposase_8 Transposase. Transposase proteins are nec 96.0
PRK13413200 mpi multiple promoter invertase; Provisional 95.96
pfam0279645 HTH_7 Helix-turn-helix domain of resolvase. 95.94
pfam0421853 CENP-B_N CENP-B N-terminal DNA-binding domain. Centrome 94.59
COG3415138 Transposase and inactivated derivatives [DNA replicatio 93.35
pfam0522545 HTH_psq helix-turn-helix, Psq domain. This DNA-binding 91.21
pfam01710120 Transposase_14 Transposase. Transposase proteins are ne 95.67
pfam07141174 Phage_term_sma Putative bacteriophage terminase small s 91.04
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella Back     alignment and domain information
>pfam01527 Transposase_8 Transposase Back     alignment and domain information
>PRK13413 mpi multiple promoter invertase; Provisional Back     alignment and domain information
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase Back     alignment and domain information
>pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain Back     alignment and domain information
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Back     alignment and domain information
>pfam05225 HTH_psq helix-turn-helix, Psq domain Back     alignment and domain information
>pfam01710 Transposase_14 Transposase Back     alignment and domain information
>pfam07141 Phage_term_sma Putative bacteriophage terminase small subunit Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target185 hypothetical protein CLIBASIA_05475 [Candidatus Liberib
3hef_A143 Crystal Structure Of The Bacteriophage Sf6 Terminas 2e-23
>gi|288562970|pdb|3HEF|A Chain A, Crystal Structure Of The Bacteriophage Sf6 Terminase Small Subunit Length = 143 Back     alignment and structure
 Score =  112 bits (280), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 34/121 (28%), Positives = 63/121 (52%), Gaps = 8/121 (6%)

Query: 10  KAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYT 69
           KA R       Y PE+   I   +++G++L  V ++ GMP  ST +RW+ K    ++ Y 
Sbjct: 9   KAGRP----SDYMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKHEDFRDKYA 64

Query: 70  EALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSV 129
           +A + R D + EE+ E       + A  V  +++R   ++   + L +++ +KYG +V+ 
Sbjct: 65  KATEARADSIFEEIFEIADNAIPDAA-EVAKARLRVDTRK---WALARMNPRKYGDKVTN 120

Query: 130 E 130
           E
Sbjct: 121 E 121


Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target185 hypothetical protein CLIBASIA_05475 [Candidatus Liberib
3hef_A143 Gene 1 protein; bacteriophage SF6, terminase small subu 8e-14
>3hef_A Gene 1 protein; bacteriophage SF6, terminase small subunit GP1, GP1 octameric assembly, GP1 channel, DNA recognition, DNA packaging; 1.65A {Enterobacteria phage SF6} Length = 143 Back     alignment and structure
 Score = 71.9 bits (176), Expect = 8e-14
 Identities = 32/122 (26%), Positives = 57/122 (46%), Gaps = 8/122 (6%)

Query: 9   KKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAY 68
            KA R       Y PE+   I   +++G++L  V ++ GMP  ST +RW+ K    ++ Y
Sbjct: 8   PKAGRPSD----YMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKHEDFRDKY 63

Query: 69  TEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVS 128
            +A + R D + EE+ E     A+              +     + L +++ +KYG +V+
Sbjct: 64  AKATEARADSIFEEIFEI----ADNAIPDAAEVAKARLRVDTRKWALARMNPRKYGDKVT 119

Query: 129 VE 130
            E
Sbjct: 120 NE 121


Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target185 hypothetical protein CLIBASIA_05475 [Candidatus Liberib
3hef_A143 Gene 1 protein; bacteriophage SF6, terminase small subu 99.93
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, nati 96.97
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated reco 96.55
2jn6_A97 Protein CGL2762, transposase; GFT PSI-2, protein struct 95.42
2r0q_C209 Putative transposon TN552 DNA-invertase BIN3; site-spec 94.68
2rn7_A108 IS629 ORFA; helix, all alpha, unknown function, structu 93.91
1u78_A141 TC3 transposase, transposable element TC3 transposase; 93.15
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn-heli 92.54
1gdt_A183 GD resolvase, protein (gamma delta resolvase); protein- 92.54
1k78_A149 Paired box protein PAX5; paired domain, ETS domain, tra 92.29
2k27_A159 Paired box protein PAX-8; paired domain, solution struc 92.19
3gzi_A218 Transcriptional regulator, TETR family; TETR family tra 91.39
>3hef_A Gene 1 protein; bacteriophage SF6, terminase small subunit GP1, GP1 octameric assembly, GP1 channel, DNA recognition, DNA packaging; 1.65A {Enterobacteria phage SF6} Back     alignment and structure
Probab=99.93  E-value=7.4e-26  Score=192.58  Aligned_cols=121  Identities=29%  Similarity=0.471  Sum_probs=105.8

Q ss_pred             HHHHHCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             55540246567644589999999999858923899961588988889999983398999999999997379999998620
Q gi|254781188|r    7 KAKKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEE   86 (185)
Q Consensus         7 ~~~Ka~R~Kk~~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~laEEILE~   86 (185)
                      +.+|.||+++    ||+|++++||++|++|.|++.||+++||||++|||+|++++++|+++|.+|++.+++.++|++++.
T Consensus         6 ~~~k~GRPtk----~t~e~~e~I~~~l~~G~sl~~i~~~~gvps~sT~~~Wl~~~~ef~e~y~~Ar~~~~~~~~~~~~~i   81 (143)
T 3hef_A            6 TEPKAGRPSD----YMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKHEDFRDKYAKATEARADSIFEEIFEI   81 (143)
T ss_dssp             -------CCS----CCHHHHHHHHHHHHTTCCHHHHHTSTTCCCHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCC----CCHHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999865----799999999999988985999987079996899999997189999999999999999999999999


Q ss_pred             CCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0230056403603789979999889999987646653434203443313
Q gi|254781188|r   87 PAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKHTI  135 (185)
Q Consensus        87 ~a~~~ee~~~~~~~~~lr~~~~~~~~w~l~k~~p~~yg~rvs~e~~h~~  135 (185)
                      .. ........+..+++++++++   |.|+|++|++||+++.+|++...
T Consensus        82 ~~-~~~~~~~~~~~~r~~~~~~k---w~l~kl~P~~ygdk~~~e~~g~~  126 (143)
T 3hef_A           82 AD-NAIPDAAEVAKARLRVDTRK---WALARMNPRKYGDKVTNELVGKD  126 (143)
T ss_dssp             HH-TCCSSHHHHHHHHHHHHHHH---HHHHHHSHHHHSCCEEEEEECGG
T ss_pred             HH-HCCCCHHHHHHHHHHHHHHH---HHHHCCCCCCCCCCCCCCCCCCC
T ss_conf             86-10246188888688899999---99976683013656431036789



>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster} Back     alignment and structure
>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C Back     alignment and structure
>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19 Back     alignment and structure
>2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific recombinase, resolvase, DNA-binding protein, protein-DNA complex, DNA integration, DNA invertase, DNA recombination; 3.20A {Staphylococcus aureus} Back     alignment and structure
>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri} Back     alignment and structure
>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2 Back     alignment and structure
>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A Back     alignment and structure
>1gdt_A GD resolvase, protein (gamma delta resolvase); protein-DNA complex, double helix, overhanging base, DNA binding protein/DNA complex; 3.00A {Escherichia coli} SCOP: a.4.1.2 c.53.1.1 PDB: 1zr4_A 1zr2_A 2gm4_A 1res_A 1ret_A Back     alignment and structure
>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Back     alignment and structure
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Back     alignment and structure
>3gzi_A Transcriptional regulator, TETR family; TETR family transcriptional regulator, structural genomics, center for structural genomics, JCSG; 2.05A {Shewanella loihica pv-4} Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

No hit with e-value below 0.005

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target185 hypothetical protein CLIBASIA_05475 [Candidatus Liberib
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 96.76
d2jn6a189 Uncharacterized protein Cgl2762 {Corynebacterium glutam 95.55
d1pdnc_123 Paired protein (prd) {Fruit fly (Drosophila melanogaste 93.62
d1k78a163 Pax-5 {Human (Homo sapiens) [TaxId: 9606]} 92.67
d1hlva166 DNA-binding domain of centromere binding protein B (CEN 90.92
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic
Probab=96.76  E-value=0.00064  Score=44.31  Aligned_cols=45  Identities=18%  Similarity=0.243  Sum_probs=39.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf             24656764458999999999985892389996158898888999998339
Q gi|254781188|r   12 VRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKD   61 (185)
Q Consensus        12 ~R~Kk~~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kd   61 (185)
                      ||.++    .|++-+..+-..+++|+|..+|++..|+ |.+|+|+|+-.+
T Consensus         1 GR~~~----lt~~q~~~a~~l~~~G~s~~~iA~~~gV-Sr~TiYry~pa~   45 (47)
T d1ijwc_           1 GRPRA----INKHEQEQISRLLEKGHPRQQLAIIFGI-GVSTLYRYFPAS   45 (47)
T ss_dssp             CCCCS----SCHHHHHHHHHHHHTTCCHHHHHHHHTC-CHHHHHHHSCST
T ss_pred             CCCCC----CCHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHCCCC
T ss_conf             98885----9999999999999889979999999796-999998557755



>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]} Back     information, alignment and structure
>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 185 hypothetical protein CLIBASIA_05475 [Candidatus Li
3hef_A_143 (A:) Gene 1 protein; bacteriophage SF6, terminase 3e-12
>3hef_A (A:) Gene 1 protein; bacteriophage SF6, terminase small subunit GP1, GP1 octameric assembly, GP1 channel, DNA recognition, DNA packaging; 1.65A {Enterobacteria phage SF6}Length = 143 Back     alignment and structure
 Score = 65.7 bits (160), Expect = 3e-12
 Identities = 33/126 (26%), Positives = 60/126 (47%), Gaps = 14/126 (11%)

Query: 21  YSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLA 80
           Y PE+   I   +++G++L  V ++ GMP  ST +RW+ K    ++ Y +A + R D + 
Sbjct: 16  YMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKHEDFRDKYAKATEARADSIF 75

Query: 81  EELLEEPAPTAEELANPVFYSKMRDRKQRMGT----FLLEKLSNQKYGPRVSVESKHTID 136
           EE+         E+A+          K R+      + L +++ +KYG +V+ E      
Sbjct: 76  EEIF--------EIADNAIPDAAEVAKARLRVDTRKWALARMNPRKYGDKVTNE--LVGK 125

Query: 137 LRPAIE 142
              AI+
Sbjct: 126 DGGAIQ 131


Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target185 hypothetical protein CLIBASIA_05475 [Candidatus Liberib
3hef_A_143 Gene 1 protein; bacteriophage SF6, terminase small 99.85
2elh_A_87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 97.16
1jko_C_52 HIN recombinase, DNA-invertase HIN; water-mediated 96.98
2cob_A_70 LCOR protein; MLR2, KIAA1795, helix-turn-helix, st 95.48
1hlv_A_1-6767 CENP-B, major centromere autoantigen B; helix-turn 95.46
2jn6_A_1-5656 Protein CGL2762, transposase; GFT PSI-2, protein s 95.26
1pdn_C_17-6953 Protein (PRD paired); protein-DNA complex, double 94.74
2rn7_A_108 IS629 ORFA; helix, all alpha, unknown function; NM 94.25
2k27_A_1-7575 Paired box protein PAX-8; paired domain, solution 92.05
2hku_A_215 A putative transcriptional regulator; structural g 91.31
>3hef_A (A:) Gene 1 protein; bacteriophage SF6, terminase small subunit GP1, GP1 octameric assembly, GP1 channel, DNA recognition, DNA packaging; 1.65A {Enterobacteria phage SF6} Back     alignment and structure
Probab=99.85  E-value=5.3e-21  Score=161.13  Aligned_cols=126  Identities=28%  Similarity=0.490  Sum_probs=106.9

Q ss_pred             HHHHHCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             55540246567644589999999999858923899961588988889999983398999999999997379999998620
Q gi|254781188|r    7 KAKKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEE   86 (185)
Q Consensus         7 ~~~Ka~R~Kk~~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~laEEILE~   86 (185)
                      +..|.||+.    +|+++++++||..+++|.|++.||...|||+++||++|+.++++|+++|.+|++.+.+.+++.+++.
T Consensus         6 ~~~k~gRps----ky~~e~~~~i~~~~~~G~s~~~Ia~~~gips~~Tl~~W~~~~~ef~e~~~~ak~~~~~~v~~~l~~~   81 (143)
T 3hef_A            6 TEPKAGRPS----DYMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKHEDFRDKYAKATEARADSIFEEIFEI   81 (143)
T ss_dssp             -------CC----SCCHHHHHHHHHHHHTTCCHHHHHTSTTCCCHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCC----CCCHHHHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999997----6899999999999987987999987279996899999998178999999999999999999999999


Q ss_pred             -CCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHH
Q ss_conf             -02300564036037899799998899999876466534342034433------13467889
Q gi|254781188|r   87 -PAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKH------TIDLRPAI  141 (185)
Q Consensus        87 -~a~~~ee~~~~~~~~~lr~~~~~~~~w~l~k~~p~~yg~rvs~e~~h------~~~~~~~~  141 (185)
                       ...+.++.-  +...++++.+++   |.|.++.|.+||+++++|++.      ++.++|+.
T Consensus        82 A~~~~~~~~~--~~~~~~~~~A~~---f~L~~~~p~~y~dk~~~e~tg~~g~~i~~~~~~~~  138 (143)
T 3hef_A           82 ADNAIPDAAE--VAKARLRVDTRK---WALARMNPRKYGDKVTNELVGKDGGAIQIETSPMS  138 (143)
T ss_dssp             HHTCCSSHHH--HHHHHHHHHHHH---HHHHHHSHHHHSCCEEEEEECGGGSCCCEEEC---
T ss_pred             HHCCCCCHHH--HHHHHHHHHHHH---HHHHCCCHHHCCCCCCCCCCCCCCCCEEEEECCCH
T ss_conf             9601135278--877778888999---99972681313654320035789986588732405



>2elh_A (A:) CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster} Back     alignment and structure
>1jko_C (C:) HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} Back     alignment and structure
>2cob_A (A:) LCOR protein; MLR2, KIAA1795, helix-turn-helix, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1hlv_A (A:1-67) CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} Back     alignment and structure
>2jn6_A (A:1-56) Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} Back     alignment and structure
>1pdn_C (C:17-69) Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} Back     alignment and structure
>2rn7_A (A:) IS629 ORFA; helix, all alpha, unknown function; NMR {Shigella flexneri} Back     alignment and structure
>2k27_A (A:1-75) Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Back     alignment and structure
>2hku_A (A:) A putative transcriptional regulator; structural genomics, APC6040, TETR family, rhodococcus SP. RHA1, PSI-2, protein structure initiative; HET: PG4; 2.00A {Rhodococcus SP} Back     alignment and structure