254780976

254780976

Holliday junction resolvase YqgF

GeneID in NCBI database:8209998Locus tag:CLIBASIA_04385
Protein GI in NCBI database:254780976Protein Accession:YP_003065389.1
Gene range:-(973456, 973938)Protein Length:160aa
Gene description:Holliday junction resolvase YqgF
COG prediction:[L] Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis)
KEGG prediction:Holliday junction resolvase YqgF; K07447 putative holliday junction resolvase [EC:3.1.-.-]
SEED prediction:Putative Holliday junction resolvase (EC 3.1.-.-)
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
TOPPRED1 TM-Helix
HMMTOP1 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
MSILLIEDLVKSLKPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLESSKG
cccccHHHHHHHccccccEEEEEccccEEEEEcccccccEEccEEEEEcccccHHHHHHHHHHHHccccEEEEEccccccccccHHHHHHHHHHHHHHHccccccEEEEcccccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
cccccHHHHHHHcccccEEEEEEccccEEEEEEccccccccccHHHHHHccccccHHHHHHHHHHccccEEEEEccccccccccHHHHHHHHHHHHHHHccccccEEEccccccHHHHHHHHHHccccHHHHHcHHHHHHHHHHHHHHHHHHHHHHcccc
MSILLIEDLVKslkpnqpiasidlgtkriglaisdpgrrfahprpflvRKKVTQTALELLSFITTENIAAFIIGlplnmngsegprvhsTRAFVHNmidrkvyvpfvfwderlttVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLESSKG
MSILLIEDLVKslkpnqpiasidlgtkRIGLAISdpgrrfahprpflvrKKVTQTALELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLESSKG
MSILLIEDLVKSLKPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLESSKG
*SILLIEDLVKSLKPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLNMNGSE*PRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQ****************VDSIAAALILQEVL****F******
MSILLIEDLVKSLKPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLESSKG
*SILLIEDLVKSLKPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLE****
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSILLIEDLVKSLKPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLESSKG
MSILLIEDLVKSLKPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLESSKG
MSILLIEDLVKSLKPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLESSKG

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

Original result of BLAST against C. L. asiaticus genome

No hits with e-value below 0.05

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

Original result of PSI-BLAST first 2 iterations

IdentityAlignment graphLength Definition Round E-value
Target160 Holliday junction resolvase YqgF [Candidatus Liberibact
315122522167 Holliday junction resolvase YqgF [Candidatus Liberibact 1 2e-76
209549118163 Holliday junction resolvase-like protein [Rhizobium leg 1 2e-47
218661529166 holliday junction resolvase protein [Rhizobium etli IE4 1 2e-47
327192100164 holliday junction resolvase protein [Rhizobium etli CNP 1 2e-47
86357479164 holliday junction resolvase protein [Rhizobium etli CFN 1 3e-47
190891542164 holliday junction resolvase [Rhizobium etli CIAT 652] L 1 4e-47
222085624164 holliday junction resolvase protein [Agrobacterium radi 1 1e-46
222148317158 Holliday junction resolvase-like protein [Agrobacterium 1 5e-46
241204443164 Holliday junction resolvase-like protein [Rhizobium leg 1 6e-46
325292676159 Holliday junction resolvase [Agrobacterium sp. H13-3] L 1 6e-46
>gi|315122522|ref|YP_004063011.1| Holliday junction resolvase YqgF [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 167 Back     alignment and organism information
 Score =  288 bits (737), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 140/159 (88%), Positives = 152/159 (95%)

Query: 1   MSILLIEDLVKSLKPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELL 60
           MSILLIEDLVKSLKPNQPIASIDLGTK+IG+AISD GRRFAHPRPFL+RKK+TQTALELL
Sbjct: 1   MSILLIEDLVKSLKPNQPIASIDLGTKKIGIAISDLGRRFAHPRPFLIRKKITQTALELL 60

Query: 61  SFITTENIAAFIIGLPLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQ 120
           SF TTENIAAF+IGLPLNMNGSEGPRV STRAFV NMIDR++ VPF+FWDERLTTVSAQQ
Sbjct: 61  SFATTENIAAFVIGLPLNMNGSEGPRVQSTRAFVQNMIDREINVPFIFWDERLTTVSAQQ 120

Query: 121 ILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLESSK 159
           ILIDM+VSRKKR QKVDSIAA+LILQEVLDRIS L+SS+
Sbjct: 121 ILIDMDVSRKKRAQKVDSIAASLILQEVLDRISSLKSSE 159



Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|209549118|ref|YP_002281035.1| Holliday junction resolvase-like protein [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 163 Back     alignment and organism information
>gi|218661529|ref|ZP_03517459.1| holliday junction resolvase protein [Rhizobium etli IE4771] Length = 166 Back     alignment and organism information
>gi|327192100|gb|EGE59078.1| holliday junction resolvase protein [Rhizobium etli CNPAF512] Length = 164 Back     alignment and organism information
>gi|86357479|ref|YP_469371.1| holliday junction resolvase protein [Rhizobium etli CFN 42] Length = 164 Back     alignment and organism information
>gi|190891542|ref|YP_001978084.1| holliday junction resolvase [Rhizobium etli CIAT 652] Length = 164 Back     alignment and organism information
>gi|222085624|ref|YP_002544154.1| holliday junction resolvase protein [Agrobacterium radiobacter K84] Length = 164 Back     alignment and organism information
>gi|222148317|ref|YP_002549274.1| Holliday junction resolvase-like protein [Agrobacterium vitis S4] Length = 158 Back     alignment and organism information
>gi|241204443|ref|YP_002975539.1| Holliday junction resolvase-like protein [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 164 Back     alignment and organism information
>gi|325292676|ref|YP_004278540.1| Holliday junction resolvase [Agrobacterium sp. H13-3] Length = 159 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

Original result of RPS-BLAST against CDD database part I

Original result of RPS-BLASTagainst CDD database part II

IdentityAlignment graphLength Definition E-value
Target160 Holliday junction resolvase YqgF [Candidatus Liberibact
PRK00109138 PRK00109, PRK00109, Holliday junction resolvase-like pr 1e-37
COG0816141 COG0816, COG0816, Predicted endonuclease involved in re 1e-32
TIGR00250130 TIGR00250, RNAse_H_YqgF, RNAse H-fold protein YqgF 4e-21
pfam03652134 pfam03652, UPF0081, Uncharacterized protein family (UPF 9e-38
smart0073299 smart00732, YqgFc, Likely ribonuclease with RNase H fol 2e-18
>gnl|CDD|178870 PRK00109, PRK00109, Holliday junction resolvase-like protein; Reviewed Back     alignment and domain information
>gnl|CDD|31158 COG0816, COG0816, Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B Back     alignment and domain information
>gnl|CDD|129352 TIGR00250, RNAse_H_YqgF, RNAse H-fold protein YqgF Back     alignment and domain information
>gnl|CDD|146342 pfam03652, UPF0081, Uncharacterized protein family (UPF0081) Back     alignment and domain information
>gnl|CDD|128971 smart00732, YqgFc, Likely ribonuclease with RNase H fold Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

Original result of HHsearch against CDD database

IdentityAlignment graphLength Definition Probability
Target 160 Holliday junction resolvase YqgF [Candidatus Liberibact
PRK00109141 Holliday junction resolvase-like protein; Reviewed 100.0
pfam03652134 UPF0081 Uncharacterized protein family (UPF0081). 100.0
COG0816141 Predicted endonuclease involved in recombination (possi 100.0
TIGR00250133 TIGR00250 conserved hypothetical protein TIGR00250; Int 100.0
COG2433 652 Uncharacterized conserved protein [Function unknown] 97.7
pfam04312138 DUF460 Protein of unknown function (DUF460). Archaeal p 97.33
TIGR00228158 ruvC crossover junction endodeoxyribonuclease RuvC; Int 90.74
smart0073299 YqgFc Likely ribonuclease with RNase H fold. YqgF prote 99.95
PRK00039169 ruvC Holliday junction resolvase; Reviewed 97.53
cd00529154 RuvC_resolvase Holliday junction resolvases (HJRs) are 97.51
COG2183 780 Tex Transcriptional accessory protein [Transcription] 97.41
pfam02075148 RuvC Crossover junction endodeoxyribonuclease RuvC. 97.16
COG1548 330 Predicted transcriptional regulator/sugar kinase [Trans 95.78
COG0817160 RuvC Holliday junction resolvasome, endonuclease subuni 95.16
COG1940 314 NagC Transcriptional regulator/sugar kinase [Transcript 95.1
PRK09698 302 D-allose kinase; Provisional 94.05
>PRK00109 Holliday junction resolvase-like protein; Reviewed Back     alignment and domain information
>pfam03652 UPF0081 Uncharacterized protein family (UPF0081) Back     alignment and domain information
>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B Back     alignment and domain information
>TIGR00250 TIGR00250 conserved hypothetical protein TIGR00250; InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination Back     alignment and domain information
>COG2433 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>pfam04312 DUF460 Protein of unknown function (DUF460) Back     alignment and domain information
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination Back     alignment and domain information
>smart00732 YqgFc Likely ribonuclease with RNase H fold Back     alignment and domain information
>PRK00039 ruvC Holliday junction resolvase; Reviewed Back     alignment and domain information
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination Back     alignment and domain information
>COG2183 Tex Transcriptional accessory protein [Transcription] Back     alignment and domain information
>pfam02075 RuvC Crossover junction endodeoxyribonuclease RuvC Back     alignment and domain information
>COG1548 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism] Back     alignment and domain information
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism] Back     alignment and domain information
>PRK09698 D-allose kinase; Provisional 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

Original result of PSI-BLAST

IdentityAlignment graphLength Definition E-value
Target160 Holliday junction resolvase YqgF [Candidatus Liberibact
1vhx_A150 Crystal Structure Of Putative Holliday Junction Res 4e-32
1nmn_A138 Structure Of Yqgf From Escherichia Coli, A Hypothet 1e-30
1ovq_A138 Solution Structure Of The Hypothetical Protein Yqgf 2e-30
1nu0_A138 Structure Of The Double Mutant (L6m; F134m, Semet F 1e-28
1iv0_A98 Solution Structure Of The Yqgf-Family Protein (N-Te 5e-11
>gi|40889964|pdb|1VHX|A Chain A, Crystal Structure Of Putative Holliday Junction Resolvase Length = 150 Back     alignment and structure 
 Score =  141 bits (355), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 50/142 (35%), Positives = 74/142 (52%), Gaps = 3/142 (2%)

Query: 18  PIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKK--VTQTALELLSFITTENIAAFIIGL 75
            I  +DLGTK +G+A+SD     A     +   +         L   I    I   ++G 
Sbjct: 4   RILGLDLGTKTLGVALSDEXGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGF 63

Query: 76  PLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQK 135
           P N NG+ GPR  +++ F   +++    VP V WDERLTT +A++ LI  +VSR+KR + 
Sbjct: 64  PKNXNGTVGPRGEASQTFAK-VLETTYNVPVVLWDERLTTXAAEKXLIAADVSRQKRKKV 122

Query: 136 VDSIAAALILQEVLDRISFLES 157
           +D  AA  ILQ  LD ++   S
Sbjct: 123 IDKXAAVXILQGYLDSLNEGGS 144
gi|46014935|pdb|1NMN|A Chain A, Structure Of Yqgf From Escherichia Coli, A Hypothetical Protein Length = 138 Back     alignment and structure
>gi|157879567|pdb|1OVQ|A Chain A, Solution Structure Of The Hypothetical Protein Yqgf From Escherichia Coli Length = 138 Back     alignment and structure
>gi|46014949|pdb|1NU0|A Chain A, Structure Of The Double Mutant (L6m; F134m, Semet Form) Of Yqgf From Escherichia Coli, A Hypothetical Protein Length = 138 Back     alignment and structure
>gi|37926502|pdb|1IV0|A Chain A, Solution Structure Of The Yqgf-Family Protein (N-Terminal Fragment) Length = 98 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

IdentityAlignment graphLength Definition E-value
Target160 Holliday junction resolvase YqgF [Candidatus Liberibact
1nu0_A138 Hypothetical protein YQGF; structural genomics, structu 1e-31
1vhx_A150 Putative holliday junction resolvase; structural genomi 4e-27
1iv0_A98 Hypothetical protein; rnaseh-like, YQGF, structural gen 4e-21
>1nu0_A Hypothetical protein YQGF; structural genomics, structure 2 function project, S2F, unknown function; 1.60A {Escherichia coli} SCOP: c.55.3.8 PDB: 1nmn_A 1ovq_A Length = 138 Back     alignment and structure
 Score =  130 bits (329), Expect = 1e-31
 Identities = 41/134 (30%), Positives = 63/134 (47%), Gaps = 1/134 (0%)

Query: 18  PIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPL 77
            + + D GTK IG+A+       A P P +  +  T     +   +        I+GLPL
Sbjct: 4   TLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPL 63

Query: 78  NMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVD 137
           NM+G+E P     R F +  I  +  V     DERL+TV A+  L +    R     KVD
Sbjct: 64  NMDGTEQPLTARARKFANR-IHGRFGVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVD 122

Query: 138 SIAAALILQEVLDR 151
           S +A +IL+  +++
Sbjct: 123 SASAVIILESYMEQ 136
>1vhx_A Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis} SCOP: c.55.3.8 Length = 150 Back     alignment and structure
>1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus} SCOP: c.55.3.8 Length = 98 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target160 Holliday junction resolvase YqgF [Candidatus Liberibact
1vhx_A150 Putative holliday junction resolvase; structural genomi 100.0
1nu0_A138 Hypothetical protein YQGF; structural genomics, structu 100.0
3bzc_A 785 TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, 97.61
1iv0_A98 Hypothetical protein; rnaseh-like, YQGF, structural gen 99.97
1hjr_A158 Holliday junction resolvase (RUVC); site-specific recom 97.75
2gup_A 292 ROK family protein; sugar kinase, APC80695, sucrose, st 96.07
3htv_A 310 D-allose kinase, allokinase; NP_418508.1, structural ge 95.26
2ap1_A 327 Putative regulator protein; zinc binding protein, struc 95.04
3epq_A 302 Putative fructokinase; SCRK, ADP binding, PSI2, MCSG, s 94.81
3eo3_A 333 Bifunctional UDP-N-acetylglucosamine 2- epimerase/N-ace 93.28
1woq_A267 Inorganic polyphosphate/ATP-glucomannokinase; transfera 92.88
2qm1_A 326 Glucokinase; alpha-beta structure, putative helix-turn- 92.33
3mcp_A 366 Glucokinase; structural genomics, joint center for stru 92.21
1z05_A 429 Transcriptional regulator, ROK family; structural genom 90.43
3lm2_A226 Putative kinase; structural genomics, joint center for 96.02
1sz2_A 332 Glucokinase, glucose kinase; ATP-dependent, glucose bin 92.63
2q2r_A 373 Glucokinase 1, putative; ATPase hexose kinase family, t 90.31
1dkg_D 383 Molecular chaperone DNAK; HSP70, GRPE, nucleotide excha 93.29
3i33_A 404 Heat shock-related 70 kDa protein 2; protein-ADP comple 90.35
>1vhx_A Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis} SCOP: c.55.3.8 Back     alignment and structure
Probab=100.00  E-value=1.3e-43  Score=283.19  Aligned_cols=142  Identities=36%  Similarity=0.532  Sum_probs=132.6

Q ss_pred             CCCEEEEECCCCEEEEEEEECCCCEECCCEEEECCCCCH--HHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHH
Q ss_conf             983999986887689996307651101210110477415--689899998651677589972135788888447999999
Q gi|254780976|r   16 NQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQ--TALELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAF   93 (160)
Q Consensus        16 ~~riLgiD~G~kriGiAisd~~~~~a~Pl~~i~~~~~~~--~~~~l~~ii~e~~i~~iVvGlP~~~~g~~~~~~~~v~~f   93 (160)
                      +.|+||||||+||||+|+||+.+.+|+|++++.+++...  .+.+|.+++++|+|+.||||+|+++||+++++++.++.|
T Consensus         2 ~MriLgiD~G~kriGvAisD~~~~~a~pl~~i~~~~~~~~~~~~~i~~ii~e~~i~~iViGlP~~~dg~~~~~~~~v~~f   81 (150)
T 1vhx_A            2 SLRILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPKNMNGTVGPRGEASQTF   81 (150)
T ss_dssp             CEEEEEEEECSSEEEEEEECTTSSSEEEEEEEECBGGGTBCCHHHHHHHHTTSEEEEEEEECCCCBTTBCCHHHHHHHHH
T ss_pred             CCEEEEEECCCCEEEEEEECCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHH
T ss_conf             86099995289979999956998833560113322345247999999999983999699857846688754889999999


Q ss_pred             HHHHHHHCCCCCEEEECCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99998404899779983671679999999986986445464378998999999999686456622
Q gi|254780976|r   94 VHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLESS  158 (160)
Q Consensus        94 ~~~L~~~~~~l~v~~~DEr~TS~~A~~~l~~~g~~~k~~k~~iD~~AA~iILq~~Ld~~~~~~~~  158 (160)
                      ++.|. +.+++||++|||||||++|++.+++.|++++++|+.+|++||++|||+|||+.+...|-
T Consensus        82 ~~~l~-~~~~l~V~~~DEr~TS~~A~~~l~~~~~~~~k~k~~iD~~AA~iILq~~Ld~~n~g~~~  145 (150)
T 1vhx_A           82 AKVLE-TTYNVPVVLWDERLTTMAAEKMLIAADVSRQKRKKVIDKMAAVMILQGYLDSLNEGGSH  145 (150)
T ss_dssp             HHHHH-HHHCSCEEEECCSSCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHTC----
T ss_pred             HHHHC-CCCCCCEEEECCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99626-58897568867886599999999976997000441476999999999999876376875
>1nu0_A Hypothetical protein YQGF; structural genomics, structure 2 function project, S2F, unknown function; 1.60A {Escherichia coli} SCOP: c.55.3.8 PDB: 1nmn_A 1ovq_A Back     alignment and structure
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A Back     alignment and structure
>1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus} SCOP: c.55.3.8 Back     alignment and structure
>1hjr_A Holliday junction resolvase (RUVC); site-specific recombinase; 2.50A {Escherichia coli} SCOP: c.55.3.6 Back     alignment and structure
>2gup_A ROK family protein; sugar kinase, APC80695, sucrose, structural genomics, PSI, protein structure initiative; HET: SUC; 2.01A {Streptococcus pneumoniae TIGR4} SCOP: c.55.1.10 c.55.1.10 Back     alignment and structure
>3htv_A D-allose kinase, allokinase; NP_418508.1, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: MSE; 1.95A {Escherichia coli k-12} Back     alignment and structure
>2ap1_A Putative regulator protein; zinc binding protein, structural genomics, PSI, protein STRU initiative; 1.90A {Salmonella typhimurium} SCOP: c.55.1.10 c.55.1.10 Back     alignment and structure
>3eo3_A Bifunctional UDP-N-acetylglucosamine 2- epimerase/N-acetylmannosamine kinase; non-protein kinase, sialic acid biosynthesis; 2.84A {Homo sapiens} Back     alignment and structure
>1woq_A Inorganic polyphosphate/ATP-glucomannokinase; transferase; HET: BGC; 1.80A {Arthrobacter SP} SCOP: c.55.1.10 c.55.1.10 Back     alignment and structure
>2qm1_A Glucokinase; alpha-beta structure, putative helix-turn-helix, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.02A {Enterococcus faecalis V583} Back     alignment and structure
>3mcp_A Glucokinase; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, transferase; 3.00A {Parabacteroides distasonis} Back     alignment and structure
>1z05_A Transcriptional regulator, ROK family; structural genomics, PSI, protein structure initiative; 2.00A {Vibrio cholerae o1 biovar eltor str} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 Back     alignment and structure
>3lm2_A Putative kinase; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2, transferase; HET: MSE; 1.70A {Agrobacterium tumefaciens} Back     alignment and structure
>1sz2_A Glucokinase, glucose kinase; ATP-dependent, glucose binding, transferase; HET: MSE BGC; 2.20A {Escherichia coli} SCOP: c.55.1.7 PDB: 1q18_A* Back     alignment and structure
>2q2r_A Glucokinase 1, putative; ATPase hexose kinase family, transferase; HET: BGC ADP; 2.10A {Trypanosoma cruzi} Back     alignment and structure
>1dkg_D Molecular chaperone DNAK; HSP70, GRPE, nucleotide exchange factor, coiled-coil, complex (HSP24/HSP70); 2.80A {Escherichia coli} SCOP: c.55.1.1 c.55.1.1 Back     alignment and structure
>3i33_A Heat shock-related 70 kDa protein 2; protein-ADP complex, ATP-binding, chaperone, nucleotide- binding, phosphoprotein, polymorphism; HET: ADP; 1.30A {Homo sapiens} PDB: 1hx1_A 3jxu_A* 2qwl_A* 2qw9_A* 2qwm_A* 1hpm_A* 1ngi_A* 1ngj_A* 3hsc_A* 1ngb_A* 3fzh_A* 3fzf_A* 3fzk_A* 3fzl_A* 3fzm_A* 1ngh_A* 1ngd_A* 1ngf_A* 1bup_A* 1nga_A* ... 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

Original result of RPS-BLAST against SCOP70(version1.75) database

IdentityAlignment graphLength Definition E-value
Target 160 Holliday junction resolvase YqgF [Candidatus Liberibact
d1nu0a_138 c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escheri 1e-28
d1vhxa_140 c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillu 7e-26
d1iv0a_98 c.55.3.8 (A:) Hypothetical protein, YqgF homologue {The 3e-19
>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]} Length = 138 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YqgF (RuvX)
species: Escherichia coli [TaxId: 562]

 Score =  119 bits (300), Expect = 1e-28
 Identities = 41/134 (30%), Positives = 63/134 (47%), Gaps = 1/134 (0%)

Query: 18  PIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPL 77
            + + D GTK IG+A+       A P P +  +  T     +   +        I+GLPL
Sbjct: 4   TLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPL 63

Query: 78  NMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVD 137
           NM+G+E P     R F + +  R   V     DERL+TV A+  L +    R     KVD
Sbjct: 64  NMDGTEQPLTARARKFANRIHGRF-GVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVD 122

Query: 138 SIAAALILQEVLDR 151
           S +A +IL+  +++
Sbjct: 123 SASAVIILESYMEQ 136
>d1vhxa_ c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillus subtilis [TaxId: 1423]} Length = 140 Back     information, alignment and structure
>d1iv0a_ c.55.3.8 (A:) Hypothetical protein, YqgF homologue {Thermus thermophilus [TaxId: 274]} Length = 98 Back     information, alignment and structure

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

Original result of HHsearch against SCOP70(version1.75) database

IdentityAlignment graphLength Definition Probability
Target160 Holliday junction resolvase YqgF [Candidatus Liberibact
d1vhxa_140 Hypothetical protein YrrK (RuvX) {Bacillus subtilis [Ta 100.0
d1nu0a_138 Hypothetical protein YqgF (RuvX) {Escherichia coli [Tax 100.0
d1iv0a_98 Hypothetical protein, YqgF homologue {Thermus thermophi 99.97
d3bzka5149 Transcriptional accessory factor Tex {Pseudomonas aerug 98.49
d1hjra_158 RuvC resolvase {Escherichia coli [TaxId: 562]} 97.7
d1xc3a1118 Putative fructokinase YhdR {Bacillus subtilis [TaxId: 1 96.01
d2gupa1114 Hypothetical protein SP2142 {Streptococcus pneumoniae [ 96.0
d2aa4a1119 N-acetylmannosamine kinase NanK {Escherichia coli [TaxI 95.7
d2ap1a2117 Putative regulator protein YcfX {Salmonella typhimurium 94.73
d1z6ra2129 Mlc protein {Escherichia coli [TaxId: 562]} 93.77
d1z05a3128 Transcriptional regulator VC2007 {Vibrio cholerae [TaxI 93.75
d1okja1106 Hypothetical protein YeaZ {Escherichia coli [TaxId: 562 93.38
d2hoea3128 N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 90.4
d1woqa1129 Inorganic polyphosphate/ATP-glucomannokinase PPGMK {Art 90.14
d1q18a1110 Glucokinase Glk {Escherichia coli [TaxId: 562]} 94.46
d1sz2a1 319 Glucokinase Glk {Escherichia coli [TaxId: 562]} 94.28
d1huxa_ 259 Hydroxyglutaryl-CoA dehydratase component A {Acidaminoc 90.8
d1dkgd1183 Heat shock protein 70kDa, ATPase fragment {Escherichia 91.31
d1bupa1185 Heat shock protein 70kDa, ATPase fragment {Cow (Bos tau 91.0
>d1vhxa_ c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YrrK (RuvX)
species: Bacillus subtilis [TaxId: 1423]

Probab=100.00  E-value=2.6e-42  Score=273.94  Aligned_cols=138  Identities=36%  Similarity=0.554  Sum_probs=128.9

Q ss_pred             CCCEEEEECCCCEEEEEEEECCCCEECCCEEEECCCCC--HHHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHH
Q ss_conf             98399998688768999630765110121011047741--5689899998651677589972135788888447999999
Q gi|254780976|r   16 NQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVT--QTALELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAF   93 (160)
Q Consensus        16 ~~riLgiD~G~kriGiAisd~~~~~a~Pl~~i~~~~~~--~~~~~l~~ii~e~~i~~iVvGlP~~~~g~~~~~~~~v~~f   93 (160)
                      +.|+||||||+||||+|+||+.+.+|+|+.++.+++..  ..+.+|.+++++|+|+.||||+|++++|+++++++.++.|
T Consensus         1 ~mriLgiD~G~kriGvAisd~~~~~a~pl~~i~~~~~~~~~~~~~l~~ii~e~~i~~iViGlP~~~dg~~~~~~~~~~~f   80 (140)
T d1vhxa_           1 SLRILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPKNMNGTVGPRGEASQTF   80 (140)
T ss_dssp             CEEEEEEEECSSEEEEEEECTTSSSEEEEEEEECBGGGTBCCHHHHHHHHTTSEEEEEEEECCCCBTTBCCHHHHHHHHH
T ss_pred             CCEEEEEEECCCEEEEEEECCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCHHHHHHHHHH
T ss_conf             95199998279989999945998822551668612566416899999999851656599835522478613677888999


Q ss_pred             HHHHHHHCCCCCEEEECCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999840489977998367167999999998698644546437899899999999968645
Q gi|254780976|r   94 VHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISF  154 (160)
Q Consensus        94 ~~~L~~~~~~l~v~~~DEr~TS~~A~~~l~~~g~~~k~~k~~iD~~AA~iILq~~Ld~~~~  154 (160)
                      ++.|. +.+++||++|||||||++|++.+++.|++++++|+.+|++||++|||+|||++|.
T Consensus        81 ~~~l~-~~~~i~V~~~DEr~TS~~A~~~l~~~~~~~~~~k~~iD~~AA~iILe~~L~~~n~  140 (140)
T d1vhxa_          81 AKVLE-TTYNVPVVLWDERLTTMAAEKMLIAADVSRQKRKKVIDKMAAVMILQGYLDSLNE  140 (140)
T ss_dssp             HHHHH-HHHCSCEEEECCSSCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHC-CCCCCCEEEEECCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             99834-6778557984144379999999997699700034147799999999999997468
>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1iv0a_ c.55.3.8 (A:) Hypothetical protein, YqgF homologue {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d3bzka5 c.55.3.13 (A:325-473) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1hjra_ c.55.3.6 (A:) RuvC resolvase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1xc3a1 c.55.1.10 (A:1-118) Putative fructokinase YhdR {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d2gupa1 c.55.1.10 (A:1-114) Hypothetical protein SP2142 {Streptococcus pneumoniae [TaxId: 1313]} Back     information, alignment and structure
>d2aa4a1 c.55.1.10 (A:1-119) N-acetylmannosamine kinase NanK {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2ap1a2 c.55.1.10 (A:1-117) Putative regulator protein YcfX {Salmonella typhimurium [TaxId: 90371]} Back     information, alignment and structure
>d1z6ra2 c.55.1.10 (A:82-210) Mlc protein {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1z05a3 c.55.1.10 (A:81-208) Transcriptional regulator VC2007 {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d1okja1 c.55.1.9 (A:1-106) Hypothetical protein YeaZ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2hoea3 c.55.1.10 (A:72-199) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1woqa1 c.55.1.10 (A:11-139) Inorganic polyphosphate/ATP-glucomannokinase PPGMK {Arthrobacter sp. KM [TaxId: 184230]} Back     information, alignment and structure
>d1q18a1 c.55.1.7 (A:2-111) Glucokinase Glk {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1sz2a1 c.55.1.7 (A:3-321) Glucokinase Glk {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1huxa_ c.55.1.5 (A:) Hydroxyglutaryl-CoA dehydratase component A {Acidaminococcus fermentans [TaxId: 905]} Back     information, alignment and structure
>d1dkgd1 c.55.1.1 (D:3-185) Heat shock protein 70kDa, ATPase fragment {Escherichia coli, gene dnaK [TaxId: 562]} Back     information, alignment and structure
>d1bupa1 c.55.1.1 (A:4-188) Heat shock protein 70kDa, ATPase fragment {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against MMDB70 database

IdentityAlignment graphLength Definition E-value
Target 160 Holliday junction resolvase YqgF [Candidatus Liber
1nu0_A_138 (A:) Hypothetical protein YQGF; structural genomic 1e-30
1vhx_A_150 (A:) Putative holliday junction resolvase; structu 1e-23
3bzc_A_326-467142 (A:326-467) TEX; helix-turn-helix, helix-hairpin-h 1e-14
1iv0_A_98 (A:) Hypothetical protein; rnaseh-like, YQGF, stru 4e-21
>1nu0_A (A:) Hypothetical protein YQGF; structural genomics, structure 2 function project, S2F, unknown function; 1.60A {Escherichia coli}Length = 138 Back     alignment and structure
 Score =  126 bits (319), Expect = 1e-30
 Identities = 41/136 (30%), Positives = 62/136 (45%), Gaps = 1/136 (0%)

Query: 16  NQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGL 75
           +  + + D GTK IG+A+       A P P +  +  T     +   +        I+GL
Sbjct: 2   SGTLXAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGL 61

Query: 76  PLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQK 135
           PLN +G+E P     R F  N I  +  V     DERL+TV A+  L +    R     K
Sbjct: 62  PLNXDGTEQPLTARARKFA-NRIHGRFGVEVKLHDERLSTVEARSGLFEQGGYRALNKGK 120

Query: 136 VDSIAAALILQEVLDR 151
           VDS +A +IL+   ++
Sbjct: 121 VDSASAVIILESYXEQ 136
>1vhx_A (A:) Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis}Length = 150 Back     alignment and structure
>3bzc_A (A:326-467) TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa}Length = 142 Back     alignment and structure
>1iv0_A (A:) Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus}Length = 98 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target160 Holliday junction resolvase YqgF [Candidatus Liberibact
1nu0_A_138 Hypothetical protein YQGF; structural genomics, st 100.0
1vhx_A_150 Putative holliday junction resolvase; structural g 100.0
3bzc_A_326-467142 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 99.92
2hoe_A_86-211_358-380149 N-acetylglucosamine kinase; TM1224, structural gen 96.01
1iv0_A_98 Hypothetical protein; rnaseh-like, YQGF, structura 99.96
1hjr_A_158 Holliday junction resolvase (RUVC); site-specific 97.97
1sz2_A_1-122_314-332141 Glucokinase, glucose kinase; ATP-dependent, glucos 96.98
2gup_A_1-114_273-292134 ROK family protein; sugar kinase, APC80695, sucros 96.7
3eo3_A_1-144_315-333163 Bifunctional UDP-N-acetylglucosamine 2- epimerase/ 96.31
3lm2_A_1-9999 Putative kinase; structural genomics, joint center 96.08
2ch5_A_1-119_314-347153 NAGK protein; transferase, N-acetylglucosamine, gl 96.01
2e2o_A_1-105_275-299130 Hexokinase; acetate and sugar kinases, HSP70, acti 95.92
2ap1_A_1-128_313-327143 Putative regulator protein; zinc binding protein, 95.67
2kho_A_1-73_115-182_364-385163 Heat shock protein 70; molecular chaperone, HSP70, 95.23
3epq_A_1-120_276-302147 Putative fructokinase; SCRK, ADP binding, PSI2, MC 94.3
2aa4_A_1-119_275-289134 Mannac kinase, putative N-acetylmannosamine kinase 94.02
2qm1_A_1-131_308-326150 Glucokinase; alpha-beta structure, putative helix- 93.69
2q2r_A_1-154_358-373170 Glucokinase 1, putative; ATPase hexose kinase fami 93.36
1z6r_A_83-194112 MLC protein; transcriptional repressor, ROK family 92.4
1hux_A_1-95_239-270127 Activator of (R)-2-hydroxyglutaryl-COA dehydratase 90.66
1jce_A_1-142_312-344175 ROD shape-determining protein MREB; MBL, actin, HS 93.52
1yuw_A_1-187_362-389215 Heat shock cognate 71 kDa protein; chaperone; 2.60 92.5
2v7y_A_1-156_333-359183 Chaperone protein DNAK; HSP70, heat shock protein, 90.93
1dkg_D_1-73_115-182_364-383161 Molecular chaperone DNAK; HSP70, GRPE, nucleotide 91.85
>1nu0_A (A:) Hypothetical protein YQGF; structural genomics, structure 2 function project, S2F, unknown function; 1.60A {Escherichia coli} Back     alignment and structure
Probab=100.00  E-value=3e-40  Score=263.84  Aligned_cols=136  Identities=29%  Similarity=0.385  Sum_probs=131.5

Q ss_pred             CCCEEEEECCCCEEEEEEEECCCCEECCCEEEECCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHHHH
Q ss_conf             98399998688768999630765110121011047741568989999865167758997213578888844799999999
Q gi|254780976|r   16 NQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLNMNGSEGPRVHSTRAFVH   95 (160)
Q Consensus        16 ~~riLgiD~G~kriGiAisd~~~~~a~Pl~~i~~~~~~~~~~~l~~ii~e~~i~~iVvGlP~~~~g~~~~~~~~v~~f~~   95 (160)
                      ++|+||||||+||||+|+||+.+.+|+|++++.+++..+.+..|..++++|+++.||||+|++++|+++++++.++.|++
T Consensus         2 ~krilgiD~G~kriGiAi~d~~~~ia~p~~~i~~~~~~~~~~~l~~li~~~~~~~iViGlP~~~~g~~~~~a~~v~~f~~   81 (138)
T 1nu0_A            2 SGTLXAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNXDGTEQPLTARARKFAN   81 (138)
T ss_dssp             CCEEEEEECCSSEEEEEEEETTTTEEEEEEEEEEETTEECHHHHHHHHHHHCCSEEEEEEEECTTSCBCHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCEEEEEEECCCCCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHHHHH
T ss_conf             97689999179979999947998740140789816772689999998642487389964434777875789999999999


Q ss_pred             HHHHHCCCCCEEEECCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             998404899779983671679999999986986445464378998999999999686
Q gi|254780976|r   96 NMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRI  152 (160)
Q Consensus        96 ~L~~~~~~l~v~~~DEr~TS~~A~~~l~~~g~~~k~~k~~iD~~AA~iILq~~Ld~~  152 (160)
                      .|. +.+++||++||||+||++|++.+.+.+++++++++.+|++||++|||+|||+.
T Consensus        82 ~L~-~~~~l~v~~vDEr~TT~~A~~~l~~~~~~~~~~k~~iD~~AA~~ILq~~L~~~  137 (138)
T 1nu0_A           82 RIH-GRFGVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVDSASAVIILESYXEQG  137 (138)
T ss_dssp             HHH-HHHCCCEEEEEEECCCCCC-------CCCCCCCHHHHTTHHHHHHHHHHHHTT
T ss_pred             HHH-HHHCCCEEEEECCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             999-86299969973664599999999973563210454364999999999999736
>1vhx_A (A:) Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis} Back     alignment and structure
>3bzc_A (A:326-467) TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} Back     alignment and structure
>2hoe_A (A:86-211,A:358-380) N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center for structural genomics, JCSG; 2.46A {Thermotoga maritima} Back     alignment and structure
>1iv0_A (A:) Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus} Back     alignment and structure
>1hjr_A (A:) Holliday junction resolvase (RUVC); site-specific recombinase; 2.50A {Escherichia coli} Back     alignment and structure
>1sz2_A (A:1-122,A:314-332) Glucokinase, glucose kinase; ATP-dependent, glucose binding, transferase; HET: MSE BGC; 2.20A {Escherichia coli} Back     alignment and structure
>2gup_A (A:1-114,A:273-292) ROK family protein; sugar kinase, APC80695, sucrose, structural genomics, PSI, protein structure initiative; HET: SUC; 2.01A {Streptococcus pneumoniae TIGR4} Back     alignment and structure
>3eo3_A (A:1-144,A:315-333) Bifunctional UDP-N-acetylglucosamine 2- epimerase/N-acetylmannosamine kinase; non-protein kinase, sialic acid biosynthesis; 2.84A {Homo sapiens} Back     alignment and structure
>3lm2_A (A:1-99) Putative kinase; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2, transferase; HET: MSE; 1.70A {Agrobacterium tumefaciens} Back     alignment and structure
>2ch5_A (A:1-119,A:314-347) NAGK protein; transferase, N-acetylglucosamine, glcnac, sugar kinase, ribonuclease H fold, sugar kinase/HSP70/actin superfamily, domain rotation; HET: NAG NDG; 1.9A {Homo sapiens} Back     alignment and structure
>2e2o_A (A:1-105,A:275-299) Hexokinase; acetate and sugar kinases, HSP70, actin superfamily, ribonuclease-H fold, sugar kinase, glucose, conformational change; HET: BGC; 1.65A {Sulfolobus tokodaii} PDB: 2e2n_A* 2e2p_A* 2e2q_A* Back     alignment and structure
>2ap1_A (A:1-128,A:313-327) Putative regulator protein; zinc binding protein, structural genomics, PSI, protein structure initiative; 1.90A {Salmonella typhimurium} Back     alignment and structure
>2kho_A (A:1-73,A:115-182,A:364-385) Heat shock protein 70; molecular chaperone, HSP70, peptide binding, protein folding, acetylation, ATP-binding, cell inner membrane; NMR {Escherichia coli} Back     alignment and structure
>2aa4_A (A:1-119,A:275-289) Mannac kinase, putative N-acetylmannosamine kinase; sugar methabolism, structural genomics, PSI, protein structure initiative; 2.20A {Escherichia coli} Back     alignment and structure
>2qm1_A (A:1-131,A:308-326) Glucokinase; alpha-beta structure, putative helix-turn-helix, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.02A {Enterococcus faecalis V583} Back     alignment and structure
>2q2r_A (A:1-154,A:358-373) Glucokinase 1, putative; ATPase hexose kinase family, transferase; HET: BGC ADP; 2.10A {Trypanosoma cruzi} Back     alignment and structure
>1z6r_A (A:83-194) MLC protein; transcriptional repressor, ROK family protein, DNA binding protein, helix-turn-helix, phosphotransferase system, metalloprotein; 2.70A {Escherichia coli} Back     alignment and structure
>1hux_A (A:1-95,A:239-270) Activator of (R)-2-hydroxyglutaryl-COA dehydratase; actin fold, metal binding protein; HET: ADP; 3.00A {Acidaminococcus fermentans} Back     alignment and structure
>1jce_A (A:1-142,A:312-344) ROD shape-determining protein MREB; MBL, actin, HSP-70, FTSZ, structural protein; 2.10A {Thermotoga maritima} Back     alignment and structure
>1yuw_A (A:1-187,A:362-389) Heat shock cognate 71 kDa protein; chaperone; 2.60A {Bos taurus} Back     alignment and structure
>2v7y_A (A:1-156,A:333-359) Chaperone protein DNAK; HSP70, heat shock protein, ATPase, domain rearrangement; HET: ADP; 2.37A {Geobacillus kaustophilus HTA426} Back     alignment and structure
>1dkg_D (D:1-73,D:115-182,D:364-383) Molecular chaperone DNAK; HSP70, GRPE, nucleotide exchange factor, coiled-coil, complex (HSP24/HSP70); 2.80A {Escherichia coli} Back     alignment and structure