Citrus Sinensis ID: 040110

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------35
Protein Sequence
MDVNLRIFCERLKRVLVGEEGTLTLPDTTKLTPIFQNLLTESEIITTPLGNYQGDMKAIYKFFIAIMRQLHQQNSETEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTSIELENGEKNRHDSALVGGPLIRIKHETWQFFILHYGSTPLENETEGPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPGNYDSEKMAEEYLKQ
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccccHHHcccccccccHHHcHHHHHHHHccccccccccccEEEEEccccccHHHHHHHHHcccccccccccEEEEEEcccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHccccEEEEEEEccccHHHHHHHHHHccccccccEEEEEcccHHHHHHccccccccccccHHHHHcccccccHHHHHHHHHHccccccccccccccHHHHHcccccccccHHHHHHHccccccccEEcHHHHHHHHHHcccccccccHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEccccEEcccccHHHHHHHHHccccccEEEEEEccccccHHHHHHHHHccHHHHHcccEEEEEEEcccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHccccEEEEEEccccHHHHHHHHccccccccccEEEEEEccHHHHHHEcccccccHHHHHHHHHHHccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHcccHHHHHHHHEHEcccccccEcHHHHHHHHHHHccccccccHHHHHHHHccc
Coil and Loop (DISEMBL)
MDVNLRIFCERLKRVLvgeegtltlpdttkltPIFQNllteseiittplgnyqgDMKAIYKFFIAIMRQLHQQNSETEEICDALLGLQSKIINLRnlhqrlppssglgqptHSVVAILdsrgfdktAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLRealpdnqigsralitvgphnilTSIElengeknrhdsalvggplirikHETWQFFILHygstplenetegpsvglklvslselpfpliVCCLYfcvfptdieLTTRQLCRLWtaeglrpgnydseKMAEEYLKQ
Flexible Loop (DISEMBL)
MDVNLRIFCERlkrvlvgeegtltlpdttklTPIFQNLLTESEIITTPLGNYQGDMKAIYKFFIAIMRQLHQQNSETEEICDALLGLQSKIINLRNLHQRLppssglgqPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTSIELengeknrhDSALVGGPLIRIKHETWQFFILHYGSTPLENETEGPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTaeglrpgnydsekMAEEYLKQ
Low Complexity Region (SEG)
MDVNLRIFCERLKRVLVGEEGtltlpdttkltpIFQNLLTESEIITTPLGNYQGDMKAIYKFFIAIMRQLHQQNSETEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTSIELENGEKNRHDSALVGGPLIRIKHETWQFFILHYGSTPLENETEGPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPGNYDSEKMAEEYLKQ
Disordered region (IsUnstruct)
***NLRIFCERLKRVLVGEEGTLTLPDTTKLTPIFQNLLTESEIITTPLGNYQGDMKAIYKFFIAIMRQLHQQNSETEEICDALLGLQSKIINLRNLHQR**********THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTSIELENG***RHDSALVGGPLIRIKHETWQFFILHYGSTPLENETEGPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGL*****************
Disordered Region (DISOPRED)
*DVNLRIFCERLKRVLVGEEGTLTLPDTTKLTPIFQNLLTESEIITTPLGNYQ******************************LLGLQSKIINLRNLHQRLPPS*G**QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLM**************SEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTSIEL*****NRHDSALVGGPLIRIKHETWQFFILHYGSTPLENETEGPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPGNYDSEKMAEEYLKQ
Disordered Region (DISEMBL)
MDVNLRIFCERLKRVLVGEEGTLTLPDTTKLTPIFQNLLTESEIITTPLGNYQGDMKAIYKFFIAIMRQLHQQNSETEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTSIELENGEKNRHDSALVGGPLIRIKHETWQFFILHYGSTPLENETEGPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPGNYDSEKMAEEYLKQ
Disordered Region (DISPRO)
*DVNLRIFCERLKRVLVGEEGTLTLPDTTKLTPIFQNLLTESEIITTPLGNYQGDMKAIYKFFIAIMRQLHQQN**TEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTSIELENGEKNRHDSALVGGPLIRIKHETWQFFILHYGSTPLENETEGPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPGNYDSEKMAEEYLKQ
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDVNLRIFCERLKRVLVGEEGTLTLPDTTKLTPIFQNLLTESEIITTPLGNYQGDMKAIYKFFIAIMRQLHQQNSETEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTSIELENGEKNRHDSALVGGPLIRIKHETWQFFILHYGSTPLENETEGPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPGNYDSEKMAEEYLKQ
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	348	2.2.26 [Sep-21-2011]
Q9FJB5	901	Disease resistance RPP8-l	yes	no	0.709	0.274	0.255	4e-14
Q9M667	835	Disease resistance protei	no	no	0.333	0.138	0.389	5e-13
Q9STE7	847	Putative disease resistan	no	no	0.640	0.263	0.289	7e-13
Q39214	926	Disease resistance protei	no	no	0.359	0.134	0.294	1e-12
Q9XIF0	906	Putative disease resistan	no	no	0.813	0.312	0.256	2e-12
Q7XBQ9	970	Disease resistance protei	N/A	no	0.655	0.235	0.266	2e-12
Q8W4J9	908	Disease resistance protei	no	no	0.827	0.317	0.243	2e-12
Q6L3Z7	1317	Putative late blight resi	N/A	no	0.781	0.206	0.256	2e-12
Q6L403	1312	Putative late blight resi	N/A	no	0.781	0.207	0.256	2e-12
P59584	910	Disease resistance protei	no	no	0.793	0.303	0.235	3e-12

>sp|Q9FJB5|RP8L3_ARATH Disease resistance RPP8-like protein 3 OS=Arabidopsis thaliana GN=RPP8L3 PE=2 SV=1

 Score = 79.3 bits (194), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 83/325 (25%), Positives = 130/325 (40%), Gaps = 78/325 (24%)

Query: 85  LGLQSKIIN----------LRNLHQRLPPSS-----GLGQPTH------------SVVAI 117
           LG+Q +II+           R + Q  P SS     G+ Q                VV+I
Sbjct: 129 LGIQQQIIDGGRSLSLQDIQREIRQTFPNSSESDLVGVEQSVEELVGPMVEIDNIQVVSI 188

Query: 118 LDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIM 177
               G  KT  A +I++++ V+ +FD  AWV VS  +  K +   I++ L P     +I+
Sbjct: 189 SGMGGIGKTTLARQIFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRILQELRPHDG--EIL 246

Query: 178 GKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALIT-----VGP 232
             D  + +  L   L   +Y  VLDDVW E+ WD ++E  P  + G + L+T     VG 
Sbjct: 247 QMDEYTIQGKLFQLLETGRYLVVLDDVWKEEDWDRIKEVFPRKR-GWKMLLTSRNEGVGL 305

Query: 233 HNILTSIELENGEKNRHDSALVGGPLIRIKHET--------WQFFILHYGSTPLENETEG 284
           H   T +       N  +S  +   ++  ++ET         +  + + G  PL  +  G
Sbjct: 306 HADPTCLSFRARILNPKESWKLFERIVPRRNETEYEEMEAIGKEMVTYCGGLPLAVKVLG 365

Query: 285 ----------------PSVGLKLV-------------------SLSELPFPLIVCCLYFC 309
                            ++G ++V                   S  +LP  L  C LY  
Sbjct: 366 GLLANKHTASEWKRVSENIGAQIVGKSCLDDNSLNSVYRILSLSYEDLPTDLKHCFLYLA 425

Query: 310 VFPTDIELTTRQLCRLWTAEGLRPG 334
            FP D ++ TR L   W AEG+  G
Sbjct: 426 HFPEDYKIKTRTLYSYWAAEGIYDG 450

Disease resistance protein.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9M667|RPP13_ARATH Disease resistance protein RPP13 OS=Arabidopsis thaliana GN=RPP13 PE=2 SV=2

 Score = 75.5 bits (184), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 46/118 (38%), Positives = 65/118 (55%), Gaps = 2/118 (1%)

Query: 114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSL-MPTSS 172
           +++I    G  KTA A ++YN+  VK  F+  AW  VS  Y    IL  I++SL M +  
Sbjct: 187 IISIFGMGGLGKTALARKLYNSRDVKERFEYRAWTYVSQEYKTGDILMRIIRSLGMTSGE 246

Query: 173 WLKIMGKDYKSE-KTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALIT 229
            L+ + K  + E +  L   L  KKY  V+DD+W  + WD L+ ALP N  GSR +IT
Sbjct: 247 ELEKIRKFAEEELEVYLYGLLEGKKYLVVVDDIWEREAWDSLKRALPCNHEGSRVIIT 304

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. In contrast to other resistance proteins, it works independently of ESD1 and NSD1 proteins and does not require the accumulation of salicylic acid, suggesting the existence of an independent signaling pathway. The specificity to avirulence proteins differs in the different cultivars.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9STE7|R13L3_ARATH Putative disease resistance RPP13-like protein 3 OS=Arabidopsis thaliana GN=RPP13L3 PE=3 SV=1

 Score = 75.1 bits (183), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 81/280 (28%), Positives = 111/280 (39%), Gaps = 57/280 (20%)

Query: 114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSS- 172
           +++I    G  KTA A ++YN+  VK  FDC AW  VS  Y  + IL  I++SL   S+ 
Sbjct: 187 IISIFGMGGLGKTALARKLYNSGDVKRRFDCRAWTYVSQEYKTRDILIRIIRSLGIVSAE 246

Query: 173 ---WLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALIT 229
               +K+  +D + E   L   L  K Y  V+DDVW    W+ L+ ALP +  GS+ +IT
Sbjct: 247 EMEKIKMFEEDEELE-VYLYGLLEGKNYMVVVDDVWDPDAWESLKRALPCDHRGSKVIIT 305

Query: 230 VGPHNILTSIE------------------------LENGEKNRHDSALVG---------- 255
                I   +E                          N EK   D    G          
Sbjct: 306 TRIRAIAEGVEGTVYAHKLRFLTFEESWTLFERKAFSNIEKVDEDLQRTGKEMVKKCGGL 365

Query: 256 --------GPLIRIKHETWQFFILHYGSTPLENETEGPSVGLKLV---SLSELPFPLIVC 304
                   G L R +   W     H     L    +  S+ +  V   S  E+   L +C
Sbjct: 366 PLAIVVLSGLLSRKRTNEW-----HEVCASLWRRLKDNSIHISTVFDLSFKEMRHELKLC 420

Query: 305 CLYFCVFPTDIELTTRQLCRLWTAEGLRPGNYDSEKMAEE 344
            LYF VFP D E+   +L  L  AEG      D E M E+
Sbjct: 421 FLYFSVFPEDYEIKVEKLIHLLVAEGF--IQEDEEMMMED 458

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q39214|RPM1_ARATH Disease resistance protein RPM1 OS=Arabidopsis thaliana GN=RPM1 PE=1 SV=1

 Score = 74.3 bits (181), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 72/136 (52%), Gaps = 11/136 (8%)

Query: 109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLM 168
           +P   VVA++   G  KT  +A I+ +  V+ +F+ +AWV +S  Y    +++D+ ++++
Sbjct: 190 EPQRIVVAVVGMGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSY----VIEDVFRTMI 245

Query: 169 P-------TSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQ 221
                   T    ++    Y+     L +YL +K+Y  VLDDVW   +W ++  ALPD  
Sbjct: 246 KEFYKEADTQIPAELYSLGYRELVEKLVEYLQSKRYIVVLDDVWTTGLWREISIALPDGI 305

Query: 222 IGSRALITVGPHNILT 237
            GSR ++T    N+ +
Sbjct: 306 YGSRVMMTTRDMNVAS 321

Disease resistance (R) protein that specifically recognizes the AvrRpm1 type III effector avirulence protein from Pseudomonas syringae. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Acts via its interaction with RIN4, and probably triggers the plant resistance when RIN4 is phosphorylated by AvrRpm1. It is then degraded at the onset of the hypersensitive response.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9XIF0|DRL13_ARATH Putative disease resistance protein At1g59780 OS=Arabidopsis thaliana GN=At1g59780 PE=2 SV=1

 Score = 73.9 bits (180), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 93/363 (25%), Positives = 149/363 (41%), Gaps = 80/363 (22%)

Query: 29  TKLTPIFQNLLTESEIITTPLGNYQGDMKAIYKFFIAIMRQL-HQQNSETEEICDALLGL 87
           +K+  + QNL  +S+I+     + Q + K          R+L H  +SE+E     L+GL
Sbjct: 117 SKVIQVMQNLGIKSDIMDGVDSHAQLERK----------RELRHTFSSESE---SNLVGL 163

Query: 88  QSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAW 147
           +    N+  L + L     +G  +   V+I    G  KT  A +I++++ VK +FD  AW
Sbjct: 164 EK---NVEKLVEEL-----VGNDSSHGVSITGLGGLGKTTLARQIFDHDKVKSHFDGLAW 215

Query: 148 VRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE 207
           V VS  +  K +   I+ +L P      +   D + +   L   L  KK   V DD+W  
Sbjct: 216 VCVSQEFTRKDVWKTILGNLSPKYKDSDLPEDDIQKK---LFQLLETKKALIVFDDLWKR 272

Query: 208 KIWDDLREALPDNQIGSRALIT-----VGPHNILTSIEL--------------------- 241
           + W  +    P+ + G + L+T     + PH +    EL                     
Sbjct: 273 EDWYRIAPMFPERKAGWKVLLTSRNDAIHPHCVTFKPELLTHDECWKLLQRIAFSKQKTI 332

Query: 242 -----------ENGEKNRH------DSALVGGPLIRIKH--ETWQFF-------ILHYGS 275
                         E  +H         L+GG L+  KH    W+         I+  G+
Sbjct: 333 TGYIIDKEMVKMAKEMTKHCKRLPLAVKLLGG-LLDAKHTLRQWKLISENIISHIVVGGT 391

Query: 276 TPLENETEGPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLR-PG 334
           +  EN++   +  L L S   LP  L  C LY   +P D E+   +L  +W AEG+  PG
Sbjct: 392 SSNENDSSSVNHVLSL-SFEGLPGYLKHCLLYLASYPEDHEIEIERLSYVWAAEGITYPG 450

Query: 335 NYD 337
           NY+
Sbjct: 451 NYE 453

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XBQ9|RGA2_SOLBU Disease resistance protein RGA2 OS=Solanum bulbocastanum GN=RGA2 PE=1 SV=1

 Score = 73.9 bits (180), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 76/285 (26%), Positives = 117/285 (41%), Gaps = 57/285 (20%)

Query: 113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSS 172
           SV+ IL   G  KT  A  ++N+  V  +F    W+ VS  ++ KR++  I++S+     
Sbjct: 176 SVLPILGMGGLGKTTLAQMVFNDQRVTEHFHSKIWICVSEDFDEKRLIKAIVESIEGRP- 234

Query: 173 WLKIMGK-DYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALIT 229
              ++G+ D    +  L++ L  K+Y  VLDDVW E  + W +LR  L     G+  L T
Sbjct: 235 ---LLGEMDLAPLQKKLQELLNGKRYLLVLDDVWNEDQQKWANLRAVLKVGASGASVLTT 291

Query: 230 VGPHNI------LTSIELEN---------------GEKNRHDSALVG------------- 255
                +      L   EL N               G +   +  LV              
Sbjct: 292 TRLEKVGSIMGTLQPYELSNLSQEDCWLLFMQRAFGHQEEINPNLVAIGKEIVKKSGGVP 351

Query: 256 ------GPLIRIKHE--TWQFFILHYGSTPLENETEGPSVGLKLVSLS--ELPFPLIVCC 305
                 G ++  K E   W+    H   +P+ N  +  S  L  + LS  +LP  L  C 
Sbjct: 352 LAAKTLGGILCFKREERAWE----HVRDSPIWNLPQDESSILPALRLSYHQLPLDLKQCF 407

Query: 306 LYFCVFPTDIELTTRQLCRLWTAEG--LRPGNYDSEKMAEEYLKQ 348
            Y  VFP D ++   +L  LW A G  L  GN + E + +E  K+
Sbjct: 408 AYCAVFPKDAKMEKEKLISLWMAHGFLLSKGNMELEDVGDEVWKE 452

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth. Confers a broad resistance to all known races of P.infestans.

Solanum bulbocastanum (taxid: 147425)

>sp|Q8W4J9|RPP8_ARATH Disease resistance protein RPP8 OS=Arabidopsis thaliana GN=RPP8 PE=1 SV=2

 Score = 73.6 bits (179), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 89/365 (24%), Positives = 144/365 (39%), Gaps = 77/365 (21%)

Query: 55  DMKAIYKFFIAIMRQLHQQNSETEEICDA--LLGLQSKIINLRNLHQRLPPSS-----GL 107
           D++ I K    ++ ++  Q+   ++I D    L LQ +    R + Q  P SS     G+
Sbjct: 111 DIEGITKRISEVIGEM--QSFGIQQIIDGGRSLSLQERQRVQREIRQTYPDSSESDLVGV 168

Query: 108 GQPT------------HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYN 155
            Q              H VV+I    G  KT  A ++++++ V+ +FD  AWV VS  + 
Sbjct: 169 EQSVKELVGHLVENDVHQVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFT 228

Query: 156 FKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLRE 215
            K +   I++ L P      I+  D  + +  L   L   +Y  VLDDVW ++ WD ++ 
Sbjct: 229 QKHVWQRILQELQPHDG--DILQMDEYALQRKLFQLLEAGRYLVVLDDVWKKEDWDVIKA 286

Query: 216 ALPDNQIGSRALIT-----VGPHNILTSIELENGEKNRHDSALVGGPL---------IRI 261
             P  + G + L+T     VG H   T +       N  +S  +   +         +R+
Sbjct: 287 VFPRKR-GWKMLLTSRNEGVGIHADPTCLTFRASILNPEESWKLCERIVFPRRDETEVRL 345

Query: 262 KHETWQF---FILHYGSTPLENETEG----------------PSVGLKLV---------- 292
             E        + H G  PL  +  G                 ++G ++V          
Sbjct: 346 DEEMEAMGKEMVTHCGGLPLAVKALGGLLANKHTVPEWKRVFDNIGSQIVGGSWLDDNSL 405

Query: 293 ---------SLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPGNYDSEKMAE 343
                    S  +LP  L  C L    FP D E++T  L   W AEG+  G+   E   E
Sbjct: 406 NSVYRILSLSYEDLPTHLKHCFLNLAHFPEDSEISTYSLFYYWAAEGIYDGS-TIEDSGE 464

Query: 344 EYLKQ 348
            YL++
Sbjct: 465 YYLEE 469

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. The interaction with TIP (TCV-interacting protein) may be essential for the recognition of the avirulence proteins, and the triggering of the defense response.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6L3Z7|R1B14_SOLDE Putative late blight resistance protein homolog R1B-14 OS=Solanum demissum GN=R1B-14 PE=3 SV=1

 Score = 73.6 bits (179), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 83/324 (25%), Positives = 130/324 (40%), Gaps = 52/324 (16%)

Query: 66  IMRQLHQQNSETEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDK 125
           ++     Q + T  + + ++G +  I NLRN   RL      G     V++I    G  K
Sbjct: 522 VITHTSSQLARTPRMNEEIVGFKDVIENLRN---RLLN----GTKGQDVISIHGMPGLGK 574

Query: 126 TAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEK 185
           T  A  +Y++  V  +FD  A   VS  Y++K +L  ++   +   S  +   ++  ++K
Sbjct: 575 TTLANRLYSDRSVVSHFDICAQCCVSQVYSYKELLLALLCDAVGDDSARRKHNENKLADK 634

Query: 186 TILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTSIELEN-- 243
             LR  L +++Y  ++DDVW    WDDLR   PD    SR ++T   H +     + +  
Sbjct: 635 --LRKTLLSRRYLILVDDVWDNSAWDDLRGCFPDANNRSRIILTTRHHEVAKYASVHSDP 692

Query: 244 --------------------GEKNRHDSALVGGPLIRIKHETWQF---FILHYGS-TPLE 279
                               GEK R  S L+    +RI     Q     +L  G  + +E
Sbjct: 693 LHLRMFDEDESWKLLEKKVFGEK-RCSSLLLKDVGLRIAKMCGQLPLSIVLVAGILSEME 751

Query: 280 NETE--------------GPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRL 325
            E E                S  +   S   LP  L  C LYF  F  D  +   +L RL
Sbjct: 752 KEVECWEQVANNLGTHIHNDSRAIVNQSYHVLPCHLKSCFLYFGAFLEDEVIDISRLIRL 811

Query: 326 WTAEGLRPGNYDS--EKMAEEYLK 347
           W +E     +     E +AE YL+
Sbjct: 812 WISESFIKSSEGRRLEDIAEGYLE 835

Confers resistance to late blight (Phytophthora infestans) races carrying the avirulence gene Avr1. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth.

Solanum demissum (taxid: 50514)

>sp|Q6L403|R1B17_SOLDE Putative late blight resistance protein homolog R1B-17 OS=Solanum demissum GN=R1B-17 PE=3 SV=1

 Score = 73.6 bits (179), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 83/324 (25%), Positives = 130/324 (40%), Gaps = 52/324 (16%)

Query: 66  IMRQLHQQNSETEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDK 125
           ++     Q + T  + + ++G +  I NLRN   RL      G     V++I    G  K
Sbjct: 522 VITHTSSQLARTPRMNEEIVGFKDVIENLRN---RLLN----GTKGQDVISIHGMPGLGK 574

Query: 126 TAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEK 185
           T  A  +Y++  V  +FD  A   VS  Y++K +L  ++   +   S  +   ++  ++K
Sbjct: 575 TTLANRLYSDRSVVSHFDICAQCCVSQVYSYKELLLALLCDAVGDDSARRKHNENKLADK 634

Query: 186 TILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTSIELEN-- 243
             LR  L +++Y  ++DDVW    WDDLR   PD    SR ++T   H +     + +  
Sbjct: 635 --LRKTLLSRRYLILVDDVWDNSAWDDLRGCFPDANNRSRIILTTRHHEVAKYASVHSDP 692

Query: 244 --------------------GEKNRHDSALVGGPLIRIKHETWQF---FILHYGS-TPLE 279
                               GEK R  S L+    +RI     Q     +L  G  + +E
Sbjct: 693 LHLRMFDEDESWKLLEKKVFGEK-RCSSLLLKDVGLRIAKMCEQLPLSIVLVAGILSEME 751

Query: 280 NETE--------------GPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRL 325
            E E                S  +   S   LP  L  C LYF  F  D  +   +L RL
Sbjct: 752 KEVECWEQVANNLGTHIHNDSRAIVNQSYHVLPCHLKSCFLYFGAFLEDEVIDISRLIRL 811

Query: 326 WTAEGLRPGNYDS--EKMAEEYLK 347
           W +E     +     E +AE YL+
Sbjct: 812 WISESFIKSSEGRRLEDIAEGYLE 835

Confers resistance to late blight (Phytophthora infestans) races carrying the avirulence gene Avr1. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth.

Solanum demissum (taxid: 50514)

>sp|P59584|RP8HA_ARATH Disease resistance protein RPH8A OS=Arabidopsis thaliana GN=RPH8A PE=3 SV=1

 Score = 73.2 bits (178), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 83/352 (23%), Positives = 140/352 (39%), Gaps = 76/352 (21%)

Query: 55  DMKAIYKFFIAIMRQLHQQNSETEEICDA--LLGLQSKIINLRNLHQRLPPSS-----GL 107
           D++ I K    ++ ++  Q+   ++I D    L LQ +    R + Q  P SS     G+
Sbjct: 111 DIEGITKRISEVIGEM--QSFGIQQIIDGGRSLSLQERQRVQREIRQTYPDSSESDLVGV 168

Query: 108 GQPT------------HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYN 155
            Q              H VV+I    G  KT  A ++++++ V+ +FD  AWV VS  + 
Sbjct: 169 EQSVTELVCHLVENDVHQVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFT 228

Query: 156 FKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLRE 215
            K +   I++ L P     +I+  D  + +  L   L   +Y  VLDDVW ++ WD ++ 
Sbjct: 229 QKHVWQRILQELQPHDG--EILQMDEYTIQGKLFQLLETGRYLVVLDDVWKKEDWDRIKA 286

Query: 216 ALPDNQIGSRALIT-----VGPHNILTSIELENGEKNRHDSALVGGPL---------IRI 261
             P  + G + L+T     VG H   T +       N  +S  +   +         +R+
Sbjct: 287 VFPRKR-GWKMLLTSRNEGVGIHADPTCLTFRASILNPEESWKLCERIVFPRRDETEVRL 345

Query: 262 KHETWQF---FILHYGSTPLENETEG----------------PSVGLKLV---------- 292
             E        + H G  PL  +  G                 ++G ++V          
Sbjct: 346 DEEMEAMGKEMVTHCGGLPLAVKALGGLLANKHTVPEWKRVSDNIGSQIVGGSCLDDNSL 405

Query: 293 ---------SLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPGN 335
                    S  +LP  L  C L+   +P D ++ T+ L   W AEG+  G+
Sbjct: 406 NSVYRILSLSYEDLPTHLKHCFLHLAHYPEDSKIYTQDLFNYWAAEGIYDGS 457

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. In contrast to RPP8, it does not specifically recognize the Emco5 avirulence protein from Hyaloperonospora parasitica.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	348
297745275	1136	unnamed protein product [Vitis vinifera]	0.658	0.201	0.300	2e-23
359489796	795	PREDICTED: disease susceptibility protei	0.669	0.293	0.311	5e-23
297745279	920	unnamed protein product [Vitis vinifera]	0.669	0.253	0.304	5e-23
359489148	897	PREDICTED: probable disease resistance R	0.672	0.260	0.306	7e-23
359489156	899	PREDICTED: probable disease resistance p	0.672	0.260	0.302	1e-22
297744819	597	unnamed protein product [Vitis vinifera]	0.672	0.391	0.302	2e-22
147780806	597	hypothetical protein VITISV_008412 [Viti	0.672	0.391	0.302	2e-22
359489158	531	PREDICTED: putative disease resistance p	0.672	0.440	0.302	2e-22
147839260	816	hypothetical protein VITISV_033801 [Viti	0.660	0.281	0.309	3e-22
359480122	934	PREDICTED: disease resistance protein RP	0.75	0.279	0.271	8e-22

>gi|297745275|emb|CBI40355.3| unnamed protein product [Vitis vinifera]

 Score =  115 bits (289), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 89/296 (30%), Positives = 123/296 (41%), Gaps = 67/296 (22%)

Query: 109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLM 168
           +   SVV+I+   G  KT FA ++YN   V+ +FDC AWV VS  +  + IL DI    M
Sbjct: 186 ETRRSVVSIVGMGGLGKTTFAKKVYNQRDVQQHFDCKAWVYVSQEFRAREILLDIANHFM 245

Query: 169 PTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALI 228
             S   K M +    EK  L +YL  KKY  V+DDVW  ++W  LR  LP+ + GS+ LI
Sbjct: 246 SLSEKEKEMRESELGEK--LCEYLKEKKYLIVMDDVWSSEVWSRLRSHLPEAKDGSKVLI 303

Query: 229 TVGPHNILTSIELENGEKNRHDSALVGGPLIRIKHETWQFFI---LHYGSTP--LENETE 283
           T     I                A +    +    E+WQ F+       STP  L  E E
Sbjct: 304 TTRNKEIALQAT---------SQAFIYELRLMNDDESWQLFLKKTFQGTSTPHTLSRELE 354

Query: 284 GPS-------------------------------------------------VGLKLVSL 294
            P                                                  +G+  +S 
Sbjct: 355 EPGKKIVAKCKGLPLAVVVLGGLLSTKEKTKPSWEKVLASIEWYLDQGPESCMGILALSY 414

Query: 295 SELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGL--RPGNYDSEKMAEEYLKQ 348
           ++LP+ L  C LY  +FP D E+   +L RLW AEG   R G    E +AE+Y+ +
Sbjct: 415 NDLPYYLKSCFLYCGIFPEDSEIKASKLIRLWLAEGFIQRRGKETLEDIAEDYMHE 470

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489796|ref|XP_003633980.1| PREDICTED: disease susceptibility protein LOV1-like [Vitis vinifera]

 Score =  114 bits (286), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 91/292 (31%), Positives = 133/292 (45%), Gaps = 59/292 (20%)

Query: 109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLM 168
           +   SVV+I+   G  KT  A ++YN   V+ +FDC AWV VS  +  + IL DI    M
Sbjct: 186 ETRRSVVSIVGMGGLGKTTLAKKVYNQRDVQQHFDCKAWVYVSQEFRAREILLDIANRFM 245

Query: 169 PTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALI 228
             S   K M +    EK  L +YL  KKY  V+DDVW  ++W  LR  LP+ + GS+ LI
Sbjct: 246 SLSEKEKEMRESELGEK--LCEYLKEKKYLVVMDDVWSSEVWSRLRSHLPEAKDGSKVLI 303

Query: 229 TV---------------------------------------GPHNILTSIELENGEKNRH 249
           T                                         PH ++  +E E G+K   
Sbjct: 304 TTRNKEIALHATSQAFIYELRLMNDDESWQLFLKKTFQGTSTPHTLIRELE-EPGKKIVA 362

Query: 250 D------SALVGGPLIRIKHET---WQFFILHYGSTPLENETEGPSVGLKLVSLS--ELP 298
                  + +V G L+  K +T   W+  +L      L+   +GP   + +++LS  +LP
Sbjct: 363 KCKGLPLAVVVLGGLLSTKEKTKPSWE-KVLASIEWYLD---QGPESCMGILALSYNDLP 418

Query: 299 FPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGL--RPGNYDSEKMAEEYLKQ 348
           + L  C LY  +FP D E+   +L RLW AEG   R G    E +AE+Y+ +
Sbjct: 419 YYLKSCFLYCGIFPEDSEIKASKLIRLWLAEGFIQRRGKETLEDIAEDYMHE 470

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745279|emb|CBI40359.3| unnamed protein product [Vitis vinifera]

 Score =  114 bits (286), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 89/292 (30%), Positives = 132/292 (45%), Gaps = 59/292 (20%)

Query: 109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLM 168
           +   SVV+I+   G  KT  A ++YN   V+ +FDC AWV VS  +  + IL DI    M
Sbjct: 186 ETRRSVVSIVGMGGLGKTTLAKKVYNQRDVQQHFDCKAWVYVSQEFRAREILLDIANRFM 245

Query: 169 PTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALI 228
             S   K M +    EK  L +YL  KKY  V+DDVW  ++W  LR  LP+ + GS+ LI
Sbjct: 246 SLSEKEKEMRESELGEK--LCEYLKEKKYLVVMDDVWSSEVWSRLRSHLPEAKDGSKVLI 303

Query: 229 TV---------------------------------------GPHNILTSIELENGEKNRH 249
           T                                         PH ++  +E E G+K   
Sbjct: 304 TTRNKEIALHATSQAFIYELRLMNDDESWQLFLKKTFQGTSTPHTLIRELE-EPGKKIVA 362

Query: 250 D------SALVGGPLIRIKHET---WQFFILHYGSTPLENETEGPSVGLKLVSLS--ELP 298
                  + +V G L+  K +T   W+  +    ++      +GP   + +++LS  +LP
Sbjct: 363 KCKGLPLAVVVLGGLLSTKEKTKPSWEKVL----ASIEWYLDQGPESCMGILALSYNDLP 418

Query: 299 FPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGL--RPGNYDSEKMAEEYLKQ 348
           + L  C LY  +FP D E+   +L RLW AEG   R G    E +AE+Y+ +
Sbjct: 419 YYLKSCFLYCGIFPEDSEIKASKLIRLWLAEGFIQRRGKETLEDIAEDYMHE 470

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489148|ref|XP_003633887.1| PREDICTED: probable disease resistance RPP8-like protein 4-like [Vitis vinifera]

 Score =  114 bits (285), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 90/294 (30%), Positives = 136/294 (46%), Gaps = 60/294 (20%)

Query: 108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSL 167
           G+   +VV+I+   G  KT  A ++YN+N V+  FDCHAW+ VS  Y  + +L       
Sbjct: 172 GEMRRAVVSIVGMGGLGKTTLAKKVYNDNDVRQCFDCHAWIYVSQEYTIRELL------- 224

Query: 168 MPTSSWLKIMGKDYKSE------KTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQ 221
           +  +  ++I+ ++ +S+         LRDYLT KKY  VLDD+W  + WD L    PD+ 
Sbjct: 225 LGVAVCVRILSEEERSKMDESELGDRLRDYLTTKKYLIVLDDMWRNEAWDRLGLYFPDSV 284

Query: 222 IGSRALIT-----VG--------PHNILTSIELENGEKNRHDSALVGGP---LIRIKHET 265
            GSR LIT     +G        PH +    E E+ E       L G       R   E 
Sbjct: 285 NGSRVLITSRNKEIGFYADPQAIPHELSFLTEEESWELFLKKIFLAGSANAVCPRELEEL 344

Query: 266 WQFFILHYGSTPLE---------------------------NETEGPSVGLKLVSLS--E 296
            +  + + G  PL                            +  +GP   L +++LS  +
Sbjct: 345 GKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQKVLDSLTWHLNQGPDSCLGVLALSYND 404

Query: 297 LPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGL--RPGNYDSEKMAEEYLKQ 348
           +P+ L  C LY  +FP D E+ T +L RLW AEG   R G   +E +AE++L++
Sbjct: 405 MPYYLKSCFLYCGLFPEDSEIWTDKLIRLWVAEGFIQRRGVEIAEDVAEDHLQE 458

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489156|ref|XP_003633889.1| PREDICTED: probable disease resistance protein RDL6/RF9-like [Vitis vinifera]

 Score =  113 bits (283), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 89/294 (30%), Positives = 135/294 (45%), Gaps = 60/294 (20%)

Query: 108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSL 167
           G+   +VV+I+   G  KT  A ++YN+N V+  FDCHAW+ VS  Y  + +L       
Sbjct: 173 GEMRRAVVSIVGMGGLGKTTLAKKVYNDNDVQQCFDCHAWIYVSQEYTIRELL------- 225

Query: 168 MPTSSWLKIMGKDYKSE------KTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQ 221
           +  +  + I+ ++ +S+         LRDYLT KKY  V+DD+W  + WD L    PD+ 
Sbjct: 226 LGVAVRVGILSEEERSKMNESDLGNSLRDYLTTKKYLIVMDDMWRNEAWDRLGLYFPDSV 285

Query: 222 IGSRALIT-----VG--------PHNILTSIELENGEKNRHDSALVGGP---LIRIKHET 265
            GSR LIT     +G        PH +    E E+ E       L G       R   E 
Sbjct: 286 NGSRVLITSRNKQIGLYADPQTIPHELSFLTEEESWELFLKKIFLAGSANAVCPRELEEL 345

Query: 266 WQFFILHYGSTPLE---------------------------NETEGPSVGLKLVSLS--E 296
            +  + + G  PL                            +  +GP   L +++LS  +
Sbjct: 346 GKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQKVLDSLTWHLNQGPDSCLGVLALSYND 405

Query: 297 LPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGL--RPGNYDSEKMAEEYLKQ 348
           +P+ L  C LY  +FP D E+ T +L RLW AEG   R G   +E +AE++L++
Sbjct: 406 MPYYLKSCFLYCGLFPEDSEIRTDKLIRLWVAEGFIQRRGEEIAEDVAEDHLQE 459

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297744819|emb|CBI38087.3| unnamed protein product [Vitis vinifera]

 Score =  112 bits (281), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 89/294 (30%), Positives = 134/294 (45%), Gaps = 60/294 (20%)

Query: 108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSL 167
           G+   +VV+I+   G  KT  A ++YN+N V+  FDCHAW+ VS  Y  + +L       
Sbjct: 173 GEMRRAVVSIVGMGGLGKTTLAKKVYNDNDVQQCFDCHAWIYVSQEYTIRELL------- 225

Query: 168 MPTSSWLKIMGKDYKSE------KTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQ 221
           +  +  + I+ ++ +S+         LRDYLT KKY  V+DD+W  + WD L    PD+ 
Sbjct: 226 LGIAVRVGILSEEERSKMNESDLGNSLRDYLTTKKYLIVMDDMWRNEAWDRLGLYFPDSV 285

Query: 222 IGSRALIT-----VG--------PHNILTSIELENGEKNRHDSALVGGP---LIRIKHET 265
            GSR LIT     +G        PH +    E E+ E       L G       R   E 
Sbjct: 286 NGSRVLITSRNKEIGLYADPQTIPHELSFLTEEESWELFLKKIFLAGSANAVCPRELEEL 345

Query: 266 WQFFILHYGSTPLE---------------------------NETEGPSVGLKLVSLS--E 296
            +  + + G  PL                            +  +GP   L +++LS  +
Sbjct: 346 GKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQKVLDSLTWHLNQGPDSCLGVLALSYND 405

Query: 297 LPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGL--RPGNYDSEKMAEEYLKQ 348
           +P+ L  C LY  +FP D E+ T +L RLW AEG   R G    E +AE++L++
Sbjct: 406 MPYYLKSCFLYCGLFPEDSEIRTDKLIRLWVAEGFIQRRGEEIGEDVAEDHLQE 459

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147780806|emb|CAN70484.1| hypothetical protein VITISV_008412 [Vitis vinifera]

 Score =  112 bits (281), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 89/294 (30%), Positives = 134/294 (45%), Gaps = 60/294 (20%)

Query: 108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSL 167
           G+   +VV+I+   G  KT  A ++YN+N V+  FDCHAW+ VS  Y  + +L       
Sbjct: 173 GEMRRAVVSIVGMGGLGKTTLAKKVYNDNDVQQCFDCHAWIYVSQEYTIRELL------- 225

Query: 168 MPTSSWLKIMGKDYKSE------KTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQ 221
           +  +  + I+ ++ +S+         LRDYLT KKY  V+DD+W  + WD L    PD+ 
Sbjct: 226 LGXAVRVGILSEEERSKMNESDLGNSLRDYLTTKKYLIVMDDMWRXEAWDRLGLYFPDSV 285

Query: 222 IGSRALIT-----VG--------PHNILTSIELENGEKNRHDSALVGGP---LIRIKHET 265
            GSR LIT     +G        PH +    E E+ E       L G       R   E 
Sbjct: 286 NGSRVLITSRNKEIGLYADPQTIPHELSFLTEEESWELFLKKIFLAGSANAVCPRELEEL 345

Query: 266 WQFFILHYGSTPLE---------------------------NETEGPSVGLKLVSLS--E 296
            +  + + G  PL                            +  +GP   L +++LS  +
Sbjct: 346 GKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQKVLDSLTWHLNQGPDSCLGVLALSYND 405

Query: 297 LPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGL--RPGNYDSEKMAEEYLKQ 348
           +P+ L  C LY  +FP D E+ T +L RLW AEG   R G    E +AE++L++
Sbjct: 406 MPYYLKSCFLYCGLFPEDSEIRTDKLIRLWVAEGFIQRRGEEIGEDVAEDHLQE 459

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489158|ref|XP_003633890.1| PREDICTED: putative disease resistance protein At1g50180-like [Vitis vinifera]

 Score =  112 bits (281), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 89/294 (30%), Positives = 134/294 (45%), Gaps = 60/294 (20%)

Query: 108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSL 167
           G+   +VV+I+   G  KT  A ++YN+N V+  FDCHAW+ VS  Y  + +L       
Sbjct: 173 GEMRRAVVSIVGMGGLGKTTLAKKVYNDNDVQQCFDCHAWIYVSQEYTIRELL------- 225

Query: 168 MPTSSWLKIMGKDYKSE------KTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQ 221
           +  +  + I+ ++ +S+         LRDYLT KKY  V+DD+W  + WD L    PD+ 
Sbjct: 226 LGIAVRVGILSEEERSKMNESDLGNSLRDYLTTKKYLIVMDDMWRNEAWDRLGLYFPDSV 285

Query: 222 IGSRALIT-----VG--------PHNILTSIELENGEKNRHDSALVGGP---LIRIKHET 265
            GSR LIT     +G        PH +    E E+ E       L G       R   E 
Sbjct: 286 NGSRVLITSRNKEIGLYADPQTIPHELSFLTEEESWELFLKKIFLAGSANAVCPRELEEL 345

Query: 266 WQFFILHYGSTPLE---------------------------NETEGPSVGLKLVSLS--E 296
            +  + + G  PL                            +  +GP   L +++LS  +
Sbjct: 346 GKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQKVLDSLTWHLNQGPDSCLGVLALSYND 405

Query: 297 LPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGL--RPGNYDSEKMAEEYLKQ 348
           +P+ L  C LY  +FP D E+ T +L RLW AEG   R G    E +AE++L++
Sbjct: 406 MPYYLKSCFLYCGLFPEDSEIRTDKLIRLWVAEGFIQRRGEEIGEDVAEDHLQE 459

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147839260|emb|CAN67961.1| hypothetical protein VITISV_033801 [Vitis vinifera]

 Score =  112 bits (280), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 134/265 (50%), Gaps = 35/265 (13%)

Query: 108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSL 167
           G+   +VV+I+   G  KT  A ++YN+N V   FDCHAW+ VS  Y  + +       L
Sbjct: 173 GEMRRAVVSIVGMGGLGKTTLAKKVYNDNDVXQCFDCHAWIYVSQEYTIREL-------L 225

Query: 168 MPTSSWLKIMGKDYKSE------KTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDN- 220
           +  +  ++ + ++ +S          LRDYLT KKY  V+DD+W  + WD L    PD+ 
Sbjct: 226 LGVAVCVRXLSEEERSXMNESELGNRLRDYLTTKKYLIVMDDMWRNEAWDRLGLYFPDSE 285

Query: 221 ---QIGSRALITVGPHNILTSIELEN-GEKNRHD------SALVGGPLIRIKHET---WQ 267
              ++  + +   G  N +   ELE  G+K   +      + +V G L+  K +T   WQ
Sbjct: 286 ESWELFLKKIFLAGSANAVCPRELEELGKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQ 345

Query: 268 FFILHYGSTPLENETEGPSVGLKLVSLS--ELPFPLIVCCLYFCVFPTDIELTTRQLCRL 325
             +     +   +  +GP   L +++LS  ++P+ L  C LY  +FP D E+ T +L R 
Sbjct: 346 KVL----DSLTWHLNQGPDSCLGVLALSYNDMPYYLKSCFLYCGLFPEDSEIRTDKLIRX 401

Query: 326 WTAEGL--RPGNYDSEKMAEEYLKQ 348
           W AEG   R G   +E +AE++L++
Sbjct: 402 WVAEGFIQRRGEEIAEDVAEDHLQE 426

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480122|ref|XP_002265617.2| PREDICTED: disease resistance protein RPM1-like [Vitis vinifera] gi|147771833|emb|CAN60254.1| hypothetical protein VITISV_025805 [Vitis vinifera]

 Score =  110 bits (276), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 84/309 (27%), Positives = 134/309 (43%), Gaps = 48/309 (15%)

Query: 88  QSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAW 147
           +++I+ +  L   L      G P  +V++++   G  KT FA ++Y+N  V  +FDC+AW
Sbjct: 167 ETEIVGIEPLRNELISRLVEGNPKRTVISVVGMGGLGKTTFAKKVYDNQRVVGHFDCNAW 226

Query: 148 VRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKT---ILRDYLTNKKYFTVLDDV 204
           V VS  +  + +L ++ K            G D   E +   ++R YL +K+Y  V DDV
Sbjct: 227 VTVSQSFKMEELLRNMTKKFYQGRKEAVPEGIDTIDEMSLIALIRQYLQDKRYVVVFDDV 286

Query: 205 WIEKIWDDLREALPDNQIGSRALITVGPHNILTSIE------------------------ 240
           W    W  ++  LP+N  GSR +IT     + +S +                        
Sbjct: 287 WKLDFWGFIKYVLPENGKGSRIIITTRNDEVASSCKESSFDYIHKLQPLSPKSSWELFCK 346

Query: 241 --LENG-----EKNRHD-----------SALVGGPLIRIKHET-WQFFILHYGSTPLENE 281
              + G     EK   D              +GG L R ++E+ W+ F  + GS    N 
Sbjct: 347 KTFQGGCPPELEKLSLDIVKRCGGLPLAIVAIGGLLSRKQNESEWKNFSDNLGSELESNS 406

Query: 282 TEGPSVGLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPG--NYDSE 339
              P   +  +S  +LP+ L  C LY  +FP D  +   +L RLW AEG          E
Sbjct: 407 RLQPINTILSLSYHDLPYYLKSCFLYLAIFPEDYTIKCTKLTRLWIAEGFVKAKKGVTME 466

Query: 340 KMAEEYLKQ 348
           ++AEE+L +
Sbjct: 467 ELAEEFLTE 475

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	348
TAIR|locus:2077572	926	RPM1 "RESISTANCE TO P. SYRINGA	0.364	0.137	0.307	6.1e-17
TAIR|locus:2075170	835	RPP13 "RECOGNITION OF PERONOSP	0.445	0.185	0.333	1.3e-16
TAIR|locus:504956483	847	AT3G46730 [Arabidopsis thalian	0.362	0.148	0.358	1.6e-16
TAIR|locus:2169523	901	AT5G35450 [Arabidopsis thalian	0.324	0.125	0.336	2e-13
TAIR|locus:2025916	906	AT1G59780 "AT1G59780" [Arabido	0.459	0.176	0.283	8.7e-13
TAIR|locus:2078012	852	ZAR1 "HOPZ-ACTIVATED RESISTANC	0.370	0.151	0.262	1.1e-12
UNIPROTKB|Q84UB1	928	Pi-ta "Pi-ta protein" [Oryza s	0.350	0.131	0.322	1.6e-12
UNIPROTKB|Q9AY26	928	Pi-ta "Pi-ta protein" [Oryza s	0.350	0.131	0.322	1.6e-12
TAIR|locus:2176486	908	RPP8 "RECOGNITION OF PERONOSPO	0.330	0.126	0.305	2.4e-12
TAIR|locus:2102857	847	AT3G46710 [Arabidopsis thalian	0.327	0.134	0.341	4.1e-12

TAIR|locus:2077572 RPM1 "RESISTANCE TO P. SYRINGAE PV MACULICOLA 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 185 (70.2 bits), Expect = 6.1e-17, Sum P(2) = 6.1e-17
 Identities = 40/130 (30%), Positives = 67/130 (51%)

Query:   109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLM 168
             +P   VVA++   G  KT  +A I+ +  V+ +F+ +AWV +S  Y  + +   ++K   
Sbjct:   190 EPQRIVVAVVGMGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSYVIEDVFRTMIKEFY 249

Query:   169 P---TSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSR 225
                 T    ++    Y+     L +YL +K+Y  VLDDVW   +W ++  ALPD   GSR
Sbjct:   250 KEADTQIPAELYSLGYRELVEKLVEYLQSKRYIVVLDDVWTTGLWREISIALPDGIYGSR 309

Query:   226 ALITVGPHNI 235
              ++T    N+
Sbjct:   310 VMMTTRDMNV 319

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0000166 "nucleotide binding" evidence=ISS

GO:0009626 "plant-type hypersensitive response" evidence=IDA

TAIR|locus:2075170 RPP13 "RECOGNITION OF PERONOSPORA PARASITICA 13" [Arabidopsis thaliana (taxid:3702)]

 Score = 196 (74.1 bits), Expect = 1.3e-16, Sum P(2) = 1.3e-16
 Identities = 55/165 (33%), Positives = 86/165 (52%)

Query:    67 MRQLHQQNSETEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKT 126
             +RQL +  S  +E  + ++GL+    + + L ++L       +    +++I    G  KT
Sbjct:   148 VRQLRRARSVDQE--EVVVGLED---DAKILLEKLLDYE---EKNRFIISIFGMGGLGKT 199

Query:   127 AFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSL-MPTSSWLKIMGKDYKSEK 185
             A A ++YN+  VK  F+  AW  VS  Y    IL  I++SL M +   L+ + K  + E 
Sbjct:   200 ALARKLYNSRDVKERFEYRAWTYVSQEYKTGDILMRIIRSLGMTSGEELEKIRKFAEEEL 259

Query:   186 TI-LRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALIT 229
              + L   L  KKY  V+DD+W  + WD L+ ALP N  GSR +IT
Sbjct:   260 EVYLYGLLEGKKYLVVVDDIWEREAWDSLKRALPCNHEGSRVIIT 304

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=TAS

GO:0009814 "defense response, incompatible interaction" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

GO:0009626 "plant-type hypersensitive response" evidence=IMP

TAIR|locus:504956483 AT3G46730 [Arabidopsis thaliana (taxid:3702)]

 Score = 191 (72.3 bits), Expect = 1.6e-16, Sum P(2) = 1.6e-16
 Identities = 47/131 (35%), Positives = 68/131 (51%)

Query:   114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW 173
             +++I    G  KTA A ++YN+  VK  FDC AW  VS  Y  + IL  I++SL   S+ 
Sbjct:   187 IISIFGMGGLGKTALARKLYNSGDVKRRFDCRAWTYVSQEYKTRDILIRIIRSLGIVSAE 246

Query:   174 ----LKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALIT 229
                 +K+  +D + E   L   L  K Y  V+DDVW    W+ L+ ALP +  GS+ +IT
Sbjct:   247 EMEKIKMFEEDEELE-VYLYGLLEGKNYMVVVDDVWDPDAWESLKRALPCDHRGSKVIIT 305

Query:   230 VGPHNILTSIE 240
                  I   +E
Sbjct:   306 TRIRAIAEGVE 316

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2169523 AT5G35450 [Arabidopsis thaliana (taxid:3702)]

 Score = 160 (61.4 bits), Expect = 2.0e-13, Sum P(2) = 2.0e-13
 Identities = 39/116 (33%), Positives = 62/116 (53%)

Query:   114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW 173
             VV+I    G  KT  A +I++++ V+ +FD  AWV VS  +  K +   I++ L P    
Sbjct:   185 VVSISGMGGIGKTTLARQIFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRILQELRPHDG- 243

Query:   174 LKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALIT 229
              +I+  D  + +  L   L   +Y  VLDDVW E+ WD ++E  P  + G + L+T
Sbjct:   244 -EILQMDEYTIQGKLFQLLETGRYLVVLDDVWKEEDWDRIKEVFPRKR-GWKMLLT 297

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:2025916 AT1G59780 "AT1G59780" [Arabidopsis thaliana (taxid:3702)]

 Score = 139 (54.0 bits), Expect = 8.7e-13, Sum P(2) = 8.7e-13
 Identities = 51/180 (28%), Positives = 83/180 (46%)

Query:    68 RQL-HQQNSETEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKT 126
             R+L H  +SE+E     L+GL+    N+  L + L     +G  +   V+I    G  KT
Sbjct:   146 RELRHTFSSESES---NLVGLEK---NVEKLVEEL-----VGNDSSHGVSITGLGGLGKT 194

Query:   127 AFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKT 186
               A +I++++ VK +FD  AWV VS  +  K +   I+ +L P      +   D + +  
Sbjct:   195 TLARQIFDHDKVKSHFDGLAWVCVSQEFTRKDVWKTILGNLSPKYKDSDLPEDDIQKK-- 252

Query:   187 ILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALIT-----VGPHNILTSIEL 241
              L   L  KK   V DD+W  + W  +    P+ + G + L+T     + PH +    EL
Sbjct:   253 -LFQLLETKKALIVFDDLWKREDWYRIAPMFPERKAGWKVLLTSRNDAIHPHCVTFKPEL 311

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2078012 ZAR1 "HOPZ-ACTIVATED RESISTANCE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 161 (61.7 bits), Expect = 1.1e-12, Sum P(2) = 1.1e-12
 Identities = 36/137 (26%), Positives = 71/137 (51%)

Query:   114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW 173
             ++A +   G  KT  A E++N+  ++  F+   WV VS  +  ++I+  I+++L   S  
Sbjct:   184 IMAFVGMGGLGKTTIAQEVFNDKEIEHRFERRIWVSVSQTFTEEQIMRSILRNLGDAS-- 241

Query:   174 LKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKI--WDDLREALPDNQIGSRALITVG 231
                +G D  +    ++ YL  K+Y  V+DDVW + +  WD + + LP  Q GS  ++T  
Sbjct:   242 ---VGDDIGTLLRKIQQYLLGKRYLIVMDDVWDKNLSWWDKIYQGLPRGQGGS-VIVTTR 297

Query:   232 PHNILTSIELENGEKNR 248
               ++   ++  + + +R
Sbjct:   298 SESVAKRVQARDDKTHR 314

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

UNIPROTKB|Q84UB1 Pi-ta "Pi-ta protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 174 (66.3 bits), Expect = 1.6e-12, Sum P(2) = 1.6e-12
 Identities = 40/124 (32%), Positives = 61/124 (49%)

Query:   108 GQPTHSVVAILDSRGFDKTAFAAEIY--NNNFVKFYFDCHAWVRVSNFYNFKRILDDIMK 165
             G+P   V +I+ S G  KT  A E Y  +   +   FDC A+VR     +  +IL D++ 
Sbjct:   225 GEPKLKVASIVGSGGVGKTTLATEFYRLHGRRLDAPFDCRAFVRTPRKPDMTKILTDMLS 284

Query:   166 SLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSR 225
              L P          +       +R +L +K+YF +++D+W   +WD +   LPDN   SR
Sbjct:   285 QLRPQHQHQSSDVWEVDRLLETIRTHLQDKRYFIIIEDLWASSMWDIVSRGLPDNNSCSR 344

Query:   226 ALIT 229
              LIT
Sbjct:   345 ILIT 348

GO:0006952 "defense response" evidence=IMP

UNIPROTKB|Q9AY26 Pi-ta "Pi-ta protein" [Oryza sativa (taxid:4530)]

 Score = 174 (66.3 bits), Expect = 1.6e-12, Sum P(2) = 1.6e-12
 Identities = 40/124 (32%), Positives = 61/124 (49%)

Query:   108 GQPTHSVVAILDSRGFDKTAFAAEIY--NNNFVKFYFDCHAWVRVSNFYNFKRILDDIMK 165
             G+P   V +I+ S G  KT  A E Y  +   +   FDC A+VR     +  +IL D++ 
Sbjct:   225 GEPKLKVASIVGSGGVGKTTLATEFYRLHGRRLDAPFDCRAFVRTPRKPDMTKILTDMLS 284

Query:   166 SLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSR 225
              L P          +       +R +L +K+YF +++D+W   +WD +   LPDN   SR
Sbjct:   285 QLRPQHQHQSSDVWEVDRLLETIRTHLQDKRYFIIIEDLWASSMWDIVSRGLPDNNSCSR 344

Query:   226 ALIT 229
              LIT
Sbjct:   345 ILIT 348

GO:0006952 "defense response" evidence=IMP

TAIR|locus:2176486 RPP8 "RECOGNITION OF PERONOSPORA PARASITICA 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 157 (60.3 bits), Expect = 2.4e-12, Sum P(2) = 2.4e-12
 Identities = 36/118 (30%), Positives = 63/118 (53%)

Query:   112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTS 171
             H VV+I    G  KT  A ++++++ V+ +FD  AWV VS  +  K +   I++ L P  
Sbjct:   185 HQVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRILQELQPHD 244

Query:   172 SWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALIT 229
               +  M  +Y  ++ + +  L   +Y  VLDDVW ++ WD ++   P  + G + L+T
Sbjct:   245 GDILQMD-EYALQRKLFQ-LLEAGRYLVVLDDVWKKEDWDVIKAVFPRKR-GWKMLLT 299

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=ISS

GO:0009416 "response to light stimulus" evidence=IMP

GO:0051607 "defense response to virus" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0051707 "response to other organism" evidence=IMP

TAIR|locus:2102857 AT3G46710 [Arabidopsis thaliana (taxid:3702)]

 Score = 166 (63.5 bits), Expect = 4.1e-12, Sum P(2) = 4.1e-12
 Identities = 40/117 (34%), Positives = 64/117 (54%)

Query:   114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW 173
             +++I    G  KT+ A +++N++ VK  F+   W  VS   N + IL  I+ SL  TS  
Sbjct:   186 MISIFGMEGLGKTSLARKLFNSSDVKESFEYRVWTNVSGECNTRDILMRIISSLEETSEG 245

Query:   174 -LKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALIT 229
              L+ M +  +  +  L D L  K+Y  V+DD+W  +  + L+ ALP +  GSR +IT
Sbjct:   246 ELEKMAQ--QELEVYLHDILQEKRYLVVVDDIWESEALESLKRALPCSYQGSRVIIT 300

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	348
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	2e-23

>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain

 Score = 97.4 bits (243), Expect = 2e-23
 Identities = 73/284 (25%), Positives = 108/284 (38%), Gaps = 55/284 (19%)

Query: 94  LRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF 153
           +  L ++L            VV I+   G  KT  A +IYN++ V  +FD  AWV VS  
Sbjct: 5   IEALIEKL--LEMSDNLG--VVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKT 60

Query: 154 YNFKRILDDIMKSLMPT-SSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDD 212
           Y   R+  DI++ L    S W++   K+       +++ L  K++  VLDDVW +  WD 
Sbjct: 61  YTEFRLQKDILQELGLDDSDWVE---KNESELAVKIKEALLRKRFLLVLDDVWEKNDWDK 117

Query: 213 LREALPDNQIGSRALIT----------------------------------VGPHNILTS 238
           +    PD + GSR ++T                                  V    +   
Sbjct: 118 IGVPFPDGENGSRVIVTTRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELPPC 177

Query: 239 IELENGEKNRHDS--------ALVGGPLIRIKHE--TWQFFILHYGSTPLEN-ETEGPSV 287
            ELE   K   +          ++GG L+  K     W+  +    +             
Sbjct: 178 PELEEVAKEIVEKCKGLPLALKVLGG-LLAFKSTVQEWEHVLEQLNNELAGRDGLNEVLS 236

Query: 288 GLKLVSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGL 331
            L L S   LP  L  C LY  +FP D  +   QL +LW AEG 
Sbjct: 237 ILSL-SYDNLPMHLKRCFLYLALFPEDYNIRKEQLIKLWIAEGF 279

Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	348
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.97
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.99
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.89
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.84
PF05729	166	NACHT: NACHT domain	98.82
PF13173	128	AAA_14: AAA domain	98.7
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.69
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.65
cd01128	249	rho_factor Transcription termination factor rho is	98.64
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.61
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.57
PTZ00202	550	tuzin; Provisional	98.54
PRK09376	416	rho transcription termination factor Rho; Provisio	98.46
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.44
PRK04841	903	transcriptional regulator MalT; Provisional	98.43
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.41
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.41
KOG2028	554	consensus ATPase related to the helicase subunit o	98.31
TIGR00767	415	rho transcription termination factor Rho. Members	98.29
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.22
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.18
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.15
PRK13342	413	recombination factor protein RarA; Reviewed	98.15
PRK12402	337	replication factor C small subunit 2; Reviewed	98.11
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.07
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.04
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.04
smart00382	148	AAA ATPases associated with a variety of cellular	98.04
PF00004	132	AAA: ATPase family associated with various cellula	98.04
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.03
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.0
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	97.98
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	97.96
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.94
PRK06893	229	DNA replication initiation factor; Validated	97.93
PRK13341	725	recombination factor protein RarA/unknown domain f	97.9
PRK08116	268	hypothetical protein; Validated	97.87
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.87
PRK04195	482	replication factor C large subunit; Provisional	97.86
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.85
PHA02544	316	44 clamp loader, small subunit; Provisional	97.84
PLN03025	319	replication factor C subunit; Provisional	97.83
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.82
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.81
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.8
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.79
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.77
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.77
PRK10536	262	hypothetical protein; Provisional	97.76
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.74
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.71
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.71
PRK08118	167	topology modulation protein; Reviewed	97.7
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.68
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.66
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.66
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.65
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.62
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.61
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.61
PRK08181	269	transposase; Validated	97.6
PRK12377	248	putative replication protein; Provisional	97.59
PRK08727	233	hypothetical protein; Validated	97.59
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.58
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.58
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.55
CHL00095	821	clpC Clp protease ATP binding subunit	97.54
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.54
PRK08084	235	DNA replication initiation factor; Provisional	97.52
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.51
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.51
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.5
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.49
PRK07261	171	topology modulation protein; Provisional	97.49
PRK10865	857	protein disaggregation chaperone; Provisional	97.48
PRK12608	380	transcription termination factor Rho; Provisional	97.47
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.47
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.46
PRK05642	234	DNA replication initiation factor; Validated	97.44
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.43
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.41
PRK06526	254	transposase; Provisional	97.39
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.38
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.37
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.37
PRK07952	244	DNA replication protein DnaC; Validated	97.36
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.35
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.35
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.34
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.34
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.33
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.33
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.32
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.31
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.3
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.3
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.29
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.29
COG3903	414	Predicted ATPase [General function prediction only	97.29
PRK09183	259	transposase/IS protein; Provisional	97.28
CHL00181	287	cbbX CbbX; Provisional	97.27
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.27
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.26
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.25
PRK05541	176	adenylylsulfate kinase; Provisional	97.25
PRK08939	306	primosomal protein DnaI; Reviewed	97.25
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.24
PRK09087	226	hypothetical protein; Validated	97.24
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.23
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.23
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.23
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.23
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.22
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.21
PHA00729	226	NTP-binding motif containing protein	97.2
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.2
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.19
PRK06921	266	hypothetical protein; Provisional	97.19
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.17
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.17
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.16
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.15
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.14
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	97.12
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	97.11
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.11
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.11
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.11
PRK04296	190	thymidine kinase; Provisional	97.1
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.1
CHL00095	821	clpC Clp protease ATP binding subunit	97.09
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.09
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.09
CHL00176	638	ftsH cell division protein; Validated	97.07
TIGR00959	428	ffh signal recognition particle protein. This mode	97.07
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.07
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.06
PRK06835	329	DNA replication protein DnaC; Validated	97.05
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.04
PRK06620	214	hypothetical protein; Validated	97.03
PRK10865	857	protein disaggregation chaperone; Provisional	97.02
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.02
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.0
PRK07667	193	uridine kinase; Provisional	97.0
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	96.99
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.97
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.97
PRK12422	445	chromosomal replication initiation protein; Provis	96.97
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.96
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	96.95
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.95
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.94
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.92
PRK06696	223	uridine kinase; Validated	96.92
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.9
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	96.89
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.88
PRK14974	336	cell division protein FtsY; Provisional	96.88
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.87
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.86
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.86
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.85
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.85
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	96.85
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.84
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	96.83
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.83
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.83
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.83
PRK10867	433	signal recognition particle protein; Provisional	96.82
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	96.81
PRK06067	234	flagellar accessory protein FlaH; Validated	96.81
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.8
PRK09354	349	recA recombinase A; Provisional	96.8
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.79
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.79
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.76
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.75
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	96.75
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.73
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.7
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.7
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.68
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.67
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.67
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	96.66
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.66
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.64
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	96.63
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	96.63
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	96.62
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.62
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.62
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.62
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.6
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.57
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.57
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	96.56
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.56
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.56
PHA02774	613	E1; Provisional	96.55
PRK05480	209	uridine/cytidine kinase; Provisional	96.54
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	96.54
PRK06547	172	hypothetical protein; Provisional	96.53
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.53
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.53
PRK08233	182	hypothetical protein; Provisional	96.51
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.51
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.51
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	96.49
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.49
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.47
PRK04040	188	adenylate kinase; Provisional	96.46
PTZ00301	210	uridine kinase; Provisional	96.46
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.45
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.44
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.43
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.43
CHL00195	489	ycf46 Ycf46; Provisional	96.42
PRK15455	644	PrkA family serine protein kinase; Provisional	96.42
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.42
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.41
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.41
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	96.4
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.4
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	96.39
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	96.39
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	96.38
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.37
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.36
cd03246	173	ABCC_Protease_Secretion This family represents the	96.35
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	96.34
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.33
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.33
PRK06762	166	hypothetical protein; Provisional	96.33
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.33
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.32
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.32
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.3
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.29
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.28
PTZ00035	337	Rad51 protein; Provisional	96.26
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.22
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.22
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.22
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	96.22
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	96.2
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.2
PRK00889	175	adenylylsulfate kinase; Provisional	96.19
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.19
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	96.16
KOG1514	767	consensus Origin recognition complex, subunit 1, a	96.16
PRK03839	180	putative kinase; Provisional	96.15
PRK14527	191	adenylate kinase; Provisional	96.14
PTZ00088	229	adenylate kinase 1; Provisional	96.14
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.14
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.13
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	96.12
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	96.11
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	96.11
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.1
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	96.09
PRK05022	509	anaerobic nitric oxide reductase transcription reg	96.09
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.08
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.07
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.07
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	96.03
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	96.03
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	96.03
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.03
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.01
PRK04328	249	hypothetical protein; Provisional	96.0
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.0
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	95.99
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.99
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	95.97
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	95.96
PRK13531	498	regulatory ATPase RavA; Provisional	95.95
PRK00131	175	aroK shikimate kinase; Reviewed	95.95
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	95.95
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	95.94
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	95.94
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	95.93
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.92
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.92
PRK05439	311	pantothenate kinase; Provisional	95.91
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	95.9
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	95.9
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	95.88
PRK10416	318	signal recognition particle-docking protein FtsY;	95.88
PRK00625	173	shikimate kinase; Provisional	95.88
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.88
PRK06936	439	type III secretion system ATPase; Provisional	95.87
PRK00279	215	adk adenylate kinase; Reviewed	95.85
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	95.85
PF00154	322	RecA: recA bacterial DNA recombination protein; In	95.84
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.83
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	95.81
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	95.81
cd03215	182	ABC_Carb_Monos_II This family represents domain II	95.81
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	95.8
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	95.8
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.79
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	95.78
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	95.76
PRK08149	428	ATP synthase SpaL; Validated	95.75
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	95.74
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	95.74
PRK06217	183	hypothetical protein; Validated	95.74
PRK14738	206	gmk guanylate kinase; Provisional	95.73
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	95.73
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	95.72
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.72
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	95.71
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	95.71
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	95.71
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	95.71
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	95.7
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	95.69
PRK13765	637	ATP-dependent protease Lon; Provisional	95.69
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	95.68
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.66
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	95.66
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	95.65
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.65
PRK13947	171	shikimate kinase; Provisional	95.65
PRK11608	326	pspF phage shock protein operon transcriptional ac	95.64
PRK14528	186	adenylate kinase; Provisional	95.64
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	95.63
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	95.59
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.59
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	95.59
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	95.57
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	95.56
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	95.56
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	95.55
PRK13948	182	shikimate kinase; Provisional	95.55
PRK03846	198	adenylylsulfate kinase; Provisional	95.54
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	95.54
PRK05922	434	type III secretion system ATPase; Validated	95.54
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	95.53
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	95.53
PRK00300	205	gmk guanylate kinase; Provisional	95.52
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	95.52
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	95.52
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	95.48
PRK09099	441	type III secretion system ATPase; Provisional	95.47
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	95.47
PRK15453	290	phosphoribulokinase; Provisional	95.46
PRK13949	169	shikimate kinase; Provisional	95.46
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	95.45
PF07726	131	AAA_3: ATPase family associated with various cellu	95.44
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.44
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	95.44
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.44
PRK11823	446	DNA repair protein RadA; Provisional	95.43
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	95.42
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	95.42
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	95.41
PTZ00185	574	ATPase alpha subunit; Provisional	95.41
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	95.41
PF14516	331	AAA_35: AAA-like domain	95.4
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	95.39
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	95.37
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	95.37
PLN02200	234	adenylate kinase family protein	95.36
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	95.36
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	95.35
PRK14526	211	adenylate kinase; Provisional	95.35
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	95.35
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	95.35
PRK14737	186	gmk guanylate kinase; Provisional	95.34
PRK07594	433	type III secretion system ATPase SsaN; Validated	95.34
PRK15064	530	ABC transporter ATP-binding protein; Provisional	95.32
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.31
PRK09519	790	recA DNA recombination protein RecA; Reviewed	95.31
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	95.31
PRK12678	672	transcription termination factor Rho; Provisional	95.3
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	95.3
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	95.3
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	95.3
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	95.29
PRK12339	197	2-phosphoglycerate kinase; Provisional	95.29
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	95.27
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.27
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	95.26
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	95.24
PRK14530	215	adenylate kinase; Provisional	95.23
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.22
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	95.22
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	95.21
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	95.2
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.2
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	95.17
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	95.17
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	95.16
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	95.15
PLN02318	656	phosphoribulokinase/uridine kinase	95.14
PRK05057	172	aroK shikimate kinase I; Reviewed	95.12
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	95.12
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	95.09
PRK13946	184	shikimate kinase; Provisional	95.09
PRK11147	635	ABC transporter ATPase component; Reviewed	95.08
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	95.07
PRK05973	237	replicative DNA helicase; Provisional	95.06
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	95.05
PRK13975	196	thymidylate kinase; Provisional	95.03
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	95.02
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	95.01
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	94.99
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	94.98
PRK04182	180	cytidylate kinase; Provisional	94.97
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	94.95
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	94.93
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	94.93
PLN02348	395	phosphoribulokinase	94.9
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	94.88
PTZ00494	664	tuzin-like protein; Provisional	94.87
COG1117	253	PstB ABC-type phosphate transport system, ATPase c	94.87
TIGR01287	275	nifH nitrogenase iron protein. This model describe	94.86
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	94.85
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	94.85
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	94.84
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	94.84
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	94.84
PRK09825	176	idnK D-gluconate kinase; Provisional	94.83
PRK13236	296	nitrogenase reductase; Reviewed	94.82
PRK15115	444	response regulator GlrR; Provisional	94.8
KOG0736	953	consensus Peroxisome assembly factor 2 containing	94.79
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	94.79
COG5635	824	Predicted NTPase (NACHT family) [Signal transducti	94.79
TIGR02546	422	III_secr_ATP type III secretion apparatus H+-trans	94.78
COG0237	201	CoaE Dephospho-CoA kinase [Coenzyme metabolism]	94.78
CHL00059	485	atpA ATP synthase CF1 alpha subunit	94.76
COG0488	530	Uup ATPase components of ABC transporters with dup	94.76
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	94.75
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	94.75
COG1157	441	FliI Flagellar biosynthesis/type III secretory pat	94.75
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	94.75
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	94.75
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	94.72
PRK14532	188	adenylate kinase; Provisional	94.71
PRK13545	549	tagH teichoic acids export protein ATP-binding sub	94.71
PF00005	137	ABC_tran: ABC transporter This structure is on hol	94.71
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	94.7
COG1100	219	GTPase SAR1 and related small G proteins [General	94.7
PLN02796	347	D-glycerate 3-kinase	94.69
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	94.69
PRK09435	332	membrane ATPase/protein kinase; Provisional	94.68
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	94.65
PRK13230	279	nitrogenase reductase-like protein; Reviewed	94.65
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	94.64
PRK06761	282	hypothetical protein; Provisional	94.63
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	94.63
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	94.63
PRK08769	319	DNA polymerase III subunit delta'; Validated	94.61
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	94.61
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	94.61
cd02117	212	NifH_like This family contains the NifH (iron prot	94.6
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	94.6
PRK08356	195	hypothetical protein; Provisional	94.6
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	94.6
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	94.6
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	94.59
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	94.59
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	94.59
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	94.58
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	94.58
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	94.58
TIGR01026	440	fliI_yscN ATPase FliI/YscN family. This family of	94.58
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	94.58
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	94.57
PRK09302	509	circadian clock protein KaiC; Reviewed	94.57
PRK13409	590	putative ATPase RIL; Provisional	94.55
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	94.55
PHA02530	300	pseT polynucleotide kinase; Provisional	94.54
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	94.54
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	94.53
PF13245	76	AAA_19: Part of AAA domain	94.53
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	94.52
PRK08699	325	DNA polymerase III subunit delta'; Validated	94.5
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	94.5
COG0714	329	MoxR-like ATPases [General function prediction onl	94.5
PRK03731	171	aroL shikimate kinase II; Reviewed	94.48
COG3638	258	ABC-type phosphate/phosphonate transport system, A	94.48
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	94.46
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	94.46
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	94.46
PRK13695	174	putative NTPase; Provisional	94.44
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	94.44
CHL00060	494	atpB ATP synthase CF1 beta subunit	94.43
cd02040	270	NifH NifH gene encodes component II (iron protein)	94.43
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	94.43
PRK01184	184	hypothetical protein; Provisional	94.42
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	94.41
cd03116	159	MobB Molybdenum is an essential trace element in t	94.41
PRK10875	615	recD exonuclease V subunit alpha; Provisional	94.38
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	94.38

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=1.5e-50  Score=415.95  Aligned_cols=253  Identities=26%  Similarity=0.425  Sum_probs=223.6

Q ss_pred             cccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCcc-ccCCcceeEEEEeCCCCCHHHHHHHH
Q 040110           85 LGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNF-VKFYFDCHAWVRVSNFYNFKRILDDI  163 (348)
Q Consensus        85 vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~-~~~~F~~~~wv~~~~~~~~~~~~~~i  163 (348)
                      ||.+..+   +.+++.|.      .++..+++|+||||+||||||++++|+.. ++++|+.++||++|+.++...++++|
T Consensus       161 VG~e~~~---~kl~~~L~------~d~~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~I  231 (889)
T KOG4658|consen  161 VGLETML---EKLWNRLM------EDDVGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTI  231 (889)
T ss_pred             ccHHHHH---HHHHHHhc------cCCCCEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHH
Confidence            9999999   99999999      33348999999999999999999999987 99999999999999999999999999


Q ss_pred             HHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhhh-cc--
Q 040110          164 MKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTS-IE--  240 (348)
Q Consensus       164 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~-~~--  240 (348)
                      +..++....  ........++...|.+.|+++||||||||||+..+|+.+..++|...+||||++|||+..||.. +.  
T Consensus       232 l~~l~~~~~--~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~  309 (889)
T KOG4658|consen  232 LERLGLLDE--EWEDKEEDELASKLLNLLEGKRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVD  309 (889)
T ss_pred             HHHhccCCc--ccchhhHHHHHHHHHHHhccCceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCC
Confidence            999988543  2333344789999999999999999999999999999999999999899999999999999998 33  


Q ss_pred             ----cC---------------------------------CCCc-CCCC-cccccCccccCC-HHHHHHHHHHhCCCCCCC
Q 040110          241 ----LE---------------------------------NGEK-NRHD-SALVGGPLIRIK-HETWQFFILHYGSTPLEN  280 (348)
Q Consensus       241 ----l~---------------------------------~~~C-~Lp~-~~~ig~~L~~~~-~~~w~~~~~~~~~~~~~~  280 (348)
                          ++                                 ..+| |||+ ++++|+.|+.+. ..+|+++.+.+.+.....
T Consensus       310 ~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~  389 (889)
T KOG4658|consen  310 YPIEVECLTPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAAD  389 (889)
T ss_pred             ccccccccCccccHHHHHHhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCC
Confidence                22                                 4677 9999 999999999999 779999999987762222


Q ss_pred             CC-CCcchhccc-cccCCCChhHHHHHhHhccCCCCceecHHHHHHHHHhcCCCCC---CCChHHHHHhhhcC
Q 040110          281 ET-EGPSVGLKL-VSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPG---NYDSEKMAEEYLKQ  348 (348)
Q Consensus       281 ~~-~~~~i~~~l-~s~~~Lp~~lk~cf~y~a~fp~~~~i~~~~Li~~W~aeG~i~~---~~~~e~~~~~y~~e  348 (348)
                      .+ ..+.+...+ +||+.||.++|+||+|||+||+||.|++++||.+|+|||||.+   +.+.++.|..|+.|
T Consensus       390 ~~~~~~~i~~iLklSyd~L~~~lK~CFLycalFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~  462 (889)
T KOG4658|consen  390 FSGMEESILPILKLSYDNLPEELKSCFLYCALFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEE  462 (889)
T ss_pred             CCchhhhhHHhhhccHhhhhHHHHHHHHhhccCCcccccchHHHHHHHHhccCcCccccccchhcchHHHHHH
Confidence            22 234665666 9999999889999999999999999999999999999999998   77889999999864

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=100.00  E-value=8.5e-43  Score=321.54  Aligned_cols=240  Identities=30%  Similarity=0.418  Sum_probs=191.8

Q ss_pred             cccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHH
Q 040110           87 LQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKS  166 (348)
Q Consensus        87 r~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~  166 (348)
                      ||.++   ++|.+.|.    ...++.++|+|+||||+||||||.+++++..++++|+.++|+.+++..+...++..|+.+
T Consensus         1 re~~~---~~l~~~L~----~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~   73 (287)
T PF00931_consen    1 REKEI---EKLKDWLL----DNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQ   73 (287)
T ss_dssp             -HHHH---HHHHHHHH----TTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHH
T ss_pred             CHHHH---HHHHHHhh----CCCCCeEEEEEEcCCcCCcceeeeeccccccccccccccccccccccccccccccccccc
Confidence            67778   99999999    334789999999999999999999999888889999999999999999999999999999


Q ss_pred             hCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhhh-------c
Q 040110          167 LMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTS-------I  239 (348)
Q Consensus       167 l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~-------~  239 (348)
                      ++..... .....+..++...+++.|+++++||||||||+...|+.+...++....||+||||||+..++..       +
T Consensus        74 l~~~~~~-~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~  152 (287)
T PF00931_consen   74 LGEPDSS-ISDPKDIEELQDQLRELLKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVI  152 (287)
T ss_dssp             HTCC-ST-SSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEE
T ss_pred             ccccccc-cccccccccccccchhhhccccceeeeeeecccccccccccccccccccccccccccccccccccccccccc
Confidence            9987432 1245688889999999999999999999999999999998888877789999999999998865       3


Q ss_pred             ccC---------------------------------CCCc-CCCC-cccccCccccCC-HHHHHHHHHHhCCCCCCCCCC
Q 040110          240 ELE---------------------------------NGEK-NRHD-SALVGGPLIRIK-HETWQFFILHYGSTPLENETE  283 (348)
Q Consensus       240 ~l~---------------------------------~~~C-~Lp~-~~~ig~~L~~~~-~~~w~~~~~~~~~~~~~~~~~  283 (348)
                      +++                                 ...| |+|+ ++++|+.|+.+. ..+|+.+++.+..........
T Consensus       153 ~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~  232 (287)
T PF00931_consen  153 ELEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDY  232 (287)
T ss_dssp             ECSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGS
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            333                                 2456 9999 999999996654 778999888866551222223


Q ss_pred             Ccchhccc-cccCCCChhHHHHHhHhccCCCCceecHHHHHHHHHhcCCCCC
Q 040110          284 GPSVGLKL-VSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPG  334 (348)
Q Consensus       284 ~~~i~~~l-~s~~~Lp~~lk~cf~y~a~fp~~~~i~~~~Li~~W~aeG~i~~  334 (348)
                      ...+...+ +||+.||+++|+||+|||+||+++.|+++.|+++|+|||||++
T Consensus       233 ~~~~~~~l~~s~~~L~~~~~~~f~~L~~f~~~~~i~~~~li~lW~~e~~i~~  284 (287)
T PF00931_consen  233 DRSVFSALELSYDSLPDELRRCFLYLSIFPEGVPIPRERLIRLWVAEGFISS  284 (287)
T ss_dssp             CHHHHHHHHHHHHSSHTCCHHHHHHGGGSGTTS-EEHHHHHHHHTT-HHTC-
T ss_pred             cccccccceechhcCCccHHHHHhhCcCCCCCceECHHHHHHHHHHCCCCcc
Confidence            46676777 9999999999999999999999999999999999999999975

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>PLN03210 Resistant to P

Probab=99.97  E-value=2.2e-30  Score=278.25  Aligned_cols=226  Identities=17%  Similarity=0.200  Sum_probs=175.4

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEe---CCC------
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRV---SNF------  153 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~---~~~------  153 (348)
                      .+|||+..+   +++..+|.    ...+.+++++|+||||+||||||+++|+.  +..+|+..+|+..   +..      
T Consensus       185 ~~vG~~~~l---~~l~~lL~----l~~~~~~vvgI~G~gGiGKTTLA~~l~~~--l~~~F~g~vfv~~~~v~~~~~~~~~  255 (1153)
T PLN03210        185 DFVGIEDHI---AKMSSLLH----LESEEVRMVGIWGSSGIGKTTIARALFSR--LSRQFQSSVFIDRAFISKSMEIYSS  255 (1153)
T ss_pred             cccchHHHH---HHHHHHHc----cccCceEEEEEEcCCCCchHHHHHHHHHH--HhhcCCeEEEeeccccccchhhccc
Confidence            899999999   99999887    44567899999999999999999999998  8889998887742   111      


Q ss_pred             -----CC-HHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEE
Q 040110          154 -----YN-FKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRAL  227 (348)
Q Consensus       154 -----~~-~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIl  227 (348)
                           ++ ...++.+++..+....   ......    ...+++.|+++|+||||||||+..+|+.+.....+.++||+||
T Consensus       256 ~~~~~~~~~~~l~~~~l~~il~~~---~~~~~~----~~~~~~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrII  328 (1153)
T PLN03210        256 ANPDDYNMKLHLQRAFLSEILDKK---DIKIYH----LGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRII  328 (1153)
T ss_pred             ccccccchhHHHHHHHHHHHhCCC---CcccCC----HHHHHHHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEE
Confidence                 11 1234455555543321   111111    2457888999999999999999999999988777777899999


Q ss_pred             EEeCChhhhhh------cccC--------------------------------CCCc-CCCC-cccccCccccCCHHHHH
Q 040110          228 ITVGPHNILTS------IELE--------------------------------NGEK-NRHD-SALVGGPLIRIKHETWQ  267 (348)
Q Consensus       228 vTTR~~~v~~~------~~l~--------------------------------~~~C-~Lp~-~~~ig~~L~~~~~~~w~  267 (348)
                      ||||+..++..      |.++                                ...| |||+ ++++|+.|+.++.++|+
T Consensus       329 iTTrd~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~~~~W~  408 (1153)
T PLN03210        329 VITKDKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGSYLRGRDKEDWM  408 (1153)
T ss_pred             EEeCcHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCCHHHHH
Confidence            99999999864      3333                                2456 9999 99999999998899999


Q ss_pred             HHHHHhCCCCCCCCCCCcchhccc-cccCCCCh-hHHHHHhHhccCCCCceecHHHHHHHHHhcCCCC
Q 040110          268 FFILHYGSTPLENETEGPSVGLKL-VSLSELPF-PLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRP  333 (348)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~~i~~~l-~s~~~Lp~-~lk~cf~y~a~fp~~~~i~~~~Li~~W~aeG~i~  333 (348)
                      .+++++... ..     ..|...+ +||++|++ ..|.||+++|+||.+..++   .+..|+|++...
T Consensus       409 ~~l~~L~~~-~~-----~~I~~~L~~SYd~L~~~~~k~~Fl~ia~ff~~~~~~---~v~~~l~~~~~~  467 (1153)
T PLN03210        409 DMLPRLRNG-LD-----GKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVN---DIKLLLANSDLD  467 (1153)
T ss_pred             HHHHHHHhC-cc-----HHHHHHHHHhhhccCccchhhhhheehhhcCCCCHH---HHHHHHHhcCCC
Confidence            999998654 21     3465677 99999987 4999999999999987654   477788876543

syringae 6; Provisional

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.99  E-value=4.3e-09  Score=101.47  Aligned_cols=123  Identities=16%  Similarity=0.172  Sum_probs=86.7

Q ss_pred             ccccCcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHH
Q 040110           78 EEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFK  157 (348)
Q Consensus        78 ~~~~~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  157 (348)
                      .+.++.++||+++.   ++|...|...  ........+.|+|++|+|||++++.++++.......-..+++++....+..
T Consensus        26 ~~~P~~l~~Re~e~---~~l~~~l~~~--~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~  100 (394)
T PRK00411         26 DYVPENLPHREEQI---EELAFALRPA--LRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRY  100 (394)
T ss_pred             CCcCCCCCCHHHHH---HHHHHHHHHH--hCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHH
Confidence            34445899999999   9999988521  112233456799999999999999999873222212245667777777888


Q ss_pred             HHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhc--CCeEEEEEeCCCCh
Q 040110          158 RILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT--NKKYFTVLDDVWIE  207 (348)
Q Consensus       158 ~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVLDdv~~~  207 (348)
                      .++..|+.++.....  .....+..++...+.+.+.  ++..+||||+++..
T Consensus       101 ~~~~~i~~~l~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l  150 (394)
T PRK00411        101 AIFSEIARQLFGHPP--PSSGLSFDELFDKIAEYLDERDRVLIVALDDINYL  150 (394)
T ss_pred             HHHHHHHHHhcCCCC--CCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHh
Confidence            999999999976311  1223456777788888775  35689999999763

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.89  E-value=1.3e-08  Score=97.06  Aligned_cols=123  Identities=17%  Similarity=0.132  Sum_probs=84.8

Q ss_pred             cccccCcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCcccc-CC--c-ceeEEEEeCC
Q 040110           77 TEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVK-FY--F-DCHAWVRVSN  152 (348)
Q Consensus        77 ~~~~~~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~-~~--F-~~~~wv~~~~  152 (348)
                      +.+.++.++||+.++   ++|...|.+.-  .......+.|+|++|+|||++++.+++..... ..  . -..+|+++..
T Consensus        10 ~~~~p~~l~gRe~e~---~~l~~~l~~~~--~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~   84 (365)
T TIGR02928        10 PDYVPDRIVHRDEQI---EELAKALRPIL--RGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQI   84 (365)
T ss_pred             CCCCCCCCCCcHHHH---HHHHHHHHHHH--cCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCC
Confidence            445556899999999   99999986311  12234467899999999999999999762110 11  1 1356777777


Q ss_pred             CCCHHHHHHHHHHHhC---CCCCccccCCCCHHHHHHHHHHHhc--CCeEEEEEeCCCCh
Q 040110          153 FYNFKRILDDIMKSLM---PTSSWLKIMGKDYKSEKTILRDYLT--NKKYFTVLDDVWIE  207 (348)
Q Consensus       153 ~~~~~~~~~~i~~~l~---~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVLDdv~~~  207 (348)
                      ..+...++..|+.++.   ...   .....+..+....+.+.+.  +++++||||+++..
T Consensus        85 ~~~~~~~~~~i~~~l~~~~~~~---~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L  141 (365)
T TIGR02928        85 LDTLYQVLVELANQLRGSGEEV---PTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYL  141 (365)
T ss_pred             CCCHHHHHHHHHHHHhhcCCCC---CCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhh
Confidence            7778889999999984   221   1122345566666766663  46889999999765

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.84  E-value=1.1e-08  Score=82.57  Aligned_cols=114  Identities=14%  Similarity=0.191  Sum_probs=79.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCC-----cceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFY-----FDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEK  185 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~-----F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~  185 (348)
                      +.+++.|+|.+|+|||++++.+.+.  ....     -..++|+.+....+...+...|+..++...    ....+..++.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~----~~~~~~~~l~   76 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQ--LNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPL----KSRQTSDELR   76 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHH--HHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SS----SSTS-HHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHH--hHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccc----cccCCHHHHH
Confidence            3457889999999999999999887  3221     235679998888899999999999999873    2345778888


Q ss_pred             HHHHHHhcCCe-EEEEEeCCCCh---hhHHHHHhhCCCCCCCcEEEEEeCC
Q 040110          186 TILRDYLTNKK-YFTVLDDVWIE---KIWDDLREALPDNQIGSRALITVGP  232 (348)
Q Consensus       186 ~~l~~~L~~kr-~LlVLDdv~~~---~~~~~l~~~l~~~~~gskIlvTTR~  232 (348)
                      +.+.+.+...+ .+||+|++...   ..++.+.... + ..+.++|+..+.
T Consensus        77 ~~~~~~l~~~~~~~lviDe~~~l~~~~~l~~l~~l~-~-~~~~~vvl~G~~  125 (131)
T PF13401_consen   77 SLLIDALDRRRVVLLVIDEADHLFSDEFLEFLRSLL-N-ESNIKVVLVGTP  125 (131)
T ss_dssp             HHHHHHHHHCTEEEEEEETTHHHHTHHHHHHHHHHT-C-SCBEEEEEEESS
T ss_pred             HHHHHHHHhcCCeEEEEeChHhcCCHHHHHHHHHHH-h-CCCCeEEEEECh
Confidence            88888887654 59999999654   2334443333 3 556677776554

>PF05729 NACHT: NACHT domain

Probab=98.82  E-value=2.3e-08  Score=83.84  Aligned_cols=113  Identities=19%  Similarity=0.229  Sum_probs=67.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCC----cceeEEEEeCCCCCHH---HHHHHHHHHhCCCCCccccCCCCHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFY----FDCHAWVRVSNFYNFK---RILDDIMKSLMPTSSWLKIMGKDYKSEK  185 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~----F~~~~wv~~~~~~~~~---~~~~~i~~~l~~~~~~~~~~~~~~~~~~  185 (348)
                      +++.|+|.+|+||||+++.++........    +...+|+.........   .+...|..+.....       .....  
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~-------~~~~~--   71 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESI-------APIEE--   71 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccch-------hhhHH--
Confidence            47889999999999999999876332222    4456677665443322   34444444443321       11111  


Q ss_pred             HHHHHHh-cCCeEEEEEeCCCChhh---------HHHHH-hhCCC-CCCCcEEEEEeCChhh
Q 040110          186 TILRDYL-TNKKYFTVLDDVWIEKI---------WDDLR-EALPD-NQIGSRALITVGPHNI  235 (348)
Q Consensus       186 ~~l~~~L-~~kr~LlVLDdv~~~~~---------~~~l~-~~l~~-~~~gskIlvTTR~~~v  235 (348)
                       .+...+ ..++++||||++++...         +..+. ..++. ..++++++||||....
T Consensus        72 -~~~~~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~  132 (166)
T PF05729_consen   72 -LLQELLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAF  132 (166)
T ss_pred             -HHHHHHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChH
Confidence             222222 56899999999975421         22222 22332 2468999999998777

>PF13173 AAA_14: AAA domain

Probab=98.70  E-value=4.2e-08  Score=79.34  Aligned_cols=102  Identities=14%  Similarity=0.237  Sum_probs=69.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      .+++.|.|+.|+|||||+++++.+..   ....+++++..........                    +.+ ..+.+.+.
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~~--------------------~~~-~~~~~~~~   57 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRLA--------------------DPD-LLEYFLEL   57 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHHh--------------------hhh-hHHHHHHh
Confidence            35789999999999999999997733   2235666655433221100                    000 23334444


Q ss_pred             hcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhh
Q 040110          192 LTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILT  237 (348)
Q Consensus       192 L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~  237 (348)
                      ...++.+++||++....+|......+.+..+..+|++|+.+.....
T Consensus        58 ~~~~~~~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~  103 (128)
T PF13173_consen   58 IKPGKKYIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGSSSSLLS  103 (128)
T ss_pred             hccCCcEEEEehhhhhccHHHHHHHHHHhccCceEEEEccchHHHh
Confidence            4457889999999998888888777776556689999999877764

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=98.69  E-value=2e-07  Score=75.87  Aligned_cols=123  Identities=15%  Similarity=0.089  Sum_probs=69.4

Q ss_pred             cccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHH
Q 040110           85 LGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIM  164 (348)
Q Consensus        85 vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~  164 (348)
                      +|++...   +.+...+.      ......+.|+|++|+|||++++.+++...  ..-..++++..............+.
T Consensus         1 ~~~~~~~---~~i~~~~~------~~~~~~v~i~G~~G~GKT~l~~~i~~~~~--~~~~~v~~~~~~~~~~~~~~~~~~~   69 (151)
T cd00009           1 VGQEEAI---EALREALE------LPPPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDLLEGLVVAELFG   69 (151)
T ss_pred             CchHHHH---HHHHHHHh------CCCCCeEEEECCCCCCHHHHHHHHHHHhh--cCCCCeEEEehhhhhhhhHHHHHhh
Confidence            3667777   78888776      22445788999999999999999998832  2223455665443332211111000


Q ss_pred             HHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh-----hhHHHHHhhCCCC---CCCcEEEEEeCChh
Q 040110          165 KSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE-----KIWDDLREALPDN---QIGSRALITVGPHN  234 (348)
Q Consensus       165 ~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~-----~~~~~l~~~l~~~---~~gskIlvTTR~~~  234 (348)
                      ..                ............+..++++||++..     ..+..+...+...   ..+..||+||....
T Consensus        70 ~~----------------~~~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          70 HF----------------LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             hh----------------hHhHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence            00                0011112223456789999999853     2233333333221   35778888887654

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=98.65  E-value=5.1e-07  Score=82.32  Aligned_cols=96  Identities=17%  Similarity=0.222  Sum_probs=62.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      +..++.|+|++|+|||||++.+++..... .+ ..+|+ +....+..+++..|+..++.+..     ..+.......+..
T Consensus        42 ~~~~~~l~G~~G~GKTtl~~~l~~~l~~~-~~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~-----~~~~~~~~~~l~~  113 (269)
T TIGR03015        42 REGFILITGEVGAGKTTLIRNLLKRLDQE-RV-VAAKL-VNTRVDAEDLLRMVAADFGLETE-----GRDKAALLRELED  113 (269)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHhcCCC-Ce-EEeee-eCCCCCHHHHHHHHHHHcCCCCC-----CCCHHHHHHHHHH
Confidence            34578899999999999999999883321 11 22233 33455778899999998877522     2233333333333


Q ss_pred             H----h-cCCeEEEEEeCCCCh--hhHHHHH
Q 040110          191 Y----L-TNKKYFTVLDDVWIE--KIWDDLR  214 (348)
Q Consensus       191 ~----L-~~kr~LlVLDdv~~~--~~~~~l~  214 (348)
                      .    + .+++.+||+||++..  ..++.+.
T Consensus       114 ~l~~~~~~~~~~vliiDe~~~l~~~~~~~l~  144 (269)
T TIGR03015       114 FLIEQFAAGKRALLVVDEAQNLTPELLEELR  144 (269)
T ss_pred             HHHHHHhCCCCeEEEEECcccCCHHHHHHHH
Confidence            2    2 568899999999875  3455554

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.64  E-value=7.4e-08  Score=86.63  Aligned_cols=103  Identities=10%  Similarity=-0.022  Sum_probs=67.2

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC--CCHHHHHHHH-----HHHh
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF--YNFKRILDDI-----MKSL  167 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~--~~~~~~~~~i-----~~~l  167 (348)
                      .+.++.+.+-    . .-..++|+|++|+|||||++.++++.... +|+..+|+.+.++  .++.++++.+     +..+
T Consensus         4 ~~~id~~~~i----~-~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~   77 (249)
T cd01128           4 TRVVDLFAPI----G-KGQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTF   77 (249)
T ss_pred             hhheeeeccc----C-CCCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecC
Confidence            3455666521    1 22367899999999999999999985444 8999999997766  7999999999     3333


Q ss_pred             CCCCCccccCCCCHHHHHHHHHHH-hcCCeEEEEEeCCCC
Q 040110          168 MPTSSWLKIMGKDYKSEKTILRDY-LTNKKYFTVLDDVWI  206 (348)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVLDdv~~  206 (348)
                      +.+.   .....-..........+ -.+++.+|++|++..
T Consensus        78 ~~~~---~~~~~~~~~~~~~a~~~~~~G~~vll~iDei~r  114 (249)
T cd01128          78 DEPP---ERHVQVAEMVLEKAKRLVEHGKDVVILLDSITR  114 (249)
T ss_pred             CCCH---HHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHH
Confidence            3210   00001111222333332 247899999999954

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=98.61  E-value=7e-08  Score=82.57  Aligned_cols=48  Identities=15%  Similarity=0.233  Sum_probs=32.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .||||+++.   +++...|. .  ......+.+.|+|.+|+|||+|.++++...
T Consensus         1 ~fvgR~~e~---~~l~~~l~-~--~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~   48 (185)
T PF13191_consen    1 QFVGREEEI---ERLRDLLD-A--AQSGSPRNLLLTGESGSGKTSLLRALLDRL   48 (185)
T ss_dssp             --TT-HHHH---HHHHHTTG-G--TSS-----EEE-B-TTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHHH---HHHHHHHH-H--HHcCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            489999999   99999994 1  224455789999999999999999998883

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=98.57  E-value=7.2e-08  Score=85.38  Aligned_cols=43  Identities=21%  Similarity=0.383  Sum_probs=35.3

Q ss_pred             ccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           84 LLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        84 ~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |+||+.++   +.|.+++.      ......+.|+|+.|+|||+|++.+.+.
T Consensus         1 F~gR~~el---~~l~~~l~------~~~~~~~~l~G~rg~GKTsLl~~~~~~   43 (234)
T PF01637_consen    1 FFGREKEL---EKLKELLE------SGPSQHILLYGPRGSGKTSLLKEFINE   43 (234)
T ss_dssp             S-S-HHHH---HHHHHCHH------H--SSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCHHHHH---HHHHHHHH------hhcCcEEEEEcCCcCCHHHHHHHHHHH
Confidence            79999999   99999887      334567889999999999999999987

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PTZ00202 tuzin; Provisional

Probab=98.54  E-value=2e-06  Score=81.91  Aligned_cols=100  Identities=13%  Similarity=0.137  Sum_probs=69.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .|+||+.++   ..|...|...   +....+++.|+|++|+|||||++.+.....    + ..++++..   +..+++..
T Consensus       263 ~FVGReaEl---a~Lr~VL~~~---d~~~privvLtG~~G~GKTTLlR~~~~~l~----~-~qL~vNpr---g~eElLr~  328 (550)
T PTZ00202        263 QFVSREAEE---SWVRQVLRRL---DTAHPRIVVFTGFRGCGKSSLCRSAVRKEG----M-PAVFVDVR---GTEDTLRS  328 (550)
T ss_pred             CCCCcHHHH---HHHHHHHhcc---CCCCceEEEEECCCCCCHHHHHHHHHhcCC----c-eEEEECCC---CHHHHHHH
Confidence            999999999   9999888622   223456899999999999999999987632    2 23333222   67999999


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHHHHHh-----c-CCeEEEEEe
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTILRDYL-----T-NKKYFTVLD  202 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L-----~-~kr~LlVLD  202 (348)
                      ++.+|+.+..      ....++...|.+.|     . +++.+||+-
T Consensus       329 LL~ALGV~p~------~~k~dLLrqIqeaLl~~~~e~GrtPVLII~  368 (550)
T PTZ00202        329 VVKALGVPNV------EACGDLLDFISEACRRAKKMNGETPLLVLK  368 (550)
T ss_pred             HHHHcCCCCc------ccHHHHHHHHHHHHHHHHHhCCCCEEEEEE
Confidence            9999997421      22244445555444     2 556666653

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.46  E-value=2.4e-07  Score=87.37  Aligned_cols=101  Identities=11%  Similarity=0.056  Sum_probs=66.8

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC--CHHHHHHHHHHHhCCCCC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY--NFKRILDDIMKSLMPTSS  172 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~--~~~~~~~~i~~~l~~~~~  172 (348)
                      -++++++.+-    ..+- ..+|+|++|+||||||+.+|+..... +|+.++||.+.+..  .+.++++.+...+-....
T Consensus       157 ~rvID~l~PI----GkGQ-R~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~  230 (416)
T PRK09376        157 TRIIDLIAPI----GKGQ-RGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTF  230 (416)
T ss_pred             eeeeeeeccc----ccCc-eEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECC
Confidence            4667777632    2222 46789999999999999999984444 89999999998887  788888888643222211


Q ss_pred             ccccCCCCHH-------HHHHHHHHH-hcCCeEEEEEeCCCC
Q 040110          173 WLKIMGKDYK-------SEKTILRDY-LTNKKYFTVLDDVWI  206 (348)
Q Consensus       173 ~~~~~~~~~~-------~~~~~l~~~-L~~kr~LlVLDdv~~  206 (348)
                           +....       .....-..+ -.++++||++|++..
T Consensus       231 -----d~~~~~~~~~a~~~ie~Ae~~~e~G~dVlL~iDsItR  267 (416)
T PRK09376        231 -----DEPAERHVQVAEMVIEKAKRLVEHGKDVVILLDSITR  267 (416)
T ss_pred             -----CCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEChHH
Confidence                 11111       111112222 257899999999953

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=98.44  E-value=6.4e-07  Score=83.68  Aligned_cols=110  Identities=19%  Similarity=0.194  Sum_probs=68.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++|-...+   .++++         ...+.-..+||++|+||||||+.+...  ....|.     .++-..+-.+    
T Consensus        31 HLlg~~~~l---rr~v~---------~~~l~SmIl~GPPG~GKTTlA~liA~~--~~~~f~-----~~sAv~~gvk----   87 (436)
T COG2256          31 HLLGEGKPL---RRAVE---------AGHLHSMILWGPPGTGKTTLARLIAGT--TNAAFE-----ALSAVTSGVK----   87 (436)
T ss_pred             hhhCCCchH---HHHHh---------cCCCceeEEECCCCCCHHHHHHHHHHh--hCCceE-----EeccccccHH----
Confidence            667776666   66665         334555668999999999999999987  555552     2222222111    


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHH-HHHhcCCeEEEEEeCCCC--hhhHHHHHhhCCCCCCCcEEEE--EeCChhh
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTIL-RDYLTNKKYFTVLDDVWI--EKIWDDLREALPDNQIGSRALI--TVGPHNI  235 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l-~~~L~~kr~LlVLDdv~~--~~~~~~l~~~l~~~~~gskIlv--TTR~~~v  235 (348)
                                       ++....+.- +....+++.+|.+|.|..  ..+-+.|...   ..+|.-|+|  ||.|..-
T Consensus        88 -----------------dlr~i~e~a~~~~~~gr~tiLflDEIHRfnK~QQD~lLp~---vE~G~iilIGATTENPsF  145 (436)
T COG2256          88 -----------------DLREIIEEARKNRLLGRRTILFLDEIHRFNKAQQDALLPH---VENGTIILIGATTENPSF  145 (436)
T ss_pred             -----------------HHHHHHHHHHHHHhcCCceEEEEehhhhcChhhhhhhhhh---hcCCeEEEEeccCCCCCe
Confidence                             222222222 222347899999999963  3444555444   456888887  8887653

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.43  E-value=2.5e-06  Score=90.87  Aligned_cols=134  Identities=13%  Similarity=0.096  Sum_probs=82.6

Q ss_pred             CcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-CCHHHHH
Q 040110           82 DALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRIL  160 (348)
Q Consensus        82 ~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~  160 (348)
                      ..+|-|+...   +.+-.         ....+++.|.|++|.||||++.+..+.      ++.++|+++... .+...+.
T Consensus        14 ~~~~~R~rl~---~~l~~---------~~~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~~~f~   75 (903)
T PRK04841         14 HNTVVRERLL---AKLSG---------ANNYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQPERFA   75 (903)
T ss_pred             cccCcchHHH---HHHhc---------ccCCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCHHHHH
Confidence            3677777666   44432         235678999999999999999998754      226889999644 4666777


Q ss_pred             HHHHHHhCCCCCc--c-------ccCCCCHHHHHHHHHHHhc--CCeEEEEEeCCCCh--hhHH-HHHhhCCCCCCCcEE
Q 040110          161 DDIMKSLMPTSSW--L-------KIMGKDYKSEKTILRDYLT--NKKYFTVLDDVWIE--KIWD-DLREALPDNQIGSRA  226 (348)
Q Consensus       161 ~~i~~~l~~~~~~--~-------~~~~~~~~~~~~~l~~~L~--~kr~LlVLDdv~~~--~~~~-~l~~~l~~~~~gskI  226 (348)
                      ..++..+......  +       .....+...+...+...+.  +.+++|||||+...  .... .+...+.....+.++
T Consensus        76 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~l  155 (903)
T PRK04841         76 SYLIAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTL  155 (903)
T ss_pred             HHHHHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEE
Confidence            7777777422111  0       0111233334444444443  57899999999653  2222 232222333446688


Q ss_pred             EEEeCCh
Q 040110          227 LITVGPH  233 (348)
Q Consensus       227 lvTTR~~  233 (348)
                      |||||..
T Consensus       156 v~~sR~~  162 (903)
T PRK04841        156 VVLSRNL  162 (903)
T ss_pred             EEEeCCC
Confidence            8999984

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.41  E-value=2.8e-06  Score=86.02  Aligned_cols=195  Identities=20%  Similarity=0.156  Sum_probs=116.3

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCcc---------ccCCC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSWL---------KIMGK  179 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~---------~~~~~  179 (348)
                      .+.+.+.|..+.|.|||||+.+....  ... =..+.|.+++.. .++..+..-++..++...+..         .....
T Consensus        35 ~~~RL~li~APAGfGKttl~aq~~~~--~~~-~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~~  111 (894)
T COG2909          35 NDYRLILISAPAGFGKTTLLAQWREL--AAD-GAAVAWLSLDESDNDPARFLSYLIAALQQATPTLGDEAQTLLQKHQYV  111 (894)
T ss_pred             CCceEEEEeCCCCCcHHHHHHHHHHh--cCc-ccceeEeecCCccCCHHHHHHHHHHHHHHhCccccHHHHHHHHhcccc
Confidence            46789999999999999999998763  222 236899998655 578888888888887432210         11223


Q ss_pred             CHHHHHHHHHHHhcC--CeEEEEEeCCCC---h---hhHHHHHhhCCCCCCCcEEEEEeCChhhhhh---------cccC
Q 040110          180 DYKSEKTILRDYLTN--KKYFTVLDDVWI---E---KIWDDLREALPDNQIGSRALITVGPHNILTS---------IELE  242 (348)
Q Consensus       180 ~~~~~~~~l~~~L~~--kr~LlVLDdv~~---~---~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~---------~~l~  242 (348)
                      +...+...+..-|.+  ++.+|||||..-   .   ..+..+....|   .+-..+||||++.-...         ..++
T Consensus       112 ~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P---~~l~lvv~SR~rP~l~la~lRlr~~llEi~  188 (894)
T COG2909         112 SLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAP---ENLTLVVTSRSRPQLGLARLRLRDELLEIG  188 (894)
T ss_pred             cHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCC---CCeEEEEEeccCCCCcccceeehhhHHhcC
Confidence            444455555555543  689999999642   2   23444444444   46789999999875554         2222


Q ss_pred             -------CCCc--------CCCC-cccccCccccCCHHHHHHHHHHhCCCCCC-C------CCCC----cchhccc--cc
Q 040110          243 -------NGEK--------NRHD-SALVGGPLIRIKHETWQFFILHYGSTPLE-N------ETEG----PSVGLKL--VS  293 (348)
Q Consensus       243 -------~~~C--------~Lp~-~~~ig~~L~~~~~~~w~~~~~~~~~~~~~-~------~~~~----~~i~~~l--~s  293 (348)
                             .++|        ++|+ ...+..+...  .+-|-..++-..-. .. +      .+.+    ..+..-+  --
T Consensus       189 ~~~Lrf~~eE~~~fl~~~~~l~Ld~~~~~~L~~~--teGW~~al~L~aLa-~~~~~~~~q~~~~LsG~~~~l~dYL~eeV  265 (894)
T COG2909         189 SEELRFDTEEAAAFLNDRGSLPLDAADLKALYDR--TEGWAAALQLIALA-LRNNTSAEQSLRGLSGAASHLSDYLVEEV  265 (894)
T ss_pred             hHhhcCChHHHHHHHHHcCCCCCChHHHHHHHhh--cccHHHHHHHHHHH-ccCCCcHHHHhhhccchHHHHHHHHHHHH
Confidence                   2222        4665 2222222222  34444443331100 11 0      0111    1232333  55


Q ss_pred             cCCCChhHHHHHhHhccCCC
Q 040110          294 LSELPFPLIVCCLYFCVFPT  313 (348)
Q Consensus       294 ~~~Lp~~lk~cf~y~a~fp~  313 (348)
                      ++.||+++|..++-||+++.
T Consensus       266 ld~Lp~~l~~FLl~~svl~~  285 (894)
T COG2909         266 LDRLPPELRDFLLQTSVLSR  285 (894)
T ss_pred             HhcCCHHHHHHHHHHHhHHH
Confidence            88999999999999999876

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=98.41  E-value=1.1e-06  Score=83.45  Aligned_cols=120  Identities=19%  Similarity=0.181  Sum_probs=90.9

Q ss_pred             cccccCcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcc--eeEEEEeCCCC
Q 040110           77 TEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD--CHAWVRVSNFY  154 (348)
Q Consensus        77 ~~~~~~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~  154 (348)
                      +.+.++.+.+|+.++   +.+...|.+.-  ....+.-+.|+|.+|+|||+.++.+.+.  +.....  ..++|++-...
T Consensus        12 ~~~iP~~l~~Re~ei---~~l~~~l~~~~--~~~~p~n~~iyG~~GTGKT~~~~~v~~~--l~~~~~~~~~~yINc~~~~   84 (366)
T COG1474          12 EDYIPEELPHREEEI---NQLASFLAPAL--RGERPSNIIIYGPTGTGKTATVKFVMEE--LEESSANVEVVYINCLELR   84 (366)
T ss_pred             CCCCcccccccHHHH---HHHHHHHHHHh--cCCCCccEEEECCCCCCHhHHHHHHHHH--HHhhhccCceEEEeeeeCC
Confidence            455566899999999   99998886431  1112223778999999999999999988  443322  26889998889


Q ss_pred             CHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcC--CeEEEEEeCCCCh
Q 040110          155 NFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTN--KKYFTVLDDVWIE  207 (348)
Q Consensus       155 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~--kr~LlVLDdv~~~  207 (348)
                      +..+++..|+++++..    ........+....+.+.+..  +.+++|||++...
T Consensus        85 t~~~i~~~i~~~~~~~----p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L  135 (366)
T COG1474          85 TPYQVLSKILNKLGKV----PLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDAL  135 (366)
T ss_pred             CHHHHHHHHHHHcCCC----CCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhh
Confidence            9999999999999733    33355667788888888854  7899999999754

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=98.31  E-value=1.8e-06  Score=79.63  Aligned_cols=101  Identities=21%  Similarity=0.200  Sum_probs=63.8

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTIL  188 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  188 (348)
                      .....-+.+||++|+||||||+.+.+..+...    ..||..|-.....+-++.|+++-...                  
T Consensus       159 q~~ipSmIlWGppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~t~dvR~ife~aq~~------------------  216 (554)
T KOG2028|consen  159 QNRIPSMILWGPPGTGKTTLARLIASTSKKHS----YRFVELSATNAKTNDVRDIFEQAQNE------------------  216 (554)
T ss_pred             cCCCCceEEecCCCCchHHHHHHHHhhcCCCc----eEEEEEeccccchHHHHHHHHHHHHH------------------
Confidence            34555677899999999999999998843333    55676665443333334444332211                  


Q ss_pred             HHHhcCCeEEEEEeCCCC--hhhHHHHHhhCCCCCCCcEEEE--EeCChhh
Q 040110          189 RDYLTNKKYFTVLDDVWI--EKIWDDLREALPDNQIGSRALI--TVGPHNI  235 (348)
Q Consensus       189 ~~~L~~kr~LlVLDdv~~--~~~~~~l~~~l~~~~~gskIlv--TTR~~~v  235 (348)
                       ..+.++|.+|.+|.|..  ..+-+   ..||...+|+.++|  ||.+.+-
T Consensus       217 -~~l~krkTilFiDEiHRFNksQQD---~fLP~VE~G~I~lIGATTENPSF  263 (554)
T KOG2028|consen  217 -KSLTKRKTILFIDEIHRFNKSQQD---TFLPHVENGDITLIGATTENPSF  263 (554)
T ss_pred             -HhhhcceeEEEeHHhhhhhhhhhh---cccceeccCceEEEecccCCCcc
Confidence             12456899999999942  22322   34555677887777  7877653

>TIGR00767 rho transcription termination factor Rho

Probab=98.29  E-value=2.9e-06  Score=80.47  Aligned_cols=90  Identities=9%  Similarity=-0.046  Sum_probs=61.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC--CCHHHHHHHHHHHhCCCCCccccCCCCH----HHHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF--YNFKRILDDIMKSLMPTSSWLKIMGKDY----KSEKTI  187 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~--~~~~~~~~~i~~~l~~~~~~~~~~~~~~----~~~~~~  187 (348)
                      .++|+|++|+|||||++.+++..... +|+..+|+.+.+.  .++.++++.+...+-.....  .+....    ....+.
T Consensus       170 ~~~IvG~~g~GKTtL~~~i~~~I~~n-hfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d--~p~~~~~~va~~v~e~  246 (415)
T TIGR00767       170 RGLIVAPPKAGKTVLLQKIAQAITRN-HPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFD--EPASRHVQVAEMVIEK  246 (415)
T ss_pred             EEEEECCCCCChhHHHHHHHHhhccc-CCceEEEEEEcCCCCccHHHHHHHhhceEEEecCC--CChHHHHHHHHHHHHH
Confidence            57899999999999999999984333 7999999998866  78999999995544332211  011111    112222


Q ss_pred             HHHH-hcCCeEEEEEeCCCC
Q 040110          188 LRDY-LTNKKYFTVLDDVWI  206 (348)
Q Consensus       188 l~~~-L~~kr~LlVLDdv~~  206 (348)
                      ...+ -.+++++|++|++..
T Consensus       247 Ae~~~~~GkdVVLlIDEitR  266 (415)
T TIGR00767       247 AKRLVEHKKDVVILLDSITR  266 (415)
T ss_pred             HHHHHHcCCCeEEEEEChhH
Confidence            2222 257899999999954

Members of this family differ in the specificity of RNA binding.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.22  E-value=8.3e-06  Score=83.53  Aligned_cols=124  Identities=11%  Similarity=-0.003  Sum_probs=82.0

Q ss_pred             cccccCcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccc---cCCcc--eeEEEEeC
Q 040110           77 TEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFV---KFYFD--CHAWVRVS  151 (348)
Q Consensus        77 ~~~~~~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~---~~~F~--~~~wv~~~  151 (348)
                      +.++++.+.||+++.   ++|...|.+.- .+.....++-|+|++|+|||++++.|.+....   ....+  ..++|++.
T Consensus       750 ~DYVPD~LPhREeEI---eeLasfL~paI-kgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm  825 (1164)
T PTZ00112        750 LDVVPKYLPCREKEI---KEVHGFLESGI-KQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGM  825 (1164)
T ss_pred             cccCCCcCCChHHHH---HHHHHHHHHHH-hcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCC
Confidence            345556899999999   99998886321 11233357789999999999999999876311   11122  35677776


Q ss_pred             CCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcC---CeEEEEEeCCCCh
Q 040110          152 NFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTN---KKYFTVLDDVWIE  207 (348)
Q Consensus       152 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~---kr~LlVLDdv~~~  207 (348)
                      .-.+...++..|..+|....+   .......+....+...+..   ...+||||+++..
T Consensus       826 ~Lstp~sIYqvI~qqL~g~~P---~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L  881 (1164)
T PTZ00112        826 NVVHPNAAYQVLYKQLFNKKP---PNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYL  881 (1164)
T ss_pred             ccCCHHHHHHHHHHHHcCCCC---CccccHHHHHHHHHhhhhcccccceEEEeehHhhh
Confidence            667788889999988854321   1223344555556555522   2468999999743

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.18  E-value=8.9e-06  Score=76.54  Aligned_cols=49  Identities=20%  Similarity=0.243  Sum_probs=37.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|+|++...   +.+..++.... ........+.++|++|+|||+||+.+++.
T Consensus        26 ~~vG~~~~~---~~l~~~l~~~~-~~~~~~~~~ll~GppG~GKT~la~~ia~~   74 (328)
T PRK00080         26 EFIGQEKVK---ENLKIFIEAAK-KRGEALDHVLLYGPPGLGKTTLANIIANE   74 (328)
T ss_pred             HhcCcHHHH---HHHHHHHHHHH-hcCCCCCcEEEECCCCccHHHHHHHHHHH
Confidence            899999999   88777664210 11233456779999999999999999988

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.15  E-value=6e-05  Score=76.62  Aligned_cols=142  Identities=13%  Similarity=0.091  Sum_probs=83.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc---ceeEEEEeCC---CCCH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF---DCHAWVRVSN---FYNF  156 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F---~~~~wv~~~~---~~~~  156 (348)
                      .++|++..+   ..+.+.+.      ......+.|+|++|+||||||+.+++.......+   ...-|+.+..   ..+.
T Consensus       155 ~iiGqs~~~---~~l~~~ia------~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~  225 (615)
T TIGR02903       155 EIVGQERAI---KALLAKVA------SPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDP  225 (615)
T ss_pred             hceeCcHHH---HHHHHHHh------cCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCH
Confidence            789999999   88887776      2234468899999999999999998774333332   1233444432   1122


Q ss_pred             HHHHHHH---------------HHHhCCCCCc--------------cccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh
Q 040110          157 KRILDDI---------------MKSLMPTSSW--------------LKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE  207 (348)
Q Consensus       157 ~~~~~~i---------------~~~l~~~~~~--------------~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~  207 (348)
                      ..+...+               +...+.....              ......+ ...+..+.+.+.+++++++.|+.|..
T Consensus       226 ~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld-~~~Q~~Ll~~Le~~~v~~~~~~~~~~  304 (615)
T TIGR02903       226 REVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELD-PLLQNKLLKVLEDKRVEFSSSYYDPD  304 (615)
T ss_pred             HHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCC-HHHHHHHHHHHhhCeEEeecceeccC
Confidence            2221111               1111211000              0111122 33567888888888988887777654


Q ss_pred             --hhHHHHHhhCCCCCCCcEEEE--EeCChh
Q 040110          208 --KIWDDLREALPDNQIGSRALI--TVGPHN  234 (348)
Q Consensus       208 --~~~~~l~~~l~~~~~gskIlv--TTR~~~  234 (348)
                        ..|+.+...+....+...|++  ||++..
T Consensus       305 ~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~  335 (615)
T TIGR02903       305 DPNVPKYIKKLFEEGAPADFVLIGATTRDPE  335 (615)
T ss_pred             CcccchhhhhhcccCccceEEEEEecccccc
Confidence              457777766666555555666  666543

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.15  E-value=6.2e-06  Score=80.09  Aligned_cols=106  Identities=18%  Similarity=0.203  Sum_probs=61.8

Q ss_pred             cccccccccccHHH---HHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHH
Q 040110           83 ALLGLQSKIINLRN---LHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRI  159 (348)
Q Consensus        83 ~~vGr~~~~~~~~~---l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  159 (348)
                      .+||++..+   ..   +..++.      ......+.++|++|+||||||+.+++.  ....|     +.++......+-
T Consensus        13 d~vGq~~~v---~~~~~L~~~i~------~~~~~~ilL~GppGtGKTtLA~~ia~~--~~~~~-----~~l~a~~~~~~~   76 (413)
T PRK13342         13 EVVGQEHLL---GPGKPLRRMIE------AGRLSSMILWGPPGTGKTTLARIIAGA--TDAPF-----EALSAVTSGVKD   76 (413)
T ss_pred             HhcCcHHHh---CcchHHHHHHH------cCCCceEEEECCCCCCHHHHHHHHHHH--hCCCE-----EEEecccccHHH
Confidence            688887775   44   666665      233446778999999999999999987  33333     222211111111


Q ss_pred             HHHHHHHhCCCCCccccCCCCHHHHHHHHHHH-hcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEE
Q 040110          160 LDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY-LTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALI  228 (348)
Q Consensus       160 ~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlv  228 (348)
                      ++.++                     +..... ..+++.+|++|+++..  .+.+.+...+..   |+.+++
T Consensus        77 ir~ii---------------------~~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le~---~~iilI  124 (413)
T PRK13342         77 LREVI---------------------EEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVED---GTITLI  124 (413)
T ss_pred             HHHHH---------------------HHHHHhhhcCCceEEEEechhhhCHHHHHHHHHHhhc---CcEEEE
Confidence            12222                     222111 1357889999999864  455566555533   455555

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.11  E-value=1.6e-05  Score=74.94  Aligned_cols=44  Identities=18%  Similarity=0.289  Sum_probs=36.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|++...   +.+..++.      .+..+.+.++|++|+||||+|+.+.+.
T Consensus        16 ~~~g~~~~~---~~L~~~~~------~~~~~~lll~Gp~GtGKT~la~~~~~~   59 (337)
T PRK12402         16 DILGQDEVV---ERLSRAVD------SPNLPHLLVQGPPGSGKTAAVRALARE   59 (337)
T ss_pred             HhcCCHHHH---HHHHHHHh------CCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            689999999   99988887      223335779999999999999998876

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.07  E-value=0.0001  Score=67.38  Aligned_cols=219  Identities=11%  Similarity=0.029  Sum_probs=131.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCcccc-----CCcceeEEEEeCCCCCHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVK-----FYFDCHAWVRVSNFYNFK  157 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~-----~~F~~~~wv~~~~~~~~~  157 (348)
                      ..+|-..-...+++|.++|..   .......-+.|+|.+|.|||+++++..+..-..     ..+ .++.|.+....+..
T Consensus        35 rWIgY~~A~~~L~~L~~Ll~~---P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~-PVv~vq~P~~p~~~  110 (302)
T PF05621_consen   35 RWIGYPRAKEALDRLEELLEY---PKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERI-PVVYVQMPPEPDER  110 (302)
T ss_pred             CeecCHHHHHHHHHHHHHHhC---CcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccc-cEEEEecCCCCChH
Confidence            577766555445777777763   234556678999999999999999988653111     111 46667788889999


Q ss_pred             HHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcC-CeEEEEEeCCCCh---------hhHHHHHhhCCCCCCCcEEE
Q 040110          158 RILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTN-KKYFTVLDDVWIE---------KIWDDLREALPDNQIGSRAL  227 (348)
Q Consensus       158 ~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~-kr~LlVLDdv~~~---------~~~~~l~~~l~~~~~gskIl  227 (348)
                      .+...|+.+++.+..    ...+...+.......|+. +--+||+|.+.+.         ..++.+ ..+.+.-.=+-|.
T Consensus       111 ~~Y~~IL~~lgaP~~----~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~L-K~L~NeL~ipiV~  185 (302)
T PF05621_consen  111 RFYSAILEALGAPYR----PRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNAL-KFLGNELQIPIVG  185 (302)
T ss_pred             HHHHHHHHHhCcccC----CCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHH-HHHhhccCCCeEE
Confidence            999999999999843    344555666666666655 5668889999763         122222 3333323345566


Q ss_pred             EEeCChhhhhh--------cccCCCCcCCCCcccccCccccCCHHHHHHHHHHhCCC-CCCCCCCC--cchhccc-cccC
Q 040110          228 ITVGPHNILTS--------IELENGEKNRHDSALVGGPLIRIKHETWQFFILHYGST-PLENETEG--PSVGLKL-VSLS  295 (348)
Q Consensus       228 vTTR~~~v~~~--------~~l~~~~C~Lp~~~~ig~~L~~~~~~~w~~~~~~~~~~-~~~~~~~~--~~i~~~l-~s~~  295 (348)
                      |-|+.---+-.        |..-    .||       ..+.  .+++..++..+... .+.....+  ..++..| ...+
T Consensus       186 vGt~~A~~al~~D~QLa~RF~~~----~Lp-------~W~~--d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~  252 (302)
T PF05621_consen  186 VGTREAYRALRTDPQLASRFEPF----ELP-------RWEL--DEEFRRLLASFERALPLRKPSNLASPELARRIHERSE  252 (302)
T ss_pred             eccHHHHHHhccCHHHHhccCCc----cCC-------CCCC--CcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcC
Confidence            66654333222        2222    111       2222  56667777765433 12222222  3455566 6666


Q ss_pred             CCChhHHHHHhHhccC---CCCceecHHHHH
Q 040110          296 ELPFPLIVCCLYFCVF---PTDIELTTRQLC  323 (348)
Q Consensus       296 ~Lp~~lk~cf~y~a~f---p~~~~i~~~~Li  323 (348)
                      |+-.++.+.+..+|+.   ...-.|+.+.|-
T Consensus       253 G~iG~l~~ll~~aA~~AI~sG~E~It~~~l~  283 (302)
T PF05621_consen  253 GLIGELSRLLNAAAIAAIRSGEERITREILD  283 (302)
T ss_pred             CchHHHHHHHHHHHHHHHhcCCceecHHHHh
Confidence            7877877777777665   333446666554

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=98.04  E-value=5.6e-06  Score=79.74  Aligned_cols=107  Identities=14%  Similarity=0.145  Sum_probs=71.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .+++.+...   +.+...|.        ..+.+.++|++|+|||++|+.+++.......|+.+.||.+++.++..+++.-
T Consensus       176 d~~i~e~~l---e~l~~~L~--------~~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G  244 (459)
T PRK11331        176 DLFIPETTI---ETILKRLT--------IKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQG  244 (459)
T ss_pred             cccCCHHHH---HHHHHHHh--------cCCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcc
Confidence            677888888   99999888        1235778999999999999999988544557778889999999887776542


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHHHHHhc--CCeEEEEEeCCCCh
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTILRDYLT--NKKYFTVLDDVWIE  207 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVLDdv~~~  207 (348)
                      +.    ....  .. .....-..+.+.....  .++++||+|++...
T Consensus       245 ~r----P~~v--gy-~~~~G~f~~~~~~A~~~p~~~~vliIDEINRa  284 (459)
T PRK11331        245 YR----PNGV--GF-RRKDGIFYNFCQQAKEQPEKKYVFIIDEINRA  284 (459)
T ss_pred             cC----CCCC--Ce-EecCchHHHHHHHHHhcccCCcEEEEehhhcc
Confidence            21    1100  00 0001112223333332  36899999999654

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.04  E-value=6e-05  Score=70.45  Aligned_cols=123  Identities=11%  Similarity=0.133  Sum_probs=77.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc----cccCCcceeEEEE-eCCCCCHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN----FVKFYFDCHAWVR-VSNFYNFK  157 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~----~~~~~F~~~~wv~-~~~~~~~~  157 (348)
                      +++|.+...   +.+.+.+.    . ..-.....++|+.|+||||+|..+++..    ....|.|...|.. -+....+.
T Consensus         5 ~i~g~~~~~---~~l~~~~~----~-~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~   76 (313)
T PRK05564          5 TIIGHENIK---NRIKNSII----K-NRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVD   76 (313)
T ss_pred             hccCcHHHH---HHHHHHHH----c-CCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHH
Confidence            578888888   88888886    2 2233466789999999999999988742    1234556555544 23333433


Q ss_pred             HHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCC--ChhhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          158 RILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVW--IEKIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       158 ~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~--~~~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      + ++++...+...                    -..+++-++|+|+++  +...++.+...+.....++.+|++|.+.+
T Consensus        77 ~-ir~~~~~~~~~--------------------p~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~  134 (313)
T PRK05564         77 D-IRNIIEEVNKK--------------------PYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLE  134 (313)
T ss_pred             H-HHHHHHHHhcC--------------------cccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChH
Confidence            3 23333333221                    011344455556554  55788999999887777888888886654

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.04  E-value=4.7e-05  Score=61.01  Aligned_cols=87  Identities=10%  Similarity=-0.045  Sum_probs=48.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHh
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL  192 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L  192 (348)
                      ..+.|+|++|+||||+++.++..  .......++.+..+........... ......     .............+....
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-----~~~~~~~~~~~~~~~~~~   74 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARE--LGPPGGGVIYIDGEDILEEVLDQLL-LIIVGG-----KKASGSGELRLRLALALA   74 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhc--cCCCCCCEEEECCEEccccCHHHHH-hhhhhc-----cCCCCCHHHHHHHHHHHH
Confidence            46889999999999999999988  3333233455544433222111111 111111     111222333334444444


Q ss_pred             cCC-eEEEEEeCCCCh
Q 040110          193 TNK-KYFTVLDDVWIE  207 (348)
Q Consensus       193 ~~k-r~LlVLDdv~~~  207 (348)
                      ... ..++++|++...
T Consensus        75 ~~~~~~viiiDei~~~   90 (148)
T smart00382       75 RKLKPDVLILDEITSL   90 (148)
T ss_pred             HhcCCCEEEEECCccc
Confidence            444 499999999875

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=98.04  E-value=2.4e-05  Score=62.82  Aligned_cols=21  Identities=19%  Similarity=0.270  Sum_probs=19.7

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|+|++|+|||++|+.+++.
T Consensus         1 ill~G~~G~GKT~l~~~la~~   21 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY   21 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh
Confidence            568999999999999999998

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.03  E-value=3.3e-05  Score=78.56  Aligned_cols=137  Identities=13%  Similarity=0.156  Sum_probs=71.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      ++||.+..+   +.|.+++.    .+. -...+.++|..|+||||+|+.+.+.......++       +..+..=.....
T Consensus        17 EVIGQe~Vv---~~L~~aL~----~gR-L~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~-------~~PCG~C~sCr~   81 (830)
T PRK07003         17 SLVGQEHVV---RALTHALD----GGR-LHHAYLFTGTRGVGKTTLSRIFAKALNCETGVT-------SQPCGVCRACRE   81 (830)
T ss_pred             HHcCcHHHH---HHHHHHHh----cCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCccCCC-------CCCCcccHHHHH
Confidence            799999999   99999887    222 234556899999999999998877632221111       001111011111


Q ss_pred             HHHHhCCCCCcc-ccCCCCHHHHHHHHHHH----hcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          163 IMKSLMPTSSWL-KIMGKDYKSEKTILRDY----LTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       163 i~~~l~~~~~~~-~~~~~~~~~~~~~l~~~----L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      |...-.....+. ..+....+++...+...    ..++.-++|||++...  ..++.++..+-......++|+||.+..
T Consensus        82 I~~G~h~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~  160 (830)
T PRK07003         82 IDEGRFVDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQ  160 (830)
T ss_pred             HhcCCCceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChh
Confidence            111000000000 00111222222222221    1245568889999764  457777777655445677777666543

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.00  E-value=1.4e-05  Score=70.87  Aligned_cols=48  Identities=8%  Similarity=0.040  Sum_probs=32.7

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEe
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRV  150 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~  150 (348)
                      +.+.+++.      ......+.|+|++|+|||+||+.+++.  ........+++++
T Consensus        27 ~~l~~~~~------~~~~~~lll~G~~G~GKT~la~~~~~~--~~~~~~~~~~i~~   74 (226)
T TIGR03420        27 AALRQLAA------GKGDRFLYLWGESGSGKSHLLQAACAA--AEERGKSAIYLPL   74 (226)
T ss_pred             HHHHHHHh------cCCCCeEEEECCCCCCHHHHHHHHHHH--HHhcCCcEEEEeH
Confidence            66666654      234557889999999999999999877  3222233455543

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=97.98  E-value=3.6e-05  Score=71.64  Aligned_cols=115  Identities=17%  Similarity=0.255  Sum_probs=81.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .+.+|+.+.   ..+..++...   +..-++.+-|+|-.|.|||.+.+++++..  ..   ..+|+++-..++..-++..
T Consensus         7 ~v~~Re~qi---~~L~~Llg~~---~~~~PS~~~iyG~sgTGKT~~~r~~l~~~--n~---~~vw~n~~ecft~~~lle~   75 (438)
T KOG2543|consen    7 NVPCRESQI---RRLKSLLGNN---SCTIPSIVHIYGHSGTGKTYLVRQLLRKL--NL---ENVWLNCVECFTYAILLEK   75 (438)
T ss_pred             CccchHHHH---HHHHHHhCCC---CcccceeEEEeccCCCchhHHHHHHHhhc--CC---cceeeehHHhccHHHHHHH
Confidence            788999999   9999999832   22345667899999999999999999984  22   4689999999999999999


Q ss_pred             HHHHhCCCCCccccCC---CCHHHHHHHHHH--Hhc--CCeEEEEEeCCCChh
Q 040110          163 IMKSLMPTSSWLKIMG---KDYKSEKTILRD--YLT--NKKYFTVLDDVWIEK  208 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~---~~~~~~~~~l~~--~L~--~kr~LlVLDdv~~~~  208 (348)
                      |+.+++....+.....   .........+.+  ...  ++.++|||||++.-.
T Consensus        76 IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lr  128 (438)
T KOG2543|consen   76 ILNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALR  128 (438)
T ss_pred             HHHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhh
Confidence            9999963322101111   222333333333  222  358999999997643

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=97.96  E-value=9.7e-06  Score=75.37  Aligned_cols=49  Identities=18%  Similarity=0.272  Sum_probs=37.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|+|++..+   +.|..++.... ........+.++|++|+|||+||+.+++.
T Consensus         5 ~~iG~~~~~---~~l~~~l~~~~-~~~~~~~~~ll~Gp~G~GKT~la~~ia~~   53 (305)
T TIGR00635         5 EFIGQEKVK---EQLQLFIEAAK-MRQEALDHLLLYGPPGLGKTTLAHIIANE   53 (305)
T ss_pred             HHcCHHHHH---HHHHHHHHHHH-hcCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            689999999   88888775211 11223445778999999999999999987

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.94  E-value=8.8e-05  Score=70.79  Aligned_cols=45  Identities=22%  Similarity=0.389  Sum_probs=36.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.+.+.+.    .+ .-...+.++|+.|+||||+|+.+++.
T Consensus        17 ~iiGq~~~~---~~l~~~~~----~~-~~~h~~L~~Gp~G~GKTtla~~la~~   61 (363)
T PRK14961         17 DIIGQKHIV---TAISNGLS----LG-RIHHAWLLSGTRGVGKTTIARLLAKS   61 (363)
T ss_pred             hccChHHHH---HHHHHHHH----cC-CCCeEEEEecCCCCCHHHHHHHHHHH
Confidence            789999999   88888887    21 22345678999999999999999876

>PRK06893 DNA replication initiation factor; Validated

Probab=97.93  E-value=1.3e-05  Score=71.52  Aligned_cols=36  Identities=8%  Similarity=0.128  Sum_probs=27.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEe
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRV  150 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~  150 (348)
                      +.+.|+|++|+|||+|++.+++.  .......+.|+++
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~y~~~   75 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNH--YLLNQRTAIYIPL   75 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEeeH
Confidence            46789999999999999999987  3333334566654

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=97.90  E-value=3.4e-05  Score=79.45  Aligned_cols=52  Identities=19%  Similarity=0.242  Sum_probs=35.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF  142 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F  142 (348)
                      .|+|.+..+.....+.+.+.      ......+.++|++|+||||||+.+++.  ...+|
T Consensus        29 d~vGQe~ii~~~~~L~~~i~------~~~~~slLL~GPpGtGKTTLA~aIA~~--~~~~f   80 (725)
T PRK13341         29 EFVGQDHILGEGRLLRRAIK------ADRVGSLILYGPPGVGKTTLARIIANH--TRAHF   80 (725)
T ss_pred             HhcCcHHHhhhhHHHHHHHh------cCCCceEEEECCCCCCHHHHHHHHHHH--hcCcc
Confidence            68888876611123555555      234445678999999999999999987  44444

>PRK08116 hypothetical protein; Validated

Probab=97.87  E-value=4.6e-05  Score=69.56  Aligned_cols=101  Identities=21%  Similarity=0.252  Sum_probs=57.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT  193 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~  193 (348)
                      -+.++|..|+|||.||.++++.  +...-..+++++      ..+++..+...+....      ..+..+    +.+.+.
T Consensus       116 gl~l~G~~GtGKThLa~aia~~--l~~~~~~v~~~~------~~~ll~~i~~~~~~~~------~~~~~~----~~~~l~  177 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANE--LIEKGVPVIFVN------FPQLLNRIKSTYKSSG------KEDENE----IIRSLV  177 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEE------HHHHHHHHHHHHhccc------cccHHH----HHHHhc
Confidence            4778999999999999999998  433323455654      4556666665554321      112222    333444


Q ss_pred             CCeEEEEEeCCCC--hhhHH--HHHhhCCC-CCCCcEEEEEeCCh
Q 040110          194 NKKYFTVLDDVWI--EKIWD--DLREALPD-NQIGSRALITVGPH  233 (348)
Q Consensus       194 ~kr~LlVLDdv~~--~~~~~--~l~~~l~~-~~~gskIlvTTR~~  233 (348)
                      +-. ||||||+-.  ..+|.  .+...+-. -.++..+|+||...
T Consensus       178 ~~d-lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        178 NAD-LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             CCC-EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            434 899999942  23332  22222111 12456688888743

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.87  E-value=9.1e-05  Score=74.53  Aligned_cols=45  Identities=27%  Similarity=0.343  Sum_probs=37.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.|.+++.    .+. -...+.++|+.|+||||+|+.+++.
T Consensus        16 dVIGQe~vv---~~L~~aI~----~gr-l~HAyLF~GPpGvGKTTlAriLAK~   60 (702)
T PRK14960         16 ELVGQNHVS---RALSSALE----RGR-LHHAYLFTGTRGVGKTTIARILAKC   60 (702)
T ss_pred             HhcCcHHHH---HHHHHHHH----cCC-CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            799999999   99999887    222 2356678999999999999998876

>PRK04195 replication factor C large subunit; Provisional

Probab=97.86  E-value=6.8e-05  Score=74.31  Aligned_cols=119  Identities=12%  Similarity=0.157  Sum_probs=70.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++|.+...   +.+.+|+..-.  .....+.+.|+|++|+||||+|..+++.  ..  |+ .+-++.+...+ ...+..
T Consensus        15 dlvg~~~~~---~~l~~~l~~~~--~g~~~~~lLL~GppG~GKTtla~ala~e--l~--~~-~ielnasd~r~-~~~i~~   83 (482)
T PRK04195         15 DVVGNEKAK---EQLREWIESWL--KGKPKKALLLYGPPGVGKTSLAHALAND--YG--WE-VIELNASDQRT-ADVIER   83 (482)
T ss_pred             HhcCCHHHH---HHHHHHHHHHh--cCCCCCeEEEECCCCCCHHHHHHHHHHH--cC--CC-EEEEccccccc-HHHHHH
Confidence            799999999   99998886211  1122567889999999999999999988  32  22 23334443322 223333


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh------hhHHHHHhhCCCCCCCcEEEEEeCC
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE------KIWDDLREALPDNQIGSRALITVGP  232 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~------~~~~~l~~~l~~~~~gskIlvTTR~  232 (348)
                      ++.......+                  ....++-+||||+++..      ..+..+...+..  .++.||+|+.+
T Consensus        84 ~i~~~~~~~s------------------l~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~--~~~~iIli~n~  139 (482)
T PRK04195         84 VAGEAATSGS------------------LFGARRKLILLDEVDGIHGNEDRGGARAILELIKK--AKQPIILTAND  139 (482)
T ss_pred             HHHHhhccCc------------------ccCCCCeEEEEecCcccccccchhHHHHHHHHHHc--CCCCEEEeccC
Confidence            3332221100                  01136789999999763      235555555442  23446666543

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.85  E-value=0.00016  Score=67.53  Aligned_cols=44  Identities=14%  Similarity=0.211  Sum_probs=36.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|++...   +.+..++.      ....+.+.++|.+|+||||+|+.+++.
T Consensus        18 ~~~g~~~~~---~~l~~~i~------~~~~~~~ll~G~~G~GKt~~~~~l~~~   61 (319)
T PRK00440         18 EIVGQEEIV---ERLKSYVK------EKNMPHLLFAGPPGTGKTTAALALARE   61 (319)
T ss_pred             HhcCcHHHH---HHHHHHHh------CCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            689999999   99999887      223334689999999999999999876

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.84  E-value=7.3e-05  Score=69.87  Aligned_cols=118  Identities=15%  Similarity=0.104  Sum_probs=68.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++|.+...   +.+..++.    . .....++.++|++|+||||+|+.+++.  ....   ...++.+. ... ..++.
T Consensus        22 ~~~~~~~~~---~~l~~~~~----~-~~~~~~lll~G~~G~GKT~la~~l~~~--~~~~---~~~i~~~~-~~~-~~i~~   86 (316)
T PHA02544         22 ECILPAADK---ETFKSIVK----K-GRIPNMLLHSPSPGTGKTTVAKALCNE--VGAE---VLFVNGSD-CRI-DFVRN   86 (316)
T ss_pred             HhcCcHHHH---HHHHHHHh----c-CCCCeEEEeeCcCCCCHHHHHHHHHHH--hCcc---ceEeccCc-ccH-HHHHH
Confidence            789999999   99998887    2 223457777999999999999999886  3221   23333333 111 11111


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh---hhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE---KIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~---~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      .+..+...                   ..+.+.+-++|+|++...   ...+.+...+.....++++|+||....
T Consensus        87 ~l~~~~~~-------------------~~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~  142 (316)
T PHA02544         87 RLTRFAST-------------------VSLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKN  142 (316)
T ss_pred             HHHHHHHh-------------------hcccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChh
Confidence            11111100                   001134567889999754   223334433433445678888886543

>PLN03025 replication factor C subunit; Provisional

Probab=97.83  E-value=9.7e-05  Score=69.24  Aligned_cols=122  Identities=10%  Similarity=0.092  Sum_probs=66.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcc-eeEEEEeCCCCCHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD-CHAWVRVSNFYNFKRILD  161 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~-~~~wv~~~~~~~~~~~~~  161 (348)
                      +++|.+...   +.|.+++.      ......+.++|++|+||||+|..+++... ...|. ..+-++.+...+.. ..+
T Consensus        14 ~~~g~~~~~---~~L~~~~~------~~~~~~lll~Gp~G~GKTtla~~la~~l~-~~~~~~~~~eln~sd~~~~~-~vr   82 (319)
T PLN03025         14 DIVGNEDAV---SRLQVIAR------DGNMPNLILSGPPGTGKTTSILALAHELL-GPNYKEAVLELNASDDRGID-VVR   82 (319)
T ss_pred             HhcCcHHHH---HHHHHHHh------cCCCceEEEECCCCCCHHHHHHHHHHHHh-cccCccceeeecccccccHH-HHH
Confidence            788988888   88877766      22333466899999999999999987621 11222 12222223222221 222


Q ss_pred             HHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCC
Q 040110          162 DIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGP  232 (348)
Q Consensus       162 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~  232 (348)
                      ++++.+.....    .             .-.++.-++|||+++.-  ...+.+...+......++++++|..
T Consensus        83 ~~i~~~~~~~~----~-------------~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~  138 (319)
T PLN03025         83 NKIKMFAQKKV----T-------------LPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNT  138 (319)
T ss_pred             HHHHHHHhccc----c-------------CCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCC
Confidence            22222211100    0             00135678999999754  3344555444333445677776644

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.82  E-value=9.1e-05  Score=76.74  Aligned_cols=46  Identities=20%  Similarity=0.256  Sum_probs=36.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .+||.+..+   +.|.+++.    .+ .-...+.++|+.|+||||+|+.+++..
T Consensus        17 dIIGQe~Iv---~~LknaI~----~~-rl~HAyLFtGPpGtGKTTLARiLAk~L   62 (944)
T PRK14949         17 QMVGQSHVL---HALTNALT----QQ-RLHHAYLFTGTRGVGKTSLARLFAKGL   62 (944)
T ss_pred             HhcCcHHHH---HHHHHHHH----hC-CCCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            789999999   88888887    11 223345789999999999999998773

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.81  E-value=0.00012  Score=72.85  Aligned_cols=124  Identities=15%  Similarity=0.130  Sum_probs=72.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccC-------------------Ccc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKF-------------------YFD  143 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-------------------~F~  143 (348)
                      .++|.+..+   +.|...+.    .+ .-...+.++|+.|+||||+|+.+++......                   .|.
T Consensus        17 diiGq~~~v---~~L~~~i~----~~-rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~   88 (546)
T PRK14957         17 EVAGQQHAL---NSLVHALE----TQ-KVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFI   88 (546)
T ss_pred             HhcCcHHHH---HHHHHHHH----cC-CCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCC
Confidence            789999999   88888887    21 2334567899999999999999986521111                   111


Q ss_pred             eeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH-hcCCeEEEEEeCCCCh--hhHHHHHhhCCCC
Q 040110          144 CHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY-LTNKKYFTVLDDVWIE--KIWDDLREALPDN  220 (348)
Q Consensus       144 ~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~  220 (348)
                      ..+++.......+.                      +..++.+.+... ..+++-++|+|++..-  ...+.+...+-..
T Consensus        89 dlieidaas~~gvd----------------------~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEep  146 (546)
T PRK14957         89 DLIEIDAASRTGVE----------------------ETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEP  146 (546)
T ss_pred             ceEEeecccccCHH----------------------HHHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcC
Confidence            22222221111111                      122222222221 2356779999999743  5677787777655


Q ss_pred             CCCcEEE-EEeCChhhh
Q 040110          221 QIGSRAL-ITVGPHNIL  236 (348)
Q Consensus       221 ~~gskIl-vTTR~~~v~  236 (348)
                      ...+++| +||....+.
T Consensus       147 p~~v~fIL~Ttd~~kil  163 (546)
T PRK14957        147 PEYVKFILATTDYHKIP  163 (546)
T ss_pred             CCCceEEEEECChhhhh
Confidence            4455555 455544444

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=97.80  E-value=6.4e-05  Score=66.92  Aligned_cols=35  Identities=17%  Similarity=0.252  Sum_probs=29.5

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEe
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRV  150 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~  150 (348)
                      .++|+|.+|+|||||...+..+  ..+.|+.+++++-
T Consensus        15 r~viIG~sGSGKT~li~~lL~~--~~~~f~~I~l~t~   49 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYY--LRHKFDHIFLITP   49 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHh--hcccCCEEEEEec
Confidence            5678999999999999999988  8888977766643

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.79  E-value=0.00018  Score=72.33  Aligned_cols=146  Identities=14%  Similarity=0.142  Sum_probs=74.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      ++||.+..+   +.|.+.+.    .+. -...+.++|..|+||||+|+.+.+.....+.-...- + .+..+..-.....
T Consensus        17 dVIGQe~vv---~~L~~al~----~gR-LpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g-~-~~~PCG~C~sC~~   86 (700)
T PRK12323         17 TLVGQEHVV---RALTHALE----QQR-LHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGG-I-TAQPCGQCRACTE   86 (700)
T ss_pred             HHcCcHHHH---HHHHHHHH----hCC-CceEEEEECCCCCCHHHHHHHHHHHhcCCCcccccc-C-CCCCCcccHHHHH
Confidence            799999999   99998887    222 234567899999999999999876532210000000 0 0000110111111


Q ss_pred             HHHHhCCCCCcc-ccCCCCHHHHHHHHHHH----hcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcE-EEEEeCChh
Q 040110          163 IMKSLMPTSSWL-KIMGKDYKSEKTILRDY----LTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSR-ALITVGPHN  234 (348)
Q Consensus       163 i~~~l~~~~~~~-~~~~~~~~~~~~~l~~~----L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gsk-IlvTTR~~~  234 (348)
                      |...-....-.. ..+...++++.+.+.+.    ..++.-++|+|++...  ..++.|+..+-.-..+++ |++||....
T Consensus        87 I~aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~k  166 (700)
T PRK12323         87 IDAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQK  166 (700)
T ss_pred             HHcCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHh
Confidence            111000000000 00112233333322221    1356678999999753  567788777755444455 455666565


Q ss_pred             hhhh
Q 040110          235 ILTS  238 (348)
Q Consensus       235 v~~~  238 (348)
                      +...
T Consensus       167 LlpT  170 (700)
T PRK12323        167 IPVT  170 (700)
T ss_pred             hhhH
Confidence            5543

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.77  E-value=6.1e-05  Score=71.92  Aligned_cols=55  Identities=20%  Similarity=0.297  Sum_probs=39.5

Q ss_pred             cccccccccccHHHHHhhcCCCC-------CCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS-------GLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF  142 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~-------~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F  142 (348)
                      ++.|++..+   ++|.+.+..+-       ..+-..++-+.++|++|+|||++|+++++.  ....|
T Consensus       123 di~Gl~~~~---~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~--l~~~~  184 (364)
T TIGR01242       123 DIGGLEEQI---REIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE--TNATF  184 (364)
T ss_pred             HhCChHHHH---HHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh--CCCCE
Confidence            788999999   88888763110       001123455889999999999999999987  44443

Many proteins may score above the trusted cutoff because an internal

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.77  E-value=1.5e-05  Score=79.00  Aligned_cols=133  Identities=13%  Similarity=0.022  Sum_probs=70.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      +++|.+...   +.|..++.    .+. -...+.++|++|+||||+|+.+++.......+...+|.|.+.        ..
T Consensus        15 dvvGq~~v~---~~L~~~i~----~~~-l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc--------~~   78 (504)
T PRK14963         15 EVVGQEHVK---EVLLAALR----QGR-LGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESC--------LA   78 (504)
T ss_pred             HhcChHHHH---HHHHHHHH----cCC-CCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhh--------HH
Confidence            789999888   88888887    211 234568899999999999999987743222232233332210        00


Q ss_pred             HHHHhCCCCCcc-ccCCCCHHH---HHHHHHH-HhcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeC
Q 040110          163 IMKSLMPTSSWL-KIMGKDYKS---EKTILRD-YLTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVG  231 (348)
Q Consensus       163 i~~~l~~~~~~~-~~~~~~~~~---~~~~l~~-~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR  231 (348)
                      +........... .......+.   +...+.. -+.+++-++|+|+++..  ..++.+...+......+.+|++|.
T Consensus        79 i~~~~h~dv~el~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~  154 (504)
T PRK14963         79 VRRGAHPDVLEIDAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATT  154 (504)
T ss_pred             HhcCCCCceEEecccccCCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcC
Confidence            000000000000 000112222   2222221 12346678999999754  567778777755444555555543

>PRK10536 hypothetical protein; Provisional

Probab=97.76  E-value=0.00013  Score=65.37  Aligned_cols=53  Identities=11%  Similarity=0.095  Sum_probs=39.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeE
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHA  146 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~  146 (348)
                      .+.++....   ..++.+|.      +  ..++.+.|+.|+|||+||.++..+.-....|+.++
T Consensus        56 ~i~p~n~~Q---~~~l~al~------~--~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIi  108 (262)
T PRK10536         56 PILARNEAQ---AHYLKAIE------S--KQLIFATGEAGCGKTWISAAKAAEALIHKDVDRII  108 (262)
T ss_pred             cccCCCHHH---HHHHHHHh------c--CCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEE
Confidence            567788888   88898887      2  23888999999999999999877532234455333

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.74  E-value=0.00024  Score=69.87  Aligned_cols=45  Identities=16%  Similarity=0.169  Sum_probs=35.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.|...+.    .+ .-...+.++|++|+||||+|+.+++.
T Consensus        15 divGq~~i~---~~L~~~i~----~~-~l~~~~Lf~GPpGtGKTTlA~~lA~~   59 (472)
T PRK14962         15 EVVGQDHVK---KLIINALK----KN-SISHAYIFAGPRGTGKTTVARILAKS   59 (472)
T ss_pred             HccCcHHHH---HHHHHHHH----cC-CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            789998888   88877776    11 22345678999999999999999876

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=97.71  E-value=5.5e-05  Score=66.24  Aligned_cols=54  Identities=19%  Similarity=0.219  Sum_probs=33.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF  142 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F  142 (348)
                      +|||.+..+   ..+.-++... ....+...-+.+||++|+||||||..+++.  ....|
T Consensus        25 efiGQ~~l~---~~l~i~i~aa-~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e--~~~~~   78 (233)
T PF05496_consen   25 EFIGQEHLK---GNLKILIRAA-KKRGEALDHMLFYGPPGLGKTTLARIIANE--LGVNF   78 (233)
T ss_dssp             CS-S-HHHH---HHHHHHHHHH-HCTTS---EEEEESSTTSSHHHHHHHHHHH--CT--E
T ss_pred             HccCcHHHH---hhhHHHHHHH-HhcCCCcceEEEECCCccchhHHHHHHHhc--cCCCe
Confidence            899999888   5544433210 012345667788999999999999999998  55554

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.71  E-value=0.0003  Score=69.93  Aligned_cols=45  Identities=20%  Similarity=0.275  Sum_probs=36.4

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++||-+..+   +.|.+++.    .+ .-...+.++|+.|+||||+|+.+++.
T Consensus        17 divGq~~v~---~~L~~~~~----~~-~l~ha~Lf~Gp~G~GKTt~A~~lAk~   61 (509)
T PRK14958         17 EVIGQAPVV---RALSNALD----QQ-YLHHAYLFTGTRGVGKTTISRILAKC   61 (509)
T ss_pred             HhcCCHHHH---HHHHHHHH----hC-CCCeeEEEECCCCCCHHHHHHHHHHH
Confidence            789999999   99999987    22 12335678999999999999998875

>PRK08118 topology modulation protein; Reviewed

Probab=97.70  E-value=2.1e-05  Score=66.62  Aligned_cols=34  Identities=18%  Similarity=0.335  Sum_probs=27.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCcccc-CCcceeEE
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVK-FYFDCHAW  147 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~-~~F~~~~w  147 (348)
                      .|.|+|++|+||||||+.+++..... -+||..+|
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            57899999999999999999885443 45777776

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.68  E-value=0.0004  Score=68.79  Aligned_cols=143  Identities=13%  Similarity=0.064  Sum_probs=73.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcce-eEEEEeCCCCCHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDC-HAWVRVSNFYNFKRILD  161 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~-~~wv~~~~~~~~~~~~~  161 (348)
                      +++|.+..+   ..|...+.    .+ .-...+.++|+.|+||||+|+.+++.......... .-+..+...    ....
T Consensus        22 dliGq~~vv---~~L~~ai~----~~-ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C----~~C~   89 (507)
T PRK06645         22 ELQGQEVLV---KVLSYTIL----ND-RLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQC----TNCI   89 (507)
T ss_pred             HhcCcHHHH---HHHHHHHH----cC-CCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCC----hHHH
Confidence            789999998   88887776    11 22345678999999999999999876322111100 000000000    0011


Q ss_pred             HHHHHhCCCCCcc-ccCCCCHHHHHHHHHHH----hcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEE-EeCCh
Q 040110          162 DIMKSLMPTSSWL-KIMGKDYKSEKTILRDY----LTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALI-TVGPH  233 (348)
Q Consensus       162 ~i~~~l~~~~~~~-~~~~~~~~~~~~~l~~~----L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlv-TTR~~  233 (348)
                      .+........... ..+....+++...+...    +.+++-++|+|+++..  ..++.+...+......+++|+ ||+..
T Consensus        90 ~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~  169 (507)
T PRK06645         90 SFNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQ  169 (507)
T ss_pred             HHhcCCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChH
Confidence            1110000000000 00111223332222221    2356778999999863  568888877765555566554 65555


Q ss_pred             hhhh
Q 040110          234 NILT  237 (348)
Q Consensus       234 ~v~~  237 (348)
                      .+..
T Consensus       170 kI~~  173 (507)
T PRK06645        170 KIPA  173 (507)
T ss_pred             HhhH
Confidence            5544

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.66  E-value=0.00046  Score=69.01  Aligned_cols=45  Identities=24%  Similarity=0.347  Sum_probs=36.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+..+   +.|.+++.    .+ .-...+.++|+.|+||||+|+.+.+.
T Consensus        17 divGq~~v~---~~L~~~i~----~~-~~~ha~Lf~Gp~G~GKTt~A~~lAk~   61 (527)
T PRK14969         17 ELVGQEHVV---RALTNALE----QQ-RLHHAYLFTGTRGVGKTTLARILAKS   61 (527)
T ss_pred             HhcCcHHHH---HHHHHHHH----cC-CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            789999999   88888887    11 22335578999999999999998766

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.66  E-value=0.00033  Score=70.85  Aligned_cols=45  Identities=18%  Similarity=0.296  Sum_probs=35.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++||-+..+   +.|.+++.    .+ .-...+.++|..|+||||+|+.+.+.
T Consensus        17 dviGQe~vv---~~L~~~l~----~~-rl~ha~Lf~Gp~GvGKTtlAr~lAk~   61 (618)
T PRK14951         17 EMVGQEHVV---QALTNALT----QQ-RLHHAYLFTGTRGVGKTTVSRILAKS   61 (618)
T ss_pred             HhcCcHHHH---HHHHHHHH----cC-CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            789988888   88888887    21 23345678999999999999998655

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.65  E-value=0.00036  Score=70.80  Aligned_cols=45  Identities=24%  Similarity=0.393  Sum_probs=36.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+..+   +.|.+++.    .+ .-...+.++|+.|+||||+|+.+.+.
T Consensus        17 dIIGQe~vv---~~L~~ai~----~~-rl~Ha~Lf~GP~GvGKTTlAriLAk~   61 (709)
T PRK08691         17 DLVGQEHVV---KALQNALD----EG-RLHHAYLLTGTRGVGKTTIARILAKS   61 (709)
T ss_pred             HHcCcHHHH---HHHHHHHH----cC-CCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            799999999   99999887    21 22345778999999999999998775

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.62  E-value=0.00047  Score=67.88  Aligned_cols=127  Identities=14%  Similarity=0.144  Sum_probs=71.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCcccc-------------------CCcc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVK-------------------FYFD  143 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~-------------------~~F~  143 (348)
                      ++||.+...   +.|.+.+.    .+. -...+.++|+.|+||||+|+.+++.....                   ..+.
T Consensus        14 dliGQe~vv---~~L~~a~~----~~r-i~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~   85 (491)
T PRK14964         14 DLVGQDVLV---RILRNAFT----LNK-IPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHP   85 (491)
T ss_pred             HhcCcHHHH---HHHHHHHH----cCC-CCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCC
Confidence            789999888   88888776    222 23367789999999999999887531100                   0111


Q ss_pred             eeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhCCCCC
Q 040110          144 CHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPDNQ  221 (348)
Q Consensus       144 ~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~  221 (348)
                      .++.+..+....+.+ .++++......                    -..++.-++|+|++...  ...+.+...+-...
T Consensus        86 Dv~eidaas~~~vdd-IR~Iie~~~~~--------------------P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp  144 (491)
T PRK14964         86 DVIEIDAASNTSVDD-IKVILENSCYL--------------------PISSKFKVYIIDEVHMLSNSAFNALLKTLEEPA  144 (491)
T ss_pred             CEEEEecccCCCHHH-HHHHHHHHHhc--------------------cccCCceEEEEeChHhCCHHHHHHHHHHHhCCC
Confidence            223333332222222 11222221110                    01346678999999653  55777777776555


Q ss_pred             CCcEEEE-EeCChhhhhh
Q 040110          222 IGSRALI-TVGPHNILTS  238 (348)
Q Consensus       222 ~gskIlv-TTR~~~v~~~  238 (348)
                      +.+++|+ ||....+...
T Consensus       145 ~~v~fIlatte~~Kl~~t  162 (491)
T PRK14964        145 PHVKFILATTEVKKIPVT  162 (491)
T ss_pred             CCeEEEEEeCChHHHHHH
Confidence            5666655 5444555443

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.61  E-value=0.00042  Score=66.98  Aligned_cols=145  Identities=13%  Similarity=0.124  Sum_probs=73.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEE-eCCCCCHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVR-VSNFYNFKRILD  161 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~-~~~~~~~~~~~~  161 (348)
                      .++|.+...   +.|.+++.    .+. -...+.++|+.|+||||+|..+++.......++..-|.. ...++..=...+
T Consensus        17 eiiGq~~~~---~~L~~~~~----~~~-~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~   88 (397)
T PRK14955         17 DITAQEHIT---RTIQNSLR----MGR-VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCR   88 (397)
T ss_pred             hccChHHHH---HHHHHHHH----hCC-cceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHH
Confidence            789999888   88888887    221 233466899999999999999877632211111111110 001111111112


Q ss_pred             HHHHHhCCCCCcc-ccCCCCHHHHHHHHHHHh-----cCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEE-eCC
Q 040110          162 DIMKSLMPTSSWL-KIMGKDYKSEKTILRDYL-----TNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALIT-VGP  232 (348)
Q Consensus       162 ~i~~~l~~~~~~~-~~~~~~~~~~~~~l~~~L-----~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvT-TR~  232 (348)
                      .+......+.... .......+++.+ +.+.+     .+++-++|+|++...  ..++.+...+....+.+.+|++ ++.
T Consensus        89 ~~~~~~~~n~~~~~~~~~~~id~Ir~-l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~  167 (397)
T PRK14955         89 DFDAGTSLNISEFDAASNNSVDDIRL-LRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTEL  167 (397)
T ss_pred             HHhcCCCCCeEeecccccCCHHHHHH-HHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCCh
Confidence            2221111110000 001112333332 22222     345668899998753  5677787777655556665554 444


Q ss_pred             hhhh
Q 040110          233 HNIL  236 (348)
Q Consensus       233 ~~v~  236 (348)
                      ..+.
T Consensus       168 ~kl~  171 (397)
T PRK14955        168 HKIP  171 (397)
T ss_pred             HHhH
Confidence            4444

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.61  E-value=0.00014  Score=66.22  Aligned_cols=25  Identities=16%  Similarity=0.007  Sum_probs=21.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...-+.++|++|+||||+|+.+++.
T Consensus        41 ~~~~vll~GppGtGKTtlA~~ia~~   65 (261)
T TIGR02881        41 QVLHMIFKGNPGTGKTTVARILGKL   65 (261)
T ss_pred             CcceEEEEcCCCCCHHHHHHHHHHH
Confidence            4455778999999999999999765

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PRK08181 transposase; Validated

Probab=97.60  E-value=0.00019  Score=65.40  Aligned_cols=71  Identities=17%  Similarity=0.074  Sum_probs=42.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT  193 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~  193 (348)
                      -+.++|++|+|||.||..+.+.  .....-.++|++      ..+++..+.....         ..+.......    + 
T Consensus       108 nlll~Gp~GtGKTHLa~Aia~~--a~~~g~~v~f~~------~~~L~~~l~~a~~---------~~~~~~~l~~----l-  165 (269)
T PRK08181        108 NLLLFGPPGGGKSHLAAAIGLA--LIENGWRVLFTR------TTDLVQKLQVARR---------ELQLESAIAK----L-  165 (269)
T ss_pred             eEEEEecCCCcHHHHHHHHHHH--HHHcCCceeeee------HHHHHHHHHHHHh---------CCcHHHHHHH----H-
Confidence            4789999999999999999876  322222345553      3455555543321         1122222222    2 


Q ss_pred             CCeEEEEEeCCCC
Q 040110          194 NKKYFTVLDDVWI  206 (348)
Q Consensus       194 ~kr~LlVLDdv~~  206 (348)
                      .+--||||||+..
T Consensus       166 ~~~dLLIIDDlg~  178 (269)
T PRK08181        166 DKFDLLILDDLAY  178 (269)
T ss_pred             hcCCEEEEecccc
Confidence            2345999999953

>PRK12377 putative replication protein; Provisional

Probab=97.59  E-value=0.00029  Score=63.37  Aligned_cols=72  Identities=19%  Similarity=0.118  Sum_probs=44.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHh
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL  192 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L  192 (348)
                      ..+.++|.+|+|||+||.++++.  .....-.++++++      .+++..+-......        .....    +.+.+
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~--l~~~g~~v~~i~~------~~l~~~l~~~~~~~--------~~~~~----~l~~l  161 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNR--LLAKGRSVIVVTV------PDVMSRLHESYDNG--------QSGEK----FLQEL  161 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEEEH------HHHHHHHHHHHhcc--------chHHH----HHHHh
Confidence            46789999999999999999998  4333334566643      35555554443221        11122    22223


Q ss_pred             cCCeEEEEEeCCC
Q 040110          193 TNKKYFTVLDDVW  205 (348)
Q Consensus       193 ~~kr~LlVLDdv~  205 (348)
                       .+--||||||+-
T Consensus       162 -~~~dLLiIDDlg  173 (248)
T PRK12377        162 -CKVDLLVLDEIG  173 (248)
T ss_pred             -cCCCEEEEcCCC
Confidence             356799999994

>PRK08727 hypothetical protein; Validated

Probab=97.59  E-value=0.00013  Score=65.19  Aligned_cols=35  Identities=14%  Similarity=0.104  Sum_probs=26.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEE
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVR  149 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~  149 (348)
                      ..+.|+|..|+|||.|++++++.  ..+....+++++
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~--~~~~~~~~~y~~   76 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAA--AEQAGRSSAYLP   76 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEe
Confidence            45889999999999999999877  333323455665

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.58  E-value=0.00032  Score=71.13  Aligned_cols=139  Identities=14%  Similarity=0.116  Sum_probs=72.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .+||.+..+   +.|.+.+.    .+. -...+.++|..|+||||+|+.+++.......+.       +.++..-...+.
T Consensus        17 divGQe~vv---~~L~~~l~----~~r-l~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~-------~~pCg~C~~C~~   81 (647)
T PRK07994         17 EVVGQEHVL---TALANALD----LGR-LHHAYLFSGTRGVGKTTIARLLAKGLNCETGIT-------ATPCGECDNCRE   81 (647)
T ss_pred             HhcCcHHHH---HHHHHHHH----cCC-CCeEEEEECCCCCCHHHHHHHHHHhhhhccCCC-------CCCCCCCHHHHH
Confidence            799999999   88888887    221 233467899999999999999987632211110       011111112222


Q ss_pred             HHHHhCCCCCcc-ccCCCCHH---HHHHHHHHH-hcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEE-EEEeCChh
Q 040110          163 IMKSLMPTSSWL-KIMGKDYK---SEKTILRDY-LTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRA-LITVGPHN  234 (348)
Q Consensus       163 i~~~l~~~~~~~-~~~~~~~~---~~~~~l~~~-L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskI-lvTTR~~~  234 (348)
                      |...-....... .......+   ++...+... ..+++-++|+|++...  ...+.++..+-......++ ++||....
T Consensus        82 i~~g~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~k  161 (647)
T PRK07994         82 IEQGRFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQK  161 (647)
T ss_pred             HHcCCCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccc
Confidence            211100000000 00011222   222222221 2456778999999753  5677777766544444544 44555555


Q ss_pred             hh
Q 040110          235 IL  236 (348)
Q Consensus       235 v~  236 (348)
                      +.
T Consensus       162 Ll  163 (647)
T PRK07994        162 LP  163 (647)
T ss_pred             cc
Confidence            54

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.58  E-value=0.00056  Score=66.03  Aligned_cols=109  Identities=16%  Similarity=0.182  Sum_probs=69.7

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCc
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSW  173 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~  173 (348)
                      .++.+.+.      .... ++.|.|+.++||||+++.+...  ..+.   .+++...... +..++              
T Consensus        27 ~~l~~~~~------~~~~-i~~i~GpR~~GKTtll~~l~~~--~~~~---~iy~~~~d~~~~~~~l--------------   80 (398)
T COG1373          27 PRLIKKLD------LRPF-IILILGPRQVGKTTLLKLLIKG--LLEE---IIYINFDDLRLDRIEL--------------   80 (398)
T ss_pred             HHHHhhcc------cCCc-EEEEECCccccHHHHHHHHHhh--CCcc---eEEEEecchhcchhhH--------------
Confidence            56666555      2222 8999999999999999777666  3222   4444322211 11111              


Q ss_pred             cccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          174 LKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       174 ~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                              .+....+...-..++.+++||.|.....|......+.+.++. +|++|+-+......
T Consensus        81 --------~d~~~~~~~~~~~~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~  136 (398)
T COG1373          81 --------LDLLRAYIELKEREKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLSK  136 (398)
T ss_pred             --------HHHHHHHHHhhccCCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhhcc
Confidence                    111111111111278899999999999999999998887766 89998888776554

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.55  E-value=0.0014  Score=56.45  Aligned_cols=40  Identities=8%  Similarity=0.076  Sum_probs=26.8

Q ss_pred             CCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCCh
Q 040110          194 NKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPH  233 (348)
Q Consensus       194 ~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~  233 (348)
                      +.+-++|+|++...  ...+.+...+......+.+|++|++.
T Consensus        95 ~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~  136 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSP  136 (188)
T ss_pred             CCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECCh
Confidence            45678999998754  45677777775544456666666543

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.54  E-value=0.00021  Score=75.33  Aligned_cols=44  Identities=23%  Similarity=0.300  Sum_probs=36.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   +++++.|.    ..  ...-+.++|++|+|||++|..++..
T Consensus       180 ~~igr~~ei---~~~~~~L~----r~--~~~n~lL~G~pGvGKTal~~~la~~  223 (821)
T CHL00095        180 PVIGREKEI---ERVIQILG----RR--TKNNPILIGEPGVGKTAIAEGLAQR  223 (821)
T ss_pred             CCCCcHHHH---HHHHHHHc----cc--ccCCeEEECCCCCCHHHHHHHHHHH
Confidence            579999999   99999998    22  2223458999999999999998876

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.54  E-value=0.00057  Score=65.70  Aligned_cols=50  Identities=12%  Similarity=0.154  Sum_probs=35.5

Q ss_pred             cccccccccccHHHHHhhcCCCCC----CCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSG----LGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~----~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.|.+.+.....    ....-...+.++|+.|+|||++|..+++.
T Consensus         6 ~IiGq~~~~---~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~   59 (394)
T PRK07940          6 DLVGQEAVV---AELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAA   59 (394)
T ss_pred             hccChHHHH---HHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            678888888   888888872100    00012445778999999999999998764

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.52  E-value=0.00018  Score=64.34  Aligned_cols=36  Identities=6%  Similarity=0.090  Sum_probs=26.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEe
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRV  150 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~  150 (348)
                      ..+.|+|+.|+|||+|++.+++.  ....-..+.++++
T Consensus        46 ~~l~l~Gp~G~GKThLl~a~~~~--~~~~~~~v~y~~~   81 (235)
T PRK08084         46 GYIYLWSREGAGRSHLLHAACAE--LSQRGRAVGYVPL   81 (235)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEEH
Confidence            46789999999999999999886  2222224456554

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.51  E-value=0.00024  Score=68.38  Aligned_cols=50  Identities=20%  Similarity=0.296  Sum_probs=37.3

Q ss_pred             cccccccccccHHHHHhhcCCCC-------CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS-------GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~-------~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.|++..+   +++.+.+..+-       .-+-..++-+.++|++|+|||++|+++++.
T Consensus       132 di~Gl~~~~---~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~  188 (389)
T PRK03992        132 DIGGLEEQI---REVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE  188 (389)
T ss_pred             HhCCcHHHH---HHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHH
Confidence            788999999   88887663110       011234556789999999999999999987

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.51  E-value=0.0011  Score=62.88  Aligned_cols=45  Identities=18%  Similarity=0.257  Sum_probs=36.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+.+++.    .+ .-...+.++|++|+||||+|+.+...
T Consensus        15 ~iig~~~~~---~~l~~~~~----~~-~~~~~~Ll~G~~G~GKt~~a~~la~~   59 (355)
T TIGR02397        15 DVIGQEHIV---QTLKNAIK----NG-RIAHAYLFSGPRGTGKTSIARIFAKA   59 (355)
T ss_pred             hccCcHHHH---HHHHHHHH----cC-CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            789999999   99998887    22 22346778999999999999888755

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.50  E-value=0.00027  Score=68.95  Aligned_cols=141  Identities=13%  Similarity=0.107  Sum_probs=73.4

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      +++|.+...   ..|..++.    .+. -...+.++|+.|+||||+|+.+++..........   ..+....+    ...
T Consensus        19 dvVGQe~iv---~~L~~~i~----~~r-i~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~---~pCg~C~s----C~~   83 (484)
T PRK14956         19 DVIHQDLAI---GALQNALK----SGK-IGHAYIFFGPRGVGKTTIARILAKRLNCENPIGN---EPCNECTS----CLE   83 (484)
T ss_pred             HHhChHHHH---HHHHHHHH----cCC-CCeEEEEECCCCCCHHHHHHHHHHhcCcccccCc---cccCCCcH----HHH
Confidence            789999888   88888887    222 2235678999999999999999877322111000   00111111    111


Q ss_pred             HHHHhCCCCCcc----ccCCCCHHHHHHHHHHH-hcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEE-EEeCChh
Q 040110          163 IMKSLMPTSSWL----KIMGKDYKSEKTILRDY-LTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRAL-ITVGPHN  234 (348)
Q Consensus       163 i~~~l~~~~~~~----~~~~~~~~~~~~~l~~~-L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIl-vTTR~~~  234 (348)
                      +...........    .....++.++.+.+... ..++.-++|+|++...  ..++.+...+-.......+| .||....
T Consensus        84 i~~g~~~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~k  163 (484)
T PRK14956         84 ITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHK  163 (484)
T ss_pred             HHccCCccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhh
Confidence            211111100000    00111222233333221 2356678999999754  66788877765433344444 4665555


Q ss_pred             hhhh
Q 040110          235 ILTS  238 (348)
Q Consensus       235 v~~~  238 (348)
                      +...
T Consensus       164 I~~T  167 (484)
T PRK14956        164 IPET  167 (484)
T ss_pred             ccHH
Confidence            5443

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.49  E-value=0.00064  Score=68.16  Aligned_cols=45  Identities=16%  Similarity=0.148  Sum_probs=36.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|++...   +.+.+.+.    .+ .-...+.++|+.|+||||+|+.+++.
T Consensus        17 dIIGQe~iv---~~L~~aI~----~~-rl~hA~Lf~GP~GvGKTTlA~~lAk~   61 (605)
T PRK05896         17 QIIGQELIK---KILVNAIL----NN-KLTHAYIFSGPRGIGKTSIAKIFAKA   61 (605)
T ss_pred             HhcCcHHHH---HHHHHHHH----cC-CCCceEEEECCCCCCHHHHHHHHHHH
Confidence            789999999   99998886    21 22345778999999999999998776

>PRK07261 topology modulation protein; Provisional

Probab=97.49  E-value=0.00029  Score=59.81  Aligned_cols=66  Identities=14%  Similarity=0.215  Sum_probs=41.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCcccc-CCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHh
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVK-FYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL  192 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~-~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L  192 (348)
                      .|.|+|++|+||||||+.+.....+. -+.|...|-.                         .....+.++....+...+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~-------------------------~~~~~~~~~~~~~~~~~~   56 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQP-------------------------NWQERDDDDMIADISNFL   56 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEecc-------------------------ccccCCHHHHHHHHHHHH
Confidence            47899999999999999998663221 1334444421                         111223455666667777


Q ss_pred             cCCeEEEEEeCCCC
Q 040110          193 TNKKYFTVLDDVWI  206 (348)
Q Consensus       193 ~~kr~LlVLDdv~~  206 (348)
                      .+.+  .|+|+.-.
T Consensus        57 ~~~~--wIidg~~~   68 (171)
T PRK07261         57 LKHD--WIIDGNYS   68 (171)
T ss_pred             hCCC--EEEcCcch
Confidence            6666  67787743

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.48  E-value=0.00029  Score=74.34  Aligned_cols=44  Identities=23%  Similarity=0.308  Sum_probs=36.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   +++++.|.    .  ....-+.++|++|+|||++|..+...
T Consensus       179 ~vigr~~ei---~~~i~iL~----r--~~~~n~lL~G~pGvGKT~l~~~la~~  222 (857)
T PRK10865        179 PVIGRDEEI---RRTIQVLQ----R--RTKNNPVLIGEPGVGKTAIVEGLAQR  222 (857)
T ss_pred             cCCCCHHHH---HHHHHHHh----c--CCcCceEEECCCCCCHHHHHHHHHHH
Confidence            689999999   99999998    2  22333558999999999999999877

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.47  E-value=0.00099  Score=63.01  Aligned_cols=104  Identities=10%  Similarity=-0.025  Sum_probs=64.7

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc-ce-eEEEEeCCC-CCHHHHHHHHHHHhCCCC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF-DC-HAWVRVSNF-YNFKRILDDIMKSLMPTS  171 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F-~~-~~wv~~~~~-~~~~~~~~~i~~~l~~~~  171 (348)
                      .++++.+.+-    ..+- ...|+|..|+|||||++.+++.  +.... +. ++|+.+++. ..+.++++.+...+....
T Consensus       121 ~RvID~l~Pi----GkGQ-R~LIvG~pGtGKTTLl~~la~~--i~~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast  193 (380)
T PRK12608        121 MRVVDLVAPI----GKGQ-RGLIVAPPRAGKTVLLQQIAAA--VAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYAST  193 (380)
T ss_pred             Hhhhhheeec----CCCc-eEEEECCCCCCHHHHHHHHHHH--HHhcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeec
Confidence            6788888732    2333 3579999999999999998886  33322 33 466666554 578889999988777643


Q ss_pred             Ccc-ccCCCCHHHHHHHHHHHh--cCCeEEEEEeCCC
Q 040110          172 SWL-KIMGKDYKSEKTILRDYL--TNKKYFTVLDDVW  205 (348)
Q Consensus       172 ~~~-~~~~~~~~~~~~~l~~~L--~~kr~LlVLDdv~  205 (348)
                      ++. .............+.+++  .+++++||+|++-
T Consensus       194 ~de~~~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDslt  230 (380)
T PRK12608        194 FDRPPDEHIRVAELVLERAKRLVEQGKDVVILLDSLT  230 (380)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCcH
Confidence            210 000011111122222333  5789999999984

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=97.47  E-value=0.00031  Score=73.19  Aligned_cols=44  Identities=20%  Similarity=0.232  Sum_probs=36.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   +++++.|..    .  ...-+.++|++|+|||++|+.+++.
T Consensus       183 ~~igr~~ei---~~~~~~L~~----~--~~~n~lL~G~pG~GKT~l~~~la~~  226 (731)
T TIGR02639       183 PLIGREDEL---ERTIQVLCR----R--KKNNPLLVGEPGVGKTAIAEGLALR  226 (731)
T ss_pred             cccCcHHHH---HHHHHHHhc----C--CCCceEEECCCCCCHHHHHHHHHHH
Confidence            689999999   999998872    2  2223558999999999999999876

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.46  E-value=0.00093  Score=63.86  Aligned_cols=45  Identities=16%  Similarity=0.178  Sum_probs=37.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.+.+.+.    .+ .-...+.++|+.|+||||+|..+.+.
T Consensus        18 ~iig~~~~~---~~l~~~i~----~~-~~~~~~L~~G~~G~GKt~~a~~la~~   62 (367)
T PRK14970         18 DVVGQSHIT---NTLLNAIE----NN-HLAQALLFCGPRGVGKTTCARILARK   62 (367)
T ss_pred             hcCCcHHHH---HHHHHHHH----cC-CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            789999999   99999887    21 23457778999999999999999776

>PRK05642 DNA replication initiation factor; Validated

Probab=97.44  E-value=0.00034  Score=62.54  Aligned_cols=37  Identities=5%  Similarity=0.077  Sum_probs=26.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEe
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRV  150 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~  150 (348)
                      ...+.|+|..|+|||.|++++++..  ...-..++|++.
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~--~~~~~~v~y~~~   81 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRF--EQRGEPAVYLPL   81 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH--HhCCCcEEEeeH
Confidence            3567899999999999999998762  221124566653

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=97.43  E-value=0.00075  Score=59.96  Aligned_cols=122  Identities=16%  Similarity=0.172  Sum_probs=69.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++|.+.+.   +.|++-...-- . ..+..-+.+||..|+|||++++++.+...-+.    .--|.+.+.         
T Consensus        28 ~L~Gie~Qk---~~l~~Nt~~Fl-~-G~pannvLL~G~rGtGKSSlVkall~~y~~~G----LRlIev~k~---------   89 (249)
T PF05673_consen   28 DLIGIERQK---EALIENTEQFL-Q-GLPANNVLLWGARGTGKSSLVKALLNEYADQG----LRLIEVSKE---------   89 (249)
T ss_pred             HhcCHHHHH---HHHHHHHHHHH-c-CCCCcceEEecCCCCCHHHHHHHHHHHHhhcC----ceEEEECHH---------
Confidence            899998888   77665332100 1 22333466799999999999999987722222    111222211         


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCC---ChhhHHHHHhhCCCC---CCCc-EEEEEeCChhh
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVW---IEKIWDDLREALPDN---QIGS-RALITVGPHNI  235 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~---~~~~~~~l~~~l~~~---~~gs-kIlvTTR~~~v  235 (348)
                                    .-.+...+.+.|+.  +..||+|.+||+.   ++.....++..+-.+   .+.. .|.+||..+++
T Consensus        90 --------------~L~~l~~l~~~l~~--~~~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHL  153 (249)
T PF05673_consen   90 --------------DLGDLPELLDLLRD--RPYKFILFCDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRRHL  153 (249)
T ss_pred             --------------HhccHHHHHHHHhc--CCCCEEEEecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchhhc
Confidence                          12234444444442  3579999999985   235566666665432   1223 34446665665


Q ss_pred             hhh
Q 040110          236 LTS  238 (348)
Q Consensus       236 ~~~  238 (348)
                      ...
T Consensus       154 v~E  156 (249)
T PF05673_consen  154 VPE  156 (249)
T ss_pred             cch
Confidence            554

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.41  E-value=0.0012  Score=66.52  Aligned_cols=45  Identities=20%  Similarity=0.236  Sum_probs=36.4

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+...   +.|.+++.    .+ .-...+.++|+.|+||||+|+.+++.
T Consensus        14 eivGq~~i~---~~L~~~i~----~~-r~~ha~Lf~Gp~G~GKTt~A~~lAk~   58 (584)
T PRK14952         14 EVVGQEHVT---EPLSSALD----AG-RINHAYLFSGPRGCGKTSSARILARS   58 (584)
T ss_pred             HhcCcHHHH---HHHHHHHH----cC-CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            789999999   88999887    22 22335678999999999999999876

>PRK06526 transposase; Provisional

Probab=97.39  E-value=0.00038  Score=62.99  Aligned_cols=23  Identities=26%  Similarity=0.213  Sum_probs=20.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .-+.++|++|+|||+||..+.+.
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~  121 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIR  121 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHH
Confidence            35789999999999999999876

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.38  E-value=0.0015  Score=66.37  Aligned_cols=134  Identities=10%  Similarity=0.092  Sum_probs=71.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++|.+..+   +.|..++.    .+ .-...+.++|+.|+||||+|+.+++.......+.      -...++.-...+.
T Consensus        17 eiiGq~~~~---~~L~~~i~----~~-~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~------~~~~c~~c~~c~~   82 (585)
T PRK14950         17 ELVGQEHVV---QTLRNAIA----EG-RVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDP------KGRPCGTCEMCRA   82 (585)
T ss_pred             HhcCCHHHH---HHHHHHHH----hC-CCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCC------CCCCCccCHHHHH
Confidence            789999999   88888887    21 1234567899999999999999987622111100      0111222233333


Q ss_pred             HHHHhCCCCCcc-ccCCCCHHHHHHHHHHHh-----cCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeC
Q 040110          163 IMKSLMPTSSWL-KIMGKDYKSEKTILRDYL-----TNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVG  231 (348)
Q Consensus       163 i~~~l~~~~~~~-~~~~~~~~~~~~~l~~~L-----~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR  231 (348)
                      |........-.. .......+++.. +.+.+     .+++-++|+|++...  ...+.|...+......+.+|++|.
T Consensus        83 i~~~~~~d~~~i~~~~~~~vd~ir~-ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~  158 (585)
T PRK14950         83 IAEGSAVDVIEMDAASHTSVDDARE-IIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATT  158 (585)
T ss_pred             HhcCCCCeEEEEeccccCCHHHHHH-HHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeC
Confidence            333222110000 001122333222 22221     245678999998643  557777776655444566655553

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.37  E-value=0.0012  Score=69.17  Aligned_cols=46  Identities=20%  Similarity=0.226  Sum_probs=36.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .+||.+..+   +.|...+.    .+. -...+.++|+.|+||||+|+.+.+..
T Consensus        16 eiiGqe~v~---~~L~~~i~----~~r-i~Ha~Lf~Gp~G~GKTt~A~~lAr~L   61 (824)
T PRK07764         16 EVIGQEHVT---EPLSTALD----SGR-INHAYLFSGPRGCGKTSSARILARSL   61 (824)
T ss_pred             HhcCcHHHH---HHHHHHHH----hCC-CCceEEEECCCCCCHHHHHHHHHHHh
Confidence            789999999   88988887    222 22356789999999999999997763

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.37  E-value=0.0013  Score=66.63  Aligned_cols=45  Identities=22%  Similarity=0.353  Sum_probs=36.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+..+   +.|.+.+.    .+. -...+.++|+.|+||||+|+.+++.
T Consensus        25 dliGq~~~v---~~L~~~~~----~gr-i~ha~L~~Gp~GvGKTt~Ar~lAk~   69 (598)
T PRK09111         25 DLIGQEAMV---RTLTNAFE----TGR-IAQAFMLTGVRGVGKTTTARILARA   69 (598)
T ss_pred             HhcCcHHHH---HHHHHHHH----cCC-CCceEEEECCCCCCHHHHHHHHHHh
Confidence            799999999   99999887    222 2335678999999999999999876

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.36  E-value=0.0031  Score=56.63  Aligned_cols=76  Identities=14%  Similarity=0.166  Sum_probs=45.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      ...+.++|.+|+|||+||.++++..  ...-..++++      +..+++..+-......       ..+...    +.+.
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l--~~~g~~v~~i------t~~~l~~~l~~~~~~~-------~~~~~~----~l~~  159 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNEL--LLRGKSVLII------TVADIMSAMKDTFSNS-------ETSEEQ----LLND  159 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHH--HhcCCeEEEE------EHHHHHHHHHHHHhhc-------cccHHH----HHHH
Confidence            3467789999999999999999883  2222345555      3455555554443211       112222    3333


Q ss_pred             hcCCeEEEEEeCCCCh
Q 040110          192 LTNKKYFTVLDDVWIE  207 (348)
Q Consensus       192 L~~kr~LlVLDdv~~~  207 (348)
                      +. +.=||||||+...
T Consensus       160 l~-~~dlLvIDDig~~  174 (244)
T PRK07952        160 LS-NVDLLVIDEIGVQ  174 (244)
T ss_pred             hc-cCCEEEEeCCCCC
Confidence            44 3458888999643

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.35  E-value=0.0019  Score=53.39  Aligned_cols=40  Identities=15%  Similarity=0.135  Sum_probs=28.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYN  155 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  155 (348)
                      ++.|+|.+|+||||++..+....  ...-..++|++......
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~--~~~~~~v~~~~~e~~~~   40 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNI--ATKGGKVVYVDIEEEIE   40 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHH--HhcCCEEEEEECCcchH
Confidence            36789999999999999998773  22233567777665543

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.35  E-value=0.0021  Score=56.88  Aligned_cols=94  Identities=12%  Similarity=0.125  Sum_probs=58.1

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCc------ceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc-----cccCC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF------DCHAWVRVSNFYNFKRILDDIMKSLMPTSSW-----LKIMG  178 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F------~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~  178 (348)
                      ..-.++.|+|.+|+|||+||.+++...  ...-      ..++|+.....++...+. ++....+.....     .-...
T Consensus        17 ~~g~v~~I~G~~GsGKT~l~~~ia~~~--~~~~~~~g~~~~v~yi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~~   93 (226)
T cd01393          17 PTGRITEIFGEFGSGKTQLCLQLAVEA--QLPGELGGLEGKVVYIDTEGAFRPERLV-QLAVRFGLDPEEVLDNIYVARP   93 (226)
T ss_pred             cCCcEEEEeCCCCCChhHHHHHHHHHh--hcccccCCCcceEEEEecCCCCCHHHHH-HHHHHhccchhhhhccEEEEeC
Confidence            445689999999999999999987652  2222      357888887777765543 333333221100     01122


Q ss_pred             CCHHHHHHHHHHHhc----CCeEEEEEeCCCC
Q 040110          179 KDYKSEKTILRDYLT----NKKYFTVLDDVWI  206 (348)
Q Consensus       179 ~~~~~~~~~l~~~L~----~kr~LlVLDdv~~  206 (348)
                      .+.+++...+.....    .+--|+|+|.+..
T Consensus        94 ~~~~~~~~~l~~~~~~~~~~~~~lvVIDsis~  125 (226)
T cd01393          94 YNGEQQLEIVEELERIMSSGRVDLVVVDSVAA  125 (226)
T ss_pred             CCHHHHHHHHHHHHHHhhcCCeeEEEEcCcch
Confidence            455666666666553    3556999999853

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.34  E-value=0.00045  Score=73.10  Aligned_cols=44  Identities=23%  Similarity=0.311  Sum_probs=36.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   ++++..|.    ..  ...-+.++|++|+|||++|..+...
T Consensus       174 ~~igr~~ei---~~~~~~l~----r~--~~~n~lL~G~pGvGKT~l~~~la~~  217 (852)
T TIGR03346       174 PVIGRDEEI---RRTIQVLS----RR--TKNNPVLIGEPGVGKTAIVEGLAQR  217 (852)
T ss_pred             cCCCcHHHH---HHHHHHHh----cC--CCCceEEEcCCCCCHHHHHHHHHHH
Confidence            589999999   99999997    22  2233457999999999999998876

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=97.34  E-value=0.00061  Score=60.27  Aligned_cols=102  Identities=13%  Similarity=0.161  Sum_probs=59.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcc--eeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD--CHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTIL  188 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  188 (348)
                      ....+.|+|..|+|||.|.+++++.  ..+..+  .++++      +..++...+...+...         ..    ..+
T Consensus        33 ~~~~l~l~G~~G~GKTHLL~Ai~~~--~~~~~~~~~v~y~------~~~~f~~~~~~~~~~~---------~~----~~~   91 (219)
T PF00308_consen   33 RYNPLFLYGPSGLGKTHLLQAIANE--AQKQHPGKRVVYL------SAEEFIREFADALRDG---------EI----EEF   91 (219)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHHHH--HHHHCTTS-EEEE------EHHHHHHHHHHHHHTT---------SH----HHH
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHH--HHhccccccceee------cHHHHHHHHHHHHHcc---------cc----hhh
Confidence            3445789999999999999999988  332221  34555      4556666766666432         22    233


Q ss_pred             HHHhcCCeEEEEEeCCCCh---hhHHHHHhhCCC--CCCCcEEEEEeCChh
Q 040110          189 RDYLTNKKYFTVLDDVWIE---KIWDDLREALPD--NQIGSRALITVGPHN  234 (348)
Q Consensus       189 ~~~L~~kr~LlVLDdv~~~---~~~~~l~~~l~~--~~~gskIlvTTR~~~  234 (348)
                      ++.++ .-=+|++||++..   ..|......+-+  ...|.+||+|++...
T Consensus        92 ~~~~~-~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P  141 (219)
T PF00308_consen   92 KDRLR-SADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPP  141 (219)
T ss_dssp             HHHHC-TSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-T
T ss_pred             hhhhh-cCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCC
Confidence            44444 3457888999753   223222211111  124668999996543

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.33  E-value=0.0016  Score=66.14  Aligned_cols=45  Identities=13%  Similarity=0.109  Sum_probs=35.4

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   ..|.+.+.    .+ .-...+.++|+.|+||||+|..+++.
T Consensus        17 eivGQe~i~---~~L~~~i~----~~-ri~ha~Lf~Gp~GvGKttlA~~lAk~   61 (620)
T PRK14954         17 DITAQEHIT---HTIQNSLR----MD-RVGHGYIFSGLRGVGKTTAARVFAKA   61 (620)
T ss_pred             HhcCcHHHH---HHHHHHHH----cC-CCCeeEEEECCCCCCHHHHHHHHHHH
Confidence            789999888   88888777    21 22234678999999999999988766

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.33  E-value=0.0019  Score=61.58  Aligned_cols=45  Identities=22%  Similarity=0.222  Sum_probs=36.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+...   +.|.+.+.    .+ .-...+.++|+.|+||+|+|..+.+.
T Consensus        20 ~iiGq~~~~---~~L~~~~~----~~-rl~HA~Lf~Gp~G~GK~~lA~~~A~~   64 (365)
T PRK07471         20 ALFGHAAAE---AALLDAYR----SG-RLHHAWLIGGPQGIGKATLAYRMARF   64 (365)
T ss_pred             hccChHHHH---HHHHHHHH----cC-CCCceEEEECCCCCCHHHHHHHHHHH
Confidence            899999999   88988887    22 22335778999999999999887765

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.32  E-value=0.0009  Score=59.33  Aligned_cols=90  Identities=11%  Similarity=0.060  Sum_probs=53.5

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHH----hCCCCCccccCCCCHHH--
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKS----LMPTSSWLKIMGKDYKS--  183 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~----l~~~~~~~~~~~~~~~~--  183 (348)
                      ..-.++.|+|.+|+|||+||.+++..  ....-..++|++.. .++...+. +++..    +..+..  -....+..+  
T Consensus        21 ~~g~i~~i~G~~GsGKT~l~~~la~~--~~~~~~~v~yi~~e-~~~~~r~~-~~~~~~~~~~~~~~~--~~~~~~~~~~~   94 (225)
T PRK09361         21 ERGTITQIYGPPGSGKTNICLQLAVE--AAKNGKKVIYIDTE-GLSPERFK-QIAGEDFEELLSNII--IFEPSSFEEQS   94 (225)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEECC-CCCHHHHH-HHHhhChHhHhhCeE--EEeCCCHHHHH
Confidence            45568899999999999999999876  32233567888877 56555443 23222    100000  011123323  


Q ss_pred             -HHHHHHHHhcCCeEEEEEeCCC
Q 040110          184 -EKTILRDYLTNKKYFTVLDDVW  205 (348)
Q Consensus       184 -~~~~l~~~L~~kr~LlVLDdv~  205 (348)
                       ....+...+..+.-++|+|.+.
T Consensus        95 ~~i~~~~~~~~~~~~lvVIDsi~  117 (225)
T PRK09361         95 EAIRKAEKLAKENVGLIVLDSAT  117 (225)
T ss_pred             HHHHHHHHHHHhcccEEEEeCcH
Confidence             3344444454677799999984

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=97.31  E-value=0.0019  Score=60.21  Aligned_cols=122  Identities=11%  Similarity=0.078  Sum_probs=72.3

Q ss_pred             ccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccC-------------------Ccce
Q 040110           84 LLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKF-------------------YFDC  144 (348)
Q Consensus        84 ~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-------------------~F~~  144 (348)
                      ++|-+...   .++..+..    ........+.++|++|+||||+|..+.+...-..                   ..+.
T Consensus         3 ~~~~~~~~---~~l~~~~~----~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d   75 (325)
T COG0470           3 LVPWQEAV---KRLLVQAL----ESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPD   75 (325)
T ss_pred             cccchhHH---HHHHHHHH----hcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCc
Confidence            45555556   67777666    1122333588899999999999999987632111                   1123


Q ss_pred             eEEEEeCCCCC---HHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhCCC
Q 040110          145 HAWVRVSNFYN---FKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPD  219 (348)
Q Consensus       145 ~~wv~~~~~~~---~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~  219 (348)
                      ...++.+....   ..+.++++.+.......                    .++.-++++|+++..  +.-+.+...+..
T Consensus        76 ~lel~~s~~~~~~i~~~~vr~~~~~~~~~~~--------------------~~~~kviiidead~mt~~A~nallk~lEe  135 (325)
T COG0470          76 FLELNPSDLRKIDIIVEQVRELAEFLSESPL--------------------EGGYKVVIIDEADKLTEDAANALLKTLEE  135 (325)
T ss_pred             eEEecccccCCCcchHHHHHHHHHHhccCCC--------------------CCCceEEEeCcHHHHhHHHHHHHHHHhcc
Confidence            44444444433   34444444444433210                    356788899999754  445666666655


Q ss_pred             CCCCcEEEEEeCC
Q 040110          220 NQIGSRALITVGP  232 (348)
Q Consensus       220 ~~~gskIlvTTR~  232 (348)
                      ....+.+|++|.+
T Consensus       136 p~~~~~~il~~n~  148 (325)
T COG0470         136 PPKNTRFILITND  148 (325)
T ss_pred             CCCCeEEEEEcCC
Confidence            5556777777763

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.30  E-value=0.00051  Score=72.40  Aligned_cols=44  Identities=20%  Similarity=0.234  Sum_probs=36.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   +++++.|.    .  ....-+.++|.+|+||||+|..+++.
T Consensus       188 ~~iGr~~ei---~~~i~~l~----r--~~~~n~lLvG~pGvGKTal~~~La~~  231 (852)
T TIGR03345       188 PVLGRDDEI---RQMIDILL----R--RRQNNPILTGEAGVGKTAVVEGLALR  231 (852)
T ss_pred             cccCCHHHH---HHHHHHHh----c--CCcCceeEECCCCCCHHHHHHHHHHH
Confidence            689999999   99999887    2  22223458999999999999999876

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.30  E-value=0.00077  Score=58.65  Aligned_cols=112  Identities=13%  Similarity=0.115  Sum_probs=64.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHH-HHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFK-RILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~-~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      .++.|.|+.|+||||++..+.+.  ........++. +..+.... .-...+..+-       . -..+.....+.++..
T Consensus         2 GlilI~GptGSGKTTll~~ll~~--~~~~~~~~i~t-~e~~~E~~~~~~~~~i~q~-------~-vg~~~~~~~~~i~~a   70 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDY--INKNKTHHILT-IEDPIEFVHESKRSLINQR-------E-VGLDTLSFENALKAA   70 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH--hhhcCCcEEEE-EcCCccccccCccceeeec-------c-cCCCccCHHHHHHHH
Confidence            47889999999999999988776  43333334443 22221100 0000011000       0 011223455667788


Q ss_pred             hcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          192 LTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       192 L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      |+...=++++|.+.+.+.+..+.....   .|..++.|+-..++...
T Consensus        71 Lr~~pd~ii~gEird~e~~~~~l~~a~---~G~~v~~t~Ha~~~~~~  114 (198)
T cd01131          71 LRQDPDVILVGEMRDLETIRLALTAAE---TGHLVMSTLHTNSAAKT  114 (198)
T ss_pred             hcCCcCEEEEcCCCCHHHHHHHHHHHH---cCCEEEEEecCCcHHHH
Confidence            877788999999988766655444432   35568888877766544

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.29  E-value=0.0064  Score=59.22  Aligned_cols=91  Identities=11%  Similarity=-0.045  Sum_probs=49.0

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTIL  188 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  188 (348)
                      ..+.++.++|.+|+||||++..++..... ..+. +.-++... .....+.++.++.+++.+... .....+........
T Consensus        93 ~~p~vI~lvG~~GsGKTTtaakLA~~L~~-~g~k-V~lV~~D~~R~aa~eQL~~la~~~gvp~~~-~~~~~d~~~i~~~a  169 (437)
T PRK00771         93 LKPQTIMLVGLQGSGKTTTAAKLARYFKK-KGLK-VGLVAADTYRPAAYDQLKQLAEKIGVPFYG-DPDNKDAVEIAKEG  169 (437)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHH-cCCe-EEEecCCCCCHHHHHHHHHHHHHcCCcEEe-cCCccCHHHHHHHH
Confidence            35789999999999999999999876322 2232 23333321 112345566666666654221 11122333333333


Q ss_pred             HHHhcCCeEEEEEeCC
Q 040110          189 RDYLTNKKYFTVLDDV  204 (348)
Q Consensus       189 ~~~L~~kr~LlVLDdv  204 (348)
                      .+.+.+. -++|+|-.
T Consensus       170 l~~~~~~-DvVIIDTA  184 (437)
T PRK00771        170 LEKFKKA-DVIIVDTA  184 (437)
T ss_pred             HHHhhcC-CEEEEECC
Confidence            3333333 45777766

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.29  E-value=0.0016  Score=60.07  Aligned_cols=22  Identities=18%  Similarity=0.172  Sum_probs=18.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -+.++|++|+|||++|+.+++.
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~   81 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQI   81 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHH
Confidence            4678999999999999777654

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>COG3903 Predicted ATPase [General function prediction only]

Probab=97.29  E-value=0.00011  Score=69.27  Aligned_cols=195  Identities=14%  Similarity=0.030  Sum_probs=122.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcce-eEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDC-HAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTIL  188 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~-~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  188 (348)
                      +..+.+.++|.|||||||++-++..   +...|.. +.++...+-.+...+.-.+...++....       +-+.....+
T Consensus        12 ~~~RlvtL~g~ggvgkttl~~~~a~---~~~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~-------~g~~~~~~~   81 (414)
T COG3903          12 TALRLVTLTGAGGVGKTTLALQAAH---AASEYADGVAFVDLAPITDPALVFPTLAGALGLHVQ-------PGDSAVDTL   81 (414)
T ss_pred             hhhheeeeeccCccceehhhhhhHh---HhhhcccceeeeeccccCchhHhHHHHHhhcccccc-------cchHHHHHH
Confidence            3567899999999999999998887   4566764 4455555555666666667776777521       223445566


Q ss_pred             HHHhcCCeEEEEEeCCCCh-hhHHHHHhhCCCCCCCcEEEEEeCChhhhhh---cccC----------------------
Q 040110          189 RDYLTNKKYFTVLDDVWIE-KIWDDLREALPDNQIGSRALITVGPHNILTS---IELE----------------------  242 (348)
Q Consensus       189 ~~~L~~kr~LlVLDdv~~~-~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~---~~l~----------------------  242 (348)
                      .....++|.++|+||..+. ++-..+...+..+++.-.|+.|+|+......   +.++                      
T Consensus        82 ~~~~~~rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~  161 (414)
T COG3903          82 VRRIGDRRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAILVAGEVHRRVPSLSLFDEAIELFVCRAVLVALS  161 (414)
T ss_pred             HHHHhhhhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhcccccccccCCccccCCchhHHHHHHHHHhccc
Confidence            7777889999999998654 3334444555555556678888888765554   2222                      


Q ss_pred             -----------CCCc----CCCC----cccccCccccCC-----HHHHHHHHHHhCCCCCCCCCCCcchhccc-cccCCC
Q 040110          243 -----------NGEK----NRHD----SALVGGPLIRIK-----HETWQFFILHYGSTPLENETEGPSVGLKL-VSLSEL  297 (348)
Q Consensus       243 -----------~~~C----~Lp~----~~~ig~~L~~~~-----~~~w~~~~~~~~~~~~~~~~~~~~i~~~l-~s~~~L  297 (348)
                                 ...|    |.|+    +...+..|..+.     .+.|..+.... .  ...... .....++ +||.-|
T Consensus       162 f~l~~~~~a~v~~icr~ldg~~laielaaarv~sl~~~~i~~~L~drf~ll~~~~-r--~a~~~~-qtl~asl~ws~~lL  237 (414)
T COG3903         162 FWLTDDNAAAVAEICRRLDGIPLAIELAAARVRSLSPDEIAAGLRDRFRLLTGGA-R--LAVLRQ-QTLRASLDWSYALL  237 (414)
T ss_pred             eeecCCchHHHHHHHHHhhcchHHHHHHHHHHHhcCHHHHHHHHhhHHHHHhccc-c--cchhHH-HhccchhhhhhHhh
Confidence                       2455    5666    222222222211     33444443331 1  111111 2333777 999999


Q ss_pred             ChhHHHHHhHhccCCCCceec
Q 040110          298 PFPLIVCCLYFCVFPTDIELT  318 (348)
Q Consensus       298 p~~lk~cf~y~a~fp~~~~i~  318 (348)
                      ....+.-|.-++.|...+.-+
T Consensus       238 tgwe~~~~~rLa~~~g~f~~~  258 (414)
T COG3903         238 TGWERALFGRLAVFVGGFDLG  258 (414)
T ss_pred             hhHHHHHhcchhhhhhhhccc
Confidence            988889999999998876554

>PRK09183 transposase/IS protein; Provisional

Probab=97.28  E-value=0.00072  Score=61.42  Aligned_cols=23  Identities=22%  Similarity=0.319  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+.|+|++|+|||+||..+.+.
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~  125 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYE  125 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHH
Confidence            35779999999999999999765

>CHL00181 cbbX CbbX; Provisional

Probab=97.27  E-value=0.003  Score=58.29  Aligned_cols=22  Identities=23%  Similarity=0.226  Sum_probs=19.5

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.++|++|+||||+|+.+++.
T Consensus        61 ~ill~G~pGtGKT~lAr~la~~   82 (287)
T CHL00181         61 HMSFTGSPGTGKTTVALKMADI   82 (287)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4678999999999999999765

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=97.27  E-value=0.00078  Score=64.91  Aligned_cols=50  Identities=16%  Similarity=0.244  Sum_probs=36.3

Q ss_pred             cccccccccccHHHHHhhcCC----C---CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----S---SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~---~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|.+...   ++|.+.+..    +   ...+-..++-+.++|++|+|||+||+++++.
T Consensus       146 digGl~~~k---~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~  202 (398)
T PTZ00454        146 DIGGLDIQK---QEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHH  202 (398)
T ss_pred             HcCCHHHHH---HHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            678888888   777765521    1   0112234566889999999999999999987

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.26  E-value=0.00078  Score=71.30  Aligned_cols=136  Identities=13%  Similarity=0.126  Sum_probs=72.1

Q ss_pred             cccccccccccHHHHHhhcCCCC-C--CCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS-G--LGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRI  159 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~-~--~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  159 (348)
                      .++|.+..+   +.+...+.... +  ..+....++.++|+.|+|||++|+.+...  ....-...+.++++.-.+... 
T Consensus       566 ~v~GQ~~av---~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~--l~~~~~~~i~~d~s~~~~~~~-  639 (852)
T TIGR03346       566 RVVGQDEAV---EAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEF--LFDDEDAMVRIDMSEYMEKHS-  639 (852)
T ss_pred             ccCCChHHH---HHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHH--hcCCCCcEEEEechhhcccch-
Confidence            689999988   88888876210 0  11223456789999999999999999876  222212334444443222111 


Q ss_pred             HHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhCCCC-----------CCCcEE
Q 040110          160 LDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPDN-----------QIGSRA  226 (348)
Q Consensus       160 ~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~-----------~~gskI  226 (348)
                         ...-++.+ +. .........+...++   +....+|+||++...  +.++.|...+..+           -..+-|
T Consensus       640 ---~~~l~g~~-~g-~~g~~~~g~l~~~v~---~~p~~vlllDeieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~ii  711 (852)
T TIGR03346       640 ---VARLIGAP-PG-YVGYEEGGQLTEAVR---RKPYSVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVI  711 (852)
T ss_pred             ---HHHhcCCC-CC-ccCcccccHHHHHHH---cCCCcEEEEeccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEE
Confidence               11112211 00 001111122322222   123458999999864  5667666665332           123446


Q ss_pred             EEEeCC
Q 040110          227 LITVGP  232 (348)
Q Consensus       227 lvTTR~  232 (348)
                      |+||..
T Consensus       712 I~TSn~  717 (852)
T TIGR03346       712 IMTSNL  717 (852)
T ss_pred             EEeCCc
Confidence            777764

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.25  E-value=0.0012  Score=57.77  Aligned_cols=93  Identities=11%  Similarity=0.038  Sum_probs=54.9

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHh-CCCCCc-cccCCCCH---HH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSL-MPTSSW-LKIMGKDY---KS  183 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l-~~~~~~-~~~~~~~~---~~  183 (348)
                      -+.-.++.|+|++|+|||+++.++...  ....-..++|++... ++...+.+. +... ...... .-.+..+.   ..
T Consensus         9 i~~g~i~~i~G~~GsGKT~l~~~~~~~--~~~~g~~v~yi~~e~-~~~~rl~~~-~~~~~~~~~~~i~~~~~~~~~~~~~   84 (209)
T TIGR02237         9 VERGTITQIYGPPGSGKTNICMILAVN--AARQGKKVVYIDTEG-LSPERFKQI-AEDRPERALSNFIVFEVFDFDEQGV   84 (209)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCC-CCHHHHHHH-HHhChHHHhcCEEEEECCCHHHHHH
Confidence            345578999999999999999998766  323335788988765 665554443 2221 000000 00111222   23


Q ss_pred             HHHHHHHHhcC-CeEEEEEeCCC
Q 040110          184 EKTILRDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       184 ~~~~l~~~L~~-kr~LlVLDdv~  205 (348)
                      ....+...+.. +.-++|+|.+.
T Consensus        85 ~~~~l~~~~~~~~~~lvVIDSis  107 (209)
T TIGR02237        85 AIQKTSKFIDRDSASLVVVDSFT  107 (209)
T ss_pred             HHHHHHHHHhhcCccEEEEeCcH
Confidence            35555555544 46689999985

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.25  E-value=0.00059  Score=58.06  Aligned_cols=36  Identities=22%  Similarity=0.344  Sum_probs=28.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEE
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWV  148 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv  148 (348)
                      ...+|.+.|+.|+||||+|+.+++.  ....+...+++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~--l~~~~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYER--LKLKYSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHH--HHHcCCcEEEE
Confidence            4458999999999999999999988  55555555555

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.25  E-value=0.0011  Score=61.65  Aligned_cols=98  Identities=15%  Similarity=0.162  Sum_probs=57.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      ..-+.++|..|+|||.||.++++... +..+ .+.++++      .+++.++.......         +..+...    .
T Consensus       156 ~~gl~L~G~~G~GKThLa~Aia~~l~-~~g~-~v~~~~~------~~l~~~lk~~~~~~---------~~~~~l~----~  214 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLAAIANELA-KKGV-SSTLLHF------PEFIRELKNSISDG---------SVKEKID----A  214 (306)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH-HcCC-CEEEEEH------HHHHHHHHHHHhcC---------cHHHHHH----H
Confidence            34577999999999999999998843 2233 3455543      45666665554321         2222222    2


Q ss_pred             hcCCeEEEEEeCCCCh--hhHH--HHHhhCCC-C-CCCcEEEEEeC
Q 040110          192 LTNKKYFTVLDDVWIE--KIWD--DLREALPD-N-QIGSRALITVG  231 (348)
Q Consensus       192 L~~kr~LlVLDdv~~~--~~~~--~l~~~l~~-~-~~gskIlvTTR  231 (348)
                      + .+-=||||||+-..  ..|.  ++...+.+ . ..+-.+|+||.
T Consensus       215 l-~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSN  259 (306)
T PRK08939        215 V-KEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSN  259 (306)
T ss_pred             h-cCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECC
Confidence            2 35678999999543  4453  34333321 1 23455777775

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.24  E-value=0.0024  Score=56.82  Aligned_cols=96  Identities=13%  Similarity=0.093  Sum_probs=57.1

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCC----cceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-----ccCCC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFY----FDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-----KIMGK  179 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~----F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-----~~~~~  179 (348)
                      -..-.++.|+|.+|+|||+||.+++-.......    -..++|++....++...+. +++..++......     -....
T Consensus        16 i~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~~~   94 (235)
T cd01123          16 IETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLV-QIAERFGLDPEEVLDNIYVARAY   94 (235)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHH-HHHHHhccChHhHhcCEEEEecC
Confidence            345578899999999999999998744222221    2578899888777755443 3334433221110     01112


Q ss_pred             CH---HHHHHHHHHHhc-C-CeEEEEEeCCC
Q 040110          180 DY---KSEKTILRDYLT-N-KKYFTVLDDVW  205 (348)
Q Consensus       180 ~~---~~~~~~l~~~L~-~-kr~LlVLDdv~  205 (348)
                      +.   ......+.+.+. . +--|+|+|.+.
T Consensus        95 ~~~~l~~~l~~l~~~l~~~~~~~liVIDSis  125 (235)
T cd01123          95 NSDHQLQLLEELEAILIESSRIKLVIVDSVT  125 (235)
T ss_pred             CHHHHHHHHHHHHHHHhhcCCeeEEEEeCcH
Confidence            22   333444555553 3 67899999985

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>PRK09087 hypothetical protein; Validated

Probab=97.24  E-value=0.0013  Score=58.47  Aligned_cols=24  Identities=25%  Similarity=0.237  Sum_probs=21.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.+.|+|+.|+|||+|++.+++.
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~   67 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREK   67 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHh
Confidence            356889999999999999988876

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.23  E-value=0.0022  Score=64.76  Aligned_cols=46  Identities=15%  Similarity=0.102  Sum_probs=35.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      +++|.+...   +.|.+.+.    .+ .-...+.++|+.|+||||+|+.+++..
T Consensus        17 dIiGQe~v~---~~L~~ai~----~~-ri~ha~Lf~GPpG~GKTtiArilAk~L   62 (624)
T PRK14959         17 EVAGQETVK---AILSRAAQ----EN-RVAPAYLFSGTRGVGKTTIARIFAKAL   62 (624)
T ss_pred             HhcCCHHHH---HHHHHHHH----cC-CCCceEEEECCCCCCHHHHHHHHHHhc
Confidence            788988888   88888777    21 123466789999999999999998773

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.23  E-value=0.00056  Score=72.14  Aligned_cols=50  Identities=14%  Similarity=0.215  Sum_probs=37.4

Q ss_pred             cccccccccccHHHHHhhcCCC---CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS---SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~---~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+.+.+...   -...+....++.++|+.|+|||.||+.++..
T Consensus       567 ~v~GQ~~Av---~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~  619 (852)
T TIGR03345       567 RVIGQDHAL---EAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAEL  619 (852)
T ss_pred             eEcChHHHH---HHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            678999988   8888877421   0122344567889999999999999988766

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.23  E-value=0.0014  Score=63.55  Aligned_cols=99  Identities=13%  Similarity=0.192  Sum_probs=54.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcc--eeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD--CHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      ...+.|+|..|+|||+|++++++.  +....+  .+++++      ..++...+...+...         ....    +.
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~--l~~~~~~~~v~yi~------~~~~~~~~~~~~~~~---------~~~~----~~  194 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNE--ILENNPNAKVVYVS------SEKFTNDFVNALRNN---------KMEE----FK  194 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH--HHHhCCCCcEEEEE------HHHHHHHHHHHHHcC---------CHHH----HH
Confidence            345789999999999999999987  433322  345553      344555555555322         2222    23


Q ss_pred             HHhcCCeEEEEEeCCCCh---hhH-HHHHhhCCC-CCCCcEEEEEeCC
Q 040110          190 DYLTNKKYFTVLDDVWIE---KIW-DDLREALPD-NQIGSRALITVGP  232 (348)
Q Consensus       190 ~~L~~kr~LlVLDdv~~~---~~~-~~l~~~l~~-~~~gskIlvTTR~  232 (348)
                      +.+++ .-+|+|||+...   ..+ +.+...+.. ...+..+|+||..
T Consensus       195 ~~~~~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~  241 (405)
T TIGR00362       195 EKYRS-VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDR  241 (405)
T ss_pred             HHHHh-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCC
Confidence            33332 348889999743   111 222222211 1234567777764

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=97.23  E-value=0.00024  Score=56.34  Aligned_cols=22  Identities=27%  Similarity=0.392  Sum_probs=20.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|.|.|++|+||||+|+.+.+.
T Consensus         1 vI~I~G~~gsGKST~a~~La~~   22 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAER   22 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999999887

...

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.22  E-value=0.0013  Score=64.42  Aligned_cols=73  Identities=22%  Similarity=0.267  Sum_probs=47.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCc-c-eeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYF-D-CHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F-~-~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      .-+.|+|.+|+|||+|++++++.  +...+ . .++|++      ..++..++...+...         ...    .+.+
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~~--l~~~~~~~~v~yi~------~~~f~~~~~~~~~~~---------~~~----~f~~  189 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGNY--VVQNEPDLRVMYIT------SEKFLNDLVDSMKEG---------KLN----EFRE  189 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHH--HHHhCCCCeEEEEE------HHHHHHHHHHHHhcc---------cHH----HHHH
Confidence            34889999999999999999987  44332 2 355664      345666666665432         122    2333


Q ss_pred             HhcCCeEEEEEeCCCC
Q 040110          191 YLTNKKYFTVLDDVWI  206 (348)
Q Consensus       191 ~L~~kr~LlVLDdv~~  206 (348)
                      .+..+.-+|++||+..
T Consensus       190 ~~~~~~dvLlIDDi~~  205 (440)
T PRK14088        190 KYRKKVDVLLIDDVQF  205 (440)
T ss_pred             HHHhcCCEEEEechhh
Confidence            3334456899999974

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=97.21  E-value=0.00095  Score=69.57  Aligned_cols=118  Identities=13%  Similarity=0.161  Sum_probs=64.2

Q ss_pred             cccccccccccHHHHHhhcCCCC-C--CCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS-G--LGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRI  159 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~-~--~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  159 (348)
                      .++|.+..+   +.+.+.+.... +  ..+....++.++|+.|+|||+||+.++..  ..   ...+.++++.-.+..  
T Consensus       455 ~v~GQ~~ai---~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~--l~---~~~~~~d~se~~~~~--  524 (731)
T TIGR02639       455 KIFGQDEAI---DSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEA--LG---VHLERFDMSEYMEKH--  524 (731)
T ss_pred             ceeCcHHHH---HHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHH--hc---CCeEEEeCchhhhcc--
Confidence            578888888   77777765210 0  11233456789999999999999999887  32   233445444321111  


Q ss_pred             HHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcC-CeEEEEEeCCCCh--hhHHHHHhhCC
Q 040110          160 LDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTN-KKYFTVLDDVWIE--KIWDDLREALP  218 (348)
Q Consensus       160 ~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~-kr~LlVLDdv~~~--~~~~~l~~~l~  218 (348)
                        .+...++.+..  .........    +.+.++. ...+++||+++..  +.++.+...+-
T Consensus       525 --~~~~lig~~~g--yvg~~~~~~----l~~~~~~~p~~VvllDEieka~~~~~~~Ll~~ld  578 (731)
T TIGR02639       525 --TVSRLIGAPPG--YVGFEQGGL----LTEAVRKHPHCVLLLDEIEKAHPDIYNILLQVMD  578 (731)
T ss_pred             --cHHHHhcCCCC--CcccchhhH----HHHHHHhCCCeEEEEechhhcCHHHHHHHHHhhc
Confidence              11122222110  011111222    3333333 4569999999854  55566665553

>PHA00729 NTP-binding motif containing protein

Probab=97.20  E-value=0.0012  Score=58.14  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=21.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+.|+|.+|+||||||..+.+.
T Consensus        16 ~f~nIlItG~pGvGKT~LA~aLa~~   40 (226)
T PHA00729         16 GFVSAVIFGKQGSGKTTYALKVARD   40 (226)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHH
Confidence            4456889999999999999999886

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.20  E-value=0.00079  Score=58.62  Aligned_cols=123  Identities=15%  Similarity=0.060  Sum_probs=60.3

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeC----CCC--CHHH-------HHH
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVS----NFY--NFKR-------ILD  161 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~----~~~--~~~~-------~~~  161 (348)
                      ...++.|.        ...++.+.|++|+|||.||.+..-+.-....|+..+++.-.    +..  -+.+       .+.
T Consensus        10 ~~~~~al~--------~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~   81 (205)
T PF02562_consen   10 KFALDALL--------NNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLR   81 (205)
T ss_dssp             HHHHHHHH--------H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTH
T ss_pred             HHHHHHHH--------hCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHH
Confidence            55666666        34478899999999999999988765455778877766321    111  0011       111


Q ss_pred             HHHHHhCCCCCccccCCCCHHHHHHH------HHHHhcCC---eEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEe
Q 040110          162 DIMKSLMPTSSWLKIMGKDYKSEKTI------LRDYLTNK---KYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITV  230 (348)
Q Consensus       162 ~i~~~l~~~~~~~~~~~~~~~~~~~~------l~~~L~~k---r~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTT  230 (348)
                      -+...+..-     ......+.+...      -..+++++   +.++|+|++.+.  .++..+...   .+.|||++++=
T Consensus        82 p~~d~l~~~-----~~~~~~~~~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~ilTR---~g~~skii~~G  153 (205)
T PF02562_consen   82 PIYDALEEL-----FGKEKLEELIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMILTR---IGEGSKIIITG  153 (205)
T ss_dssp             HHHHHHTTT-----S-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTT---B-TT-EEEEEE
T ss_pred             HHHHHHHHH-----hChHhHHHHhhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHHHcc---cCCCcEEEEec
Confidence            222222211     011122222211      01245553   689999999875  455555444   46689999875


Q ss_pred             CCh
Q 040110          231 GPH  233 (348)
Q Consensus       231 R~~  233 (348)
                      -..
T Consensus       154 D~~  156 (205)
T PF02562_consen  154 DPS  156 (205)
T ss_dssp             ---
T ss_pred             Cce
Confidence            443

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=97.19  E-value=0.00023  Score=60.82  Aligned_cols=73  Identities=21%  Similarity=0.260  Sum_probs=42.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHh
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL  192 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L  192 (348)
                      .-+.++|..|+|||.||..+.+.... ..+ .+.|++      ..+++..+-..-.         .....+....    +
T Consensus        48 ~~l~l~G~~G~GKThLa~ai~~~~~~-~g~-~v~f~~------~~~L~~~l~~~~~---------~~~~~~~~~~----l  106 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAIANEAIR-KGY-SVLFIT------ASDLLDELKQSRS---------DGSYEELLKR----L  106 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHH-TT---EEEEE------HHHHHHHHHCCHC---------CTTHCHHHHH----H
T ss_pred             eEEEEEhhHhHHHHHHHHHHHHHhcc-CCc-ceeEee------cCceecccccccc---------ccchhhhcCc----c
Confidence            35889999999999999999876322 233 355663      4455555432211         1122233222    3


Q ss_pred             cCCeEEEEEeCCCCh
Q 040110          193 TNKKYFTVLDDVWIE  207 (348)
Q Consensus       193 ~~kr~LlVLDdv~~~  207 (348)
                      . +-=||||||+-..
T Consensus       107 ~-~~dlLilDDlG~~  120 (178)
T PF01695_consen  107 K-RVDLLILDDLGYE  120 (178)
T ss_dssp             H-TSSCEEEETCTSS
T ss_pred             c-cccEeccccccee
Confidence            2 3467889998643

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>PRK06921 hypothetical protein; Provisional

Probab=97.19  E-value=0.0022  Score=58.45  Aligned_cols=37  Identities=16%  Similarity=0.076  Sum_probs=27.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCC-cceeEEEEe
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFY-FDCHAWVRV  150 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~-F~~~~wv~~  150 (348)
                      ..-+.++|..|+|||.||.++++.  +... -..+++++.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~--l~~~~g~~v~y~~~  154 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANE--LMRKKGVPVLYFPF  154 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH--HhhhcCceEEEEEH
Confidence            346789999999999999999987  4332 234566653

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.17  E-value=0.0019  Score=63.52  Aligned_cols=73  Identities=15%  Similarity=0.166  Sum_probs=45.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcc--eeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD--CHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      ..-+.|+|.+|+|||+|++++++.  ....++  .+++++      ..++...+...+...         ...    .+.
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~v~yi~------~~~~~~~~~~~~~~~---------~~~----~~~  206 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNY--ILEKNPNAKVVYVT------SEKFTNDFVNALRNN---------TME----EFK  206 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEEE------HHHHHHHHHHHHHcC---------cHH----HHH
Confidence            345789999999999999999988  444432  344553      334445555555321         122    233


Q ss_pred             HHhcCCeEEEEEeCCCC
Q 040110          190 DYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       190 ~~L~~kr~LlVLDdv~~  206 (348)
                      +.++ +.-+|+|||+..
T Consensus       207 ~~~~-~~dlLiiDDi~~  222 (450)
T PRK00149        207 EKYR-SVDVLLIDDIQF  222 (450)
T ss_pred             HHHh-cCCEEEEehhhh
Confidence            3333 344889999964

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.17  E-value=0.0013  Score=64.56  Aligned_cols=103  Identities=12%  Similarity=0.073  Sum_probs=57.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHh
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL  192 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L  192 (348)
                      .-+.|+|..|+|||+|++++.+.......--.++++      +..++...+...+...    .       .....+.+.+
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv------~~~~f~~~~~~~l~~~----~-------~~~~~~~~~~  204 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYM------SGDEFARKAVDILQKT----H-------KEIEQFKNEI  204 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEE------EHHHHHHHHHHHHHHh----h-------hHHHHHHHHh
Confidence            347799999999999999998862111111133444      3456777777666432    0       1223344444


Q ss_pred             cCCeEEEEEeCCCCh---hhH-HHHHhhCCC-CCCCcEEEEEeCCh
Q 040110          193 TNKKYFTVLDDVWIE---KIW-DDLREALPD-NQIGSRALITVGPH  233 (348)
Q Consensus       193 ~~kr~LlVLDdv~~~---~~~-~~l~~~l~~-~~~gskIlvTTR~~  233 (348)
                      +. .-+|||||+...   ..+ +.+...+-. ...|..||+|+...
T Consensus       205 ~~-~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~  249 (450)
T PRK14087        205 CQ-NDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKS  249 (450)
T ss_pred             cc-CCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCC
Confidence            43 447888999643   222 233222211 12345688886644

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.16  E-value=0.0002  Score=67.26  Aligned_cols=51  Identities=10%  Similarity=0.178  Sum_probs=41.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .++|.++.+   +++++++...........+++.++|++|+||||||..+.+..
T Consensus        52 ~~~G~~~~i---~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l  102 (361)
T smart00763       52 DFFGMEEAI---ERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGL  102 (361)
T ss_pred             hccCcHHHH---HHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            799999999   999999973221223456789999999999999999998873

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.15  E-value=0.0017  Score=64.26  Aligned_cols=50  Identities=20%  Similarity=0.254  Sum_probs=36.0

Q ss_pred             cccccccccccHHHHHhhcCCC-------CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-------SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-------~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.|.+..+   +++.+.+.-+       ...+-..++-+.++|++|+|||++|+++++.
T Consensus       183 dIgGl~~~i---~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~e  239 (512)
T TIGR03689       183 DIGGLDSQI---EQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANS  239 (512)
T ss_pred             HcCChHHHH---HHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHh
Confidence            677899998   8887765310       0011223445778999999999999999988

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.14  E-value=0.0037  Score=63.29  Aligned_cols=45  Identities=22%  Similarity=0.280  Sum_probs=36.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+...   +.|.+.+.    .+ .-...+.++|+.|+||||+|+.+++.
T Consensus        17 ~iiGq~~v~---~~L~~~i~----~~-~~~hayLf~Gp~G~GKtt~A~~lak~   61 (576)
T PRK14965         17 DLTGQEHVS---RTLQNAID----TG-RVAHAFLFTGARGVGKTSTARILAKA   61 (576)
T ss_pred             HccCcHHHH---HHHHHHHH----cC-CCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            799999888   88888887    22 22345678999999999999998766

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=97.12  E-value=0.0025  Score=58.00  Aligned_cols=92  Identities=13%  Similarity=0.218  Sum_probs=55.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcc-eeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHH------
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFD-CHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKS------  183 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~-~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~------  183 (348)
                      .++|.|.+|+|||||++.+++.  .+.+|+ .++++-+++.. .+.++..++...=.......  ...+.....      
T Consensus        71 r~~If~~~G~GKTtLa~~i~~~--i~~~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~~~  148 (274)
T cd01133          71 KIGLFGGAGVGKTVLIMELINN--IAKAHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARVAL  148 (274)
T ss_pred             EEEEecCCCCChhHHHHHHHHH--HHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHH
Confidence            4789999999999999999998  554554 45556665554 45566666654321111110  111111111      


Q ss_pred             HHHHHHHHh--c-CCeEEEEEeCCCCh
Q 040110          184 EKTILRDYL--T-NKKYFTVLDDVWIE  207 (348)
Q Consensus       184 ~~~~l~~~L--~-~kr~LlVLDdv~~~  207 (348)
                      ..-.+.+++  + ++++|+++||+-..
T Consensus       149 ~a~~~AEyfr~~~g~~Vl~~~Dsltr~  175 (274)
T cd01133         149 TGLTMAEYFRDEEGQDVLLFIDNIFRF  175 (274)
T ss_pred             HHHHHHHHHHHhcCCeEEEEEeChhHH
Confidence            112344555  3 78999999998543

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=97.11  E-value=0.0032  Score=53.62  Aligned_cols=23  Identities=17%  Similarity=0.306  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|.|..|.|||||++.+...
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G~   51 (178)
T cd03247          29 EKIALLGRSGSGKSTLLQLLTGD   51 (178)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcc
Confidence            47899999999999999999876

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.11  E-value=0.0058  Score=60.48  Aligned_cols=45  Identities=20%  Similarity=0.251  Sum_probs=36.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.|.+++.    .+ .-.....++|+.|+||||+|+.++..
T Consensus        17 diiGq~~i~---~~L~~~i~----~~-~i~hayLf~Gp~G~GKTtlAr~lAk~   61 (486)
T PRK14953         17 EVIGQEIVV---RILKNAVK----LQ-RVSHAYIFAGPRGTGKTTIARILAKV   61 (486)
T ss_pred             HccChHHHH---HHHHHHHH----cC-CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            788999999   99999887    21 22335667999999999999998765

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=97.11  E-value=0.0013  Score=57.16  Aligned_cols=57  Identities=18%  Similarity=0.086  Sum_probs=38.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPT  170 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~  170 (348)
                      ++++.++|+.|+||||.+-.++.....+  =..+..++... .....+-++..++.++.+
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~--~~~v~lis~D~~R~ga~eQL~~~a~~l~vp   58 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLK--GKKVALISADTYRIGAVEQLKTYAEILGVP   58 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHT--T--EEEEEESTSSTHHHHHHHHHHHHHTEE
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhc--cccceeecCCCCCccHHHHHHHHHHHhccc
Confidence            4689999999999999887777664333  22455666543 235566777788888765

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.11  E-value=0.0024  Score=58.75  Aligned_cols=86  Identities=19%  Similarity=0.183  Sum_probs=48.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCcccc-CCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVK-FYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTIL  188 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~-~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  188 (348)
                      ..++++++|++|+||||++..++.....+ ..+ .+..++.... ....+.+....+.++.+.    ....+..++...+
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~-~V~li~~D~~r~~a~eql~~~~~~~~~p~----~~~~~~~~l~~~l  267 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNK-KVALITTDTYRIGAVEQLKTYAKILGVPV----KVARDPKELRKAL  267 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCC-eEEEEECCccchhHHHHHHHHHHHhCCce----eccCCHHHHHHHH
Confidence            46799999999999999999988763322 223 3444544321 123344444555555442    2223445554444


Q ss_pred             HHHhcCCeEEEEEeC
Q 040110          189 RDYLTNKKYFTVLDD  203 (348)
Q Consensus       189 ~~~L~~kr~LlVLDd  203 (348)
                      .. +.+ .=++++|.
T Consensus       268 ~~-~~~-~d~vliDt  280 (282)
T TIGR03499       268 DR-LRD-KDLILIDT  280 (282)
T ss_pred             HH-ccC-CCEEEEeC
Confidence            43 333 34666664

>PRK04296 thymidine kinase; Provisional

Probab=97.10  E-value=0.0013  Score=56.82  Aligned_cols=115  Identities=9%  Similarity=-0.071  Sum_probs=64.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHh
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL  192 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L  192 (348)
                      .++.|+|..|.||||+|..+..+.  ..+-..++.+.  ..++.......++.+++....  ........++...+.+ .
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~--~~~g~~v~i~k--~~~d~~~~~~~i~~~lg~~~~--~~~~~~~~~~~~~~~~-~   75 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNY--EERGMKVLVFK--PAIDDRYGEGKVVSRIGLSRE--AIPVSSDTDIFELIEE-E   75 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHH--HHcCCeEEEEe--ccccccccCCcEecCCCCccc--ceEeCChHHHHHHHHh-h
Confidence            367789999999999998888773  22222233331  222222223445666654321  1112334555555555 3


Q ss_pred             cCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCChhhh
Q 040110          193 TNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPHNIL  236 (348)
Q Consensus       193 ~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~~v~  236 (348)
                      .++.-+||+|.+.-.  ++..++...+.  ..|..|++|.++.+..
T Consensus        76 ~~~~dvviIDEaq~l~~~~v~~l~~~l~--~~g~~vi~tgl~~~~~  119 (190)
T PRK04296         76 GEKIDCVLIDEAQFLDKEQVVQLAEVLD--DLGIPVICYGLDTDFR  119 (190)
T ss_pred             CCCCCEEEEEccccCCHHHHHHHHHHHH--HcCCeEEEEecCcccc
Confidence            334568999998642  33444443321  3477899999985543

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.10  E-value=0.0048  Score=58.53  Aligned_cols=45  Identities=22%  Similarity=0.278  Sum_probs=37.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.+...+.    .+ .-+..+.|+|+.|+||||+|..+.+.
T Consensus        24 ~l~Gh~~a~---~~L~~a~~----~g-rl~ha~L~~G~~G~GKttlA~~lA~~   68 (351)
T PRK09112         24 RLFGHEEAE---AFLAQAYR----EG-KLHHALLFEGPEGIGKATLAFHLANH   68 (351)
T ss_pred             hccCcHHHH---HHHHHHHH----cC-CCCeeEeeECCCCCCHHHHHHHHHHH
Confidence            899999999   99999887    22 23346778999999999999988776

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.09  E-value=0.00093  Score=70.49  Aligned_cols=135  Identities=11%  Similarity=0.095  Sum_probs=71.1

Q ss_pred             cccccccccccHHHHHhhcCCC-C--CCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-S--GLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRI  159 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-~--~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  159 (348)
                      .++|.+..+   +.+.+.+... .  ...+.....+.++|+.|+|||+||+.+++.  +-..-...+-+.++.-.+...+
T Consensus       510 ~v~GQ~~ai---~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~--l~~~~~~~~~~d~s~~~~~~~~  584 (821)
T CHL00095        510 RIIGQDEAV---VAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASY--FFGSEDAMIRLDMSEYMEKHTV  584 (821)
T ss_pred             cCcChHHHH---HHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHH--hcCCccceEEEEchhccccccH
Confidence            688988888   8887776411 0  012233446678999999999999999876  2111122333444332221111


Q ss_pred             HHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCe-EEEEEeCCCCh--hhHHHHHhhCCCC-----------CCCcE
Q 040110          160 LDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKK-YFTVLDDVWIE--KIWDDLREALPDN-----------QIGSR  225 (348)
Q Consensus       160 ~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr-~LlVLDdv~~~--~~~~~l~~~l~~~-----------~~gsk  225 (348)
                          .+-++.+. . ........    .+.+.++.++ .+++||++...  +.++.+...+-.+           ...+-
T Consensus       585 ----~~l~g~~~-g-yvg~~~~~----~l~~~~~~~p~~VvllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i  654 (821)
T CHL00095        585 ----SKLIGSPP-G-YVGYNEGG----QLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTL  654 (821)
T ss_pred             ----HHhcCCCC-c-ccCcCccc----hHHHHHHhCCCeEEEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceE
Confidence                11122110 0 01111112    2334444444 68889999754  5566666655432           13455


Q ss_pred             EEEEeCC
Q 040110          226 ALITVGP  232 (348)
Q Consensus       226 IlvTTR~  232 (348)
                      +|+||..
T Consensus       655 ~I~Tsn~  661 (821)
T CHL00095        655 IIMTSNL  661 (821)
T ss_pred             EEEeCCc
Confidence            6667664

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.09  E-value=0.0011  Score=67.13  Aligned_cols=49  Identities=16%  Similarity=0.208  Sum_probs=38.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +++..+|.... .......++.|+|++|+||||+++.++..
T Consensus        85 el~~~~~ki---~~l~~~l~~~~-~~~~~~~illL~GP~GsGKTTl~~~la~~  133 (637)
T TIGR00602        85 ELAVHKKKI---EEVETWLKAQV-LENAPKRILLITGPSGCGKSTTIKILSKE  133 (637)
T ss_pred             HhcCcHHHH---HHHHHHHHhcc-cccCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            789999999   88888886321 11233457899999999999999999876

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=97.09  E-value=0.0011  Score=68.90  Aligned_cols=44  Identities=20%  Similarity=0.241  Sum_probs=35.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   +++++.|..    ..  ..-+.++|++|+|||++|+.+++.
T Consensus       187 ~liGR~~ei---~~~i~iL~r----~~--~~n~LLvGppGvGKT~lae~la~~  230 (758)
T PRK11034        187 PLIGREKEL---ERAIQVLCR----RR--KNNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_pred             cCcCCCHHH---HHHHHHHhc----cC--CCCeEEECCCCCCHHHHHHHHHHH
Confidence            589999999   999998882    12  223457999999999999998865

>CHL00176 ftsH cell division protein; Validated

Probab=97.07  E-value=0.0016  Score=66.34  Aligned_cols=53  Identities=17%  Similarity=0.228  Sum_probs=35.9

Q ss_pred             cccccccccccHHHHHhhcCCCCC---CCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSG---LGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~---~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|.++....+.+++..|..+..   -+....+-+.++|++|+|||+||+.+++.
T Consensus       184 dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e  239 (638)
T CHL00176        184 DIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE  239 (638)
T ss_pred             hccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            678888877334555555542211   01223445789999999999999999886

>TIGR00959 ffh signal recognition particle protein

Probab=97.07  E-value=0.0079  Score=58.44  Aligned_cols=26  Identities=15%  Similarity=0.220  Sum_probs=21.8

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+.++.++|.+|+||||+|..++..
T Consensus        97 ~~p~vi~~vG~~GsGKTTtaakLA~~  122 (428)
T TIGR00959        97 KPPTVILMVGLQGSGKTTTCGKLAYY  122 (428)
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHH
Confidence            34679999999999999998777655

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.07  E-value=0.0021  Score=57.03  Aligned_cols=24  Identities=4%  Similarity=0.162  Sum_probs=21.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+.|+|..|+|||+||..+++.
T Consensus        42 ~~~~~l~G~~G~GKT~La~ai~~~   65 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQALVAD   65 (227)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            446789999999999999999886

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=97.06  E-value=0.0016  Score=58.97  Aligned_cols=75  Identities=19%  Similarity=0.191  Sum_probs=47.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      ...-+.++|.+|+|||.||.++.+... +..+ .+.++      +..+++.++.......            .....|.+
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~-sv~f~------~~~el~~~Lk~~~~~~------------~~~~~l~~  163 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELL-KAGI-SVLFI------TAPDLLSKLKAAFDEG------------RLEEKLLR  163 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHH-HcCC-eEEEE------EHHHHHHHHHHHHhcC------------chHHHHHH
Confidence            344577999999999999999999943 3233 34455      4556666666655431            11222333


Q ss_pred             HhcCCeEEEEEeCCCC
Q 040110          191 YLTNKKYFTVLDDVWI  206 (348)
Q Consensus       191 ~L~~kr~LlVLDdv~~  206 (348)
                      .+ .+-=||||||+-.
T Consensus       164 ~l-~~~dlLIiDDlG~  178 (254)
T COG1484         164 EL-KKVDLLIIDDIGY  178 (254)
T ss_pred             Hh-hcCCEEEEecccC
Confidence            22 2445899999864

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.05  E-value=0.0019  Score=60.63  Aligned_cols=35  Identities=11%  Similarity=-0.032  Sum_probs=25.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEE
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVR  149 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~  149 (348)
                      .-+.++|..|+|||.||.++++...- ..+ .+++++
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~-~g~-~V~y~t  218 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLD-RGK-SVIYRT  218 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHH-CCC-eEEEEE
Confidence            45889999999999999999987322 222 455664

>cd01394 radB RadB

Probab=97.04  E-value=0.0052  Score=54.08  Aligned_cols=90  Identities=12%  Similarity=0.099  Sum_probs=50.7

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHH----hCCCCCccccCCCCHHHH-
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKS----LMPTSSWLKIMGKDYKSE-  184 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~----l~~~~~~~~~~~~~~~~~-  184 (348)
                      ..-.++.|.|.+|+||||||.+++..  ....=..++|++....+.  +-+++++..    +.....  -....+..++ 
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~~a~~--~~~~g~~v~yi~~e~~~~--~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~   90 (218)
T cd01394          17 ERGTVTQVYGPPGTGKTNIAIQLAVE--TAGQGKKVAYIDTEGLSS--ERFRQIAGDRPERAASSII--VFEPMDFNEQG   90 (218)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEECCCCCH--HHHHHHHhHChHhhhcCEE--EEeCCCHHHHH
Confidence            44568899999999999999998866  222223567776655543  223333322    111100  1112222232 


Q ss_pred             --HHHHHHHhcCCeEEEEEeCCC
Q 040110          185 --KTILRDYLTNKKYFTVLDDVW  205 (348)
Q Consensus       185 --~~~l~~~L~~kr~LlVLDdv~  205 (348)
                        ...+...+..+.-++|+|.+.
T Consensus        91 ~~~~~~~~~~~~~~~lvvIDsi~  113 (218)
T cd01394          91 RAIQETETFADEKVDLVVVDSAT  113 (218)
T ss_pred             HHHHHHHHHHhcCCcEEEEechH
Confidence              334455555556789999984

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK06620 hypothetical protein; Validated

Probab=97.03  E-value=0.0012  Score=58.08  Aligned_cols=23  Identities=17%  Similarity=-0.026  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.+.|+|++|+|||+|++.+++.
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~   67 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNL   67 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhc
Confidence            56889999999999999998877

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.02  E-value=0.0017  Score=68.77  Aligned_cols=50  Identities=16%  Similarity=0.239  Sum_probs=35.8

Q ss_pred             cccccccccccHHHHHhhcCCCC-C--CCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS-G--LGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~-~--~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+.... +  ..+....++.++|+.|+|||+||+.+++.
T Consensus       569 ~viGQ~~ai---~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~  621 (857)
T PRK10865        569 RVIGQNEAV---EAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANF  621 (857)
T ss_pred             eEeCCHHHH---HHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            578988888   77777664210 0  11223357889999999999999999876

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=97.02  E-value=0.0055  Score=51.48  Aligned_cols=114  Identities=10%  Similarity=0.056  Sum_probs=64.5

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccC------------------CcceeEEEEeCCC---
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKF------------------YFDCHAWVRVSNF---  153 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~------------------~F~~~~wv~~~~~---  153 (348)
                      +.|.+.+.    . +.-+..+.++|+.|+||+++|..+++..--..                  ..+...|+.-...   
T Consensus         7 ~~L~~~~~----~-~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~   81 (162)
T PF13177_consen    7 ELLKNLIK----S-GRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKKS   81 (162)
T ss_dssp             HHHHHHHH----C-TC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSSS
T ss_pred             HHHHHHHH----c-CCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccch
Confidence            55666555    1 12233567899999999999988865421111                  1223344432221   


Q ss_pred             CCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeC
Q 040110          154 YNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVG  231 (348)
Q Consensus       154 ~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR  231 (348)
                      ..+.++. ++...+....                    ..++.=++|+|+++..  +..+.++..+-.-..++.+|++|.
T Consensus        82 i~i~~ir-~i~~~~~~~~--------------------~~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~  140 (162)
T PF13177_consen   82 IKIDQIR-EIIEFLSLSP--------------------SEGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITN  140 (162)
T ss_dssp             BSHHHHH-HHHHHCTSS---------------------TTSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES
T ss_pred             hhHHHHH-HHHHHHHHHH--------------------hcCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEEC
Confidence            2332222 3333332221                    1235678889999753  677888877766566788888887


Q ss_pred             Chh
Q 040110          232 PHN  234 (348)
Q Consensus       232 ~~~  234 (348)
                      +..
T Consensus       141 ~~~  143 (162)
T PF13177_consen  141 NPS  143 (162)
T ss_dssp             -GG
T ss_pred             ChH
Confidence            765

...

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.00  E-value=0.0015  Score=60.77  Aligned_cols=136  Identities=15%  Similarity=0.119  Sum_probs=74.5

Q ss_pred             ccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc-cccCCcceeE-E---EEeCCCCC---
Q 040110           84 LLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN-FVKFYFDCHA-W---VRVSNFYN---  155 (348)
Q Consensus        84 ~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~-~~~~~F~~~~-w---v~~~~~~~---  155 (348)
                      +-+|..+.   .-.+++|+      ++....|.+.|.+|+|||.||.+..-.. ..+..|..++ .   +.+++...   
T Consensus       226 i~prn~eQ---~~ALdlLl------d~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIGfLP  296 (436)
T COG1875         226 IRPRNAEQ---RVALDLLL------DDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIGFLP  296 (436)
T ss_pred             cCcccHHH---HHHHHHhc------CCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccccCcCC
Confidence            44566666   77778888      7788999999999999999997754222 2233444222 1   22333221   


Q ss_pred             ------HHHHHHHHHHHhCCCCCccccCCCCHHHHHHHH----------HHHhcCC---eEEEEEeCCCChhhHHHHHhh
Q 040110          156 ------FKRILDDIMKSLMPTSSWLKIMGKDYKSEKTIL----------RDYLTNK---KYFTVLDDVWIEKIWDDLREA  216 (348)
Q Consensus       156 ------~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l----------~~~L~~k---r~LlVLDdv~~~~~~~~l~~~  216 (348)
                            +.-.++.|...+..-.   +..... ......+          ..+++++   +.++|+|...+... ..++..
T Consensus       297 G~eEeKm~PWmq~i~DnLE~L~---~~~~~~-~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLTp-heikTi  371 (436)
T COG1875         297 GTEEEKMGPWMQAIFDNLEVLF---SPNEPG-DRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLTP-HELKTI  371 (436)
T ss_pred             CchhhhccchHHHHHhHHHHHh---cccccc-hHHHHHHHhccceeeeeeeeecccccccceEEEehhhccCH-HHHHHH
Confidence                  1112333333322111   111112 2222222          1233453   68999999987621 334455


Q ss_pred             CCCCCCCcEEEEEeCCh
Q 040110          217 LPDNQIGSRALITVGPH  233 (348)
Q Consensus       217 l~~~~~gskIlvTTR~~  233 (348)
                      +...+.||||+.|---.
T Consensus       372 ltR~G~GsKIVl~gd~a  388 (436)
T COG1875         372 LTRAGEGSKIVLTGDPA  388 (436)
T ss_pred             HHhccCCCEEEEcCCHH
Confidence            55567899999875433

>PRK07667 uridine kinase; Provisional

Probab=97.00  E-value=0.00081  Score=58.26  Aligned_cols=38  Identities=18%  Similarity=0.174  Sum_probs=30.9

Q ss_pred             HHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           94 LRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        94 ~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.+.+.+.    .......+|+|.|.+|+||||+|..+...
T Consensus         3 ~~~~~~~~~----~~~~~~~iIgI~G~~gsGKStla~~L~~~   40 (193)
T PRK07667          3 TNELINIMK----KHKENRFILGIDGLSRSGKTTFVANLKEN   40 (193)
T ss_pred             HHHHHHHHH----hcCCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            477777776    33445589999999999999999999876

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=96.99  E-value=0.0082  Score=54.60  Aligned_cols=42  Identities=12%  Similarity=0.051  Sum_probs=27.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRIL  160 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  160 (348)
                      -+.+.|++|+|||+||+.+++.  ....   .+.++.....+..+++
T Consensus        23 ~vLL~G~~GtGKT~lA~~la~~--lg~~---~~~i~~~~~~~~~dll   64 (262)
T TIGR02640        23 PVHLRGPAGTGKTTLAMHVARK--RDRP---VMLINGDAELTTSDLV   64 (262)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHH--hCCC---EEEEeCCccCCHHHHh
Confidence            3558999999999999999874  3222   3445555554444443

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.97  E-value=0.0063  Score=61.96  Aligned_cols=45  Identities=16%  Similarity=0.210  Sum_probs=35.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.|.+.+.    .+ .-...+.++|+.|+||||+|..+...
T Consensus        18 ~viGq~~~~---~~L~~~i~----~~-~l~hayLf~Gp~G~GKtt~A~~lAk~   62 (614)
T PRK14971         18 SVVGQEALT---TTLKNAIA----TN-KLAHAYLFCGPRGVGKTTCARIFAKT   62 (614)
T ss_pred             HhcCcHHHH---HHHHHHHH----cC-CCCeeEEEECCCCCCHHHHHHHHHHH
Confidence            789999999   99999887    21 23345778999999999999887765

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.97  E-value=0.0059  Score=59.95  Aligned_cols=45  Identities=20%  Similarity=0.240  Sum_probs=36.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+..+   +.|.+.+.    .+ .-...+.++|+.|+||||+|+.+.+.
T Consensus        18 diiGq~~~v---~~L~~~i~----~~-~i~ha~Lf~Gp~G~GKtt~A~~lAk~   62 (451)
T PRK06305         18 EILGQDAVV---AVLKNALR----FN-RAAHAYLFSGIRGTGKTTLARIFAKA   62 (451)
T ss_pred             HhcCcHHHH---HHHHHHHH----cC-CCceEEEEEcCCCCCHHHHHHHHHHH
Confidence            789999999   88888887    11 22345678999999999999998765

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.97  E-value=0.0041  Score=60.88  Aligned_cols=73  Identities=11%  Similarity=0.177  Sum_probs=44.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      ..-+.|+|+.|+|||+|++++++.  +...-..+++++      ...+...+...+...         .    ...++..
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~--l~~~~~~v~yi~------~~~f~~~~~~~l~~~---------~----~~~f~~~  199 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHA--LRESGGKILYVR------SELFTEHLVSAIRSG---------E----MQRFRQF  199 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHH--HHHcCCCEEEee------HHHHHHHHHHHHhcc---------h----HHHHHHH
Confidence            345779999999999999999987  332222344553      344555555555321         1    1224444


Q ss_pred             hcCCeEEEEEeCCCC
Q 040110          192 LTNKKYFTVLDDVWI  206 (348)
Q Consensus       192 L~~kr~LlVLDdv~~  206 (348)
                      ++. .-+|++||+..
T Consensus       200 ~~~-~dvLiIDDiq~  213 (445)
T PRK12422        200 YRN-VDALFIEDIEV  213 (445)
T ss_pred             ccc-CCEEEEcchhh
Confidence            433 44788899864

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=96.96  E-value=0.0033  Score=54.45  Aligned_cols=84  Identities=13%  Similarity=0.048  Sum_probs=45.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcc---eeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFD---CHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~---~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      ||+|.|.+|+||||||+.+...... ..+.   ....++....+........ -...............+.+.+...|..
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~-~~~~~~~~~~~~~~d~~~~~~~~~~~-~~~~~~~~~~~~p~a~d~~~l~~~l~~   78 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNK-RGIPAMEMDIILSLDDFYDDYHLRDR-KGRGENRYNFDHPDAFDFDLLKEDLKA   78 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTT-CTTTCCCSEEEEEGGGGBHHHHHHHH-HHHCTTTSSTTSGGGBSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCc-cCcCccceeEEEeecccccccchhhH-hhccccccCCCCccccCHHHHHHHHHH
Confidence            6899999999999999999876221 1122   1333333332222222222 111111100003445677788888877


Q ss_pred             HhcCCeEEE
Q 040110          191 YLTNKKYFT  199 (348)
Q Consensus       191 ~L~~kr~Ll  199 (348)
                      ..+++..-+
T Consensus        79 L~~g~~i~~   87 (194)
T PF00485_consen   79 LKNGGSIEI   87 (194)
T ss_dssp             HHTTSCEEE
T ss_pred             HhCCCcccc
Confidence            666665444

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.95  E-value=0.0034  Score=55.34  Aligned_cols=123  Identities=15%  Similarity=0.133  Sum_probs=68.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++|.+...   +.|++-..+-- . .-...-|.+||..|+|||+|++++.+.  +....-..+=|  .+.         
T Consensus        61 ~l~Gvd~qk---~~L~~NT~~F~-~-G~pANnVLLwGaRGtGKSSLVKA~~~e--~~~~glrLVEV--~k~---------  122 (287)
T COG2607          61 DLVGVDRQK---EALVRNTEQFA-E-GLPANNVLLWGARGTGKSSLVKALLNE--YADEGLRLVEV--DKE---------  122 (287)
T ss_pred             HHhCchHHH---HHHHHHHHHHH-c-CCcccceEEecCCCCChHHHHHHHHHH--HHhcCCeEEEE--cHH---------
Confidence            789988887   66665332100 1 222334678999999999999999988  54443322222  111         


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCC---hhhHHHHHhhCCCC---CCCcEEEEEeC-Chhh
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWI---EKIWDDLREALPDN---QIGSRALITVG-PHNI  235 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~---~~~~~~l~~~l~~~---~~gskIlvTTR-~~~v  235 (348)
                                    +-.+...+.+.|+.  ..+||+|..||+.=   .+....++..+-.+   .+...++..|. .++.
T Consensus       123 --------------dl~~Lp~l~~~Lr~--~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNRRHL  186 (287)
T COG2607         123 --------------DLATLPDLVELLRA--RPEKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSNRRHL  186 (287)
T ss_pred             --------------HHhhHHHHHHHHhc--CCceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecCCccc
Confidence                          11122222222221  35799999999863   24566666666432   23444444444 4444


Q ss_pred             hhhc
Q 040110          236 LTSI  239 (348)
Q Consensus       236 ~~~~  239 (348)
                      ...+
T Consensus       187 l~e~  190 (287)
T COG2607         187 LPED  190 (287)
T ss_pred             ccHh
Confidence            4433

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.95  E-value=0.0098  Score=59.26  Aligned_cols=45  Identities=22%  Similarity=0.148  Sum_probs=35.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|-+...   +.|...+.    .+ .-..+..++|+.|+||||+|+.+.+.
T Consensus        15 eiiGqe~v~---~~L~~~I~----~g-rl~hayLf~Gp~G~GKTt~Ar~LAk~   59 (535)
T PRK08451         15 ELIGQESVS---KTLSLALD----NN-RLAHAYLFSGLRGSGKTSSARIFARA   59 (535)
T ss_pred             HccCcHHHH---HHHHHHHH----cC-CCCeeEEEECCCCCcHHHHHHHHHHH
Confidence            789998888   88888887    22 23345678999999999999987765

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.94  E-value=0.0025  Score=64.07  Aligned_cols=96  Identities=11%  Similarity=0.152  Sum_probs=55.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCc--ceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYF--DCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F--~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      ..+.|+|..|+|||.|++++++.  ....+  -.++++      +..++..++...+...         ..    ..+++
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~--a~~~~~g~~V~Yi------taeef~~el~~al~~~---------~~----~~f~~  373 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHY--ARRLYPGTRVRYV------SSEEFTNEFINSIRDG---------KG----DSFRR  373 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEe------eHHHHHHHHHHHHHhc---------cH----HHHHH
Confidence            34789999999999999999987  33322  134555      3455555555544321         11    22333


Q ss_pred             HhcCCeEEEEEeCCCCh---hhHH----HHHhhCCCCCCCcEEEEEeCC
Q 040110          191 YLTNKKYFTVLDDVWIE---KIWD----DLREALPDNQIGSRALITVGP  232 (348)
Q Consensus       191 ~L~~kr~LlVLDdv~~~---~~~~----~l~~~l~~~~~gskIlvTTR~  232 (348)
                      .+++ -=+|||||+...   ..|.    .+...+.  ..|..|||||..
T Consensus       374 ~y~~-~DLLlIDDIq~l~gke~tqeeLF~l~N~l~--e~gk~IIITSd~  419 (617)
T PRK14086        374 RYRE-MDILLVDDIQFLEDKESTQEEFFHTFNTLH--NANKQIVLSSDR  419 (617)
T ss_pred             Hhhc-CCEEEEehhccccCCHHHHHHHHHHHHHHH--hcCCCEEEecCC
Confidence            3433 357888999643   2222    2222222  234568888876

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.92  E-value=0.0064  Score=56.93  Aligned_cols=96  Identities=10%  Similarity=0.061  Sum_probs=58.4

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCc----ceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-----ccCCCC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF----DCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-----KIMGKD  180 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F----~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-----~~~~~~  180 (348)
                      +.-.++-|+|++|+|||+|+.+++-.......+    ..++|++....++...+.+ +++.++......     -....+
T Consensus       100 ~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~-~~~~~g~~~~~~l~~i~~~~~~~  178 (317)
T PRK04301        100 ETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQ-MAEALGLDPDEVLDNIHVARAYN  178 (317)
T ss_pred             cCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHH-HHHHcCCChHhhhccEEEEeCCC
Confidence            456688899999999999999987552221111    3788999888888776544 445554432110     001111


Q ss_pred             ---HHHHHHHHHHHhcC--CeEEEEEeCCCC
Q 040110          181 ---YKSEKTILRDYLTN--KKYFTVLDDVWI  206 (348)
Q Consensus       181 ---~~~~~~~l~~~L~~--kr~LlVLDdv~~  206 (348)
                         ...+...+...+..  +--|||+|.+..
T Consensus       179 ~~~~~~~~~~l~~~i~~~~~~~lvVIDSisa  209 (317)
T PRK04301        179 SDHQMLLAEKAEELIKEGENIKLVIVDSLTA  209 (317)
T ss_pred             HHHHHHHHHHHHHHHhccCceeEEEEECchH
Confidence               12334555555644  445999999853

>PRK06696 uridine kinase; Validated

Probab=96.92  E-value=0.00063  Score=60.33  Aligned_cols=43  Identities=26%  Similarity=0.247  Sum_probs=32.6

Q ss_pred             cccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           87 LQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        87 r~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.+.+   ++|.+.+..   .....+.+|+|.|.+|+||||||+.+...
T Consensus         3 ~~~~~---~~la~~~~~---~~~~~~~iI~I~G~sgsGKSTlA~~L~~~   45 (223)
T PRK06696          3 RKQLI---KELAEHILT---LNLTRPLRVAIDGITASGKTTFADELAEE   45 (223)
T ss_pred             HHHHH---HHHHHHHHH---hCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            44445   666666652   12456789999999999999999999876

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=96.90  E-value=0.0035  Score=57.10  Aligned_cols=124  Identities=15%  Similarity=0.165  Sum_probs=74.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEE-EEeCCCCCHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAW-VRVSNFYNFKRILD  161 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~w-v~~~~~~~~~~~~~  161 (348)
                      .++|.+..+   +.|.+.+.      .........+|++|.|||+-|...+...--.+.|++++- .++|..-... +..
T Consensus        37 e~~gQe~vV---~~L~~a~~------~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGis-vvr  106 (346)
T KOG0989|consen   37 ELAGQEHVV---QVLKNALL------RRILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGIS-VVR  106 (346)
T ss_pred             hhcchHHHH---HHHHHHHh------hcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhccccccccc-chh
Confidence            789999999   88888888      245567778999999999999888776444566765543 3444332221 000


Q ss_pred             HHHHHhCCCCCccccCCCCHHHHHHHHHHHhc--CCe-EEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEe
Q 040110          162 DIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT--NKK-YFTVLDDVWIE--KIWDDLREALPDNQIGSRALITV  230 (348)
Q Consensus       162 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr-~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTT  230 (348)
                      +              ...+...+.........  .++ -.+|||++++-  +.|..+...+-+....++.+..|
T Consensus       107 ~--------------Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIc  166 (346)
T KOG0989|consen  107 E--------------KIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILIC  166 (346)
T ss_pred             h--------------hhcCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEc
Confidence            0              00011111111110000  123 46788999864  88999988887655556554433

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=96.89  E-value=0.0082  Score=61.65  Aligned_cols=45  Identities=18%  Similarity=0.222  Sum_probs=36.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.|...+.    .+ .-.....++|+.|+||||+|+.+++.
T Consensus        19 dIiGQe~~v---~~L~~aI~----~~-rl~HAYLF~GP~GtGKTt~AriLAk~   63 (725)
T PRK07133         19 DIVGQDHIV---QTLKNIIK----SN-KISHAYLFSGPRGTGKTSVAKIFANA   63 (725)
T ss_pred             HhcCcHHHH---HHHHHHHH----cC-CCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            789999988   88888887    21 22345668999999999999998765

>TIGR02012 tigrfam_recA protein RecA

Probab=96.88  E-value=0.003  Score=58.89  Aligned_cols=89  Identities=13%  Similarity=0.069  Sum_probs=56.8

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTIL  188 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l  188 (348)
                      +.-+++-|+|++|+||||||.++...  ....-..++|++....++..     .+++++.+.... .....+.++....+
T Consensus        53 p~G~iteI~G~~GsGKTtLaL~~~~~--~~~~g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~  125 (321)
T TIGR02012        53 PRGRIIEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIA  125 (321)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHH
Confidence            45568889999999999999987766  22222457788776665543     355555432211 11223456666666


Q ss_pred             HHHhc-CCeEEEEEeCCC
Q 040110          189 RDYLT-NKKYFTVLDDVW  205 (348)
Q Consensus       189 ~~~L~-~kr~LlVLDdv~  205 (348)
                      ...++ +.--++|+|.|-
T Consensus       126 ~~li~~~~~~lIVIDSv~  143 (321)
T TIGR02012       126 ETLVRSGAVDIIVVDSVA  143 (321)
T ss_pred             HHHhhccCCcEEEEcchh
Confidence            65554 356789999985

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>PRK14974 cell division protein FtsY; Provisional

Probab=96.88  E-value=0.0091  Score=56.17  Aligned_cols=92  Identities=13%  Similarity=0.033  Sum_probs=49.5

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC--CHHHHHHHHHHHhCCCCCccccCCCCHHHH-HHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY--NFKRILDDIMKSLMPTSSWLKIMGKDYKSE-KTI  187 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~--~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~-~~~  187 (348)
                      ++.++.++|+.|+||||++..++.... ...+. ++.+. ...+  ...+.++..+..++.+... .....+.... ...
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~-~~g~~-V~li~-~Dt~R~~a~eqL~~~a~~lgv~v~~-~~~g~dp~~v~~~a  214 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLK-KNGFS-VVIAA-GDTFRAGAIEQLEEHAERLGVKVIK-HKYGADPAAVAYDA  214 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHH-HcCCe-EEEec-CCcCcHHHHHHHHHHHHHcCCceec-ccCCCCHHHHHHHH
Confidence            468999999999999998887776522 12233 22333 2233  2334456667777654321 1222333332 233


Q ss_pred             HHHHhcCCeEEEEEeCCCC
Q 040110          188 LRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       188 l~~~L~~kr~LlVLDdv~~  206 (348)
                      +........=++++|-.-.
T Consensus       215 i~~~~~~~~DvVLIDTaGr  233 (336)
T PRK14974        215 IEHAKARGIDVVLIDTAGR  233 (336)
T ss_pred             HHHHHhCCCCEEEEECCCc
Confidence            3332222233888888743

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.87  E-value=0.012  Score=56.29  Aligned_cols=101  Identities=13%  Similarity=0.131  Sum_probs=54.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      ..++|+++|++|+||||++..++.... ...+ .+..++.... ....+-++.....++.+    -....+...+...+.
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L~-~~Gk-kVglI~aDt~RiaAvEQLk~yae~lgip----v~v~~d~~~L~~aL~  313 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQFH-GKKK-TVGFITTDHSRIGTVQQLQDYVKTIGFE----VIAVRDEAAMTRALT  313 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHHH-HcCC-cEEEEecCCcchHHHHHHHHHhhhcCCc----EEecCCHHHHHHHHH
Confidence            457899999999999999999986532 2222 2334443221 12333344555555544    222345566665554


Q ss_pred             HHhcC-CeEEEEEeCCCC----hhhHHHHHhhC
Q 040110          190 DYLTN-KKYFTVLDDVWI----EKIWDDLREAL  217 (348)
Q Consensus       190 ~~L~~-kr~LlVLDdv~~----~~~~~~l~~~l  217 (348)
                      ..-.. +.=++++|-.-.    ...+.++...+
T Consensus       314 ~lk~~~~~DvVLIDTaGRs~kd~~lm~EL~~~l  346 (436)
T PRK11889        314 YFKEEARVDYILIDTAGKNYRASETVEEMIETM  346 (436)
T ss_pred             HHHhccCCCEEEEeCccccCcCHHHHHHHHHHH
Confidence            44321 234566676532    23455554444

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=96.86  E-value=0.0023  Score=65.77  Aligned_cols=122  Identities=13%  Similarity=0.182  Sum_probs=70.3

Q ss_pred             cccccccccccHHHHHhhcCCCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRI  159 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  159 (348)
                      .++|.+.-+   ..+.+.+....   ...+.+..+....|+.|||||-||++++..  +-..=+..+-+.+|.--.-   
T Consensus       492 rViGQd~AV---~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~--Lfg~e~aliR~DMSEy~Ek---  563 (786)
T COG0542         492 RVIGQDEAV---EAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEA--LFGDEQALIRIDMSEYMEK---  563 (786)
T ss_pred             ceeChHHHH---HHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHH--hcCCCccceeechHHHHHH---
Confidence            689999999   88888774220   123455667788999999999999998876  2111133444433322111   


Q ss_pred             HHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeE-EEEEeCCCCh--hhHHHHHhhCCC
Q 040110          160 LDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKY-FTVLDDVWIE--KIWDDLREALPD  219 (348)
Q Consensus       160 ~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~-LlVLDdv~~~--~~~~~l~~~l~~  219 (348)
                       ..+.+-+|.+ +. -..-..    -..|-+..+.++| ++.||.+...  +.++-|...|-+
T Consensus       564 -HsVSrLIGaP-PG-YVGyee----GG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDd  619 (786)
T COG0542         564 -HSVSRLIGAP-PG-YVGYEE----GGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDD  619 (786)
T ss_pred             -HHHHHHhCCC-CC-Cceecc----ccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcC
Confidence             1222223322 11 111111    2334555667776 6778999864  667777776654

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.86  E-value=0.014  Score=56.83  Aligned_cols=86  Identities=17%  Similarity=0.088  Sum_probs=47.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCcc-ccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNF-VKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~-~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      .+++.++|++|+||||++..++.... ....+ .+..++.... ....+.+....+.++.+.    ....+..++...+.
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~-~V~li~~D~~r~~a~eqL~~~a~~~~vp~----~~~~~~~~l~~~l~  295 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKK-KVALITLDTYRIGAVEQLKTYAKIMGIPV----EVVYDPKELAKALE  295 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCC-eEEEEECCccHHHHHHHHHHHHHHhCCce----EccCCHHhHHHHHH
Confidence            46899999999999999888876532 12222 3445554321 112233444455555442    22234455555554


Q ss_pred             HHhcCCeEEEEEeCC
Q 040110          190 DYLTNKKYFTVLDDV  204 (348)
Q Consensus       190 ~~L~~kr~LlVLDdv  204 (348)
                      . +. ..=++++|..
T Consensus       296 ~-~~-~~DlVlIDt~  308 (424)
T PRK05703        296 Q-LR-DCDVILIDTA  308 (424)
T ss_pred             H-hC-CCCEEEEeCC
Confidence            3 33 3466777865

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.85  E-value=0.0031  Score=65.89  Aligned_cols=50  Identities=20%  Similarity=0.254  Sum_probs=35.4

Q ss_pred             cccccccccccHHHHHhhcCCC-------CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-------SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-------~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|.+..+   +.+.+.+.-+       ...+-...+-+.++|++|+|||+||+.+++.
T Consensus       179 di~G~~~~~---~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~  235 (733)
T TIGR01243       179 DIGGLKEAK---EKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANE  235 (733)
T ss_pred             HhcCHHHHH---HHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHH
Confidence            578999888   7776665310       0011123455779999999999999999987

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.85  E-value=0.01  Score=60.46  Aligned_cols=136  Identities=10%  Similarity=0.034  Sum_probs=70.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++|.+...   +.|..++.    .+. -...+.++|+.|+||||+|..+++..........     ....+..-...+.
T Consensus        17 ~liGq~~i~---~~L~~~l~----~~r-l~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~-----~~~~Cg~C~~C~~   83 (620)
T PRK14948         17 ELVGQEAIA---TTLKNALI----SNR-IAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKP-----TPEPCGKCELCRA   83 (620)
T ss_pred             hccChHHHH---HHHHHHHH----cCC-CCceEEEECCCCCChHHHHHHHHHHhcCCCcCCC-----CCCCCcccHHHHH
Confidence            788999999   88888887    222 2235678999999999999999877322111100     0011121122333


Q ss_pred             HHHHhCCCCCcc-ccCCCCHHHHHHHHHHH----hcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeC
Q 040110          163 IMKSLMPTSSWL-KIMGKDYKSEKTILRDY----LTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVG  231 (348)
Q Consensus       163 i~~~l~~~~~~~-~~~~~~~~~~~~~l~~~----L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR  231 (348)
                      +........... .......+++.+.+...    ..+++-++|+|++...  ..++.|...+-.....+.+|++|.
T Consensus        84 i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~  159 (620)
T PRK14948         84 IAAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATT  159 (620)
T ss_pred             HhcCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeC
Confidence            322222110000 00112233332222111    1245568899999753  567777777655444454444443

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=96.85  E-value=0.005  Score=59.15  Aligned_cols=115  Identities=13%  Similarity=0.122  Sum_probs=75.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++||+.+.   ..+.+++...  -.....+-+-|.|-+|.|||.+...++.+......=.+++.++...-.....++..
T Consensus       151 ~l~gRe~e~---~~v~~F~~~h--le~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~k  225 (529)
T KOG2227|consen  151 TLKGRELEM---DIVREFFSLH--LELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKK  225 (529)
T ss_pred             CccchHHHH---HHHHHHHHhh--hhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHH
Confidence            799999999   8888888632  12344556778999999999999999988322222124566665544456666777


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHHHHHhcCC--eEEEEEeCCCC
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNK--KYFTVLDDVWI  206 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~k--r~LlVLDdv~~  206 (348)
                      |...+-..    ........+.+..+.......  -+|+|||..+.
T Consensus       226 I~~~~~q~----~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~  267 (529)
T KOG2227|consen  226 IFSSLLQD----LVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDH  267 (529)
T ss_pred             HHHHHHHH----hcCCchhHHHHHHHHHHHhcccceEEEEechhhH
Confidence            76666111    001112256667777777553  58899998853

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.84  E-value=0.0024  Score=55.83  Aligned_cols=26  Identities=23%  Similarity=0.309  Sum_probs=24.0

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.+.+|+|-|.+|+||||+|+.++..
T Consensus         6 ~~~iiIgIaG~SgSGKTTva~~l~~~   31 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSEQ   31 (218)
T ss_pred             CceEEEEEeCCCCCCHHHHHHHHHHH
Confidence            46689999999999999999999988

>TIGR01817 nifA Nif-specific regulatory protein

Probab=96.83  E-value=0.03  Score=56.36  Aligned_cols=46  Identities=17%  Similarity=0.216  Sum_probs=35.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|....+   +++.+.+...    .....-|.|+|..|+|||++|+.+++.
T Consensus       197 ~liG~s~~~---~~~~~~~~~~----a~~~~pvli~Ge~GtGK~~lA~~ih~~  242 (534)
T TIGR01817       197 GIIGKSPAM---RQVVDQARVV----ARSNSTVLLRGESGTGKELIAKAIHYL  242 (534)
T ss_pred             ceEECCHHH---HHHHHHHHHH----hCcCCCEEEECCCCccHHHHHHHHHHh
Confidence            899999999   8887777521    122234669999999999999999876

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=96.83  E-value=0.0092  Score=50.48  Aligned_cols=22  Identities=27%  Similarity=0.342  Sum_probs=19.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.++|++|+||||++..++..
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~   23 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALY   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6788999999999999988866

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.83  E-value=0.016  Score=58.49  Aligned_cols=45  Identities=18%  Similarity=0.240  Sum_probs=36.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.|.+++.    .+. -...+.++|+.|+||||+|+.+.+.
T Consensus        17 ~viGq~~v~---~~L~~~i~----~~~-~~hayLf~Gp~GtGKTt~Ak~lAka   61 (559)
T PRK05563         17 DVVGQEHIT---KTLKNAIK----QGK-ISHAYLFSGPRGTGKTSAAKIFAKA   61 (559)
T ss_pred             hccCcHHHH---HHHHHHHH----cCC-CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            799999999   99999887    222 2345667999999999999998765

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.83  E-value=0.003  Score=58.99  Aligned_cols=89  Identities=15%  Similarity=0.078  Sum_probs=56.7

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTIL  188 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l  188 (348)
                      +.-+++-|+|++|+||||||.+++..  ....-..++|++....++..     .+++++.+.... -....+.++....+
T Consensus        53 p~G~iteI~Gp~GsGKTtLal~~~~~--~~~~g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~  125 (325)
T cd00983          53 PKGRIIEIYGPESSGKTTLALHAIAE--AQKLGGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIA  125 (325)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHH
Confidence            34568889999999999999998765  22233467788877666643     344444432210 11223456666666


Q ss_pred             HHHhcC-CeEEEEEeCCC
Q 040110          189 RDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       189 ~~~L~~-kr~LlVLDdv~  205 (348)
                      ...++. .--++|+|.|-
T Consensus       126 ~~li~s~~~~lIVIDSva  143 (325)
T cd00983         126 DSLVRSGAVDLIVVDSVA  143 (325)
T ss_pred             HHHHhccCCCEEEEcchH
Confidence            665544 56789999975

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK10867 signal recognition particle protein; Provisional

Probab=96.82  E-value=0.0052  Score=59.70  Aligned_cols=26  Identities=19%  Similarity=0.285  Sum_probs=21.4

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+.++.++|++|+||||++..++..
T Consensus        98 ~~p~vI~~vG~~GsGKTTtaakLA~~  123 (433)
T PRK10867         98 KPPTVIMMVGLQGAGKTTTAGKLAKY  123 (433)
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHH
Confidence            34789999999999999977776654

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.81  E-value=0.0043  Score=56.94  Aligned_cols=82  Identities=10%  Similarity=0.155  Sum_probs=51.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccc--cCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFV--KFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTIL  188 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~--~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  188 (348)
                      ..++|.++|++|.|||+|+++++++..+  .+.|....-+.+.    -..+.....          +.+..-+..+-+.|
T Consensus       176 ~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEin----shsLFSKWF----------sESgKlV~kmF~kI  241 (423)
T KOG0744|consen  176 WNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEIN----SHSLFSKWF----------SESGKLVAKMFQKI  241 (423)
T ss_pred             eeeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEe----hhHHHHHHH----------hhhhhHHHHHHHHH
Confidence            3678899999999999999999998643  3455444434332    122222222          12233456667777


Q ss_pred             HHHhcCCe--EEEEEeCCCC
Q 040110          189 RDYLTNKK--YFTVLDDVWI  206 (348)
Q Consensus       189 ~~~L~~kr--~LlVLDdv~~  206 (348)
                      .+.+.++.  +++.+|.|.+
T Consensus       242 ~ELv~d~~~lVfvLIDEVES  261 (423)
T KOG0744|consen  242 QELVEDRGNLVFVLIDEVES  261 (423)
T ss_pred             HHHHhCCCcEEEEEeHHHHH
Confidence            88887764  3344688853

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.81  E-value=0.013  Score=52.14  Aligned_cols=93  Identities=14%  Similarity=0.152  Sum_probs=57.8

Q ss_pred             CCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-------------
Q 040110          108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-------------  174 (348)
Q Consensus       108 ~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-------------  174 (348)
                      +-+.-+++.|.|.+|+|||+|+.++.... .++. ..++|++....  ..++.+++ .+++....+.             
T Consensus        21 G~~~g~~~~i~G~~GsGKt~l~~~~~~~~-~~~g-~~~~y~~~e~~--~~~~~~~~-~~~g~~~~~~~~~g~l~i~~~~~   95 (234)
T PRK06067         21 GIPFPSLILIEGDHGTGKSVLSQQFVYGA-LKQG-KKVYVITTENT--SKSYLKQM-ESVKIDISDFFLWGYLRIFPLNT   95 (234)
T ss_pred             CCcCCcEEEEECCCCCChHHHHHHHHHHH-HhCC-CEEEEEEcCCC--HHHHHHHH-HHCCCChhHHHhCCCceEEeccc
Confidence            34556788999999999999999985441 2222 36778877544  44555553 3343221110             


Q ss_pred             ---ccCCCCHHHHHHHHHHHhcC-CeEEEEEeCCC
Q 040110          175 ---KIMGKDYKSEKTILRDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       175 ---~~~~~~~~~~~~~l~~~L~~-kr~LlVLDdv~  205 (348)
                         .....+.+.+...+.+.+.. +.-++|+|.+-
T Consensus        96 ~~~~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067         96 EGFEWNSTLANKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             cccccCcchHHHHHHHHHHHHHhcCCCEEEEecHH
Confidence               01123446777777777764 56689999975

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.80  E-value=0.014  Score=58.74  Aligned_cols=45  Identities=18%  Similarity=0.187  Sum_probs=37.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|-+...   +.|...+.    .+ .-...+.++|+.|+||||+|+.+++.
T Consensus        17 diiGqe~iv---~~L~~~i~----~~-~i~hayLf~Gp~G~GKTt~Ar~lAk~   61 (563)
T PRK06647         17 SLEGQDFVV---ETLKHSIE----SN-KIANAYIFSGPRGVGKTSSARAFARC   61 (563)
T ss_pred             HccCcHHHH---HHHHHHHH----cC-CCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            789999999   89999887    22 23346778999999999999999876

>PRK09354 recA recombinase A; Provisional

Probab=96.80  E-value=0.0037  Score=58.84  Aligned_cols=89  Identities=16%  Similarity=0.070  Sum_probs=58.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTIL  188 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l  188 (348)
                      +.-+++-|+|++|+||||||.++...  ....-..++|+.....++.     ..+++++...... .....+.++....+
T Consensus        58 p~G~IteI~G~~GsGKTtLal~~~~~--~~~~G~~~~yId~E~s~~~-----~~a~~lGvdld~lli~qp~~~Eq~l~i~  130 (349)
T PRK09354         58 PRGRIVEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDP-----VYAKKLGVDIDNLLVSQPDTGEQALEIA  130 (349)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEECCccchHH-----HHHHHcCCCHHHeEEecCCCHHHHHHHH
Confidence            45568889999999999999998765  2223346788887777665     2455555432211 11223456666666


Q ss_pred             HHHhcC-CeEEEEEeCCC
Q 040110          189 RDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       189 ~~~L~~-kr~LlVLDdv~  205 (348)
                      ...++. .--++|+|.|-
T Consensus       131 ~~li~s~~~~lIVIDSva  148 (349)
T PRK09354        131 DTLVRSGAVDLIVVDSVA  148 (349)
T ss_pred             HHHhhcCCCCEEEEeChh
Confidence            666544 56789999985

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.79  E-value=0.026  Score=54.72  Aligned_cols=26  Identities=15%  Similarity=0.217  Sum_probs=22.4

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+.+|.++|+.|+||||++..++..
T Consensus        98 ~~~~vi~lvG~~GvGKTTtaaKLA~~  123 (429)
T TIGR01425        98 GKQNVIMFVGLQGSGKTTTCTKLAYY  123 (429)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34689999999999999999888754

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=96.79  E-value=0.018  Score=48.51  Aligned_cols=114  Identities=11%  Similarity=0.045  Sum_probs=57.5

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCcccc-CC--cc---eeEEEEeCCCC--CHHHHHHHHHHHhCCCCCccccCCCCHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVK-FY--FD---CHAWVRVSNFY--NFKRILDDIMKSLMPTSSWLKIMGKDYKS  183 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~-~~--F~---~~~wv~~~~~~--~~~~~~~~i~~~l~~~~~~~~~~~~~~~~  183 (348)
                      -.+++|+|..|.|||||++.+....... ..  ++   .+.++  .+..  ....+...+... ..     . .-..-..
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~~~~~i~~~--~q~~~~~~~tv~~nl~~~-~~-----~-~LS~G~~   97 (166)
T cd03223          27 GDRLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLFL--PQRPYLPLGTLREQLIYP-WD-----D-VLSGGEQ   97 (166)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCCceEEEE--CCCCccccccHHHHhhcc-CC-----C-CCCHHHH
Confidence            3478999999999999999998763221 11  11   12222  2222  111333333211 00     1 1111223


Q ss_pred             HHHHHHHHhcCCeEEEEEeCCCCh---hhHHHHHhhCCCCCCCcEEEEEeCChhhh
Q 040110          184 EKTILRDYLTNKKYFTVLDDVWIE---KIWDDLREALPDNQIGSRALITVGPHNIL  236 (348)
Q Consensus       184 ~~~~l~~~L~~kr~LlVLDdv~~~---~~~~~l~~~l~~~~~gskIlvTTR~~~v~  236 (348)
                      ..-.+.+.|..++=+++||+.-+.   .....+...+...  +..||++|.+....
T Consensus        98 ~rv~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~~  151 (166)
T cd03223          98 QRLAFARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSLW  151 (166)
T ss_pred             HHHHHHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhHH
Confidence            333455566667788889987543   2222222222221  34577777776543

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.76  E-value=0.016  Score=55.27  Aligned_cols=89  Identities=20%  Similarity=0.122  Sum_probs=51.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      .-.+++++|+.|+||||++..+......+.....+..++... .....+.++...+.++.+..    ...+..++...+.
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~----~~~~~~~l~~~l~  211 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVH----AVKDGGDLQLALA  211 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceE----ecCCcccHHHHHH
Confidence            346899999999999999999987632222122344554322 23445666666777766522    2223333333333


Q ss_pred             HHhcCCeEEEEEeCCC
Q 040110          190 DYLTNKKYFTVLDDVW  205 (348)
Q Consensus       190 ~~L~~kr~LlVLDdv~  205 (348)
                       .+.++ -++++|..-
T Consensus       212 -~l~~~-DlVLIDTaG  225 (374)
T PRK14722        212 -ELRNK-HMVLIDTIG  225 (374)
T ss_pred             -HhcCC-CEEEEcCCC
Confidence             34444 455588874

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=96.75  E-value=0.021  Score=48.73  Aligned_cols=120  Identities=13%  Similarity=0.071  Sum_probs=63.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEE---eCCCCCHHHH------HHHHHHHhCCCCCcc-ccCCCCHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVR---VSNFYNFKRI------LDDIMKSLMPTSSWL-KIMGKDYK  182 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~---~~~~~~~~~~------~~~i~~~l~~~~~~~-~~~~~~~~  182 (348)
                      .+++|+|..|.|||||++.++...   ......+++.   +. ..+....      .-++++.++...... .....+..
T Consensus        26 ~~~~l~G~nGsGKStLl~~i~G~~---~~~~G~v~~~g~~~~-~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~G  101 (180)
T cd03214          26 EIVGILGPNGAGKSTLLKTLAGLL---KPSSGEILLDGKDLA-SLSPKELARKIAYVPQALELLGLAHLADRPFNELSGG  101 (180)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC---CCCCcEEEECCEECC-cCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCHH
Confidence            478999999999999999998762   2233444332   21 1122221      112455554431100 11112222


Q ss_pred             H-HHHHHHHHhcCCeEEEEEeCCCCh---hhHHHHHhhCCCC-CC-CcEEEEEeCChhhh
Q 040110          183 S-EKTILRDYLTNKKYFTVLDDVWIE---KIWDDLREALPDN-QI-GSRALITVGPHNIL  236 (348)
Q Consensus       183 ~-~~~~l~~~L~~kr~LlVLDdv~~~---~~~~~l~~~l~~~-~~-gskIlvTTR~~~v~  236 (348)
                      + ..-.+.+.|-..+-+++||+.-+.   ...+.+...+... .. +..||++|.+....
T Consensus       102 ~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~~  161 (180)
T cd03214         102 ERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNLA  161 (180)
T ss_pred             HHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHH
Confidence            2 223455666678889999997643   2223333332211 11 56788888776644

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=96.75  E-value=0.0074  Score=51.46  Aligned_cols=22  Identities=36%  Similarity=0.409  Sum_probs=20.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|.|+|++|+||||+|+.+...
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~   22 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVEN   22 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999876

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=96.73  E-value=0.012  Score=50.07  Aligned_cols=116  Identities=12%  Similarity=0.099  Sum_probs=60.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc-cc--cC---Ccc--eeEEEEeCCCCCHHHHHHHHHHHhCCCCC--ccccCCCCH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN-FV--KF---YFD--CHAWVRVSNFYNFKRILDDIMKSLMPTSS--WLKIMGKDY  181 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~-~~--~~---~F~--~~~wv~~~~~~~~~~~~~~i~~~l~~~~~--~~~~~~~~~  181 (348)
                      -.+++|+|+.|+|||||.+.+..+. .+  ..   .|.  ...|+  .+        .+.+..++....  .......+.
T Consensus        21 G~~~~l~G~nG~GKSTLl~~il~~~G~v~~~~~~~~~~~~~~~~~--~q--------~~~l~~~~L~~~~~~~~~~~LSg   90 (176)
T cd03238          21 NVLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIFI--DQ--------LQFLIDVGLGYLTLGQKLSTLSG   90 (176)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhcCCcEEECCcccccccccEEEE--hH--------HHHHHHcCCCccccCCCcCcCCH
Confidence            3478999999999999999886321 11  11   111  12232  11        456666665321  001111222


Q ss_pred             HH-HHHHHHHHhcCC--eEEEEEeCCCCh---hhHHHHHhhCCC-CCCCcEEEEEeCChhhhh
Q 040110          182 KS-EKTILRDYLTNK--KYFTVLDDVWIE---KIWDDLREALPD-NQIGSRALITVGPHNILT  237 (348)
Q Consensus       182 ~~-~~~~l~~~L~~k--r~LlVLDdv~~~---~~~~~l~~~l~~-~~~gskIlvTTR~~~v~~  237 (348)
                      .+ ..-.+.+.|..+  .-+++||..-+.   ...+.+...+.. ...|..||++|.+.....
T Consensus        91 Gq~qrl~laral~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~~~~  153 (176)
T cd03238          91 GELQRVKLASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLDVLS  153 (176)
T ss_pred             HHHHHHHHHHHHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHH
Confidence            22 222344555556  778888987543   222333322221 113566888888876553

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.70  E-value=0.0079  Score=50.52  Aligned_cols=113  Identities=11%  Similarity=0.014  Sum_probs=58.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeC--CCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVS--NFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~--~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      .+++|.|..|.|||||.+.++...   ......+++.-.  ...+..+..   .+.++.-     .+-..-+...-.+.+
T Consensus        27 e~~~l~G~nGsGKSTLl~~i~G~~---~~~~G~v~~~g~~~~~~~~~~~~---~~~i~~~-----~qLS~G~~qrl~lar   95 (163)
T cd03216          27 EVHALLGENGAGKSTLMKILSGLY---KPDSGEILVDGKEVSFASPRDAR---RAGIAMV-----YQLSVGERQMVEIAR   95 (163)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC---CCCCeEEEECCEECCcCCHHHHH---hcCeEEE-----EecCHHHHHHHHHHH
Confidence            378999999999999999998762   233444544211  111111111   1111110     001111223334555


Q ss_pred             HhcCCeEEEEEeCCCCh---hhHHHHHhhCCC-CCCCcEEEEEeCChhhh
Q 040110          191 YLTNKKYFTVLDDVWIE---KIWDDLREALPD-NQIGSRALITVGPHNIL  236 (348)
Q Consensus       191 ~L~~kr~LlVLDdv~~~---~~~~~l~~~l~~-~~~gskIlvTTR~~~v~  236 (348)
                      .+-.++-+++||+.-+.   .....+...+.. ...|..||++|.+...+
T Consensus        96 al~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~~  145 (163)
T cd03216          96 ALARNARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLDEV  145 (163)
T ss_pred             HHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHH
Confidence            66677888999997653   222233222221 12355688888886643

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=96.70  E-value=0.0027  Score=65.94  Aligned_cols=50  Identities=16%  Similarity=0.252  Sum_probs=36.8

Q ss_pred             cccccccccccHHHHHhhcCCC-CC--CCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-SG--LGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-~~--~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.|.+.+... .+  ........+.++|++|+|||++|+.++..
T Consensus       459 ~ViGQ~~ai---~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~  511 (758)
T PRK11034        459 LVFGQDKAI---EALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA  511 (758)
T ss_pred             eEeCcHHHH---HHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHH
Confidence            578988888   7777776521 00  11233457889999999999999999887

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=96.68  E-value=0.012  Score=47.89  Aligned_cols=22  Identities=14%  Similarity=0.309  Sum_probs=19.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|.+.|++|+||||+|+.+...
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~   22 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKR   22 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5778999999999999999865

...

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=96.67  E-value=0.004  Score=62.00  Aligned_cols=53  Identities=21%  Similarity=0.245  Sum_probs=33.0

Q ss_pred             cccccccccccHHHHHhhcCCCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+.....+.+++.++..+.   ..+....+-+.++|++|+|||+||+.+++.
T Consensus        56 di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~  111 (495)
T TIGR01241        56 DVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE  111 (495)
T ss_pred             HhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            67887777622233344333110   011223344778999999999999999987

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.67  E-value=0.016  Score=54.11  Aligned_cols=96  Identities=10%  Similarity=0.059  Sum_probs=57.1

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCC----cceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc----c-cCCCC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFY----FDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL----K-IMGKD  180 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~----F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~----~-~~~~~  180 (348)
                      ..-.++-|+|.+|+|||+|+.+++........    =..++|++....++...+. +++..++......    . ....+
T Consensus        93 ~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~gl~~~~~~~~i~i~~~~~  171 (310)
T TIGR02236        93 ETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARGLDPDEVLKNIYVARAYN  171 (310)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcCCCHHHHhhceEEEecCC
Confidence            44678889999999999999998765322110    1268899988888877654 4455554431100    0 00111


Q ss_pred             H---HHHHHHHHHHhcCC---eEEEEEeCCCC
Q 040110          181 Y---KSEKTILRDYLTNK---KYFTVLDDVWI  206 (348)
Q Consensus       181 ~---~~~~~~l~~~L~~k---r~LlVLDdv~~  206 (348)
                      .   ..+.+.+.+.+...   .-++|+|.+..
T Consensus       172 ~~~~~~lld~l~~~i~~~~~~~~lVVIDSisa  203 (310)
T TIGR02236       172 SNHQMLLVEKAEDLIKELNNPVKLLIVDSLTS  203 (310)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCceEEEEecchH
Confidence            1   12344455555432   45899998853

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=96.66  E-value=0.00072  Score=67.93  Aligned_cols=55  Identities=15%  Similarity=0.198  Sum_probs=43.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF  142 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F  142 (348)
                      +-+|.++..   ++|++.|....-...-.-.+++++|++|+|||+|++.+++.  ..+.|
T Consensus       324 dHYGLekVK---eRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~a--l~Rkf  378 (782)
T COG0466         324 DHYGLEKVK---ERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKA--LGRKF  378 (782)
T ss_pred             cccCchhHH---HHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHH--hCCCE
Confidence            679999999   99999995211122233369999999999999999999988  76666

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.66  E-value=0.0015  Score=53.96  Aligned_cols=25  Identities=20%  Similarity=0.193  Sum_probs=21.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .--|+|.|++|+||||+++.+.+..
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~L   29 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEKL   29 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHHH
Confidence            3458899999999999999999773

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=96.64  E-value=0.023  Score=46.63  Aligned_cols=101  Identities=12%  Similarity=0.030  Sum_probs=54.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHh
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL  192 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L  192 (348)
                      .+++|+|..|.|||||++.+.....   .....+++.-.             ..++.-     ..-..-....-.+.+.|
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~~---~~~G~i~~~~~-------------~~i~~~-----~~lS~G~~~rv~laral   85 (144)
T cd03221          27 DRIGLVGRNGAGKSTLLKLIAGELE---PDEGIVTWGST-------------VKIGYF-----EQLSGGEKMRLALAKLL   85 (144)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCCC---CCceEEEECCe-------------EEEEEE-----ccCCHHHHHHHHHHHHH
Confidence            4789999999999999999987632   22333433110             000000     00001122233355566


Q ss_pred             cCCeEEEEEeCCCCh---hhHHHHHhhCCCCCCCcEEEEEeCChhhh
Q 040110          193 TNKKYFTVLDDVWIE---KIWDDLREALPDNQIGSRALITVGPHNIL  236 (348)
Q Consensus       193 ~~kr~LlVLDdv~~~---~~~~~l~~~l~~~~~gskIlvTTR~~~v~  236 (348)
                      ..+.-+++||+.-..   .....+...+..-  +..||++|.+...+
T Consensus        86 ~~~p~illlDEP~~~LD~~~~~~l~~~l~~~--~~til~~th~~~~~  130 (144)
T cd03221          86 LENPNLLLLDEPTNHLDLESIEALEEALKEY--PGTVILVSHDRYFL  130 (144)
T ss_pred             hcCCCEEEEeCCccCCCHHHHHHHHHHHHHc--CCEEEEEECCHHHH
Confidence            667788999997643   2233333332221  24578888776654

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.63  E-value=0.0088  Score=58.36  Aligned_cols=106  Identities=17%  Similarity=0.142  Sum_probs=60.4

Q ss_pred             CCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHH
Q 040110          108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTI  187 (348)
Q Consensus       108 ~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  187 (348)
                      ...+...+.+.|++|+|||+||..++..    ..|+.+--++.      ++                 .-..+.......
T Consensus       534 ~~s~lvSvLl~Gp~~sGKTaLAA~iA~~----S~FPFvKiiSp------e~-----------------miG~sEsaKc~~  586 (744)
T KOG0741|consen  534 ERSPLVSVLLEGPPGSGKTALAAKIALS----SDFPFVKIISP------ED-----------------MIGLSESAKCAH  586 (744)
T ss_pred             ccCcceEEEEecCCCCChHHHHHHHHhh----cCCCeEEEeCh------HH-----------------ccCccHHHHHHH
Confidence            3455666778999999999999999865    56764433321      11                 011122223333


Q ss_pred             HHHH----hcCCeEEEEEeCCCChhhHH------------HHHhhCCC-CCCCcEE--EEEeCChhhhhhcc
Q 040110          188 LRDY----LTNKKYFTVLDDVWIEKIWD------------DLREALPD-NQIGSRA--LITVGPHNILTSIE  240 (348)
Q Consensus       188 l~~~----L~~kr~LlVLDdv~~~~~~~------------~l~~~l~~-~~~gskI--lvTTR~~~v~~~~~  240 (348)
                      +++.    -+..=..||+||+...-+|-            .+...+.. ...|-|.  +-||....+.+.++
T Consensus       587 i~k~F~DAYkS~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~  658 (744)
T KOG0741|consen  587 IKKIFEDAYKSPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMG  658 (744)
T ss_pred             HHHHHHHhhcCcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcC
Confidence            3333    34556789999997543332            23222221 1124444  44888888888733

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=96.63  E-value=0.0055  Score=57.80  Aligned_cols=27  Identities=11%  Similarity=0.219  Sum_probs=24.7

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -..+..++|+|++|+|||.+|+.+++.
T Consensus       145 ik~PlgllL~GPPGcGKTllAraiA~e  171 (413)
T PLN00020        145 IKVPLILGIWGGKGQGKSFQCELVFKK  171 (413)
T ss_pred             CCCCeEEEeeCCCCCCHHHHHHHHHHH
Confidence            356788999999999999999999998

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=96.62  E-value=0.0016  Score=63.43  Aligned_cols=55  Identities=20%  Similarity=0.324  Sum_probs=37.2

Q ss_pred             cccccccccccHHHHHhhcCCC-C------CCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-S------GLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF  142 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-~------~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F  142 (348)
                      ++.|.+..+   ++|.+.+.-+ .      .-+-...+-+.++|++|+|||++|+.+++.  ....|
T Consensus       184 DIgGl~~qi---~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~e--l~~~f  245 (438)
T PTZ00361        184 DIGGLEQQI---QEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANE--TSATF  245 (438)
T ss_pred             HhcCHHHHH---HHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHh--hCCCE
Confidence            567888888   7776665311 0      011223455778999999999999999987  44444

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.62  E-value=0.016  Score=54.69  Aligned_cols=107  Identities=12%  Similarity=0.102  Sum_probs=63.8

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccC----CcceeEEEEeCCCCCHHHHHHHHHHHhCCC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKF----YFDCHAWVRVSNFYNFKRILDDIMKSLMPT  170 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~----~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~  170 (348)
                      ..|-.+|.    .+-..-.++-|.|.+|+|||+|+..++-......    .-..++|++....|+...+ .+|++.++..
T Consensus       110 ~~LD~lL~----GG~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl-~qia~~~~~~  184 (342)
T PLN03186        110 RELDKILE----GGIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRL-IQIAERFGLN  184 (342)
T ss_pred             HHHHHhhc----CCCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHH-HHHHHHcCCC
Confidence            44444444    2334566888999999999999988774421111    1126889999998888775 4556666554


Q ss_pred             CCcc-----ccCCCCHHHHHHHHH---HHh-cCCeEEEEEeCCCC
Q 040110          171 SSWL-----KIMGKDYKSEKTILR---DYL-TNKKYFTVLDDVWI  206 (348)
Q Consensus       171 ~~~~-----~~~~~~~~~~~~~l~---~~L-~~kr~LlVLDdv~~  206 (348)
                      ....     -....+.+.+...+.   ..+ ..+--|||+|.+-.
T Consensus       185 ~~~~l~~i~~~~~~~~e~~~~ll~~~~~~~~~~~~~LIVIDSI~a  229 (342)
T PLN03186        185 GADVLENVAYARAYNTDHQSELLLEAASMMAETRFALMIVDSATA  229 (342)
T ss_pred             hhhhccceEEEecCCHHHHHHHHHHHHHHhhccCCCEEEEeCcHH
Confidence            2110     111234444433333   223 34567899999853

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=96.62  E-value=0.013  Score=53.40  Aligned_cols=94  Identities=16%  Similarity=0.041  Sum_probs=59.6

Q ss_pred             CCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHH---H
Q 040110          108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKS---E  184 (348)
Q Consensus       108 ~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~---~  184 (348)
                      +-+.-+++=|+|+.|+||||+|.+++-.  ....-..++|++..+.+++..+..-....+..-.   -....+.++   +
T Consensus        56 Gl~~g~ItEiyG~~gsGKT~lal~~~~~--aq~~g~~a~fIDtE~~l~p~r~~~l~~~~~d~l~---v~~~~~~e~q~~i  130 (279)
T COG0468          56 GLPRGRITEIYGPESSGKTTLALQLVAN--AQKPGGKAAFIDTEHALDPERAKQLGVDLLDNLL---VSQPDTGEQQLEI  130 (279)
T ss_pred             CcccceEEEEecCCCcchhhHHHHHHHH--hhcCCCeEEEEeCCCCCCHHHHHHHHHhhhccee---EecCCCHHHHHHH
Confidence            3456678899999999999999998876  4444447899999999998765433322122110   112223333   3


Q ss_pred             HHHHHHHhcCCeEEEEEeCCCC
Q 040110          185 KTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       185 ~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                      ...+......+--|+|+|.+-.
T Consensus       131 ~~~~~~~~~~~i~LvVVDSvaa  152 (279)
T COG0468         131 AEKLARSGAEKIDLLVVDSVAA  152 (279)
T ss_pred             HHHHHHhccCCCCEEEEecCcc
Confidence            3333333333468999999854

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=96.62  E-value=0.0057  Score=58.61  Aligned_cols=100  Identities=17%  Similarity=0.121  Sum_probs=59.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      ....+.|+|..|.|||.|++++.+.  .....+....+.+    +.+.....++..+...             -...+++
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~--~~~~~~~a~v~y~----~se~f~~~~v~a~~~~-------------~~~~Fk~  172 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNE--ALANGPNARVVYL----TSEDFTNDFVKALRDN-------------EMEKFKE  172 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHH--HHhhCCCceEEec----cHHHHHHHHHHHHHhh-------------hHHHHHH
Confidence            4567889999999999999999998  5555553333332    3344555555444332             1234555


Q ss_pred             HhcCCeEEEEEeCCCCh---hhH----HHHHhhCCCCCCCcEEEEEeCCh
Q 040110          191 YLTNKKYFTVLDDVWIE---KIW----DDLREALPDNQIGSRALITVGPH  233 (348)
Q Consensus       191 ~L~~kr~LlVLDdv~~~---~~~----~~l~~~l~~~~~gskIlvTTR~~  233 (348)
                      ..  .-=++++||++-.   +.|    -.+...+..  .|-.||+|++..
T Consensus       173 ~y--~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~--~~kqIvltsdr~  218 (408)
T COG0593         173 KY--SLDLLLIDDIQFLAGKERTQEEFFHTFNALLE--NGKQIVLTSDRP  218 (408)
T ss_pred             hh--ccCeeeechHhHhcCChhHHHHHHHHHHHHHh--cCCEEEEEcCCC
Confidence            55  3347888999752   122    222333332  233788888643

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.60  E-value=0.045  Score=52.12  Aligned_cols=101  Identities=11%  Similarity=0.109  Sum_probs=60.0

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTIL  188 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  188 (348)
                      .+.++++++|+.|+||||++..++.....+ . ..+.+++.... ....+-++..++.++.+    -....+..++...+
T Consensus       204 ~~~~ii~lvGptGvGKTTt~akLA~~l~~~-g-~~V~lItaDtyR~gAveQLk~yae~lgvp----v~~~~dp~dL~~al  277 (407)
T PRK12726        204 SNHRIISLIGQTGVGKTTTLVKLGWQLLKQ-N-RTVGFITTDTFRSGAVEQFQGYADKLDVE----LIVATSPAELEEAV  277 (407)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHc-C-CeEEEEeCCccCccHHHHHHHHhhcCCCC----EEecCCHHHHHHHH
Confidence            456799999999999999999888653222 2 23555655322 23345666667766654    22234666666655


Q ss_pred             HHHhc-CCeEEEEEeCCCC----hhhHHHHHhh
Q 040110          189 RDYLT-NKKYFTVLDDVWI----EKIWDDLREA  216 (348)
Q Consensus       189 ~~~L~-~kr~LlVLDdv~~----~~~~~~l~~~  216 (348)
                      ...-. +..=++++|-.-.    ....+++...
T Consensus       278 ~~l~~~~~~D~VLIDTAGr~~~d~~~l~EL~~l  310 (407)
T PRK12726        278 QYMTYVNCVDHILIDTVGRNYLAEESVSEISAY  310 (407)
T ss_pred             HHHHhcCCCCEEEEECCCCCccCHHHHHHHHHH
Confidence            54431 3446777787643    2344555443

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.57  E-value=0.0084  Score=62.63  Aligned_cols=50  Identities=18%  Similarity=0.235  Sum_probs=33.6

Q ss_pred             cccccccccccHHHHHhhcCCC-------CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-------SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-------~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.|.+...   +.|.+.+.-+       ...+-...+-+.++|++|+|||+||+++++.
T Consensus       454 di~g~~~~k---~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e  510 (733)
T TIGR01243       454 DIGGLEEVK---QELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATE  510 (733)
T ss_pred             hcccHHHHH---HHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            567777777   6665554310       0011223445778999999999999999987

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.57  E-value=0.0099  Score=58.80  Aligned_cols=89  Identities=16%  Similarity=0.073  Sum_probs=46.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      ...+++|+|++|+||||++..+......+.....+..++... .....+.++...+.++...    ....+...+...+.
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v----~~a~d~~~L~~aL~  424 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAV----HEADSAESLLDLLE  424 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCcee----EecCcHHHHHHHHH
Confidence            457899999999999999988876522221112334444321 1122233334444444321    11223344444443


Q ss_pred             HHhcCCeEEEEEeCCC
Q 040110          190 DYLTNKKYFTVLDDVW  205 (348)
Q Consensus       190 ~~L~~kr~LlVLDdv~  205 (348)
                      . +.+ .-+|++|..-
T Consensus       425 ~-l~~-~DLVLIDTaG  438 (559)
T PRK12727        425 R-LRD-YKLVLIDTAG  438 (559)
T ss_pred             H-hcc-CCEEEecCCC
Confidence            3 333 4567777763

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=96.56  E-value=0.0035  Score=55.06  Aligned_cols=44  Identities=14%  Similarity=0.130  Sum_probs=35.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++||-++.+   +++.-.-.      +.++.-+.|.||+|+||||-+..+++.
T Consensus        28 dIVGNe~tv---~rl~via~------~gnmP~liisGpPG~GKTTsi~~LAr~   71 (333)
T KOG0991|consen   28 DIVGNEDTV---ERLSVIAK------EGNMPNLIISGPPGTGKTTSILCLARE   71 (333)
T ss_pred             HhhCCHHHH---HHHHHHHH------cCCCCceEeeCCCCCchhhHHHHHHHH
Confidence            799999999   77766655      445666889999999999988777765

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.56  E-value=0.0073  Score=58.14  Aligned_cols=25  Identities=24%  Similarity=0.263  Sum_probs=21.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...++.++|++|+||||++..++..
T Consensus       222 ~~~vi~lvGptGvGKTTtaaKLA~~  246 (432)
T PRK12724        222 QRKVVFFVGPTGSGKTTSIAKLAAK  246 (432)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999999999999865

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=96.56  E-value=0.0095  Score=52.71  Aligned_cols=22  Identities=18%  Similarity=0.173  Sum_probs=20.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.|.+|+||||||+.+...
T Consensus         1 IigI~G~sGSGKTTla~~L~~~   22 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQAL   22 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHH
Confidence            5899999999999999999876

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PHA02774 E1; Provisional

Probab=96.55  E-value=0.012  Score=58.50  Aligned_cols=37  Identities=16%  Similarity=0.263  Sum_probs=27.4

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEe
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRV  150 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~  150 (348)
                      +....+.|+|++|+|||.+|..+.+-  ...  ..+.|++.
T Consensus       432 PKknciv~~GPP~TGKS~fa~sL~~~--L~G--~vi~fvN~  468 (613)
T PHA02774        432 PKKNCLVIYGPPDTGKSMFCMSLIKF--LKG--KVISFVNS  468 (613)
T ss_pred             CcccEEEEECCCCCCHHHHHHHHHHH--hCC--CEEEEEEC
Confidence            44557889999999999999999877  321  23456653

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.54  E-value=0.0024  Score=55.94  Aligned_cols=26  Identities=27%  Similarity=0.433  Sum_probs=23.4

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+|+|.|.+|+|||||++.+...
T Consensus         4 ~~~~iI~I~G~sGsGKTTl~~~l~~~   29 (209)
T PRK05480          4 KKPIIIGIAGGSGSGKTTVASTIYEE   29 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            35679999999999999999999887

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=96.54  E-value=0.027  Score=58.45  Aligned_cols=46  Identities=22%  Similarity=0.278  Sum_probs=34.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|+...+   ..+.+.+...    .....-|.|+|..|+|||++|+.+++.
T Consensus       377 ~liG~S~~~---~~~~~~~~~~----a~~~~pVLI~GE~GTGK~~lA~~ih~~  422 (686)
T PRK15429        377 EIIGRSEAM---YSVLKQVEMV----AQSDSTVLILGETGTGKELIARAIHNL  422 (686)
T ss_pred             ceeecCHHH---HHHHHHHHHH----hCCCCCEEEECCCCcCHHHHHHHHHHh
Confidence            799999888   7776655411    122234779999999999999999876

>PRK06547 hypothetical protein; Provisional

Probab=96.53  E-value=0.0033  Score=53.39  Aligned_cols=27  Identities=22%  Similarity=0.135  Sum_probs=23.9

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....+|+|.|++|+||||+|..+...
T Consensus        12 ~~~~~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         12 GGGMITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             cCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            356779999999999999999999876

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=96.53  E-value=0.014  Score=52.93  Aligned_cols=94  Identities=17%  Similarity=0.157  Sum_probs=57.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccC----CcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-----ccCCCCH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKF----YFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-----KIMGKDY  181 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~----~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-----~~~~~~~  181 (348)
                      .-.+.=|+|.+|+|||.|+.+++-...+..    .=..++|++-...|+...+. +|++..+......     -....+.
T Consensus        37 ~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~~~~~~l~~I~v~~~~~~  115 (256)
T PF08423_consen   37 TGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGLDPEEILDNIFVIRVFDL  115 (256)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS-HHHHHHTEEEEE-SSH
T ss_pred             CCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccccccchhhhceeeeecCCH
Confidence            445888999999999999988864422221    12368899988889887765 4666654432110     1112344


Q ss_pred             HHHHHHHH---HHh-cCCeEEEEEeCCC
Q 040110          182 KSEKTILR---DYL-TNKKYFTVLDDVW  205 (348)
Q Consensus       182 ~~~~~~l~---~~L-~~kr~LlVLDdv~  205 (348)
                      .++...+.   ..+ ..+--|||+|.+-
T Consensus       116 ~~l~~~L~~l~~~l~~~~ikLIVIDSIa  143 (256)
T PF08423_consen  116 EELLELLEQLPKLLSESKIKLIVIDSIA  143 (256)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETSS
T ss_pred             HHHHHHHHHHHhhccccceEEEEecchH
Confidence            44444443   333 3456799999984

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=96.53  E-value=0.0018  Score=51.53  Aligned_cols=21  Identities=29%  Similarity=0.343  Sum_probs=19.5

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|.|.+|+||||+|+.+...
T Consensus         1 I~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            678999999999999999887

...

>PRK08233 hypothetical protein; Provisional

Probab=96.51  E-value=0.0023  Score=54.38  Aligned_cols=24  Identities=17%  Similarity=0.302  Sum_probs=21.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|+|.|.+|+||||||..+...
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~   26 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHK   26 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhh
Confidence            368999999999999999999876

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.51  E-value=0.013  Score=55.68  Aligned_cols=101  Identities=14%  Similarity=0.092  Sum_probs=57.2

Q ss_pred             CcEEEEEECCCCCcHHH-HHHHHhcCccccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTA-FAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTIL  188 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTt-LA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  188 (348)
                      +.++++++|+.|+|||| ||+..+.-.....+. .+..++...- ....+-++..++-++.+    -.-..+..++...+
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~-kVaiITtDtYRIGA~EQLk~Ya~im~vp----~~vv~~~~el~~ai  276 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARYVMLKKKK-KVAIITTDTYRIGAVEQLKTYADIMGVP----LEVVYSPKELAEAI  276 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHHHHhhccCc-ceEEEEeccchhhHHHHHHHHHHHhCCc----eEEecCHHHHHHHH
Confidence            47899999999999998 666655442223332 3455554322 34556677777777776    33345566666555


Q ss_pred             HHHhcCCeEEEEEeCCCC----hhhHHHHHhhCC
Q 040110          189 RDYLTNKKYFTVLDDVWI----EKIWDDLREALP  218 (348)
Q Consensus       189 ~~~L~~kr~LlVLDdv~~----~~~~~~l~~~l~  218 (348)
                      .. |++.++.| +|=+-.    .....++...+.
T Consensus       277 ~~-l~~~d~IL-VDTaGrs~~D~~~i~el~~~~~  308 (407)
T COG1419         277 EA-LRDCDVIL-VDTAGRSQYDKEKIEELKELID  308 (407)
T ss_pred             HH-hhcCCEEE-EeCCCCCccCHHHHHHHHHHHh
Confidence            43 34444433 355432    234445544443

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.51  E-value=0.013  Score=53.55  Aligned_cols=92  Identities=14%  Similarity=0.049  Sum_probs=49.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCH--HHHHHHHHHHhCCCCCccccCCCCHHH-HHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNF--KRILDDIMKSLMPTSSWLKIMGKDYKS-EKT  186 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~--~~~~~~i~~~l~~~~~~~~~~~~~~~~-~~~  186 (348)
                      ...+++.++|++|+||||++..++...  ...-..+..+... .+..  .+-+....+..+.+... .....+... ...
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~~l--~~~g~~V~li~~D-~~r~~a~~ql~~~~~~~~i~~~~-~~~~~dp~~~~~~  145 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLANKL--KKQGKSVLLAAGD-TFRAAAIEQLEEWAKRLGVDVIK-QKEGADPAAVAFD  145 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHH--HhcCCEEEEEeCC-CCCHHHHHHHHHHHHhCCeEEEe-CCCCCCHHHHHHH
Confidence            456899999999999999998888663  2221234445433 2322  23444455555533110 111223322 233


Q ss_pred             HHHHHhcCCeEEEEEeCCC
Q 040110          187 ILRDYLTNKKYFTVLDDVW  205 (348)
Q Consensus       187 ~l~~~L~~kr~LlVLDdv~  205 (348)
                      .+........=++++|-.-
T Consensus       146 ~l~~~~~~~~D~ViIDT~G  164 (272)
T TIGR00064       146 AIQKAKARNIDVVLIDTAG  164 (272)
T ss_pred             HHHHHHHCCCCEEEEeCCC
Confidence            4444444445567777763

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>TIGR00763 lon ATP-dependent protease La

Probab=96.49  E-value=0.0026  Score=66.69  Aligned_cols=55  Identities=16%  Similarity=0.249  Sum_probs=38.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF  142 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F  142 (348)
                      .++|.+...   +++.+++......+.....++.++|++|+|||++|+.+++.  ....|
T Consensus       321 ~~~G~~~~k---~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~--l~~~~  375 (775)
T TIGR00763       321 DHYGLKKVK---ERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKA--LNRKF  375 (775)
T ss_pred             hcCChHHHH---HHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHH--hcCCe
Confidence            578888888   88887663110011222347889999999999999999988  44443

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.49  E-value=0.024  Score=53.34  Aligned_cols=45  Identities=13%  Similarity=0.106  Sum_probs=31.3

Q ss_pred             cccc-cccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLG-LQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vG-r~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++| -+...   +.+.+.+.    . ..-.....++|+.|+||||+|..+.+.
T Consensus         6 ~i~~~q~~~~---~~L~~~~~----~-~~l~ha~Lf~G~~G~gk~~~a~~la~~   51 (329)
T PRK08058          6 QLTALQPVVV---KMLQNSIA----K-NRLSHAYLFEGAKGTGKKATALWLAKS   51 (329)
T ss_pred             HHHhhHHHHH---HHHHHHHH----c-CCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            3555 55555   66777665    1 223446678999999999999988665

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.47  E-value=0.028  Score=53.01  Aligned_cols=96  Identities=13%  Similarity=0.095  Sum_probs=59.0

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCcccc----CCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-----ccCCC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVK----FYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-----KIMGK  179 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~----~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-----~~~~~  179 (348)
                      =+.-++.-|+|.+|+|||+|+.+++-.....    ..-..++|++....|+...+.+ +++.++.+....     -....
T Consensus       123 i~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d~~~~l~~I~~~~~~  201 (344)
T PLN03187        123 IETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMDADAVLDNIIYARAY  201 (344)
T ss_pred             CCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCChhhhcCeEEEecCC
Confidence            3455688899999999999999886432111    1123688999999899887654 566666542110     11223


Q ss_pred             CHHHHHHH---HHHHh-cCCeEEEEEeCCC
Q 040110          180 DYKSEKTI---LRDYL-TNKKYFTVLDDVW  205 (348)
Q Consensus       180 ~~~~~~~~---l~~~L-~~kr~LlVLDdv~  205 (348)
                      +.+++...   +...+ ..+--|||+|.+-
T Consensus       202 ~~e~~~~~l~~l~~~i~~~~~~LvVIDSit  231 (344)
T PLN03187        202 TYEHQYNLLLGLAAKMAEEPFRLLIVDSVI  231 (344)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcH
Confidence            44443333   33333 2345688999985

>PRK04040 adenylate kinase; Provisional

Probab=96.46  E-value=0.0083  Score=51.73  Aligned_cols=24  Identities=21%  Similarity=0.272  Sum_probs=21.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|+|+|++|+||||+++.+.+.
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~   25 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEK   25 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH
Confidence            357899999999999999999887

>PTZ00301 uridine kinase; Provisional

Probab=96.46  E-value=0.0034  Score=55.07  Aligned_cols=24  Identities=21%  Similarity=0.405  Sum_probs=21.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|+|.|.+|+||||||+.+.+.
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~   26 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSE   26 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHH
Confidence            468999999999999999988765

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.45  E-value=0.026  Score=52.72  Aligned_cols=96  Identities=9%  Similarity=0.052  Sum_probs=58.6

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCcccc----CCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-----ccCCC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVK----FYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-----KIMGK  179 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~----~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-----~~~~~  179 (348)
                      =+.-+++-|+|++|+|||+|+.+++-.....    ..=..++|++....++.+.+. ++++.++.+....     .....
T Consensus        93 i~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~-~~a~~~g~d~~~~l~~i~~~~~~  171 (313)
T TIGR02238        93 IESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIR-AIAERFGVDPDAVLDNILYARAY  171 (313)
T ss_pred             CcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHH-HHHHHcCCChHHhcCcEEEecCC
Confidence            3455688899999999999998876432111    111368899988888888765 4566666542210     01112


Q ss_pred             CHHHHH---HHHHHHhc-CCeEEEEEeCCC
Q 040110          180 DYKSEK---TILRDYLT-NKKYFTVLDDVW  205 (348)
Q Consensus       180 ~~~~~~---~~l~~~L~-~kr~LlVLDdv~  205 (348)
                      +.++..   ..+...+. .+--|+|+|.+.
T Consensus       172 ~~e~~~~~l~~l~~~i~~~~~~LvVIDSis  201 (313)
T TIGR02238       172 TSEHQMELLDYLAAKFSEEPFRLLIVDSIM  201 (313)
T ss_pred             CHHHHHHHHHHHHHHhhccCCCEEEEEcch
Confidence            333333   33333443 356689999985

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.44  E-value=0.013  Score=51.67  Aligned_cols=122  Identities=11%  Similarity=0.149  Sum_probs=59.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      .+++.|+|+.|.|||||.+.+.......   ....|+.... ..+ ....++...++...+. .........-...+...
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~~~~la---~~G~~v~a~~-~~~-~~~d~i~~~l~~~~si-~~~~S~f~~el~~l~~~  102 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVALIVFLA---HIGSFVPADS-ATI-GLVDKIFTRMSSRESV-SSGQSAFMIDLYQVSKA  102 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHHHHHHH---hCCCeeEcCC-cEE-eeeeeeeeeeCCccCh-hhccchHHHHHHHHHHH
Confidence            4788999999999999999887331110   0111111110 000 0111122222221110 00011112222223322


Q ss_pred             h--cCCeEEEEEeCCCChhh-------HHHHHhhCCCC-CCCcEEEEEeCChhhhhhc
Q 040110          192 L--TNKKYFTVLDDVWIEKI-------WDDLREALPDN-QIGSRALITVGPHNILTSI  239 (348)
Q Consensus       192 L--~~kr~LlVLDdv~~~~~-------~~~l~~~l~~~-~~gskIlvTTR~~~v~~~~  239 (348)
                      +  ..++.|++||..-...+       ...+...+... ..+..+|+||-+..++...
T Consensus       103 l~~~~~~slvllDE~~~gtd~~~~~~~~~ail~~l~~~~~~~~~vli~TH~~~l~~~~  160 (213)
T cd03281         103 LRLATRRSLVLIDEFGKGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTHFHELFNRS  160 (213)
T ss_pred             HHhCCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEcChHHHHHhh
Confidence            2  36789999999875421       11233333222 2345799999998887763

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>TIGR00235 udk uridine kinase

Probab=96.43  E-value=0.0031  Score=55.22  Aligned_cols=26  Identities=31%  Similarity=0.486  Sum_probs=22.9

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +...+++|.|++|+|||||++.+...
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~   29 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQ   29 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHH
Confidence            34578999999999999999999876

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.43  E-value=0.012  Score=59.38  Aligned_cols=77  Identities=14%  Similarity=0.208  Sum_probs=53.9

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTIL  188 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  188 (348)
                      .+.-+++.++|++|.||||||.-++++    ..| .++=+++|..-+...+-..|...+....    ..+.         
T Consensus       323 RP~kKilLL~GppGlGKTTLAHViAkq----aGY-sVvEINASDeRt~~~v~~kI~~avq~~s----~l~a---------  384 (877)
T KOG1969|consen  323 RPPKKILLLCGPPGLGKTTLAHVIAKQ----AGY-SVVEINASDERTAPMVKEKIENAVQNHS----VLDA---------  384 (877)
T ss_pred             CCccceEEeecCCCCChhHHHHHHHHh----cCc-eEEEecccccccHHHHHHHHHHHHhhcc----cccc---------
Confidence            456788999999999999999999987    223 3556778888777777777766665431    1100         


Q ss_pred             HHHhcCCeEEEEEeCCCCh
Q 040110          189 RDYLTNKKYFTVLDDVWIE  207 (348)
Q Consensus       189 ~~~L~~kr~LlVLDdv~~~  207 (348)
                          .+++.-||+|.++..
T Consensus       385 ----dsrP~CLViDEIDGa  399 (877)
T KOG1969|consen  385 ----DSRPVCLVIDEIDGA  399 (877)
T ss_pred             ----CCCcceEEEecccCC
Confidence                146677888888754

>CHL00195 ycf46 Ycf46; Provisional

Probab=96.42  E-value=0.014  Score=57.71  Aligned_cols=50  Identities=26%  Similarity=0.311  Sum_probs=32.2

Q ss_pred             cccccccccccHHHHHhhcCC----CCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----SSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|.+..+   +.+.+....    ....+-..++-+.++|++|+|||.+|+.+++.
T Consensus       229 dvgGl~~lK---~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e  282 (489)
T CHL00195        229 DIGGLDNLK---DWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIAND  282 (489)
T ss_pred             HhcCHHHHH---HHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            567777666   555432110    00011234456779999999999999999987

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.42  E-value=0.0012  Score=65.54  Aligned_cols=50  Identities=12%  Similarity=0.204  Sum_probs=39.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.++.+   ++|++.|...........+++.++|++|+||||||+.+.+-
T Consensus        77 d~yGlee~i---eriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~  126 (644)
T PRK15455         77 EFYGMEEAI---EQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSL  126 (644)
T ss_pred             cccCcHHHH---HHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHH
Confidence            689999999   99999993211122345579999999999999999999876

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.42  E-value=0.028  Score=53.89  Aligned_cols=102  Identities=12%  Similarity=0.072  Sum_probs=57.7

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccC-Ccc-eeEEEEeCCCCC--HHHHHHHHHHHhCCCCCccccCCCCHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKF-YFD-CHAWVRVSNFYN--FKRILDDIMKSLMPTSSWLKIMGKDYKSEK  185 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~F~-~~~wv~~~~~~~--~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~  185 (348)
                      ...+++.++|+.|+||||.+..++....... .-. .+..+++. .+.  ....++..++.++.+.    ....+...+.
T Consensus       172 ~~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~D-t~R~aa~eQL~~~a~~lgvpv----~~~~~~~~l~  246 (388)
T PRK12723        172 LKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITID-NYRIGAKKQIQTYGDIMGIPV----KAIESFKDLK  246 (388)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEecc-CccHHHHHHHHHHhhcCCcce----EeeCcHHHHH
Confidence            3467999999999999999988886632221 111 34444443 332  2334666666666642    2233445555


Q ss_pred             HHHHHHhcCCeEEEEEeCCCCh----hhHHHHHhhCC
Q 040110          186 TILRDYLTNKKYFTVLDDVWIE----KIWDDLREALP  218 (348)
Q Consensus       186 ~~l~~~L~~kr~LlVLDdv~~~----~~~~~l~~~l~  218 (348)
                      ..+.+.  .+.-++++|-.-..    ..+..+...+.
T Consensus       247 ~~L~~~--~~~DlVLIDTaGr~~~~~~~l~el~~~l~  281 (388)
T PRK12723        247 EEITQS--KDFDLVLVDTIGKSPKDFMKLAEMKELLN  281 (388)
T ss_pred             HHHHHh--CCCCEEEEcCCCCCccCHHHHHHHHHHHH
Confidence            555443  34567777877432    23445544443

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.41  E-value=0.026  Score=46.62  Aligned_cols=22  Identities=18%  Similarity=0.244  Sum_probs=19.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|+|.+|+||||||+.+...
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~   22 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEK   22 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH
Confidence            4778999999999999998876

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.41  E-value=0.028  Score=50.24  Aligned_cols=94  Identities=16%  Similarity=0.174  Sum_probs=57.0

Q ss_pred             CCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc--------------
Q 040110          108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW--------------  173 (348)
Q Consensus       108 ~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~--------------  173 (348)
                      +-+.-+++.|.|.+|+|||+||.++.... .++ -..++|++...  +..++.+.+. +++.+...              
T Consensus        17 G~~~gs~~lI~G~pGsGKT~la~~~l~~~-~~~-ge~~lyvs~ee--~~~~i~~~~~-~~g~~~~~~~~~g~l~~~d~~~   91 (237)
T TIGR03877        17 GIPERNVVLLSGGPGTGKSIFSQQFLWNG-LQM-GEPGIYVALEE--HPVQVRRNMA-QFGWDVRKYEEEGKFAIVDAFT   91 (237)
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHHH-HHc-CCcEEEEEeeC--CHHHHHHHHH-HhCCCHHHHhhcCCEEEEeccc
Confidence            34456788999999999999998865442 122 23677877654  4455555433 33322100              


Q ss_pred             ---------c---ccCCCCHHHHHHHHHHHhcC-CeEEEEEeCCCC
Q 040110          174 ---------L---KIMGKDYKSEKTILRDYLTN-KKYFTVLDDVWI  206 (348)
Q Consensus       174 ---------~---~~~~~~~~~~~~~l~~~L~~-kr~LlVLDdv~~  206 (348)
                               .   .....+..++...+.+.+.. +.-++|+|.+..
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDSls~  137 (237)
T TIGR03877        92 GGIGEAAEREKYVVKDPTDVRELIDVLRQAIRDINAKRVVIDSVTT  137 (237)
T ss_pred             cccccccccccccccCcccHHHHHHHHHHHHHHhCCCEEEEcChhH
Confidence                     0   01224667777777777644 445799999854

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=96.40  E-value=0.0027  Score=63.81  Aligned_cols=72  Identities=14%  Similarity=0.205  Sum_probs=51.8

Q ss_pred             ccCcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHH
Q 040110           80 ICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRI  159 (348)
Q Consensus        80 ~~~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  159 (348)
                      .+++-+|.++..   ++|+++|....-.++..-++++.+|++|||||++|+.++..  ..+.|   +-++++.-.|+.+|
T Consensus       409 LdeDHYgm~dVK---eRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~A--LnRkF---fRfSvGG~tDvAeI  480 (906)
T KOG2004|consen  409 LDEDHYGMEDVK---ERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARA--LNRKF---FRFSVGGMTDVAEI  480 (906)
T ss_pred             hcccccchHHHH---HHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHH--hCCce---EEEeccccccHHhh
Confidence            334679999999   99999985322234455679999999999999999999988  65555   12345555555443

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.40  E-value=0.023  Score=51.22  Aligned_cols=123  Identities=9%  Similarity=0.024  Sum_probs=72.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-----CCCHHHHHHHHHHHhCCCCCcc--ccCCCCHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-----FYNFKRILDDIMKSLMPTSSWL--KIMGKDYKSE  184 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-----~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~~  184 (348)
                      -.+++|+|.+|+||||+++.+..-  ..-.. +.+++.-.+     .....+-..+++..++....-.  ....-+-.+.
T Consensus        39 ge~~glVGESG~GKSTlgr~i~~L--~~pt~-G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQr  115 (268)
T COG4608          39 GETLGLVGESGCGKSTLGRLILGL--EEPTS-GEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQR  115 (268)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHcC--cCCCC-ceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhh
Confidence            347999999999999999999877  33232 233332111     2233455677777777543210  1111222333


Q ss_pred             HH-HHHHHhcCCeEEEEEeCCCCh------hhHHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          185 KT-ILRDYLTNKKYFTVLDDVWIE------KIWDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       185 ~~-~l~~~L~~kr~LlVLDdv~~~------~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      +. .+.+.|.-+.-|+|.|..-+.      .+.-.+...+. ...|-..+..|-+-.++..
T Consensus       116 QRi~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq-~~~~lt~lFIsHDL~vv~~  175 (268)
T COG4608         116 QRIGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQ-EELGLTYLFISHDLSVVRY  175 (268)
T ss_pred             hhHHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHH-HHhCCeEEEEEEEHHhhhh
Confidence            33 467778889999999987543      12222222221 1235668888888888877

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=96.39  E-value=0.015  Score=56.25  Aligned_cols=90  Identities=11%  Similarity=0.121  Sum_probs=53.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHH------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKS------  183 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~------  183 (348)
                      ..++|+|..|+|||||++.+.+.  ..  .+.++.+-++... .+.++..+++..-+...+..  ...+.....      
T Consensus       163 qrigI~G~sG~GKSTLL~~I~~~--~~--~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~  238 (444)
T PRK08972        163 QRMGLFAGSGVGKSVLLGMMTRG--TT--ADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGCE  238 (444)
T ss_pred             CEEEEECCCCCChhHHHHHhccC--CC--CCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHHH
Confidence            36899999999999999999865  22  2456666666554 45566666654422221110  111221111      


Q ss_pred             HHHHHHHHh--cCCeEEEEEeCCCC
Q 040110          184 EKTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       184 ~~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      ..-.+.+++  +++++||++||+-.
T Consensus       239 ~A~tiAEyfrd~G~~VLl~~DslTR  263 (444)
T PRK08972        239 TATTIAEYFRDQGLNVLLLMDSLTR  263 (444)
T ss_pred             HHHHHHHHHHHcCCCEEEEEcChHH
Confidence            111234444  57899999999853

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=96.39  E-value=0.076  Score=50.93  Aligned_cols=42  Identities=17%  Similarity=0.178  Sum_probs=30.6

Q ss_pred             HHHHhhcCCCCCC---CCCCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110           95 RNLHQRLPPSSGL---GQPTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus        95 ~~l~~~L~~~~~~---~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ++|+++|...+..   ....+.+|-.+|.-|.||||.|-.+++..
T Consensus        80 eELv~llG~~~~~~~l~~~~P~vImmvGLQGsGKTTt~~KLA~~l  124 (451)
T COG0541          80 EELVKLLGGENSELNLAKKPPTVILMVGLQGSGKTTTAGKLAKYL  124 (451)
T ss_pred             HHHHHHhCCCCcccccCCCCCeEEEEEeccCCChHhHHHHHHHHH
Confidence            6677777631111   13457899999999999999998888773

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=96.38  E-value=0.019  Score=53.64  Aligned_cols=106  Identities=10%  Similarity=0.047  Sum_probs=61.1

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccC----CcceeEEEEeCCCCCHHHHHHHHHHHhCCC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKF----YFDCHAWVRVSNFYNFKRILDDIMKSLMPT  170 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~----~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~  170 (348)
                      ..|-.+|.    .+-..-.++.|.|.+|+|||+|+..++.......    .-..++|++....++...+ .++++.++..
T Consensus        83 ~~lD~ll~----gGi~~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl-~~ia~~~~~~  157 (316)
T TIGR02239        83 KELDKLLG----GGIETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERL-LAIAERYGLN  157 (316)
T ss_pred             HHHHHHhc----CCCCCCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHH-HHHHHHcCCC
Confidence            44445454    3334567889999999999999998875321211    1125689988877777763 4455555443


Q ss_pred             CCcc-----ccCCCCHHHHHH---HHHHHhc-CCeEEEEEeCCC
Q 040110          171 SSWL-----KIMGKDYKSEKT---ILRDYLT-NKKYFTVLDDVW  205 (348)
Q Consensus       171 ~~~~-----~~~~~~~~~~~~---~l~~~L~-~kr~LlVLDdv~  205 (348)
                      ....     -....+.+++..   .+...+. .+--|+|+|.+-
T Consensus       158 ~~~~l~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~LvVIDSI~  201 (316)
T TIGR02239       158 PEDVLDNVAYARAYNTDHQLQLLQQAAAMMSESRFALLIVDSAT  201 (316)
T ss_pred             hHHhhccEEEEecCChHHHHHHHHHHHHhhccCCccEEEEECcH
Confidence            2110     011123333333   3333343 356789999984

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=96.37  E-value=0.03  Score=47.31  Aligned_cols=24  Identities=21%  Similarity=0.223  Sum_probs=21.5

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+++|+|..|.|||||.+.++.-
T Consensus        28 G~~~~l~G~nGsGKstLl~~i~G~   51 (171)
T cd03228          28 GEKVAIVGPSGSGKSTLLKLLLRL   51 (171)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcC
Confidence            347899999999999999999876

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.36  E-value=0.012  Score=59.36  Aligned_cols=72  Identities=18%  Similarity=0.206  Sum_probs=45.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC--CCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF--YNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~--~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      ..-|.|.|+.|+|||+||+++++... +.+.-.+..++++.-  ..++.+++.                     +...+.
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk~---------------------l~~vfs  488 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQKF---------------------LNNVFS  488 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHHH---------------------HHHHHH
Confidence            44678999999999999999998844 333333445554422  122222222                     223344


Q ss_pred             HHhcCCeEEEEEeCCC
Q 040110          190 DYLTNKKYFTVLDDVW  205 (348)
Q Consensus       190 ~~L~~kr~LlVLDdv~  205 (348)
                      +.+.-.+.++||||++
T Consensus       489 e~~~~~PSiIvLDdld  504 (952)
T KOG0735|consen  489 EALWYAPSIIVLDDLD  504 (952)
T ss_pred             HHHhhCCcEEEEcchh
Confidence            4555679999999996

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=96.35  E-value=0.019  Score=48.69  Aligned_cols=23  Identities=26%  Similarity=0.322  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|..|.|||||.+.+..-
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G~   51 (173)
T cd03246          29 ESLAIIGPSGSGKSTLARLILGL   51 (173)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc
Confidence            47899999999999999999876

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=96.34  E-value=0.049  Score=48.94  Aligned_cols=124  Identities=15%  Similarity=0.145  Sum_probs=73.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCcc-----cc---C---Cc---ceeEEEEeCCCC------CH----------------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNF-----VK---F---YF---DCHAWVRVSNFY------NF----------------  156 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~-----~~---~---~F---~~~~wv~~~~~~------~~----------------  156 (348)
                      .+++|+|+.|.|||||.+.+..-..     +.   .   .+   ..+.||+-...+      ++                
T Consensus        31 ~~~~iiGPNGaGKSTLlK~iLGll~p~~G~i~~~g~~~~~~~~~~~IgYVPQ~~~~d~~fP~tV~d~V~~g~~~~~g~~~  110 (254)
T COG1121          31 EITALIGPNGAGKSTLLKAILGLLKPSSGEIKIFGKPVRKRRKRLRIGYVPQKSSVDRSFPITVKDVVLLGRYGKKGWFR  110 (254)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCCcCCcceEEEccccccccccCCeEEEcCcccccCCCCCcCHHHHHHccCcccccccc
Confidence            5899999999999999999987311     10   0   01   124444321111      11                


Q ss_pred             ------HHHHHHHHHHhCCCCCcc-ccCCCCHHHHHH-HHHHHhcCCeEEEEEeCCCCh------hhHHHHHhhCCCCCC
Q 040110          157 ------KRILDDIMKSLMPTSSWL-KIMGKDYKSEKT-ILRDYLTNKKYFTVLDDVWIE------KIWDDLREALPDNQI  222 (348)
Q Consensus       157 ------~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~-~l~~~L~~kr~LlVLDdv~~~------~~~~~l~~~l~~~~~  222 (348)
                            .+...+.++.++...... ....-+-.+.+. .|.+.|..+.=||+||.--..      ..+-++...+...  
T Consensus       111 ~~~~~d~~~v~~aL~~Vgm~~~~~r~i~~LSGGQ~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~e--  188 (254)
T COG1121         111 RLNKKDKEKVDEALERVGMEDLRDRQIGELSGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQE--  188 (254)
T ss_pred             cccHHHHHHHHHHHHHcCchhhhCCcccccCcHHHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHHC--
Confidence                  244555666665542210 223334444444 466778999999999985432      3344444444333  


Q ss_pred             CcEEEEEeCChhhhhh
Q 040110          223 GSRALITVGPHNILTS  238 (348)
Q Consensus       223 gskIlvTTR~~~v~~~  238 (348)
                      |+-||+.|-+-+....
T Consensus       189 g~tIl~vtHDL~~v~~  204 (254)
T COG1121         189 GKTVLMVTHDLGLVMA  204 (254)
T ss_pred             CCEEEEEeCCcHHhHh
Confidence            7889999998776555

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=96.33  E-value=0.031  Score=47.32  Aligned_cols=23  Identities=22%  Similarity=0.299  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|..|.|||||++.++..
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~   49 (173)
T cd03230          27 EIYGLLGPNGAGKTTLIKIILGL   49 (173)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            47899999999999999999876

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=96.33  E-value=0.0067  Score=52.68  Aligned_cols=102  Identities=10%  Similarity=0.046  Sum_probs=49.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      .++..|.|.+|+||||++..+...  .... ...+.+.....    +....+....+....       ++..........
T Consensus        18 ~~~~~l~G~aGtGKT~~l~~~~~~--~~~~-g~~v~~~apT~----~Aa~~L~~~~~~~a~-------Ti~~~l~~~~~~   83 (196)
T PF13604_consen   18 DRVSVLQGPAGTGKTTLLKALAEA--LEAA-GKRVIGLAPTN----KAAKELREKTGIEAQ-------TIHSFLYRIPNG   83 (196)
T ss_dssp             CSEEEEEESTTSTHHHHHHHHHHH--HHHT-T--EEEEESSH----HHHHHHHHHHTS-EE-------EHHHHTTEECCE
T ss_pred             CeEEEEEECCCCCHHHHHHHHHHH--HHhC-CCeEEEECCcH----HHHHHHHHhhCcchh-------hHHHHHhcCCcc
Confidence            457778999999999999988766  2222 12333332222    222223333332211       111100000000


Q ss_pred             h------cCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEE
Q 040110          192 L------TNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALIT  229 (348)
Q Consensus       192 L------~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvT  229 (348)
                      -      ..++-+||+|++.-.  ..+..+....+.  .|+|+|+.
T Consensus        84 ~~~~~~~~~~~~vliVDEasmv~~~~~~~ll~~~~~--~~~klilv  127 (196)
T PF13604_consen   84 DDEGRPELPKKDVLIVDEASMVDSRQLARLLRLAKK--SGAKLILV  127 (196)
T ss_dssp             ECCSSCC-TSTSEEEESSGGG-BHHHHHHHHHHS-T---T-EEEEE
T ss_pred             cccccccCCcccEEEEecccccCHHHHHHHHHHHHh--cCCEEEEE
Confidence            0      123459999998643  567777776654  35677653

>PRK06762 hypothetical protein; Provisional

Probab=96.33  E-value=0.0032  Score=52.93  Aligned_cols=23  Identities=22%  Similarity=0.369  Sum_probs=21.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|.|.|++|+||||+|+.+.+.
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~   25 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQER   25 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999999999877

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.33  E-value=0.036  Score=49.37  Aligned_cols=54  Identities=11%  Similarity=0.075  Sum_probs=33.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMP  169 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~  169 (348)
                      .-.++.|.|.+|+||||||.++.... .++. ..+++++  ..-+..++++.+ .+++.
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~-~~~g-~~~~yi~--~e~~~~~~~~~~-~~~g~   76 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGF-LQNG-YSVSYVS--TQLTTTEFIKQM-MSLGY   76 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH-HhCC-CcEEEEe--CCCCHHHHHHHH-HHhCC
Confidence            34589999999999999986665442 1222 2345555  333556666666 34443

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.32  E-value=0.01  Score=50.63  Aligned_cols=22  Identities=23%  Similarity=0.374  Sum_probs=20.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|++|+||||+|+.+.+.
T Consensus         2 riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            3678999999999999999988

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.32  E-value=0.08  Score=48.33  Aligned_cols=119  Identities=13%  Similarity=0.011  Sum_probs=64.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCC-CCCcc--ccCCCCHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMP-TSSWL--KIMGKDYKSEKTIL  188 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~-~~~~~--~~~~~~~~~~~~~l  188 (348)
                      ..-++|+|+.|+|||||.+.+...  +... ...+++. +......+-..++...... +....  ..+..+-......+
T Consensus       111 ~~~~~i~g~~g~GKttl~~~l~~~--~~~~-~G~i~~~-g~~v~~~d~~~ei~~~~~~~~q~~~~~r~~v~~~~~k~~~~  186 (270)
T TIGR02858       111 VLNTLIISPPQCGKTTLLRDLARI--LSTG-ISQLGLR-GKKVGIVDERSEIAGCVNGVPQHDVGIRTDVLDGCPKAEGM  186 (270)
T ss_pred             eeEEEEEcCCCCCHHHHHHHHhCc--cCCC-CceEEEC-CEEeecchhHHHHHHHhcccccccccccccccccchHHHHH
Confidence            457899999999999999999977  3322 2333331 1111111111233332221 10000  00000101112223


Q ss_pred             HHHhc-CCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhh
Q 040110          189 RDYLT-NKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILT  237 (348)
Q Consensus       189 ~~~L~-~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~  237 (348)
                      ...+. ..+-++++|.+-..+.+..+...+.   .|..||+||-+..+..
T Consensus       187 ~~~i~~~~P~villDE~~~~e~~~~l~~~~~---~G~~vI~ttH~~~~~~  233 (270)
T TIGR02858       187 MMLIRSMSPDVIVVDEIGREEDVEALLEALH---AGVSIIATAHGRDVED  233 (270)
T ss_pred             HHHHHhCCCCEEEEeCCCcHHHHHHHHHHHh---CCCEEEEEechhHHHH
Confidence            33333 4788999999987777777766653   3677999998766644

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.30  E-value=0.021  Score=50.77  Aligned_cols=27  Identities=19%  Similarity=0.223  Sum_probs=24.1

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....+++|.|+.|+|||||++.+...
T Consensus        30 ~~~~~iigi~G~~GsGKTTl~~~L~~~   56 (229)
T PRK09270         30 PQRRTIVGIAGPPGAGKSTLAEFLEAL   56 (229)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            356789999999999999999999876

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.29  E-value=0.046  Score=51.42  Aligned_cols=24  Identities=17%  Similarity=0.213  Sum_probs=20.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+.++|+.|+||||+|..+++.
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~   45 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAA   45 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHH
Confidence            445778999999999999988765

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=96.28  E-value=0.039  Score=47.19  Aligned_cols=124  Identities=12%  Similarity=0.131  Sum_probs=69.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEE---eC------------------CC-----------------
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVR---VS------------------NF-----------------  153 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~---~~------------------~~-----------------  153 (348)
                      -..+.++|++|.|||||.+.+|...+...   +.+|+.   ++                  ++                 
T Consensus        28 Gef~fl~GpSGAGKSTllkLi~~~e~pt~---G~i~~~~~dl~~l~~~~iP~LRR~IGvVFQD~rLL~~~tvyeNVA~pL  104 (223)
T COG2884          28 GEFVFLTGPSGAGKSTLLKLIYGEERPTR---GKILVNGHDLSRLKGREIPFLRRQIGVVFQDFRLLPDRTVYENVALPL  104 (223)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhhcCCC---ceEEECCeecccccccccchhhheeeeEeeeccccccchHhhhhhhhh
Confidence            34788999999999999999997743221   222321   00                  00                 


Q ss_pred             ----C---CHHHHHHHHHHHhCCCCCcc--ccCCCCHHHHHHHHHHHhcCCeEEEEEeCC----CChhhHHHHHhhCCCC
Q 040110          154 ----Y---NFKRILDDIMKSLMPTSSWL--KIMGKDYKSEKTILRDYLTNKKYFTVLDDV----WIEKIWDDLREALPDN  220 (348)
Q Consensus       154 ----~---~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv----~~~~~~~~l~~~l~~~  220 (348)
                          .   ...+-..+.++.++......  ...-..-++.--.|.+.+-+++-+|+-|.-    +....|+-+...-.-+
T Consensus       105 ~v~G~~~~~i~~rV~~~L~~VgL~~k~~~lP~~LSGGEQQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeein  184 (223)
T COG2884         105 RVIGKPPREIRRRVSEVLDLVGLKHKARALPSQLSGGEQQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEIN  184 (223)
T ss_pred             hccCCCHHHHHHHHHHHHHHhccchhhhcCccccCchHHHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHh
Confidence                1   12222333344444432210  011122233344567777788888888864    3333444332222224


Q ss_pred             CCCcEEEEEeCChhhhhh
Q 040110          221 QIGSRALITVGPHNILTS  238 (348)
Q Consensus       221 ~~gskIlvTTR~~~v~~~  238 (348)
                      ..|..||++|-+.++-..
T Consensus       185 r~GtTVl~ATHd~~lv~~  202 (223)
T COG2884         185 RLGTTVLMATHDLELVNR  202 (223)
T ss_pred             hcCcEEEEEeccHHHHHh
Confidence            568999999999988776

>PTZ00035 Rad51 protein; Provisional

Probab=96.26  E-value=0.054  Score=51.10  Aligned_cols=107  Identities=11%  Similarity=0.052  Sum_probs=61.4

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCcccc---C-CcceeEEEEeCCCCCHHHHHHHHHHHhCCC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVK---F-YFDCHAWVRVSNFYNFKRILDDIMKSLMPT  170 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~---~-~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~  170 (348)
                      ..|-.+|.    .+-+.-.++.|+|.+|+|||+|+..++-.....   . .=..++|++-...++...+ .++++.++..
T Consensus       105 ~~LD~lLg----GGi~~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri-~~ia~~~g~~  179 (337)
T PTZ00035        105 TQLDKLLG----GGIETGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERI-VQIAERFGLD  179 (337)
T ss_pred             HHHHHHhC----CCCCCCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHH-HHHHHHhCCC
Confidence            34444444    334556789999999999999999887542211   1 1124668887777777663 4445555543


Q ss_pred             CCcc-----ccCCCCHHHHHHHH---HHHh-cCCeEEEEEeCCCC
Q 040110          171 SSWL-----KIMGKDYKSEKTIL---RDYL-TNKKYFTVLDDVWI  206 (348)
Q Consensus       171 ~~~~-----~~~~~~~~~~~~~l---~~~L-~~kr~LlVLDdv~~  206 (348)
                      ....     -....+.+++...+   ...+ ..+--|||+|.+..
T Consensus       180 ~~~~l~nI~~~~~~~~e~~~~~l~~~~~~l~~~~~~lvVIDSita  224 (337)
T PTZ00035        180 PEDVLDNIAYARAYNHEHQMQLLSQAAAKMAEERFALLIVDSATA  224 (337)
T ss_pred             hHhHhhceEEEccCCHHHHHHHHHHHHHHhhccCccEEEEECcHH
Confidence            2110     11122334444433   3333 34567899999853

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.22  E-value=0.012  Score=55.64  Aligned_cols=114  Identities=13%  Similarity=0.148  Sum_probs=67.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      ...+.|.|+.|+||||++..+.+.  +..+....++. +..+...  ..... ..+-...   . ...+.......++..
T Consensus       122 ~g~ili~G~tGSGKTT~l~al~~~--i~~~~~~~i~t-iEdp~E~--~~~~~-~~~i~q~---e-vg~~~~~~~~~l~~~  191 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTLASMIDY--INKNAAGHIIT-IEDPIEY--VHRNK-RSLINQR---E-VGLDTLSFANALRAA  191 (343)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHh--hCcCCCCEEEE-EcCChhh--hccCc-cceEEcc---c-cCCCCcCHHHHHHHh
Confidence            467899999999999999998876  44444445543 2322111  00000 0000000   0 011223456667888


Q ss_pred             hcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          192 LTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       192 L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      |+...=.|++|.+.+.+.+.......   ..|..|+.|+-..++...
T Consensus       192 lr~~pd~i~vgEird~~~~~~~l~aa---~tGh~v~~T~Ha~~~~~~  235 (343)
T TIGR01420       192 LREDPDVILIGEMRDLETVELALTAA---ETGHLVFGTLHTNSAAQT  235 (343)
T ss_pred             hccCCCEEEEeCCCCHHHHHHHHHHH---HcCCcEEEEEcCCCHHHH
Confidence            88899999999998876665543332   235557777777666554

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=96.22  E-value=0.0038  Score=44.40  Aligned_cols=22  Identities=23%  Similarity=0.400  Sum_probs=19.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|.|..|+||||+++.+.+.
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~   22 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQ   22 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4788999999999999999877

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.22  E-value=0.0081  Score=49.81  Aligned_cols=45  Identities=22%  Similarity=0.212  Sum_probs=33.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTS  171 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~  171 (348)
                      +|.|-|++|+||||+|+.++++.-..-       +      +...++++|++..+.+.
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl~~-------v------saG~iFR~~A~e~gmsl   46 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGLKL-------V------SAGTIFREMARERGMSL   46 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCCce-------e------eccHHHHHHHHHcCCCH
Confidence            688999999999999999998832221       1      33467788888777653

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=96.22  E-value=0.0043  Score=50.57  Aligned_cols=22  Identities=23%  Similarity=0.211  Sum_probs=19.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|+|..|+||+++|+.++..
T Consensus        23 pvli~GE~GtGK~~~A~~lh~~   44 (138)
T PF14532_consen   23 PVLITGEPGTGKSLLARALHRY   44 (138)
T ss_dssp             -EEEECCTTSSHHHHHHCCHHT
T ss_pred             cEEEEcCCCCCHHHHHHHHHhh
Confidence            4678999999999999999877

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=96.20  E-value=0.014  Score=54.03  Aligned_cols=146  Identities=16%  Similarity=0.132  Sum_probs=80.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC-ccccCCcceeEEEEeCCCCCH-HHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN-NFVKFYFDCHAWVRVSNFYNF-KRIL  160 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~-~~~~~~F~~~~wv~~~~~~~~-~~~~  160 (348)
                      .++|-.++.   .++-.+|.+.-  -.....-+.|+|+.|.|||+|......+ ....++|   +-|.+...... .-.+
T Consensus        25 ~l~g~~~~~---~~l~~~lkqt~--~~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~---l~v~Lng~~~~dk~al   96 (408)
T KOG2228|consen   25 NLFGVQDEQ---KHLSELLKQTI--LHGESNSVIIIGPRGSGKTILIDTRLSDIQENGENF---LLVRLNGELQTDKIAL   96 (408)
T ss_pred             ceeehHHHH---HHHHHHHHHHH--HhcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeE---EEEEECccchhhHHHH
Confidence            799999999   77777775321  0122234668999999999988777665 1233333   33444443332 2245


Q ss_pred             HHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcC------CeEEEEEeCCCCh----h---hHHHHHhhCCCCCCCcEEE
Q 040110          161 DDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTN------KKYFTVLDDVWIE----K---IWDDLREALPDNQIGSRAL  227 (348)
Q Consensus       161 ~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~------kr~LlVLDdv~~~----~---~~~~l~~~l~~~~~gskIl  227 (348)
                      +.|.+++...-........+..+-..++...|+.      -++++|+|.++--    .   -.+.+...-....+-|-|-
T Consensus        97 ~~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig  176 (408)
T KOG2228|consen   97 KGITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIG  176 (408)
T ss_pred             HHHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEE
Confidence            5555555332111022233444555566666643      3689999887532    1   1111211111234667788


Q ss_pred             EEeCChhhh
Q 040110          228 ITVGPHNIL  236 (348)
Q Consensus       228 vTTR~~~v~  236 (348)
                      +|||-...-
T Consensus       177 ~Ttrld~lE  185 (408)
T KOG2228|consen  177 VTTRLDILE  185 (408)
T ss_pred             eeccccHHH
Confidence            899976543

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.20  E-value=0.023  Score=54.34  Aligned_cols=88  Identities=13%  Similarity=0.060  Sum_probs=51.7

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTIL  188 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l  188 (348)
                      ..-.++.|.|.+|+|||||+.+++..  ....-..++|++....  ..++ +.-+..++...... -....+.+.+.+.+
T Consensus        80 ~~GslvLI~G~pG~GKStLllq~a~~--~a~~g~~VlYvs~EEs--~~qi-~~Ra~rlg~~~~~l~l~~e~~le~I~~~i  154 (372)
T cd01121          80 VPGSVILIGGDPGIGKSTLLLQVAAR--LAKRGGKVLYVSGEES--PEQI-KLRADRLGISTENLYLLAETNLEDILASI  154 (372)
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHH--HHhcCCeEEEEECCcC--HHHH-HHHHHHcCCCcccEEEEccCcHHHHHHHH
Confidence            34568899999999999999998866  3222235677765432  3333 23344555432210 11223445554444


Q ss_pred             HHHhcCCeEEEEEeCCC
Q 040110          189 RDYLTNKKYFTVLDDVW  205 (348)
Q Consensus       189 ~~~L~~kr~LlVLDdv~  205 (348)
                      .   ..+.-++|+|.+.
T Consensus       155 ~---~~~~~lVVIDSIq  168 (372)
T cd01121         155 E---ELKPDLVIIDSIQ  168 (372)
T ss_pred             H---hcCCcEEEEcchH
Confidence            3   2367789999984

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.19  E-value=0.032  Score=47.27  Aligned_cols=24  Identities=21%  Similarity=0.151  Sum_probs=21.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++.|.|++|+||||+|+.+...
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~   27 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEK   27 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999999887

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=96.19  E-value=0.0022  Score=57.84  Aligned_cols=49  Identities=18%  Similarity=0.227  Sum_probs=38.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|+|.++..   +.|.=.+... ....+..--+.++|++|.||||||.-+++.
T Consensus        27 efiGQ~~vk---~~L~ifI~AA-k~r~e~lDHvLl~GPPGlGKTTLA~IIA~E   75 (332)
T COG2255          27 EFIGQEKVK---EQLQIFIKAA-KKRGEALDHVLLFGPPGLGKTTLAHIIANE   75 (332)
T ss_pred             HhcChHHHH---HHHHHHHHHH-HhcCCCcCeEEeeCCCCCcHHHHHHHHHHH
Confidence            899999988   7666555421 123455667889999999999999999988

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=96.16  E-value=0.023  Score=55.62  Aligned_cols=91  Identities=12%  Similarity=0.169  Sum_probs=55.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHH------H
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKS------E  184 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~------~  184 (348)
                      .++|.|.+|+|||||+.++.+.... ++-+.++++-++... .+.+++.++...=....+..  ...+.....      .
T Consensus       145 R~gIfa~~G~GKt~Ll~~~~~~~~~-~~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~~~  223 (461)
T PRK12597        145 KTGLFGGAGVGKTVLMMELIFNISK-QHSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVVLT  223 (461)
T ss_pred             EEEeecCCCCChhHHHHHHHHHHHh-hCCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHHHH
Confidence            5889999999999999998877322 244677777666543 55667666655322221110  111222211      2


Q ss_pred             HHHHHHHh---cCCeEEEEEeCCC
Q 040110          185 KTILRDYL---TNKKYFTVLDDVW  205 (348)
Q Consensus       185 ~~~l~~~L---~~kr~LlVLDdv~  205 (348)
                      .-.+.+++   .++++||++|++-
T Consensus       224 a~tiAEyfrd~~G~~VLl~~DslT  247 (461)
T PRK12597        224 GLTIAEYLRDEEKEDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHHhcCCceEEEeccch
Confidence            22344555   3789999999993

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=96.16  E-value=0.04  Score=55.55  Aligned_cols=139  Identities=15%  Similarity=0.081  Sum_probs=88.0

Q ss_pred             ccCcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCcc------ccCCcceeEEEEeCCC
Q 040110           80 ICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNF------VKFYFDCHAWVRVSNF  153 (348)
Q Consensus        80 ~~~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~------~~~~F~~~~wv~~~~~  153 (348)
                      +++.+-+|+.+.   .+|-..+...-.. +..-+.+-|.|-+|+|||..+..|.+...      .-..|+ .+.|+.-.-
T Consensus       394 vp~sLpcRe~E~---~~I~~f~~~~i~~-~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~-yveINgm~l  468 (767)
T KOG1514|consen  394 VPESLPCRENEF---SEIEDFLRSFISD-QGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFD-YVEINGLRL  468 (767)
T ss_pred             ccccccchhHHH---HHHHHHHHhhcCC-CCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCcc-EEEEcceee
Confidence            334677999999   8888888632111 33445888999999999999999987521      223453 455555555


Q ss_pred             CCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhc-----CCeEEEEEeCCCCh-hhHHHHHhhC-CC-CCCCcE
Q 040110          154 YNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT-----NKKYFTVLDDVWIE-KIWDDLREAL-PD-NQIGSR  225 (348)
Q Consensus       154 ~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~-----~kr~LlVLDdv~~~-~~~~~l~~~l-~~-~~~gsk  225 (348)
                      ....+++..|...+....       .........|..+..     .+.+++++|+++.. .--.++...+ -+ ..++||
T Consensus       469 ~~~~~~Y~~I~~~lsg~~-------~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sK  541 (767)
T KOG1514|consen  469 ASPREIYEKIWEALSGER-------VTWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSK  541 (767)
T ss_pred             cCHHHHHHHHHHhcccCc-------ccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCc
Confidence            678999999999998752       233444555555553     24688888887543 1112233222 22 346788


Q ss_pred             EEEEe
Q 040110          226 ALITV  230 (348)
Q Consensus       226 IlvTT  230 (348)
                      ++|-+
T Consensus       542 Lvvi~  546 (767)
T KOG1514|consen  542 LVVIA  546 (767)
T ss_pred             eEEEE
Confidence            76644

>PRK03839 putative kinase; Provisional

Probab=96.15  E-value=0.0041  Score=53.04  Aligned_cols=22  Identities=23%  Similarity=0.386  Sum_probs=20.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|++|+||||+++.+++.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~   23 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4788999999999999999988

>PRK14527 adenylate kinase; Provisional

Probab=96.14  E-value=0.016  Score=49.87  Aligned_cols=25  Identities=24%  Similarity=0.288  Sum_probs=22.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...++.|.|++|+||||+|+.+.+.
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~   29 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQE   29 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4568999999999999999999866

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.14  E-value=0.0087  Score=53.27  Aligned_cols=21  Identities=19%  Similarity=0.430  Sum_probs=19.5

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|.|++|+||||+|+.+...
T Consensus         9 Ivl~G~PGsGK~T~a~~La~~   29 (229)
T PTZ00088          9 IVLFGAPGVGKGTFAEILSKK   29 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            778999999999999999877

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.14  E-value=0.0037  Score=53.70  Aligned_cols=21  Identities=19%  Similarity=0.118  Sum_probs=18.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhc
Q 040110          114 VVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      ++.|+|+.|.||||+.+.+.-
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~   21 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGL   21 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHH
Confidence            367999999999999999873

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.13  E-value=0.0046  Score=52.86  Aligned_cols=25  Identities=16%  Similarity=0.248  Sum_probs=22.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...++.|.|++|+||||+|+.+...
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~   26 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEK   26 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999999999999865

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=96.12  E-value=0.037  Score=53.85  Aligned_cols=91  Identities=11%  Similarity=0.149  Sum_probs=49.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc-cccCCCCHH------HHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW-LKIMGKDYK------SEK  185 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-~~~~~~~~~------~~~  185 (348)
                      ..++|+|..|+|||||+..+.....   ....++++.-.+.-++.++....+.......-. ....+....      ...
T Consensus       166 qri~I~G~SGsGKTTLL~~Ia~l~~---pd~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~~a  242 (450)
T PRK06002        166 QRIGIFAGSGVGKSTLLAMLARADA---FDTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPLTA  242 (450)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCCC---CCeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHHHH
Confidence            3689999999999999998876522   222444443334445555555444433111000 011111111      111


Q ss_pred             HHHHHHh--cCCeEEEEEeCCCC
Q 040110          186 TILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       186 ~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      -.+.+++  +++++|+++||+-.
T Consensus       243 ~~iAEyfrd~G~~Vll~~DslTr  265 (450)
T PRK06002        243 TAIAEYFRDRGENVLLIVDSVTR  265 (450)
T ss_pred             HHHHHHHHHcCCCEEEeccchHH
Confidence            2234444  47899999999853

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=96.11  E-value=0.021  Score=52.61  Aligned_cols=80  Identities=13%  Similarity=0.057  Sum_probs=43.9

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc--ceeEEEEeCCCCCHHHHHHHHHHHhCCC-CCccccCCCCHHHHH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF--DCHAWVRVSNFYNFKRILDDIMKSLMPT-SSWLKIMGKDYKSEK  185 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F--~~~~wv~~~~~~~~~~~~~~i~~~l~~~-~~~~~~~~~~~~~~~  185 (348)
                      ...+.+|+|.|..|+||||+|+.+..-  .....  ..+..++...-+...+.+..    .+.. ... .....+...+.
T Consensus        59 ~~~p~IIGIaG~~GSGKSTlar~L~~l--l~~~~~~g~V~vi~~D~f~~~~~~l~~----~g~~~~~g-~P~s~D~~~l~  131 (290)
T TIGR00554        59 AKIPYIISIAGSVAVGKSTTARILQAL--LSRWPEHRKVELITTDGFLHPNQVLKE----RNLMKKKG-FPESYDMHRLV  131 (290)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH--HhhcCCCCceEEEecccccccHHHHHH----cCCccccC-CChhccHHHHH
Confidence            345689999999999999999877544  22111  12334444433322222222    1111 001 23456777777


Q ss_pred             HHHHHHhcCC
Q 040110          186 TILRDYLTNK  195 (348)
Q Consensus       186 ~~l~~~L~~k  195 (348)
                      ..+.....++
T Consensus       132 ~~L~~Lk~g~  141 (290)
T TIGR00554       132 KFLSDLKSGK  141 (290)
T ss_pred             HHHHHHHCCC
Confidence            7776666554

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=96.11  E-value=0.036  Score=46.02  Aligned_cols=113  Identities=13%  Similarity=0.106  Sum_probs=59.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC--CCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN--FYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~--~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      .+++|+|..|.|||||.+.+....  . .....+++.-..  ......    ....+...    . +-..-+...-.+..
T Consensus        26 ~~~~i~G~nGsGKStll~~l~g~~--~-~~~G~i~~~~~~~~~~~~~~----~~~~i~~~----~-qlS~G~~~r~~l~~   93 (157)
T cd00267          26 EIVALVGPNGSGKSTLLRAIAGLL--K-PTSGEILIDGKDIAKLPLEE----LRRRIGYV----P-QLSGGQRQRVALAR   93 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC--C-CCccEEEECCEEcccCCHHH----HHhceEEE----e-eCCHHHHHHHHHHH
Confidence            588999999999999999998762  2 234445442211  111111    11111110    0 00111223333566


Q ss_pred             HhcCCeEEEEEeCCCCh---hhHHHHHhhCCC-CCCCcEEEEEeCChhhhh
Q 040110          191 YLTNKKYFTVLDDVWIE---KIWDDLREALPD-NQIGSRALITVGPHNILT  237 (348)
Q Consensus       191 ~L~~kr~LlVLDdv~~~---~~~~~l~~~l~~-~~~gskIlvTTR~~~v~~  237 (348)
                      .+....-+++||+.-..   .....+...+.. ...+..++++|.+.....
T Consensus        94 ~l~~~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~  144 (157)
T cd00267          94 ALLLNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPELAE  144 (157)
T ss_pred             HHhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHH
Confidence            66667889999998653   222222222211 112456888887766544

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.10  E-value=0.037  Score=53.59  Aligned_cols=25  Identities=24%  Similarity=0.339  Sum_probs=21.5

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++++|+.|+||||++..+...
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~  214 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAAR  214 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999887654

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.09  E-value=0.0043  Score=55.35  Aligned_cols=53  Identities=19%  Similarity=0.216  Sum_probs=45.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+.....+.-|++.|..+..-++-.++-|..+|++|.|||-+|+++++.
T Consensus       122 dViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane  174 (368)
T COG1223         122 DVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANE  174 (368)
T ss_pred             hhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcc
Confidence            68999999988888999998554445667888999999999999999999998

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=96.09  E-value=0.067  Score=53.52  Aligned_cols=46  Identities=20%  Similarity=0.301  Sum_probs=36.4

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|....+   +++.+.+...    .....-|.|+|..|+|||++|+.+++.
T Consensus       188 ~iig~s~~~---~~~~~~i~~~----a~~~~pVlI~Ge~GtGK~~~A~~ih~~  233 (509)
T PRK05022        188 EMIGQSPAM---QQLKKEIEVV----AASDLNVLILGETGVGKELVARAIHAA  233 (509)
T ss_pred             ceeecCHHH---HHHHHHHHHH----hCCCCcEEEECCCCccHHHHHHHHHHh
Confidence            799999999   8888777621    222335779999999999999999876

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=96.08  E-value=0.0087  Score=62.64  Aligned_cols=50  Identities=16%  Similarity=0.262  Sum_probs=38.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.+..+   ++|+++|......+.....++.++|++|+||||+|+.++..
T Consensus       323 ~~~g~~~vK---~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~  372 (784)
T PRK10787        323 DHYGLERVK---DRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKA  372 (784)
T ss_pred             hccCHHHHH---HHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            589999999   99998886211112223447889999999999999999976

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=96.07  E-value=0.085  Score=47.96  Aligned_cols=52  Identities=12%  Similarity=0.118  Sum_probs=34.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKS  166 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~  166 (348)
                      -.++.|.|.+|+||||++.+++........ ..++|++...  +..++...+...
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g-~~vl~iS~E~--~~~~~~~r~~~~   81 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALDLITQHG-VRVGTISLEE--PVVRTARRLLGQ   81 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHHhcC-ceEEEEEccc--CHHHHHHHHHHH
Confidence            347778999999999999998766222212 3577877654  344555555443

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=96.07  E-value=0.016  Score=57.48  Aligned_cols=97  Identities=19%  Similarity=0.278  Sum_probs=61.1

Q ss_pred             cccccccccccHHHHHhhcCC---CC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCH
Q 040110           83 ALLGLQSKIINLRNLHQRLPP---SS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNF  156 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~---~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  156 (348)
                      ++=|.+..+   .+|.+++..   ++   ..+-..++=|.++|++|+|||.||+++++.  ..-.|     +.++-+   
T Consensus       191 diGG~d~~~---~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAge--l~vPf-----~~isAp---  257 (802)
T KOG0733|consen  191 DIGGLDKTL---AELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGE--LGVPF-----LSISAP---  257 (802)
T ss_pred             hccChHHHH---HHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhh--cCCce-----Eeecch---
Confidence            677899888   777776642   10   112234455678999999999999999998  43333     222211   


Q ss_pred             HHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 040110          157 KRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       157 ~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                           +|+...         ...+.+.+-+.+.+.-+.-.+++.+|+++-
T Consensus       258 -----eivSGv---------SGESEkkiRelF~~A~~~aPcivFiDeIDA  293 (802)
T KOG0733|consen  258 -----EIVSGV---------SGESEKKIRELFDQAKSNAPCIVFIDEIDA  293 (802)
T ss_pred             -----hhhccc---------CcccHHHHHHHHHHHhccCCeEEEeecccc
Confidence                 222222         233445555555555566899999999963

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=96.03  E-value=0.032  Score=54.45  Aligned_cols=91  Identities=13%  Similarity=0.215  Sum_probs=53.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHH------H
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKS------E  184 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~------~  184 (348)
                      .++|.|.+|+|||||+.++......... +.++++-++... .+.+++.++...=....+..  ...+.....      .
T Consensus       146 R~gIfa~~GvGKt~Ll~~i~~~~~~~~~-~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~~~  224 (463)
T PRK09280        146 KIGLFGGAGVGKTVLIQELINNIAKEHG-GYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVALT  224 (463)
T ss_pred             EEEeecCCCCChhHHHHHHHHHHHhcCC-CEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHH
Confidence            5789999999999999988766221111 356666665543 56677777765422221110  112222221      1


Q ss_pred             HHHHHHHh---cCCeEEEEEeCCC
Q 040110          185 KTILRDYL---TNKKYFTVLDDVW  205 (348)
Q Consensus       185 ~~~l~~~L---~~kr~LlVLDdv~  205 (348)
                      .-.+.+++   +++++||++|++-
T Consensus       225 a~tiAEyfrd~~G~~VLll~DslT  248 (463)
T PRK09280        225 GLTMAEYFRDVEGQDVLLFIDNIF  248 (463)
T ss_pred             HHHHHHHHHHhcCCceEEEecchH
Confidence            22355555   5689999999984

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=96.03  E-value=0.047  Score=49.70  Aligned_cols=94  Identities=15%  Similarity=0.115  Sum_probs=56.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccc--cCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHH-----
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFV--KFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKS-----  183 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~--~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~-----  183 (348)
                      .++|.|-.|+|||+|+..+.++..+  +.+-+.++++-+++.. .+.+++.++...=....+..  ...+.....     
T Consensus        71 R~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~~a~  150 (276)
T cd01135          71 KIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERIITP  150 (276)
T ss_pred             EEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHHHHH
Confidence            4789999999999999998877331  1234678888887665 56677776665422221110  111111111     


Q ss_pred             -HHHHHHHHhc---CCeEEEEEeCCCCh
Q 040110          184 -EKTILRDYLT---NKKYFTVLDDVWIE  207 (348)
Q Consensus       184 -~~~~l~~~L~---~kr~LlVLDdv~~~  207 (348)
                       ..-.+.++++   ++++|+++||+-..
T Consensus       151 ~~a~aiAEyfrd~~g~~VLl~~D~ltr~  178 (276)
T cd01135         151 RMALTTAEYLAYEKGKHVLVILTDMTNY  178 (276)
T ss_pred             HHHHHHHHHHHhccCCeEEEEEcChhHH
Confidence             1123445542   68999999999543

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=96.03  E-value=0.037  Score=48.05  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|..|.|||||.+.+...
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~   49 (200)
T cd03217          27 EVHALMGPNGSGKSTLAKTIMGH   49 (200)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999876

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.03  E-value=0.0044  Score=53.74  Aligned_cols=22  Identities=32%  Similarity=0.471  Sum_probs=20.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|+|.|.+|+|||||++.+...
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~   22 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQ   22 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999776

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=96.01  E-value=0.065  Score=45.68  Aligned_cols=23  Identities=22%  Similarity=0.306  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|..|+|||||.+.+..-
T Consensus        26 e~~~l~G~nGsGKSTLl~~l~Gl   48 (177)
T cd03222          26 EVIGIVGPNGTGKTTAVKILAGQ   48 (177)
T ss_pred             CEEEEECCCCChHHHHHHHHHcC
Confidence            48999999999999999999876

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>PRK04328 hypothetical protein; Provisional

Probab=96.00  E-value=0.029  Score=50.60  Aligned_cols=91  Identities=16%  Similarity=0.170  Sum_probs=54.0

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc---------------
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL---------------  174 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~---------------  174 (348)
                      +.-+++.|.|.+|+|||+|+.++.... .++ -..++|++....  ..++.+ .+++++.+....               
T Consensus        21 p~gs~ili~G~pGsGKT~l~~~fl~~~-~~~-ge~~lyis~ee~--~~~i~~-~~~~~g~d~~~~~~~~~l~iid~~~~~   95 (249)
T PRK04328         21 PERNVVLLSGGPGTGKSIFSQQFLWNG-LQM-GEPGVYVALEEH--PVQVRR-NMRQFGWDVRKYEEEGKFAIVDAFTGG   95 (249)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHHHHH-Hhc-CCcEEEEEeeCC--HHHHHH-HHHHcCCCHHHHhhcCCEEEEeccccc
Confidence            455688899999999999999865442 222 235777776553  333333 333443321000               


Q ss_pred             -----------ccCCCCHHHHHHHHHHHhcC-CeEEEEEeCCC
Q 040110          175 -----------KIMGKDYKSEKTILRDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       175 -----------~~~~~~~~~~~~~l~~~L~~-kr~LlVLDdv~  205 (348)
                                 .....+...+...+.+.++. +.-++|+|.+.
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDSlt  138 (249)
T PRK04328         96 IGSAAKREKYVVKDPDDVRELIDVLRQAIKDIGAKRVVIDSVS  138 (249)
T ss_pred             cccccccccccccCcccHHHHHHHHHHHHHhhCCCEEEEeChh
Confidence                       00123556667777776654 45679999984

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.00  E-value=0.033  Score=52.04  Aligned_cols=45  Identities=13%  Similarity=0.125  Sum_probs=35.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.+.+.+.    .+ .-.....++|+.|+||+++|..+.+.
T Consensus         5 ~iiGq~~~~---~~L~~~i~----~~-rl~ha~Lf~G~~G~Gk~~~A~~~a~~   49 (314)
T PRK07399          5 NLIGQPLAI---ELLTAAIK----QN-RIAPAYLFAGPEGVGRKLAALCFIEG   49 (314)
T ss_pred             HhCCHHHHH---HHHHHHHH----hC-CCCceEEEECCCCCCHHHHHHHHHHH
Confidence            578988888   88888887    22 22357778999999999999887654

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=95.99  E-value=0.078  Score=43.51  Aligned_cols=22  Identities=9%  Similarity=0.339  Sum_probs=19.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.+.|++|+||||+|+.+...
T Consensus         1 li~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhh
Confidence            3678999999999999999876

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.99  E-value=0.042  Score=49.85  Aligned_cols=95  Identities=17%  Similarity=0.098  Sum_probs=52.3

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCH-HHHHHHHHHHhCCCCCc----c---ccCC--
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNF-KRILDDIMKSLMPTSSW----L---KIMG--  178 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~-~~~~~~i~~~l~~~~~~----~---~~~~--  178 (348)
                      -+.-+++.|.|.+|+|||+||.+++.... ++. ..+++++...+.+. .+-+...+..++.....    .   ....  
T Consensus        33 ip~gs~~lI~G~pGtGKT~l~~qf~~~~a-~~G-e~vlyis~Ee~~~~~~~~l~~~a~~~g~d~~~~~~~l~~id~~~~~  110 (259)
T TIGR03878        33 IPAYSVINITGVSDTGKSLMVEQFAVTQA-SRG-NPVLFVTVESPANFVYTSLKERAKAMGVDFDKIEENIILIDAASST  110 (259)
T ss_pred             eECCcEEEEEcCCCCCHHHHHHHHHHHHH-hCC-CcEEEEEecCCchHHHHHHHHHHHHcCCCHHHHhCCEEEEECCCch
Confidence            34566888999999999999999765421 221 25677777643321 11122223334332110    0   0001  


Q ss_pred             ---CCHHHHHHHHHHHhcC-CeEEEEEeCCC
Q 040110          179 ---KDYKSEKTILRDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       179 ---~~~~~~~~~l~~~L~~-kr~LlVLDdv~  205 (348)
                         .+.+++...+....+. +.-++|+|.+.
T Consensus       111 ~~~~~~~~l~~~l~~~i~~~~~~~vVIDSls  141 (259)
T TIGR03878       111 ELRENVPNLLATLAYAIKEYKVKNTVIDSIT  141 (259)
T ss_pred             hhhhhHHHHHHHHHHHHHhhCCCEEEEcCch
Confidence               2345556666655533 45688999985

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=95.97  E-value=0.13  Score=45.14  Aligned_cols=23  Identities=13%  Similarity=0.151  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|..|.|||||.+.+...
T Consensus        38 e~~~i~G~nGsGKSTLl~~i~G~   60 (214)
T PRK13543         38 EALLVQGDNGAGKTTLLRVLAGL   60 (214)
T ss_pred             CEEEEEcCCCCCHHHHHHHHhCC
Confidence            47899999999999999999865

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=95.96  E-value=0.0065  Score=55.30  Aligned_cols=63  Identities=17%  Similarity=0.031  Sum_probs=44.1

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHH
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILD  161 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~  161 (348)
                      .+|+..|.    ....+..+|+|+|.||+|||||.-.+......+.+==.++=|.-|++++--.++-
T Consensus        38 ~~ll~~l~----p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSSp~TGGsiLG  100 (323)
T COG1703          38 RELLRALY----PRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGSILG  100 (323)
T ss_pred             HHHHHHHh----hcCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEECCCCCCCCccccc
Confidence            56777777    3355677999999999999999988877754444433555666677776544443

>PRK13531 regulatory ATPase RavA; Provisional

Probab=95.95  E-value=0.0054  Score=59.99  Aligned_cols=42  Identities=19%  Similarity=0.113  Sum_probs=36.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||++.+   +.+...+.      ..+  -+.|.|++|+|||+||+.+...
T Consensus        21 ~i~gre~vI---~lll~aal------ag~--hVLL~GpPGTGKT~LAraLa~~   62 (498)
T PRK13531         21 GLYERSHAI---RLCLLAAL------SGE--SVFLLGPPGIAKSLIARRLKFA   62 (498)
T ss_pred             hccCcHHHH---HHHHHHHc------cCC--CEEEECCCChhHHHHHHHHHHH
Confidence            699999999   99998888      222  3668999999999999999886

>PRK00131 aroK shikimate kinase; Reviewed

Probab=95.95  E-value=0.0064  Score=51.15  Aligned_cols=24  Identities=8%  Similarity=0.151  Sum_probs=21.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|.++|++|+||||+|+.++..
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~   27 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKR   27 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHH
Confidence            347889999999999999999987

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=95.95  E-value=0.066  Score=46.54  Aligned_cols=23  Identities=26%  Similarity=0.156  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++++|+|+.|.|||||.+.+...
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~~   48 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGVN   48 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHHH
Confidence            78999999999999999988643

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=95.94  E-value=0.046  Score=48.63  Aligned_cols=93  Identities=13%  Similarity=0.086  Sum_probs=53.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCcccc------------CCcceeE----------EEEeCCCC------------CHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVK------------FYFDCHA----------WVRVSNFY------------NFKR  158 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~------------~~F~~~~----------wv~~~~~~------------~~~~  158 (348)
                      -+++|+|++|+|||||.+.++.-..-.            ..-+.+.          |.++-++.            ...+
T Consensus        30 EfvsilGpSGcGKSTLLriiAGL~~p~~G~V~~~g~~v~~p~~~~~~vFQ~~~LlPW~Tv~~NV~l~l~~~~~~~~e~~~  109 (248)
T COG1116          30 EFVAILGPSGCGKSTLLRLIAGLEKPTSGEVLLDGRPVTGPGPDIGYVFQEDALLPWLTVLDNVALGLELRGKSKAEARE  109 (248)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCCCCceEEECCcccCCCCCCEEEEeccCcccchhhHHhhheehhhccccchHhHHH
Confidence            379999999999999999987532111            1101111          43332221            1234


Q ss_pred             HHHHHHHHhCCCCCcc---ccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 040110          159 ILDDIMKSLMPTSSWL---KIMGKDYKSEKTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       159 ~~~~i~~~l~~~~~~~---~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                      ...++++.++......   ..-+..+.+.. .|.+.|..++=+|.||.--.
T Consensus       110 ~a~~~L~~VgL~~~~~~~P~qLSGGMrQRV-aiARAL~~~P~lLLlDEPFg  159 (248)
T COG1116         110 RAKELLELVGLAGFEDKYPHQLSGGMRQRV-AIARALATRPKLLLLDEPFG  159 (248)
T ss_pred             HHHHHHHHcCCcchhhcCccccChHHHHHH-HHHHHHhcCCCEEEEcCCcc
Confidence            6777777777764431   11222333433 35666667777888888654

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=95.94  E-value=0.0063  Score=51.77  Aligned_cols=22  Identities=9%  Similarity=0.173  Sum_probs=20.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|+|++|+|||||++.+...
T Consensus         3 ~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         3 LIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6889999999999999998876

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.93  E-value=0.04  Score=56.98  Aligned_cols=59  Identities=17%  Similarity=0.054  Sum_probs=35.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPT  170 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~  170 (348)
                      ..+++++|+.|+||||.+..++...........+..++... .....+.++...+.++.+
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvp  244 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVP  244 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCCC
Confidence            47999999999999999988887632222112334443321 122445556666666554

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.92  E-value=0.0081  Score=52.52  Aligned_cols=119  Identities=13%  Similarity=0.057  Sum_probs=59.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      ..++.|.|+.|.||||+.+.+....-..+   ..+++.... .. -.+...|...++...+. .........-...+...
T Consensus        29 ~~~~~l~G~n~~GKstll~~i~~~~~la~---~G~~vpa~~-~~-l~~~d~I~~~~~~~d~~-~~~~S~fs~e~~~~~~i  102 (204)
T cd03282          29 SRFHIITGPNMSGKSTYLKQIALLAIMAQ---IGCFVPAEY-AT-LPIFNRLLSRLSNDDSM-ERNLSTFASEMSETAYI  102 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHHH---cCCCcchhh-cC-ccChhheeEecCCcccc-chhhhHHHHHHHHHHHH
Confidence            36899999999999999988764321110   111221111 01 12223333333332110 00001111111122222


Q ss_pred             h--cCCeEEEEEeCCCCh---hh----HHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          192 L--TNKKYFTVLDDVWIE---KI----WDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       192 L--~~kr~LlVLDdv~~~---~~----~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      +  ..++-|++||..-..   .+    ...+...+..  .|+.+|++|-+..++..
T Consensus       103 l~~~~~~~lvllDE~~~gt~~~~~~~l~~~il~~l~~--~~~~~i~~TH~~~l~~~  156 (204)
T cd03282         103 LDYADGDSLVLIDELGRGTSSADGFAISLAILECLIK--KESTVFFATHFRDIAAI  156 (204)
T ss_pred             HHhcCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHh--cCCEEEEECChHHHHHH
Confidence            2  356889999998442   11    1223333322  27789999999888775

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.92  E-value=0.066  Score=47.44  Aligned_cols=116  Identities=15%  Similarity=0.052  Sum_probs=63.9

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc---------------
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL---------------  174 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~---------------  174 (348)
                      +.-.++.|.|.+|+||||||.++.... .+ .-..++|++....  ..++... +++++......               
T Consensus        18 ~~G~~~~i~G~~G~GKT~l~~~~~~~~-~~-~g~~~~~is~e~~--~~~i~~~-~~~~g~~~~~~~~~~~l~i~d~~~~~   92 (229)
T TIGR03881        18 PRGFFVAVTGEPGTGKTIFCLHFAYKG-LR-DGDPVIYVTTEES--RESIIRQ-AAQFGMDFEKAIEEGKLVIIDALMKE   92 (229)
T ss_pred             cCCeEEEEECCCCCChHHHHHHHHHHH-Hh-cCCeEEEEEccCC--HHHHHHH-HHHhCCCHHHHhhcCCEEEEEccccc
Confidence            345688999999999999999876542 12 2236778876433  3343332 33332211100               


Q ss_pred             -----ccCCCCHHHHHHHHHHHhcC---CeEEEEEeCCCCh-----hhHH----HHHhhCCCCCCCcEEEEEeCC
Q 040110          175 -----KIMGKDYKSEKTILRDYLTN---KKYFTVLDDVWIE-----KIWD----DLREALPDNQIGSRALITVGP  232 (348)
Q Consensus       175 -----~~~~~~~~~~~~~l~~~L~~---kr~LlVLDdv~~~-----~~~~----~l~~~l~~~~~gskIlvTTR~  232 (348)
                           .....+.+++...+.+.++.   +.-++|+|.+...     ....    .+...+  ...|+.+++|+..
T Consensus        93 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~vvIDsl~~l~~~~~~~~r~~~~~l~~~l--~~~~~tvil~~~~  165 (229)
T TIGR03881        93 KEDEWSLRELSIEELLNKVIEAKKYLGYGHARLVIDSMSAFWLDKPAMARKYSYYLKRVL--NRWNFTILLTSQY  165 (229)
T ss_pred             cccccccccCCHHHHHHHHHHHHHhhccCceEEEecCchhhhccChHHHHHHHHHHHHHH--HhCCCEEEEEecc
Confidence                 01124567777777776643   3467889997532     1111    122222  2347778888763

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK05439 pantothenate kinase; Provisional

Probab=95.91  E-value=0.037  Score=51.46  Aligned_cols=81  Identities=17%  Similarity=0.163  Sum_probs=44.9

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCC--cceeEEEEeCCCCCHHHHHHHHHHHhC-CCCCccccCCCCHHHHH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFY--FDCHAWVRVSNFYNFKRILDDIMKSLM-PTSSWLKIMGKDYKSEK  185 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~--F~~~~wv~~~~~~~~~~~~~~i~~~l~-~~~~~~~~~~~~~~~~~  185 (348)
                      ...+.+|+|.|.+|+||||+|..+...  ....  -..+.-+++..-+...+.+..  ..+. ...   .+..-|.+.+.
T Consensus        83 ~~~~~iIgIaG~~gsGKSTla~~L~~~--l~~~~~~~~v~vi~~DdFy~~~~~l~~--~~l~~~kg---~Pes~D~~~l~  155 (311)
T PRK05439         83 QKVPFIIGIAGSVAVGKSTTARLLQAL--LSRWPEHPKVELVTTDGFLYPNAVLEE--RGLMKRKG---FPESYDMRALL  155 (311)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH--HHhhCCCCceEEEeccccccCHHHHhh--hhccccCC---CcccccHHHHH
Confidence            456789999999999999999988765  2221  112333444333322222221  1111 111   22345677777


Q ss_pred             HHHHHHhcCCe
Q 040110          186 TILRDYLTNKK  196 (348)
Q Consensus       186 ~~l~~~L~~kr  196 (348)
                      ..|....+++.
T Consensus       156 ~~L~~Lk~G~~  166 (311)
T PRK05439        156 RFLSDVKSGKP  166 (311)
T ss_pred             HHHHHHHcCCC
Confidence            77776666654

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=95.90  E-value=0.039  Score=53.65  Aligned_cols=90  Identities=13%  Similarity=0.110  Sum_probs=52.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHH------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKS------  183 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~------  183 (348)
                      ..++|+|..|+|||||++.+++...   . +.++++-++... .+.++..+.+..-+...+..  ...+.....      
T Consensus       159 qri~I~G~sG~GKTtLL~~I~~~~~---~-d~~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~a~~  234 (442)
T PRK08927        159 QRMGIFAGSGVGKSVLLSMLARNAD---A-DVSVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQAAY  234 (442)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhccC---C-CEEEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHHHHH
Confidence            4679999999999999999987722   1 345556565544 45566655554432221110  111221111      


Q ss_pred             HHHHHHHHh--cCCeEEEEEeCCCC
Q 040110          184 EKTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       184 ~~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      ..-.+.+++  +++++|+++||+-.
T Consensus       235 ~a~tiAEyfrd~G~~Vll~~DslTr  259 (442)
T PRK08927        235 LTLAIAEYFRDQGKDVLCLMDSVTR  259 (442)
T ss_pred             HHHHHHHHHHHCCCcEEEEEeCcHH
Confidence            111244444  47899999999843

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=95.90  E-value=0.12  Score=45.02  Aligned_cols=23  Identities=13%  Similarity=0.326  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|.|..|+|||||++.+...
T Consensus        35 ~~~~i~G~nGsGKSTLl~~l~Gl   57 (207)
T cd03369          35 EKIGIVGRTGAGKSTLILALFRF   57 (207)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcc
Confidence            47999999999999999999764

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=95.88  E-value=0.0072  Score=53.57  Aligned_cols=23  Identities=13%  Similarity=0.095  Sum_probs=20.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHh
Q 040110          111 THSVVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~  133 (348)
                      ..+++.|+|+.|.||||+.+.+.
T Consensus        29 ~~~~~~l~G~n~~GKstll~~i~   51 (222)
T cd03285          29 KSRFLIITGPNMGGKSTYIRQIG   51 (222)
T ss_pred             CCeEEEEECCCCCChHHHHHHHH
Confidence            45689999999999999988865

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.88  E-value=0.042  Score=51.42  Aligned_cols=27  Identities=15%  Similarity=0.226  Sum_probs=23.5

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ....+++++|++|+||||++..++...
T Consensus       112 ~~~~vi~lvGpnGsGKTTt~~kLA~~l  138 (318)
T PRK10416        112 KKPFVILVVGVNGVGKTTTIGKLAHKY  138 (318)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            356899999999999999999988763

>PRK00625 shikimate kinase; Provisional

Probab=95.88  E-value=0.0063  Score=51.71  Aligned_cols=22  Identities=14%  Similarity=0.138  Sum_probs=19.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.++||+|+||||+++.+.+.
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~   23 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKF   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3778999999999999999877

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=95.88  E-value=0.02  Score=52.07  Aligned_cols=111  Identities=12%  Similarity=0.074  Sum_probs=61.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      ...++.|.|..|+||||++..+.+.  +...-..++  .+.++....  +.. ..++..       ...........++.
T Consensus        79 ~~GlilisG~tGSGKTT~l~all~~--i~~~~~~ii--tiEdp~E~~--~~~-~~q~~v-------~~~~~~~~~~~l~~  144 (264)
T cd01129          79 PHGIILVTGPTGSGKTTTLYSALSE--LNTPEKNII--TVEDPVEYQ--IPG-INQVQV-------NEKAGLTFARGLRA  144 (264)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHhh--hCCCCCeEE--EECCCceec--CCC-ceEEEe-------CCcCCcCHHHHHHH
Confidence            3457889999999999999988766  322111222  232221110  000 011111       11111235567778


Q ss_pred             HhcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          191 YLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       191 ~L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      .|+...=.++++++.+.+....+.....   .|..++-|....++...
T Consensus       145 ~lR~~PD~i~vgEiR~~e~a~~~~~aa~---tGh~v~tTlHa~~~~~a  189 (264)
T cd01129         145 ILRQDPDIIMVGEIRDAETAEIAVQAAL---TGHLVLSTLHTNDAPGA  189 (264)
T ss_pred             HhccCCCEEEeccCCCHHHHHHHHHHHH---cCCcEEEEeccCCHHHH
Confidence            8888888999999988876554444332   24446656665555443

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>PRK06936 type III secretion system ATPase; Provisional

Probab=95.87  E-value=0.043  Score=53.30  Aligned_cols=90  Identities=12%  Similarity=0.182  Sum_probs=52.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHHH-----
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKSE-----  184 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~~-----  184 (348)
                      ..++|.|..|+|||||.+.+++.  ...  +.++++-++... .+.++....+..-+...+..  ...+......     
T Consensus       163 q~~~I~G~sG~GKStLl~~Ia~~--~~~--dv~V~~liGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~  238 (439)
T PRK06936        163 QRMGIFAAAGGGKSTLLASLIRS--AEV--DVTVLALIGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAKAGF  238 (439)
T ss_pred             CEEEEECCCCCChHHHHHHHhcC--CCC--CEEEEEEEccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHHHHH
Confidence            36899999999999999999987  222  456677666554 45555544433222111110  1122222211     


Q ss_pred             -HHHHHHHh--cCCeEEEEEeCCCC
Q 040110          185 -KTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       185 -~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                       .-.+.+++  .++++||++||+-.
T Consensus       239 ~a~tiAEyfrd~G~~Vll~~DslTR  263 (439)
T PRK06936        239 VATSIAEYFRDQGKRVLLLMDSVTR  263 (439)
T ss_pred             HHHHHHHHHHHcCCCEEEeccchhH
Confidence             11233444  57899999999953

>PRK00279 adk adenylate kinase; Reviewed

Probab=95.85  E-value=0.022  Score=50.04  Aligned_cols=22  Identities=23%  Similarity=0.176  Sum_probs=19.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|++|+||||+|+.++..
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~   23 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEK   23 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3778999999999999998866

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=95.85  E-value=0.057  Score=56.55  Aligned_cols=117  Identities=16%  Similarity=0.205  Sum_probs=70.6

Q ss_pred             cccccccccccHHHHHhhcCCCC-CCCC-CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS-GLGQ-PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRIL  160 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~-~~~~-~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  160 (348)
                      .++|.++.+   ..|.+.+.... +..+ .+...+.+.|+.|+|||-||++++.-  +-+..+.-+-+.++      +..
T Consensus       563 ~V~gQ~eAv---~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~--~Fgse~~~IriDms------e~~  631 (898)
T KOG1051|consen  563 RVIGQDEAV---AAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEY--VFGSEENFIRLDMS------EFQ  631 (898)
T ss_pred             hccchHHHH---HHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHH--HcCCccceEEechh------hhh
Confidence            578888888   88888776431 1222 25567788999999999999999877  54444455555443      222


Q ss_pred             HHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeE-EEEEeCCCCh--hhHHHHHhhC
Q 040110          161 DDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKY-FTVLDDVWIE--KIWDDLREAL  217 (348)
Q Consensus       161 ~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~-LlVLDdv~~~--~~~~~l~~~l  217 (348)
                      . +.+..+.+      +..--.+....|-+.++.++| .+.||||+..  +...-+...+
T Consensus       632 e-vskligsp------~gyvG~e~gg~LteavrrrP~sVVLfdeIEkAh~~v~n~llq~l  684 (898)
T KOG1051|consen  632 E-VSKLIGSP------PGYVGKEEGGQLTEAVKRRPYSVVLFEEIEKAHPDVLNILLQLL  684 (898)
T ss_pred             h-hhhccCCC------cccccchhHHHHHHHHhcCCceEEEEechhhcCHHHHHHHHHHH
Confidence            2 33333332      111223344567777877765 4556999765  3444444443

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=95.84  E-value=0.04  Score=51.35  Aligned_cols=90  Identities=16%  Similarity=0.109  Sum_probs=56.0

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTIL  188 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l  188 (348)
                      +.-+++-|+|+.|+||||||.++...  ....-..++|+.....++.     ..+..++.+.+.. -......++..+.+
T Consensus        51 p~G~ivEi~G~~ssGKttLaL~~ia~--~q~~g~~~a~ID~e~~ld~-----~~a~~lGvdl~rllv~~P~~~E~al~~~  123 (322)
T PF00154_consen   51 PRGRIVEIYGPESSGKTTLALHAIAE--AQKQGGICAFIDAEHALDP-----EYAESLGVDLDRLLVVQPDTGEQALWIA  123 (322)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHH--HHHTT-EEEEEESSS---H-----HHHHHTT--GGGEEEEE-SSHHHHHHHH
T ss_pred             ccCceEEEeCCCCCchhhhHHHHHHh--hhcccceeEEecCcccchh-----hHHHhcCccccceEEecCCcHHHHHHHH
Confidence            34568999999999999999998876  3333347889988777765     3455566554331 11233456666766


Q ss_pred             HHHhcC-CeEEEEEeCCCC
Q 040110          189 RDYLTN-KKYFTVLDDVWI  206 (348)
Q Consensus       189 ~~~L~~-kr~LlVLDdv~~  206 (348)
                      ...++. .--++|+|.|-.
T Consensus       124 e~lirsg~~~lVVvDSv~a  142 (322)
T PF00154_consen  124 EQLIRSGAVDLVVVDSVAA  142 (322)
T ss_dssp             HHHHHTTSESEEEEE-CTT
T ss_pred             HHHhhcccccEEEEecCcc
Confidence            666654 456889999854

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=95.83  E-value=0.015  Score=47.19  Aligned_cols=42  Identities=17%  Similarity=0.123  Sum_probs=30.0

Q ss_pred             EEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHH
Q 040110          115 VAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILD  161 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~  161 (348)
                      |.++|++|+|||+||+.++..  ...   ...-+.++...+..+++.
T Consensus         2 vlL~G~~G~GKt~l~~~la~~--~~~---~~~~i~~~~~~~~~dl~g   43 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAAL--LGR---PVIRINCSSDTTEEDLIG   43 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHH--HTC---EEEEEE-TTTSTHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hhc---ceEEEEecccccccccee
Confidence            568999999999999999887  311   233456777777766554

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=95.81  E-value=0.029  Score=57.67  Aligned_cols=22  Identities=27%  Similarity=0.288  Sum_probs=20.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -+.++|++|+|||++|+.+++.
T Consensus       187 gill~G~~G~GKt~~~~~~a~~  208 (644)
T PRK10733        187 GVLMVGPPGTGKTLLAKAIAGE  208 (644)
T ss_pred             cEEEECCCCCCHHHHHHHHHHH
Confidence            3889999999999999999887

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=95.81  E-value=0.0074  Score=54.08  Aligned_cols=61  Identities=18%  Similarity=0.103  Sum_probs=35.6

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHH
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRI  159 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  159 (348)
                      .++++.|.+    ...+..+|+|.|++|+|||||...+....+.+.+=-.++=|.-|++++--.+
T Consensus        16 ~~ll~~l~~----~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~~g~~VaVlAVDPSSp~tGGAl   76 (266)
T PF03308_consen   16 RELLKRLYP----HTGRAHVIGITGPPGAGKSTLIDALIRELRERGKRVAVLAVDPSSPFTGGAL   76 (266)
T ss_dssp             HHHHHHHGG----GTT-SEEEEEEE-TTSSHHHHHHHHHHHHHHTT--EEEEEE-GGGGCC---S
T ss_pred             HHHHHHHHh----hcCCceEEEeeCCCCCcHHHHHHHHHHHHhhcCCceEEEEECCCCCCCCCcc
Confidence            566666662    2345679999999999999999888766333222224445555666654433

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=95.81  E-value=0.079  Score=45.20  Aligned_cols=23  Identities=22%  Similarity=0.339  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|..|.|||||.+.+..-
T Consensus        27 ~~~~i~G~nGsGKSTLl~~l~G~   49 (182)
T cd03215          27 EIVGIAGLVGNGQTELAEALFGL   49 (182)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            47899999999999999999876

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=95.80  E-value=0.039  Score=54.09  Aligned_cols=55  Identities=18%  Similarity=0.201  Sum_probs=39.8

Q ss_pred             cccccccccccHHHHHhhcCCCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcCcc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNNNF  137 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~  137 (348)
                      ++-|-++...-+++++++|..+.   .-+..-++=|.++|++|.|||-||++++....
T Consensus       305 dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~  362 (752)
T KOG0734|consen  305 DVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAG  362 (752)
T ss_pred             cccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccC
Confidence            45576666555599999998432   12333455677899999999999999998733

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=95.80  E-value=0.0057  Score=50.87  Aligned_cols=34  Identities=15%  Similarity=-0.060  Sum_probs=25.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEE
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWV  148 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv  148 (348)
                      .+|-|+|.+|+||||||+++.+.  ....-..++.+
T Consensus         3 ~vIwltGlsGsGKtTlA~~L~~~--L~~~g~~~~~L   36 (156)
T PF01583_consen    3 FVIWLTGLSGSGKTTLARALERR--LFARGIKVYLL   36 (156)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHH--HHHTTS-EEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEe
Confidence            47889999999999999999988  43333344444

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.79  E-value=0.008  Score=51.10  Aligned_cols=23  Identities=13%  Similarity=0.342  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++++|+|+.|+|||||++.+.+.
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~   24 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEE   24 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHcc
Confidence            47899999999999999999886

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=95.78  E-value=0.012  Score=50.46  Aligned_cols=36  Identities=11%  Similarity=0.135  Sum_probs=28.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEE
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVR  149 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~  149 (348)
                      .+++.|+|+.|+|||||+..+...  ....|...+..+
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~--~~~~~~~~v~~T   37 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQE--FPDKFGRVVSHT   37 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHH--STTTEEEEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh--cccccccceeec
Confidence            357889999999999999999987  666775444443

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=95.76  E-value=0.059  Score=54.17  Aligned_cols=122  Identities=16%  Similarity=0.145  Sum_probs=67.1

Q ss_pred             CcEEEEEECCCCCcHHH-HHHHHhcCccccCCcceeEEEEeCCCCC--HHHHHHHHHHHhCCCCCcc-------------
Q 040110          111 THSVVAILDSRGFDKTA-FAAEIYNNNFVKFYFDCHAWVRVSNFYN--FKRILDDIMKSLMPTSSWL-------------  174 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTt-LA~~v~~~~~~~~~F~~~~wv~~~~~~~--~~~~~~~i~~~l~~~~~~~-------------  174 (348)
                      ...||.|+|..|+|||| |++.+|.+     .|...--+.+.++-.  ...+.+.+...++......             
T Consensus       370 ~n~vvvivgETGSGKTTQl~QyL~ed-----GY~~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGYsIRFEdvT~~  444 (1042)
T KOG0924|consen  370 ENQVVVIVGETGSGKTTQLAQYLYED-----GYADNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGYSIRFEDVTSE  444 (1042)
T ss_pred             hCcEEEEEecCCCCchhhhHHHHHhc-----ccccCCeeeecCchHHHHHHHHHHHHHHhCCccccccceEEEeeecCCC
Confidence            34588999999999999 88888877     232222344455543  3456667777775443220             


Q ss_pred             --ccCCCCHH-HHHHHHHHHhcCCeEEEEEeCCCCh----hhHHH-HHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          175 --KIMGKDYK-SEKTILRDYLTNKKYFTVLDDVWIE----KIWDD-LREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       175 --~~~~~~~~-~~~~~l~~~L~~kr~LlVLDdv~~~----~~~~~-l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                        .+.-.+.. -+.+.|....-+|=..+|+|...+.    +.+-- ++..+. ....-|+||||-.-+.-+.
T Consensus       445 ~T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~la-rRrdlKliVtSATm~a~kf  515 (1042)
T KOG0924|consen  445 DTKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLA-RRRDLKLIVTSATMDAQKF  515 (1042)
T ss_pred             ceeEEEeccchHHHHHhhhhhhhheeEEEechhhhcccchHHHHHHHHHHHH-hhccceEEEeeccccHHHH
Confidence              00011111 1222333333345567888988653    22222 223322 2236799999877665544

>PRK08149 ATP synthase SpaL; Validated

Probab=95.75  E-value=0.047  Score=52.93  Aligned_cols=90  Identities=13%  Similarity=0.122  Sum_probs=51.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeC-CCCCHHHHHHHHHHHhCCCCCcc--ccCCCCHH------H
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVS-NFYNFKRILDDIMKSLMPTSSWL--KIMGKDYK------S  183 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~------~  183 (348)
                      ..++|+|..|+|||||+..+++....    +.++...+. +.-++.++..+............  ...+....      .
T Consensus       152 q~i~I~G~sG~GKTTLl~~i~~~~~~----dv~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a~~  227 (428)
T PRK08149        152 QRMGIFASAGCGKTSLMNMLIEHSEA----DVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAAL  227 (428)
T ss_pred             CEEEEECCCCCChhHHHHHHhcCCCC----CeEEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhHHH
Confidence            36899999999999999999876221    233333343 33456667666666433221110  11111111      1


Q ss_pred             HHHHHHHHh--cCCeEEEEEeCCCC
Q 040110          184 EKTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       184 ~~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      ..-.+.+++  +++++||++||+-.
T Consensus       228 ~a~tiAE~fr~~G~~Vll~~DslTr  252 (428)
T PRK08149        228 VATTVAEYFRDQGKRVVLFIDSMTR  252 (428)
T ss_pred             HHHHHHHHHHHcCCCEEEEccchHH
Confidence            222233444  47899999999854

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=95.74  E-value=0.092  Score=51.84  Aligned_cols=46  Identities=13%  Similarity=0.186  Sum_probs=34.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.....   .++.+.+...    .....-+.|+|.+|+|||++|+.+++.
T Consensus       139 ~lig~s~~~---~~l~~~~~~~----~~~~~~vli~Ge~GtGK~~lA~~ih~~  184 (469)
T PRK10923        139 DIIGEAPAM---QDVFRIIGRL----SRSSISVLINGESGTGKELVAHALHRH  184 (469)
T ss_pred             cceecCHHH---HHHHHHHHHH----hccCCeEEEEeCCCCcHHHHHHHHHhc
Confidence            689988877   6666655411    122334679999999999999999876

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=95.74  E-value=0.062  Score=45.90  Aligned_cols=25  Identities=16%  Similarity=0.183  Sum_probs=22.3

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...++.|.|.+|+||||+|+.+...
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~~   41 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEKK   41 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4568999999999999999999876

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>PRK06217 hypothetical protein; Validated

Probab=95.74  E-value=0.0086  Score=51.28  Aligned_cols=23  Identities=17%  Similarity=0.216  Sum_probs=20.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .|.|.|.+|+||||+|+.+....
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERL   25 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48899999999999999999874

>PRK14738 gmk guanylate kinase; Provisional

Probab=95.73  E-value=0.012  Score=51.40  Aligned_cols=27  Identities=22%  Similarity=0.255  Sum_probs=23.0

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+.+.|+|++|+|||||++.+...
T Consensus        10 ~~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         10 PAKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            446678889999999999999999755

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=95.73  E-value=0.041  Score=53.61  Aligned_cols=92  Identities=9%  Similarity=0.192  Sum_probs=56.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHH------H
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKS------E  184 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~------~  184 (348)
                      .++|.|.+|+|||+|+.++.++.. +.+-+.++++-++... .+.+++.++...=....+..  ...+.....      .
T Consensus       140 r~~Ifg~~G~GKt~l~~~~~~~~~-~~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~~~~  218 (449)
T TIGR03305       140 KAGLFGGAGVGKTVLLTEMIHNMV-GQHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVGHT  218 (449)
T ss_pred             EEEeecCCCCChhHHHHHHHHHHH-hcCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHHHHH
Confidence            578999999999999999887732 2233678888776654 45666666655322211110  111121111      2


Q ss_pred             HHHHHHHhc---CCeEEEEEeCCCC
Q 040110          185 KTILRDYLT---NKKYFTVLDDVWI  206 (348)
Q Consensus       185 ~~~l~~~L~---~kr~LlVLDdv~~  206 (348)
                      .-.+.++++   ++++||++||+-.
T Consensus       219 a~tiAEyfrd~~G~~VLl~~DslTR  243 (449)
T TIGR03305       219 ALTMAEYFRDDEKQDVLLLIDNIFR  243 (449)
T ss_pred             HHHHHHHHHHhcCCceEEEecChHH
Confidence            223555554   5899999999854

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=95.72  E-value=0.0071  Score=52.05  Aligned_cols=22  Identities=23%  Similarity=0.178  Sum_probs=20.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|+|.|.+|+||||||+.+...
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~   22 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999999887

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=95.72  E-value=0.014  Score=51.66  Aligned_cols=124  Identities=13%  Similarity=0.130  Sum_probs=67.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccc-------------cC-----Cccee--EEEEeCCCC----CHHHH---------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFV-------------KF-----YFDCH--AWVRVSNFY----NFKRI---------  159 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~-------------~~-----~F~~~--~wv~~~~~~----~~~~~---------  159 (348)
                      .+++|+|.+|+|||||++.+..-.+-             ..     .|..+  +|=.-....    ++.++         
T Consensus        34 e~lgivGeSGsGKSTL~r~l~Gl~~p~~G~I~~~G~~~~~~~~~~~~~~~VQmVFQDp~~SLnP~~tv~~~l~Epl~~~~  113 (252)
T COG1124          34 ETLGIVGESGSGKSTLARLLAGLEKPSSGSILLDGKPLAPKKRAKAFYRPVQMVFQDPYSSLNPRRTVGRILSEPLRPHG  113 (252)
T ss_pred             CEEEEEcCCCCCHHHHHHHHhcccCCCCceEEECCcccCccccchhhccceeEEecCCccccCcchhHHHHHhhhhccCC
Confidence            37999999999999999998644211             00     12211  121111111    22222         


Q ss_pred             -------HHHHHHHhCCCCCcc--ccCCCCHHHHHH-HHHHHhcCCeEEEEEeCCCCh-------hhHHHHHhhCCCCCC
Q 040110          160 -------LDDIMKSLMPTSSWL--KIMGKDYKSEKT-ILRDYLTNKKYFTVLDDVWIE-------KIWDDLREALPDNQI  222 (348)
Q Consensus       160 -------~~~i~~~l~~~~~~~--~~~~~~~~~~~~-~l~~~L~~kr~LlVLDdv~~~-------~~~~~l~~~l~~~~~  222 (348)
                             ..+++++++.+.+..  .+..-+-.+++. .|.+.|.-+.-+||+|..-+.       ..|+.+...-  ...
T Consensus       114 ~~~~~~~i~~~L~~VgL~~~~l~R~P~eLSGGQ~QRiaIARAL~~~PklLIlDEptSaLD~siQa~IlnlL~~l~--~~~  191 (252)
T COG1124         114 LSKSQQRIAELLDQVGLPPSFLDRRPHELSGGQRQRIAIARALIPEPKLLILDEPTSALDVSVQAQILNLLLELK--KER  191 (252)
T ss_pred             ccHHHHHHHHHHHHcCCCHHHHhcCchhcChhHHHHHHHHHHhccCCCEEEecCchhhhcHHHHHHHHHHHHHHH--Hhc
Confidence                   345566666653321  111223333333 477788889999999987543       2344333221  123


Q ss_pred             CcEEEEEeCChhhhhh
Q 040110          223 GSRALITVGPHNILTS  238 (348)
Q Consensus       223 gskIlvTTR~~~v~~~  238 (348)
                      +--+|+.|.+-.++..
T Consensus       192 ~lt~l~IsHdl~~v~~  207 (252)
T COG1124         192 GLTYLFISHDLALVEH  207 (252)
T ss_pred             CceEEEEeCcHHHHHH
Confidence            4568888888777765

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=95.71  E-value=0.02  Score=59.06  Aligned_cols=44  Identities=23%  Similarity=0.330  Sum_probs=35.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   +++++.|.    ....+..++  +|.+|||||+++.-++.+
T Consensus       171 PvIGRd~EI---~r~iqIL~----RR~KNNPvL--iGEpGVGKTAIvEGLA~r  214 (786)
T COG0542         171 PVIGRDEEI---RRTIQILS----RRTKNNPVL--VGEPGVGKTAIVEGLAQR  214 (786)
T ss_pred             CCcChHHHH---HHHHHHHh----ccCCCCCeE--ecCCCCCHHHHHHHHHHH
Confidence            579999999   99999998    444555554  899999999987766654

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=95.71  E-value=0.009  Score=53.64  Aligned_cols=59  Identities=10%  Similarity=0.137  Sum_probs=37.0

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEE---------eCCCCCHHHH--HHHHHHHhCC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVR---------VSNFYNFKRI--LDDIMKSLMP  169 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~---------~~~~~~~~~~--~~~i~~~l~~  169 (348)
                      -..+.+|.++||+|+||||+.+.++.+  ....+....-++         ..-+.++.+.  .++..++.+.
T Consensus        16 ~~~p~~ilVvGMAGSGKTTF~QrL~~h--l~~~~~ppYviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~L   85 (366)
T KOG1532|consen   16 IQRPVIILVVGMAGSGKTTFMQRLNSH--LHAKKTPPYVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQL   85 (366)
T ss_pred             ccCCcEEEEEecCCCCchhHHHHHHHH--HhhccCCCeEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCC
Confidence            345567788999999999999999987  444433222222         2334455554  4566665544

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.71  E-value=0.05  Score=53.58  Aligned_cols=59  Identities=17%  Similarity=0.055  Sum_probs=35.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPT  170 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~  170 (348)
                      ..|++++|+.|+||||++..++.....+..-..+..+.... .....+-++...+.++.+
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilGVp  315 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILGVP  315 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHHHHHHhCCC
Confidence            47999999999999999999987632222111234444322 223344555555555543

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=95.71  E-value=0.063  Score=47.99  Aligned_cols=22  Identities=18%  Similarity=0.211  Sum_probs=18.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +..|+|++|+|||+||..++-.
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~   24 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALA   24 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHH
Confidence            4567999999999999998764

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=95.70  E-value=0.0082  Score=50.99  Aligned_cols=23  Identities=9%  Similarity=0.174  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|.+.|++|+||||+|+.+...
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~   25 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSV   25 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            47889999999999999999876

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=95.69  E-value=0.18  Score=45.99  Aligned_cols=115  Identities=15%  Similarity=0.115  Sum_probs=75.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .|+|-....    ++..++.+    ....-+...++|+.|+|||+-++.+++.      .+..+-+..++.++...++..
T Consensus        73 ~~l~tkt~r----~~~~~~~~----A~k~g~l~~vyg~~g~gKt~a~~~y~~s------~p~~~l~~~~p~~~a~~~i~~  138 (297)
T COG2842          73 DFLETKTVR----RIFFRTRP----ASKTGSLVVVYGYAGLGKTQAAKNYAPS------NPNALLIEADPSYTALVLILI  138 (297)
T ss_pred             cccccchhH----hHhhhhhh----hhhcCceEEEeccccchhHHHHHhhccc------CccceeecCChhhHHHHHHHH
Confidence            777765543    45555552    2223337788999999999999998877      222333456666776666666


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhC
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREAL  217 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l  217 (348)
                      +.......      ...........+...+++..-+++.|+....  ..++.+....
T Consensus       139 i~~~~~~~------~~~~~~d~~~~~~~~l~~~~~~iivDEA~~L~~~ale~lr~i~  189 (297)
T COG2842         139 ICAAAFGA------TDGTINDLTERLMIRLRDTVRLIIVDEADRLPYRALEELRRIH  189 (297)
T ss_pred             HHHHHhcc------cchhHHHHHHHHHHHHccCcceeeeehhhccChHHHHHHHHHH
Confidence            66655543      2335566667777778888889999998764  5556655443

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=95.69  E-value=0.0079  Score=61.26  Aligned_cols=75  Identities=11%  Similarity=-0.004  Sum_probs=56.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++|.+..+   +.|...+.      ..  +.+.++|.+|+||||+|+.+.+.. -..+|+..+|..- ...+...+++.
T Consensus        32 ~vigq~~a~---~~L~~~~~------~~--~~~l~~G~~G~GKttla~~l~~~l-~~~~~~~~~~~~n-p~~~~~~~~~~   98 (637)
T PRK13765         32 QVIGQEHAV---EVIKKAAK------QR--RHVMMIGSPGTGKSMLAKAMAELL-PKEELQDILVYPN-PEDPNNPKIRT   98 (637)
T ss_pred             HcCChHHHH---HHHHHHHH------hC--CeEEEECCCCCcHHHHHHHHHHHc-ChHhHHHheEeeC-CCcchHHHHHH
Confidence            789998888   87777676      11  257789999999999999998772 2234577778654 44477888888


Q ss_pred             HHHHhCCC
Q 040110          163 IMKSLMPT  170 (348)
Q Consensus       163 i~~~l~~~  170 (348)
                      ++.+++..
T Consensus        99 v~~~~G~~  106 (637)
T PRK13765         99 VPAGKGKQ  106 (637)
T ss_pred             HHHhcCHH
Confidence            88877654

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=95.68  E-value=0.012  Score=49.92  Aligned_cols=25  Identities=20%  Similarity=0.214  Sum_probs=22.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|+|..|+|||||+..+...
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~   29 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPA   29 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHH
Confidence            4669999999999999999999877

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.66  E-value=0.0099  Score=48.45  Aligned_cols=21  Identities=10%  Similarity=0.346  Sum_probs=19.6

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|+|+.|+|||||++.+...
T Consensus         2 i~i~GpsGsGKstl~~~L~~~   22 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEE   22 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhc
Confidence            678999999999999999877

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=95.66  E-value=0.058  Score=52.26  Aligned_cols=91  Identities=13%  Similarity=0.099  Sum_probs=49.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc--ccCCCCH-HH-----H
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL--KIMGKDY-KS-----E  184 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~-~~-----~  184 (348)
                      ..++|+|..|+|||||++.+...  .+. ...++...-.+.-.+.++..+.+..-+...+..  ...+... ..     .
T Consensus       141 q~i~I~G~sG~GKTtLl~~I~~~--~~~-~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a~~~  217 (418)
T TIGR03498       141 QRLGIFAGSGVGKSTLLSMLARN--TDA-DVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQAAYT  217 (418)
T ss_pred             cEEEEECCCCCChHHHHHHHhCC--CCC-CEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHHHHH
Confidence            46899999999999999988876  222 222332222333445556665544332221110  1111111 11     1


Q ss_pred             HHHHHHHh--cCCeEEEEEeCCCC
Q 040110          185 KTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       185 ~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      .-.+.+++  +++++||++||+-.
T Consensus       218 a~~iAEyfrd~G~~Vll~~DslTr  241 (418)
T TIGR03498       218 ATAIAEYFRDQGKDVLLLMDSVTR  241 (418)
T ss_pred             HHHHHHHHHHcCCCEEEeccchhH
Confidence            11244444  46899999999854

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=95.65  E-value=0.038  Score=52.02  Aligned_cols=44  Identities=20%  Similarity=0.279  Sum_probs=29.2

Q ss_pred             cccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           85 LGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        85 vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|....+   +++.+.+...    .....-|.|+|..|+||+++|+.+++.
T Consensus         2 iG~S~~m---~~~~~~~~~~----a~~~~pVLI~GE~GtGK~~lAr~iH~~   45 (329)
T TIGR02974         2 IGESNAF---LEVLEQVSRL----APLDRPVLIIGERGTGKELIAARLHYL   45 (329)
T ss_pred             CcCCHHH---HHHHHHHHHH----hCCCCCEEEECCCCChHHHHHHHHHHh
Confidence            5555555   5555555411    112233679999999999999999865

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.65  E-value=0.012  Score=52.10  Aligned_cols=93  Identities=19%  Similarity=0.187  Sum_probs=56.0

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc-------------cc
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW-------------LK  175 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-------------~~  175 (348)
                      =+.-+++.|.|.+|+|||+|+.++.... .++.=..++|++...+  ..++.+.+. .++.+...             +.
T Consensus        16 ip~gs~~li~G~~GsGKT~l~~q~l~~~-~~~~ge~vlyvs~ee~--~~~l~~~~~-s~g~d~~~~~~~g~l~~~d~~~~   91 (226)
T PF06745_consen   16 IPKGSVVLISGPPGSGKTTLALQFLYNG-LKNFGEKVLYVSFEEP--PEELIENMK-SFGWDLEEYEDSGKLKIIDAFPE   91 (226)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHH-HHHHT--EEEEESSS---HHHHHHHHH-TTTS-HHHHHHTTSEEEEESSGG
T ss_pred             CCCCcEEEEEeCCCCCcHHHHHHHHHHh-hhhcCCcEEEEEecCC--HHHHHHHHH-HcCCcHHHHhhcCCEEEEecccc
Confidence            3455688999999999999999866442 2220125677776544  344444433 44432111             01


Q ss_pred             cC---CCCHHHHHHHHHHHhcC-CeEEEEEeCCC
Q 040110          176 IM---GKDYKSEKTILRDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       176 ~~---~~~~~~~~~~l~~~L~~-kr~LlVLDdv~  205 (348)
                      ..   ..+...+...+.+.++. +...+|+|.+.
T Consensus        92 ~~~~~~~~~~~l~~~i~~~i~~~~~~~vVIDsls  125 (226)
T PF06745_consen   92 RIGWSPNDLEELLSKIREAIEELKPDRVVIDSLS  125 (226)
T ss_dssp             GST-TSCCHHHHHHHHHHHHHHHTSSEEEEETHH
T ss_pred             cccccccCHHHHHHHHHHHHHhcCCCEEEEECHH
Confidence            01   45778888888888765 55899999874

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>PRK13947 shikimate kinase; Provisional

Probab=95.65  E-value=0.0087  Score=50.41  Aligned_cols=22  Identities=14%  Similarity=0.237  Sum_probs=20.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|+|++|+||||+|+.+.+.
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~   24 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATT   24 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHH
Confidence            3789999999999999999887

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=95.64  E-value=0.037  Score=52.00  Aligned_cols=46  Identities=22%  Similarity=0.296  Sum_probs=34.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.....   .++.+.+...    .....-|.|+|..|+||+++|+.++..
T Consensus         7 ~liG~S~~~---~~~~~~i~~~----a~~~~pVlI~GE~GtGK~~lA~~iH~~   52 (326)
T PRK11608          7 NLLGEANSF---LEVLEQVSRL----APLDKPVLIIGERGTGKELIASRLHYL   52 (326)
T ss_pred             ccEECCHHH---HHHHHHHHHH----hCCCCCEEEECCCCCcHHHHHHHHHHh
Confidence            688988888   7777766521    112224668999999999999999865

>PRK14528 adenylate kinase; Provisional

Probab=95.64  E-value=0.037  Score=47.53  Aligned_cols=23  Identities=13%  Similarity=0.160  Sum_probs=20.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.+.|.|++|+||||+|+.+...
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~   24 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCER   24 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            35788999999999999999766

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=95.63  E-value=0.076  Score=48.33  Aligned_cols=98  Identities=13%  Similarity=0.137  Sum_probs=53.2

Q ss_pred             EEEEECCCCCcHHHHH-HHHhcCccccCCccee-EEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHH-----
Q 040110          114 VVAILDSRGFDKTAFA-AEIYNNNFVKFYFDCH-AWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKS-----  183 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA-~~v~~~~~~~~~F~~~-~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~-----  183 (348)
                      .++|.|..|+|||+|| ..+.+.  .  +-+.+ +++-++... .+.++..++...-.......  ...+.....     
T Consensus        71 r~~Ifg~~g~GKt~L~l~~i~~~--~--~~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~a~  146 (274)
T cd01132          71 RELIIGDRQTGKTAIAIDTIINQ--K--GKKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLAP  146 (274)
T ss_pred             EEEeeCCCCCCccHHHHHHHHHh--c--CCCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHHHHH
Confidence            4789999999999996 556554  2  22333 566666554 45666666664322111110  111111111     


Q ss_pred             -HHHHHHHHh--cCCeEEEEEeCCCCh-hhHHHHHh
Q 040110          184 -EKTILRDYL--TNKKYFTVLDDVWIE-KIWDDLRE  215 (348)
Q Consensus       184 -~~~~l~~~L--~~kr~LlVLDdv~~~-~~~~~l~~  215 (348)
                       ..-.+.+++  +++.+|+++||+-.. ..+.++..
T Consensus       147 ~~a~aiAE~fr~~G~~Vlvl~DslTr~A~A~rEisl  182 (274)
T cd01132         147 YTGCAMGEYFMDNGKHALIIYDDLSKQAVAYRQMSL  182 (274)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEcChHHHHHHHHHHHH
Confidence             112233333  478999999999654 44555443

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=95.59  E-value=0.044  Score=48.22  Aligned_cols=87  Identities=15%  Similarity=0.196  Sum_probs=51.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCc--cccCCCCH---------
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSW--LKIMGKDY---------  181 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~--~~~~~~~~---------  181 (348)
                      .++|.|.+|+|||+|+..+.++.  .  -+..+++.+++. ..+.++.+++...-......  ....+...         
T Consensus        17 r~~I~g~~g~GKt~Ll~~i~~~~--~--~d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~~   92 (215)
T PF00006_consen   17 RIGIFGGAGVGKTVLLQEIANNQ--D--ADVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPYT   92 (215)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHC--T--TTEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHHH
T ss_pred             EEEEEcCcccccchhhHHHHhcc--c--ccceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhhhcc
Confidence            47899999999999999998883  2  234477777655 45666666664431111100  01111111         


Q ss_pred             -HHHHHHHHHHhcCCeEEEEEeCCCC
Q 040110          182 -KSEKTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       182 -~~~~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                       -...++++.  +++++|+++||+-.
T Consensus        93 a~t~AEyfrd--~G~dVlli~Dsltr  116 (215)
T PF00006_consen   93 ALTIAEYFRD--QGKDVLLIIDSLTR  116 (215)
T ss_dssp             HHHHHHHHHH--TTSEEEEEEETHHH
T ss_pred             chhhhHHHhh--cCCceeehhhhhHH
Confidence             112223333  68999999999843

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.59  E-value=0.0089  Score=51.11  Aligned_cols=22  Identities=41%  Similarity=0.549  Sum_probs=20.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|+|.|.+|+||||||..+...
T Consensus         1 ii~i~G~sgsGKttla~~l~~~   22 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQ   22 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999876

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=95.59  E-value=0.012  Score=53.77  Aligned_cols=34  Identities=18%  Similarity=0.208  Sum_probs=25.0

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+++.+.      ..+. -+.++|+.|+|||++++...+.
T Consensus        23 ~~ll~~l~------~~~~-pvLl~G~~GtGKT~li~~~l~~   56 (272)
T PF12775_consen   23 SYLLDLLL------SNGR-PVLLVGPSGTGKTSLIQNFLSS   56 (272)
T ss_dssp             HHHHHHHH------HCTE-EEEEESSTTSSHHHHHHHHHHC
T ss_pred             HHHHHHHH------HcCC-cEEEECCCCCchhHHHHhhhcc
Confidence            45556565      2233 4568999999999999998866

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=95.57  E-value=0.059  Score=45.61  Aligned_cols=83  Identities=8%  Similarity=0.061  Sum_probs=45.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT  193 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~  193 (348)
                      ++.|.|.+|+||||+|..+...  ...   ..+++.-...+ -.++.+.|.......... -..-+....+...+.....
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~--~~~---~~~~iat~~~~-~~e~~~ri~~h~~~R~~~-w~t~E~~~~l~~~i~~~~~   75 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQ--SGL---QVLYIATAQPF-DDEMAARIAHHRQRRPAH-WQTVEEPLDLAELLRADAA   75 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHH--cCC---CcEeCcCCCCC-hHHHHHHHHHHHhcCCCC-CeEecccccHHHHHHhhcC
Confidence            5789999999999999998866  211   23344333333 345556665544332111 1111122234444544343


Q ss_pred             CCeEEEEEeCC
Q 040110          194 NKKYFTVLDDV  204 (348)
Q Consensus       194 ~kr~LlVLDdv  204 (348)
                      + .-++++|.+
T Consensus        76 ~-~~~VlID~L   85 (170)
T PRK05800         76 P-GRCVLVDCL   85 (170)
T ss_pred             C-CCEEEehhH
Confidence            3 336888886

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=95.56  E-value=0.12  Score=45.72  Aligned_cols=108  Identities=10%  Similarity=0.003  Sum_probs=57.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccc--cC-----------CcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFV--KF-----------YFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIM  177 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~--~~-----------~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~  177 (348)
                      ...++.|.|+.|.||||+.+.+......  ..           .|+ .++..+...-++..                  .
T Consensus        30 ~g~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~-~i~~~~~~~d~~~~------------------~   90 (222)
T cd03287          30 GGYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFD-SVLTRMGASDSIQH------------------G   90 (222)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccc-eEEEEecCcccccc------------------c
Confidence            3457889999999999999888652100  01           111 22222222211111                  1


Q ss_pred             CCCHHHHHHHHHHHh--cCCeEEEEEeCCCCh----h--h-HHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          178 GKDYKSEKTILRDYL--TNKKYFTVLDDVWIE----K--I-WDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       178 ~~~~~~~~~~l~~~L--~~kr~LlVLDdv~~~----~--~-~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      ......-...+...+  .+++.|++||..-..    +  . ...+...+... .++.+|++|....++..
T Consensus        91 ~StF~~e~~~~~~il~~~~~~sLvllDE~~~gT~~~d~~~i~~~il~~l~~~-~~~~~i~~TH~~~l~~~  159 (222)
T cd03287          91 MSTFMVELSETSHILSNCTSRSLVILDELGRGTSTHDGIAIAYATLHYLLEE-KKCLVLFVTHYPSLGEI  159 (222)
T ss_pred             cchHHHHHHHHHHHHHhCCCCeEEEEccCCCCCChhhHHHHHHHHHHHHHhc-cCCeEEEEcccHHHHHH
Confidence            111222222333333  247899999997432    1  1 12233444332 47889999999888664

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=95.56  E-value=0.0092  Score=48.66  Aligned_cols=22  Identities=23%  Similarity=0.292  Sum_probs=20.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|.|.|.+|+||||+|+.+...
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~   22 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKK   22 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999876

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=95.55  E-value=0.089  Score=54.17  Aligned_cols=46  Identities=17%  Similarity=0.190  Sum_probs=33.4

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.....   .++.+.+...   ..... -|.|+|..|+||+++|+.+++.
T Consensus       326 ~l~g~s~~~---~~~~~~~~~~---a~~~~-pvli~Ge~GtGK~~~A~~ih~~  371 (638)
T PRK11388        326 HMPQDSPQM---RRLIHFGRQA---AKSSF-PVLLCGEEGVGKALLAQAIHNE  371 (638)
T ss_pred             ceEECCHHH---HHHHHHHHHH---hCcCC-CEEEECCCCcCHHHHHHHHHHh
Confidence            688888777   6666665421   11222 3679999999999999999876

>PRK13948 shikimate kinase; Provisional

Probab=95.55  E-value=0.013  Score=50.28  Aligned_cols=26  Identities=19%  Similarity=0.132  Sum_probs=22.8

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....|.++|+.|+||||+++.+.+.
T Consensus         8 ~~~~~I~LiG~~GsGKSTvg~~La~~   33 (182)
T PRK13948          8 RPVTWVALAGFMGTGKSRIGWELSRA   33 (182)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            34567889999999999999999987

>PRK03846 adenylylsulfate kinase; Provisional

Probab=95.54  E-value=0.014  Score=50.69  Aligned_cols=26  Identities=15%  Similarity=0.112  Sum_probs=23.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....++.|+|++|+||||||+.+...
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~   47 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEA   47 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            45679999999999999999999876

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=95.54  E-value=0.0078  Score=46.79  Aligned_cols=21  Identities=24%  Similarity=0.434  Sum_probs=18.6

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |-|+|.+|+|||+||..++.+
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~   21 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKD   21 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999998876

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>PRK05922 type III secretion system ATPase; Validated

Probab=95.54  E-value=0.12  Score=50.20  Aligned_cols=89  Identities=8%  Similarity=0.184  Sum_probs=49.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCCCCcc--ccCCCCHHH------H
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPTSSWL--KIMGKDYKS------E  184 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~------~  184 (348)
                      .++|+|..|+|||||.+.+.+..  . . +....+.++. ...+...+.+....+....+..  ...+.....      .
T Consensus       159 rigI~G~nG~GKSTLL~~Ia~~~--~-~-d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~a~~~  234 (434)
T PRK05922        159 RIGVFSEPGSGKSSLLSTIAKGS--K-S-TINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVIAGRA  234 (434)
T ss_pred             EEEEECCCCCChHHHHHHHhccC--C-C-CceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHHHHHH
Confidence            58999999999999999998762  1 1 3333333333 2344455555544433322110  111111111      1


Q ss_pred             HHHHHHHh--cCCeEEEEEeCCCC
Q 040110          185 KTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       185 ~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      .-.+.+++  +++++||++||+-.
T Consensus       235 a~tiAEyfrd~G~~VLl~~DslTR  258 (434)
T PRK05922        235 AMTIAEYFRDQGHRVLFIMDSLSR  258 (434)
T ss_pred             HHHHHHHHHHcCCCEEEeccchhH
Confidence            12244444  47899999999853

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=95.53  E-value=0.034  Score=51.85  Aligned_cols=114  Identities=13%  Similarity=0.116  Sum_probs=59.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      ...+.|.|..|+|||||++.+...  +.... .++.+.-..+.....  .... ++....   .......-...+.+...
T Consensus       144 ~~~ili~G~tGsGKTTll~al~~~--~~~~~-~iv~ied~~El~~~~--~~~~-~l~~~~---~~~~~~~~~~~~~l~~~  214 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKSLVDE--IPKDE-RIITIEDTREIFLPH--PNYV-HLFYSK---GGQGLAKVTPKDLLQSC  214 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcc--CCccc-cEEEEcCccccCCCC--CCEE-EEEecC---CCCCcCccCHHHHHHHH
Confidence            457889999999999999998876  32221 122221111111100  0000 000000   00011112344556667


Q ss_pred             hcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhh
Q 040110          192 LTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILT  237 (348)
Q Consensus       192 L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~  237 (348)
                      |+...=.+++|.+.+.+.++.+ ..+..+..|  ++.|+...+.+.
T Consensus       215 Lr~~pd~ii~gE~r~~e~~~~l-~a~~~g~~~--~i~T~Ha~~~~~  257 (308)
T TIGR02788       215 LRMRPDRIILGELRGDEAFDFI-RAVNTGHPG--SITTLHAGSPEE  257 (308)
T ss_pred             hcCCCCeEEEeccCCHHHHHHH-HHHhcCCCe--EEEEEeCCCHHH
Confidence            8888888999999987666544 333332222  577777666544

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.53  E-value=0.18  Score=44.49  Aligned_cols=126  Identities=18%  Similarity=0.157  Sum_probs=70.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCcccc--C---Ccc--------------eeEEEEeCCC-----CCHHHHHH-------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVK--F---YFD--------------CHAWVRVSNF-----YNFKRILD-------  161 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~--~---~F~--------------~~~wv~~~~~-----~~~~~~~~-------  161 (348)
                      -+-+|-|+.|.||||||..+.-++.++  +   .|+              ..+++....+     .++.++++       
T Consensus        31 EvhaiMGPNGsGKSTLa~~i~G~p~Y~Vt~G~I~~~GedI~~l~~~ERAr~GifLafQ~P~ei~GV~~~~fLr~a~n~~~  110 (251)
T COG0396          31 EVHAIMGPNGSGKSTLAYTIMGHPKYEVTEGEILFDGEDILELSPDERARAGIFLAFQYPVEIPGVTNSDFLRAAMNARR  110 (251)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCCCceEecceEEECCcccccCCHhHHHhcCCEEeecCCccCCCeeHHHHHHHHHHhhh
Confidence            477899999999999999999887432  1   121              2233332222     12333333       


Q ss_pred             --------------HHHHHhCCCCCc----cccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHH------hhC
Q 040110          162 --------------DIMKSLMPTSSW----LKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLR------EAL  217 (348)
Q Consensus       162 --------------~i~~~l~~~~~~----~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~~~~~~l~------~~l  217 (348)
                                    +.++.++.+..-    .+..-..-+.....|.+.+--++-|.|||..++.-+.+.+.      ..+
T Consensus       111 ~~~~~~~~~~~~~~e~~~~l~~~~~~l~R~vN~GFSGGEkKR~EilQ~~~lePkl~ILDE~DSGLDIdalk~V~~~i~~l  190 (251)
T COG0396         111 GARGILPEFIKELKEKAELLGLDEEFLERYVNEGFSGGEKKRNEILQLLLLEPKLAILDEPDSGLDIDALKIVAEGINAL  190 (251)
T ss_pred             ccccccHHHHHHHHHHHHHcCCCHHHhhcccCCCcCcchHHHHHHHHHHhcCCCEEEecCCCcCccHHHHHHHHHHHHHH
Confidence                          333333332100    00011111233445566666678899999998864443332      222


Q ss_pred             CCCCCCcEEEEEeCChhhhhhcc
Q 040110          218 PDNQIGSRALITVGPHNILTSIE  240 (348)
Q Consensus       218 ~~~~~gskIlvTTR~~~v~~~~~  240 (348)
                      .  ..|+-+++.|..+.++..+.
T Consensus       191 r--~~~~~~liITHy~rll~~i~  211 (251)
T COG0396         191 R--EEGRGVLIITHYQRLLDYIK  211 (251)
T ss_pred             h--cCCCeEEEEecHHHHHhhcC
Confidence            2  23666888888888888743

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.52  E-value=0.012  Score=51.15  Aligned_cols=24  Identities=8%  Similarity=0.250  Sum_probs=21.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+++|+|++|+|||||++.++..
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            357999999999999999999887

>TIGR01351 adk adenylate kinases

Probab=95.52  E-value=0.038  Score=48.37  Aligned_cols=21  Identities=24%  Similarity=0.291  Sum_probs=19.1

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|.|++|+||||+|+.+...
T Consensus         2 I~i~G~pGsGKsT~a~~La~~   22 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEK   22 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            678999999999999999866

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=95.52  E-value=0.021  Score=48.97  Aligned_cols=90  Identities=14%  Similarity=0.070  Sum_probs=46.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCc--------ceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-----c-----
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYF--------DCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-----K-----  175 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F--------~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-----~-----  175 (348)
                      ++.|.|++|+||||++..+.........|        ..++|++...+  ...+.+.+...........     .     
T Consensus        34 l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~--~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~  111 (193)
T PF13481_consen   34 LTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS--ESQIARRLRALLQDYDDDANLFFVDLSNWG  111 (193)
T ss_dssp             EEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS---HHHHHHHHHHHHTTS-HHHHHHHHHH--E-
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC--HHHHHHHHHHHhcccCCccceEEeeccccc
Confidence            67789999999999999887663322222        25677766555  3333333332222110000     0     


Q ss_pred             --------cCCCCHHHHHHHHHHHhcC--CeEEEEEeCCC
Q 040110          176 --------IMGKDYKSEKTILRDYLTN--KKYFTVLDDVW  205 (348)
Q Consensus       176 --------~~~~~~~~~~~~l~~~L~~--kr~LlVLDdv~  205 (348)
                              ..........+.+.+.+..  +.-++|+|++.
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~lvviD~l~  151 (193)
T PF13481_consen  112 CIRLFEPDSGGPLLDEDLEELEAALKELYGPDLVVIDPLQ  151 (193)
T ss_dssp             EE---TTS---TTSHHHHHHHHHHHTT----SEEEEE-GG
T ss_pred             cceeeecccccccchHHHHHHHHHHhhcCCCcEEEEcCHH
Confidence                    0011134455666776655  46799999775

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=95.48  E-value=0.015  Score=53.15  Aligned_cols=23  Identities=17%  Similarity=0.104  Sum_probs=18.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..|.|.|.+|+||||+|+.+...
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~   24 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKY   24 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHH
Confidence            46889999999999999999876

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PRK09099 type III secretion system ATPase; Provisional

Probab=95.47  E-value=0.073  Score=51.89  Aligned_cols=91  Identities=9%  Similarity=0.059  Sum_probs=50.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc--ccCCCCHHH------H
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL--KIMGKDYKS------E  184 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~------~  184 (348)
                      ..++|.|..|+|||||++.+.......   ..+++..-.+...+.++...+...-+......  ...+.....      .
T Consensus       164 q~~~I~G~sG~GKTtLl~~ia~~~~~d---~~vi~~iGer~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~a~~~  240 (441)
T PRK09099        164 QRMGIFAPAGVGKSTLMGMFARGTQCD---VNVIALIGERGREVREFIELILGEDGMARSVVVCATSDRSSIERAKAAYV  240 (441)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCCC---eEEEEEEccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHHHHHH
Confidence            478999999999999999998763221   13333332334455566666654422221110  111111111      1


Q ss_pred             HHHHHHHh--cCCeEEEEEeCCCC
Q 040110          185 KTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       185 ~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      .-.+.+++  +++++|+++||+-.
T Consensus       241 a~tiAEyfrd~G~~VLl~~DslTr  264 (441)
T PRK09099        241 ATAIAEYFRDRGLRVLLMMDSLTR  264 (441)
T ss_pred             HHHHHHHHHHcCCCEEEeccchhH
Confidence            12244444  47899999999854

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=95.47  E-value=0.098  Score=45.45  Aligned_cols=22  Identities=14%  Similarity=0.046  Sum_probs=20.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      .+++|+|+.|.|||||.+.+..
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            6899999999999999999873

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>PRK15453 phosphoribulokinase; Provisional

Probab=95.46  E-value=0.097  Score=47.81  Aligned_cols=82  Identities=15%  Similarity=0.143  Sum_probs=44.9

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcc-eeEEEEeCCCC--CHHHHHHHH--HHHhCCCCCccccCCCCHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD-CHAWVRVSNFY--NFKRILDDI--MKSLMPTSSWLKIMGKDYKSE  184 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~-~~~wv~~~~~~--~~~~~~~~i--~~~l~~~~~~~~~~~~~~~~~  184 (348)
                      ....+|+|.|.+|+||||+|+.+.+.  ... .. ....++...-+  +-..+-..+  ...-+.+.+-.+.+..+.+.+
T Consensus         3 ~k~piI~ItG~SGsGKTTva~~l~~i--f~~-~~~~~~vi~~D~yh~ydr~~~~~~~~~~~r~g~nfdhf~PdAnd~dlL   79 (290)
T PRK15453          3 AKHPIIAVTGSSGAGTTTVKRAFEKI--FRR-ENINAAVVEGDSFHRYTRPEMKAAIAKARAAGRHFSHFGPEANLFDEL   79 (290)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH--Hhh-cCCCeEEEecccccccChhhHhhhhHHHHhcCCCCCCCCCCcccHHHH
Confidence            34579999999999999999988754  221 11 12333332222  322222222  111221111002566778888


Q ss_pred             HHHHHHHhcC
Q 040110          185 KTILRDYLTN  194 (348)
Q Consensus       185 ~~~l~~~L~~  194 (348)
                      ...++.+.++
T Consensus        80 ~~~l~~l~~~   89 (290)
T PRK15453         80 EQLFREYGET   89 (290)
T ss_pred             HHHHHHHhcC
Confidence            8888877654

>PRK13949 shikimate kinase; Provisional

Probab=95.46  E-value=0.013  Score=49.60  Aligned_cols=22  Identities=14%  Similarity=0.221  Sum_probs=20.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|+|++|+||||+++.+++.
T Consensus         3 ~I~liG~~GsGKstl~~~La~~   24 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARE   24 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999987

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=95.45  E-value=0.049  Score=46.07  Aligned_cols=79  Identities=9%  Similarity=0.071  Sum_probs=44.4

Q ss_pred             EEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTN  194 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~  194 (348)
                      +.|.|.+|+|||++|.++...     .....+++.-...++. ++.+.|.+.......     .....+....+.+.+..
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~-----~~~~~~y~at~~~~d~-em~~rI~~H~~~R~~-----~w~t~E~~~~l~~~l~~   70 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE-----LGGPVTYIATAEAFDD-EMAERIARHRKRRPA-----HWRTIETPRDLVSALKE   70 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh-----cCCCeEEEEccCcCCH-HHHHHHHHHHHhCCC-----CceEeecHHHHHHHHHh
Confidence            568999999999999998754     1125666666666654 355554443322211     11122222333333321


Q ss_pred             --CeEEEEEeCC
Q 040110          195 --KKYFTVLDDV  204 (348)
Q Consensus       195 --kr~LlVLDdv  204 (348)
                        +.-.+++|.+
T Consensus        71 ~~~~~~VLIDcl   82 (169)
T cd00544          71 LDPGDVVLIDCL   82 (169)
T ss_pred             cCCCCEEEEEcH
Confidence              2337888986

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=95.44  E-value=0.0077  Score=48.21  Aligned_cols=27  Identities=22%  Similarity=0.342  Sum_probs=19.1

Q ss_pred             EEEECCCCCcHHHHHHHHhcCccccCCcc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNNFVKFYFD  143 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~~~~~~F~  143 (348)
                      +.|+|.+|+||||+|+.++..  +...|.
T Consensus         2 vLleg~PG~GKT~la~~lA~~--~~~~f~   28 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARS--LGLSFK   28 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHH--TT--EE
T ss_pred             EeeECCCccHHHHHHHHHHHH--cCCcee
Confidence            568999999999999999988  666674

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=95.44  E-value=0.02  Score=47.92  Aligned_cols=32  Identities=16%  Similarity=0.315  Sum_probs=28.1

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|.+.|.        + +++.++|.+|+|||||...+...
T Consensus        27 ~~l~~~l~--------~-k~~vl~G~SGvGKSSLiN~L~~~   58 (161)
T PF03193_consen   27 EELKELLK--------G-KTSVLLGQSGVGKSSLINALLPE   58 (161)
T ss_dssp             HHHHHHHT--------T-SEEEEECSTTSSHHHHHHHHHTS
T ss_pred             HHHHHHhc--------C-CEEEEECCCCCCHHHHHHHHHhh
Confidence            78888887        2 57889999999999999999987

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=95.44  E-value=0.021  Score=46.72  Aligned_cols=67  Identities=10%  Similarity=0.151  Sum_probs=38.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT  193 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~  193 (348)
                      -|.|.|-+|+|||||+.+++...       ..-|+++|.-..-..+....=...       ....-+.+.+.+.|...+.
T Consensus         9 NILvtGTPG~GKstl~~~lae~~-------~~~~i~isd~vkEn~l~~gyDE~y-------~c~i~DEdkv~D~Le~~m~   74 (176)
T KOG3347|consen    9 NILVTGTPGTGKSTLAERLAEKT-------GLEYIEISDLVKENNLYEGYDEEY-------KCHILDEDKVLDELEPLMI   74 (176)
T ss_pred             CEEEeCCCCCCchhHHHHHHHHh-------CCceEehhhHHhhhcchhcccccc-------cCccccHHHHHHHHHHHHh
Confidence            46789999999999999998651       223555554332222222111111       2223455666666666654


Q ss_pred             C
Q 040110          194 N  194 (348)
Q Consensus       194 ~  194 (348)
                      .
T Consensus        75 ~   75 (176)
T KOG3347|consen   75 E   75 (176)
T ss_pred             c
Confidence            4

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=95.44  E-value=0.1  Score=44.73  Aligned_cols=96  Identities=13%  Similarity=0.081  Sum_probs=50.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      -..+.|.|..|+|||||++.+...  +.... ..+-+  ........-..... ++.....  ...........+.+...
T Consensus        25 g~~i~I~G~tGSGKTTll~aL~~~--i~~~~-~~i~i--ed~~E~~~~~~~~~-~~~~~~~--~~~~~~~~~~~~~l~~~   96 (186)
T cd01130          25 RKNILISGGTGSGKTTLLNALLAF--IPPDE-RIITI--EDTAELQLPHPNWV-RLVTRPG--NVEGSGEVTMADLLRSA   96 (186)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh--cCCCC-CEEEE--CCccccCCCCCCEE-EEEEecC--CCCCCCccCHHHHHHHH
Confidence            357899999999999999998876  32221 12222  11100000000000 0000000  00011123345566677


Q ss_pred             hcCCeEEEEEeCCCChhhHHHHHh
Q 040110          192 LTNKKYFTVLDDVWIEKIWDDLRE  215 (348)
Q Consensus       192 L~~kr~LlVLDdv~~~~~~~~l~~  215 (348)
                      ++..+=.++++.+.+.+.++.+..
T Consensus        97 lR~~pd~i~igEir~~ea~~~~~a  120 (186)
T cd01130          97 LRMRPDRIIVGEVRGGEALDLLQA  120 (186)
T ss_pred             hccCCCEEEEEccCcHHHHHHHHH
Confidence            777788899999998877665443

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK11823 DNA repair protein RadA; Provisional

Probab=95.43  E-value=0.047  Score=53.60  Aligned_cols=88  Identities=16%  Similarity=0.090  Sum_probs=51.0

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTIL  188 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l  188 (348)
                      ..-.++.|.|.+|+|||||+.+++..  ....-..++|++....  ..++.. -++.++...... -....+.+++...+
T Consensus        78 ~~Gs~~lI~G~pG~GKTtL~lq~a~~--~a~~g~~vlYvs~Ees--~~qi~~-ra~rlg~~~~~l~~~~e~~l~~i~~~i  152 (446)
T PRK11823         78 VPGSVVLIGGDPGIGKSTLLLQVAAR--LAAAGGKVLYVSGEES--ASQIKL-RAERLGLPSDNLYLLAETNLEAILATI  152 (446)
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEcccc--HHHHHH-HHHHcCCChhcEEEeCCCCHHHHHHHH
Confidence            34558889999999999999998876  2221124677765433  333322 245555432110 11223445444444


Q ss_pred             HHHhcCCeEEEEEeCCC
Q 040110          189 RDYLTNKKYFTVLDDVW  205 (348)
Q Consensus       189 ~~~L~~kr~LlVLDdv~  205 (348)
                      .+   .+.-++|+|.+.
T Consensus       153 ~~---~~~~lVVIDSIq  166 (446)
T PRK11823        153 EE---EKPDLVVIDSIQ  166 (446)
T ss_pred             Hh---hCCCEEEEechh
Confidence            32   356689999985

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=95.42  E-value=0.013  Score=50.24  Aligned_cols=22  Identities=14%  Similarity=0.314  Sum_probs=20.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|+|+.|+|||||++.++..
T Consensus         4 ~i~l~G~sGsGKsTl~~~l~~~   25 (186)
T PRK10078          4 LIWLMGPSGSGKDSLLAALRQR   25 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHhcc
Confidence            6889999999999999999876

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=95.42  E-value=0.086  Score=45.15  Aligned_cols=21  Identities=19%  Similarity=0.276  Sum_probs=19.4

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|.|++|+||||+|+.+...
T Consensus         2 I~i~G~pGsGKst~a~~La~~   22 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKK   22 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            678999999999999999876

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=95.41  E-value=0.045  Score=52.05  Aligned_cols=86  Identities=14%  Similarity=0.118  Sum_probs=53.5

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTILRD  190 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l~~  190 (348)
                      -.++.|=|-+|+|||||..++..+  ....- .+++|+-..  +..+ .+--+..|+.+.... -....+.+.+...+.+
T Consensus        93 Gs~iLIgGdPGIGKSTLLLQva~~--lA~~~-~vLYVsGEE--S~~Q-iklRA~RL~~~~~~l~l~aEt~~e~I~~~l~~  166 (456)
T COG1066          93 GSVILIGGDPGIGKSTLLLQVAAR--LAKRG-KVLYVSGEE--SLQQ-IKLRADRLGLPTNNLYLLAETNLEDIIAELEQ  166 (456)
T ss_pred             ccEEEEccCCCCCHHHHHHHHHHH--HHhcC-cEEEEeCCc--CHHH-HHHHHHHhCCCccceEEehhcCHHHHHHHHHh
Confidence            457888999999999999999888  44333 566664333  3332 334456666543211 1223455554444443


Q ss_pred             HhcCCeEEEEEeCCCC
Q 040110          191 YLTNKKYFTVLDDVWI  206 (348)
Q Consensus       191 ~L~~kr~LlVLDdv~~  206 (348)
                         .+.-|+|+|.+..
T Consensus       167 ---~~p~lvVIDSIQT  179 (456)
T COG1066         167 ---EKPDLVVIDSIQT  179 (456)
T ss_pred             ---cCCCEEEEeccce
Confidence               5789999999863

>PTZ00185 ATPase alpha subunit; Provisional

Probab=95.41  E-value=0.14  Score=50.65  Aligned_cols=93  Identities=14%  Similarity=0.128  Sum_probs=52.0

Q ss_pred             EEEEECCCCCcHHHHH-HHHhcCcccc-----CCcceeEEEEeCCCCCHHHHHHHHHHHhC-CCCCcc--ccCCCCHHH-
Q 040110          114 VVAILDSRGFDKTAFA-AEIYNNNFVK-----FYFDCHAWVRVSNFYNFKRILDDIMKSLM-PTSSWL--KIMGKDYKS-  183 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA-~~v~~~~~~~-----~~F~~~~wv~~~~~~~~~~~~~~i~~~l~-~~~~~~--~~~~~~~~~-  183 (348)
                      .++|.|-.|+|||+|| -.+.|...+.     ++-..++++-+++..+-..-+.+.++.-+ ......  ...+..... 
T Consensus       191 R~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~ei~~~L~e~GaL~~TvVV~AtAdep~~~r  270 (574)
T PTZ00185        191 RELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVARIHRLLRSYGALRYTTVMAATAAEPAGLQ  270 (574)
T ss_pred             EEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHHHHHHHHhcCCccceEEEEECCCCCHHHH
Confidence            4789999999999997 5566663221     23346788888877654333444444433 211110  111111111 


Q ss_pred             -----HHHHHHHHh--cCCeEEEEEeCCCC
Q 040110          184 -----EKTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       184 -----~~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                           ..-.+-+++  +++.+|+|+||+-.
T Consensus       271 ~~Apy~a~tiAEYFrd~GkdVLiv~DDLTr  300 (574)
T PTZ00185        271 YLAPYSGVTMGEYFMNRGRHCLCVYDDLSK  300 (574)
T ss_pred             HHHHHHHHHHHHHHHHcCCCEEEEEcCchH
Confidence                 111233333  47899999999964

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=95.41  E-value=0.05  Score=53.28  Aligned_cols=93  Identities=13%  Similarity=0.157  Sum_probs=54.5

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcc--eeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHH-----
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFD--CHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKS-----  183 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~-----  183 (348)
                      .++|.|-.|+|||||+..+.+.....+.+.  .++++-+++.. .+.+++..+...=....+..  ...+.....     
T Consensus       143 R~gIfgg~G~GKs~L~~~ia~~~~ad~~~~~~v~V~~~iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R~~a~  222 (458)
T TIGR01041       143 KLPIFSGSGLPHNELAAQIARQATVRGEESEFAVVFAAMGITYEEANFFMKDFEETGALERAVVFLNLADDPAVERIVTP  222 (458)
T ss_pred             EEEeeCCCCCCHHHHHHHHHHhhcccCCCCceEEEEEEccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHHHHH
Confidence            478999999999999999988743322221  55666665543 56667776664332221110  111111111     


Q ss_pred             -HHHHHHHHhc---CCeEEEEEeCCCC
Q 040110          184 -EKTILRDYLT---NKKYFTVLDDVWI  206 (348)
Q Consensus       184 -~~~~l~~~L~---~kr~LlVLDdv~~  206 (348)
                       ..-.+.++++   ++++||++||+-.
T Consensus       223 ~~a~tiAEyfr~d~G~~VLli~DslTR  249 (458)
T TIGR01041       223 RMALTAAEYLAFEKDMHVLVILTDMTN  249 (458)
T ss_pred             HHHHHHHHHHHHccCCcEEEEEcChhH
Confidence             1122555555   6799999999853

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PF14516 AAA_35: AAA-like domain

Probab=95.40  E-value=0.13  Score=48.57  Aligned_cols=113  Identities=14%  Similarity=0.169  Sum_probs=68.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-----CCHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-----YNFK  157 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-----~~~~  157 (348)
                      -.|.|....   +++.+.|.      .+ -..+.|.|+..+|||+|...+.+..... .| .++++++..-     .+..
T Consensus        12 ~Yi~R~~~e---~~~~~~i~------~~-G~~~~I~apRq~GKTSll~~l~~~l~~~-~~-~~v~id~~~~~~~~~~~~~   79 (331)
T PF14516_consen   12 FYIERPPAE---QECYQEIV------QP-GSYIRIKAPRQMGKTSLLLRLLERLQQQ-GY-RCVYIDLQQLGSAIFSDLE   79 (331)
T ss_pred             cccCchHHH---HHHHHHHh------cC-CCEEEEECcccCCHHHHHHHHHHHHHHC-CC-EEEEEEeecCCCcccCCHH
Confidence            567898666   67887777      21 2368899999999999999998774332 33 3456665431     2455


Q ss_pred             HHH----HHHHHHhCCCCCcc---ccCCCCHHHHHHHHHHHh---cCCeEEEEEeCCCCh
Q 040110          158 RIL----DDIMKSLMPTSSWL---KIMGKDYKSEKTILRDYL---TNKKYFTVLDDVWIE  207 (348)
Q Consensus       158 ~~~----~~i~~~l~~~~~~~---~~~~~~~~~~~~~l~~~L---~~kr~LlVLDdv~~~  207 (348)
                      +++    ..+.++++....-.   .............+.+.+   .+++.+|+||+++..
T Consensus        80 ~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l  139 (331)
T PF14516_consen   80 QFLRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRL  139 (331)
T ss_pred             HHHHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhh
Confidence            444    45555555432100   001123334445555543   257999999999753

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=95.39  E-value=0.014  Score=50.64  Aligned_cols=25  Identities=20%  Similarity=0.209  Sum_probs=22.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..+|+|-||=|+||||||+.+.++.
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l   28 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHL   28 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHh
Confidence            4589999999999999999999883

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=95.37  E-value=0.13  Score=51.47  Aligned_cols=46  Identities=13%  Similarity=0.130  Sum_probs=32.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.....   .++++.+...   ..... -|.|+|..|+||+++|+.+++.
T Consensus       205 ~~ig~s~~~---~~~~~~~~~~---A~~~~-pvlI~GE~GtGK~~lA~aiH~~  250 (520)
T PRK10820        205 QIVAVSPKM---RQVVEQARKL---AMLDA-PLLITGDTGTGKDLLAYACHLR  250 (520)
T ss_pred             ceeECCHHH---HHHHHHHHHH---hCCCC-CEEEECCCCccHHHHHHHHHHh
Confidence            788888777   6666655411   01122 3679999999999999998765

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=95.37  E-value=0.01  Score=49.65  Aligned_cols=21  Identities=14%  Similarity=0.321  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.|+|++|+||||+|+.+.+.
T Consensus         1 i~l~G~~GsGKSTla~~l~~~   21 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHR   21 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHh
Confidence            458999999999999999877

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PLN02200 adenylate kinase family protein

Probab=95.36  E-value=0.018  Score=51.49  Aligned_cols=27  Identities=19%  Similarity=0.214  Sum_probs=23.1

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+.+|.|.|++|+||||+|+.+...
T Consensus        40 ~~~~~ii~I~G~PGSGKsT~a~~La~~   66 (234)
T PLN02200         40 EKTPFITFVLGGPGSGKGTQCEKIVET   66 (234)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            344668899999999999999999876

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=95.36  E-value=0.077  Score=51.76  Aligned_cols=90  Identities=11%  Similarity=0.097  Sum_probs=50.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCcc--ccCCCC-HHH-----
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSWL--KIMGKD-YKS-----  183 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~--~~~~~~-~~~-----  183 (348)
                      ..++|+|..|+|||||++.+.+..   . .+.++...++.. ..+.++...+...-....+..  ...+.. ...     
T Consensus       169 qrigI~G~sG~GKSTLl~~I~g~~---~-~dv~V~g~Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~a~~  244 (451)
T PRK05688        169 QRLGLFAGTGVGKSVLLGMMTRFT---E-ADIIVVGLIGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLRAAM  244 (451)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC---C-CCEEEEEEeCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHHHHH
Confidence            368999999999999999988752   1 133334334333 345566666555433322110  111111 111     


Q ss_pred             HHHHHHHHh--cCCeEEEEEeCCCC
Q 040110          184 EKTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       184 ~~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      ..-.+.+++  +++++||++||+-.
T Consensus       245 ~a~aiAEyfrd~G~~VLl~~DslTR  269 (451)
T PRK05688        245 YCTRIAEYFRDKGKNVLLLMDSLTR  269 (451)
T ss_pred             HHHHHHHHHHHCCCCEEEEecchhH
Confidence            111244444  57899999999854

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=95.35  E-value=0.09  Score=51.31  Aligned_cols=92  Identities=13%  Similarity=0.173  Sum_probs=53.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCcc--ccCCCCHHH------H
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSWL--KIMGKDYKS------E  184 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~------~  184 (348)
                      .++|.|.+|+|||||+..+..+... ++=..++++-++.. -.+.+++.++...=....+..  ...+.....      .
T Consensus       145 r~~If~~~G~GKt~L~~~~~~~~~~-~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~~~  223 (461)
T TIGR01039       145 KIGLFGGAGVGKTVLIQELINNIAK-EHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVALT  223 (461)
T ss_pred             EEEeecCCCCChHHHHHHHHHHHHh-cCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHH
Confidence            5789999999999999998766211 12135667767554 356677777654322111110  111222111      2


Q ss_pred             HHHHHHHh---cCCeEEEEEeCCCC
Q 040110          185 KTILRDYL---TNKKYFTVLDDVWI  206 (348)
Q Consensus       185 ~~~l~~~L---~~kr~LlVLDdv~~  206 (348)
                      .-.+.+++   +++++||++||+-.
T Consensus       224 a~tiAEyfrd~~G~~VLll~DslTR  248 (461)
T TIGR01039       224 GLTMAEYFRDEQGQDVLLFIDNIFR  248 (461)
T ss_pred             HHHHHHHHHHhcCCeeEEEecchhH
Confidence            22355565   45799999999853

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>PRK14526 adenylate kinase; Provisional

Probab=95.35  E-value=0.037  Score=48.62  Aligned_cols=21  Identities=24%  Similarity=0.303  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.|+|++|+||||+|+.+...
T Consensus         3 i~l~G~pGsGKsT~a~~La~~   23 (211)
T PRK14526          3 LVFLGPPGSGKGTIAKILSNE   23 (211)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            668999999999999998865

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=95.35  E-value=0.015  Score=46.99  Aligned_cols=25  Identities=20%  Similarity=0.235  Sum_probs=22.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -.++.+.|.-|+|||||++.+++..
T Consensus        22 ~~~i~l~G~lGaGKTtl~~~l~~~l   46 (133)
T TIGR00150        22 GTVVLLKGDLGAGKTTLVQGLLQGL   46 (133)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            3489999999999999999999874

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=95.35  E-value=0.02  Score=51.92  Aligned_cols=91  Identities=19%  Similarity=0.097  Sum_probs=59.4

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc-------------c--
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW-------------L--  174 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-------------~--  174 (348)
                      +.-+++.|+|.+|+|||+++.+....  ..+....++||+.....  .++.+.+.. ++.....             .  
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~--~~~~ge~vlyvs~~e~~--~~l~~~~~~-~g~d~~~~~~~g~l~i~d~~~~~   95 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYE--GAREGEPVLYVSTEESP--EELLENARS-FGWDLEVYIEKGKLAILDAFLSE   95 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHH--HHhcCCcEEEEEecCCH--HHHHHHHHH-cCCCHHHHhhcCCEEEEEccccc
Confidence            45678999999999999999998877  55557789999876543  333333322 3222110             0  


Q ss_pred             -c------cCCCCHHHHHHHHHHHhcC-CeEEEEEeCCC
Q 040110          175 -K------IMGKDYKSEKTILRDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       175 -~------~~~~~~~~~~~~l~~~L~~-kr~LlVLDdv~  205 (348)
                       .      ....+...+...+.+.... +..-+|+|++-
T Consensus        96 ~~~~~~~~~~~~~~~~l~~~I~~~~~~~~~~~~ViDsi~  134 (260)
T COG0467          96 KGLVSIVVGDPLDLEELLDRIREIVEKEGADRVVIDSIT  134 (260)
T ss_pred             cccccccccCCccHHHHHHHHHHHHHHhCCCEEEEeCCc
Confidence             0      0123556677777777654 47788999986

>PRK14737 gmk guanylate kinase; Provisional

Probab=95.34  E-value=0.018  Score=49.57  Aligned_cols=25  Identities=12%  Similarity=0.186  Sum_probs=22.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...++.|+|++|+|||||++.+...
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~   27 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEE   27 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            4568899999999999999999876

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=95.34  E-value=0.1  Score=50.79  Aligned_cols=90  Identities=13%  Similarity=0.194  Sum_probs=49.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCc--cccCCCC-HHHH----
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSW--LKIMGKD-YKSE----  184 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~--~~~~~~~-~~~~----  184 (348)
                      ..++|+|..|+|||||++.+.+..    +.+..++..++.. ..+.+++.+....=......  ....+.. ....    
T Consensus       156 qrigI~G~sG~GKSTLL~~I~~~~----~~d~~vi~~iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~~a~~  231 (433)
T PRK07594        156 QRVGIFSAPGVGKSTLLAMLCNAP----DADSNVLVLIGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERVRALF  231 (433)
T ss_pred             CEEEEECCCCCCccHHHHHhcCCC----CCCEEEEEEECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHHHHHH
Confidence            368999999999999999998762    2334555555543 44545555543211010000  0111111 1111    


Q ss_pred             -HHHHHHHh--cCCeEEEEEeCCCC
Q 040110          185 -KTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       185 -~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                       .-.+.+++  +++++||++||+-.
T Consensus       232 ~a~tiAEyfrd~G~~VLl~~Dsltr  256 (433)
T PRK07594        232 VATTIAEFFRDNGKRVVLLADSLTR  256 (433)
T ss_pred             HHHHHHHHHHHCCCcEEEEEeCHHH
Confidence             11244444  47899999999853

>PRK15064 ABC transporter ATP-binding protein; Provisional

Probab=95.32  E-value=0.29  Score=49.18  Aligned_cols=23  Identities=13%  Similarity=0.309  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++..
T Consensus        28 e~~~liG~NGsGKSTLl~~l~Gl   50 (530)
T PRK15064         28 NRYGLIGANGCGKSTFMKILGGD   50 (530)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            47999999999999999999875

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.31  E-value=0.13  Score=43.05  Aligned_cols=120  Identities=8%  Similarity=0.075  Sum_probs=59.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeE--EEEeCCCCCHHHHHHHHHHHhCCCCCc--cccCCCCH-------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHA--WVRVSNFYNFKRILDDIMKSLMPTSSW--LKIMGKDY-------  181 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~--wv~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~-------  181 (348)
                      ..|-|++..|.||||+|..+.-+.. ...+.+.+  |+.-........+++.+ ..+......  ......+.       
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~ra~-~~g~~v~~vQFlKg~~~~gE~~~l~~l-~~v~~~~~g~~~~~~~~~~~~~~~~a   80 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALRAL-GHGYRVGVVQFLKGGWKYGELKALERL-PNIEIHRMGRGFFWTTENDEEDIAAA   80 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEEEeCCCCccCHHHHHHhC-CCcEEEECCCCCccCCCChHHHHHHH
Confidence            3677788889999999987765421 22232222  23322233433443333 001000000  00000111       


Q ss_pred             HHHHHHHHHHhcC-CeEEEEEeCCCCh-----hhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          182 KSEKTILRDYLTN-KKYFTVLDDVWIE-----KIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       182 ~~~~~~l~~~L~~-kr~LlVLDdv~~~-----~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      .+..+..++.+.. .-=|||||++-..     -..+++...+.....+.-||+|.|+..
T Consensus        81 ~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p  139 (159)
T cd00561          81 AEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAP  139 (159)
T ss_pred             HHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCC
Confidence            1223334444433 5579999998543     234455555444445678999999854

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=95.31  E-value=0.063  Score=55.78  Aligned_cols=89  Identities=18%  Similarity=0.111  Sum_probs=58.0

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTIL  188 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l  188 (348)
                      +.-+++-|.|.+|+|||||+.+++...  ...=..++|+.....++.     ..+++++.+.... -......+.....+
T Consensus        58 p~GsiteI~G~~GsGKTtLal~~~~~a--~~~G~~v~yId~E~t~~~-----~~A~~lGvDl~~llv~~~~~~E~~l~~i  130 (790)
T PRK09519         58 PRGRVIEIYGPESSGKTTVALHAVANA--QAAGGVAAFIDAEHALDP-----DYAKKLGVDTDSLLVSQPDTGEQALEIA  130 (790)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHH--HHcCCcEEEECCccchhH-----HHHHHcCCChhHeEEecCCCHHHHHHHH
Confidence            456788899999999999998765542  111235788887777663     3667777653321 11223445566666


Q ss_pred             HHHhcC-CeEEEEEeCCC
Q 040110          189 RDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       189 ~~~L~~-kr~LlVLDdv~  205 (348)
                      ...++. +--|+|+|.+.
T Consensus       131 ~~lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        131 DMLIRSGALDIVVIDSVA  148 (790)
T ss_pred             HHHhhcCCCeEEEEcchh
Confidence            666644 56789999985

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=95.31  E-value=0.19  Score=49.40  Aligned_cols=213  Identities=13%  Similarity=0.103  Sum_probs=101.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++|.....   .++.+.+..    .......+.|.|..|+||+++|+.+....  .......+-+++..- + .+.+..
T Consensus       135 ~lig~s~~~---~~v~~~i~~----~a~~~~~vli~Ge~GtGK~~~A~~ih~~~--~~~~~~~~~~~c~~~-~-~~~~~~  203 (463)
T TIGR01818       135 ELIGEAPAM---QEVFRAIGR----LSRSDITVLINGESGTGKELVARALHRHS--PRANGPFIALNMAAI-P-KDLIES  203 (463)
T ss_pred             ceeecCHHH---HHHHHHHHH----HhCcCCeEEEECCCCCCHHHHHHHHHHhC--CCCCCCeEEEeCCCC-C-HHHHHH
Confidence            578877766   666665541    11222346789999999999999998762  212122223333322 2 233333


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhCCCCC-----------CCcEEEEE
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPDNQ-----------IGSRALIT  229 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~-----------~gskIlvT  229 (348)
                      .+  ++....  ...... ..   .....-....-.|+||++...  .....+...+..+.           ...+||+|
T Consensus       204 ~l--fg~~~~--~~~~~~-~~---~~g~~~~a~~gtl~l~ei~~l~~~~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~  275 (463)
T TIGR01818       204 EL--FGHEKG--AFTGAN-TR---RQGRFEQADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAA  275 (463)
T ss_pred             Hh--cCCCCC--CCCCcc-cC---CCCcEEECCCCeEEEEchhhCCHHHHHHHHHHHhcCcEEECCCCceeeeeeEEEEe
Confidence            22  221100  000000 00   000011122344889999764  34445554443221           14578887


Q ss_pred             eCChhhh---hh-------cccCCCCcCCCCcccccCccccCC---HHHHHHHHHHhCCCCCCC-CCCCc-chhcccccc
Q 040110          230 VGPHNIL---TS-------IELENGEKNRHDSALVGGPLIRIK---HETWQFFILHYGSTPLEN-ETEGP-SVGLKLVSL  294 (348)
Q Consensus       230 TR~~~v~---~~-------~~l~~~~C~Lp~~~~ig~~L~~~~---~~~w~~~~~~~~~~~~~~-~~~~~-~i~~~l~s~  294 (348)
                      |......   ..       |.+....+.+|       .|+++.   ..-...+++.+... ... ...+. .....|..|
T Consensus       276 ~~~~l~~~~~~~~f~~~L~~rl~~~~i~lP-------pLr~R~~Di~~l~~~~l~~~~~~-~~~~~~~~~~~a~~~L~~~  347 (463)
T TIGR01818       276 THQNLEALVRQGKFREDLFHRLNVIRIHLP-------PLRERREDIPRLARHFLALAARE-LDVEPKLLDPEALERLKQL  347 (463)
T ss_pred             CCCCHHHHHHcCCcHHHHHHHhCcceecCC-------CcccchhhHHHHHHHHHHHHHHH-hCCCCCCcCHHHHHHHHhC
Confidence            7554311   11       22221111333       788765   55555666555332 211 11111 121222344


Q ss_pred             CCCC---hhHHHHHhHhccCCCCceecHHHHH
Q 040110          295 SELP---FPLIVCCLYFCVFPTDIELTTRQLC  323 (348)
Q Consensus       295 ~~Lp---~~lk~cf~y~a~fp~~~~i~~~~Li  323 (348)
                       +-|   .+++.+.-.+.+...+-.|..+.|-
T Consensus       348 -~wpgNvreL~~~~~~~~~~~~~~~i~~~~l~  378 (463)
T TIGR01818       348 -RWPGNVRQLENLCRWLTVMASGDEVLVSDLP  378 (463)
T ss_pred             -CCCChHHHHHHHHHHHHHhCCCCcccHHhch
Confidence             456   5677777777776666667766654

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PRK12678 transcription termination factor Rho; Provisional

Probab=95.30  E-value=0.031  Score=55.71  Aligned_cols=105  Identities=13%  Similarity=0.066  Sum_probs=53.4

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccC-CcceeEEE-EeCCCC-CHHHHHHHHHHHhCCCC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKF-YFDCHAWV-RVSNFY-NFKRILDDIMKSLMPTS  171 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~F~~~~wv-~~~~~~-~~~~~~~~i~~~l~~~~  171 (348)
                      -+++++|.+-    ..+- ..+|+|.+|+|||||++.+.+.  +.. +=++.++| -++... .+.++.+.+-..+-...
T Consensus       404 iRvIDll~PI----GkGQ-R~LIvgpp~aGKTtLL~~IAn~--i~~n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT  476 (672)
T PRK12678        404 TRVIDLIMPI----GKGQ-RGLIVSPPKAGKTTILQNIANA--ITTNNPECHLMVVLVDERPEEVTDMQRSVKGEVIAST  476 (672)
T ss_pred             ceeeeeeccc----ccCC-EeEEeCCCCCCHHHHHHHHHHH--HhhcCCCeEEEEEEEeCchhhHHHHHHhccceEEEEC
Confidence            4667777632    2222 4679999999999999999986  322 22344333 344333 33333333211111110


Q ss_pred             Cc-cccCCCCHHHHHHHHHHHh--cCCeEEEEEeCCCC
Q 040110          172 SW-LKIMGKDYKSEKTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       172 ~~-~~~~~~~~~~~~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      +. +.........+.-.+.++|  .++.+||+||++-.
T Consensus       477 ~D~p~~~~~~~a~~ai~~Ae~fre~G~dVlillDSlTR  514 (672)
T PRK12678        477 FDRPPSDHTTVAELAIERAKRLVELGKDVVVLLDSITR  514 (672)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCchH
Confidence            00 0000011122223344444  57899999999843

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=95.30  E-value=0.066  Score=52.12  Aligned_cols=93  Identities=14%  Similarity=0.143  Sum_probs=56.5

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccC--Ccc---------eeEEEEeCCCCCHHHHHHHHHHHhC-CCCCcc--ccCCC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKF--YFD---------CHAWVRVSNFYNFKRILDDIMKSLM-PTSSWL--KIMGK  179 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~--~F~---------~~~wv~~~~~~~~~~~~~~i~~~l~-~~~~~~--~~~~~  179 (348)
                      -++|.|-+|+|||||+..+.+.....+  ..|         .++++-+++.....+.+.+.+..-+ ...+..  ...+.
T Consensus       143 RigIfagsGvGKs~L~~~i~~~~~~~~~~~aD~~~~~~~~~v~V~a~IGerre~~efi~~~l~~~g~l~rtvvv~atsd~  222 (466)
T TIGR01040       143 KIPIFSAAGLPHNEIAAQICRQAGLVKLPTKDVHDGHEDNFAIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNLAND  222 (466)
T ss_pred             eeeeecCCCCCHHHHHHHHHHhhccccccccccccccCCceEEEEEEeeeehHHHHHHHHHHHhcCCcceEEEEEECCCC
Confidence            478999999999999999987743100  011         5667777877666676666666555 222110  11111


Q ss_pred             CHHH------HHHHHHHHhc---CCeEEEEEeCCCC
Q 040110          180 DYKS------EKTILRDYLT---NKKYFTVLDDVWI  206 (348)
Q Consensus       180 ~~~~------~~~~l~~~L~---~kr~LlVLDdv~~  206 (348)
                      ..-.      ..-.+.++++   ++++||++||+-.
T Consensus       223 p~~~R~~a~~~a~tiAEyfr~~~G~~VLl~~DslTr  258 (466)
T TIGR01040       223 PTIERIITPRLALTTAEYLAYQCEKHVLVILTDMSS  258 (466)
T ss_pred             CHHHHHHHHhhhHHHHHHHHHhcCCcEEEeccChHH
Confidence            1111      1122555555   5899999999943

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=95.30  E-value=0.026  Score=57.52  Aligned_cols=74  Identities=8%  Similarity=0.012  Sum_probs=49.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCC-cceeEEEEeCCCCCHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFY-FDCHAWVRVSNFYNFKRILD  161 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~-F~~~~wv~~~~~~~~~~~~~  161 (348)
                      .++|.+...   +.+...+.      ...  .+.++|++|+||||+|+.+.+.  +... |...+++. ....+...+++
T Consensus        19 ~viG~~~a~---~~l~~a~~------~~~--~~ll~G~pG~GKT~la~~la~~--l~~~~~~~~~~~~-n~~~~~~~~~~   84 (608)
T TIGR00764        19 QVIGQEEAV---EIIKKAAK------QKR--NVLLIGEPGVGKSMLAKAMAEL--LPDEELEDILVYP-NPEDPNMPRIV   84 (608)
T ss_pred             hccCHHHHH---HHHHHHHH------cCC--CEEEECCCCCCHHHHHHHHHHH--cCchhheeEEEEe-CCCCCchHHHH
Confidence            789999888   77777776      112  4458999999999999999977  4333 23233322 22335556677


Q ss_pred             HHHHHhCCC
Q 040110          162 DIMKSLMPT  170 (348)
Q Consensus       162 ~i~~~l~~~  170 (348)
                      .++.+++..
T Consensus        85 ~v~~~~g~~   93 (608)
T TIGR00764        85 EVPAGEGRE   93 (608)
T ss_pred             HHHHhhchH
Confidence            777777654

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=95.30  E-value=0.014  Score=48.07  Aligned_cols=21  Identities=14%  Similarity=0.237  Sum_probs=19.3

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|++|+||||+|+.+...
T Consensus         2 i~l~G~~GsGKstla~~la~~   22 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKA   22 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            678999999999999999876

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=95.29  E-value=0.17  Score=47.35  Aligned_cols=90  Identities=11%  Similarity=0.137  Sum_probs=50.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeC-CCCCHHHHHHHHHHHhCCCCCcc--ccCCCCHH------H
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVS-NFYNFKRILDDIMKSLMPTSSWL--KIMGKDYK------S  183 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~------~  183 (348)
                      ..++|+|..|+|||||.+.+.+.  ...  +..+..-++ +.-++.++.......-+......  ...+....      .
T Consensus        70 qri~I~G~sG~GKTtLl~~Ia~~--~~~--~~~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~~~  145 (326)
T cd01136          70 QRLGIFAGSGVGKSTLLGMIARG--TTA--DVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKAAY  145 (326)
T ss_pred             cEEEEECCCCCChHHHHHHHhCC--CCC--CEEEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHHHH
Confidence            36899999999999999998877  222  233334443 33456666666655433221110  11111111      1


Q ss_pred             HHHHHHHHh--cCCeEEEEEeCCCC
Q 040110          184 EKTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       184 ~~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      ..-.+.+++  +++.+|+++||+-.
T Consensus       146 ~a~~~AEyfr~~g~~Vll~~Dsltr  170 (326)
T cd01136         146 TATAIAEYFRDQGKDVLLLMDSLTR  170 (326)
T ss_pred             HHHHHHHHHHHcCCCeEEEeccchH
Confidence            112233333  47899999999843

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=95.29  E-value=0.017  Score=50.24  Aligned_cols=24  Identities=21%  Similarity=0.195  Sum_probs=21.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++.|.|.+|+||||+|+.+...
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~   26 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARH   26 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh
Confidence            458899999999999999999887

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=95.27  E-value=0.27  Score=47.81  Aligned_cols=121  Identities=15%  Similarity=0.091  Sum_probs=65.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc--ccCCCCH------HHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL--KIMGKDY------KSE  184 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~------~~~  184 (348)
                      ..++|+|..|+|||||+..++...  +. ...++...-.+...+.+++...+..-+...+..  ...+...      ...
T Consensus       157 qri~I~G~sG~GKTtLl~~Ia~~~--~~-~~gvI~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra~~~  233 (432)
T PRK06793        157 QKIGIFAGSGVGKSTLLGMIAKNA--KA-DINVISLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRAAKL  233 (432)
T ss_pred             cEEEEECCCCCChHHHHHHHhccC--CC-CeEEEEeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHHHHH
Confidence            367999999999999999998873  21 123333322334667777666655533221110  1111111      112


Q ss_pred             HHHHHHHh--cCCeEEEEEeCCCCh-hhHHHHHhh---CCCCCCCcEEEEEeCChhhhhh
Q 040110          185 KTILRDYL--TNKKYFTVLDDVWIE-KIWDDLREA---LPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       185 ~~~l~~~L--~~kr~LlVLDdv~~~-~~~~~l~~~---l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      ...+.+++  ++++.||++|++-.. +...++...   .|. . |-...+.|....++..
T Consensus       234 a~~iAEyfr~~G~~VLlilDslTr~a~A~reisl~~~e~p~-~-G~~~~~~s~l~~L~ER  291 (432)
T PRK06793        234 ATSIAEYFRDQGNNVLLMMDSVTRFADARRSVDIAVKELPI-G-GKTLLMESYMKKLLER  291 (432)
T ss_pred             HHHHHHHHHHcCCcEEEEecchHHHHHHHHHHHHHhcCCCC-C-CeeeeeeccchhHHHH
Confidence            22233344  468999999999654 333333322   332 2 5555565555555544

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.27  E-value=0.18  Score=50.70  Aligned_cols=24  Identities=25%  Similarity=0.220  Sum_probs=21.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -..++|+|+.|+|||||++.+..-
T Consensus       361 G~~vaIvG~SGsGKSTLl~lL~g~  384 (529)
T TIGR02868       361 GERVAILGPSGSGKSTLLMLLTGL  384 (529)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            347899999999999999999755

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=95.26  E-value=0.017  Score=45.26  Aligned_cols=23  Identities=22%  Similarity=0.527  Sum_probs=19.9

Q ss_pred             EEEECCCCCcHHHHHHHHhcCcc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNNF  137 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~~  137 (348)
                      |.|+|..|+|||||.+.+.+...
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~~   24 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGEF   24 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS-
T ss_pred             EEEECcCCCCHHHHHHHHhcCCC
Confidence            67899999999999999987743

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=95.24  E-value=0.033  Score=49.13  Aligned_cols=22  Identities=9%  Similarity=0.152  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      .++.|+|+.|.||||+.+.+..
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~   52 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVAL   52 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            7899999999999999999853

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam

>PRK14530 adenylate kinase; Provisional

Probab=95.23  E-value=0.015  Score=51.17  Aligned_cols=22  Identities=14%  Similarity=0.259  Sum_probs=20.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|+|++|+||||+|+.++..
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~   26 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEE   26 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999999876

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.22  E-value=0.11  Score=51.73  Aligned_cols=92  Identities=11%  Similarity=0.035  Sum_probs=57.5

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc-----------cccC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW-----------LKIM  177 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----------~~~~  177 (348)
                      -..-+++.|.|++|+|||||+.++......  .=..+++++..  -+..++...+ +.++.+...           ....
T Consensus       260 ~~~gs~~li~G~~G~GKt~l~~~f~~~~~~--~ge~~~y~s~e--Es~~~i~~~~-~~lg~~~~~~~~~g~l~~~~~~p~  334 (484)
T TIGR02655       260 FFKDSIILATGATGTGKTLLVSKFLENACA--NKERAILFAYE--ESRAQLLRNA-YSWGIDFEEMEQQGLLKIICAYPE  334 (484)
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHHH--CCCeEEEEEee--CCHHHHHHHH-HHcCCChHHHhhCCcEEEEEcccc
Confidence            345668889999999999999998776321  11245555443  3455555554 455543211           0112


Q ss_pred             CCCHHHHHHHHHHHhcC-CeEEEEEeCCC
Q 040110          178 GKDYKSEKTILRDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       178 ~~~~~~~~~~l~~~L~~-kr~LlVLDdv~  205 (348)
                      ....++....+.+.+.. +.-.+|+|.+.
T Consensus       335 ~~~~~~~~~~i~~~i~~~~~~~vvIDsi~  363 (484)
T TIGR02655       335 SAGLEDHLQIIKSEIADFKPARIAIDSLS  363 (484)
T ss_pred             cCChHHHHHHHHHHHHHcCCCEEEEcCHH
Confidence            23456777777777754 56689999985

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=95.22  E-value=0.029  Score=52.40  Aligned_cols=47  Identities=15%  Similarity=0.048  Sum_probs=30.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRIL  160 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  160 (348)
                      .+++...|.|||||||+|.+.+-.  .......++=|+.....++.+++
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~~--lA~~g~kvLlvStDPAhsL~d~f   48 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAVK--LAESGKKVLLVSTDPAHSLGDVF   48 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHHH--HHHcCCcEEEEEeCCCCchHhhh
Confidence            468889999999999999886544  22222335555555544544443

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=95.21  E-value=0.03  Score=53.48  Aligned_cols=25  Identities=12%  Similarity=0.076  Sum_probs=21.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+.|.|.||+|||+|.+++.+.
T Consensus        21 ~~~~~fv~G~~GtGKs~l~~~i~~~   45 (364)
T PF05970_consen   21 EGLNFFVTGPAGTGKSFLIKAIIDY   45 (364)
T ss_pred             CCcEEEEEcCCCCChhHHHHHHHHH
Confidence            3456789999999999999999887

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=95.20  E-value=0.019  Score=44.57  Aligned_cols=22  Identities=32%  Similarity=0.363  Sum_probs=19.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHh
Q 040110          112 HSVVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~  133 (348)
                      -..++|.|++|+|||||+..+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            3578999999999999999976

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=95.20  E-value=0.038  Score=47.39  Aligned_cols=22  Identities=14%  Similarity=0.160  Sum_probs=20.5

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|+|.|+.|+||||+++.+.+.
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~   23 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAER   23 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6889999999999999999887

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>TIGR00416 sms DNA repair protein RadA

Probab=95.17  E-value=0.093  Score=51.60  Aligned_cols=99  Identities=13%  Similarity=0.070  Sum_probs=54.5

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL  174 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~  174 (348)
                      ..+-..|.    .+-..-.++.|.|.+|+|||||+.++....  ...=..++|++...  +..++.. -+..++......
T Consensus        81 ~~LD~vLg----GGi~~GsvilI~G~pGsGKTTL~lq~a~~~--a~~g~kvlYvs~EE--s~~qi~~-ra~rlg~~~~~l  151 (454)
T TIGR00416        81 GELDRVLG----GGIVPGSLILIGGDPGIGKSTLLLQVACQL--AKNQMKVLYVSGEE--SLQQIKM-RAIRLGLPEPNL  151 (454)
T ss_pred             HHHHHHhc----CCccCCeEEEEEcCCCCCHHHHHHHHHHHH--HhcCCcEEEEECcC--CHHHHHH-HHHHcCCChHHe
Confidence            44444444    233455688999999999999999987652  22112467776543  3333322 233444322110


Q ss_pred             -ccCCCCHHHHHHHHHHHhcCCeEEEEEeCCC
Q 040110          175 -KIMGKDYKSEKTILRDYLTNKKYFTVLDDVW  205 (348)
Q Consensus       175 -~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~  205 (348)
                       -....+.+.+...+.+   .+.-++|+|.+.
T Consensus       152 ~~~~e~~~~~I~~~i~~---~~~~~vVIDSIq  180 (454)
T TIGR00416       152 YVLSETNWEQICANIEE---ENPQACVIDSIQ  180 (454)
T ss_pred             EEcCCCCHHHHHHHHHh---cCCcEEEEecch
Confidence             1122344544444432   356689999985

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=95.17  E-value=0.017  Score=47.30  Aligned_cols=39  Identities=13%  Similarity=0.171  Sum_probs=27.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN  152 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  152 (348)
                      ++|.|+|..|+|||||+..+.+... ++.+...+..+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~-~~g~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELK-RRGYRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHH-HTT--EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHh-HcCCceEEEEEccC
Confidence            3789999999999999999998832 24555555555544

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=95.16  E-value=0.012  Score=55.03  Aligned_cols=50  Identities=14%  Similarity=0.228  Sum_probs=43.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|+|.++.+   +++++.+.......+..-+++-++|+.|.||||||..+.+-
T Consensus        62 ~~~G~~~~i---~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~  111 (358)
T PF08298_consen   62 EFYGMEETI---ERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRG  111 (358)
T ss_pred             cccCcHHHH---HHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHH
Confidence            799999999   99999997544445667789999999999999999998776

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=95.15  E-value=0.017  Score=48.49  Aligned_cols=20  Identities=25%  Similarity=0.371  Sum_probs=18.6

Q ss_pred             EEEEECCCCCcHHHHHHHHh
Q 040110          114 VVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~  133 (348)
                      .|+|.|.+|+||||+++.+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58899999999999999987

>PLN02318 phosphoribulokinase/uridine kinase

Probab=95.14  E-value=0.021  Score=57.22  Aligned_cols=27  Identities=22%  Similarity=0.318  Sum_probs=24.1

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++.+|+|.|.+|+||||||+.+...
T Consensus        62 ~~~riIIGIaGpSGSGKTTLAk~Lagl   88 (656)
T PLN02318         62 NDGIILVGVAGPSGAGKTVFTEKVLNF   88 (656)
T ss_pred             CCCeEEEEEECCCCCcHHHHHHHHHhh
Confidence            456789999999999999999999876

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=95.12  E-value=0.019  Score=48.68  Aligned_cols=23  Identities=9%  Similarity=0.235  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..|.|+|+.|+||||+++.+.+.
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~   27 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQ   27 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHH
Confidence            35889999999999999999987

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=95.12  E-value=0.062  Score=50.60  Aligned_cols=22  Identities=9%  Similarity=0.066  Sum_probs=19.2

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      +.+.|++|.||||+++.+.+..
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~l   23 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSATL   23 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHHH
Confidence            5679999999999999998763

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=95.09  E-value=0.043  Score=52.82  Aligned_cols=55  Identities=15%  Similarity=0.180  Sum_probs=35.7

Q ss_pred             cccccccccccHHHHHhhcCC--------CCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPP--------SSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF  142 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~--------~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F  142 (348)
                      .++|.++.+   +.+.-.+..        ++......++-+.++|++|+|||++|+.+...  ....|
T Consensus        13 ~IiGQ~eAk---k~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~--l~~~f   75 (441)
T TIGR00390        13 YIIGQDNAK---KSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKL--ANAPF   75 (441)
T ss_pred             hccCHHHHH---HHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHH--hCCeE
Confidence            577777777   666544431        00011123356789999999999999999887  44443

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>PRK13946 shikimate kinase; Provisional

Probab=95.09  E-value=0.019  Score=49.17  Aligned_cols=24  Identities=13%  Similarity=0.194  Sum_probs=21.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.|.++|++|+||||+++.+.+.
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~   33 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATM   33 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            346889999999999999999987

>PRK11147 ABC transporter ATPase component; Reviewed

Probab=95.08  E-value=0.34  Score=49.92  Aligned_cols=23  Identities=13%  Similarity=0.255  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+...
T Consensus        30 e~v~LvG~NGsGKSTLLriiaG~   52 (635)
T PRK11147         30 ERVCLVGRNGAGKSTLMKILNGE   52 (635)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCC
Confidence            37999999999999999999876

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=95.07  E-value=0.11  Score=50.63  Aligned_cols=91  Identities=12%  Similarity=0.057  Sum_probs=47.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc--cccCCCCH------HH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW--LKIMGKDY------KS  183 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~------~~  183 (348)
                      -..++|+|..|+|||||++.+.+....   -...+++.-.+.-++.++..+.+..-......  ....+...      ..
T Consensus       158 Gq~i~I~G~sG~GKStLl~~I~~~~~~---~~gvI~~~Gerg~ev~e~~~~~l~~~~l~r~v~vv~~~~~~~~~r~~~~~  234 (438)
T PRK07721        158 GQRVGIFAGSGVGKSTLMGMIARNTSA---DLNVIALIGERGREVREFIERDLGPEGLKRSIVVVATSDQPALMRIKGAY  234 (438)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcccCC---CeEEEEEEecCCccHHHHHHhhcChhhhcCeEEEEECCCCCHHHHHHHHH
Confidence            347899999999999999988876221   12344432223334555444322211111000  01111111      11


Q ss_pred             HHHHHHHHh--cCCeEEEEEeCCC
Q 040110          184 EKTILRDYL--TNKKYFTVLDDVW  205 (348)
Q Consensus       184 ~~~~l~~~L--~~kr~LlVLDdv~  205 (348)
                      ..-.+.+++  +++++||++||+-
T Consensus       235 ~a~~iAEyfr~~g~~Vll~~Dslt  258 (438)
T PRK07721        235 TATAIAEYFRDQGLNVMLMMDSVT  258 (438)
T ss_pred             HHHHHHHHHHHCCCcEEEEEeChH
Confidence            112244444  4789999999984

>PRK05973 replicative DNA helicase; Provisional

Probab=95.06  E-value=0.13  Score=45.95  Aligned_cols=48  Identities=15%  Similarity=0.129  Sum_probs=31.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDI  163 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i  163 (348)
                      -.++.|.|.+|+|||+|+.++..... ++. ..+++++....  ..++...+
T Consensus        64 Gsl~LIaG~PG~GKT~lalqfa~~~a-~~G-e~vlyfSlEes--~~~i~~R~  111 (237)
T PRK05973         64 GDLVLLGARPGHGKTLLGLELAVEAM-KSG-RTGVFFTLEYT--EQDVRDRL  111 (237)
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHH-hcC-CeEEEEEEeCC--HHHHHHHH
Confidence            34778899999999999999876532 222 24556655443  44554444

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=95.05  E-value=0.052  Score=54.08  Aligned_cols=100  Identities=14%  Similarity=0.137  Sum_probs=55.5

Q ss_pred             cccccccccccHHHHHhhcCCCCC----CCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSG----LGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKR  158 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~----~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~  158 (348)
                      .+.|.+.....+.+.+.++.....    .+-...+.+.++|++|.|||.||+++++.  ...+|-.+.     .. +   
T Consensus       243 diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~--~~~~fi~v~-----~~-~---  311 (494)
T COG0464         243 DIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALE--SRSRFISVK-----GS-E---  311 (494)
T ss_pred             hhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhh--CCCeEEEee-----CH-H---
Confidence            555666666222333443332111    12345557889999999999999999996  444443222     11 1   


Q ss_pred             HHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 040110          159 ILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       159 ~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                          ++..         .-......+...+....+...+.|.+|.++.
T Consensus       312 ----l~sk---------~vGesek~ir~~F~~A~~~~p~iiFiDEiDs  346 (494)
T COG0464         312 ----LLSK---------WVGESEKNIRELFEKARKLAPSIIFIDEIDS  346 (494)
T ss_pred             ----Hhcc---------ccchHHHHHHHHHHHHHcCCCcEEEEEchhh
Confidence                1110         1112233344444444557889999999864

>PRK13975 thymidylate kinase; Provisional

Probab=95.03  E-value=0.021  Score=49.26  Aligned_cols=24  Identities=17%  Similarity=0.082  Sum_probs=21.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .+|.|.|+.|+||||+|+.+....
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l   26 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKL   26 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999999883

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=95.02  E-value=0.034  Score=48.97  Aligned_cols=41  Identities=24%  Similarity=0.160  Sum_probs=25.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYN  155 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  155 (348)
                      .|+|+|-||+||||+|..+.....-++.|+ ++=|....+++
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l~~~~~~~-VLvVDaDpd~n   42 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRLLSKGGYN-VLVVDADPDSN   42 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHHHHhcCCce-EEEEeCCCCCC
Confidence            589999999999999988554422233243 33344444444

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=95.01  E-value=0.024  Score=47.27  Aligned_cols=48  Identities=23%  Similarity=0.212  Sum_probs=33.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTS  171 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~  171 (348)
                      .+++.|+|.+|+||||+.+.+.... +..+           -.+...+.-+++...+...
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~l-~~~~-----------ivNyG~~Mle~A~k~glve   51 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKEL-VKHK-----------IVNYGDLMLEIAKKKGLVE   51 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHHH-hhce-----------eeeHhHHHHHHHHHhCCcc
Confidence            6789999999999999998877662 1111           1144566667777666653

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.99  E-value=0.02  Score=53.46  Aligned_cols=128  Identities=16%  Similarity=0.204  Sum_probs=74.9

Q ss_pred             cccccccccccHHHHHhhcCCC-------CCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-------SGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYN  155 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-------~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  155 (348)
                      .+=|-++++   ++|.+...-+       ..-+=+.++=|.++|++|.|||-||++|+++  ....|     +.+..   
T Consensus       152 dIGGL~~Qi---~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~--T~AtF-----Irvvg---  218 (406)
T COG1222         152 DIGGLDEQI---QEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQ--TDATF-----IRVVG---  218 (406)
T ss_pred             hccCHHHHH---HHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhc--cCceE-----EEecc---
Confidence            344688888   7777765311       0112234555678999999999999999999  55554     32221   


Q ss_pred             HHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcC-CeEEEEEeCCCCh-------------h---hHHHHHhhCC
Q 040110          156 FKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTN-KKYFTVLDDVWIE-------------K---IWDDLREALP  218 (348)
Q Consensus       156 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~-kr~LlVLDdv~~~-------------~---~~~~l~~~l~  218 (348)
                       .++.+..+    +          +-..+...+.+.-+. ...+|.+|.++..             +   .+-++...+-
T Consensus       219 -SElVqKYi----G----------EGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlD  283 (406)
T COG1222         219 -SELVQKYI----G----------EGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLD  283 (406)
T ss_pred             -HHHHHHHh----c----------cchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhcc
Confidence             12222221    1          224455555555555 4788889988631             1   1223344443


Q ss_pred             CCC--CCcEEEEEeCChhhhhh
Q 040110          219 DNQ--IGSRALITVGPHNILTS  238 (348)
Q Consensus       219 ~~~--~gskIlvTTR~~~v~~~  238 (348)
                      .++  ..-|||..|...++...
T Consensus       284 GFD~~~nvKVI~ATNR~D~LDP  305 (406)
T COG1222         284 GFDPRGNVKVIMATNRPDILDP  305 (406)
T ss_pred             CCCCCCCeEEEEecCCccccCh
Confidence            322  34689988887777665

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=94.98  E-value=0.042  Score=46.47  Aligned_cols=44  Identities=23%  Similarity=0.308  Sum_probs=28.1

Q ss_pred             cccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           85 LGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        85 vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|....+   .++.+.+...   ..... -|.|+|..|+||+.+|+.+++.
T Consensus         2 iG~s~~m---~~~~~~~~~~---a~~~~-pVlI~GE~GtGK~~lA~~IH~~   45 (168)
T PF00158_consen    2 IGESPAM---KRLREQAKRA---ASSDL-PVLITGETGTGKELLARAIHNN   45 (168)
T ss_dssp             S--SHHH---HHHHHHHHHH---TTSTS--EEEECSTTSSHHHHHHHHHHC
T ss_pred             EeCCHHH---HHHHHHHHHH---hCCCC-CEEEEcCCCCcHHHHHHHHHHh
Confidence            5656666   5555555411   11223 3559999999999999999986

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>PRK04182 cytidylate kinase; Provisional

Probab=94.97  E-value=0.02  Score=48.41  Aligned_cols=22  Identities=23%  Similarity=0.303  Sum_probs=20.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|.|.|+.|+||||+|+.+...
T Consensus         2 ~I~i~G~~GsGKstia~~la~~   23 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6889999999999999999877

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=94.95  E-value=0.02  Score=48.37  Aligned_cols=21  Identities=19%  Similarity=0.351  Sum_probs=18.2

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.|+|.+|+|||||++.+.+.
T Consensus         2 i~iTG~pG~GKTTll~k~i~~   22 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEE   22 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHH
Confidence            679999999999999998876

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=94.93  E-value=0.094  Score=50.98  Aligned_cols=91  Identities=11%  Similarity=0.091  Sum_probs=48.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCCCCcc--cc------CCCCHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPTSSWL--KI------MGKDYK  182 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~~~~~--~~------~~~~~~  182 (348)
                      -..++|+|..|+|||||+..+.+....    +..+...++. .-.+.++....+..-+......  ..      ......
T Consensus       155 GQ~igI~G~sGaGKSTLl~~I~g~~~~----dv~vig~IGerg~ev~ef~~~~l~~~gl~rsvvv~~~~d~s~~~rl~a~  230 (434)
T PRK07196        155 GQRVGLMAGSGVGKSVLLGMITRYTQA----DVVVVGLIGERGREVKEFIEHSLQAAGMAKSVVVAAPADESPLMRIKAT  230 (434)
T ss_pred             ceEEEEECCCCCCccHHHHHHhcccCC----CeEEEEEEeeecHHHHHHHHHHhhhcccceEEEEEecCCCChhhhHHHH
Confidence            347899999999999999998876221    2222222322 2234444444443332211100  00      111222


Q ss_pred             HHHHHHHHHh--cCCeEEEEEeCCCC
Q 040110          183 SEKTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       183 ~~~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      +....+.+++  .++++||++||+-.
T Consensus       231 e~a~~iAEyfr~~g~~Vll~~Dsltr  256 (434)
T PRK07196        231 ELCHAIATYYRDKGHDVLLLVDSLTR  256 (434)
T ss_pred             HHHHHHHHHhhhccCCEEEeecchhH
Confidence            3333445554  46899999999854

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=94.93  E-value=0.024  Score=48.17  Aligned_cols=23  Identities=9%  Similarity=0.343  Sum_probs=21.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++.|.|++|+|||||+++++.+
T Consensus         5 ~l~vlsgPSG~GKsTl~k~L~~~   27 (191)
T COG0194           5 LLIVLSGPSGVGKSTLVKALLED   27 (191)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            46788999999999999999988

>PLN02348 phosphoribulokinase

Probab=94.90  E-value=0.027  Score=53.72  Aligned_cols=27  Identities=15%  Similarity=0.289  Sum_probs=24.0

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.+.+|+|.|.+|+||||||+.+.+.
T Consensus        46 ~~~p~IIGIaG~SGSGKSTfA~~L~~~   72 (395)
T PLN02348         46 DDGTVVIGLAADSGCGKSTFMRRLTSV   72 (395)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            356789999999999999999999876

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=94.88  E-value=0.026  Score=49.36  Aligned_cols=27  Identities=22%  Similarity=0.342  Sum_probs=24.4

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++++++++|..|+|||||..++.+.
T Consensus        19 ~~~~~~i~~~G~~gsGKTTli~~l~~~   45 (207)
T TIGR00073        19 KHGLVVLNFMSSPGSGKTTLIEKLIDN   45 (207)
T ss_pred             hcCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999999998876

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>PTZ00494 tuzin-like protein; Provisional

Probab=94.87  E-value=0.32  Score=47.15  Aligned_cols=74  Identities=12%  Similarity=0.091  Sum_probs=56.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .+|.|+.+.   ..+.+.|.+   .+...++++.+.|..|.||++|.+.....+.+     ..++|.+...   ++.++.
T Consensus       372 ~~V~R~~eE---~~vRqvL~q---ld~aHPRIvV~TG~~GcGKSslcRsAvrkE~~-----paV~VDVRg~---EDtLrs  437 (664)
T PTZ00494        372 FEVRREDEE---ALVRSVLTQ---MAPSHPRIVALAGGSGGGRCVPCRRAVRVEGV-----ALVHVDVGGT---EDTLRS  437 (664)
T ss_pred             cccchhhHH---HHHHHHHhh---ccCCCCcEEEEecCCCCCchHHHHHHHHHcCC-----CeEEEEecCC---cchHHH
Confidence            799999999   666666652   23567889999999999999999988776333     4567777644   456788


Q ss_pred             HHHHhCCC
Q 040110          163 IMKSLMPT  170 (348)
Q Consensus       163 i~~~l~~~  170 (348)
                      +.+.++.+
T Consensus       438 VVKALgV~  445 (664)
T PTZ00494        438 VVRALGVS  445 (664)
T ss_pred             HHHHhCCC
Confidence            88899887

>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=94.87  E-value=0.1  Score=45.58  Aligned_cols=26  Identities=19%  Similarity=0.368  Sum_probs=22.3

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +...|.++.|++|+|||||.+.+.+-
T Consensus        31 ~~~~VTAlIGPSGcGKST~LR~lNRm   56 (253)
T COG1117          31 PKNKVTALIGPSGCGKSTLLRCLNRM   56 (253)
T ss_pred             cCCceEEEECCCCcCHHHHHHHHHhh
Confidence            45679999999999999999987654

>TIGR01287 nifH nitrogenase iron protein

Probab=94.86  E-value=0.02  Score=52.30  Aligned_cols=23  Identities=22%  Similarity=0.296  Sum_probs=19.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.|+|.|-||+||||++..++..
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~~   23 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAAA   23 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHHH
Confidence            36899999999999988877655

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>TIGR01069 mutS2 MutS2 family protein

Probab=94.85  E-value=0.019  Score=60.07  Aligned_cols=25  Identities=20%  Similarity=0.001  Sum_probs=21.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +..++.|+|+.|.|||||.+.+...
T Consensus       321 ~~~~liItGpNg~GKSTlLK~i~~~  345 (771)
T TIGR01069       321 EKRVLAITGPNTGGKTVTLKTLGLL  345 (771)
T ss_pred             CceEEEEECCCCCCchHHHHHHHHH
Confidence            3468999999999999999988644

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=94.85  E-value=0.031  Score=48.75  Aligned_cols=123  Identities=9%  Similarity=0.061  Sum_probs=65.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEe-------------------CCCC-------------------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRV-------------------SNFY-------------------  154 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~-------------------~~~~-------------------  154 (348)
                      .|++|+|++|+|||||.+.+..-+...   .+.+|+.-                   =+.|                   
T Consensus        29 evv~iiGpSGSGKSTlLRclN~LE~~~---~G~I~i~g~~~~~~~~~~~~R~~vGmVFQ~fnLFPHlTvleNv~lap~~v  105 (240)
T COG1126          29 EVVVIIGPSGSGKSTLLRCLNGLEEPD---SGSITVDGEDVGDKKDILKLRRKVGMVFQQFNLFPHLTVLENVTLAPVKV  105 (240)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCcCCC---CceEEECCEeccchhhHHHHHHhcCeecccccccccchHHHHHHhhhHHH
Confidence            488999999999999999886553332   23444421                   0111                   


Q ss_pred             ------CHHHHHHHHHHHhCCCCCcc-ccCC-CCHHHHHHHHHHHhcCCeEEEEEeCCCCh---hhHHHHHhhCCC-CCC
Q 040110          155 ------NFKRILDDIMKSLMPTSSWL-KIMG-KDYKSEKTILRDYLTNKKYFTVLDDVWIE---KIWDDLREALPD-NQI  222 (348)
Q Consensus       155 ------~~~~~~~~i~~~l~~~~~~~-~~~~-~~~~~~~~~l~~~L~~kr~LlVLDdv~~~---~~~~~l~~~l~~-~~~  222 (348)
                            ..++...+++..++...... -+.. ..-.+---.|.+.|.-++-++.+|..-+.   +-..++...+.. ...
T Consensus       106 ~~~~k~eA~~~A~~lL~~VGL~~ka~~yP~qLSGGQqQRVAIARALaM~P~vmLFDEPTSALDPElv~EVL~vm~~LA~e  185 (240)
T COG1126         106 KKLSKAEAREKALELLEKVGLADKADAYPAQLSGGQQQRVAIARALAMDPKVMLFDEPTSALDPELVGEVLDVMKDLAEE  185 (240)
T ss_pred             cCCCHHHHHHHHHHHHHHcCchhhhhhCccccCcHHHHHHHHHHHHcCCCCEEeecCCcccCCHHHHHHHHHHHHHHHHc
Confidence                  12234445555555543220 0111 12223334577888888889999998664   222222222211 123


Q ss_pred             CcEEEEEeCChhhhhh
Q 040110          223 GSRALITVGPHNILTS  238 (348)
Q Consensus       223 gskIlvTTR~~~v~~~  238 (348)
                      |-..++.|..-.-|+.
T Consensus       186 GmTMivVTHEM~FAr~  201 (240)
T COG1126         186 GMTMIIVTHEMGFARE  201 (240)
T ss_pred             CCeEEEEechhHHHHH
Confidence            5556666666554443

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=94.84  E-value=0.035  Score=48.73  Aligned_cols=52  Identities=19%  Similarity=0.097  Sum_probs=29.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCcc-----ccCCcceeEEEEeCCCCCHHHHHHHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNF-----VKFYFDCHAWVRVSNFYNFKRILDDIMK  165 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~-----~~~~F~~~~wv~~~~~~~~~~~~~~i~~  165 (348)
                      +..|+|++|+||||++..+.....     ....-...+-++...+..+..++..+..
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            678899999999987766665521     0122234444445555556666666655

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=94.84  E-value=0.02  Score=47.92  Aligned_cols=21  Identities=14%  Similarity=0.191  Sum_probs=17.4

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |+|+|..|+|||||+..+...
T Consensus         2 I~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc
Confidence            789999999999999999866

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=94.84  E-value=0.18  Score=44.88  Aligned_cols=49  Identities=20%  Similarity=0.168  Sum_probs=31.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDI  163 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i  163 (348)
                      -.++.|.|.+|+|||+++.++..+....... .++|++...  +..++...+
T Consensus        13 G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~-~vly~s~E~--~~~~~~~r~   61 (242)
T cd00984          13 GDLIIIAARPSMGKTAFALNIAENIAKKQGK-PVLFFSLEM--SKEQLLQRL   61 (242)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhCCC-ceEEEeCCC--CHHHHHHHH
Confidence            3578889999999999999887663222122 466665443  333444444

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=94.83  E-value=0.024  Score=48.29  Aligned_cols=23  Identities=13%  Similarity=0.169  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|++|+|||||++.++..
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~   26 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAAL   26 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHh
Confidence            37899999999999999999987

>PRK13236 nitrogenase reductase; Reviewed

Probab=94.82  E-value=0.028  Score=52.13  Aligned_cols=27  Identities=11%  Similarity=0.176  Sum_probs=22.5

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++.+++++.|-|||||||+|..++.-
T Consensus         3 ~~~~~~~~~~GKGGVGKTt~a~NLA~~   29 (296)
T PRK13236          3 DENIRQIAFYGKGGIGKSTTSQNTLAA   29 (296)
T ss_pred             CcCceEEEEECCCcCCHHHHHHHHHHH
Confidence            457799999999999999988776543

>PRK15115 response regulator GlrR; Provisional

Probab=94.80  E-value=0.34  Score=47.44  Aligned_cols=46  Identities=22%  Similarity=0.174  Sum_probs=31.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.....   .++.+.....   .... ..+.|.|.+|+|||++|+.+.+.
T Consensus       135 ~lig~s~~~---~~~~~~~~~~---a~~~-~~vli~Ge~GtGk~~lA~~ih~~  180 (444)
T PRK15115        135 AIVTRSPLM---LRLLEQARMV---AQSD-VSVLINGQSGTGKEILAQAIHNA  180 (444)
T ss_pred             cccccCHHH---HHHHHHHHhh---ccCC-CeEEEEcCCcchHHHHHHHHHHh
Confidence            577777666   6665544311   1122 24668999999999999999876

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=94.79  E-value=0.11  Score=53.11  Aligned_cols=97  Identities=12%  Similarity=0.188  Sum_probs=58.6

Q ss_pred             cccccccccccHHHHHhhcCCC-C-----CCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-S-----GLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNF  156 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-~-----~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  156 (348)
                      ++=|.++.+   .+|.+-+.-+ .     ..+-...+=|.++|++|.|||-||++|+..  .     ..-|+++..+   
T Consensus       673 DVGGLeevK---~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATE--c-----sL~FlSVKGP---  739 (953)
T KOG0736|consen  673 DVGGLEEVK---TEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATE--C-----SLNFLSVKGP---  739 (953)
T ss_pred             cccCHHHHH---HHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhh--c-----eeeEEeecCH---
Confidence            566788888   8887766421 0     112222344668999999999999999977  2     1235555443   


Q ss_pred             HHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 040110          157 KRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       157 ~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                       +++....             ..+.+.+.+.+.+.-..+++.|.+|.+++
T Consensus       740 -ELLNMYV-------------GqSE~NVR~VFerAR~A~PCVIFFDELDS  775 (953)
T KOG0736|consen  740 -ELLNMYV-------------GQSEENVREVFERARSAAPCVIFFDELDS  775 (953)
T ss_pred             -HHHHHHh-------------cchHHHHHHHHHHhhccCCeEEEeccccc
Confidence             2222211             11233344444444456899999999975

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=94.79  E-value=0.025  Score=50.72  Aligned_cols=32  Identities=16%  Similarity=0.058  Sum_probs=21.0

Q ss_pred             EECCCCCcHHHHHHHHhcCccccCCcceeEEEEe
Q 040110          117 ILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRV  150 (348)
Q Consensus       117 I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~  150 (348)
                      |+|++|+||||+++.+.+..  ...-..++-|++
T Consensus         1 ViGpaGSGKTT~~~~~~~~~--~~~~~~~~~vNL   32 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWL--ESNGRDVYIVNL   32 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHH--TTT-S-EEEEE-
T ss_pred             CCCCCCCCHHHHHHHHHHHH--HhccCCceEEEc
Confidence            68999999999999998873  333223444444

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>COG5635 Predicted NTPase (NACHT family) [Signal transduction mechanisms]

Probab=94.79  E-value=0.052  Score=57.49  Aligned_cols=116  Identities=16%  Similarity=0.160  Sum_probs=62.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCcccc--CCcceeEEEEeCC-----CCCHH-HHHHHHHHHhCCCCCccccCCCCHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVK--FYFDCHAWVRVSN-----FYNFK-RILDDIMKSLMPTSSWLKIMGKDYKSE  184 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~--~~F~~~~wv~~~~-----~~~~~-~~~~~i~~~l~~~~~~~~~~~~~~~~~  184 (348)
                      .-+.|+|.+|.||||+.+.++-....+  ..=+..+++.+..     .+.-. .+..-+...+....        ...+.
T Consensus       223 ~~~~Ilg~pGsGKTtfl~~lA~~~~~~~~~~~~vpi~~~l~~~~~~~~~~~q~~~~~~l~~~~~~~~--------~~~~~  294 (824)
T COG5635         223 AKLLILGAPGSGKTTFLQRLALWLAQRTLEPEDVPIFLLLNAFALARKFEKQLSLIDYLAEELFSQG--------IAKQL  294 (824)
T ss_pred             hheeeecCCCCCceehHHHHHHHhccCcCCcccCceeeechhHHHhhhhHhhccHHHHHHHHHhccC--------Ccchh
Confidence            368899999999999998876442111  2223444543321     11111 23333333333221        11223


Q ss_pred             HHHHHHHhcCCeEEEEEeCCCCh------hhHHHHHhhCCCCCCCcEEEEEeCChhhhh
Q 040110          185 KTILRDYLTNKKYFTVLDDVWIE------KIWDDLREALPDNQIGSRALITVGPHNILT  237 (348)
Q Consensus       185 ~~~l~~~L~~kr~LlVLDdv~~~------~~~~~l~~~l~~~~~gskIlvTTR~~~v~~  237 (348)
                      .....+.++..++|+.+|.++..      .....+...++ .-+.+++|+|+|....-.
T Consensus       295 ~~~~~e~l~~g~~llLlDGlDe~~~~~~~~~~~~i~~f~~-~~~~~~~iltcR~~~~~~  352 (824)
T COG5635         295 IEAHQELLKTGKLLLLLDGLDELEPKNQRALIREINKFLQ-EYPDAQVLLTCRPDTYKE  352 (824)
T ss_pred             hHHHHHHHhccchhhHhhccchhhhhhHHHHHHHHHHHhh-hccCCeEEEEeccchhhh
Confidence            33336788899999999998653      11112222222 234788999998755443

>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase

Probab=94.78  E-value=0.27  Score=47.83  Aligned_cols=90  Identities=12%  Similarity=0.177  Sum_probs=49.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCCCCcc--ccCCCCHH------H
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPTSSWL--KIMGKDYK------S  183 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~------~  183 (348)
                      ..++|.|..|+|||||.+.+.+.  ...  +....+.++. ...+.++..+............  ........      .
T Consensus       146 q~~~I~G~sG~GKStLl~~I~~~--~~~--~~~vi~~iG~~~~ev~~~~~~~~~~~~~~~tvvv~~~s~~p~~~r~~~~~  221 (422)
T TIGR02546       146 QRIGIFAGAGVGKSTLLGMIARG--ASA--DVNVIALIGERGREVREFIEHHLGEEGRKRSVLVVSTSDRPSLERLKAAY  221 (422)
T ss_pred             CEEEEECCCCCChHHHHHHHhCC--CCC--CEEEEEEEccCCcCHHHHHHHHhccccccceEEEeccccCCHHHHHHHHH
Confidence            36799999999999999999876  222  2333333433 3455555555443322211110  11111111      1


Q ss_pred             HHHHHHHHh--cCCeEEEEEeCCCC
Q 040110          184 EKTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       184 ~~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      ..-.+.+++  .+++.|+++|++-.
T Consensus       222 ~a~~~AE~f~~~g~~Vl~~~Dsltr  246 (422)
T TIGR02546       222 TATAIAEYFRDQGKRVLLMMDSLTR  246 (422)
T ss_pred             HHHHHHHHHHHCCCcEEEEEeCchH
Confidence            222344444  46899999999953

>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]

Probab=94.78  E-value=0.027  Score=49.04  Aligned_cols=24  Identities=13%  Similarity=0.141  Sum_probs=20.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|+|+|+.|+||||+|+.+.+.
T Consensus         2 ~~iIglTG~igsGKStva~~~~~~   25 (201)
T COG0237           2 MLIIGLTGGIGSGKSTVAKILAEL   25 (201)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHHc
Confidence            468999999999999999987653

>CHL00059 atpA ATP synthase CF1 alpha subunit

Probab=94.76  E-value=0.12  Score=50.79  Aligned_cols=89  Identities=15%  Similarity=0.162  Sum_probs=49.4

Q ss_pred             EEEEECCCCCcHHHHHH-HHhcCccccCCcce-eEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCH-HHH---
Q 040110          114 VVAILDSRGFDKTAFAA-EIYNNNFVKFYFDC-HAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDY-KSE---  184 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~-~v~~~~~~~~~F~~-~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~-~~~---  184 (348)
                      .++|.|..|+|||+||. .+.+.  .  .-+. ++++-+++.. .+.++...+...=....+..  ...+... .+.   
T Consensus       143 R~~I~g~~g~GKt~Lal~~I~~q--~--~~dv~cV~~~IGer~rev~e~~~~l~~~~~l~~tvvV~atad~~~~~r~~ap  218 (485)
T CHL00059        143 RELIIGDRQTGKTAVATDTILNQ--K--GQNVICVYVAIGQKASSVAQVVTTLQERGAMEYTIVVAETADSPATLQYLAP  218 (485)
T ss_pred             EEEeecCCCCCHHHHHHHHHHhc--c--cCCeEEEEEEecCCchHHHHHHHHhhcccchhceEEEEeCCCCCHHHHHHHH
Confidence            47899999999999964 45555  2  2243 3677776554 55666666654322221110  1111111 110   


Q ss_pred             --HHHHHHHh--cCCeEEEEEeCCCC
Q 040110          185 --KTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       185 --~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                        .-.+.+++  +++++|||+||+-.
T Consensus       219 ~~a~aiAEyfr~~G~~VLlv~DdlTr  244 (485)
T CHL00059        219 YTGAALAEYFMYRGRHTLIIYDDLSK  244 (485)
T ss_pred             HHHhhHHHHHHHcCCCEEEEEcChhH
Confidence              11133333  47899999999954

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=94.76  E-value=0.28  Score=49.14  Aligned_cols=111  Identities=15%  Similarity=0.084  Sum_probs=0.0

Q ss_pred             EEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeC--------------------------CCCCHHHHHHHHHHHhC
Q 040110          115 VAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVS--------------------------NFYNFKRILDDIMKSLM  168 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~--------------------------~~~~~~~~~~~i~~~l~  168 (348)
                      |+|+|+.|+|||||.+.+...  .... .+.+.+..+                          .+.....-.+.++..++
T Consensus       351 iaiiG~NG~GKSTLlk~l~g~--~~~~-~G~v~~g~~v~igyf~Q~~~~l~~~~t~~d~l~~~~~~~~e~~~r~~L~~f~  427 (530)
T COG0488         351 IAIVGPNGAGKSTLLKLLAGE--LGPL-SGTVKVGETVKIGYFDQHRDELDPDKTVLEELSEGFPDGDEQEVRAYLGRFG  427 (530)
T ss_pred             EEEECCCCCCHHHHHHHHhhh--cccC-CceEEeCCceEEEEEEehhhhcCccCcHHHHHHhhCccccHHHHHHHHHHcC


Q ss_pred             CCCCc---cccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh---hhHHHHHhhCCCCCCCcEEEEE
Q 040110          169 PTSSW---LKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE---KIWDDLREALPDNQIGSRALIT  229 (348)
Q Consensus       169 ~~~~~---~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~---~~~~~l~~~l~~~~~gskIlvT  229 (348)
                      .+...   +-..-..-+...-.+...+-.+.=+||||.--|.   +..+.+...+.... |+.|+|+
T Consensus       428 F~~~~~~~~v~~LSGGEk~Rl~La~ll~~~pNvLiLDEPTNhLDi~s~~aLe~aL~~f~-Gtvl~VS  493 (530)
T COG0488         428 FTGEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPTNHLDIESLEALEEALLDFE-GTVLLVS  493 (530)
T ss_pred             CChHHHhCchhhcCHhHHHHHHHHHHhccCCCEEEEcCCCccCCHHHHHHHHHHHHhCC-CeEEEEe

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=94.75  E-value=0.11  Score=47.59  Aligned_cols=50  Identities=20%  Similarity=0.147  Sum_probs=35.3

Q ss_pred             cccccccccccHHHHHhhcCCC-CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.--..   +.++..+..- .......+-+++.+|.+|+||.-+++.++++
T Consensus        83 ~lfGQHla~---~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n  133 (344)
T KOG2170|consen   83 ALFGQHLAK---QLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAEN  133 (344)
T ss_pred             HhhchHHHH---HHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHH
Confidence            466755555   5555555311 1234567779999999999999999999877

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=94.75  E-value=0.027  Score=47.27  Aligned_cols=22  Identities=23%  Similarity=0.308  Sum_probs=20.5

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|.|.|+.|+||||+|+.+.+.
T Consensus         2 iI~i~G~~GSGKstia~~la~~   23 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEK   23 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999876

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.75  E-value=0.14  Score=48.93  Aligned_cols=88  Identities=13%  Similarity=0.164  Sum_probs=58.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEe-CCCCCHHHHHHHHHHHhCCCCCcc--ccCC-CCHH-----HH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRV-SNFYNFKRILDDIMKSLMPTSSWL--KIMG-KDYK-----SE  184 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~-~~~~~~~~~~~~i~~~l~~~~~~~--~~~~-~~~~-----~~  184 (348)
                      .++|..-+|+|||||.-++++.    ..+|..+-.-+ .+.-.+.+++.+.+..-+...+..  ...+ ....     ..
T Consensus       165 RiGIFAgsGVGKStLLgMiar~----t~aDv~ViaLIGERGREVrEFIE~~Lg~egl~rsViVvATSD~s~l~R~~aa~~  240 (441)
T COG1157         165 RIGIFAGSGVGKSTLLGMIARN----TEADVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESALMRLKAAFT  240 (441)
T ss_pred             eeEEEecCCCcHHHHHHHHhcc----ccCCEEEEEEeeccchhHHHHHHHhcchhhccceEEEEECCCCCHHHHHHHHHH
Confidence            5889999999999999999987    44564443333 345678888888887776654431  1111 1112     22


Q ss_pred             HHHHHHHhc--CCeEEEEEeCCC
Q 040110          185 KTILRDYLT--NKKYFTVLDDVW  205 (348)
Q Consensus       185 ~~~l~~~L~--~kr~LlVLDdv~  205 (348)
                      .-.+.++++  +|++||++|.+-
T Consensus       241 At~IAEyFRDqG~~VLL~mDSlT  263 (441)
T COG1157         241 ATTIAEYFRDQGKRVLLIMDSLT  263 (441)
T ss_pred             HHHHHHHHHhCCCeEEEEeecHH
Confidence            334666664  589999999983

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=94.75  E-value=0.16  Score=47.48  Aligned_cols=100  Identities=13%  Similarity=0.118  Sum_probs=53.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      ...+.|.|..|+||||+++.+...  +...++..--+++.....+.--...   .+...    ....   ....+.++..
T Consensus       148 ~~~ilI~G~tGSGKTTll~aL~~~--~~~~~~~~rivtIEd~~El~~~~~~---~v~~~----~~~~---~~~~~ll~~a  215 (319)
T PRK13894        148 HRNILVIGGTGSGKTTLVNAIINE--MVIQDPTERVFIIEDTGEIQCAAEN---YVQYH----TSID---VNMTALLKTT  215 (319)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHh--hhhcCCCceEEEEcCCCccccCCCC---EEEEe----cCCC---CCHHHHHHHH
Confidence            356788999999999999998865  2111111111223222211000000   00000    0011   1345567778


Q ss_pred             hcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCc
Q 040110          192 LTNKKYFTVLDDVWIEKIWDDLREALPDNQIGS  224 (348)
Q Consensus       192 L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gs  224 (348)
                      |+...=.||+..+.+.+.++.+ .....+..|+
T Consensus       216 LR~~PD~IivGEiR~~Ea~~~l-~A~~tGh~G~  247 (319)
T PRK13894        216 LRMRPDRILVGEVRGPEALDLL-MAWNTGHEGG  247 (319)
T ss_pred             hcCCCCEEEEeccCCHHHHHHH-HHHHcCCCce
Confidence            8888888999999988776644 4443434443

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=94.75  E-value=0.064  Score=46.12  Aligned_cols=23  Identities=22%  Similarity=0.104  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..|+|.|..|+||||+++.+.+.
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~   26 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKL   26 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999999877

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=94.72  E-value=0.07  Score=48.34  Aligned_cols=81  Identities=16%  Similarity=0.058  Sum_probs=43.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC--CHHHHHHHHHHHh--CCCCCccccCCCCHHHHHHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY--NFKRILDDIMKSL--MPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~--~~~~~~~~i~~~l--~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      +|+|.|.+|+||||++..+........  .....++...-+  +-...-..+....  +.+-+-.+++..+.+.+.+.++
T Consensus         1 IIgItG~SGSGKTTv~~~l~~~l~~~g--~~v~vI~~D~yyr~~r~~~~~~~~~a~~~~~nfdHf~PeAnd~dlL~~~l~   78 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHIFAREG--IHPAVVEGDSFHRYERMEMKMAIAEALDAGRNFSHFGPEANLFDLLEELFR   78 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhcC--CceEEEeccccccCCchhHHHHHHHHhhcCCCCCCCCcccccHHHHHHHHH
Confidence            589999999999999998876521111  112333322211  2222222222221  1111100245677888888888


Q ss_pred             HHhcCCe
Q 040110          190 DYLTNKK  196 (348)
Q Consensus       190 ~~L~~kr  196 (348)
                      .+.+++.
T Consensus        79 ~L~~g~~   85 (277)
T cd02029          79 TYGETGR   85 (277)
T ss_pred             HHHcCCC
Confidence            8877653

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>PRK14532 adenylate kinase; Provisional

Probab=94.71  E-value=0.024  Score=48.66  Aligned_cols=21  Identities=10%  Similarity=0.156  Sum_probs=19.2

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.+.|++|+||||+|+.+...
T Consensus         3 i~~~G~pGsGKsT~a~~la~~   23 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVEE   23 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            668999999999999999876

>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional

Probab=94.71  E-value=0.38  Score=47.95  Aligned_cols=23  Identities=22%  Similarity=0.313  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|..|.|||||++.++..
T Consensus        51 EivgIiGpNGSGKSTLLkiLaGL   73 (549)
T PRK13545         51 EIVGIIGLNGSGKSTLSNLIAGV   73 (549)
T ss_pred             CEEEEEcCCCCCHHHHHHHHhCC
Confidence            47999999999999999999876

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=94.71  E-value=0.026  Score=45.53  Aligned_cols=23  Identities=22%  Similarity=0.339  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|..|+|||||.+.++..
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~g~   34 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALAGL   34 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CEEEEEccCCCccccceeeeccc
Confidence            47899999999999999998766

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=94.70  E-value=0.1  Score=50.51  Aligned_cols=90  Identities=16%  Similarity=0.168  Sum_probs=48.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHH------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKS------  183 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~------  183 (348)
                      ..++|+|..|+|||||++.+.+..  ..  +..+..-++... .+.++..+.+.+-+......  ...+.....      
T Consensus       138 qri~I~G~sG~GKTtLl~~i~~~~--~~--~~gvi~~~Ger~~ev~e~~~~~l~~~~~~~~v~v~~tsd~~~~~r~~~~~  213 (413)
T TIGR03497       138 QRVGIFAGSGVGKSTLLGMIARNA--KA--DINVIALIGERGREVRDFIEKDLGEEGLKRSVVVVATSDQPALMRLKAAF  213 (413)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC--CC--CeEEEEEEccchHHHHHHHHHHhcccccceEEEEEECCCCCHHHHHHHHH
Confidence            478999999999999999888762  22  222223344332 45555555444322111110  111111111      


Q ss_pred             HHHHHHHHh--cCCeEEEEEeCCCC
Q 040110          184 EKTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       184 ~~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      ..-.+.+++  +++++||++||+-.
T Consensus       214 ~a~tiAEyfr~~G~~Vll~~Dsltr  238 (413)
T TIGR03497       214 TATAIAEYFRDQGKDVLLMMDSVTR  238 (413)
T ss_pred             HHHHHHHHHHHCCCCEEEEEcCcHH
Confidence            112234444  47899999999843

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=94.70  E-value=0.025  Score=49.52  Aligned_cols=24  Identities=17%  Similarity=0.343  Sum_probs=21.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .-|.++|++|+|||||+.++.++.
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~~   29 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGDE   29 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcCc
Confidence            457899999999999999998774

>PLN02796 D-glycerate 3-kinase

Probab=94.69  E-value=0.082  Score=49.70  Aligned_cols=26  Identities=19%  Similarity=0.183  Sum_probs=23.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+-+++|.|..|+|||||++.+...
T Consensus        98 ~~pliIGI~G~sGSGKSTLa~~L~~l  123 (347)
T PLN02796         98 IPPLVIGISAPQGCGKTTLVFALVYL  123 (347)
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHH
Confidence            35678999999999999999999877

>TIGR00750 lao LAO/AO transport system ATPase

Probab=94.69  E-value=0.045  Score=50.81  Aligned_cols=37  Identities=16%  Similarity=0.150  Sum_probs=28.4

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+++.+.    .......+++|.|++|+|||||+..+...
T Consensus        21 ~~~~~~~~----~~~~~~~~i~i~G~~G~GKttl~~~l~~~   57 (300)
T TIGR00750        21 KQLLDRIM----PYTGNAHRVGITGTPGAGKSTLLEALGME   57 (300)
T ss_pred             HHHHHhCC----cccCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            45555554    23456789999999999999999998765

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=94.68  E-value=0.05  Score=51.09  Aligned_cols=37  Identities=16%  Similarity=0.159  Sum_probs=28.4

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+++.+.    ....+..+|+|.|.+|+|||||+..+...
T Consensus        43 ~~l~~~~~----~~~~~~~~igi~G~~GaGKSTl~~~l~~~   79 (332)
T PRK09435         43 QELLDALL----PHTGNALRIGITGVPGVGKSTFIEALGMH   79 (332)
T ss_pred             HHHHHHHh----hcCCCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            45666555    22346779999999999999999987766

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=94.65  E-value=0.33  Score=50.56  Aligned_cols=23  Identities=22%  Similarity=0.228  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++|+|..|+|||||++.+..-
T Consensus       492 ~~iaIvG~sGsGKSTLlklL~gl  514 (694)
T TIGR03375       492 EKVAIIGRIGSGKSTLLKLLLGL  514 (694)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            47899999999999999998755

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=94.65  E-value=0.028  Score=51.55  Aligned_cols=23  Identities=13%  Similarity=0.182  Sum_probs=19.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++++|+|-||+||||+|..++..
T Consensus         2 ~~i~~~gKGGVGKTT~a~nLA~~   24 (279)
T PRK13230          2 RKFCFYGKGGIGKSTTVCNIAAA   24 (279)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH
Confidence            57889999999999988877654

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.64  E-value=0.46  Score=43.38  Aligned_cols=101  Identities=14%  Similarity=0.151  Sum_probs=52.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      +..+++++|.+|+||||++..+......+ . ..+.+++..... ....-++.....++.+    .....+...+...+.
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l~~~-~-~~v~~i~~D~~ri~~~~ql~~~~~~~~~~----~~~~~~~~~l~~~l~  147 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFHGK-K-KTVGFITTDHSRIGTVQQLQDYVKTIGFE----VIAVRDEAAMTRALT  147 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHHHc-C-CeEEEEecCCCCHHHHHHHHHHhhhcCce----EEecCCHHHHHHHHH
Confidence            34689999999999999999887652111 1 134455443221 2222333444444433    222235555554444


Q ss_pred             HHhc-CCeEEEEEeCCCC----hhhHHHHHhhC
Q 040110          190 DYLT-NKKYFTVLDDVWI----EKIWDDLREAL  217 (348)
Q Consensus       190 ~~L~-~kr~LlVLDdv~~----~~~~~~l~~~l  217 (348)
                      ..-+ .+.=++++|..-.    ...++++...+
T Consensus       148 ~l~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~  180 (270)
T PRK06731        148 YFKEEARVDYILIDTAGKNYRASETVEEMIETM  180 (270)
T ss_pred             HHHhcCCCCEEEEECCCCCcCCHHHHHHHHHHH
Confidence            3322 2456777787643    23455554443

>PRK06761 hypothetical protein; Provisional

Probab=94.63  E-value=0.059  Score=49.37  Aligned_cols=24  Identities=21%  Similarity=0.239  Sum_probs=21.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      +++.|.|++|+||||+++.+++..
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L   27 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDIL   27 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhc
Confidence            478899999999999999999883

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=94.63  E-value=0.11  Score=51.91  Aligned_cols=103  Identities=15%  Similarity=0.210  Sum_probs=58.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      +.=|.++|++|+|||-||++|+|.  -.-.|     +++..+    +++....   |          .+....-..+++.
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVANE--ag~NF-----isVKGP----ELlNkYV---G----------ESErAVR~vFqRA  600 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVANE--AGANF-----ISVKGP----ELLNKYV---G----------ESERAVRQVFQRA  600 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhhh--ccCce-----EeecCH----HHHHHHh---h----------hHHHHHHHHHHHh
Confidence            444678999999999999999998  33333     444332    2222211   1          1223333334444


Q ss_pred             hcCCeEEEEEeCCCCh-------------hhHHHHHhhCCCCC--CCcEEEEEeCChhhhhh
Q 040110          192 LTNKKYFTVLDDVWIE-------------KIWDDLREALPDNQ--IGSRALITVGPHNILTS  238 (348)
Q Consensus       192 L~~kr~LlVLDdv~~~-------------~~~~~l~~~l~~~~--~gskIlvTTR~~~v~~~  238 (348)
                      -..-.+.|.+|.++..             ...++++..+-...  .|--||-.|...++-..
T Consensus       601 R~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDp  662 (802)
T KOG0733|consen  601 RASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDP  662 (802)
T ss_pred             hcCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccch
Confidence            4557999999998631             23455555554322  34445555555555443

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=94.63  E-value=0.11  Score=49.40  Aligned_cols=107  Identities=17%  Similarity=0.162  Sum_probs=59.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      .++=+-|||..|.|||.|+-..|+...++..-  +        .....+..++-+.+.....    .    ......+.+
T Consensus        61 ~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~--R--------~HFh~Fm~~vh~~l~~~~~----~----~~~l~~va~  122 (362)
T PF03969_consen   61 PPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKR--R--------VHFHEFMLDVHSRLHQLRG----Q----DDPLPQVAD  122 (362)
T ss_pred             CCceEEEECCCCCchhHHHHHHHHhCCccccc--c--------ccccHHHHHHHHHHHHHhC----C----CccHHHHHH
Confidence            34557789999999999999999885432210  0        0111233333333322100    0    112344455


Q ss_pred             HhcCCeEEEEEeCCCChh-----hHHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          191 YLTNKKYFTVLDDVWIEK-----IWDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       191 ~L~~kr~LlVLDdv~~~~-----~~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      .+.++..||.||.+.-.+     -+..+...+.  ..|. |||+|-|......
T Consensus       123 ~l~~~~~lLcfDEF~V~DiaDAmil~rLf~~l~--~~gv-vlVaTSN~~P~~L  172 (362)
T PF03969_consen  123 ELAKESRLLCFDEFQVTDIADAMILKRLFEALF--KRGV-VLVATSNRPPEDL  172 (362)
T ss_pred             HHHhcCCEEEEeeeeccchhHHHHHHHHHHHHH--HCCC-EEEecCCCChHHH
Confidence            666777899999875432     2333334332  2343 7777777766665

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=94.61  E-value=0.39  Score=44.92  Aligned_cols=24  Identities=21%  Similarity=0.241  Sum_probs=20.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+.++|+.|+||+++|..+++.
T Consensus        26 ~HA~Lf~Gp~G~GK~~lA~~lA~~   49 (319)
T PRK08769         26 GHGLLICGPEGLGKRAVALALAEH   49 (319)
T ss_pred             ceeEeeECCCCCCHHHHHHHHHHH
Confidence            345778999999999999888765

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=94.61  E-value=0.049  Score=49.97  Aligned_cols=92  Identities=11%  Similarity=0.045  Sum_probs=49.3

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccc---cCCCCHHHHH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLK---IMGKDYKSEK  185 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~---~~~~~~~~~~  185 (348)
                      ..+..++.|.|.+|+|||||...+.+.  ........+.  .....+..+  .+.++..+.+.-...   .-..+...+.
T Consensus       101 ~~~~~~v~l~G~pGsGKTTLl~~l~~~--l~~~~~~~VI--~gD~~t~~D--a~rI~~~g~pvvqi~tG~~Chl~a~mv~  174 (290)
T PRK10463        101 ARKQLVLNLVSSPGSGKTTLLTETLMR--LKDSVPCAVI--EGDQQTVND--AARIRATGTPAIQVNTGKGCHLDAQMIA  174 (290)
T ss_pred             hcCCeEEEEECCCCCCHHHHHHHHHHH--hccCCCEEEE--CCCcCcHHH--HHHHHhcCCcEEEecCCCCCcCcHHHHH
Confidence            456889999999999999999999887  4433332222  122122222  222344433211100   0012333344


Q ss_pred             HHHHHHhcCCeEEEEEeCCCC
Q 040110          186 TILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       186 ~~l~~~L~~kr~LlVLDdv~~  206 (348)
                      ..+........-+||++++-+
T Consensus       175 ~Al~~L~~~~~d~liIEnvGn  195 (290)
T PRK10463        175 DAAPRLPLDDNGILFIENVGN  195 (290)
T ss_pred             HHHHHHhhcCCcEEEEECCCC
Confidence            445444444456778898854

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=94.61  E-value=0.25  Score=46.58  Aligned_cols=47  Identities=17%  Similarity=0.190  Sum_probs=34.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIM  164 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~  164 (348)
                      .++|.|..|+|||+|++++.+..    +-+.++++-++... .+.+++.++-
T Consensus       159 r~~I~G~~G~GKT~L~~~Iak~~----~~dvvVyv~iGERg~Ev~e~l~ef~  206 (369)
T cd01134         159 TAAIPGPFGCGKTVIQQSLSKYS----NSDIVIYVGCGERGNEMTEVLEEFP  206 (369)
T ss_pred             EEEEECCCCCChHHHHHHHHhCC----CCCEEEEEEeCCChHHHHHHHHHHH
Confidence            68899999999999999999872    22467778776554 4555666653

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.

>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase

Probab=94.60  E-value=0.028  Score=49.32  Aligned_cols=23  Identities=17%  Similarity=0.290  Sum_probs=18.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|+|.|-||+||||++..++..
T Consensus         1 ~~iav~gKGGvGKTt~~~nLA~~   23 (212)
T cd02117           1 RQIAIYGKGGIGKSTTSQNLSAA   23 (212)
T ss_pred             CEEEEECCCcCcHHHHHHHHHHH
Confidence            46889999999999988776544

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=94.60  E-value=0.18  Score=46.84  Aligned_cols=90  Identities=13%  Similarity=0.101  Sum_probs=51.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcc-eeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFD-CHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~-~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      ..+.|.|..|+||||++..+.+.  +....+ .++ +++.....+   .-.--..+..     .. ..........++..
T Consensus       133 ~~ilI~G~tGSGKTTll~al~~~--i~~~~~~~ri-~tiEd~~El---~~~~~~~v~~-----~~-~~~~~~~~~~l~~a  200 (299)
T TIGR02782       133 KNILVVGGTGSGKTTLANALLAE--IAKNDPTDRV-VIIEDTREL---QCAAPNVVQL-----RT-SDDAISMTRLLKAT  200 (299)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--hhccCCCceE-EEECCchhh---cCCCCCEEEE-----Ee-cCCCCCHHHHHHHH
Confidence            35679999999999999999876  332211 222 233322111   0000000000     00 01112556678888


Q ss_pred             hcCCeEEEEEeCCCChhhHHHHH
Q 040110          192 LTNKKYFTVLDDVWIEKIWDDLR  214 (348)
Q Consensus       192 L~~kr~LlVLDdv~~~~~~~~l~  214 (348)
                      |+...=.+|+..+.+.+.++.+.
T Consensus       201 LR~~pD~iivGEiR~~ea~~~l~  223 (299)
T TIGR02782       201 LRLRPDRIIVGEVRGGEALDLLK  223 (299)
T ss_pred             hcCCCCEEEEeccCCHHHHHHHH
Confidence            88888888999999887666543

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PRK08356 hypothetical protein; Provisional

Probab=94.60  E-value=0.037  Score=47.90  Aligned_cols=21  Identities=19%  Similarity=0.151  Sum_probs=19.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHh
Q 040110          113 SVVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~  133 (348)
                      .+++|.|++|+||||+|+.+.
T Consensus         6 ~~i~~~G~~gsGK~t~a~~l~   26 (195)
T PRK08356          6 MIVGVVGKIAAGKTTVAKFFE   26 (195)
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            578999999999999999994

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=94.60  E-value=0.031  Score=52.79  Aligned_cols=44  Identities=20%  Similarity=0.252  Sum_probs=36.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+||.++.+   ..|...+.      ++...-+.|.|..|+||||+|+.+++-
T Consensus        18 ~ivGq~~~k---~al~~~~~------~p~~~~vli~G~~GtGKs~~ar~~~~~   61 (350)
T CHL00081         18 AIVGQEEMK---LALILNVI------DPKIGGVMIMGDRGTGKSTTIRALVDL   61 (350)
T ss_pred             HHhChHHHH---HHHHHhcc------CCCCCeEEEEcCCCCCHHHHHHHHHHH
Confidence            899999988   88887777      345555669999999999999998654

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=94.60  E-value=0.15  Score=49.61  Aligned_cols=23  Identities=17%  Similarity=0.330  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++|.|..|+|||||+..+...
T Consensus       158 q~~~i~G~sG~GKStLl~~i~~~  180 (434)
T PRK08472        158 QKLGIFAGSGVGKSTLMGMIVKG  180 (434)
T ss_pred             CEEEEECCCCCCHHHHHHHHhhc
Confidence            36899999999999999999876

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=94.59  E-value=0.24  Score=47.95  Aligned_cols=90  Identities=13%  Similarity=0.147  Sum_probs=49.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHH------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKS------  183 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~------  183 (348)
                      ..++|+|..|+|||||+..+.+..  ..  +..+...++... .+.++...+...=.......  ...+.....      
T Consensus       138 q~~~I~G~sG~GKTtLl~~I~~~~--~~--~~~vi~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~a~~  213 (411)
T TIGR03496       138 QRMGIFAGSGVGKSTLLGMMARYT--EA--DVVVVGLIGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLRAAF  213 (411)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCC--CC--CEEEEEEEecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHHHHH
Confidence            368999999999999999888762  21  234444555433 34455555443321111110  111111111      


Q ss_pred             HHHHHHHHh--cCCeEEEEEeCCCC
Q 040110          184 EKTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       184 ~~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                      ..-.+.+++  +++++||++||+-.
T Consensus       214 ~a~tiAEyfr~~G~~Vll~~Dsltr  238 (411)
T TIGR03496       214 YATAIAEYFRDQGKDVLLLMDSLTR  238 (411)
T ss_pred             HHHHHHHHHHHCCCCEEEEEeChHH
Confidence            112233444  57899999999843

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=94.59  E-value=0.036  Score=45.73  Aligned_cols=23  Identities=17%  Similarity=0.371  Sum_probs=20.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .|+++|.+|+|||||+..+.+..
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~~~   24 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMYDE   24 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            37899999999999999998653

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=94.59  E-value=0.083  Score=50.26  Aligned_cols=117  Identities=15%  Similarity=0.125  Sum_probs=60.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcc-eeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD-CHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~-~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      -..+.|+|+.|+||||++..+.+.  +....+ ...-+++..+...  .+..+......-..  .....+.......++.
T Consensus       134 ~glilI~GpTGSGKTTtL~aLl~~--i~~~~~~~~~Ivt~EdpiE~--~~~~~~~~~~~v~Q--~~v~~~~~~~~~~l~~  207 (358)
T TIGR02524       134 EGIVFITGATGSGKSTLLAAIIRE--LAEAPDSHRKILTYEAPIEF--VYDEIETISASVCQ--SEIPRHLNNFAAGVRN  207 (358)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH--HhhcCCCCcEEEEeCCCceE--eccccccccceeee--eeccccccCHHHHHHH
Confidence            468999999999999999998766  322222 1111222222110  01111000000000  0001122345566777


Q ss_pred             HhcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhh
Q 040110          191 YLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILT  237 (348)
Q Consensus       191 ~L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~  237 (348)
                      .|+...-.+++..+.+.+..........   .|-.|+-|--..++..
T Consensus       208 aLR~~Pd~i~vGEiRd~et~~~al~aa~---tGh~v~tTlHa~~~~~  251 (358)
T TIGR02524       208 ALRRKPHAILVGEARDAETISAALEAAL---TGHPVYTTLHSSGVAE  251 (358)
T ss_pred             HhccCCCEEeeeeeCCHHHHHHHHHHHH---cCCcEEEeeccCCHHH
Confidence            8888888999999988766654433322   2444555555444443

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=94.58  E-value=0.026  Score=47.03  Aligned_cols=33  Identities=12%  Similarity=0.115  Sum_probs=24.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEE
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAW  147 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~w  147 (348)
                      +++|+|+.|+|||||+..+....+- ..+...+.
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~l~~-~G~~V~vi   33 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKALKA-RGYRVATI   33 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHh-cCCeEEEE
Confidence            5789999999999999999887322 23444433

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=94.58  E-value=0.034  Score=52.37  Aligned_cols=44  Identities=18%  Similarity=0.220  Sum_probs=34.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+||.+..+   ..++-.+.      ++...-+.|.|..|+|||||++.+..-
T Consensus         5 ~ivgq~~~~---~al~~~~~------~~~~g~vli~G~~G~gKttl~r~~~~~   48 (337)
T TIGR02030         5 AIVGQDEMK---LALLLNVI------DPKIGGVMVMGDRGTGKSTAVRALAAL   48 (337)
T ss_pred             ccccHHHHH---HHHHHHhc------CCCCCeEEEEcCCCCCHHHHHHHHHHh
Confidence            678988888   88776666      333445779999999999999999754

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=94.58  E-value=0.051  Score=54.55  Aligned_cols=44  Identities=27%  Similarity=0.371  Sum_probs=34.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+..      ....-+.|+|++|+|||++|+.+++.
T Consensus        66 ~iiGqs~~i---~~l~~al~~------~~~~~vLi~Ge~GtGKt~lAr~i~~~  109 (531)
T TIGR02902        66 EIIGQEEGI---KALKAALCG------PNPQHVIIYGPPGVGKTAAARLVLEE  109 (531)
T ss_pred             HeeCcHHHH---HHHHHHHhC------CCCceEEEECCCCCCHHHHHHHHHHH
Confidence            799999999   888877661      22234568999999999999999764

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>TIGR01026 fliI_yscN ATPase FliI/YscN family

Probab=94.58  E-value=0.11  Score=50.67  Aligned_cols=89  Identities=13%  Similarity=0.174  Sum_probs=46.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCCCCcc--ccCCCCHH------H
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPTSSWL--KIMGKDYK------S  183 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~~~~~--~~~~~~~~------~  183 (348)
                      ..++|.|..|+|||||++.+.+..  . . +..+...++. .-.+.++..+.+..-.......  ...+....      .
T Consensus       164 q~~~I~G~sG~GKStLl~~I~~~~--~-~-~~~vi~~iG~r~~ev~~~~~~~~~~~~l~~tvvv~~~~d~~p~~r~~~~~  239 (440)
T TIGR01026       164 QRIGIFAGSGVGKSTLLGMIARNT--E-A-DVNVIALIGERGREVREFIEHDLGEEGLKRSVVVVATSDQSPLLRLKGAY  239 (440)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC--C-C-CEEEEEEEeecchHHHHHHHHHhcccccceEEEEEECCCCCHHHHHHHHH
Confidence            367999999999999999988762  2 1 2223333333 2244444444333211111000  11111111      1


Q ss_pred             HHHHHHHHh--cCCeEEEEEeCCC
Q 040110          184 EKTILRDYL--TNKKYFTVLDDVW  205 (348)
Q Consensus       184 ~~~~l~~~L--~~kr~LlVLDdv~  205 (348)
                      ..-.+.+++  +++++||++||+-
T Consensus       240 ~a~t~AE~frd~G~~Vll~~DslT  263 (440)
T TIGR01026       240 VATAIAEYFRDQGKDVLLLMDSVT  263 (440)
T ss_pred             HHHHHHHHHHHCCCCEEEEEeChH
Confidence            112233444  5789999999984

This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=94.58  E-value=0.21  Score=41.74  Aligned_cols=20  Identities=25%  Similarity=0.325  Sum_probs=18.4

Q ss_pred             EEEEEECCCCCcHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEI  132 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v  132 (348)
                      ++..|+|+.|.|||++.+.+
T Consensus        22 ~~~~i~G~NgsGKS~~l~~i   41 (162)
T cd03227          22 SLTIITGPNGSGKSTILDAI   41 (162)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            68899999999999999886

These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.

>smart00072 GuKc Guanylate kinase homologues

Probab=94.57  E-value=0.039  Score=47.23  Aligned_cols=23  Identities=17%  Similarity=0.323  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.+.|+|++|+||+||+..+...
T Consensus         3 r~ivl~Gpsg~GK~tl~~~L~~~   25 (184)
T smart00072        3 RPIVLSGPSGVGKGTLLAELIQE   25 (184)
T ss_pred             cEEEEECCCCCCHHHHHHHHHhc
Confidence            57889999999999999999887

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=94.57  E-value=0.19  Score=50.32  Aligned_cols=91  Identities=10%  Similarity=0.038  Sum_probs=55.6

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-----------ccCC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-----------KIMG  178 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-----------~~~~  178 (348)
                      +.-.++.|.|.+|+|||+||.++....  ...-..++|++....  ..++...+ ..++.+....           ....
T Consensus       271 ~~g~~~li~G~~G~GKT~l~~~~~~~~--~~~g~~~~yis~e~~--~~~i~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~  345 (509)
T PRK09302        271 FRGSIILVSGATGTGKTLLASKFAEAA--CRRGERCLLFAFEES--RAQLIRNA-RSWGIDLEKMEEKGLLKIICARPES  345 (509)
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHHH--HhCCCcEEEEEecCC--HHHHHHHH-HHcCCChHHHhhcCCceeecCCccc
Confidence            345678889999999999999987662  222246778776543  44444443 4444321110           1122


Q ss_pred             CCHHHHHHHHHHHhcC-CeEEEEEeCCC
Q 040110          179 KDYKSEKTILRDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       179 ~~~~~~~~~l~~~L~~-kr~LlVLDdv~  205 (348)
                      ...++....+.+.+.. +.-++|+|.+.
T Consensus       346 ~~~~~~~~~i~~~i~~~~~~~vVIDslt  373 (509)
T PRK09302        346 YGLEDHLIIIKREIEEFKPSRVAIDPLS  373 (509)
T ss_pred             CCHHHHHHHHHHHHHHcCCCEEEEcCHH
Confidence            3445666677776644 55689999984

>PRK13409 putative ATPase RIL; Provisional

Probab=94.55  E-value=0.28  Score=50.03  Aligned_cols=125  Identities=12%  Similarity=0.066  Sum_probs=63.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccC-C--cce-eEEEEeC----CCCCHHHH-------------HHHHHHHhCCCC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKF-Y--FDC-HAWVRVS----NFYNFKRI-------------LDDIMKSLMPTS  171 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~--F~~-~~wv~~~----~~~~~~~~-------------~~~i~~~l~~~~  171 (348)
                      .+++|+|+.|+|||||++.++....... .  ++. +.++.-.    ...++.+.             ..++++.++...
T Consensus       366 eiv~l~G~NGsGKSTLlk~L~Gl~~p~~G~I~~~~~i~y~~Q~~~~~~~~tv~e~l~~~~~~~~~~~~~~~~L~~l~l~~  445 (590)
T PRK13409        366 EVIGIVGPNGIGKTTFAKLLAGVLKPDEGEVDPELKISYKPQYIKPDYDGTVEDLLRSITDDLGSSYYKSEIIKPLQLER  445 (590)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCCCceEEEEeeeEEEecccccCCCCCcHHHHHHHHhhhcChHHHHHHHHHHCCCHH
Confidence            4899999999999999999987622111 0  111 1111110    11122222             233444444321


Q ss_pred             Cc-cccCCCCHHHHHH-HHHHHhcCCeEEEEEeCCCCh---h---hHHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          172 SW-LKIMGKDYKSEKT-ILRDYLTNKKYFTVLDDVWIE---K---IWDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       172 ~~-~~~~~~~~~~~~~-~l~~~L~~kr~LlVLDdv~~~---~---~~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      .. .....-+..+.+. .|...|....-+++||.--+.   .   ....+...+.. ..|..||++|.+...+..
T Consensus       446 ~~~~~~~~LSGGe~QRvaiAraL~~~p~llLLDEPt~~LD~~~~~~l~~~l~~l~~-~~g~tviivsHD~~~~~~  519 (590)
T PRK13409        446 LLDKNVKDLSGGELQRVAIAACLSRDADLYLLDEPSAHLDVEQRLAVAKAIRRIAE-EREATALVVDHDIYMIDY  519 (590)
T ss_pred             HHhCCcccCCHHHHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHH-hCCCEEEEEeCCHHHHHH
Confidence            00 0112223333332 356667778899999987643   2   22222222222 124568888888765554

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=94.55  E-value=0.024  Score=51.03  Aligned_cols=21  Identities=19%  Similarity=0.422  Sum_probs=19.3

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|++|+||||+|+.+...
T Consensus         2 Ivl~G~pGSGKST~a~~La~~   22 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKK   22 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            678999999999999999876

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=94.54  E-value=0.03  Score=51.78  Aligned_cols=23  Identities=17%  Similarity=0.320  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++.+.|++|+||||+|+.+...
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~   25 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAK   25 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHH
Confidence            46788999999999999999876

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=94.54  E-value=0.18  Score=52.91  Aligned_cols=139  Identities=10%  Similarity=0.026  Sum_probs=83.8

Q ss_pred             cccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHH
Q 040110           87 LQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKS  166 (348)
Q Consensus        87 r~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~  166 (348)
                      -....   .+|.+.+.        ...|+.|.|..|+||||-.-+.+-+.-.  .....+=++-.+......+...+++.
T Consensus        51 v~~~~---~~i~~ai~--------~~~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAee  117 (845)
T COG1643          51 VTAVR---DEILKAIE--------QNQVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEE  117 (845)
T ss_pred             cHHHH---HHHHHHHH--------hCCEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHH
Confidence            34455   77778777        4558889999999999976665544111  22234444444455667888899999


Q ss_pred             hCCCCCcc---------------ccCCCCHHHHHHHHH-HHhcCCeEEEEEeCCCChh-hH----HHHHhhCCCCCCCcE
Q 040110          167 LMPTSSWL---------------KIMGKDYKSEKTILR-DYLTNKKYFTVLDDVWIEK-IW----DDLREALPDNQIGSR  225 (348)
Q Consensus       167 l~~~~~~~---------------~~~~~~~~~~~~~l~-~~L~~kr~LlVLDdv~~~~-~~----~~l~~~l~~~~~gsk  225 (348)
                      ++.+..+.               ...-.+...+...++ ..+-.+=-.+|+|.+.+.. +-    ..++..++....--|
T Consensus       118 l~~~~G~~VGY~iRfe~~~s~~Trik~mTdGiLlrei~~D~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLK  197 (845)
T COG1643         118 LGEKLGETVGYSIRFESKVSPRTRIKVMTDGILLREIQNDPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLK  197 (845)
T ss_pred             hCCCcCceeeEEEEeeccCCCCceeEEeccHHHHHHHhhCcccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCce
Confidence            98763320               122234555655555 3334456678899997642 11    222222222222479


Q ss_pred             EEEEeCChhhhhh
Q 040110          226 ALITVGPHNILTS  238 (348)
Q Consensus       226 IlvTTR~~~v~~~  238 (348)
                      |||+|=.-+..+.
T Consensus       198 iIimSATld~~rf  210 (845)
T COG1643         198 LIIMSATLDAERF  210 (845)
T ss_pred             EEEEecccCHHHH
Confidence            9999887776655

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=94.53  E-value=0.034  Score=51.77  Aligned_cols=22  Identities=23%  Similarity=0.211  Sum_probs=18.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      +++.+.|-||+||||+|.+++-
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~   23 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALAL   23 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCcHHHHHHHHH
Confidence            5788999999999999977654

...

>PF13245 AAA_19: Part of AAA domain

Probab=94.53  E-value=0.038  Score=40.09  Aligned_cols=22  Identities=18%  Similarity=0.154  Sum_probs=16.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHh
Q 040110          112 HSVVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~  133 (348)
                      .+++.|.|++|.|||+++....
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i   31 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARI   31 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHH
Confidence            4467789999999995554443

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=94.52  E-value=0.057  Score=43.08  Aligned_cols=50  Identities=12%  Similarity=0.109  Sum_probs=33.4

Q ss_pred             cccccccccccHHHHHhhcCCC-CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|..-..   +.+++.|..- .......+-|++.+|.+|+|||.+++.+++.
T Consensus        26 ~l~GQhla~---~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   26 NLFGQHLAV---EVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HccCcHHHH---HHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            466655444   4444444210 0134566789999999999999988888766

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=94.50  E-value=0.39  Score=45.10  Aligned_cols=25  Identities=24%  Similarity=0.224  Sum_probs=20.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -...+.++|+.|+||||+|..+...
T Consensus        20 ~~hA~Lf~G~~G~GK~~la~~~a~~   44 (325)
T PRK08699         20 RPNAWLFAGKKGIGKTAFARFAAQA   44 (325)
T ss_pred             cceEEEeECCCCCCHHHHHHHHHHH
Confidence            3446778999999999999988765

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.50  E-value=0.22  Score=48.07  Aligned_cols=21  Identities=24%  Similarity=0.346  Sum_probs=19.2

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.++|++|.|||++..+++|.
T Consensus       238 YLLYGPPGTGKSS~IaAmAn~  258 (457)
T KOG0743|consen  238 YLLYGPPGTGKSSFIAAMANY  258 (457)
T ss_pred             ceeeCCCCCCHHHHHHHHHhh
Confidence            457999999999999999988

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=94.50  E-value=0.044  Score=51.55  Aligned_cols=64  Identities=14%  Similarity=0.083  Sum_probs=44.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++|.++..   ..+...+.      ..+  -+.+.|.+|+|||+||+.++..  ....   ..++.+.......++...
T Consensus        25 ~~~g~~~~~---~~~l~a~~------~~~--~vll~G~PG~gKT~la~~lA~~--l~~~---~~~i~~t~~l~p~d~~G~   88 (329)
T COG0714          25 VVVGDEEVI---ELALLALL------AGG--HVLLEGPPGVGKTLLARALARA--LGLP---FVRIQCTPDLLPSDLLGT   88 (329)
T ss_pred             eeeccHHHH---HHHHHHHH------cCC--CEEEECCCCccHHHHHHHHHHH--hCCC---eEEEecCCCCCHHHhcCc
Confidence            588888888   77777776      122  3668999999999999999988  4433   345555666665554433

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=94.48  E-value=0.031  Score=47.05  Aligned_cols=22  Identities=18%  Similarity=0.324  Sum_probs=20.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.|+|++|+||||+|+.+.+.
T Consensus         4 ~i~~~G~~GsGKst~~~~la~~   25 (171)
T PRK03731          4 PLFLVGARGCGKTTVGMALAQA   25 (171)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4778999999999999999977

>COG3638 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=94.48  E-value=0.083  Score=46.71  Aligned_cols=23  Identities=22%  Similarity=0.343  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..|+|+|++|.|||||.+.+..-
T Consensus        31 E~VaiIG~SGaGKSTLLR~lngl   53 (258)
T COG3638          31 EMVAIIGPSGAGKSTLLRSLNGL   53 (258)
T ss_pred             cEEEEECCCCCcHHHHHHHHhcc
Confidence            37899999999999999999875

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=94.46  E-value=0.28  Score=53.79  Aligned_cols=129  Identities=12%  Similarity=0.043  Sum_probs=68.3

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL  174 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~  174 (348)
                      ++|++.|.        +..++.|+|..|+||||..-.+.-.  ......+.+.++-.+......+...++..++......
T Consensus        73 ~~Il~~l~--------~~~vvii~g~TGSGKTTqlPq~lle--~~~~~~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~  142 (1283)
T TIGR01967        73 EDIAEAIA--------ENQVVIIAGETGSGKTTQLPKICLE--LGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEK  142 (1283)
T ss_pred             HHHHHHHH--------hCceEEEeCCCCCCcHHHHHHHHHH--cCCCCCceEecCCccHHHHHHHHHHHHHHhCCCcceE
Confidence            66777776        2347889999999999977655543  1111223343333333455667778888876542210


Q ss_pred             ---------------ccCCCCHHHHHHHHHH-HhcCCeEEEEEeCCCCh----hhH-HHHHhhCCCCCCCcEEEEEeCCh
Q 040110          175 ---------------KIMGKDYKSEKTILRD-YLTNKKYFTVLDDVWIE----KIW-DDLREALPDNQIGSRALITVGPH  233 (348)
Q Consensus       175 ---------------~~~~~~~~~~~~~l~~-~L~~kr~LlVLDdv~~~----~~~-~~l~~~l~~~~~gskIlvTTR~~  233 (348)
                                     .+.-.+..-+...+.. .+-++=-.||||.+...    +-. ..+...+.. .+..|+|++|=.-
T Consensus       143 VGY~vR~~~~~s~~T~I~~~TdGiLLr~l~~d~~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~-rpdLKlIlmSATl  221 (1283)
T TIGR01967       143 VGYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPR-RPDLKIIITSATI  221 (1283)
T ss_pred             EeeEEcCCcccCCCceeeeccccHHHHHhhhCcccccCcEEEEcCcchhhccchhHHHHHHHHHhh-CCCCeEEEEeCCc
Confidence                           0111233444444432 11123356889999752    111 122322222 2356888877554


Q ss_pred             h
Q 040110          234 N  234 (348)
Q Consensus       234 ~  234 (348)
                      +
T Consensus       222 d  222 (1283)
T TIGR01967       222 D  222 (1283)
T ss_pred             C
Confidence            4

This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=94.46  E-value=0.45  Score=42.61  Aligned_cols=100  Identities=15%  Similarity=0.130  Sum_probs=60.4

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeC-CCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVS-NFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTI  187 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  187 (348)
                      .++-+++.++|.-|+|||.+.+.+.....  +  +.++-+.+. +..+...+...|+..+..+...  .-.....+....
T Consensus        48 ~d~qg~~~vtGevGsGKTv~~Ral~~s~~--~--d~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~--~~~~~~e~~~~~  121 (269)
T COG3267          48 ADGQGILAVTGEVGSGKTVLRRALLASLN--E--DQVAVVVIDKPTLSDATLLEAIVADLESQPKV--NVNAVLEQIDRE  121 (269)
T ss_pred             hcCCceEEEEecCCCchhHHHHHHHHhcC--C--CceEEEEecCcchhHHHHHHHHHHHhccCccc--hhHHHHHHHHHH
Confidence            35566899999999999999996554411  1  112223333 4467888999999988874211  001122333333


Q ss_pred             HHHHh-cCCe-EEEEEeCCCCh--hhHHHHH
Q 040110          188 LRDYL-TNKK-YFTVLDDVWIE--KIWDDLR  214 (348)
Q Consensus       188 l~~~L-~~kr-~LlVLDdv~~~--~~~~~l~  214 (348)
                      +.... +++| ..++.|+....  +.++.++
T Consensus       122 L~al~~~g~r~v~l~vdEah~L~~~~le~Lr  152 (269)
T COG3267         122 LAALVKKGKRPVVLMVDEAHDLNDSALEALR  152 (269)
T ss_pred             HHHHHHhCCCCeEEeehhHhhhChhHHHHHH
Confidence            44443 4567 89999998654  4455544

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=94.46  E-value=0.028  Score=47.91  Aligned_cols=21  Identities=14%  Similarity=0.262  Sum_probs=19.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhc
Q 040110          114 VVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      +|+|+|+.|+||||+++.+.+
T Consensus         1 ii~itG~~gsGKst~~~~l~~   21 (179)
T cd02022           1 IIGLTGGIGSGKSTVAKLLKE   21 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            479999999999999999876

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>PRK13695 putative NTPase; Provisional

Probab=94.44  E-value=0.036  Score=46.95  Aligned_cols=22  Identities=23%  Similarity=0.291  Sum_probs=19.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|+|.+|+|||||++.+++.
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~   23 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAEL   23 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3789999999999999998876

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=94.44  E-value=0.035  Score=49.03  Aligned_cols=53  Identities=13%  Similarity=0.103  Sum_probs=33.6

Q ss_pred             HHHHHHHhcCCeEEEEEeCCCC------hhhHHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          185 KTILRDYLTNKKYFTVLDDVWI------EKIWDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       185 ~~~l~~~L~~kr~LlVLDdv~~------~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      .-.+.+.|-..+-+|+.|.--.      ....-.+...+. ...|..||+.|-+..+|..
T Consensus       150 RVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~-~~~g~tii~VTHd~~lA~~  208 (226)
T COG1136         150 RVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELN-KERGKTIIMVTHDPELAKY  208 (226)
T ss_pred             HHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHH-HhcCCEEEEEcCCHHHHHh
Confidence            3457777888888888887532      122222222221 1346789999999999886

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=94.43  E-value=0.13  Score=50.54  Aligned_cols=92  Identities=14%  Similarity=0.142  Sum_probs=54.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCC-------Cc--cccCCCCHH-
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTS-------SW--LKIMGKDYK-  182 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~-------~~--~~~~~~~~~-  182 (348)
                      .++|.|.+|+|||||+..+...... .+=+.++++-++... .+.+++..+...-....       +.  ....+.... 
T Consensus       163 R~gIfgg~GvGKs~L~~~~~~~~~~-~~~dv~V~~lIGERgrEv~efi~~~~~~~~~~~~~~~~~rsvvv~atsd~p~~~  241 (494)
T CHL00060        163 KIGLFGGAGVGKTVLIMELINNIAK-AHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMNEPPGA  241 (494)
T ss_pred             EEeeecCCCCChhHHHHHHHHHHHH-hcCCeEEEEEeccCchHHHHHHHHHHhcCccccCcccccceEEEEECCCCCHHH
Confidence            5789999999999999988766111 111577788776654 45677777765221110       00  011111211 


Q ss_pred             -----HHHHHHHHHhc--CC-eEEEEEeCCCC
Q 040110          183 -----SEKTILRDYLT--NK-KYFTVLDDVWI  206 (348)
Q Consensus       183 -----~~~~~l~~~L~--~k-r~LlVLDdv~~  206 (348)
                           -..-.+.++++  ++ ++||++||+-.
T Consensus       242 R~~a~~~A~tiAEyfrd~g~~~VLll~DslTR  273 (494)
T CHL00060        242 RMRVGLTALTMAEYFRDVNKQDVLLFIDNIFR  273 (494)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCEEEEcccchH
Confidence                 12223566664  34 99999999954

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=94.43  E-value=0.031  Score=50.72  Aligned_cols=23  Identities=17%  Similarity=0.283  Sum_probs=19.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|+|.|-||+||||++..++..
T Consensus         2 ~~iav~~KGGvGKTT~~~nLA~~   24 (270)
T cd02040           2 RQIAIYGKGGIGKSTTTQNLSAA   24 (270)
T ss_pred             cEEEEEeCCcCCHHHHHHHHHHH
Confidence            46888899999999999887665

Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=94.43  E-value=0.037  Score=47.09  Aligned_cols=44  Identities=14%  Similarity=0.231  Sum_probs=28.8

Q ss_pred             EEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110          115 VAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      +.|.|.+|+|||+|+.++..... ++. ..++|++...  +..++...
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~-~~g-~~v~~~s~e~--~~~~~~~~   45 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGL-ARG-EPGLYVTLEE--SPEELIEN   45 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH-HCC-CcEEEEECCC--CHHHHHHH
Confidence            56899999999999998766522 222 3466776543  34444443

A related protein is found in archaea.

>PRK01184 hypothetical protein; Provisional

Probab=94.42  E-value=0.035  Score=47.39  Aligned_cols=22  Identities=18%  Similarity=0.398  Sum_probs=18.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|+|+|++|+||||+|+ ++..
T Consensus         2 ~~i~l~G~~GsGKsT~a~-~~~~   23 (184)
T PRK01184          2 KIIGVVGMPGSGKGEFSK-IARE   23 (184)
T ss_pred             cEEEEECCCCCCHHHHHH-HHHH
Confidence            478999999999999987 4443

>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse

Probab=94.41  E-value=0.036  Score=43.39  Aligned_cols=21  Identities=19%  Similarity=0.327  Sum_probs=19.4

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |+|+|+.|+|||||...+.+.
T Consensus         2 V~iiG~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTGK   22 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            689999999999999999974

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=94.41  E-value=0.04  Score=46.10  Aligned_cols=23  Identities=17%  Similarity=0.306  Sum_probs=21.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++++|+|..|+|||||+..+...
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~~   24 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIPA   24 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999999876

In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=94.38  E-value=0.091  Score=53.53  Aligned_cols=52  Identities=13%  Similarity=0.125  Sum_probs=30.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCcc-ccCCcceeEEEEeCCCCCHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNF-VKFYFDCHAWVRVSNFYNFKRILDDI  163 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~-~~~~F~~~~wv~~~~~~~~~~~~~~i  163 (348)
                      .++..|.|.+|+||||++..+..... ....=...+.+.....-....+...+
T Consensus       167 ~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~  219 (615)
T PRK10875        167 RRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESL  219 (615)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHH
Confidence            35778899999999999988776521 11111134555555444444444444

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=94.38  E-value=0.1  Score=52.94  Aligned_cols=23  Identities=22%  Similarity=0.177  Sum_probs=19.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++..|.|.+|+||||++..+...
T Consensus       161 ~~~vitGgpGTGKTt~v~~ll~~  183 (586)
T TIGR01447       161 NFSLITGGPGTGKTTTVARLLLA  183 (586)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHH
Confidence            57788999999999998887654

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	348
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-27
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-08
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	4e-22
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	2e-17

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score =  112 bits (281), Expect = 2e-27
 Identities = 66/420 (15%), Positives = 122/420 (29%), Gaps = 110/420 (26%)

Query: 2   DVNLRIFCERLKRVLVGEE--GTLTLPDT-TKLTPIFQNLLTESEIITTPLGNYQGDMKA 58
           + + +   +  K +L  EE    +   D  +    +F  LL++ E +       +  ++ 
Sbjct: 32  NFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKF--VEEVLRI 89

Query: 59  IYKFFIAIMRQLHQQNSETEEICDALLGLQSKIIN------------------LRNLHQR 100
            YKF   +M  +  +  +   +    +  + ++ N                  LR     
Sbjct: 90  NYKF---LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLE 146

Query: 101 LPPSSGL---GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHA-WVRVSNFYNF 156
           L P+  +   G             G  KT  A ++  +  V+   D    W+ + N  + 
Sbjct: 147 LRPAKNVLIDGVL-----------GSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP 195

Query: 157 KRILD-------DIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFT---VLDDVWI 206
           + +L+        I  +    S     +     S +  LR  L +K Y     VL +V  
Sbjct: 196 ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN 255

Query: 207 EKIWDDLREALPDNQIGSRALITVGPHNILTS--------IELENGEKNRHDS------- 251
            K W+       +  +  + L+T     +           I L++               
Sbjct: 256 AKAWNAF-----N--LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL 308

Query: 252 -------------ALVGGPL--------IRIKHETWQFFILHYGSTPLENETEGPSVGLK 290
                         L   P         IR    TW  +  H     L    E       
Sbjct: 309 KYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNW-KHVNCDKLTTIIE------- 360

Query: 291 LVSLSELPFPLIVCCLY--FCVFPTDIELTTRQLCRLWTAEGLRPGNYDSEKMAEEYLKQ 348
             SL+ L  P     ++    VFP    + T  L  +W          D   +  +  K 
Sbjct: 361 -SSLNVLE-PAEYRKMFDRLSVFPPSAHIPTILLSLIWFD----VIKSDVMVVVNKLHKY 414

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 55.6 bits (133), Expect = 1e-08
 Identities = 47/271 (17%), Positives = 87/271 (32%), Gaps = 58/271 (21%)

Query: 5   LRIFCERLKRVLVGEEGTLTLPDTTKLTPIFQNL--LTESEIITTP-LGNYQGDMKAIYK 61
             + C++L  ++   E +L + +  +   +F  L     S  I T  L     D+  I  
Sbjct: 348 KHVNCDKLTTII---ESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDV--IKS 402

Query: 62  FFIAIMRQLH-------QQNSETEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSV 114
             + ++ +LH       Q    T  I    L L+ K+ N   LH+               
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRS-------------- 448

Query: 115 VAILDS----RGFDKTAFAAEIYNNNFVKFYFDCHAWV--RVSNFYNFKRILDDIMKSLM 168
             I+D     + FD        Y + +   +   H            F+ +  D      
Sbjct: 449 --IVDHYNIPKTFDSDDLIPP-YLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDF----- 500

Query: 169 PTSSWL--KIMGKDY-----KSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQ 221
               +L  KI           S    L+     K Y    D  + E++ + + + LP  +
Sbjct: 501 ---RFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKY-ERLVNAILDFLP--K 554

Query: 222 IGSRALITVGPHNILTSIELENGEKNRHDSA 252
           I    + +   +  L  I L   ++   + A
Sbjct: 555 IEENLICS--KYTDLLRIALMAEDEAIFEEA 583

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score = 96.1 bits (239), Expect = 4e-22
 Identities = 46/292 (15%), Positives = 92/292 (31%), Gaps = 68/292 (23%)

Query: 108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVK--FYFDCHAWVRVSNFYNFKRI--LDDI 163
            +     V I    G  K+  AAE   ++ +    +     WV V        +  L ++
Sbjct: 143 LKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNL 202

Query: 164 MKSLMPTSSWLKIMGKDYKSEKTILRDYLTNK--KYFTVLDDVWIEKIWDDLREALPDNQ 221
              L    S+ + +  + +  K  LR  +  K  +   +LDDVW   +            
Sbjct: 203 CTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF-------D 255

Query: 222 IGSRALIT----------VGPHNILTSIELENGEK---------NRHDSAL--------- 253
              + L+T          +GP  ++        EK         N   + L         
Sbjct: 256 SQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIK 315

Query: 254 -----------VGGPLIRIKHETWQFFILHYGSTPLENETEGPSVGLKLV------SLSE 296
                      +G  L+R     W++++    +   +   +  S   + +      S+  
Sbjct: 316 ECKGSPLVVSLIGA-LLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEM 374

Query: 297 LPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAEGLRPGNYDSEKMAEEYLKQ 348
           L   +        +   D+++ T+ LC LW  E          +  E+ L++
Sbjct: 375 LREDIKDYYTDLSILQKDVKVPTKVLCILWDME---------TEEVEDILQE 417

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score = 82.0 bits (202), Expect = 2e-17
 Identities = 27/278 (9%), Positives = 61/278 (21%), Gaps = 60/278 (21%)

Query: 125 KTAFAAEIYNNN--FVKFYFDCHAWVRVSNFYNFK--RILDDIMKSLMPTSSWLKIMGKD 180
           K+  A++  + +   +   +D   W++ S         +  DI+  L      L     +
Sbjct: 165 KSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVE 224

Query: 181 YKSEKTILRDYLT----NKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALIT------- 229
           + +   + R              V DDV  E+            ++  R L+T       
Sbjct: 225 HVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIR------WAQELRLRCLVTTRDVEIS 278

Query: 230 --VGPHNILTSIELENGE----------KNRHDS---------------------ALVGG 256
                      +     +                                      +   
Sbjct: 279 NAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFK 338

Query: 257 PLIRIKHETWQFFILHYGSTPLENETEGPSVGLKLV------SLSELPFPLIVCCLYFCV 310
                  E          S  L           K +       +  L         +  V
Sbjct: 339 SCEPKTFEKMAQLNNKLESRGLVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVV 398

Query: 311 FPTDIELTTRQLCRLWTAEGLRPGNYDSEKMAEEYLKQ 348
            P  +++  +    +   +         +    + LK+
Sbjct: 399 MPPGVDIPVKLWSCVIPVDICSNEEEQLDDEVADRLKR 436

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	348
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.97
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.97
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.95
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.2
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.06
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.04
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.04
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.03
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.01
2fna_A	357	Conserved hypothetical protein; structural genomic	98.99
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.88
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.75
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.49
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.47
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.43
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.24
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.21
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.1
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.09
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.02
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.97
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.97
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.96
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.93
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.86
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.85
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.84
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.84
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.79
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.78
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.76
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.73
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.73
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.72
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.72
3co5_A	143	Putative two-component system transcriptional RES	97.67
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.62
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.61
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.58
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.58
3bos_A	242	Putative DNA replication factor; P-loop containing	97.58
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.58
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.53
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.52
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.52
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.49
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.43
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.43
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.41
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.4
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.37
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.36
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.35
3pvs_A	447	Replication-associated recombination protein A; ma	97.34
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.32
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.31
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.3
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.3
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.3
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.27
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	97.26
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.24
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.15
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	97.13
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.08
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.07
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.06
2xxa_A	433	Signal recognition particle protein; protein trans	97.02
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.97
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.92
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.92
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	96.89
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.88
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.85
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.83
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.81
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.77
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.77
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.76
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.75
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.75
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.68
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	96.66
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.65
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.65
3io5_A	333	Recombination and repair protein; storage dimer, i	96.63
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.63
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	96.57
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.56
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.55
2qgz_A	308	Helicase loader, putative primosome component; str	96.45
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	96.41
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.39
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.38
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	96.37
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.35
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.34
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.33
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	96.33
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.33
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.3
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.29
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.22
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.2
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.16
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.15
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	96.14
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.1
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.1
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	96.06
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.04
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.03
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.03
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.03
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	96.02
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	96.0
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	95.99
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	95.99
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	95.97
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	95.97
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	95.95
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.95
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	95.94
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	95.93
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	95.9
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	95.88
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.88
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.86
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	95.85
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	95.83
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.83
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.82
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	95.81
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	95.78
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	95.76
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.74
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	95.74
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.73
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.73
3fwy_A	314	Light-independent protochlorophyllide reductase I	95.73
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	95.72
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	95.71
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.71
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.71
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.71
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.69
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.69
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	95.67
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.66
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	95.66
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	95.65
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.65
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	95.65
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	95.65
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	95.62
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	95.59
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	95.57
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	95.55
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	95.54
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.54
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.52
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.52
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	95.52
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.51
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.5
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.5
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	95.49
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	95.49
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	95.48
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	95.48
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.48
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.47
1via_A	175	Shikimate kinase; structural genomics, transferase	95.47
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	95.44
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.42
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	95.41
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.41
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	95.41
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.41
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	95.4
2r44_A	331	Uncharacterized protein; putative ATPase, structur	95.37
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.36
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	95.36
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.35
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.33
2vli_A	183	Antibiotic resistance protein; transferase, tunica	95.33
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.33
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	95.33
3ice_A	422	Transcription termination factor RHO; transcriptio	95.32
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.3
4a74_A	231	DNA repair and recombination protein RADA; hydrola	95.26
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.24
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	95.21
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.2
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.19
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.18
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	95.17
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	95.15
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.14
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	95.12
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	95.1
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	95.09
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.08
2ged_A	193	SR-beta, signal recognition particle receptor beta	95.05
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.04
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	95.03
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.02
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	95.0
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	94.95
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	94.94
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	94.94
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	94.92
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	94.91
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	94.91
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	94.9
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.85
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	94.8
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.74
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	94.73
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	94.72
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.7
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.69
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	94.69
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.69
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	94.65
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.61
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	94.6
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	94.6
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	94.59
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.58
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.58
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	94.57
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.57
2r6a_A	454	DNAB helicase, replicative helicase; replication,	94.56
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	94.55
2hf9_A	226	Probable hydrogenase nickel incorporation protein	94.55
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	94.47
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	94.46
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	94.46
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	94.45
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	94.44
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	94.44
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	94.44
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.44
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.43
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.42
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.41
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	94.4
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.39
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	94.35
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	94.34
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	94.34
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	94.33
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.31
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.31
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.31
3end_A	307	Light-independent protochlorophyllide reductase ir	94.3
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	94.29
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.29
2wji_A	165	Ferrous iron transport protein B homolog; membrane	94.28
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.28
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	94.27
1g6h_A	257	High-affinity branched-chain amino acid transport	94.27
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	94.26
3l0o_A	427	Transcription termination factor RHO; helicase, RH	94.23
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.22
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.21
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.2
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.2
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.18
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	94.15
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	94.15
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.13
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.12
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	94.11
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	94.11
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	94.1
2og2_A	359	Putative signal recognition particle receptor; nuc	94.09
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	94.08
1tue_A	212	Replication protein E1; helicase, replication, E1E	94.08
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	94.07
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	94.06
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.05
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	94.0
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.99
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	93.97
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	93.96
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	93.94
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	93.94
2eyu_A	261	Twitching motility protein PILT; pilus retraction	93.92
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	93.92
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	93.92
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	93.91
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	93.9
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	93.9
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	93.89
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	93.85
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	93.84
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	93.84
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	93.74
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	93.68
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	93.66
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	93.66
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	93.66
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	93.64
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	93.64
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	93.63
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	93.62
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	93.61
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	93.58
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	93.58
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	93.54
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	93.53
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	93.52
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	93.52
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	93.51
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	93.48
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	93.43
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	93.42
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	93.42
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	93.42
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	93.41
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	93.39
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.38
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	93.35
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	93.35
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.34
1nrj_B	218	SR-beta, signal recognition particle receptor beta	93.29
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	93.27
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	93.27
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	93.2
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	93.17
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	93.16
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	93.16
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.14
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.12
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	93.12
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	93.12
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	93.1
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	93.09
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.09
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	93.08
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	93.05
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	93.03
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	93.02
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.01
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.0
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	92.98
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	92.97
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	92.96
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	92.94
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	92.93
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	92.87
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	92.86
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	92.86
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	92.85
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	92.84
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	92.84
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	92.83
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	92.82
3kta_A	182	Chromosome segregation protein SMC; structural mai	92.82
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	92.78
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	92.77
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	92.75
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	92.75
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	92.74
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	92.73
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	92.72
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	92.68
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	92.66
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	92.65
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	92.65
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	92.62
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	92.62
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	92.59
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	92.59
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	92.59
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	92.57
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	92.56
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	92.56
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	92.55
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	92.55
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	92.55
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	92.54
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	92.54
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	92.53
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	92.52
3llu_A	196	RAS-related GTP-binding protein C; structural geno	92.48
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	92.47
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	92.45
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	92.44
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	92.42
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	92.4
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	92.38
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	92.36
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	92.36
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	92.34
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	92.33
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	92.33
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	92.32
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	92.32
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	92.32
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	92.32
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	92.29
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	92.28
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	92.28
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	92.28
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	92.27
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	92.26
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	92.25
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	92.21
2ewv_A	372	Twitching motility protein PILT; pilus retraction	92.2
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	92.17
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	92.17
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	92.16
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	92.09
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	92.09
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.08
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	92.02
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	91.98
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	91.98
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	91.97
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	91.97
2fh5_B	214	SR-beta, signal recognition particle receptor beta	91.96
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	91.94
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	91.91
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	91.89
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	91.88
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	91.88
3t34_A	360	Dynamin-related protein 1A, linker, dynamin-relat	91.87
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	91.86
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	91.85
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	91.83
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	91.82
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	91.8
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	91.79
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	91.79
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	91.79
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	91.79
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	91.76
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	91.75
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	91.73
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	91.73
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	91.7
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	91.68
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	91.68
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	91.65
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	91.63
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	91.62
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	91.62
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	91.6
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	91.55
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	91.55
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	91.54
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	91.49
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	91.47
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	91.47
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	91.47
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	91.46
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	91.46
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	91.44
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	91.36
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	91.32
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	91.31
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	91.31
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	91.31
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	91.31
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	91.29
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	91.26
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	91.24
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	91.23
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	91.17
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	91.13
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	91.13
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	91.1
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	91.09
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	91.09
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	91.09
1p9r_A	418	General secretion pathway protein E; bacterial typ	91.07
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	91.03
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	91.01
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	91.0
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	91.0
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	90.98
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	90.93
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	90.88
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	90.82
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	90.77
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	90.73
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	90.72
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	90.69
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	90.66
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	90.63
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	90.61
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	90.57
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	90.51
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	90.5
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	90.45
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	90.39

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=100.00  E-value=1.9e-38  Score=316.42  Aligned_cols=243  Identities=15%  Similarity=0.206  Sum_probs=187.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhc--CccccCCcceeEEEEeCCCC--CHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYN--NNFVKFYFDCHAWVRVSNFY--NFKR  158 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~--~~~~~~~F~~~~wv~~~~~~--~~~~  158 (348)
                      ..|||+.++   ++|.++|..   ..+...++|+|+||||+||||||+++|+  +.+++.+|+.++||++++.+  +...
T Consensus       129 ~~~GR~~~~---~~l~~~L~~---~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~  202 (549)
T 2a5y_B          129 TCYIREYHV---DRVIKKLDE---MCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFD  202 (549)
T ss_dssp             CSCCCHHHH---HHHHHHHHH---HTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHH
T ss_pred             ccCCchHHH---HHHHHHHhc---ccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHH
Confidence            336999999   999999972   1244689999999999999999999998  66799999999999999885  8999


Q ss_pred             HHHHHHHHhCCCCC---ccccCCCCHHHHHHHHHHHhcCC-eEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          159 ILDDIMKSLMPTSS---WLKIMGKDYKSEKTILRDYLTNK-KYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       159 ~~~~i~~~l~~~~~---~~~~~~~~~~~~~~~l~~~L~~k-r~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      ++..|+.+++....   .......+...+...+++.|+++ |+||||||||+.+++ .+..     .+||+||||||+..
T Consensus       203 ~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~~~-----~~gs~ilvTTR~~~  276 (549)
T 2a5y_B          203 LFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RWAQ-----ELRLRCLVTTRDVE  276 (549)
T ss_dssp             HHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HHHH-----HTTCEEEEEESBGG
T ss_pred             HHHHHHHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-cccc-----cCCCEEEEEcCCHH
Confidence            99999999987522   11223446677899999999996 999999999998765 2221     16899999999999


Q ss_pred             hhhh-------cccC-------------------------------CCCc-CCCC-cccccCccccCCHHHHHHHHHHhC
Q 040110          235 ILTS-------IELE-------------------------------NGEK-NRHD-SALVGGPLIRIKHETWQFFILHYG  274 (348)
Q Consensus       235 v~~~-------~~l~-------------------------------~~~C-~Lp~-~~~ig~~L~~~~~~~w~~~~~~~~  274 (348)
                      ++..       |.++                               ...| |||+ ++++|+.|+.+.   |+.+ +.+.
T Consensus       277 v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~~---w~~~-~~l~  352 (549)
T 2a5y_B          277 ISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKT---FEKM-AQLN  352 (549)
T ss_dssp             GGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSS---HHHH-HHHH
T ss_pred             HHHHcCCCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHHHHHhccch---HHHH-HHhH
Confidence            8875       3333                               2346 9999 999999998864   3332 2221


Q ss_pred             CCCCCCCCCCcchhccc-cccCCCChhHHHHHh-----------HhccCCCCceecHHHHHHHHHhc--CCCCC---CCC
Q 040110          275 STPLENETEGPSVGLKL-VSLSELPFPLIVCCL-----------YFCVFPTDIELTTRQLCRLWTAE--GLRPG---NYD  337 (348)
Q Consensus       275 ~~~~~~~~~~~~i~~~l-~s~~~Lp~~lk~cf~-----------y~a~fp~~~~i~~~~Li~~W~ae--G~i~~---~~~  337 (348)
                      .. ....+ ...+...+ +||+.||+++|.||+           |||+||+++.|+    +++|+|+  ||+..   +.+
T Consensus       353 ~~-l~~~~-~~~i~~~l~~Sy~~L~~~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~----i~~w~a~~~G~i~~~~~~~~  426 (549)
T 2a5y_B          353 NK-LESRG-LVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIP----VKLWSCVIPVDICSNEEEQL  426 (549)
T ss_dssp             HH-HHHHC-SSTTCCCSSSSSSSHHHHHHHHHHTSCHHHHHHTTGGGSSCTTCCEE----HHHHHHHSCC-------CCC
T ss_pred             HH-hhccc-HHHHHHHHhcccccccHHHHHHHhccchhhhhHhhheeeeCCCCeee----eeeeeeeccceeccCCCCCC
Confidence            11 11001 23465667 999999999999999           999999999999    8999999  99987   567


Q ss_pred             hHHHHHhhhcC
Q 040110          338 SEKMAEEYLKQ  348 (348)
Q Consensus       338 ~e~~~~~y~~e  348 (348)
                      .+++++ ||++
T Consensus       427 ~~~~~~-~l~~  436 (549)
T 2a5y_B          427 DDEVAD-RLKR  436 (549)
T ss_dssp             THHHHH-HHHH
T ss_pred             HHHHHH-HHHH
Confidence            899998 8864

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.97  E-value=6.6e-33  Score=284.98  Aligned_cols=219  Identities=17%  Similarity=0.168  Sum_probs=174.5

Q ss_pred             ccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcce-eEEEEeCCCCCHHHHHHH
Q 040110           84 LLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDC-HAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        84 ~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~-~~wv~~~~~~~~~~~~~~  162 (348)
                      .|||+.++   ++|.++|..    . +..++|+|+||||+||||||+++|++.+++.+|+. ++|+++++.++...++..
T Consensus       130 ~VGRe~eL---eeL~elL~~----~-d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~  201 (1221)
T 1vt4_I          130 NVSRLQPY---LKLRQALLE----L-RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEM  201 (1221)
T ss_dssp             CCCCHHHH---HHHHHHHHH----C-CSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHH
T ss_pred             CCCcHHHH---HHHHHHHhc----c-CCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHH
Confidence            49999999   999999972    1 24789999999999999999999998778899996 899999999998888888


Q ss_pred             HHHHhCCCCCcc--cc-----CCCCHHHHHHHHHHHh---cCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCC
Q 040110          163 IMKSLMPTSSWL--KI-----MGKDYKSEKTILRDYL---TNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGP  232 (348)
Q Consensus       163 i~~~l~~~~~~~--~~-----~~~~~~~~~~~l~~~L---~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~  232 (348)
                      |+..++......  ..     ...+.+.+...+++.|   .++|+||||||||+.+.|+.+.       +||+||||||+
T Consensus       202 Ll~lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~-------pGSRILVTTRd  274 (1221)
T 1vt4_I          202 LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRF  274 (1221)
T ss_dssp             HHHHHHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHH-------SSCCEEEECSC
T ss_pred             HHHHHhhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhC-------CCeEEEEeccC
Confidence            777543211000  00     0113455667777766   6799999999999998888763       58999999999


Q ss_pred             hhhhhh------cc---------cC--------------------CCCc-CCCC-cccccCccccCC--HHHHHHHHHHh
Q 040110          233 HNILTS------IE---------LE--------------------NGEK-NRHD-SALVGGPLIRIK--HETWQFFILHY  273 (348)
Q Consensus       233 ~~v~~~------~~---------l~--------------------~~~C-~Lp~-~~~ig~~L~~~~--~~~w~~~~~~~  273 (348)
                      +.++..      |.         +.                    .+.| |||+ ++++|+.|+.+.  .+.|+..    
T Consensus       275 ~~Va~~l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~~eeL~~eICgGLPLALkLaGs~Lr~k~~s~eeW~~~----  350 (1221)
T 1vt4_I          275 KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV----  350 (1221)
T ss_dssp             SHHHHHHHHHSSCEEEECSSSSCCCHHHHHHHHHHHHCCCTTTHHHHHCCCCHHHHHHHHHHHHHSCSSHHHHHHC----
T ss_pred             hHHHHhcCCCeEEEecCccccCCcCHHHHHHHHHHHcCCCHHHHHHHHhCCCHHHHHHHHHHHhCCCCCHHHHhcC----
Confidence            998742      22         22                    2347 9999 899999999874  7888653    


Q ss_pred             CCCCCCCCCCCcchhccc-cccCCCChhH-HHHHhHhccCCCCceecHHHHHHHHHhcC
Q 040110          274 GSTPLENETEGPSVGLKL-VSLSELPFPL-IVCCLYFCVFPTDIELTTRQLCRLWTAEG  330 (348)
Q Consensus       274 ~~~~~~~~~~~~~i~~~l-~s~~~Lp~~l-k~cf~y~a~fp~~~~i~~~~Li~~W~aeG  330 (348)
                        .       ...+...+ +||+.||+++ |.||+|||+||+++.|+++.|+.+|+++|
T Consensus       351 --~-------~~~I~aaLelSYd~Lp~eelK~cFL~LAIFPed~~I~~elLa~LW~aeG  400 (1221)
T 1vt4_I          351 --N-------CDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVI  400 (1221)
T ss_dssp             --S-------CHHHHHHHHHHHHHSCTTHHHHHHHHTTSSCTTSCEEHHHHHHHHCSSC
T ss_pred             --C-------hhHHHHHHHHHHHhCCHHHHHHHHHHHhCCCCCCCCCHHHHHHHhcCCC
Confidence              1       14576667 9999999998 99999999999999999999999999986

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=99.97  E-value=2.8e-32  Score=294.24  Aligned_cols=232  Identities=18%  Similarity=0.290  Sum_probs=181.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccc-cCCcc-eeEEEEeCCCCC--HHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFV-KFYFD-CHAWVRVSNFYN--FKR  158 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~-~~~F~-~~~wv~~~~~~~--~~~  158 (348)
                      .||||+.++   ++|.++|.    ..++..++|+|+||||+||||||+++|++.+. ..+|. .++|+++++..+  ...
T Consensus       125 ~~vgR~~~~---~~l~~~l~----~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~  197 (1249)
T 3sfz_A          125 IFVTRKKLV---HAIQQKLW----KLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLM  197 (1249)
T ss_dssp             SCCCCHHHH---HHHHHHHH----TTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHH
T ss_pred             eeccHHHHH---HHHHHHHh----hccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHH
Confidence            799999999   99999997    33467899999999999999999999998543 45564 777999988543  445


Q ss_pred             HHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCC--eEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhh
Q 040110          159 ILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNK--KYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNIL  236 (348)
Q Consensus       159 ~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~k--r~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~  236 (348)
                      .+..++..+............+.+.+...++..|.++  |+||||||||+..+|..+       .+||+||||||++.++
T Consensus       198 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~-------~~~~~ilvTtR~~~~~  270 (1249)
T 3sfz_A          198 KLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAF-------DNQCQILLTTRDKSVT  270 (1249)
T ss_dssp             HHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTT-------CSSCEEEEEESSTTTT
T ss_pred             HHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhh-------cCCCEEEEEcCCHHHH
Confidence            5777888887653321233467888999999999887  999999999998776543       5689999999999988


Q ss_pred             hh-------cc----cC--------------------------CCCc-CCCC-cccccCccccCCHHHHHHHHHHhCCCC
Q 040110          237 TS-------IE----LE--------------------------NGEK-NRHD-SALVGGPLIRIKHETWQFFILHYGSTP  277 (348)
Q Consensus       237 ~~-------~~----l~--------------------------~~~C-~Lp~-~~~ig~~L~~~~~~~w~~~~~~~~~~~  277 (348)
                      ..       +.    +.                          ...| |||+ |+++|+.|+.++ ..|..+++.+....
T Consensus       271 ~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~-~~~~~~l~~l~~~~  349 (1249)
T 3sfz_A          271 DSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQNKQ  349 (1249)
T ss_dssp             TTCCSCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS-SCHHHHHHHHHSCC
T ss_pred             HhhcCCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh-hHHHHHHHHHhhhh
Confidence            43       22    22                          2356 9999 999999999876 56777777764331


Q ss_pred             ---CCC--CCCCcchhccc-cccCCCChhHHHHHhHhccCCCCceecHHHHHHHHHhc
Q 040110          278 ---LEN--ETEGPSVGLKL-VSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAE  329 (348)
Q Consensus       278 ---~~~--~~~~~~i~~~l-~s~~~Lp~~lk~cf~y~a~fp~~~~i~~~~Li~~W~ae  329 (348)
                         +..  ......+...+ +||+.||+++|.||+|||+||+++.|+++.++.+|.++
T Consensus       350 ~~~~~~~~~~~~~~~~~~l~~s~~~L~~~~~~~~~~l~~f~~~~~i~~~~~~~~~~~~  407 (1249)
T 3sfz_A          350 FKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE  407 (1249)
T ss_dssp             CCCSSCTTCTTHHHHHHHHHHHHHTSCTTTHHHHHHGGGSCTTCCEEHHHHHHHHTCC
T ss_pred             hhhcccccccchHHHHHHHHHHHHhCCHHHHHHHHHhCccCCCCeeCHHHHHHHhCCC
Confidence               111  11223465666 99999999999999999999999999999999999775

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.95  E-value=6e-29  Score=249.81  Aligned_cols=231  Identities=18%  Similarity=0.292  Sum_probs=173.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccc-cCCcc-eeEEEEeCCCCCHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFV-KFYFD-CHAWVRVSNFYNFKRIL  160 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~-~~~F~-~~~wv~~~~~~~~~~~~  160 (348)
                      .||||+.++   ++|.++|.    ....+.++++|+||||+||||||.+++++..+ ..+|+ .++|++++.. +...++
T Consensus       125 ~~vGR~~~l---~~L~~~L~----~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~  196 (591)
T 1z6t_A          125 VFVTRKKLV---NAIQQKLS----KLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLL  196 (591)
T ss_dssp             SCCCCHHHH---HHHHHHHT----TSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHH
T ss_pred             eecccHHHH---HHHHHHHh----cccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHH
Confidence            899999999   99999998    33456789999999999999999999998655 78895 8999999765 333333


Q ss_pred             H---HHHHHhCCCCCccccCCCCHHHHHHHHHHHhcC--CeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhh
Q 040110          161 D---DIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTN--KKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNI  235 (348)
Q Consensus       161 ~---~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~--kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v  235 (348)
                      .   .++..++...........+...+...+...+.+  +++||||||+|+...+..    +   .+||+||||||+..+
T Consensus       197 ~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~----l---~~~~~ilvTsR~~~~  269 (591)
T 1z6t_A          197 MKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKA----F---DSQCQILLTTRDKSV  269 (591)
T ss_dssp             HHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHT----T---CSSCEEEEEESCGGG
T ss_pred             HHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHH----h---cCCCeEEEECCCcHH
Confidence            3   344455532111022345677888889988876  789999999998765543    2   458999999999987


Q ss_pred             hhh-----ccc------C--------------------------CCCc-CCCC-cccccCccccCCHHHHHHHHHHhCCC
Q 040110          236 LTS-----IEL------E--------------------------NGEK-NRHD-SALVGGPLIRIKHETWQFFILHYGST  276 (348)
Q Consensus       236 ~~~-----~~l------~--------------------------~~~C-~Lp~-~~~ig~~L~~~~~~~w~~~~~~~~~~  276 (348)
                      +..     +.+      +                          ...| |+|+ +..+|+.|+.+. ..|..+++.+...
T Consensus       270 ~~~~~~~~~~v~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~-~~w~~~l~~l~~~  348 (591)
T 1z6t_A          270 TDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-NRWEYYLKQLQNK  348 (591)
T ss_dssp             GTTCCSCEEEEECCSSCCHHHHHHHHHHHHTSCGGGSCTHHHHHHHHHTTCHHHHHHHHHHHHHST-TCHHHHHHHHHSC
T ss_pred             HHhcCCCceEeecCCCCCHHHHHHHHHHHhCCCcccccHHHHHHHHHhCCCcHHHHHHHHHHhcCc-hhHHHHHHHHHHh
Confidence            754     222      2                          1245 9998 888898888763 4688888776543


Q ss_pred             CCC---C--CCCCcchhccc-cccCCCChhHHHHHhHhccCCCCceecHHHHHHHHHhc
Q 040110          277 PLE---N--ETEGPSVGLKL-VSLSELPFPLIVCCLYFCVFPTDIELTTRQLCRLWTAE  329 (348)
Q Consensus       277 ~~~---~--~~~~~~i~~~l-~s~~~Lp~~lk~cf~y~a~fp~~~~i~~~~Li~~W~ae  329 (348)
                      ...   .  ......+...+ .||+.||++.|.||++||+||+++.|+.+.|+.+|.++
T Consensus       349 ~~~~~~~~~~~~~~~l~~~l~~s~~~L~~~~~~~l~~la~f~~~~~i~~~~l~~l~~~~  407 (591)
T 1z6t_A          349 QFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDME  407 (591)
T ss_dssp             CCCCSSCCCSSCCHHHHHHHHHHHHTSCTTTHHHHHHGGGCCTTCCEEHHHHHHHHTCC
T ss_pred             HHHHhhhccccchHHHHHHHHHHHHhCCHHHHHHHHHccccCCCCccCHHHHHHHhccC
Confidence            111   1  11223565666 99999999999999999999999999999999999654

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.20  E-value=3.8e-11  Score=114.38  Aligned_cols=149  Identities=16%  Similarity=0.040  Sum_probs=97.1

Q ss_pred             ccCcccccccccccHHHHHhhc-CCCCCCCCCCcEEEEE--ECCCCCcHHHHHHHHhcCcccc---CCcc-eeEEEEeCC
Q 040110           80 ICDALLGLQSKIINLRNLHQRL-PPSSGLGQPTHSVVAI--LDSRGFDKTAFAAEIYNNNFVK---FYFD-CHAWVRVSN  152 (348)
Q Consensus        80 ~~~~~vGr~~~~~~~~~l~~~L-~~~~~~~~~~~~vi~I--~G~gGvGKTtLA~~v~~~~~~~---~~F~-~~~wv~~~~  152 (348)
                      .++.++||+.++   +.|.++| .............+.|  +|++|+||||||+.+++.....   ..|+ ..+|+++..
T Consensus        20 ~p~~l~gR~~el---~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (412)
T 1w5s_A           20 IPPELRVRRGEA---EALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFN   96 (412)
T ss_dssp             CCSSCSSSCHHH---HHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGG
T ss_pred             CCCCCCChHHHH---HHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCC
Confidence            335899999999   9998888 3100010023445666  9999999999999999873211   1123 357888777


Q ss_pred             CCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhc--CCeEEEEEeCCCCh--------hhHHHHHhhC---CC
Q 040110          153 FYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT--NKKYFTVLDDVWIE--------KIWDDLREAL---PD  219 (348)
Q Consensus       153 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVLDdv~~~--------~~~~~l~~~l---~~  219 (348)
                      ..+...++..++.+++...+   ....+..++...+...+.  +++++|||||++..        ..+..+...+   +.
T Consensus        97 ~~~~~~~~~~l~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~  173 (412)
T 1w5s_A           97 APNLYTILSLIVRQTGYPIQ---VRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPS  173 (412)
T ss_dssp             CCSHHHHHHHHHHHHTCCCC---CTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCC
T ss_pred             CCCHHHHHHHHHHHhCCCCC---CCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhccc
Confidence            77889999999999976421   123345667777777775  67999999999763        2333333322   21


Q ss_pred             CC--CCcEEEEEeCChh
Q 040110          220 NQ--IGSRALITVGPHN  234 (348)
Q Consensus       220 ~~--~gskIlvTTR~~~  234 (348)
                      .+  ....+|+||+...
T Consensus       174 ~~~~~~v~lI~~~~~~~  190 (412)
T 1w5s_A          174 RDGVNRIGFLLVASDVR  190 (412)
T ss_dssp             TTSCCBEEEEEEEEETH
T ss_pred             CCCCceEEEEEEecccc
Confidence            12  3445777887654

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.06  E-value=6e-10  Score=104.89  Aligned_cols=143  Identities=17%  Similarity=0.122  Sum_probs=96.7

Q ss_pred             CcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCC------cceeEEEEeCCCCC
Q 040110           82 DALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFY------FDCHAWVRVSNFYN  155 (348)
Q Consensus        82 ~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~------F~~~~wv~~~~~~~  155 (348)
                      +.++||+.+.   +.+.++|...  ........+.|+|++|+||||||+.+++.  ....      -...+|+++....+
T Consensus        19 ~~~~gr~~~~---~~l~~~l~~~--~~~~~~~~vll~G~~G~GKT~l~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~   91 (387)
T 2v1u_A           19 DVLPHREAEL---RRLAEVLAPA--LRGEKPSNALLYGLTGTGKTAVARLVLRR--LEARASSLGVLVKPIYVNARHRET   91 (387)
T ss_dssp             SCCTTCHHHH---HHHHHTTGGG--TSSCCCCCEEECBCTTSSHHHHHHHHHHH--HHHHHHHHTCCEEEEEEETTTSCS
T ss_pred             CCCCCHHHHH---HHHHHHHHHH--HcCCCCCcEEEECCCCCCHHHHHHHHHHH--HHHHHhccCCCeEEEEEECCcCCC
Confidence            5899999999   9999988521  11234456889999999999999999987  3221      12466788888888


Q ss_pred             HHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhc--CCeEEEEEeCCCChh----hHHHH---HhhCCCC--CCCc
Q 040110          156 FKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT--NKKYFTVLDDVWIEK----IWDDL---REALPDN--QIGS  224 (348)
Q Consensus       156 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVLDdv~~~~----~~~~l---~~~l~~~--~~gs  224 (348)
                      ...++..++.+++...+   ....+..++...+...+.  +++.+|+||+++...    ..+.+   .......  ..+.
T Consensus        92 ~~~~~~~l~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~  168 (387)
T 2v1u_A           92 PYRVASAIAEAVGVRVP---FTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWV  168 (387)
T ss_dssp             HHHHHHHHHHHHSCCCC---SSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----C
T ss_pred             HHHHHHHHHHHhCCCCC---CCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceE
Confidence            89999999999976432   233456677777777774  468999999997642    22222   2222111  3355


Q ss_pred             EEEEEeCChh
Q 040110          225 RALITVGPHN  234 (348)
Q Consensus       225 kIlvTTR~~~  234 (348)
                      .+|.||+...
T Consensus       169 ~~I~~t~~~~  178 (387)
T 2v1u_A          169 SLVGITNSLG  178 (387)
T ss_dssp             EEEEECSCST
T ss_pred             EEEEEECCCc
Confidence            6777777653

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.04  E-value=1.7e-10  Score=108.79  Aligned_cols=146  Identities=14%  Similarity=0.010  Sum_probs=96.6

Q ss_pred             CcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccc----cCC--cceeEEEEeCCCC-
Q 040110           82 DALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFV----KFY--FDCHAWVRVSNFY-  154 (348)
Q Consensus        82 ~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~----~~~--F~~~~wv~~~~~~-  154 (348)
                      +.++||+.++   +.+.++|...  ......+.+.|+|++|+||||||+.+++...-    ...  ....+|+++.... 
T Consensus        20 ~~l~gr~~~~---~~l~~~l~~~--~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~   94 (384)
T 2qby_B           20 KEIPFREDIL---RDAAIAIRYF--VKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGG   94 (384)
T ss_dssp             SSCTTCHHHH---HHHHHHHHHH--HTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCS
T ss_pred             CCCCChHHHH---HHHHHHHHHH--HcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCC
Confidence            5899999999   8888777521  01233457889999999999999999986211    111  2256778777666 


Q ss_pred             CHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCChhh---HHHHHhhCCCCCCCcEEEEEeC
Q 040110          155 NFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKI---WDDLREALPDNQIGSRALITVG  231 (348)
Q Consensus       155 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~~~---~~~l~~~l~~~~~gskIlvTTR  231 (348)
                      +...++..++..+.....  .....+...+...+...+..++.+||||+++....   .+.+...+.....+..+|+||+
T Consensus        95 ~~~~~~~~l~~~l~~~~~--~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~  172 (384)
T 2qby_B           95 TPQAVLSSLAGKLTGFSV--PKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISN  172 (384)
T ss_dssp             CHHHHHHHHHHHHHCSCC--CSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECS
T ss_pred             CHHHHHHHHHHHhcCCCC--CCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEEC
Confidence            888888999888832211  12233456777888888887766999999975421   1220222211115778888988


Q ss_pred             Chh
Q 040110          232 PHN  234 (348)
Q Consensus       232 ~~~  234 (348)
                      ...
T Consensus       173 ~~~  175 (384)
T 2qby_B          173 DIN  175 (384)
T ss_dssp             STT
T ss_pred             CCc
Confidence            764

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.04  E-value=2.9e-10  Score=106.96  Aligned_cols=146  Identities=18%  Similarity=0.178  Sum_probs=97.2

Q ss_pred             ccCcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc---ceeEEEEeCCCCCH
Q 040110           80 ICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF---DCHAWVRVSNFYNF  156 (348)
Q Consensus        80 ~~~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F---~~~~wv~~~~~~~~  156 (348)
                      .++.|+||+.++   +.+.+++...  ........+.|+|++|+||||||+.+++.  ....+   ...+|+++....+.
T Consensus        18 ~p~~~~gr~~e~---~~l~~~l~~~--~~~~~~~~vli~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~i~~~~~~~~   90 (386)
T 2qby_A           18 IPDELPHREDQI---RKIASILAPL--YREEKPNNIFIYGLTGTGKTAVVKFVLSK--LHKKFLGKFKHVYINTRQIDTP   90 (386)
T ss_dssp             CCSCCTTCHHHH---HHHHHSSGGG--GGTCCCCCEEEEECTTSSHHHHHHHHHHH--HHHHTCSSCEEEEEEHHHHCSH
T ss_pred             CCCCCCChHHHH---HHHHHHHHHH--HcCCCCCeEEEECCCCCCHHHHHHHHHHH--HHHHhcCCceEEEEECCCCCCH
Confidence            335899999999   9999988721  01234457889999999999999999987  33322   24667777666677


Q ss_pred             HHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcC--CeEEEEEeCCCCh------hhHHHHHhhCCC-CCCCcEEE
Q 040110          157 KRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTN--KKYFTVLDDVWIE------KIWDDLREALPD-NQIGSRAL  227 (348)
Q Consensus       157 ~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~--kr~LlVLDdv~~~------~~~~~l~~~l~~-~~~gskIl  227 (348)
                      ..++..++..++....   ....+..+....+...+..  ++.+||||+++..      ..+..+...+.. ...+..+|
T Consensus        91 ~~~~~~i~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I  167 (386)
T 2qby_A           91 YRVLADLLESLDVKVP---FTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFI  167 (386)
T ss_dssp             HHHHHHHTTTTSCCCC---SSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEE
T ss_pred             HHHHHHHHHHhCCCCC---CCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEE
Confidence            8888888888865421   1233566666777777653  4899999999652      334444333311 22355677


Q ss_pred             EEeCChhh
Q 040110          228 ITVGPHNI  235 (348)
Q Consensus       228 vTTR~~~v  235 (348)
                      +||+....
T Consensus       168 ~~~~~~~~  175 (386)
T 2qby_A          168 GITNDVKF  175 (386)
T ss_dssp             EEESCGGG
T ss_pred             EEECCCCh
Confidence            78877654

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.03  E-value=2.4e-10  Score=106.16  Aligned_cols=134  Identities=12%  Similarity=0.162  Sum_probs=88.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC------CH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY------NF  156 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~------~~  156 (348)
                      .|+||+.++   +.|.+++.    .   + +++.|+|++|+|||||++++++.  .    . .+|+++....      +.
T Consensus        13 ~~~gR~~el---~~L~~~l~----~---~-~~v~i~G~~G~GKT~Ll~~~~~~--~----~-~~~~~~~~~~~~~~~~~~   74 (350)
T 2qen_A           13 DIFDREEES---RKLEESLE----N---Y-PLTLLLGIRRVGKSSLLRAFLNE--R----P-GILIDCRELYAERGHITR   74 (350)
T ss_dssp             GSCSCHHHH---HHHHHHHH----H---C-SEEEEECCTTSSHHHHHHHHHHH--S----S-EEEEEHHHHHHTTTCBCH
T ss_pred             hcCChHHHH---HHHHHHHh----c---C-CeEEEECCCcCCHHHHHHHHHHH--c----C-cEEEEeecccccccCCCH
Confidence            899999999   99999887    1   1 58899999999999999999877  2    1 6677664332      56


Q ss_pred             HHHHHHHHHHhCCC--------------CCccccCCCCHHHHHHHHHHHhcC-CeEEEEEeCCCChh--------h-HHH
Q 040110          157 KRILDDIMKSLMPT--------------SSWLKIMGKDYKSEKTILRDYLTN-KKYFTVLDDVWIEK--------I-WDD  212 (348)
Q Consensus       157 ~~~~~~i~~~l~~~--------------~~~~~~~~~~~~~~~~~l~~~L~~-kr~LlVLDdv~~~~--------~-~~~  212 (348)
                      ..++..+...+...              .........+..++...+.+.+.. ++.+|||||++...        . +..
T Consensus        75 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~  154 (350)
T 2qen_A           75 EELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLAL  154 (350)
T ss_dssp             HHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHH
Confidence            66677666655420              000011124566677777766653 49999999997643        2 233


Q ss_pred             HHhhCCCCCCCcEEEEEeCChhh
Q 040110          213 LREALPDNQIGSRALITVGPHNI  235 (348)
Q Consensus       213 l~~~l~~~~~gskIlvTTR~~~v  235 (348)
                      +.... ....+.++|+|++...+
T Consensus       155 L~~~~-~~~~~~~~il~g~~~~~  176 (350)
T 2qen_A          155 FAYAY-DSLPNLKIILTGSEVGL  176 (350)
T ss_dssp             HHHHH-HHCTTEEEEEEESSHHH
T ss_pred             HHHHH-HhcCCeEEEEECCcHHH
Confidence            32221 11246789999887653

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=99.01  E-value=2.3e-09  Score=101.04  Aligned_cols=147  Identities=16%  Similarity=0.111  Sum_probs=101.4

Q ss_pred             cCcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc-ceeEEEEeCCCCCHHHH
Q 040110           81 CDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF-DCHAWVRVSNFYNFKRI  159 (348)
Q Consensus        81 ~~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F-~~~~wv~~~~~~~~~~~  159 (348)
                      ++.++||+.+.   +.+.++|...-.......+.+.|+|++|+|||||++.+++.  ..... ...++++++...+...+
T Consensus        16 p~~l~gr~~~~---~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~i~~~~~~~~~~~   90 (389)
T 1fnn_A           16 PKRLPHREQQL---QQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWEL--YKDKTTARFVYINGFIYRNFTAI   90 (389)
T ss_dssp             CSCCTTCHHHH---HHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHH--HTTSCCCEEEEEETTTCCSHHHH
T ss_pred             CCCCCChHHHH---HHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHH--HhhhcCeeEEEEeCccCCCHHHH
Confidence            35899999999   99988886210001222347889999999999999999987  33321 24667777777788899


Q ss_pred             HHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhc--CCeEEEEEeCCCCh--hhHHHHHhhCCCCC----CCcEEEEEeC
Q 040110          160 LDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT--NKKYFTVLDDVWIE--KIWDDLREALPDNQ----IGSRALITVG  231 (348)
Q Consensus       160 ~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVLDdv~~~--~~~~~l~~~l~~~~----~gskIlvTTR  231 (348)
                      +..++..++....   ....+...+...+...+.  +++.+||||+++..  ..+..+...+....    .+..||++|+
T Consensus        91 ~~~l~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~  167 (389)
T 1fnn_A           91 IGEIARSLNIPFP---RRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGH  167 (389)
T ss_dssp             HHHHHHHTTCCCC---SSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEES
T ss_pred             HHHHHHHhCccCC---CCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEEC
Confidence            9999999876421   123456677777777664  56889999999763  45556655553311    3667888887


Q ss_pred             Chhh
Q 040110          232 PHNI  235 (348)
Q Consensus       232 ~~~v  235 (348)
                      ....
T Consensus       168 ~~~~  171 (389)
T 1fnn_A          168 NDAV  171 (389)
T ss_dssp             STHH
T ss_pred             CchH
Confidence            7643

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=98.99  E-value=1.2e-09  Score=101.45  Aligned_cols=135  Identities=13%  Similarity=0.114  Sum_probs=83.3

Q ss_pred             CcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-----CCH
Q 040110           82 DALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-----YNF  156 (348)
Q Consensus        82 ~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-----~~~  156 (348)
                      +.|+||+.++   +.|.+ +.    .     +++.|+|++|+|||||++++.+.  ...   ..+|+++...     .+.
T Consensus        13 ~~~~gR~~el---~~L~~-l~----~-----~~v~i~G~~G~GKT~L~~~~~~~--~~~---~~~~~~~~~~~~~~~~~~   74 (357)
T 2fna_A           13 KDFFDREKEI---EKLKG-LR----A-----PITLVLGLRRTGKSSIIKIGINE--LNL---PYIYLDLRKFEERNYISY   74 (357)
T ss_dssp             GGSCCCHHHH---HHHHH-TC----S-----SEEEEEESTTSSHHHHHHHHHHH--HTC---CEEEEEGGGGTTCSCCCH
T ss_pred             HHhcChHHHH---HHHHH-hc----C-----CcEEEECCCCCCHHHHHHHHHHh--cCC---CEEEEEchhhccccCCCH
Confidence            3899999999   99999 76    1     48999999999999999999887  322   2578876542     344


Q ss_pred             HHHHHHHHHHhCC-------------CC-----C--cccc-----CCCCHHHHHHHHHHHhcCCeEEEEEeCCCChh---
Q 040110          157 KRILDDIMKSLMP-------------TS-----S--WLKI-----MGKDYKSEKTILRDYLTNKKYFTVLDDVWIEK---  208 (348)
Q Consensus       157 ~~~~~~i~~~l~~-------------~~-----~--~~~~-----~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~~---  208 (348)
                      ..++..+...+..             ..     .  ....     .......+...+.+..+ ++++|||||++..+   
T Consensus        75 ~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~-~~~vlvlDe~~~~~~~~  153 (357)
T 2fna_A           75 KDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASK-DNVIIVLDEAQELVKLR  153 (357)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCS-SCEEEEEETGGGGGGCT
T ss_pred             HHHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCC-CCeEEEEECHHHhhccC
Confidence            5555554443310             00     0  0000     12345555555554433 49999999997632   


Q ss_pred             --hHHHHHhhCCCCCCCcEEEEEeCChhh
Q 040110          209 --IWDDLREALPDNQIGSRALITVGPHNI  235 (348)
Q Consensus       209 --~~~~l~~~l~~~~~gskIlvTTR~~~v  235 (348)
                        ++..+...+.....+..+|+|++....
T Consensus       154 ~~~~~~~l~~~~~~~~~~~~i~~g~~~~~  182 (357)
T 2fna_A          154 GVNLLPALAYAYDNLKRIKFIMSGSEMGL  182 (357)
T ss_dssp             TCCCHHHHHHHHHHCTTEEEEEEESSHHH
T ss_pred             chhHHHHHHHHHHcCCCeEEEEEcCchHH
Confidence              222222222221236789999998653

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.88  E-value=1.1e-08  Score=89.23  Aligned_cols=204  Identities=12%  Similarity=0.085  Sum_probs=103.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++||+..+   +.+..++..    + .....+.|+|++|+||||||+.+++.......+..      ........ ...
T Consensus        24 ~~~g~~~~~---~~l~~~l~~----~-~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~------~~~~~~~~-~~~   88 (250)
T 1njg_A           24 DVVGQEHVL---TALANGLSL----G-RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA------TPCGVCDN-CRE   88 (250)
T ss_dssp             GCCSCHHHH---HHHHHHHHH----T-CCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCS------SCCSCSHH-HHH
T ss_pred             HHhCcHHHH---HHHHHHHHc----C-CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC------CCCcccHH-HHH
Confidence            799999999   999988872    1 12347889999999999999999876321111100      00000000 001


Q ss_pred             HHHHhCCCCCccccCC-CCHHHHHHHHHHHh-----cCCeEEEEEeCCCC--hhhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          163 IMKSLMPTSSWLKIMG-KDYKSEKTILRDYL-----TNKKYFTVLDDVWI--EKIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~-~~~~~~~~~l~~~L-----~~kr~LlVLDdv~~--~~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      +............... .....+ ..+.+.+     .+++.+||+||++.  ...++.+...+.....+..+|+||+...
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~  167 (250)
T 1njg_A           89 IEQGRFVDLIEIDAASRTKVEDT-RDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQ  167 (250)
T ss_dssp             HHTTCCSSEEEEETTCGGGHHHH-HHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGG
T ss_pred             HhccCCcceEEecCcccccHHHH-HHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChH
Confidence            1100000000000000 111112 2222222     34679999999965  3566777666654455778888887654


Q ss_pred             hhhh--------cccCCCCcCCCCcccccCccccCCHHHHHHHHHHhCCCCCCCCCCCcchhccc-cccCCCChhHHHHH
Q 040110          235 ILTS--------IELENGEKNRHDSALVGGPLIRIKHETWQFFILHYGSTPLENETEGPSVGLKL-VSLSELPFPLIVCC  305 (348)
Q Consensus       235 v~~~--------~~l~~~~C~Lp~~~~ig~~L~~~~~~~w~~~~~~~~~~~~~~~~~~~~i~~~l-~s~~~Lp~~lk~cf  305 (348)
                      ....        +.++              .+..  .+.++.+...+......-+   ......| ....+.|..+....
T Consensus       168 ~~~~~l~~r~~~i~l~--------------~l~~--~e~~~~l~~~~~~~~~~~~---~~~~~~l~~~~~G~~~~~~~~~  228 (250)
T 1njg_A          168 KLPVTILSRCLQFHLK--------------ALDV--EQIRHQLEHILNEEHIAHE---PRALQLLARAAEGSLRDALSLT  228 (250)
T ss_dssp             GSCHHHHTTSEEEECC--------------CCCH--HHHHHHHHHHHHHTTCCBC---HHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hCCHHHHHHhhhccCC--------------CCCH--HHHHHHHHHHHHhcCCCCC---HHHHHHHHHHcCCCHHHHHHHH
Confidence            2221        2333              3333  3444433333322101111   2233566 55577887776665


Q ss_pred             hHhccCCCCceecHHHH
Q 040110          306 LYFCVFPTDIELTTRQL  322 (348)
Q Consensus       306 ~y~a~fp~~~~i~~~~L  322 (348)
                      ..+..+-.+ .|+.+.+
T Consensus       229 ~~~~~~~~~-~i~~~~v  244 (250)
T 1njg_A          229 DQAIASGDG-QVSTQAV  244 (250)
T ss_dssp             HHHHTTTTS-SBCHHHH
T ss_pred             HHHHhccCc-eecHHHH
Confidence            555555443 5665554

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.75  E-value=2.6e-08  Score=85.73  Aligned_cols=123  Identities=13%  Similarity=0.054  Sum_probs=73.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcc-eeEEEEeCCCCCHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD-CHAWVRVSNFYNFKRILD  161 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~-~~~wv~~~~~~~~~~~~~  161 (348)
                      .++|++...   +.+.+++.    ..  ....+.|+|++|+|||+||+.+++... ...+. ..+.+..+.......+..
T Consensus        18 ~~~g~~~~~---~~l~~~l~----~~--~~~~~ll~G~~G~GKT~l~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~   87 (226)
T 2chg_A           18 EVVGQDEVI---QRLKGYVE----RK--NIPHLLFSGPPGTGKTATAIALARDLF-GENWRDNFIEMNASDERGIDVVRH   87 (226)
T ss_dssp             GCCSCHHHH---HHHHHHHH----TT--CCCCEEEECSTTSSHHHHHHHHHHHHH-GGGGGGGEEEEETTCTTCHHHHHH
T ss_pred             HHcCcHHHH---HHHHHHHh----CC--CCCeEEEECCCCCCHHHHHHHHHHHHh-ccccccceEEeccccccChHHHHH
Confidence            799999999   99999987    22  222378999999999999999987621 11122 233344333333322222


Q ss_pred             HHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          162 DIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       162 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      .+........                   ...+++.+||+||++..  ...+.+...+.....++++|+||+...
T Consensus        88 ~~~~~~~~~~-------------------~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~  143 (226)
T 2chg_A           88 KIKEFARTAP-------------------IGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVS  143 (226)
T ss_dssp             HHHHHHTSCC-------------------STTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGG
T ss_pred             HHHHHhcccC-------------------CCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChh
Confidence            2211111100                   01257899999999764  344555544443445678888887654

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.49  E-value=1e-07  Score=87.29  Aligned_cols=121  Identities=15%  Similarity=0.102  Sum_probs=71.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccC-Ccc-eeEEEEeCCCCCHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKF-YFD-CHAWVRVSNFYNFKRIL  160 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~F~-~~~wv~~~~~~~~~~~~  160 (348)
                      .++|++...   +.+.+++.    .+  ....+.++|++|+||||+|+.+++.  ... .+. ..++++.+....... +
T Consensus        22 ~~~g~~~~~---~~l~~~l~----~~--~~~~~ll~G~~G~GKt~la~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~-i   89 (323)
T 1sxj_B           22 DIVGNKETI---DRLQQIAK----DG--NMPHMIISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNASDDRGIDV-V   89 (323)
T ss_dssp             GCCSCTHHH---HHHHHHHH----SC--CCCCEEEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTTSCCSHHH-H
T ss_pred             HHHCCHHHH---HHHHHHHH----cC--CCCeEEEECcCCCCHHHHHHHHHHH--hcCCcccCCEEEecCccccChHH-H
Confidence            799999999   99999887    22  2222789999999999999999877  321 121 233444333223222 2


Q ss_pred             HHHHHHhCCCCCccccCCCCHHHHHHHHHHHh-cCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCCh
Q 040110          161 DDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL-TNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPH  233 (348)
Q Consensus       161 ~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~  233 (348)
                      ++++..+....                  ..+ .+++.++|+||++..  ..++.+...+.....++.+|+||+..
T Consensus        90 ~~~~~~~~~~~------------------~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~  147 (323)
T 1sxj_B           90 RNQIKHFAQKK------------------LHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  147 (323)
T ss_dssp             HTHHHHHHHBC------------------CCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             HHHHHHHHhcc------------------ccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCCh
Confidence            22222221000                  001 346899999999763  34444444443334567888888664

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.47  E-value=1.2e-07  Score=79.46  Aligned_cols=44  Identities=23%  Similarity=0.336  Sum_probs=37.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+..+   +.+.+.+.      ......+.|+|++|+|||+||+.+++.
T Consensus        23 ~~~g~~~~~---~~l~~~l~------~~~~~~~ll~G~~G~GKT~l~~~~~~~   66 (195)
T 1jbk_A           23 PVIGRDEEI---RRTIQVLQ------RRTKNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CCCSCHHHH---HHHHHHHT------SSSSCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             ccccchHHH---HHHHHHHh------cCCCCceEEECCCCCCHHHHHHHHHHH
Confidence            799999999   99999988      233445789999999999999999876

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.43  E-value=4.6e-07  Score=83.29  Aligned_cols=116  Identities=7%  Similarity=0.054  Sum_probs=76.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccC------CcceeEEEEeCCCCCH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKF------YFDCHAWVRVSNFYNF  156 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~------~F~~~~wv~~~~~~~~  156 (348)
                      .+.||+++.   +.|...|.+.  -.......+.|+|++|+|||++++.+++......      .| ..+.++...-.+.
T Consensus        21 ~L~~Re~E~---~~i~~~L~~~--i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~-~~v~INc~~~~t~   94 (318)
T 3te6_A           21 LLKSQVEDF---TRIFLPIYDS--LMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIF-DYIHIDALELAGM   94 (318)
T ss_dssp             HHHHHHHHH---HHHHHHHHHH--HHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCE-EEEEEETTCCC--
T ss_pred             ccCCHHHHH---HHHHHHHHHH--hcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCce-EEEEEeccccCCH
Confidence            588999999   9998888621  1133455778999999999999999998732111      12 3556776677788


Q ss_pred             HHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH--hcCCeEEEEEeCCCCh
Q 040110          157 KRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY--LTNKKYFTVLDDVWIE  207 (348)
Q Consensus       157 ~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~--L~~kr~LlVLDdv~~~  207 (348)
                      ..++..|++++.....   ........+...+...  -.+++++++||+++..
T Consensus        95 ~~~~~~I~~~L~g~~~---~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l  144 (318)
T 3te6_A           95 DALYEKIWFAISKENL---CGDISLEALNFYITNVPKAKKRKTLILIQNPENL  144 (318)
T ss_dssp             HHHHHHHHHHHSCCC-----CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSS
T ss_pred             HHHHHHHHHHhcCCCC---CchHHHHHHHHHHHHhhhccCCceEEEEecHHHh
Confidence            8999999999965421   1122333333333332  2456899999999764

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=98.24  E-value=3.8e-07  Score=83.63  Aligned_cols=122  Identities=11%  Similarity=0.098  Sum_probs=70.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCC-cc-eeEEEEeCCCCCHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFY-FD-CHAWVRVSNFYNFKRIL  160 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~-F~-~~~wv~~~~~~~~~~~~  160 (348)
                      .++|++..+   +.+.+++.    .  .....+.++|++|+||||+|+.+++.  .... +. ..+.+..+..... ..+
T Consensus        26 ~~~g~~~~~---~~l~~~l~----~--~~~~~~ll~G~~G~GKT~la~~l~~~--l~~~~~~~~~~~~~~~~~~~~-~~~   93 (327)
T 1iqp_A           26 DIVGQEHIV---KRLKHYVK----T--GSMPHLLFAGPPGVGKTTAALALARE--LFGENWRHNFLELNASDERGI-NVI   93 (327)
T ss_dssp             TCCSCHHHH---HHHHHHHH----H--TCCCEEEEESCTTSSHHHHHHHHHHH--HHGGGHHHHEEEEETTCHHHH-HTT
T ss_pred             HhhCCHHHH---HHHHHHHH----c--CCCCeEEEECcCCCCHHHHHHHHHHH--hcCCcccCceEEeeccccCch-HHH
Confidence            799999999   99998887    2  22334789999999999999999876  3211 11 1223332221111 101


Q ss_pred             HHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          161 DDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       161 ~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      ...+..+...                  .....+++.++|+|+++..  ...+.+...+.....++++|+||....
T Consensus        94 ~~~~~~~~~~------------------~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~  151 (327)
T 1iqp_A           94 REKVKEFART------------------KPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSS  151 (327)
T ss_dssp             HHHHHHHHHS------------------CCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGG
T ss_pred             HHHHHHHHhh------------------CCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCcc
Confidence            1111111000                  0001256889999999753  455556555544445678888887643

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.21  E-value=6.8e-07  Score=74.64  Aligned_cols=44  Identities=25%  Similarity=0.330  Sum_probs=37.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   +.+.+.+.      ......+.|+|++|+|||+||+.+++.
T Consensus        23 ~~~g~~~~~---~~l~~~l~------~~~~~~vll~G~~G~GKT~la~~~~~~   66 (187)
T 2p65_A           23 PVIGRDTEI---RRAIQILS------RRTKNNPILLGDPGVGKTAIVEGLAIK   66 (187)
T ss_dssp             CCCSCHHHH---HHHHHHHT------SSSSCEEEEESCGGGCHHHHHHHHHHH
T ss_pred             hhhcchHHH---HHHHHHHh------CCCCCceEEECCCCCCHHHHHHHHHHH
Confidence            799999999   99999988      233445679999999999999999876

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=98.10  E-value=3.7e-06  Score=76.66  Aligned_cols=120  Identities=13%  Similarity=0.064  Sum_probs=71.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcc-eeEEEEeCCCCCHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD-CHAWVRVSNFYNFKRILD  161 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~-~~~wv~~~~~~~~~~~~~  161 (348)
                      .++|++...   +.+.+++.    .+  ....+.++|++|+|||++|+.+++... ...+. ..+.++.+.....     
T Consensus        18 ~~~g~~~~~---~~l~~~l~----~~--~~~~~ll~G~~G~GKt~la~~l~~~l~-~~~~~~~~~~~~~~~~~~~-----   82 (319)
T 2chq_A           18 EVVGQDEVI---QRLKGYVE----RK--NIPHLLFSGPPGTGKTATAIALARDLF-GENWRDNFIEMNASDERGI-----   82 (319)
T ss_dssp             GSCSCHHHH---HHHHTTTT----TT--CCCCEEEESSSSSSHHHHHHHHHHHHH-TTCHHHHCEEEETTSTTCT-----
T ss_pred             HHhCCHHHH---HHHHHHHh----CC--CCCeEEEECcCCcCHHHHHHHHHHHhc-CCcccCCeEEEeCccccCh-----
Confidence            799999999   99999887    22  222378899999999999999987621 11111 1223333321110     


Q ss_pred             HHHHHhCCCCCccccCCCCHHHHHHHHHHH--h-cCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          162 DIMKSLMPTSSWLKIMGKDYKSEKTILRDY--L-TNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       162 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~--L-~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                                       ....+....+...  + .+++.++|+|++...  ...+.+...+.....++++|+||....
T Consensus        83 -----------------~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~  143 (319)
T 2chq_A           83 -----------------DVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVS  143 (319)
T ss_dssp             -----------------TTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGG
T ss_pred             -----------------HHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChh
Confidence                             0111111111111  1 256889999999653  445666666655455677888776543

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.09  E-value=6.9e-06  Score=73.92  Aligned_cols=50  Identities=14%  Similarity=0.228  Sum_probs=36.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCC-------CCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGL-------GQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~-------~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.|.+.+...-..       +-....-+.|+|++|+|||+||+.+++.
T Consensus        18 ~i~G~~~~~---~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~   74 (285)
T 3h4m_A           18 DIGGLEKQM---QEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATE   74 (285)
T ss_dssp             GSCSCHHHH---HHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHH
T ss_pred             HhcCHHHHH---HHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            899999999   8888777410000       0123445789999999999999999887

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.02  E-value=7.1e-06  Score=66.38  Aligned_cols=46  Identities=17%  Similarity=0.174  Sum_probs=32.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|+...+   +++.+.+...   ..... -|.|+|.+|+|||++|+.+++.
T Consensus         2 ~iiG~s~~~---~~~~~~~~~~---a~~~~-~vll~G~~GtGKt~lA~~i~~~   47 (145)
T 3n70_A            2 ELIGRSEWI---NQYRRRLQQL---SETDI-AVWLYGAPGTGRMTGARYLHQF   47 (145)
T ss_dssp             --CCSSHHH---HHHHHHHHHH---TTCCS-CEEEESSTTSSHHHHHHHHHHS
T ss_pred             CceeCCHHH---HHHHHHHHHH---hCCCC-CEEEECCCCCCHHHHHHHHHHh
Confidence            478888888   7777766411   01122 3669999999999999999886

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.97  E-value=3.4e-06  Score=76.84  Aligned_cols=50  Identities=14%  Similarity=0.132  Sum_probs=33.9

Q ss_pred             cccccccccccHHHHHhhcCCC---------CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS---------SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~---------~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.|.+++...         .-........+.|+|++|+|||++|+.+++.
T Consensus        32 ~i~G~~~~~---~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~   90 (309)
T 3syl_A           32 ELIGLKPVK---DRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGL   90 (309)
T ss_dssp             HSSSCHHHH---HHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             HccChHHHH---HHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            488988888   6666554200         0001233446789999999999999988766

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=97.97  E-value=1.5e-05  Score=70.65  Aligned_cols=50  Identities=16%  Similarity=0.248  Sum_probs=33.5

Q ss_pred             cccccccccccHHHHHhhc---CCCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRL---PPSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L---~~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+..+   +.+.+++   ..+.   ..+-...+-+.|+|++|+|||++|+.+++.
T Consensus         7 ~i~G~~~~~---~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~   62 (262)
T 2qz4_A            7 DVAGMHEAK---LEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATE   62 (262)
T ss_dssp             SSCSCHHHH---HHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             HhCCHHHHH---HHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            688888888   5554433   2110   011133445779999999999999999986

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=97.96  E-value=1.4e-05  Score=74.63  Aligned_cols=45  Identities=24%  Similarity=0.397  Sum_probs=36.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|++..+   +.+...+.    .+. ....+.|+|++|+||||+|+.+++.
T Consensus        17 ~~vg~~~~~---~~L~~~l~----~~~-~~~~~ll~G~~G~GKT~la~~la~~   61 (373)
T 1jr3_A           17 DVVGQEHVL---TALANGLS----LGR-IHHAYLFSGTRGVGKTSIARLLAKG   61 (373)
T ss_dssp             TSCSCHHHH---HHHHHHHH----HTC-CCSEEEEESCTTSSHHHHHHHHHHH
T ss_pred             hccCcHHHH---HHHHHHHH----hCC-CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            699999999   99988886    212 2236779999999999999999876

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.93  E-value=6e-06  Score=69.17  Aligned_cols=101  Identities=14%  Similarity=0.081  Sum_probs=55.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      ...+.|+|++|+||||||+.+++.......+. ++++      +..++...+...+....       .  ......+   
T Consensus        38 g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~-~~~~------~~~~~~~~~~~~~~~~~-------~--~~~~~~~---   98 (180)
T 3ec2_A           38 GKGLTFVGSPGVGKTHLAVATLKAIYEKKGIR-GYFF------DTKDLIFRLKHLMDEGK-------D--TKFLKTV---   98 (180)
T ss_dssp             CCEEEECCSSSSSHHHHHHHHHHHHHHHSCCC-CCEE------EHHHHHHHHHHHHHHTC-------C--SHHHHHH---
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHcCCe-EEEE------EHHHHHHHHHHHhcCch-------H--HHHHHHh---
Confidence            45789999999999999999988732122222 2333      34555555554443220       0  1222222   


Q ss_pred             hcCCeEEEEEeCCCC--hhhHH--HHHhhCCC-CCCCcEEEEEeCCh
Q 040110          192 LTNKKYFTVLDDVWI--EKIWD--DLREALPD-NQIGSRALITVGPH  233 (348)
Q Consensus       192 L~~kr~LlVLDdv~~--~~~~~--~l~~~l~~-~~~gskIlvTTR~~  233 (348)
                       . +.-+||||++..  .+.|.  .+...+.. ...|..+|+||...
T Consensus        99 -~-~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~~  143 (180)
T 3ec2_A           99 -L-NSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNYS  143 (180)
T ss_dssp             -H-TCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCCC
T ss_pred             -c-CCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence             2 456899999973  23332  22221111 12356788888654

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.86  E-value=2.4e-05  Score=72.39  Aligned_cols=44  Identities=11%  Similarity=0.118  Sum_probs=36.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|++..+   +.+..++.    .+...  .+.++|++|+||||+|+.+++.
T Consensus        38 ~i~g~~~~~---~~l~~~l~----~~~~~--~~ll~G~~G~GKT~la~~la~~   81 (353)
T 1sxj_D           38 EVTAQDHAV---TVLKKTLK----SANLP--HMLFYGPPGTGKTSTILALTKE   81 (353)
T ss_dssp             TCCSCCTTH---HHHHHHTT----CTTCC--CEEEECSTTSSHHHHHHHHHHH
T ss_pred             HhhCCHHHH---HHHHHHHh----cCCCC--EEEEECCCCCCHHHHHHHHHHH
Confidence            799999999   99999988    22222  2789999999999999999877

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.85  E-value=1e-05  Score=68.98  Aligned_cols=72  Identities=19%  Similarity=0.158  Sum_probs=42.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHh
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL  192 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L  192 (348)
                      ..+.|+|++|+|||+||+.+++.  .......++++++      ..+...+...+...         ........+.   
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~--~~~~~~~~~~~~~------~~~~~~~~~~~~~~---------~~~~~~~~~~---  114 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANE--LAKRNVSSLIVYV------PELFRELKHSLQDQ---------TMNEKLDYIK---  114 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH--HHTTTCCEEEEEH------HHHHHHHHHC---C---------CCHHHHHHHH---
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEh------HHHHHHHHHHhccc---------hHHHHHHHhc---
Confidence            56789999999999999999987  3333334556643      34445544433211         1233333332   


Q ss_pred             cCCeEEEEEeCCCC
Q 040110          193 TNKKYFTVLDDVWI  206 (348)
Q Consensus       193 ~~kr~LlVLDdv~~  206 (348)
                       . .-+|||||++.
T Consensus       115 -~-~~~lilDei~~  126 (202)
T 2w58_A          115 -K-VPVLMLDDLGA  126 (202)
T ss_dssp             -H-SSEEEEEEECC
T ss_pred             -C-CCEEEEcCCCC
Confidence             2 23999999954

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=97.84  E-value=3.6e-05  Score=70.80  Aligned_cols=50  Identities=14%  Similarity=0.155  Sum_probs=36.7

Q ss_pred             cccccccccccHHHHHhhcCC----C--CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----S--SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~--~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.|.+.+.-    +  -.......+-+.++|++|+|||+||+.+++.
T Consensus        19 di~G~~~~~---~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~   74 (322)
T 3eie_A           19 DVAGLEGAK---EALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE   74 (322)
T ss_dssp             GSCSCHHHH---HHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHH
T ss_pred             HhcChHHHH---HHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            789999999   888777610    0  0012233456789999999999999999887

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=97.84  E-value=2.9e-05  Score=71.26  Aligned_cols=118  Identities=13%  Similarity=0.130  Sum_probs=69.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      .++|.+...   +.+.+++.    .+ ....++.+.|++|+|||++|+.+++.  ..   ...+.++.+. .... .+..
T Consensus        27 ~ivg~~~~~---~~l~~~l~----~~-~~~~~~L~~G~~G~GKT~la~~la~~--l~---~~~~~i~~~~-~~~~-~i~~   91 (324)
T 3u61_B           27 ECILPAFDK---ETFKSITS----KG-KIPHIILHSPSPGTGKTTVAKALCHD--VN---ADMMFVNGSD-CKID-FVRG   91 (324)
T ss_dssp             TSCCCHHHH---HHHHHHHH----TT-CCCSEEEECSSTTSSHHHHHHHHHHH--TT---EEEEEEETTT-CCHH-HHHT
T ss_pred             HHhCcHHHH---HHHHHHHH----cC-CCCeEEEeeCcCCCCHHHHHHHHHHH--hC---CCEEEEcccc-cCHH-HHHH
Confidence            799999999   99998887    22 23346778899999999999999877  32   1233444332 2222 2222


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCChh---hHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEK---IWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~~---~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      ++..+....                   ...+++.++++|++....   ..+.+...+.....+.++|+||....
T Consensus        92 ~~~~~~~~~-------------------~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~  147 (324)
T 3u61_B           92 PLTNFASAA-------------------SFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNID  147 (324)
T ss_dssp             HHHHHHHBC-------------------CCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGG
T ss_pred             HHHHHHhhc-------------------ccCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCcc
Confidence            221111000                   012368899999998643   44444444332223567777776644

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.79  E-value=0.0001  Score=68.36  Aligned_cols=44  Identities=11%  Similarity=0.043  Sum_probs=35.5

Q ss_pred             cccccccccccHHHHHhhc-CCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRL-PPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L-~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.+.+++ .    .+. ... +.|+|+.|+||||+|+.+++.
T Consensus        15 ~~vg~~~~~---~~l~~~~~~----~~~-~~~-~ll~Gp~G~GKTtl~~~la~~   59 (354)
T 1sxj_E           15 ALSHNEELT---NFLKSLSDQ----PRD-LPH-LLLYGPNGTGKKTRCMALLES   59 (354)
T ss_dssp             GCCSCHHHH---HHHHTTTTC----TTC-CCC-EEEECSTTSSHHHHHHTHHHH
T ss_pred             HhcCCHHHH---HHHHHHHhh----CCC-CCe-EEEECCCCCCHHHHHHHHHHH
Confidence            789999999   9999988 4    222 223 789999999999999988773

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.78  E-value=0.0002  Score=65.81  Aligned_cols=50  Identities=12%  Similarity=0.161  Sum_probs=35.0

Q ss_pred             cccccccccccHHHHHhhcCC----CC--CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----SS--GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~~--~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+..+   +.|.+.+.-    +.  .......+-+.++|++|+|||+||+.+++.
T Consensus        13 di~G~~~~k---~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~   68 (322)
T 1xwi_A           13 DVAGLEGAK---EALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE   68 (322)
T ss_dssp             GSCSCHHHH---HHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHH
T ss_pred             HhcCHHHHH---HHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHH
Confidence            788888888   666655410    00  011223456789999999999999999987

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.76  E-value=0.00014  Score=65.68  Aligned_cols=50  Identities=14%  Similarity=0.114  Sum_probs=36.5

Q ss_pred             cccccccccccHHHHHhhcCCCC------CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS------GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~------~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+.+.+..+.      .........+.|+|++|+||||+|+.+++.
T Consensus        22 ~i~G~~~~~---~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~   77 (297)
T 3b9p_A           22 DIAGQDVAK---QALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATE   77 (297)
T ss_dssp             GSCCCHHHH---HHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHH
T ss_pred             HhCChHHHH---HHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            799999999   88877763100      000123456789999999999999999987

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=97.73  E-value=3.2e-05  Score=69.17  Aligned_cols=47  Identities=15%  Similarity=0.138  Sum_probs=33.5

Q ss_pred             cccccccccccHHHHHh-------hcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQ-------RLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~-------~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.....   +.+..       .+..   ........+.|+|++|+|||+||+.+++.
T Consensus        34 ~~i~~~~~~---~~i~~~~~~l~~~l~~---~~~~~~~~vLl~G~~GtGKT~la~~ia~~   87 (272)
T 1d2n_A           34 GIIKWGDPV---TRVLDDGELLVQQTKN---SDRTPLVSVLLEGPPHSGKTALAAKIAEE   87 (272)
T ss_dssp             CCCCCSHHH---HHHHHHHHHHHHHHHH---CSSCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCccHHH---HHHHHHHHHHHHHHhc---cCCCCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            677877766   55555       2320   11345567889999999999999999986

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=97.73  E-value=4.3e-05  Score=71.39  Aligned_cols=50  Identities=10%  Similarity=0.050  Sum_probs=36.6

Q ss_pred             cccccccccccHHHHHhhcCC----CC--CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----SS--GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~~--~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.|.+.+..    +.  .......+.+.|+|++|+|||+||+.+++.
T Consensus        85 ~i~G~~~~~---~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~  140 (357)
T 3d8b_A           85 DIAGVEFAK---ATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQ  140 (357)
T ss_dssp             GSCSCHHHH---HHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHH
T ss_pred             HhCChHHHH---HHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            799999999   887776631    00  001123456789999999999999999876

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.72  E-value=7.9e-05  Score=69.45  Aligned_cols=49  Identities=18%  Similarity=0.158  Sum_probs=35.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|++.....+..+.+.+.    .+......+.|+|++|+|||++|+.+++.
T Consensus        45 ~ivG~~~~~~~l~~l~~~~~----~~~~~~~~vLl~GppGtGKT~la~~la~~   93 (368)
T 3uk6_A           45 GMVGQLAARRAAGVVLEMIR----EGKIAGRAVLIAGQPGTGKTAIAMGMAQA   93 (368)
T ss_dssp             TEESCHHHHHHHHHHHHHHH----TTCCTTCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             hccChHHHHHHHHHHHHHHH----cCCCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            79999998722233555555    22223357789999999999999999987

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.72  E-value=0.00013  Score=68.80  Aligned_cols=50  Identities=12%  Similarity=0.086  Sum_probs=36.6

Q ss_pred             cccccccccccHHHHHhhcCCC----C--CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS----S--GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~----~--~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.|.+.+..+    .  .......+-+.|+|++|+|||+||+.+++.
T Consensus       116 ~iiG~~~~~---~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~  171 (389)
T 3vfd_A          116 DIAGQDLAK---QALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAE  171 (389)
T ss_dssp             GSCSCHHHH---HHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHH
T ss_pred             HhCCHHHHH---HHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            799999999   8888877210    0  000122356789999999999999999876

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.67  E-value=1.4e-05  Score=64.57  Aligned_cols=46  Identities=17%  Similarity=0.204  Sum_probs=31.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|+...+   +++.+.+...   ..... -|.|+|.+|+|||++|+.+++.
T Consensus         5 ~~iG~s~~~---~~l~~~~~~~---~~~~~-~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A            5 DKLGNSAAI---QEMNREVEAA---AKRTS-PVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             ---CCCHHH---HHHHHHHHHH---HTCSS-CEEEEEETTCCHHHHHGGGCCT
T ss_pred             CceeCCHHH---HHHHHHHHHH---hCCCC-cEEEECCCCccHHHHHHHHHHh
Confidence            678988888   7777766411   01122 3668999999999999999877

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=97.62  E-value=0.00017  Score=67.26  Aligned_cols=50  Identities=14%  Similarity=0.172  Sum_probs=36.0

Q ss_pred             cccccccccccHHHHHhhcCC----CC--CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----SS--GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~~--~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.|.+.+..    +.  .......+-+.|+|++|+|||+||+.+++.
T Consensus        52 di~G~~~~~---~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~  107 (355)
T 2qp9_X           52 DVAGLEGAK---EALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE  107 (355)
T ss_dssp             GSCCGGGHH---HHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHH
T ss_pred             HhCCHHHHH---HHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            799999999   888776620    00  011122344778999999999999999987

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=97.61  E-value=5.7e-05  Score=72.64  Aligned_cols=100  Identities=18%  Similarity=0.222  Sum_probs=58.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcc--eeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD--CHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      ...+.|+|++|+||||||+.+++.  ....|+  ..++++      ...+...+...+...         ..    ..+.
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~--l~~~~~~~~v~~v~------~~~~~~~~~~~~~~~---------~~----~~~~  188 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNY--VVQNEPDLRVMYIT------SEKFLNDLVDSMKEG---------KL----NEFR  188 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHH--HHHHCCSSCEEEEE------HHHHHHHHHHHHHTT---------CH----HHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEee------HHHHHHHHHHHHHcc---------cH----HHHH
Confidence            456789999999999999999987  433332  234443      233445555544332         11    2233


Q ss_pred             HHhcCCeEEEEEeCCCChh----hHHHHHhhCCC-CCCCcEEEEEeCC
Q 040110          190 DYLTNKKYFTVLDDVWIEK----IWDDLREALPD-NQIGSRALITVGP  232 (348)
Q Consensus       190 ~~L~~kr~LlVLDdv~~~~----~~~~l~~~l~~-~~~gskIlvTTR~  232 (348)
                      ..+..+.-+|+|||+....    ..+.+...+.. ...|..||+||.+
T Consensus       189 ~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~  236 (440)
T 2z4s_A          189 EKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDR  236 (440)
T ss_dssp             HHHTTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             HHhcCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            4444467799999996431    22333332211 1346778888876

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.58  E-value=0.00012  Score=64.70  Aligned_cols=53  Identities=23%  Similarity=0.232  Sum_probs=33.0

Q ss_pred             cccccccccccHHHHHhhcCCCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+..+..+.+++.++..+.   ..+....+-+.|+|++|+||||||+.+++.
T Consensus        13 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   68 (257)
T 1lv7_A           13 DVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE   68 (257)
T ss_dssp             GSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            78898877722234444432110   001112334779999999999999999876

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=97.58  E-value=0.00019  Score=61.49  Aligned_cols=89  Identities=11%  Similarity=0.029  Sum_probs=53.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc-------cc-cCCCCHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW-------LK-IMGKDYKS  183 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-------~~-~~~~~~~~  183 (348)
                      -.++.|+|.+|+|||||+..++.    . .-..++|++....++...+.. +...++.....       .. ....+..+
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~----~-~~~~v~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGL----L-SGKKVAYVDTEGGFSPERLVQ-MAETRGLNPEEALSRFILFTPSDFKEQRR   93 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHH----H-HCSEEEEEESSCCCCHHHHHH-HHHTTTCCHHHHHHHEEEECCTTTSHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH----H-cCCcEEEEECCCCCCHHHHHH-HHHhcCCChHHHhhcEEEEecCCHHHHHH
Confidence            34889999999999999999987    1 113577887766556655443 33333321000       01 11112234


Q ss_pred             HHHHHHHHhcCCeEEEEEeCCCC
Q 040110          184 EKTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       184 ~~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                      ....++..++.+.-++|+|.+..
T Consensus        94 ~~~~~~~l~~~~~~lliiD~~~~  116 (220)
T 2cvh_A           94 VIGSLKKTVDSNFALVVVDSITA  116 (220)
T ss_dssp             HHHHHHHHCCTTEEEEEEECCCC
T ss_pred             HHHHHHHHhhcCCCEEEEcCcHH
Confidence            55555555544578999999864

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=97.58  E-value=1.4e-05  Score=69.55  Aligned_cols=61  Identities=3%  Similarity=-0.063  Sum_probs=36.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVS  151 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~  151 (348)
                      .|+|.+......+.+..++.      ......+.|+|++|+||||||+.+++.  .......+.+++.+
T Consensus        29 ~~~~~~~~~~~~~~l~~~~~------~~~~~~~ll~G~~G~GKT~la~~l~~~--~~~~~~~~~~~~~~   89 (242)
T 3bos_A           29 SYYPAAGNDELIGALKSAAS------GDGVQAIYLWGPVKSGRTHLIHAACAR--ANELERRSFYIPLG   89 (242)
T ss_dssp             TSCC--CCHHHHHHHHHHHH------TCSCSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEEGG
T ss_pred             hccCCCCCHHHHHHHHHHHh------CCCCCeEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEHH
Confidence            67874321101145555444      123456789999999999999999877  32222345566543

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=97.58  E-value=3.8e-05  Score=70.25  Aligned_cols=49  Identities=16%  Similarity=0.236  Sum_probs=36.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|++..+   +.+..++.... ........+.|+|++|+|||++|+.+++.
T Consensus        13 ~~ig~~~~~---~~l~~~l~~~~-~~~~~~~~vll~G~~GtGKT~la~~i~~~   61 (324)
T 1hqc_A           13 EYIGQERLK---QKLRVYLEAAK-ARKEPLEHLLLFGPPGLGKTTLAHVIAHE   61 (324)
T ss_dssp             TCCSCHHHH---HHHHHHHHHHH-HHCSCCCCCEEECCTTCCCHHHHHHHHHH
T ss_pred             HhhCHHHHH---HHHHHHHHHHH-ccCCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            799999998   77777764110 00122345778999999999999999876

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=97.53  E-value=0.00023  Score=68.51  Aligned_cols=50  Identities=12%  Similarity=0.161  Sum_probs=36.2

Q ss_pred             cccccccccccHHHHHhhcCC----CC--CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----SS--GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~~--~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.|.+.+..    +.  .......+-+.|+|++|+|||+||+.+++.
T Consensus       135 di~G~~~~k---~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~  190 (444)
T 2zan_A          135 DVAGLEGAK---EALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE  190 (444)
T ss_dssp             GSCSCHHHH---HHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HhcCHHHHH---HHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            789999988   777776520    00  001123456789999999999999999987

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=97.52  E-value=0.00028  Score=64.15  Aligned_cols=50  Identities=24%  Similarity=0.276  Sum_probs=35.5

Q ss_pred             cccccccccccHHHHHhhcCCC-------CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-------SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-------~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.|.+++..+       ...+-...+.+.|+|++|+|||+||+.+++.
T Consensus        16 di~G~~~~~---~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~   72 (301)
T 3cf0_A           16 DIGGLEDVK---RELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE   72 (301)
T ss_dssp             GSCSCHHHH---HHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             HhCCHHHHH---HHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHH
Confidence            788988888   7666655310       0001123456789999999999999999987

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.52  E-value=0.00013  Score=67.28  Aligned_cols=49  Identities=18%  Similarity=0.216  Sum_probs=37.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|++..+   +.+..++.... ........+.|+|++|+|||+||+.+++.
T Consensus        30 ~iiG~~~~~---~~l~~~l~~~~-~~~~~~~~vll~G~~GtGKT~la~~ia~~   78 (338)
T 3pfi_A           30 GYIGQESIK---KNLNVFIAAAK-KRNECLDHILFSGPAGLGKTTLANIISYE   78 (338)
T ss_dssp             GCCSCHHHH---HHHHHHHHHHH-HTTSCCCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             HhCChHHHH---HHHHHHHHHHH-hcCCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            799999999   88888775210 01223345789999999999999999877

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=97.49  E-value=0.00012  Score=67.14  Aligned_cols=99  Identities=12%  Similarity=0.108  Sum_probs=52.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDY  191 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  191 (348)
                      ...+.|+|++|+||||||+.+++..... .+ ..++++      ...+...+...+...         ....    +...
T Consensus        37 ~~~lll~G~~GtGKT~la~~i~~~~~~~-~~-~~~~i~------~~~~~~~~~~~~~~~---------~~~~----~~~~   95 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQAAGNEAKKR-GY-RVIYSS------ADDFAQAMVEHLKKG---------TINE----FRNM   95 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHHHHHHHHHHT-TC-CEEEEE------HHHHHHHHHHHHHHT---------CHHH----HHHH
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHC-CC-EEEEEE------HHHHHHHHHHHHHcC---------cHHH----HHHH
Confidence            3457799999999999999999862111 11 234443      233444444433211         1122    2222


Q ss_pred             hcCCeEEEEEeCCCChh----hHHHHHhhCCC-CCCCcEEEEEeCC
Q 040110          192 LTNKKYFTVLDDVWIEK----IWDDLREALPD-NQIGSRALITVGP  232 (348)
Q Consensus       192 L~~kr~LlVLDdv~~~~----~~~~l~~~l~~-~~~gskIlvTTR~  232 (348)
                      +. +..+|+||++....    ..+.+...+.. ...+..||+||.+
T Consensus        96 ~~-~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~  140 (324)
T 1l8q_A           96 YK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDR  140 (324)
T ss_dssp             HH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             hc-CCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecC
Confidence            22 36799999996532    12233222211 1235578887754

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=97.43  E-value=0.00048  Score=62.78  Aligned_cols=112  Identities=7%  Similarity=-0.048  Sum_probs=65.0

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc-cccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCCCC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN-FVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPTSS  172 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~-~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~~~  172 (348)
                      +.|.+.+.    .+.  .....++|+.|+||||+|..+.+.. ...........+..+. ...+.. .+++...+.... 
T Consensus         7 ~~L~~~i~----~~~--~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~id~-ir~li~~~~~~p-   78 (305)
T 2gno_A            7 ETLKRIIE----KSE--GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDD-IRTIKDFLNYSP-   78 (305)
T ss_dssp             HHHHHHHH----TCS--SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHH-HHHHHHHHTSCC-
T ss_pred             HHHHHHHH----CCC--CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCHHH-HHHHHHHHhhcc-
Confidence            66666666    222  5678899999999999999997641 1111122334554432 233322 233444443210 


Q ss_pred             ccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCC--hhhHHHHHhhCCCCCCCcEEEEEeCCh
Q 040110          173 WLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWI--EKIWDDLREALPDNQIGSRALITVGPH  233 (348)
Q Consensus       173 ~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~--~~~~~~l~~~l~~~~~gskIlvTTR~~  233 (348)
                                         ..+++-++|+|++..  ....+.+...+-...+.+.+|++|.+.
T Consensus        79 -------------------~~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~  122 (305)
T 2gno_A           79 -------------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRW  122 (305)
T ss_dssp             -------------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             -------------------ccCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECCh
Confidence                               124577889999975  355666766665444567777766543

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.43  E-value=0.0002  Score=70.29  Aligned_cols=50  Identities=16%  Similarity=0.181  Sum_probs=38.6

Q ss_pred             cccccccccccHHHHHhhcCCC-----------CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-----------SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-----------~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|++...   +.+.++|...           ...+....+.+.|+|++|+||||+|+.+++.
T Consensus        40 dliG~~~~~---~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~  100 (516)
T 1sxj_A           40 QVCGNKGSV---MKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE  100 (516)
T ss_dssp             GCCSCHHHH---HHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HhcCCHHHH---HHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            799999999   9999888620           0001123467889999999999999999987

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.41  E-value=0.00019  Score=66.40  Aligned_cols=44  Identities=14%  Similarity=0.183  Sum_probs=34.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.|...+.    .+  ....+.++|++|+||||+|+.+++.
T Consensus        26 ~~~g~~~~~---~~L~~~i~----~g--~~~~~ll~Gp~G~GKTtla~~la~~   69 (340)
T 1sxj_C           26 EVYGQNEVI---TTVRKFVD----EG--KLPHLLFYGPPGTGKTSTIVALARE   69 (340)
T ss_dssp             GCCSCHHHH---HHHHHHHH----TT--CCCCEEEECSSSSSHHHHHHHHHHH
T ss_pred             HhcCcHHHH---HHHHHHHh----cC--CCceEEEECCCCCCHHHHHHHHHHH
Confidence            678888888   88887777    22  2222788999999999999999876

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=97.40  E-value=0.00045  Score=62.56  Aligned_cols=26  Identities=12%  Similarity=0.245  Sum_probs=22.8

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++.+.++|++|+|||+||+.+++.
T Consensus        34 ~~p~~lLl~GppGtGKT~la~aiA~~   59 (293)
T 3t15_A           34 KVPLILGIWGGKGQGKSFQCELVFRK   59 (293)
T ss_dssp             CCCSEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            44567888999999999999999987

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=97.37  E-value=0.00017  Score=69.89  Aligned_cols=44  Identities=20%  Similarity=0.318  Sum_probs=36.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   +.+.+.|.    .  ....-+.++|++|+|||++|+.+++.
T Consensus       181 ~iiGr~~~i---~~l~~~l~----r--~~~~~~LL~G~pG~GKT~la~~la~~  224 (468)
T 3pxg_A          181 PVIGRSKEI---QRVIEVLS----R--RTKNNPVLIGEPGVGKTAIAEGLAQQ  224 (468)
T ss_dssp             CCCCCHHHH---HHHHHHHH----C--SSSCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             CccCcHHHH---HHHHHHHh----c--cCCCCeEEECCCCCCHHHHHHHHHHH
Confidence            689999999   99999986    1  22234568999999999999999876

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.36  E-value=0.00045  Score=56.00  Aligned_cols=36  Identities=11%  Similarity=0.078  Sum_probs=26.9

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      +.++..|..    -  .-..++|+|+.|+|||||++.+++..
T Consensus        25 ~~~~~~l~~----~--~g~~~~l~G~~G~GKTtL~~~i~~~~   60 (149)
T 2kjq_A           25 AELVYVLRH----K--HGQFIYVWGEEGAGKSHLLQAWVAQA   60 (149)
T ss_dssp             HHHHHHCCC----C--CCSEEEEESSSTTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHh----c--CCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            445555651    1  33478899999999999999998863

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=97.35  E-value=0.0002  Score=63.57  Aligned_cols=46  Identities=20%  Similarity=0.233  Sum_probs=31.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.....   .++.+.+...   .... .-+.|+|.+|+|||++|+.+++.
T Consensus         7 ~~ig~~~~~---~~~~~~~~~~---~~~~-~~vll~G~~GtGKt~la~~i~~~   52 (265)
T 2bjv_A            7 NLLGEANSF---LEVLEQVSHL---APLD-KPVLIIGERGTGKELIASRLHYL   52 (265)
T ss_dssp             ---CCCHHH---HHHHHHHHHH---TTSC-SCEEEECCTTSCHHHHHHHHHHT
T ss_pred             cceeCCHHH---HHHHHHHHHH---hCCC-CCEEEECCCCCcHHHHHHHHHHh
Confidence            578988888   7776555311   0112 34668999999999999999987

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.34  E-value=8.2e-05  Score=71.63  Aligned_cols=47  Identities=17%  Similarity=0.176  Sum_probs=31.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+.....|...+.      ......+.|+|++|+||||||+.+++.
T Consensus        27 ~ivGq~~~~~~~~~L~~~i~------~~~~~~vLL~GppGtGKTtlAr~ia~~   73 (447)
T 3pvs_A           27 QYIGQQHLLAAGKPLPRAIE------AGHLHSMILWGPPGTGKTTLAEVIARY   73 (447)
T ss_dssp             TCCSCHHHHSTTSHHHHHHH------HTCCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HhCCcHHHHhchHHHHHHHH------cCCCcEEEEECCCCCcHHHHHHHHHHH
Confidence            67776655411123444444      223356789999999999999999987

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=97.32  E-value=0.00015  Score=75.43  Aligned_cols=44  Identities=23%  Similarity=0.312  Sum_probs=36.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   +++.+.|.    .  ....-+.++|++|+|||++|+.+++.
T Consensus       171 ~viGr~~~i---~~l~~~l~----~--~~~~~vlL~G~pG~GKT~la~~la~~  214 (854)
T 1qvr_A          171 PVIGRDEEI---RRVIQILL----R--RTKNNPVLIGEPGVGKTAIVEGLAQR  214 (854)
T ss_dssp             CCCSCHHHH---HHHHHHHH----C--SSCCCCEEEECTTSCHHHHHHHHHHH
T ss_pred             ccCCcHHHH---HHHHHHHh----c--CCCCceEEEcCCCCCHHHHHHHHHHH
Confidence            589999999   99999887    2  22223578999999999999999876

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.31  E-value=8.8e-05  Score=67.37  Aligned_cols=50  Identities=16%  Similarity=0.203  Sum_probs=35.7

Q ss_pred             cccccccccccHHHHHhhcCCC---CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS---SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~---~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+...   -.........+.++|++|+|||++|+.+++.
T Consensus        18 ~i~G~~~~~---~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~   70 (311)
T 4fcw_A           18 RVVGQDEAI---RAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT   70 (311)
T ss_dssp             TCCSCHHHH---HHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHH
T ss_pred             hcCCHHHHH---HHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHH
Confidence            578888887   7776666411   0011223457889999999999999999876

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=97.30  E-value=0.0002  Score=69.65  Aligned_cols=50  Identities=14%  Similarity=0.234  Sum_probs=35.8

Q ss_pred             cccccccccccHHHHHhhcCCCC-------CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS-------GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~-------~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   ++|.+++..+-       ..+.....-+.|+|++|+|||++|+.+++.
T Consensus       205 ~i~G~~~~~---~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~  261 (489)
T 3hu3_A          205 DIGGCRKQL---AQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE  261 (489)
T ss_dssp             GCCSCHHHH---HHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HcCCHHHHH---HHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHH
Confidence            688999999   77777664100       000123345779999999999999999877

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=97.30  E-value=0.00039  Score=67.27  Aligned_cols=53  Identities=19%  Similarity=0.259  Sum_probs=33.3

Q ss_pred             cccccccccccHHHHHhhcCCCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+..+..+.+++..+..+.   .-+....+-+.|+|++|+|||+||+.+++.
T Consensus        17 di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~   72 (476)
T 2ce7_A           17 DVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGE   72 (476)
T ss_dssp             GCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            78898888722244444332110   001112233779999999999999999986

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.30  E-value=0.00093  Score=68.54  Aligned_cols=44  Identities=20%  Similarity=0.229  Sum_probs=36.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   +++.+.|..      ....-+.|+|.+|+|||++|+.+++.
T Consensus       187 ~~iGr~~~i---~~l~~~l~~------~~~~~vlL~G~~GtGKT~la~~la~~  230 (758)
T 1r6b_X          187 PLIGREKEL---ERAIQVLCR------RRKNNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_dssp             CCCSCHHHH---HHHHHHHTS------SSSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CccCCHHHH---HHHHHHHhc------cCCCCeEEEcCCCCCHHHHHHHHHHH
Confidence            689999999   999999882      23334678999999999999999875

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.27  E-value=0.0015  Score=60.13  Aligned_cols=40  Identities=8%  Similarity=0.018  Sum_probs=27.3

Q ss_pred             CCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCCh
Q 040110          194 NKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPH  233 (348)
Q Consensus       194 ~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~  233 (348)
                      +++-++|+|+++.-  ...+.+...+.....++.+|++|.+.
T Consensus       107 ~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~  148 (334)
T 1a5t_A          107 GGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREP  148 (334)
T ss_dssp             SSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCG
T ss_pred             CCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCCh
Confidence            46788999999753  45666776665544567777777664

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.26  E-value=0.00081  Score=64.23  Aligned_cols=50  Identities=22%  Similarity=0.302  Sum_probs=34.6

Q ss_pred             cccccccccccHHHHHhhcCC----CC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----SS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|.+..+   ++|.+.+.-    ++   ..+-..++=+.++|++|+|||+||+++++.
T Consensus       182 digGl~~~k---~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e  238 (437)
T 4b4t_L          182 GIGGLTEQI---RELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAAT  238 (437)
T ss_dssp             GGCSCHHHH---HHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             HhCChHHHH---HHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            567888888   666554420    00   012234556778999999999999999988

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=97.24  E-value=0.00034  Score=63.95  Aligned_cols=69  Identities=10%  Similarity=0.090  Sum_probs=46.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEe--CCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRV--SNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~--~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      -+++.|+|++|+|||+||.+++..     .-..++|++.  ....+             .       ...+.+.....+.
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~-----~G~~VlyIs~~~eE~v~-------------~-------~~~~le~~l~~i~  177 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA-----LGGKDKYATVRFGEPLS-------------G-------YNTDFNVFVDDIA  177 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH-----HHTTSCCEEEEBSCSST-------------T-------CBCCHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh-----CCCCEEEEEecchhhhh-------------h-------hhcCHHHHHHHHH
Confidence            356789999999999999999865     1113456666  32211             1       0135566777777


Q ss_pred             HHhcCCeEEEEEeCCCC
Q 040110          190 DYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       190 ~~L~~kr~LlVLDdv~~  206 (348)
                      +.+...+ +||+|++..
T Consensus       178 ~~l~~~~-LLVIDsI~a  193 (331)
T 2vhj_A          178 RAMLQHR-VIVIDSLKN  193 (331)
T ss_dssp             HHHHHCS-EEEEECCTT
T ss_pred             HHHhhCC-EEEEecccc
Confidence            7776666 999999964

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.15  E-value=0.00043  Score=71.06  Aligned_cols=44  Identities=20%  Similarity=0.328  Sum_probs=36.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||+.++   +++...|..      ....-+.++|++|+|||++|+.+++.
T Consensus       181 ~iiG~~~~i---~~l~~~l~~------~~~~~vLL~G~pGtGKT~la~~la~~  224 (758)
T 3pxi_A          181 PVIGRSKEI---QRVIEVLSR------RTKNNPVLIGEPGVGKTAIAEGLAQQ  224 (758)
T ss_dssp             CCCCCHHHH---HHHHHHHHC------SSSCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             CccCchHHH---HHHHHHHhC------CCCCCeEEECCCCCCHHHHHHHHHHH
Confidence            689999999   999999872      22223678999999999999999876

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=97.13  E-value=7.5e-05  Score=66.45  Aligned_cols=50  Identities=16%  Similarity=0.203  Sum_probs=33.3

Q ss_pred             cccccccccccHHHHHhhcC---CCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLP---PSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~---~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+.+.+.   .+.   ..+....+-+.|+|++|+|||+||+.+++.
T Consensus        12 ~i~G~~~~~---~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   67 (268)
T 2r62_A           12 DMAGNEEAK---EEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGE   67 (268)
T ss_dssp             TSSSCTTTH---HHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHH
T ss_pred             HhCCcHHHH---HHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            799999988   66655442   000   000111223668999999999999999986

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.08  E-value=0.00027  Score=64.45  Aligned_cols=46  Identities=17%  Similarity=0.288  Sum_probs=33.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|+...+   .++.+.+...    .....-+.|+|.+|+|||++|+.+++.
T Consensus         3 ~iig~s~~~---~~~~~~~~~~----a~~~~~vLi~Ge~GtGKt~lAr~i~~~   48 (304)
T 1ojl_A            3 HMIGSSPAM---QHLLNEIAMV----APSDATVLIHGDSGTGKELVARALHAC   48 (304)
T ss_dssp             CCCCCSHHH---HHHHHHHHHH----CSTTSCEEEESCTTSCHHHHHHHHHHH
T ss_pred             CcEECCHHH---HHHHHHHHHH----hCCCCcEEEECCCCchHHHHHHHHHHh
Confidence            578888888   7777766421    112234668999999999999999875

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=97.07  E-value=0.0015  Score=60.75  Aligned_cols=89  Identities=15%  Similarity=0.074  Sum_probs=58.5

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l~  189 (348)
                      .-.++.|.|++|+||||||.+++...  ...=..++|++....++..     .++.++...... -....+.++....+.
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~~--~~~gg~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~  132 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAEA--QKMGGVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIVD  132 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHH--HHTTCCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH--HhcCCeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHHH
Confidence            34689999999999999999998762  2111246788777766654     556665542211 122345667777776


Q ss_pred             HHhc-CCeEEEEEeCCCC
Q 040110          190 DYLT-NKKYFTVLDDVWI  206 (348)
Q Consensus       190 ~~L~-~kr~LlVLDdv~~  206 (348)
                      ..++ .+.-++|+|.+..
T Consensus       133 ~l~~~~~~dlvVIDSi~~  150 (356)
T 3hr8_A          133 ELVRSGVVDLIVVDSVAA  150 (356)
T ss_dssp             HHHHTSCCSEEEEECTTT
T ss_pred             HHhhhcCCCeEEehHhhh
Confidence            6654 4566899998753

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.06  E-value=0.0018  Score=55.64  Aligned_cols=116  Identities=13%  Similarity=0.023  Sum_probs=61.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc------------------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL------------------  174 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~------------------  174 (348)
                      .+++|.|.+|+|||||++.++.......  ..++|+...  .....+...+. .++......                  
T Consensus        24 ~~~~i~G~~GsGKTtl~~~l~~~~~~~~--~~v~~~~~~--~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (235)
T 2w0m_A           24 FFIALTGEPGTGKTIFSLHFIAKGLRDG--DPCIYVTTE--ESRDSIIRQAK-QFNWDFEEYIEKKLIIIDALMKEKEDQ   98 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHT--CCEEEEESS--SCHHHHHHHHH-HTTCCCGGGBTTTEEEEECCC----CT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHCC--CeEEEEEcc--cCHHHHHHHHH-HhcchHHHHhhCCEEEEeccccccCce
Confidence            5889999999999999999885521111  235565543  24444444332 443321100                  


Q ss_pred             -ccCCCCHHHHHHHHHHHhcC-C--eEEEEEeCCCC-----hhhHHHHHhhCCC--CCCCcEEEEEeCCh
Q 040110          175 -KIMGKDYKSEKTILRDYLTN-K--KYFTVLDDVWI-----EKIWDDLREALPD--NQIGSRALITVGPH  233 (348)
Q Consensus       175 -~~~~~~~~~~~~~l~~~L~~-k--r~LlVLDdv~~-----~~~~~~l~~~l~~--~~~gskIlvTTR~~  233 (348)
                       .....+..++...+...+.. +  ..+||||....     ......+...+..  ...|..||++|...
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~llilDe~~~~~~~d~~~~~~~~~~l~~~~~~~~~~vi~~~h~~  168 (235)
T 2w0m_A           99 WSLVNLTPEELVNKVIEAKQKLGYGKARLVIDSVSALFLDKPAMARKISYYLKRVLNKWNFTIYATSQYA  168 (235)
T ss_dssp             TBCSSCCHHHHHHHHHHHHHHHCSSCEEEEEETGGGGSSSCGGGHHHHHHHHHHHHHHTTEEEEEEEC--
T ss_pred             eeecCCCHHHHHHHHHHHHHhhCCCceEEEEECchHhhcCCHHHHHHHHHHHHHHHHhCCCeEEEEeccC
Confidence             00112556666666655532 3  34999999862     2222333222211  12467788888765

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=97.02  E-value=0.017  Score=55.07  Aligned_cols=41  Identities=17%  Similarity=0.165  Sum_probs=28.7

Q ss_pred             HHHHhhcCCCCC---CCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSG---LGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~---~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++.++|.+...   ......++|.++|.+|+||||++..++..
T Consensus        80 ~~l~~~l~~~~~~~~~~~~~~~vI~ivG~~GvGKTT~a~~LA~~  123 (433)
T 2xxa_A           80 NELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLGKF  123 (433)
T ss_dssp             HHHHHHHCSSSCCCCCCSSSSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHhccccccccccCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            555666653211   12245789999999999999999888755

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.97  E-value=0.00068  Score=63.93  Aligned_cols=50  Identities=20%  Similarity=0.311  Sum_probs=34.6

Q ss_pred             cccccccccccHHHHHhhcCC----CC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----SS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|.+..+   ++|.+.+.-    ++   .-+-..++=+.++|++|+|||.||+++++.
T Consensus       149 dIgGl~~~k---~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e  205 (405)
T 4b4t_J          149 MVGGLTKQI---KEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHH  205 (405)
T ss_dssp             GSCSCHHHH---HHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHH
T ss_pred             HhCCHHHHH---HHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHh
Confidence            567888888   666655421    00   012233445778999999999999999987

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=96.92  E-value=0.004  Score=57.10  Aligned_cols=95  Identities=15%  Similarity=0.142  Sum_probs=58.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCC----cceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc----c-ccCCCCH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFY----FDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW----L-KIMGKDY  181 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~----F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~----~-~~~~~~~  181 (348)
                      .-.++.|+|.+|+||||||.+++........    -..++|++....++...+. +++..++.....    . -....+.
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~-~~~~~~g~~~~~~~~~l~~~~~~~~  184 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIE-NMAKALGLDIDNVMNNIYYIRAINT  184 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHhCCCHHHHhccEEEEeCCCH
Confidence            3458889999999999999998865212211    1367899888877776655 345566543210    0 0112233


Q ss_pred             H---HHHHHHHHHhc--CCeEEEEEeCCCC
Q 040110          182 K---SEKTILRDYLT--NKKYFTVLDDVWI  206 (348)
Q Consensus       182 ~---~~~~~l~~~L~--~kr~LlVLDdv~~  206 (348)
                      +   ++...+...++  .+.-+||+|.+..
T Consensus       185 ~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~  214 (324)
T 2z43_A          185 DHQIAIVDDLQELVSKDPSIKLIVVDSVTS  214 (324)
T ss_dssp             HHHHHHHHHHHHHHHHCTTEEEEEETTTTH
T ss_pred             HHHHHHHHHHHHHHHhccCCCEEEEeCcHH
Confidence            3   34455565664  4678999999853

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=96.92  E-value=0.0076  Score=55.70  Aligned_cols=96  Identities=7%  Similarity=0.020  Sum_probs=58.5

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccC----CcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc----c----ccC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKF----YFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW----L----KIM  177 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~----~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~----~----~~~  177 (348)
                      +.-.++.|+|.+|+||||||.+++.......    .-..++|++....++...+. .++..++.....    .    ...
T Consensus       120 ~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~-~~~~~~g~~~~~~l~~l~~~~~~~  198 (343)
T 1v5w_A          120 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLR-DIADRFNVDHDAVLDNVLYARAYT  198 (343)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHcCCCHHHHHhceeEeecCC
Confidence            3456889999999999999999886522211    12367899888877776654 344555543110    0    011


Q ss_pred             CCCHHHHHHHHHHHhc---CCeEEEEEeCCCC
Q 040110          178 GKDYKSEKTILRDYLT---NKKYFTVLDDVWI  206 (348)
Q Consensus       178 ~~~~~~~~~~l~~~L~---~kr~LlVLDdv~~  206 (348)
                      .....++...+...++   .+.-+||+|.+..
T Consensus       199 ~e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~  230 (343)
T 1v5w_A          199 SEHQMELLDYVAAKFHEEAGIFKLLIIDSIMA  230 (343)
T ss_dssp             TTHHHHHHHHHHHHHHHSCSSEEEEEEETSGG
T ss_pred             HHHHHHHHHHHHHHHHhcCCCccEEEEechHH
Confidence            1222244444555553   5677999999853

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=96.89  E-value=0.00078  Score=64.93  Aligned_cols=50  Identities=18%  Similarity=0.162  Sum_probs=34.8

Q ss_pred             CcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           82 DALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        82 ~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.++|.+..+..+..+++.+.    .+....+-+.++|++|+|||+||+.+++.
T Consensus        37 ~~iiG~~~~~~~l~~~~~~~~----~~~~~~~~iLl~GppGtGKT~la~ala~~   86 (456)
T 2c9o_A           37 SGLVGQENAREACGVIVELIK----SKKMAGRAVLLAGPPGTGKTALALAIAQE   86 (456)
T ss_dssp             TTEESCHHHHHHHHHHHHHHH----TTCCTTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHH----hCCCCCCeEEEECCCcCCHHHHHHHHHHH
Confidence            379999998822223444443    22223345778999999999999999987

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=96.88  E-value=0.0033  Score=54.44  Aligned_cols=94  Identities=6%  Similarity=-0.019  Sum_probs=55.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccC----CcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc----c-ccCCCCHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKF----YFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW----L-KIMGKDYK  182 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~----~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~----~-~~~~~~~~  182 (348)
                      -.++.|+|++|+|||||+..+........    .-..++|+.....++...+ ..++..++.....    . -....+..
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~~~~  102 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERL-LAVAERYGLSGSDVLDNVAYARAFNTD  102 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTCCHHHHHHTEEEEECCSHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHH-HHHHHHcCCCHHHHhhCeEEEecCCHH
Confidence            35899999999999999999887421211    1246788877665555444 3344555443100    0 01122333


Q ss_pred             H---HHHHHHHHhc-CCeEEEEEeCCCC
Q 040110          183 S---EKTILRDYLT-NKKYFTVLDDVWI  206 (348)
Q Consensus       183 ~---~~~~l~~~L~-~kr~LlVLDdv~~  206 (348)
                      +   ....+.+.+. .+.-+||||.+..
T Consensus       103 ~~~~~~~~~~~~~~~~~~~lliiD~~~~  130 (243)
T 1n0w_A          103 HQTQLLYQASAMMVESRYALLIVDSATA  130 (243)
T ss_dssp             HHHHHHHHHHHHHHHSCEEEEEEETSSG
T ss_pred             HHHHHHHHHHHHHhcCCceEEEEeCchH
Confidence            3   2333555553 4678999999864

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=96.85  E-value=0.004  Score=56.37  Aligned_cols=86  Identities=10%  Similarity=0.019  Sum_probs=46.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeC-CCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVS-NFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~-~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  189 (348)
                      ...+++++|.+|+||||++..++......... .+..+... ......+.+.......+.+..    ...+...+...+.
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~-~V~lv~~D~~r~~a~eqL~~~~~~~gl~~~----~~~~~~~l~~al~  178 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKHK-KIAFITTDTYRIAAVEQLKTYAELLQAPLE----VCYTKEEFQQAKE  178 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTCC-CEEEEECCCSSTTHHHHHHHHHTTTTCCCC----BCSSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCC-EEEEEecCcccchHHHHHHHHHHhcCCCeE----ecCCHHHHHHHHH
Confidence            45699999999999999999988663221222 23344332 223344444444444444321    1223444444444


Q ss_pred             HHhcCCeEEEEEeC
Q 040110          190 DYLTNKKYFTVLDD  203 (348)
Q Consensus       190 ~~L~~kr~LlVLDd  203 (348)
                      . + .+.=++|+|-
T Consensus       179 ~-~-~~~dlvIiDT  190 (296)
T 2px0_A          179 L-F-SEYDHVFVDT  190 (296)
T ss_dssp             H-G-GGSSEEEEEC
T ss_pred             H-h-cCCCEEEEeC
Confidence            3 3 3445777884

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=96.83  E-value=0.0032  Score=58.77  Aligned_cols=87  Identities=14%  Similarity=0.055  Sum_probs=56.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTILRD  190 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l~~  190 (348)
                      -.++.|.|.+|+||||||.++....  ...=..++|++....++..     ++..++.+.... -....+.+++...+..
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~--~~~g~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i~~~~~~e~~l~~l~~  146 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQA--QKAGGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMEL  146 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHH--HHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHH--HHCCCeEEEEECCCChhHH-----HHHHcCCCHHHceeecCCcHHHHHHHHHH
Confidence            3478889999999999999987662  2111368899888777654     245555432110 1122456777777766


Q ss_pred             HhcC-CeEEEEEeCCC
Q 040110          191 YLTN-KKYFTVLDDVW  205 (348)
Q Consensus       191 ~L~~-kr~LlVLDdv~  205 (348)
                      ..+. .--+||+|.+.
T Consensus       147 l~~~~~~~lVVIDsl~  162 (366)
T 1xp8_A          147 LVRSGAIDVVVVDSVA  162 (366)
T ss_dssp             HHTTTCCSEEEEECTT
T ss_pred             HHhcCCCCEEEEeChH
Confidence            6654 45689999975

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.81  E-value=0.0011  Score=63.12  Aligned_cols=50  Identities=16%  Similarity=0.245  Sum_probs=35.1

Q ss_pred             cccccccccccHHHHHhhcCC----C---CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----S---SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~---~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|.+..+   ++|.+.+.-    +   ..-+-..++=+.++|++|+|||+||+++++.
T Consensus       173 digGl~~~k---~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~  229 (428)
T 4b4t_K          173 DVGGLDMQK---QEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANS  229 (428)
T ss_dssp             GSCSCHHHH---HHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHH
T ss_pred             HhccHHHHH---HHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            567888888   777665521    0   0012234555779999999999999999987

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=96.77  E-value=0.0014  Score=67.23  Aligned_cols=97  Identities=13%  Similarity=0.215  Sum_probs=56.9

Q ss_pred             cccccccccccHHHHHhhc----CCC---CCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCC
Q 040110           83 ALLGLQSKIINLRNLHQRL----PPS---SGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYN  155 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L----~~~---~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  155 (348)
                      ++.|.+..+   ++|.+.+    ..+   ..-+-..++-|.++|++|+|||+||+++++.  ...+|   +.++.+    
T Consensus       205 dIgGl~~~~---~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~e--lg~~~---~~v~~~----  272 (806)
T 3cf2_A          205 DIGGCRKQL---AQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE--TGAFF---FLINGP----  272 (806)
T ss_dssp             GCCSCCTTH---HHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTT--TTCEE---EEEEHH----
T ss_pred             hhcCHHHHH---HHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHH--hCCeE---EEEEhH----
Confidence            577889888   6665543    211   1122344566789999999999999999988  43332   333221    


Q ss_pred             HHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 040110          156 FKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       156 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                        +    +.   +..      .......+...+.......+.+|+||+++.
T Consensus       273 --~----l~---sk~------~gese~~lr~lF~~A~~~~PsIIfIDEiDa  308 (806)
T 3cf2_A          273 --E----IM---SKL------AGESESNLRKAFEEAEKNAPAIIFIDELDA  308 (806)
T ss_dssp             --H----HH---SSC------TTHHHHHHHHHHHHHTTSCSEEEEEESGGG
T ss_pred             --H----hh---ccc------chHHHHHHHHHHHHHHHcCCeEEEEehhcc
Confidence              1    11   110      111223333334444456789999999863

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.76  E-value=0.0013  Score=62.98  Aligned_cols=50  Identities=20%  Similarity=0.265  Sum_probs=35.1

Q ss_pred             cccccccccccHHHHHhhcC----CCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLP----PSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~----~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|.+..+   ++|.+.+.    .++   .-+-..++=|.++|++|+|||+||+++++.
T Consensus       210 DIgGl~~~k---~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e  266 (467)
T 4b4t_H          210 DVGGCKDQI---EKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANR  266 (467)
T ss_dssp             SCTTCHHHH---HHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHH
T ss_pred             HhccHHHHH---HHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhc
Confidence            567888888   77766542    000   012234556779999999999999999987

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.75  E-value=0.0062  Score=55.63  Aligned_cols=94  Identities=12%  Similarity=0.039  Sum_probs=58.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccC---------Cc-----ceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc---
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKF---------YF-----DCHAWVRVSNFYNFKRILDDIMKSLMPTSSW---  173 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~---------~F-----~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~---  173 (348)
                      .-.++.|.|.+|+|||+||.+++.......         ..     ..++|++....++...+.. ++..++.+...   
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~~~~~~~~  175 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGIDGQTVLD  175 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTCCHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCCCHHHHhc
Confidence            456889999999999999999876421111         11     3678898888877776654 45556543210   


Q ss_pred             -c-ccCCCCHH---HHHHHHHHHhcC--CeEEEEEeCCC
Q 040110          174 -L-KIMGKDYK---SEKTILRDYLTN--KKYFTVLDDVW  205 (348)
Q Consensus       174 -~-~~~~~~~~---~~~~~l~~~L~~--kr~LlVLDdv~  205 (348)
                       . -....+.+   ++...+...++.  +.-+||+|.+.
T Consensus       176 ~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~  214 (322)
T 2i1q_A          176 NTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLT  214 (322)
T ss_dssp             TEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSS
T ss_pred             CEEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcH
Confidence             0 01112333   344556666643  56799999985

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=96.75  E-value=0.0037  Score=57.98  Aligned_cols=89  Identities=16%  Similarity=0.057  Sum_probs=56.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l~  189 (348)
                      .-.++.|.|.+|+||||||.++....  ...=..++|++....++..     .++.++...... -....+.++....+.
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~--~~~g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~~  132 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANA--QAAGGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIAD  132 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHH--HHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH--HhCCCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            34588999999999999999987652  2111357888887776653     345555432210 112235666666666


Q ss_pred             HHhcC-CeEEEEEeCCCC
Q 040110          190 DYLTN-KKYFTVLDDVWI  206 (348)
Q Consensus       190 ~~L~~-kr~LlVLDdv~~  206 (348)
                      ...+. +.-+||+|.+..
T Consensus       133 ~l~~~~~~~lIVIDsl~~  150 (349)
T 2zr9_A          133 MLVRSGALDIIVIDSVAA  150 (349)
T ss_dssp             HHHTTTCCSEEEEECGGG
T ss_pred             HHHhcCCCCEEEEcChHh
Confidence            55543 567999999853

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.68  E-value=0.002  Score=66.14  Aligned_cols=50  Identities=12%  Similarity=0.175  Sum_probs=35.6

Q ss_pred             cccccccccccHHHHHhhcCCC---CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS---SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~---~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+...   ..........+.++|++|+|||++|+.+++.
T Consensus       492 ~viGq~~a~---~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~  544 (758)
T 3pxi_A          492 RVIGQDEAV---VAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAES  544 (758)
T ss_dssp             TSCSCHHHH---HHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHH
T ss_pred             cCcChHHHH---HHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            578888877   7766666411   0111233446889999999999999999877

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=96.66  E-value=0.0075  Score=58.61  Aligned_cols=53  Identities=19%  Similarity=0.266  Sum_probs=34.2

Q ss_pred             cccccccccccHHHHHhhcCCCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+..+..++++...+..+.   .-+-.-.+=+.|+|++|+||||||+.+++.
T Consensus        32 dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~   87 (499)
T 2dhr_A           32 DVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   87 (499)
T ss_dssp             SSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             HcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            78998888733344444443110   001111223789999999999999999987

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.65  E-value=0.00079  Score=58.46  Aligned_cols=114  Identities=11%  Similarity=-0.068  Sum_probs=62.5

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      .-.++.|+|..|+||||++..+.++...+ ... ++.+.....  .. ....++..++....  ........++...+.+
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~~-g~k-Vli~~~~~d--~r-~~~~i~srlG~~~~--~~~~~~~~~i~~~i~~   83 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEYA-DVK-YLVFKPKID--TR-SIRNIQSRTGTSLP--SVEVESAPEILNYIMS   83 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHHT-TCC-EEEEEECCC--GG-GCSSCCCCCCCSSC--CEEESSTHHHHHHHHS
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHhc-CCE-EEEEEeccC--ch-HHHHHHHhcCCCcc--ccccCCHHHHHHHHHH
Confidence            34688899999999999998887763222 122 333322221  11 11234444544322  1112334556666666


Q ss_pred             HhcCCe-EEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          191 YLTNKK-YFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       191 ~L~~kr-~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      .+.+.+ -+||+|.+...  ++.+.+.. +.+  .|-.||+|-+..+
T Consensus        84 ~~~~~~~dvViIDEaQ~l~~~~ve~l~~-L~~--~gi~Vil~Gl~~d  127 (223)
T 2b8t_A           84 NSFNDETKVIGIDEVQFFDDRICEVANI-LAE--NGFVVIISGLDKN  127 (223)
T ss_dssp             TTSCTTCCEEEECSGGGSCTHHHHHHHH-HHH--TTCEEEEECCSBC
T ss_pred             HhhCCCCCEEEEecCccCcHHHHHHHHH-HHh--CCCeEEEEecccc
Confidence            555444 49999998642  34444432 222  2678999988433

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.65  E-value=0.0018  Score=55.18  Aligned_cols=37  Identities=24%  Similarity=0.435  Sum_probs=28.6

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|.+.+..    ......+++|+|+.|+|||||++.+...
T Consensus         9 ~~~~~~~~~----~~~~g~~v~I~G~sGsGKSTl~~~l~~~   45 (208)
T 3c8u_A            9 QGVLERLDP----RQPGRQLVALSGAPGSGKSTLSNPLAAA   45 (208)
T ss_dssp             HHHHHHSCT----TCCSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             HHHHHHHHh----cCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            566666651    1345579999999999999999998766

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=96.63  E-value=0.0052  Score=55.97  Aligned_cols=86  Identities=6%  Similarity=0.029  Sum_probs=56.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCc--ceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHH-HHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYF--DCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSE-KTILR  189 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F--~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~-~~~l~  189 (348)
                      ++-|.|++|+|||||+.++...  ....+  ..++|++....++..     .+++++.+.... -....+.++. ...+.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~--~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~i~~  102 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSS--YMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRIDMVN  102 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHH--HHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH--HHhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHHHHH
Confidence            6889999999999999988766  22221  357899888777753     367777653321 1123355555 44333


Q ss_pred             HH--h-cCCeEEEEEeCCCC
Q 040110          190 DY--L-TNKKYFTVLDDVWI  206 (348)
Q Consensus       190 ~~--L-~~kr~LlVLDdv~~  206 (348)
                      ..  + +.+.-|+|+|.+..
T Consensus       103 ~l~~i~~~~~~lvVIDSI~a  122 (333)
T 3io5_A          103 QLDAIERGEKVVVFIDSLGN  122 (333)
T ss_dssp             HHHTCCTTCCEEEEEECSTT
T ss_pred             HHHHhhccCceEEEEecccc
Confidence            32  3 34688999999864

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.63  E-value=0.0015  Score=62.29  Aligned_cols=50  Identities=18%  Similarity=0.230  Sum_probs=35.9

Q ss_pred             cccccccccccHHHHHhhcC----CCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLP----PSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~----~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|.+..+   ++|.+.+.    .++   ..+-..++=+.++|++|+|||.||+++++.
T Consensus       182 digGl~~~k---~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e  238 (434)
T 4b4t_M          182 DVGGLDKQI---EELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQ  238 (434)
T ss_dssp             GSCSCHHHH---HHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             hcCcHHHHH---HHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHH
Confidence            677888888   77776542    110   012234556778999999999999999987

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=96.57  E-value=0.033  Score=50.29  Aligned_cols=90  Identities=13%  Similarity=-0.026  Sum_probs=45.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRD  190 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  190 (348)
                      ..+++++|.+|+||||++..++.......  ..+.++..... ......+.......+.+... .....+..++.....+
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g--~~v~l~~~D~~r~~a~~ql~~~~~~~~v~v~~-~~~~~~p~~~~~~~l~  174 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKG--FKVGLVGADVYRPAALEQLQQLGQQIGVPVYG-EPGEKDVVGIAKRGVE  174 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTT--CCEEEEECCCSSSHHHHHHHHHHHHHTCCEEC-CTTCCCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCC--CeEEEEecCCCCHHHHHHHHHHhccCCeEEEe-cCCCCCHHHHHHHHHH
Confidence            67899999999999999998876632111  12344443221 22223334444444443111 1112344444433344


Q ss_pred             Hhc-CCeEEEEEeCC
Q 040110          191 YLT-NKKYFTVLDDV  204 (348)
Q Consensus       191 ~L~-~kr~LlVLDdv  204 (348)
                      .++ ..-=++|+|-.
T Consensus       175 ~~~~~~~D~ViIDTp  189 (297)
T 1j8m_F          175 KFLSEKMEIIIVDTA  189 (297)
T ss_dssp             HHHHTTCSEEEEECC
T ss_pred             HHHhCCCCEEEEeCC
Confidence            443 33236666754

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.56  E-value=0.032  Score=53.10  Aligned_cols=25  Identities=16%  Similarity=0.185  Sum_probs=22.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...++.++|.+|+||||++..++..
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~  120 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYF  120 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999888755

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=96.55  E-value=0.006  Score=56.72  Aligned_cols=88  Identities=13%  Similarity=0.020  Sum_probs=54.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l~  189 (348)
                      .-.++.|.|.+|+||||||.+++...  ...=..++|++....++..     .+..++...... -....+.+++...+.
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~--~~~g~~vlyid~E~s~~~~-----~a~~~g~~~~~l~i~~~~~~e~~~~~~~  134 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAA--QREGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  134 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHH--HHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH--HHCCCeEEEEeCCCCccHH-----HHHHcCCChhheeeeCCCCHHHHHHHHH
Confidence            34588899999999999999988662  2111257889887777643     245555432110 111234555655555


Q ss_pred             HHhc-CCeEEEEEeCCC
Q 040110          190 DYLT-NKKYFTVLDDVW  205 (348)
Q Consensus       190 ~~L~-~kr~LlVLDdv~  205 (348)
                      ...+ .+--+||+|.+.
T Consensus       135 ~l~~~~~~~lVVIDsl~  151 (356)
T 1u94_A          135 ALARSGAVDVIVVDSVA  151 (356)
T ss_dssp             HHHHHTCCSEEEEECGG
T ss_pred             HHHhccCCCEEEEcCHH
Confidence            4443 455689999974

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.45  E-value=0.0012  Score=60.23  Aligned_cols=24  Identities=13%  Similarity=0.212  Sum_probs=21.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+.|+|++|+|||+||..+++.
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~  175 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHE  175 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH
Confidence            346779999999999999999986

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=96.41  E-value=0.0048  Score=55.15  Aligned_cols=21  Identities=29%  Similarity=0.373  Sum_probs=19.9

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.++|++|+||||||+.++..
T Consensus        47 vlL~Gp~GtGKTtLakala~~   67 (274)
T 2x8a_A           47 VLLAGPPGCGKTLLAKAVANE   67 (274)
T ss_dssp             EEEESSTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHH
Confidence            889999999999999999986

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=96.39  E-value=0.04  Score=50.51  Aligned_cols=26  Identities=23%  Similarity=0.187  Sum_probs=22.9

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+++|+|+.|+||||++..++..
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~  152 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANW  152 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45679999999999999999998765

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=96.38  E-value=0.013  Score=55.92  Aligned_cols=25  Identities=16%  Similarity=0.262  Sum_probs=22.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.+|.++|.+|+||||++..++..
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~  123 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARY  123 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHH
Confidence            4789999999999999999888754

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=96.37  E-value=0.011  Score=53.26  Aligned_cols=23  Identities=17%  Similarity=0.348  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|.|.+|+|||||++.++..
T Consensus        36 ~~~~i~G~~G~GKTTl~~~ia~~   58 (296)
T 1cr0_A           36 EVIMVTSGSGMGKSTFVRQQALQ   58 (296)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHH
Confidence            47899999999999999998876

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=96.35  E-value=0.0025  Score=66.25  Aligned_cols=50  Identities=16%  Similarity=0.216  Sum_probs=34.6

Q ss_pred             cccccccccccHHHHHhhcCCCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+....   .........+.|+|++|+|||++|+.+++.
T Consensus       559 ~viG~~~a~---~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~  611 (854)
T 1qvr_A          559 RVVGQDEAI---RAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT  611 (854)
T ss_dssp             HSCSCHHHH---HHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHH
T ss_pred             ccCCcHHHH---HHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            468888877   66666553110   011223457889999999999999999876

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=96.34  E-value=0.0018  Score=53.39  Aligned_cols=23  Identities=4%  Similarity=0.067  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|.|.|++|+||||+|+.+...
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~   26 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSV   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            47889999999999999999876

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=96.33  E-value=0.0019  Score=52.81  Aligned_cols=23  Identities=13%  Similarity=0.183  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|.|.|++|+||||+|+.+...
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~   24 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKE   24 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999999866

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=96.33  E-value=0.06  Score=47.67  Aligned_cols=23  Identities=30%  Similarity=0.289  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~Gl   53 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISGL   53 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC
Confidence            37899999999999999999765

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.33  E-value=0.0018  Score=54.92  Aligned_cols=38  Identities=16%  Similarity=0.132  Sum_probs=28.2

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.|.+.+..   .......+++|.|..|+||||+++.+...
T Consensus         8 ~~l~~~~~~---~~~~~~~~i~i~G~~GsGKstl~~~l~~~   45 (201)
T 1rz3_A            8 DFLCKTILA---IKTAGRLVLGIDGLSRSGKTTLANQLSQT   45 (201)
T ss_dssp             HHHHHHHHT---SCCSSSEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHH---hccCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            556665551   11345579999999999999999998764

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=96.30  E-value=0.011  Score=53.75  Aligned_cols=107  Identities=11%  Similarity=0.013  Sum_probs=56.2

Q ss_pred             HHHHhhcCCCCC--CCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCH--HHHHHHHHHHhCCC
Q 040110           95 RNLHQRLPPSSG--LGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNF--KRILDDIMKSLMPT  170 (348)
Q Consensus        95 ~~l~~~L~~~~~--~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~--~~~~~~i~~~l~~~  170 (348)
                      +.|.+.|.+...  .......+++|+|++|+||||++..++.......  ..+..+.. ..+..  .+-+...++.++.+
T Consensus        85 ~~l~~~l~~~~~~~~~~~~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g--~kV~lv~~-D~~r~~a~eqL~~~~~~~gl~  161 (306)
T 1vma_A           85 EIILEILNFDTKLNVPPEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEG--KSVVLAAA-DTFRAAAIEQLKIWGERVGAT  161 (306)
T ss_dssp             HHHHHHTCSCCCCCCCSSSCEEEEEECCTTSSHHHHHHHHHHHHHHTT--CCEEEEEE-CTTCHHHHHHHHHHHHHHTCE
T ss_pred             HHHHHHhCCCCCCcccCCCCeEEEEEcCCCChHHHHHHHHHHHHHhcC--CEEEEEcc-ccccHHHHHHHHHHHHHcCCc
Confidence            556666653210  1124567999999999999999999887632211  12334433 22322  22234455555543


Q ss_pred             CCccccCCCCHHHH-HHHHHHHhcCCeEEEEEeCCC
Q 040110          171 SSWLKIMGKDYKSE-KTILRDYLTNKKYFTVLDDVW  205 (348)
Q Consensus       171 ~~~~~~~~~~~~~~-~~~l~~~L~~kr~LlVLDdv~  205 (348)
                      ... .....+...+ ...+...+..+.-++|+|-.-
T Consensus       162 ~~~-~~s~~~~~~v~~~al~~a~~~~~dvvIiDtpg  196 (306)
T 1vma_A          162 VIS-HSEGADPAAVAFDAVAHALARNKDVVIIDTAG  196 (306)
T ss_dssp             EEC-CSTTCCHHHHHHHHHHHHHHTTCSEEEEEECC
T ss_pred             EEe-cCCccCHHHHHHHHHHHHHhcCCCEEEEECCC
Confidence            111 1112233332 334555555555578888653

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=96.29  E-value=0.0022  Score=52.34  Aligned_cols=20  Identities=30%  Similarity=0.393  Sum_probs=18.6

Q ss_pred             EEEEEECCCCCcHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEI  132 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v  132 (348)
                      .+|.|.|++|+||||+|+.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            37889999999999999999

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.22  E-value=0.0028  Score=52.16  Aligned_cols=22  Identities=18%  Similarity=0.377  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            4788999999999999999987

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=96.20  E-value=0.0044  Score=55.96  Aligned_cols=27  Identities=19%  Similarity=0.262  Sum_probs=23.5

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....+|+|.|..|+||||||+.+...
T Consensus        28 ~~~~~ii~I~G~sGsGKSTla~~L~~~   54 (290)
T 1odf_A           28 NKCPLFIFFSGPQGSGKSFTSIQIYNH   54 (290)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            346779999999999999999988765

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=96.16  E-value=0.0032  Score=52.50  Aligned_cols=24  Identities=17%  Similarity=0.236  Sum_probs=21.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+++|+|++|+|||||++.+...
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhc
Confidence            458999999999999999999876

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.15  E-value=0.0029  Score=53.47  Aligned_cols=24  Identities=13%  Similarity=0.102  Sum_probs=21.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.|+|++|+||||+++.+...
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~   48 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARK   48 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            458899999999999999999876

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.14  E-value=0.0065  Score=57.61  Aligned_cols=50  Identities=22%  Similarity=0.349  Sum_probs=34.3

Q ss_pred             cccccccccccHHHHHhhcC----CCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLP----PSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~----~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|.+..+   ++|.+.+.    .++   ..+-..++=+.++|++|+|||.||+++++.
T Consensus       183 DIgGld~~k---~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e  239 (437)
T 4b4t_I          183 DIGGLESQI---QEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQ  239 (437)
T ss_dssp             GTCSCHHHH---HHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHH
T ss_pred             ecCcHHHHH---HHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHH
Confidence            566788888   66655442    110   012234456779999999999999999988

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.10  E-value=0.021  Score=51.95  Aligned_cols=49  Identities=20%  Similarity=0.131  Sum_probs=33.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMK  165 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~  165 (348)
                      .++.|.|.+|+||||||..++.+.....  ..++|++..  -+..++...++.
T Consensus        69 ~l~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE--~s~~~l~~R~~~  117 (315)
T 3bh0_A           69 NFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLE--MGKKENIKRLIV  117 (315)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESS--SCHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECC--CCHHHHHHHHHH
Confidence            4788899999999999999876532222  467777654  445555555544

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.10  E-value=0.003  Score=52.55  Aligned_cols=23  Identities=9%  Similarity=0.330  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|++|+|||||++.+...
T Consensus         6 ~~i~i~GpsGsGKSTL~~~L~~~   28 (180)
T 1kgd_A            6 KTLVLLGAHGVGRRHIKNTLITK   28 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            48999999999999999999865

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=96.06  E-value=0.021  Score=54.26  Aligned_cols=25  Identities=20%  Similarity=0.171  Sum_probs=22.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++++|.+|+||||++..++..
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~  121 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALY  121 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            5678999999999999999988765

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=96.04  E-value=0.0041  Score=52.58  Aligned_cols=25  Identities=16%  Similarity=0.206  Sum_probs=22.5

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|+|++|+|||||++.+...
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~La~~   48 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACALNQM   48 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4568999999999999999999877

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.03  E-value=0.0029  Score=51.92  Aligned_cols=23  Identities=9%  Similarity=0.235  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|+|+|+.|+|||||++.+...
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~   27 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQ   27 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            36899999999999999999876

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=96.03  E-value=0.034  Score=52.46  Aligned_cols=95  Identities=8%  Similarity=0.019  Sum_probs=53.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccC----CcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc-----cccCCCCH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKF----YFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW-----LKIMGKDY  181 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~----~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~  181 (348)
                      .-.++.|+|.+|+|||||+..++-......    .-..++|++....++...+ ..+++.++.....     .-....+.
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl-~~~a~~~gl~~~~vleni~~~~~~~~  255 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL-VSIAQRFGLDPDDALNNVAYARAYNA  255 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHH-HHHHHHcCCChHhHhhcEEEeccCCh
Confidence            345899999999999999997653211111    1235788877666665544 3366666543110     00111222


Q ss_pred             H---HHHHHHHHHh-cCCeEEEEEeCCCC
Q 040110          182 K---SEKTILRDYL-TNKKYFTVLDDVWI  206 (348)
Q Consensus       182 ~---~~~~~l~~~L-~~kr~LlVLDdv~~  206 (348)
                      .   +....+...+ ..+.-+||+|.+..
T Consensus       256 ~~~~~~l~~~~~~l~~~~~~llVIDs~t~  284 (400)
T 3lda_A          256 DHQLRLLDAAAQMMSESRFSLIVVDSVMA  284 (400)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETGGG
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEecchhh
Confidence            2   2333333333 24678999999753

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=96.03  E-value=0.0051  Score=50.57  Aligned_cols=25  Identities=24%  Similarity=0.446  Sum_probs=22.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|+|+.|+||||+++.+...
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~~   31 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAHQ   31 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHh
Confidence            3468999999999999999998765

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=96.02  E-value=0.018  Score=53.24  Aligned_cols=97  Identities=12%  Similarity=0.115  Sum_probs=55.5

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCc---c-eeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-------c-cC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF---D-CHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-------K-IM  177 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F---~-~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-------~-~~  177 (348)
                      +.-.++.|+|+.|+|||||+..++.........   . .++|++....+....+ ..++..++......       . ..
T Consensus       129 ~~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~~~~~~v~~ni~~~~~~~  207 (349)
T 1pzn_A          129 ETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRGLDPDEVLKHIYVARAFN  207 (349)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTTCCHHHHGGGEEEEECCS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcCCCHHHHhhCEEEEecCC
Confidence            345689999999999999999988662111111   2 3478876655543333 33455444321100       0 00


Q ss_pred             CCCHHHHHHHHHHHhc------CCeEEEEEeCCCCh
Q 040110          178 GKDYKSEKTILRDYLT------NKKYFTVLDDVWIE  207 (348)
Q Consensus       178 ~~~~~~~~~~l~~~L~------~kr~LlVLDdv~~~  207 (348)
                      .....++...+...+.      .+.-+||+|.+-..
T Consensus       208 ~~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~  243 (349)
T 1pzn_A          208 SNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSH  243 (349)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTT
T ss_pred             hHHHHHHHHHHHHHHHHhccccCCCCEEEEeCchHh
Confidence            1112334455555554      46889999998654

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=96.00  E-value=0.0017  Score=59.84  Aligned_cols=49  Identities=18%  Similarity=0.264  Sum_probs=34.1

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+.... ........+.++|++|+||||||+.+++.
T Consensus        26 ~~~g~~~~~---~~l~~~i~~~~-~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~   74 (334)
T 1in4_A           26 EFIGQENVK---KKLSLALEAAK-MRGEVLDHVLLAGPPGLGKTTLAHIIASE   74 (334)
T ss_dssp             GCCSCHHHH---HHHHHHHHHHH-HHTCCCCCEEEESSTTSSHHHHHHHHHHH
T ss_pred             HccCcHHHH---HHHHHHHHHHH-hcCCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            678887777   66655553100 00123356889999999999999999987

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=95.99  E-value=0.011  Score=58.22  Aligned_cols=50  Identities=16%  Similarity=0.183  Sum_probs=33.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.+.+.+.-..-........+.++|++|+||||||+.++..
T Consensus        82 di~G~~~vk---~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~  131 (543)
T 3m6a_A           82 EHHGLEKVK---ERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKS  131 (543)
T ss_dssp             HCSSCHHHH---HHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHH
T ss_pred             HhccHHHHH---HHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHh
Confidence            578877776   65544331000001113457899999999999999999877

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=95.99  E-value=0.0024  Score=59.47  Aligned_cols=112  Identities=12%  Similarity=0.073  Sum_probs=65.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc--cccCCCCHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW--LKIMGKDYKSEKTILR  189 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~~~~~~~l~  189 (348)
                      -.+++|+|+.|+|||||.+.+...  +.......+ +++..+....         +......  ......+.......+.
T Consensus       123 ~g~i~I~GptGSGKTTlL~~l~g~--~~~~~~~~i-~t~ed~~e~~---------~~~~~~~v~q~~~~~~~~~~~~~La  190 (356)
T 3jvv_A          123 RGLVLVTGPTGSGKSTTLAAMLDY--LNNTKYHHI-LTIEDPIEFV---------HESKKCLVNQREVHRDTLGFSEALR  190 (356)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHH--HHHHCCCEE-EEEESSCCSC---------CCCSSSEEEEEEBTTTBSCHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc--ccCCCCcEE-EEccCcHHhh---------hhccccceeeeeeccccCCHHHHHH
Confidence            448999999999999999998765  221111222 2222221100         0000000  0000111123445788


Q ss_pred             HHhcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          190 DYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       190 ~~L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      ..|...+=+|++|.+.+.+.++.+....   ..|.-|++||-..+.+..
T Consensus       191 ~aL~~~PdvillDEp~d~e~~~~~~~~~---~~G~~vl~t~H~~~~~~~  236 (356)
T 3jvv_A          191 SALREDPDIILVGEMRDLETIRLALTAA---ETGHLVFGTLHTTSAAKT  236 (356)
T ss_dssp             HHTTSCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEESCSSHHHH
T ss_pred             HHhhhCcCEEecCCCCCHHHHHHHHHHH---hcCCEEEEEEccChHHHH
Confidence            8899999999999998776666554442   235568999988777644

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=95.97  E-value=0.0038  Score=51.86  Aligned_cols=24  Identities=13%  Similarity=0.185  Sum_probs=21.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.|.|+|++|+||||+|+.+...
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~   28 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKL   28 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            347889999999999999999876

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=95.97  E-value=0.017  Score=55.60  Aligned_cols=90  Identities=12%  Similarity=0.179  Sum_probs=56.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCcccc-CCcceeEEEEeCCCC-CHHHHHHHHHHHhCCC-------CCc--cccCCCC--
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVK-FYFDCHAWVRVSNFY-NFKRILDDIMKSLMPT-------SSW--LKIMGKD--  180 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~-~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~-------~~~--~~~~~~~--  180 (348)
                      .++|.|.+|+|||+|+..+.++  +. .+-+.++++-++... .+.+++.++...=...       ...  ....+..  
T Consensus       167 r~gIfgg~GvGKT~L~~~l~~~--~a~~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rtvvV~~t~d~p~~  244 (498)
T 1fx0_B          167 KIGLFGGAGVGKTVLIMELINN--IAKAHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMNEPPG  244 (498)
T ss_dssp             CEEEEECSSSSHHHHHHHHHHH--TTTTCSSCEEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCEEEEEECTTSCHH
T ss_pred             eEEeecCCCCCchHHHHHHHHH--HHhhCCCEEEEEEcccCcHHHHHHHHhhhcccccccccccccceEEEEeCCCCCHH
Confidence            4789999999999999998876  32 234677888887765 4567777776542221       111  0111111  


Q ss_pred             ----HHHHHHHHHHHhc---CCeEEEEEeCCC
Q 040110          181 ----YKSEKTILRDYLT---NKKYFTVLDDVW  205 (348)
Q Consensus       181 ----~~~~~~~l~~~L~---~kr~LlVLDdv~  205 (348)
                          .....-.+.++++   ++.+||++||+-
T Consensus       245 ~R~~~~~~altiAEyfrd~~G~dVLl~~Dsit  276 (498)
T 1fx0_B          245 ARMRVGLTALTMAEYFRDVNEQDVLLFIDNIF  276 (498)
T ss_dssp             HHTTHHHHHHHTHHHHTTTSCCEEEEEEECSH
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence                1122233455554   479999999984

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=95.95  E-value=0.0034  Score=58.34  Aligned_cols=50  Identities=16%  Similarity=0.130  Sum_probs=34.0

Q ss_pred             cccccccccccHHHHHhhcC--------C-CCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLP--------P-SSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~--------~-~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+.        . ...........+.++|++|+|||++|+.+++.
T Consensus        16 ~i~G~~~~~---~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~   74 (363)
T 3hws_A           16 YVIGQEQAK---KVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARL   74 (363)
T ss_dssp             HCCSCHHHH---HHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             hccCHHHHH---HHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            467888877   77766661        0 00011123345778999999999999999987

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=95.95  E-value=0.0047  Score=51.95  Aligned_cols=26  Identities=19%  Similarity=0.179  Sum_probs=23.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+|+|.|+.|+||||+++.+...
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            45678999999999999999999875

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=95.94  E-value=0.0041  Score=51.70  Aligned_cols=23  Identities=13%  Similarity=0.176  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|.|.|++|+||||+|+.+...
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~   24 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47889999999999999999876

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=95.93  E-value=0.0023  Score=57.69  Aligned_cols=50  Identities=18%  Similarity=0.225  Sum_probs=34.9

Q ss_pred             cccccccccccHHHHHhhcCCC---CCC-----CCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS---SGL-----GQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~---~~~-----~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+...   ...     ......-+.++|++|+|||++|+.+++.
T Consensus        16 ~i~G~~~~~---~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~   73 (310)
T 1ofh_A           16 HIIGQADAK---RAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   73 (310)
T ss_dssp             TCCSCHHHH---HHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             hcCChHHHH---HHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            588999888   8777766410   000     0112335678999999999999999876

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=95.90  E-value=0.0053  Score=51.17  Aligned_cols=25  Identities=12%  Similarity=0.222  Sum_probs=22.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+|.|.|++|+||||+|+.+...
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~~~   28 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALATG   28 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3468899999999999999999875

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=95.88  E-value=0.0033  Score=53.13  Aligned_cols=24  Identities=13%  Similarity=0.266  Sum_probs=21.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~   41 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEA   41 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            457999999999999999999876

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=95.88  E-value=0.005  Score=54.17  Aligned_cols=27  Identities=11%  Similarity=0.107  Sum_probs=22.6

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....+|+|.|+.|+||||+|+.+...
T Consensus        19 ~~~~~iI~I~G~~GSGKST~a~~L~~~   45 (252)
T 1uj2_A           19 GGEPFLIGVSGGTASGKSSVCAKIVQL   45 (252)
T ss_dssp             --CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            345678999999999999999999875

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.86  E-value=0.0046  Score=52.14  Aligned_cols=23  Identities=17%  Similarity=0.273  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.+...
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKA   30 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cEEEEECcCCCCHHHHHHHHHhh
Confidence            48999999999999999999865

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=95.85  E-value=0.0049  Score=52.11  Aligned_cols=25  Identities=20%  Similarity=0.294  Sum_probs=22.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|+|+.|+|||||++.+...
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~~   52 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVADE   52 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHh
Confidence            3458999999999999999999876

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=95.83  E-value=0.0063  Score=51.32  Aligned_cols=27  Identities=19%  Similarity=0.262  Sum_probs=23.4

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....+|+|.|+.|+||||+|+.+.+.
T Consensus        12 ~~~~~~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           12 PDQVSVIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             TTTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            345678999999999999999999865

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.83  E-value=0.005  Score=52.33  Aligned_cols=25  Identities=20%  Similarity=0.215  Sum_probs=22.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|+|+.|+|||||++.+...
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~   29 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALART   29 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHH
Confidence            4468999999999999999998775

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=95.82  E-value=0.0056  Score=52.19  Aligned_cols=24  Identities=8%  Similarity=0.317  Sum_probs=21.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+++|+|+.|+|||||++.+...
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhh
Confidence            458999999999999999999877

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=95.81  E-value=0.023  Score=52.30  Aligned_cols=89  Identities=11%  Similarity=0.017  Sum_probs=53.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCC---------C-----------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTS---------S-----------  172 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~---------~-----------  172 (348)
                      .++.|.|.+|+||||||..++.+.....  ..++|++.  .-+..++...++.....-.         +           
T Consensus        47 ~LiiIaG~pG~GKTt~al~ia~~~a~~g--~~Vl~fSl--Ems~~ql~~Rlls~~~~v~~~~l~~g~Ls~~e~~~l~~a~  122 (338)
T 4a1f_A           47 SLVIIGARPSMGKTSLMMNMVLSALNDD--RGVAVFSL--EMSAEQLALRALSDLTSINMHDLESGRLDDDQWENLAKCF  122 (338)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTT--CEEEEEES--SSCHHHHHHHHHHHHHCCCHHHHHHTCCCHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEeC--CCCHHHHHHHHHHHhhCCCHHHHhcCCCCHHHHHHHHHHH
Confidence            4788899999999999999887632211  24566654  3445555555543321100         0           


Q ss_pred             ------c---cccCCCCHHHHHHHHHHHhcC--CeEEEEEeCCC
Q 040110          173 ------W---LKIMGKDYKSEKTILRDYLTN--KKYFTVLDDVW  205 (348)
Q Consensus       173 ------~---~~~~~~~~~~~~~~l~~~L~~--kr~LlVLDdv~  205 (348)
                            .   ...+..++.++...+++..+.  +.-++|+|.+.
T Consensus       123 ~~l~~~~l~I~d~~~~si~~i~~~ir~l~~~~gg~~lIVIDyLq  166 (338)
T 4a1f_A          123 DHLSQKKLFFYDKSYVRIEQIRLQLRKLKSQHKELGIAFIDYLQ  166 (338)
T ss_dssp             HHHHHSCEEEECCTTCCHHHHHHHHHHHHHHCTTEEEEEEEEEE
T ss_pred             HHHhcCCeEEeCCCCCcHHHHHHHHHHHHHhcCCCCEEEEechH
Confidence                  0   022334667777777665533  46788888764

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=95.78  E-value=0.0053  Score=51.01  Aligned_cols=23  Identities=22%  Similarity=0.253  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|.|.|++|+||||+++.+...
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~   26 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDN   26 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999999875

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=95.76  E-value=0.006  Score=50.77  Aligned_cols=24  Identities=29%  Similarity=0.285  Sum_probs=21.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.|.|++|+||||+|+.+...
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~   26 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEK   26 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999999998765

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.74  E-value=0.0056  Score=50.46  Aligned_cols=22  Identities=32%  Similarity=0.540  Sum_probs=19.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHh
Q 040110          112 HSVVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~  133 (348)
                      -.+++|+|+.|+|||||++.++
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHS
T ss_pred             CEEEEEECCCCCCHHHHHHHHc
Confidence            4589999999999999999754

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=95.74  E-value=0.049  Score=52.24  Aligned_cols=65  Identities=17%  Similarity=0.218  Sum_probs=43.0

Q ss_pred             HHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHH
Q 040110           96 NLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKS  166 (348)
Q Consensus        96 ~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~  166 (348)
                      +.++.|.+-    ..+ ..++|.|.+|+|||+|+..+.++.. +.+-+.++++-++... .+.++++++...
T Consensus       142 r~ID~l~pi----gkG-Qr~~Ifgg~G~GKT~L~~~i~~~~~-~~~~~v~V~~~iGER~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          142 KVVDLLAPY----AKG-GKIGLFGGAGVGKTVLIMELINNVA-KAHGGYSVFAGVGERTREGNDLYHEMIES  207 (482)
T ss_dssp             HHHHHHSCE----ETT-CEEEEEECTTSSHHHHHHHHHHHTT-TTCSSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             EEEeccccc----ccC-CeeeeecCCCCChHHHHHHHHHhhH-hhCCCEEEEEECCCcchHHHHHHHHhhhc
Confidence            556666521    112 2578999999999999999987621 2233566777777664 456777777654

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=95.73  E-value=0.0063  Score=51.58  Aligned_cols=26  Identities=15%  Similarity=0.218  Sum_probs=22.8

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+++|+|++|+||||+|+.+...
T Consensus        19 ~~~~~i~i~G~~GsGKSTl~~~L~~~   44 (207)
T 2qt1_A           19 SKTFIIGISGVTNSGKTTLAKNLQKH   44 (207)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            34578999999999999999999876

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.73  E-value=0.006  Score=51.43  Aligned_cols=23  Identities=13%  Similarity=0.365  Sum_probs=21.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+||||+++.+...
T Consensus         7 ~~i~l~G~~GsGKSTl~~~L~~~   29 (207)
T 2j41_A            7 LLIVLSGPSGVGKGTVRKRIFED   29 (207)
T ss_dssp             CEEEEECSTTSCHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            48999999999999999999876

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=95.73  E-value=0.0062  Score=55.63  Aligned_cols=26  Identities=15%  Similarity=0.267  Sum_probs=21.7

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.+||+|.|-|||||||.+..+.--
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~a   71 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSAA   71 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHH
Confidence            46789999999999999988776544

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=95.72  E-value=0.0056  Score=50.01  Aligned_cols=25  Identities=16%  Similarity=0.171  Sum_probs=21.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+|+|.|+.|+||||+|+.+...
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~~   30 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGLA   30 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHHH
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHH
Confidence            4568999999999999999999876

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=95.71  E-value=0.0061  Score=53.76  Aligned_cols=23  Identities=22%  Similarity=0.144  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++.|.|+.|+||||||+.++..
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~   24 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQE   24 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHhc
Confidence            47899999999999999999875

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=95.71  E-value=0.0056  Score=52.54  Aligned_cols=23  Identities=17%  Similarity=0.261  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|+|+|+.|+||||+++.+...
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~   28 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEA   28 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47999999999999999998765

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=95.71  E-value=0.0062  Score=50.80  Aligned_cols=22  Identities=14%  Similarity=0.203  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      .+++|+|+.|+|||||++.+..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            4789999999999999999975

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.71  E-value=0.036  Score=47.82  Aligned_cols=90  Identities=16%  Similarity=0.104  Sum_probs=50.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc---------c-------
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL---------K-------  175 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~---------~-------  175 (348)
                      -.++.|.|.+|+||||||.+++...  ...=..++|++...  ...++...+ ..++......         .       
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~~--~~~~~~v~~~~~e~--~~~~~~~~~-~~~g~~~~~~~~~~~l~~~~~~~~~~~   97 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWNG--LKMGEPGIYVALEE--HPVQVRQNM-AQFGWDVKPYEEKGMFAMVDAFTAGIG   97 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHH--HHTTCCEEEEESSS--CHHHHHHHH-HTTTCCCHHHHHHTSEEEEECSTTTTC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH--HhcCCeEEEEEccC--CHHHHHHHH-HHcCCCHHHHhhCCcEEEEecchhhcc
Confidence            3478999999999999998876552  11112566766443  344444333 2333221000         0       


Q ss_pred             ----------cCCCCHHHHHHHHHHHhcC-CeEEEEEeCCCC
Q 040110          176 ----------IMGKDYKSEKTILRDYLTN-KKYFTVLDDVWI  206 (348)
Q Consensus       176 ----------~~~~~~~~~~~~l~~~L~~-kr~LlVLDdv~~  206 (348)
                                ....+..++...+.+.++. +.-++|+|.+..
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~vviD~~~~  139 (247)
T 2dr3_A           98 KSKEYEKYIVHDLTDIREFIEVLRQAIRDINAKRVVVDSVTT  139 (247)
T ss_dssp             C--CCCSCBCSCCSSHHHHHHHHHHHHHHHTCCEEEEETSGG
T ss_pred             cccccccccccCccCHHHHHHHHHHHHHHhCCCEEEECCchH
Confidence                      0123555666667666642 445899998853

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.69  E-value=0.0059  Score=51.29  Aligned_cols=22  Identities=32%  Similarity=0.469  Sum_probs=20.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|+|.|+.|+||||+++.+...
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~   23 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKK   23 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHh
Confidence            5889999999999999999876

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=95.69  E-value=0.0052  Score=51.88  Aligned_cols=22  Identities=14%  Similarity=0.205  Sum_probs=20.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      .+|+|+|+.|+||||+++.+..
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            3689999999999999999987

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=95.67  E-value=0.0051  Score=50.89  Aligned_cols=24  Identities=17%  Similarity=0.300  Sum_probs=21.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.|.|++|+||||+++.+...
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~   34 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASK   34 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHH
Confidence            456889999999999999999866

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=95.66  E-value=0.0068  Score=51.30  Aligned_cols=22  Identities=23%  Similarity=0.252  Sum_probs=20.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      .+++|+|+.|+||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=95.65  E-value=0.0075  Score=50.86  Aligned_cols=25  Identities=24%  Similarity=0.311  Sum_probs=21.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+|.|.|++|+||||+|+.+...
T Consensus        19 ~~~~I~l~G~~GsGKST~a~~La~~   43 (201)
T 2cdn_A           19 SHMRVLLLGPPGAGKGTQAVKLAEK   43 (201)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3457899999999999999999875

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.65  E-value=0.0055  Score=51.95  Aligned_cols=25  Identities=8%  Similarity=0.220  Sum_probs=21.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...++.|+|++|+|||||++.+...
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~   35 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSE   35 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHh
Confidence            3457889999999999999999876

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=95.65  E-value=0.015  Score=55.83  Aligned_cols=50  Identities=12%  Similarity=0.222  Sum_probs=33.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCc-ceeEEEEeCCCC-CHHHHHHHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYF-DCHAWVRVSNFY-NFKRILDDIMK  165 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F-~~~~wv~~~~~~-~~~~~~~~i~~  165 (348)
                      .++|+|.+|+|||||+..+..+  ....+ +.++++.+++.. ...+++.++..
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~--~~~~~~~i~V~~~iGerttev~el~~~l~~  204 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHN--IAQEHGGISVFAGVGERTREGNDLYHEMKD  204 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHH--HHHHTCCCEEEEEESSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCccHHHHHHHhh--hhhccCcEEEEeeeccCchHHHHHHHHhhh
Confidence            4789999999999999998877  33222 345666666654 34455555543

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=95.65  E-value=0.0075  Score=50.23  Aligned_cols=24  Identities=25%  Similarity=0.219  Sum_probs=21.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|.|+|+.|+||||+++.+...
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            457899999999999999998865

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=95.62  E-value=0.0063  Score=50.80  Aligned_cols=24  Identities=13%  Similarity=0.267  Sum_probs=21.5

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~   32 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQK   32 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999999865

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=95.59  E-value=0.00096  Score=56.09  Aligned_cols=23  Identities=13%  Similarity=-0.070  Sum_probs=19.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++.|+|+.|+||||++..++.+
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~   26 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEI   26 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            36789999999999999766654

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=95.57  E-value=0.0077  Score=49.91  Aligned_cols=23  Identities=22%  Similarity=0.264  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..|.+.|+.|+||||+++.+.+.
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~   27 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQE   27 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47889999999999999999865

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=95.55  E-value=0.0073  Score=50.29  Aligned_cols=22  Identities=23%  Similarity=0.347  Sum_probs=19.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|+|+.|+|||||++.++..
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~   23 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999998765

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=95.54  E-value=0.0081  Score=53.13  Aligned_cols=24  Identities=13%  Similarity=0.257  Sum_probs=21.5

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.|.|++|+||||+|+.+...
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~   27 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKI   27 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHH
Confidence            468899999999999999999875

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=95.54  E-value=0.046  Score=49.31  Aligned_cols=90  Identities=12%  Similarity=-0.024  Sum_probs=47.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHH--HHHHHHHHHhCCCCCccccCCCCHHHHHH-H
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFK--RILDDIMKSLMPTSSWLKIMGKDYKSEKT-I  187 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~--~~~~~i~~~l~~~~~~~~~~~~~~~~~~~-~  187 (348)
                      ...+++++|.+|+||||++..++.......  ..+.++... .....  ..+..+....+...-. .....+..++.. .
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~~--~~v~l~~~d-~~~~~~~~ql~~~~~~~~l~~~~-~~~~~~p~~l~~~~  172 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKG--RRPLLVAAD-TQRPAAREQLRLLGEKVGVPVLE-VMDGESPESIRRRV  172 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTT--CCEEEEECC-SSCHHHHHHHHHHHHHHTCCEEE-CCTTCCHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEecCC-cccHhHHHHHHHhcccCCeEEEE-cCCCCCHHHHHHHH
Confidence            567899999999999999999887632211  123344332 22221  2233444445443111 111234555543 3


Q ss_pred             HHHHhcCCeEEEEEeCC
Q 040110          188 LRDYLTNKKYFTVLDDV  204 (348)
Q Consensus       188 l~~~L~~kr~LlVLDdv  204 (348)
                      +......+.=++|+|-.
T Consensus       173 l~~~~~~~~D~viiDtp  189 (295)
T 1ls1_A          173 EEKARLEARDLILVDTA  189 (295)
T ss_dssp             HHHHHHHTCCEEEEECC
T ss_pred             HHHHHhCCCCEEEEeCC
Confidence            33333344457778875

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.52  E-value=0.01  Score=53.35  Aligned_cols=26  Identities=15%  Similarity=0.287  Sum_probs=22.6

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....++.|.|++|+||||+|+.+...
T Consensus        31 ~~~~livl~G~sGsGKSTla~~L~~~   56 (287)
T 1gvn_B           31 ESPTAFLLGGQPGSGKTSLRSAIFEE   56 (287)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34578889999999999999999865

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=95.52  E-value=0.071  Score=51.78  Aligned_cols=26  Identities=15%  Similarity=0.224  Sum_probs=21.3

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...++|+|+|.+|+||||++..+...
T Consensus        99 ~~~~vI~ivG~~GvGKTTl~~kLA~~  124 (504)
T 2j37_W           99 GKQNVIMFVGLQGSGKTTTCSKLAYY  124 (504)
T ss_dssp             S--EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45779999999999999999998744

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=95.52  E-value=0.0087  Score=50.54  Aligned_cols=23  Identities=17%  Similarity=0.134  Sum_probs=21.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|.|.|++|+||||+|+.+...
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~   27 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDW   27 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHH
Confidence            57899999999999999999876

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=95.51  E-value=0.0082  Score=50.67  Aligned_cols=26  Identities=19%  Similarity=0.294  Sum_probs=23.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+|+|+|+.|+||||+++.+...
T Consensus        10 ~~~~iIgltG~~GSGKSTva~~L~~~   35 (192)
T 2grj_A           10 HHHMVIGVTGKIGTGKSTVCEILKNK   35 (192)
T ss_dssp             CCEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccceEEEEECCCCCCHHHHHHHHHHh
Confidence            45789999999999999999998865

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.50  E-value=0.011  Score=49.08  Aligned_cols=25  Identities=24%  Similarity=0.177  Sum_probs=22.3

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+|.|.|++|+||||+++.+...
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~   36 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADL   36 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            4568899999999999999999876

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=95.50  E-value=0.0052  Score=51.65  Aligned_cols=22  Identities=14%  Similarity=0.357  Sum_probs=19.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|++|+|||||++.+...
T Consensus         3 pIVi~GPSG~GK~Tl~~~L~~~   24 (186)
T 1ex7_A            3 PIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            4678999999999999998766

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=95.49  E-value=0.0063  Score=49.75  Aligned_cols=23  Identities=17%  Similarity=0.309  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|.|.|+.|+||||+|+.+...
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~   25 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARA   25 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            36889999999999999999875

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=95.49  E-value=0.0068  Score=51.28  Aligned_cols=51  Identities=16%  Similarity=0.031  Sum_probs=30.5

Q ss_pred             HHHHHHHHhcC-CeEEEEEeCCCCh-----hhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          184 EKTILRDYLTN-KKYFTVLDDVWIE-----KIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       184 ~~~~l~~~L~~-kr~LlVLDdv~~~-----~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      .....++.+.+ +-=|||||++-..     -..+++...+.......-||+|+|+..
T Consensus       108 ~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap  164 (196)
T 1g5t_A          108 VWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCH  164 (196)
T ss_dssp             HHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCC
T ss_pred             HHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCc
Confidence            44445556644 4569999998431     233444444433334567999999853

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=95.48  E-value=0.0097  Score=49.39  Aligned_cols=24  Identities=29%  Similarity=0.338  Sum_probs=21.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|+|.|+.|+||||+|+.+...
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~   29 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999875

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=95.48  E-value=0.0055  Score=50.84  Aligned_cols=22  Identities=9%  Similarity=0.181  Sum_probs=20.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|.|.|++|+||||+|+.+...
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~   25 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKA   25 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999999875

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.48  E-value=0.0061  Score=51.60  Aligned_cols=23  Identities=13%  Similarity=0.339  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++++|+|+.|+|||||++.+...
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~   27 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQE   27 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            46899999999999999998764

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=95.47  E-value=0.0081  Score=52.51  Aligned_cols=24  Identities=25%  Similarity=0.217  Sum_probs=21.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+++|+|+.|+|||||++.+...
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~   50 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQN   50 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999844

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=95.47  E-value=0.0074  Score=49.67  Aligned_cols=22  Identities=14%  Similarity=0.259  Sum_probs=20.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|++|+||||+|+.+...
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~   27 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKD   27 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            5889999999999999999876

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=95.44  E-value=0.0073  Score=50.55  Aligned_cols=23  Identities=13%  Similarity=0.284  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|+|.|++|+||||+|+.+...
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~   35 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEK   35 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            47999999999999999999876

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.42  E-value=0.012  Score=53.72  Aligned_cols=27  Identities=11%  Similarity=0.074  Sum_probs=23.6

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+.+++|.|+.|+|||||++.+...
T Consensus        89 ~~~p~iigI~GpsGSGKSTl~~~L~~l  115 (321)
T 3tqc_A           89 PKVPYIIGIAGSVAVGKSTTSRVLKAL  115 (321)
T ss_dssp             CCCCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            456779999999999999999998765

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=95.41  E-value=0.012  Score=50.72  Aligned_cols=27  Identities=15%  Similarity=0.223  Sum_probs=24.0

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -...++|.|.|++|+||||+|+.+...
T Consensus        26 ~~k~kiI~llGpPGsGKgTqa~~L~~~   52 (217)
T 3umf_A           26 LAKAKVIFVLGGPGSGKGTQCEKLVQK   52 (217)
T ss_dssp             TTSCEEEEEECCTTCCHHHHHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            356789999999999999999999876

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.41  E-value=0.01  Score=51.93  Aligned_cols=25  Identities=8%  Similarity=0.125  Sum_probs=22.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|.|+.|+|||||++.+...
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~~   48 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIMEL   48 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4468999999999999999998764

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=95.41  E-value=0.0088  Score=49.42  Aligned_cols=25  Identities=12%  Similarity=0.106  Sum_probs=22.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|.|..|+|||||+..+...
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~   27 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAA   27 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHh
Confidence            4568999999999999999999876

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=95.41  E-value=0.0055  Score=59.62  Aligned_cols=43  Identities=19%  Similarity=0.089  Sum_probs=35.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .++|++..+   +.+...+.      ..  .-+.++|++|+|||+||+.+++..
T Consensus        23 ~ivGq~~~i---~~l~~al~------~~--~~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           23 GLYERSHAI---RLCLLAAL------SG--ESVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             TCSSCHHHH---HHHHHHHH------HT--CEEEEECCSSSSHHHHHHHGGGGB
T ss_pred             hhHHHHHHH---HHHHHHHh------cC--CeeEeecCchHHHHHHHHHHHHHH
Confidence            689999999   88888777      11  247789999999999999999873

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=95.40  E-value=0.009  Score=48.59  Aligned_cols=22  Identities=5%  Similarity=0.028  Sum_probs=20.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|+.|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRS   23 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999999875

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=95.37  E-value=0.0034  Score=57.45  Aligned_cols=42  Identities=14%  Similarity=0.142  Sum_probs=35.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|++..+   +.+...+.    .  .  .-+.++|++|+|||+||+.+.+.
T Consensus        28 ~i~g~~~~~---~~l~~~l~----~--~--~~vll~G~pGtGKT~la~~la~~   69 (331)
T 2r44_A           28 VVVGQKYMI---NRLLIGIC----T--G--GHILLEGVPGLAKTLSVNTLAKT   69 (331)
T ss_dssp             TCCSCHHHH---HHHHHHHH----H--T--CCEEEESCCCHHHHHHHHHHHHH
T ss_pred             ceeCcHHHH---HHHHHHHH----c--C--CeEEEECCCCCcHHHHHHHHHHH
Confidence            689999999   88888877    1  1  24678999999999999999886

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.36  E-value=0.0089  Score=49.70  Aligned_cols=22  Identities=27%  Similarity=0.371  Sum_probs=20.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|+|.|+.|+||||+|+.+.+.
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~   23 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEY   23 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6889999999999999999875

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=95.36  E-value=0.0093  Score=51.08  Aligned_cols=24  Identities=13%  Similarity=0.187  Sum_probs=21.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|.|.|++|+||||+|+.+...
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~   27 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQER   27 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            347889999999999999999876

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=95.35  E-value=0.011  Score=53.94  Aligned_cols=26  Identities=15%  Similarity=0.183  Sum_probs=22.8

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+++|.|+.|+|||||++.+..-
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gl  113 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQAL  113 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhh
Confidence            35579999999999999999998765

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=95.33  E-value=0.006  Score=50.37  Aligned_cols=24  Identities=21%  Similarity=0.195  Sum_probs=17.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~   28 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHER   28 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHh
Confidence            457899999999999999999866

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=95.33  E-value=0.0094  Score=50.64  Aligned_cols=23  Identities=13%  Similarity=0.183  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.+..-
T Consensus        21 ei~~l~GpnGsGKSTLl~~l~gl   43 (207)
T 1znw_A           21 RVVVLSGPSAVGKSTVVRCLRER   43 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            48999999999999999998765

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=95.33  E-value=0.011  Score=52.11  Aligned_cols=27  Identities=11%  Similarity=0.036  Sum_probs=23.2

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....++.|.|++|+||||+|+.+...
T Consensus        29 ~~~~~~i~l~G~~GsGKSTla~~L~~~   55 (253)
T 2p5t_B           29 SKQPIAILLGGQSGAGKTTIHRIKQKE   55 (253)
T ss_dssp             CSSCEEEEEESCGGGTTHHHHHHHHHH
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            344578899999999999999999876

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=95.32  E-value=0.015  Score=54.47  Aligned_cols=40  Identities=10%  Similarity=-0.147  Sum_probs=26.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCcccc-CCcceeEEEEeCCCC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVK-FYFDCHAWVRVSNFY  154 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~-~~F~~~~wv~~~~~~  154 (348)
                      .++|+|.+|+|||||++.+.+....+ ..+. ++++-+++..
T Consensus       176 r~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~-~I~~lIGER~  216 (422)
T 3ice_A          176 RGLIVAPPKAGKTMLLQNIAQSIAYNHPDCV-LMVLLIDERP  216 (422)
T ss_dssp             EEEEECCSSSSHHHHHHHHHHHHHHHCTTSE-EEEEEESSCH
T ss_pred             EEEEecCCCCChhHHHHHHHHHHhhcCCCee-EEEEEecCCh
Confidence            68899999999999999887652111 1222 3456666543

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=95.30  E-value=0.012  Score=48.63  Aligned_cols=24  Identities=17%  Similarity=0.122  Sum_probs=21.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+|+|.|+.|+||||+++.+...
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~   28 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEY   28 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            457889999999999999999875

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=95.26  E-value=0.031  Score=47.66  Aligned_cols=57  Identities=16%  Similarity=0.214  Sum_probs=34.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCcccc---C-CcceeEEEEeCCCCCHHHHHHHHHHHhC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVK---F-YFDCHAWVRVSNFYNFKRILDDIMKSLM  168 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~---~-~F~~~~wv~~~~~~~~~~~~~~i~~~l~  168 (348)
                      .-.+++|+|+.|+|||||++.++......   . .-...+|+.-...+.... +..+...++
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~~-i~~~~~~~~   84 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER-IREIAQNRG   84 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHH-HHHHHHHTT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHHH-HHHHHHHcC
Confidence            34689999999999999999997631111   1 123577776554444333 333444443

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=95.24  E-value=0.01  Score=50.35  Aligned_cols=25  Identities=4%  Similarity=0.308  Sum_probs=21.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++++|+|+.|+|||||++.+...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~   42 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQ   42 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhh
Confidence            3468899999999999999999865

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=95.21  E-value=0.012  Score=49.87  Aligned_cols=24  Identities=4%  Similarity=-0.053  Sum_probs=21.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|+|.|+.|+||||+++.+...
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~   33 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEY   33 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            458999999999999999999876

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=95.20  E-value=0.01  Score=50.23  Aligned_cols=24  Identities=4%  Similarity=0.099  Sum_probs=21.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.|.|+.|+||||+|+.+...
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~   32 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEA   32 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            457999999999999999999876

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=95.19  E-value=0.012  Score=52.64  Aligned_cols=25  Identities=20%  Similarity=0.238  Sum_probs=22.1

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhc
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      ..+.+|+|.|+.|+||||+|+.+..
T Consensus        73 ~~~~iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           73 SGLYVLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             TTCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4567899999999999999999883

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.18  E-value=0.012  Score=51.79  Aligned_cols=24  Identities=13%  Similarity=0.248  Sum_probs=21.5

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|+|+|+.|+||||+++.+...
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~~   50 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAES   50 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHh
Confidence            358999999999999999999855

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=95.17  E-value=0.012  Score=49.40  Aligned_cols=23  Identities=13%  Similarity=0.121  Sum_probs=21.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|+|.|+.|+||||+++.+...
T Consensus         5 ~~I~l~G~~GsGKsT~~~~L~~~   27 (204)
T 2v54_A            5 ALIVFEGLDKSGKTTQCMNIMES   27 (204)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHT
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHH
Confidence            47899999999999999999887

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=95.15  E-value=0.0046  Score=56.78  Aligned_cols=44  Identities=16%  Similarity=0.108  Sum_probs=31.4

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+...   +.+...+..    ..  ..-+.|+|++|+|||+||+.+++.
T Consensus        25 ~i~G~~~~~---~~l~~~~~~----~~--~~~vLl~G~~GtGKT~la~~la~~   68 (350)
T 1g8p_A           25 AIVGQEDMK---LALLLTAVD----PG--IGGVLVFGDRGTGKSTAVRALAAL   68 (350)
T ss_dssp             GSCSCHHHH---HHHHHHHHC----GG--GCCEEEECCGGGCTTHHHHHHHHH
T ss_pred             hccChHHHH---HHHHHHhhC----CC--CceEEEECCCCccHHHHHHHHHHh
Confidence            789988866   554444331    11  112778999999999999999875

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.14  E-value=0.0087  Score=51.45  Aligned_cols=23  Identities=17%  Similarity=0.291  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.+...
T Consensus        24 ~~~~lvGpsGsGKSTLl~~L~g~   46 (218)
T 1z6g_A           24 YPLVICGPSGVGKGTLIKKLLNE   46 (218)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            47899999999999999998865

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=95.12  E-value=0.015  Score=49.71  Aligned_cols=23  Identities=22%  Similarity=0.286  Sum_probs=20.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      ..+|+|.|+.|+||||+++.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999875

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=95.10  E-value=0.011  Score=51.03  Aligned_cols=24  Identities=17%  Similarity=0.202  Sum_probs=21.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|.|.|++|+||||+|+.+...
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~   30 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTH   30 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999999876

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=95.09  E-value=0.012  Score=50.13  Aligned_cols=22  Identities=18%  Similarity=0.264  Sum_probs=19.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|++|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4779999999999999999765

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=95.08  E-value=0.014  Score=52.95  Aligned_cols=25  Identities=24%  Similarity=0.266  Sum_probs=21.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|+|++|+||||++..++..
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagl  125 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRY  125 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4569999999999999999998754

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=95.05  E-value=0.021  Score=47.30  Aligned_cols=26  Identities=12%  Similarity=0.167  Sum_probs=22.1

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....|+|+|.+|+|||||...+...
T Consensus        46 ~~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           46 SYQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            34457889999999999999999876

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=95.04  E-value=0.015  Score=50.79  Aligned_cols=25  Identities=12%  Similarity=0.129  Sum_probs=22.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|.|.|++|+||||+|+.+.+.
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~   52 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKS   52 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4568899999999999999999865

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=95.03  E-value=0.011  Score=51.67  Aligned_cols=21  Identities=24%  Similarity=0.384  Sum_probs=19.9

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.|+|++|+|||||++.+++.
T Consensus        52 ~ll~G~~G~GKTtl~~~i~~~   72 (254)
T 1ixz_A           52 VLLVGPPGVGKTHLARAVAGE   72 (254)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            889999999999999999987

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=95.02  E-value=0.013  Score=50.55  Aligned_cols=24  Identities=8%  Similarity=0.227  Sum_probs=21.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+++|+|+.|+|||||.+.+...
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g~   39 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLKT   39 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcc
Confidence            458999999999999999999875

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=95.00  E-value=0.013  Score=49.89  Aligned_cols=22  Identities=14%  Similarity=0.190  Sum_probs=19.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|+|.|++|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4788999999999999999765

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=94.95  E-value=0.016  Score=47.19  Aligned_cols=24  Identities=17%  Similarity=0.195  Sum_probs=21.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+++|+|+.|.|||||++.+..-
T Consensus        33 Ge~v~L~G~nGaGKTTLlr~l~g~   56 (158)
T 1htw_A           33 AIMVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            358999999999999999998865

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=94.94  E-value=0.076  Score=51.29  Aligned_cols=26  Identities=15%  Similarity=0.239  Sum_probs=22.8

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+++|+|..|+|||||++.++..
T Consensus       291 ~~GeVI~LVGpNGSGKTTLl~~LAgl  316 (503)
T 2yhs_A          291 KAPFVILMVGVNGVGKTTTIGKLARQ  316 (503)
T ss_dssp             CTTEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cCCeEEEEECCCcccHHHHHHHHHHH
Confidence            34679999999999999999998865

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=94.94  E-value=0.011  Score=50.64  Aligned_cols=24  Identities=17%  Similarity=-0.014  Sum_probs=21.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|.|.|++|+||||+++.+...
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~   28 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTK   28 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            346889999999999999999876

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=94.91  E-value=0.012  Score=54.86  Aligned_cols=23  Identities=22%  Similarity=0.328  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+.++|++|+|||++|+.+++.
T Consensus        73 ~~ill~Gp~GtGKT~la~~la~~   95 (376)
T 1um8_A           73 SNILLIGPTGSGKTLMAQTLAKH   95 (376)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHH
Confidence            34778999999999999999987

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=94.91  E-value=0.0065  Score=51.55  Aligned_cols=22  Identities=18%  Similarity=0.299  Sum_probs=20.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|+|.|+.|+||||+++.+...
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~   23 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGA   23 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            6889999999999999998765

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=94.90  E-value=0.017  Score=49.07  Aligned_cols=24  Identities=13%  Similarity=0.120  Sum_probs=21.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.|.|+.|+||||+++.+...
T Consensus        25 ~~~i~~~G~~GsGKsT~~~~l~~~   48 (211)
T 1m7g_A           25 GLTIWLTGLSASGKSTLAVELEHQ   48 (211)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999999999876

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=94.85  E-value=0.018  Score=52.26  Aligned_cols=26  Identities=15%  Similarity=0.097  Sum_probs=22.7

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+++|+|+.|+|||||++.+...
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~  103 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQAL  103 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            34579999999999999999998875

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=94.80  E-value=0.016  Score=48.76  Aligned_cols=22  Identities=18%  Similarity=0.208  Sum_probs=20.5

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|+|.|+.|+||||+|+.+...
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~   25 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAA   25 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            7999999999999999999875

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.74  E-value=0.01  Score=51.23  Aligned_cols=23  Identities=17%  Similarity=0.368  Sum_probs=15.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHh-cC
Q 040110          113 SVVAILDSRGFDKTAFAAEIY-NN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~-~~  135 (348)
                      .+++|+|+.|+|||||++.+. ..
T Consensus        28 ~ii~l~Gp~GsGKSTl~~~L~~~~   51 (231)
T 3lnc_A           28 VILVLSSPSGCGKTTVANKLLEKQ   51 (231)
T ss_dssp             CEEEEECSCC----CHHHHHHC--
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcC
Confidence            589999999999999999998 54

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=94.73  E-value=0.0091  Score=49.42  Aligned_cols=23  Identities=13%  Similarity=0.228  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|..|+|||||++.+..-
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~   25 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPI   25 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47999999999999999998766

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=94.72  E-value=0.013  Score=50.07  Aligned_cols=23  Identities=13%  Similarity=0.128  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..|.|.|++|+||||+|+.+...
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~   28 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKE   28 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            46889999999999999999876

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=94.70  E-value=0.017  Score=50.39  Aligned_cols=23  Identities=22%  Similarity=0.200  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        32 e~~~iiG~nGsGKSTLl~~l~Gl   54 (235)
T 3tif_A           32 EFVSIMGPSGSGKSTMLNIIGCL   54 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcC
Confidence            47999999999999999998754

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.69  E-value=0.018  Score=50.37  Aligned_cols=23  Identities=22%  Similarity=0.265  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl   47 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGI   47 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC
Confidence            68999999999999999998754

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=94.69  E-value=0.14  Score=49.73  Aligned_cols=51  Identities=8%  Similarity=0.084  Sum_probs=33.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMK  165 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~  165 (348)
                      -.++.|.|.+|+||||||.+++.+...... ..++|++...  +..++...++.
T Consensus       242 G~l~li~G~pG~GKT~lal~~a~~~a~~~g-~~vl~~s~E~--s~~~l~~r~~~  292 (503)
T 1q57_A          242 GEVIMVTSGSGMVMSTFVRQQALQWGTAMG-KKVGLAMLEE--SVEETAEDLIG  292 (503)
T ss_dssp             TCEEEEEESSCHHHHHHHHHHHHHHTTTSC-CCEEEEESSS--CHHHHHHHHHH
T ss_pred             CeEEEEeecCCCCchHHHHHHHHHHHHhcC-CcEEEEeccC--CHHHHHHHHHH
Confidence            347788999999999999998876322211 2466776543  45566665543

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.69  E-value=0.13  Score=48.95  Aligned_cols=50  Identities=22%  Similarity=0.089  Sum_probs=33.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMK  165 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~  165 (348)
                      .++.|.|.+|+||||||..++.+...... ..++|++..  -+..++...++.
T Consensus       201 ~l~ii~G~pg~GKT~lal~ia~~~a~~~g-~~vl~~slE--~~~~~l~~R~~~  250 (444)
T 2q6t_A          201 SLNIIAARPAMGKTAFALTIAQNAALKEG-VGVGIYSLE--MPAAQLTLRMMC  250 (444)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTTC-CCEEEEESS--SCHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHHhCC-CeEEEEECC--CCHHHHHHHHHH
Confidence            47888999999999999998876322111 246676554  345566666553

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=94.65  E-value=0.016  Score=51.52  Aligned_cols=52  Identities=17%  Similarity=0.224  Sum_probs=31.8

Q ss_pred             cccccccccccHHHHHhhcCCCC---C-CCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS---G-LGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~---~-~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+.....++.+...+....   . .-.-... +.|+|++|+|||||++.+++.
T Consensus        41 ~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~g-vll~Gp~GtGKTtl~~~i~~~   96 (278)
T 1iy2_A           41 DVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAGE   96 (278)
T ss_dssp             GSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCE-EEEECCTTSSHHHHHHHHHHH
T ss_pred             HhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCcChHHHHHHHHHHH
Confidence            78888877722233333221000   0 0011223 889999999999999999987

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.61  E-value=0.053  Score=60.63  Aligned_cols=88  Identities=13%  Similarity=0.020  Sum_probs=55.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l~  189 (348)
                      ..+.+.|+|++|+|||+||.++........  ..++|+++...++...     ++.++.+.... -......++....+.
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~~G--~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~~ 1498 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICD 1498 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTTT--CCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC--CcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHHH
Confidence            456788999999999999999876522221  2567888777776655     44555321110 111223345555555


Q ss_pred             HHhc-CCeEEEEEeCCC
Q 040110          190 DYLT-NKKYFTVLDDVW  205 (348)
Q Consensus       190 ~~L~-~kr~LlVLDdv~  205 (348)
                      ...+ .+.-+||+|.+.
T Consensus      1499 ~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1499 ALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             HHHHHTCCSEEEESCGG
T ss_pred             HHHhcCCCCEEEEcChh
Confidence            5543 467899999994

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=94.60  E-value=0.016  Score=53.68  Aligned_cols=25  Identities=24%  Similarity=0.304  Sum_probs=21.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+.|+|++|+||||+++.++..
T Consensus        23 ~~~~i~l~G~~G~GKTTl~~~la~~   47 (359)
T 2ga8_A           23 YRVCVILVGSPGSGKSTIAEELCQI   47 (359)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeeEEEEECCCCCcHHHHHHHHHHH
Confidence            4556889999999999999988765

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=94.60  E-value=0.14  Score=44.07  Aligned_cols=93  Identities=14%  Similarity=0.054  Sum_probs=49.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHh-cCccccCCcc-eeEEEEeCCCCCHHHHHHHHHHHhCCCCCc----------------c
Q 040110          113 SVVAILDSRGFDKTAFAAEIY-NNNFVKFYFD-CHAWVRVSNFYNFKRILDDIMKSLMPTSSW----------------L  174 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~-~~~~~~~~F~-~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~----------------~  174 (348)
                      ..+.|.|..|+||||+...+. +......... ..+.+.........++.+.+...++.....                .
T Consensus        77 ~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  156 (235)
T 3llm_A           77 SVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHA  156 (235)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTTSSEEEEETTEEECCCSSS
T ss_pred             CEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccCceEEEeechhhccCCCCC
Confidence            368899999999998665443 2211112222 233333333333345555555554432110                0


Q ss_pred             ccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 040110          175 KIMGKDYKSEKTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       175 ~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                      ..--.+...+...+...+.+ --+||+|.+..
T Consensus       157 ~Ivv~Tpg~l~~~l~~~l~~-~~~lVlDEah~  187 (235)
T 3llm_A          157 SIMFCTVGVLLRKLEAGIRG-ISHVIVDEIHE  187 (235)
T ss_dssp             EEEEEEHHHHHHHHHHCCTT-CCEEEECCTTS
T ss_pred             eEEEECHHHHHHHHHhhhcC-CcEEEEECCcc
Confidence            11123566677777665544 34788999976

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=94.59  E-value=0.017  Score=48.61  Aligned_cols=22  Identities=18%  Similarity=0.167  Sum_probs=19.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|+|+.|+|||||++.++..
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~   24 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhh
Confidence            5889999999999999998765

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=94.58  E-value=0.02  Score=47.41  Aligned_cols=25  Identities=16%  Similarity=0.174  Sum_probs=22.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|.|..|+|||||+..+...
T Consensus         5 ~~~~i~i~G~sGsGKTTl~~~l~~~   29 (174)
T 1np6_A            5 MIPLLAFAAWSGTGKTTLLKKLIPA   29 (174)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cceEEEEEeCCCCCHHHHHHHHHHh
Confidence            3568999999999999999998876

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.58  E-value=0.011  Score=53.30  Aligned_cols=25  Identities=12%  Similarity=0.258  Sum_probs=19.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+|+|.|..|+||||+|+.+...
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~   28 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQI   28 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHH
Confidence            4568999999999999999998764

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=94.57  E-value=0.015  Score=51.23  Aligned_cols=23  Identities=13%  Similarity=0.133  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|+|+|+.|+||||+++.+...
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~   71 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARS   71 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            36899999999999999999875

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.57  E-value=0.017  Score=49.85  Aligned_cols=23  Identities=17%  Similarity=0.154  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        31 e~~~iiG~nGsGKSTLl~~l~Gl   53 (224)
T 2pcj_A           31 EFVSIIGASGSGKSTLLYILGLL   53 (224)
T ss_dssp             CEEEEEECTTSCHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            47999999999999999998754

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=94.56  E-value=0.06  Score=51.57  Aligned_cols=49  Identities=18%  Similarity=0.217  Sum_probs=32.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIM  164 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~  164 (348)
                      .++.|.|.+|+||||||..++........ ..++|++...  +..++...++
T Consensus       204 ~liiI~G~pG~GKTtl~l~ia~~~~~~~g-~~Vl~~s~E~--s~~~l~~r~~  252 (454)
T 2r6a_A          204 DLIIVAARPSVGKTAFALNIAQNVATKTN-ENVAIFSLEM--SAQQLVMRML  252 (454)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHHSS-CCEEEEESSS--CHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHhCC-CcEEEEECCC--CHHHHHHHHH
Confidence            47889999999999999998876322111 1466765433  3445555443

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=94.55  E-value=0.023  Score=51.50  Aligned_cols=25  Identities=20%  Similarity=0.251  Sum_probs=21.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|+|+.|+||||++..++..
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~  123 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHR  123 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            4579999999999999999988754

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=94.55  E-value=0.022  Score=48.66  Aligned_cols=25  Identities=16%  Similarity=0.232  Sum_probs=22.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|+|+|.+|+|||||+..+...
T Consensus        37 ~~~~i~ivG~~gvGKTtl~~~l~~~   61 (226)
T 2hf9_A           37 GVVAFDFMGAIGSGKTLLIEKLIDN   61 (226)
T ss_dssp             TCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            4678899999999999999998876

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=94.47  E-value=0.027  Score=52.20  Aligned_cols=27  Identities=15%  Similarity=0.097  Sum_probs=23.1

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....+|+|+|.+|+|||||+..+...
T Consensus        76 ~~~~~~I~i~G~~G~GKSTl~~~L~~~  102 (355)
T 3p32_A           76 SGNAHRVGITGVPGVGKSTAIEALGMH  102 (355)
T ss_dssp             CCCSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            346779999999999999999988755

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=94.46  E-value=0.024  Score=49.05  Aligned_cols=24  Identities=21%  Similarity=0.221  Sum_probs=21.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|.|.|+.|+||||+|+.+...
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~   39 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKN   39 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            356889999999999999999876

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=94.46  E-value=0.022  Score=49.63  Aligned_cols=24  Identities=21%  Similarity=0.232  Sum_probs=21.5

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+++|.|++|+||||+|+.+...
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~   32 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARA   32 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999999866

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=94.45  E-value=0.023  Score=51.00  Aligned_cols=23  Identities=17%  Similarity=0.372  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|.|.|++|+||||+|+.+...
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAK   25 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            47889999999999999999873

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=94.44  E-value=0.032  Score=53.24  Aligned_cols=105  Identities=11%  Similarity=0.148  Sum_probs=57.5

Q ss_pred             HHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccC-Ccc-eeEEEEeCCCC-CHHHHHHHHHHHhCCCCC
Q 040110           96 NLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKF-YFD-CHAWVRVSNFY-NFKRILDDIMKSLMPTSS  172 (348)
Q Consensus        96 ~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~F~-~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~  172 (348)
                      +.++.|.+-    ..+- .++|.|..|+|||+|+.++.+...... +=+ .++++-+++.. .+.++++++...=.....
T Consensus       140 raID~l~pi----grGQ-r~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rt  214 (465)
T 3vr4_D          140 SAIDHLNTL----VRGQ-KLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRS  214 (465)
T ss_dssp             HHHHTTSCC----BTTC-BCCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGE
T ss_pred             eEEeccccc----ccCC-EEEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccce
Confidence            556666632    2222 267899999999999999988743311 111 56666666543 456666665543111100


Q ss_pred             c--cccCCCCHHHH------HHHHHHHhc---CCeEEEEEeCCC
Q 040110          173 W--LKIMGKDYKSE------KTILRDYLT---NKKYFTVLDDVW  205 (348)
Q Consensus       173 ~--~~~~~~~~~~~------~~~l~~~L~---~kr~LlVLDdv~  205 (348)
                      .  ....+......      .-.+.++++   ++.+||++||+-
T Consensus       215 vvV~atsd~p~~~r~~a~~~a~tiAEyfrd~~G~~VLl~~DslT  258 (465)
T 3vr4_D          215 VMFMNLANDPAIERIATPRMALTAAEYLAYEKGMHVLVIMTDMT  258 (465)
T ss_dssp             EEEEEETTSCHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECHH
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence            0  01122222211      112445553   689999999984

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=94.44  E-value=0.023  Score=49.21  Aligned_cols=26  Identities=19%  Similarity=0.088  Sum_probs=22.5

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+|+|.|+.|+||||+++.+...
T Consensus        14 ~~~~~i~i~G~~gsGKst~~~~l~~~   39 (236)
T 1q3t_A           14 MKTIQIAIDGPASSGKSTVAKIIAKD   39 (236)
T ss_dssp             CCCCEEEEECSSCSSHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            34568999999999999999998875

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=94.44  E-value=0.022  Score=48.96  Aligned_cols=22  Identities=14%  Similarity=0.182  Sum_probs=19.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|+.|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~   23 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDK   23 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999876

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=94.44  E-value=0.021  Score=49.82  Aligned_cols=23  Identities=17%  Similarity=0.420  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        32 e~~~i~G~nGsGKSTLl~~l~Gl   54 (237)
T 2cbz_A           32 ALVAVVGQVGCGKSSLLSALLAE   54 (237)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            47999999999999999999866

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.43  E-value=0.021  Score=50.60  Aligned_cols=23  Identities=30%  Similarity=0.362  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        33 e~~~liG~nGsGKSTLlk~l~Gl   55 (262)
T 1b0u_A           33 DVISIIGSSGSGKSTFLRCINFL   55 (262)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999998754

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.42  E-value=0.023  Score=52.31  Aligned_cols=23  Identities=17%  Similarity=0.294  Sum_probs=21.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|+|.|+.|+||||||..++..
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~   30 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKK   30 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHHHHHHH
Confidence            58999999999999999998876

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.41  E-value=0.018  Score=49.20  Aligned_cols=22  Identities=27%  Similarity=0.137  Sum_probs=19.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|+|+.|+|||||++.+..-
T Consensus        24 ~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           24 IVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             EEEEECCTTSSTTHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            7899999999999999998753

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=94.40  E-value=0.037  Score=45.49  Aligned_cols=25  Identities=8%  Similarity=0.186  Sum_probs=21.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|+++|.+|+|||||...+...
T Consensus         6 ~~~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            6 KSYEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3457889999999999999999874

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=94.39  E-value=0.022  Score=50.93  Aligned_cols=23  Identities=26%  Similarity=0.356  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.+..-
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~Gl   57 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNGI   57 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            47899999999999999998754

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=94.35  E-value=0.03  Score=51.44  Aligned_cols=24  Identities=8%  Similarity=0.361  Sum_probs=21.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.|+|+.|+||||||..++..
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~   63 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAH   63 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH
Confidence            358999999999999999999877

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=94.34  E-value=0.021  Score=48.59  Aligned_cols=22  Identities=18%  Similarity=0.090  Sum_probs=19.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|++|+||||+|+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEK   23 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3789999999999999999876

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=94.34  E-value=0.035  Score=48.54  Aligned_cols=26  Identities=19%  Similarity=0.256  Sum_probs=22.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....++.+.|.||+||||++..+...
T Consensus        12 ~~~~i~~~~GkgGvGKTTl~~~La~~   37 (262)
T 1yrb_A           12 MASMIVVFVGTAGSGKTTLTGEFGRY   37 (262)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cceEEEEEeCCCCCCHHHHHHHHHHH
Confidence            44678888999999999999999855

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=94.33  E-value=0.026  Score=48.03  Aligned_cols=26  Identities=19%  Similarity=0.216  Sum_probs=22.8

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+++|+|.+|+|||||+..+...
T Consensus        28 ~~~~~i~i~G~~g~GKTTl~~~l~~~   53 (221)
T 2wsm_A           28 SGTVAVNIMGAIGSGKTLLIERTIER   53 (221)
T ss_dssp             HTCEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             cCceEEEEEcCCCCCHHHHHHHHHHH
Confidence            35678999999999999999998876

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=94.31  E-value=0.027  Score=46.93  Aligned_cols=25  Identities=16%  Similarity=0.278  Sum_probs=21.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...++|+|..|+|||||.+.+....
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcCC
Confidence            4578999999999999999998763

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=94.31  E-value=0.026  Score=53.53  Aligned_cols=27  Identities=26%  Similarity=0.341  Sum_probs=23.3

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....+|.|+|++|+||||+|+.+...
T Consensus       255 ~~~~~lIil~G~pGSGKSTla~~L~~~  281 (416)
T 3zvl_A          255 SPNPEVVVAVGFPGAGKSTFIQEHLVS  281 (416)
T ss_dssp             CSSCCEEEEESCTTSSHHHHHHHHTGG
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHh
Confidence            345678999999999999999999876

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=94.31  E-value=0.023  Score=50.46  Aligned_cols=23  Identities=22%  Similarity=0.323  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.+..-
T Consensus        38 e~~~liG~nGsGKSTLl~~l~Gl   60 (266)
T 4g1u_C           38 EMVAIIGPNGAGKSTLLRLLTGY   60 (266)
T ss_dssp             CEEEEECCTTSCHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcC
Confidence            47999999999999999999764

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=94.29  E-value=0.046  Score=47.29  Aligned_cols=26  Identities=19%  Similarity=0.327  Sum_probs=22.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .-.+|.|.|+.|+||||+++.+....
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l   50 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRL   50 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            44688999999999999999998873

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.29  E-value=0.023  Score=49.58  Aligned_cols=23  Identities=22%  Similarity=0.320  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~Gl   55 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            47999999999999999998754

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=94.28  E-value=0.038  Score=44.68  Aligned_cols=23  Identities=9%  Similarity=0.203  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++|+|.+|+|||||...+...
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            46889999999999999999865

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=94.28  E-value=0.026  Score=49.36  Aligned_cols=24  Identities=17%  Similarity=0.185  Sum_probs=21.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+++|+|+.|+|||||.+.++.-
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLERF   51 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            358999999999999999998754

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=94.27  E-value=0.025  Score=48.21  Aligned_cols=22  Identities=18%  Similarity=0.286  Sum_probs=19.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|.|.|++|+||+|+|+.+...
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~   23 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKE   23 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5778999999999999999876

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=94.27  E-value=0.024  Score=50.11  Aligned_cols=23  Identities=22%  Similarity=0.261  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        34 e~~~liG~nGsGKSTLlk~l~Gl   56 (257)
T 1g6h_A           34 DVTLIIGPNGSGKSTLINVITGF   56 (257)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999998654

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=94.26  E-value=0.025  Score=49.69  Aligned_cols=23  Identities=17%  Similarity=0.330  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        30 e~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            37999999999999999999874

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=94.23  E-value=0.17  Score=47.27  Aligned_cols=36  Identities=22%  Similarity=0.171  Sum_probs=26.4

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -++++.|.+-    ..+- .++|+|.+|+|||+|+..+.+.
T Consensus       163 iraID~l~Pi----grGQ-R~lIfg~~g~GKT~Ll~~Ia~~  198 (427)
T 3l0o_A          163 TRLIDLFAPI----GKGQ-RGMIVAPPKAGKTTILKEIANG  198 (427)
T ss_dssp             HHHHHHHSCC----BTTC-EEEEEECTTCCHHHHHHHHHHH
T ss_pred             chhhhhcccc----cCCc-eEEEecCCCCChhHHHHHHHHH
Confidence            4566777632    2222 5789999999999999988876

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.22  E-value=0.033  Score=44.32  Aligned_cols=23  Identities=13%  Similarity=0.248  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..|.++|.+|+|||||...+.+.
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45789999999999999999866

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=94.21  E-value=0.025  Score=50.17  Aligned_cols=23  Identities=22%  Similarity=0.293  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        51 ei~~liG~NGsGKSTLlk~l~Gl   73 (263)
T 2olj_A           51 EVVVVIGPSGSGKSTFLRCLNLL   73 (263)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEEcCCCCcHHHHHHHHHcC
Confidence            48999999999999999998754

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=94.20  E-value=0.026  Score=48.93  Aligned_cols=23  Identities=26%  Similarity=0.358  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        35 e~~~i~G~nGsGKSTLl~~l~Gl   57 (229)
T 2pze_A           35 QLLAVAGSTGAGKTSLLMMIMGE   57 (229)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            47899999999999999999876

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=94.20  E-value=0.025  Score=49.64  Aligned_cols=23  Identities=22%  Similarity=0.303  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        36 e~~~i~G~nGsGKSTLl~~l~Gl   58 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTKLIQRF   58 (247)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            47999999999999999998765

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.18  E-value=0.097  Score=58.60  Aligned_cols=88  Identities=13%  Similarity=0.026  Sum_probs=58.5

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l~  189 (348)
                      .-+++.|.|.+|+||||||.+++...  ...=..++|++.....+..     .++.++.+.... -.+..+.+++...+.
T Consensus       382 ~G~lilI~G~pGsGKTtLaLqia~~~--a~~G~~vlyis~E~s~~~~-----~a~~lGvd~~~L~I~~~~~~e~il~~~~  454 (2050)
T 3cmu_A          382 MGRIVEIYGPESSGKTTLTLQVIAAA--QREGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  454 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHH--HTTTCCEEEECTTSCCCHH-----HHHHTTCCTTTCEEECCSSHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHH--HhcCCeEEEEEcCCCHHHH-----HHHHcCCCHHHeEEeCCCCHHHHHHHHH
Confidence            34588899999999999999998763  2222367888887777654     255666543221 112346677777776


Q ss_pred             HHh-cCCeEEEEEeCCC
Q 040110          190 DYL-TNKKYFTVLDDVW  205 (348)
Q Consensus       190 ~~L-~~kr~LlVLDdv~  205 (348)
                      ... +.+.-++|+|.+.
T Consensus       455 ~lv~~~~~~lIVIDSL~  471 (2050)
T 3cmu_A          455 ALARSGAVDVIVVDSVA  471 (2050)
T ss_dssp             HHHHHTCCSEEEESCGG
T ss_pred             HHHHhcCCcEEEECCHH
Confidence            554 3456799999985

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=94.15  E-value=0.033  Score=50.62  Aligned_cols=24  Identities=21%  Similarity=0.264  Sum_probs=21.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+|.|.|+.|+||||||..++..
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~   26 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKR   26 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHT
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHh
Confidence            357899999999999999999876

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=94.15  E-value=0.069  Score=51.45  Aligned_cols=101  Identities=15%  Similarity=0.149  Sum_probs=56.1

Q ss_pred             HHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHH-HHHhcCccccCCcc-eeEEEEeCCCC-CHHHHHHHHHHHhCCCCC
Q 040110           96 NLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFA-AEIYNNNFVKFYFD-CHAWVRVSNFY-NFKRILDDIMKSLMPTSS  172 (348)
Q Consensus        96 ~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA-~~v~~~~~~~~~F~-~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~  172 (348)
                      +.++.|.+-    ..+- .++|.|.+|+|||+|| ..+.+..    .-+ .++++-+++.. .+.++.+++...=.....
T Consensus       151 raID~l~Pi----grGQ-R~~Ifg~~g~GKT~Lal~~I~~~~----~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~t  221 (502)
T 2qe7_A          151 KAIDSMIPI----GRGQ-RELIIGDRQTGKTTIAIDTIINQK----GQDVICIYVAIGQKQSTVAGVVETLRQHDALDYT  221 (502)
T ss_dssp             HHHHHSSCC----BTTC-BCEEEECSSSCHHHHHHHHHHGGG----SCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTE
T ss_pred             eeccccccc----ccCC-EEEEECCCCCCchHHHHHHHHHhh----cCCcEEEEEECCCcchHHHHHHHHHhhCCCccee
Confidence            556666632    1222 3678999999999995 4677762    234 34667777654 455666666653222211


Q ss_pred             cc--ccCCCCHHHH------HHHHHHHh--cCCeEEEEEeCCC
Q 040110          173 WL--KIMGKDYKSE------KTILRDYL--TNKKYFTVLDDVW  205 (348)
Q Consensus       173 ~~--~~~~~~~~~~------~~~l~~~L--~~kr~LlVLDdv~  205 (348)
                      ..  ...+......      .-.+-+++  .++.+|+++||+-
T Consensus       222 vvV~atad~p~~~r~~a~~~a~tiAEyfrd~G~dVLl~~Dslt  264 (502)
T 2qe7_A          222 IVVTASASEPAPLLYLAPYAGCAMGEYFMYKGKHALVVYDDLS  264 (502)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEECHH
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEecHH
Confidence            10  1111221111      11233444  4689999999984

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=94.13  E-value=0.028  Score=49.95  Aligned_cols=23  Identities=26%  Similarity=0.400  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        47 e~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           47 EVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            47999999999999999999874

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=94.12  E-value=0.022  Score=48.84  Aligned_cols=23  Identities=26%  Similarity=0.332  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl   58 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTY   58 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            36899999999999999998765

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=94.11  E-value=0.027  Score=46.51  Aligned_cols=22  Identities=18%  Similarity=0.341  Sum_probs=19.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|+|+|.+|+|||||...+...
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999999874

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.11  E-value=0.027  Score=49.72  Aligned_cols=23  Identities=17%  Similarity=0.203  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        42 ei~~l~G~NGsGKSTLlk~l~Gl   64 (256)
T 1vpl_A           42 EIFGLIGPNGAGKTTTLRIISTL   64 (256)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999999765

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=94.10  E-value=0.03  Score=51.17  Aligned_cols=23  Identities=13%  Similarity=0.250  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|.|+|+.|+||||||+.++..
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~   28 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADA   28 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999999999876

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=94.09  E-value=0.032  Score=51.77  Aligned_cols=26  Identities=19%  Similarity=0.230  Sum_probs=22.4

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+++|+|+.|+||||++..++..
T Consensus       155 ~~g~vi~lvG~nGsGKTTll~~Lag~  180 (359)
T 2og2_A          155 RKPAVIMIVGVNGGGKTTSLGKLAHR  180 (359)
T ss_dssp             SSSEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCeEEEEEcCCCChHHHHHHHHHhh
Confidence            34679999999999999999988764

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=94.08  E-value=0.083  Score=58.29  Aligned_cols=89  Identities=12%  Similarity=0.001  Sum_probs=58.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l~  189 (348)
                      .-+++.|.|.+|+||||||.+++....  ..=..++|++....++..     .++.++.+.... -....+.+++...+.
T Consensus       382 ~G~lilI~G~pGsGKTtLaLq~a~~~~--~~G~~vlyis~E~s~~~~-----~a~~lGvd~~~L~i~~~~~~e~~l~~l~  454 (1706)
T 3cmw_A          382 MGRIVEIYGPESSGKTTLTLQVIAAAQ--REGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  454 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHH--HTTCCEEEECTTSCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHH--HhCCCeEEEEccCchHHH-----HHHHcCCCHHHeEEcCCCCHHHHHHHHH
Confidence            345888999999999999999876632  222368888888777753     256666543221 122345666666666


Q ss_pred             HHhc-CCeEEEEEeCCCC
Q 040110          190 DYLT-NKKYFTVLDDVWI  206 (348)
Q Consensus       190 ~~L~-~kr~LlVLDdv~~  206 (348)
                      ...+ .+.-++|+|.+..
T Consensus       455 ~lv~~~~~~lVVIDSL~a  472 (1706)
T 3cmw_A          455 ALARSGAVDVIVVDSVAA  472 (1706)
T ss_dssp             HHHHHTCCSEEEESCSTT
T ss_pred             HHHHhcCCCEEEECCHHH
Confidence            5553 4567999999864

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=94.08  E-value=0.025  Score=48.22  Aligned_cols=24  Identities=8%  Similarity=0.127  Sum_probs=20.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+.|+|++|+||||+|..+++.
T Consensus        58 kn~ili~GPPGtGKTt~a~ala~~   81 (212)
T 1tue_A           58 KNCLVFCGPANTGKSYFGMSFIHF   81 (212)
T ss_dssp             CSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHH
Confidence            345889999999999999998876

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=94.07  E-value=0.027  Score=50.16  Aligned_cols=23  Identities=30%  Similarity=0.356  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        46 e~~~i~G~nGsGKSTLlk~l~Gl   68 (271)
T 2ixe_A           46 KVTALVGPNGSGKSTVAALLQNL   68 (271)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            47999999999999999999765

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=94.06  E-value=0.031  Score=48.26  Aligned_cols=26  Identities=19%  Similarity=0.132  Sum_probs=22.5

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..-.+++|.|+.|+|||||++.+...
T Consensus        18 ~~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           18 TQPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhc
Confidence            34568999999999999999998765

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.05  E-value=0.028  Score=49.76  Aligned_cols=23  Identities=22%  Similarity=0.369  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        47 e~~~i~G~nGsGKSTLl~~l~Gl   69 (260)
T 2ghi_A           47 TTCALVGHTGSGKSTIAKLLYRF   69 (260)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcc
Confidence            48999999999999999999765

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=94.00  E-value=0.054  Score=43.91  Aligned_cols=25  Identities=24%  Similarity=0.300  Sum_probs=21.5

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|+|+|.+|+|||||...+.+.
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4556889999999999999999765

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=93.99  E-value=0.03  Score=49.26  Aligned_cols=23  Identities=13%  Similarity=0.313  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        27 e~~~liG~NGsGKSTLlk~l~Gl   49 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAGM   49 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            37899999999999999998765

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=93.97  E-value=0.21  Score=47.69  Aligned_cols=38  Identities=24%  Similarity=0.111  Sum_probs=27.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN  152 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  152 (348)
                      .++.|.|.+|+||||||.+++.+.....  ..++|++...
T Consensus       198 ~liiIaG~pG~GKTtlal~ia~~~a~~g--~~vl~fSlEm  235 (444)
T 3bgw_A          198 NFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLEM  235 (444)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHHHHTT--CEEEEECSSS
T ss_pred             cEEEEEeCCCCChHHHHHHHHHHHHHcC--CEEEEEECCC
Confidence            4788899999999999999887732221  2566765543

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=93.96  E-value=0.037  Score=50.58  Aligned_cols=26  Identities=19%  Similarity=0.226  Sum_probs=23.0

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+++|+|.+|+||||++..++..
T Consensus       103 ~~~~vI~ivG~~G~GKTT~~~~LA~~  128 (320)
T 1zu4_A          103 NRLNIFMLVGVNGTGKTTSLAKMANY  128 (320)
T ss_dssp             TSCEEEEEESSTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45679999999999999999998866

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=93.94  E-value=0.031  Score=46.70  Aligned_cols=24  Identities=17%  Similarity=0.277  Sum_probs=21.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...++|+|..|+|||||.+.+...
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            346889999999999999999876

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=93.94  E-value=0.03  Score=49.71  Aligned_cols=23  Identities=9%  Similarity=0.131  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        34 e~~~liG~nGsGKSTLl~~i~Gl   56 (266)
T 2yz2_A           34 ECLLVAGNTGSGKSTLLQIVAGL   56 (266)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            47999999999999999998754

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=93.92  E-value=0.038  Score=48.92  Aligned_cols=109  Identities=12%  Similarity=0.119  Sum_probs=58.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHH---HHHH--HhCCCCCccccCCCCHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILD---DIMK--SLMPTSSWLKIMGKDYKSEK  185 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~---~i~~--~l~~~~~~~~~~~~~~~~~~  185 (348)
                      .-.+++|+|+.|+|||||++.+..-  +...+...+.+. ..+...  +..   .+..  .++.       ..   ..+.
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~--~~~~~~G~I~~~-g~~i~~--~~~~~~~~v~q~~~gl-------~~---~~l~   88 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDY--INQTKSYHIITI-EDPIEY--VFKHKKSIVNQREVGE-------DT---KSFA   88 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHH--HHHHCCCEEEEE-ESSCCS--CCCCSSSEEEEEEBTT-------TB---SCHH
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHh--CCCCCCCEEEEc-CCccee--ecCCcceeeeHHHhCC-------CH---HHHH
Confidence            3458999999999999999998765  221112333221 111000  000   0000  0000       11   2234


Q ss_pred             HHHHHHhcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhh
Q 040110          186 TILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILT  237 (348)
Q Consensus       186 ~~l~~~L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~  237 (348)
                      ..+.+.|...+=+|++|...+.+....+....   ..|.-|++||-+.++..
T Consensus        89 ~~la~aL~~~p~illlDEp~D~~~~~~~l~~~---~~g~~vl~t~H~~~~~~  137 (261)
T 2eyu_A           89 DALRAALREDPDVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNTAID  137 (261)
T ss_dssp             HHHHHHHHHCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEECCSSHHH
T ss_pred             HHHHHHHhhCCCEEEeCCCCCHHHHHHHHHHH---ccCCEEEEEeCcchHHH
Confidence            56677776677788999997554443333322   23566888888766543

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=93.92  E-value=0.037  Score=46.84  Aligned_cols=23  Identities=26%  Similarity=0.244  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.+.|.|++|+||||||..+...
T Consensus        35 ~~ilI~GpsGsGKStLA~~La~~   57 (205)
T 2qmh_A           35 LGVLITGDSGVGKSETALELVQR   57 (205)
T ss_dssp             EEEEEECCCTTTTHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            46789999999999999999876

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=93.92  E-value=0.042  Score=49.85  Aligned_cols=25  Identities=20%  Similarity=0.223  Sum_probs=22.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...++.|.|+.|+||||||..++..
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~~   33 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRKI   33 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCCccCHHHHHHHHHHh
Confidence            3568899999999999999999865

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=93.91  E-value=0.031  Score=49.23  Aligned_cols=124  Identities=12%  Similarity=0.078  Sum_probs=63.2

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCcccc-CC---cceeEEEEeCC----CCCH----------------------HHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVK-FY---FDCHAWVRVSN----FYNF----------------------KRILDD  162 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~-~~---F~~~~wv~~~~----~~~~----------------------~~~~~~  162 (348)
                      .+++|+|+.|+|||||.+.++.-.... ..   ...+.++.-..    ..++                      .+-..+
T Consensus        32 e~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~I~~~~~i~~v~q~~~~~~~~tv~enl~~~~~~~~~~~~~~~~~~~~~~~~  111 (253)
T 2nq2_C           32 DILAVLGQNGCGKSTLLDLLLGIHRPIQGKIEVYQSIGFVPQFFSSPFAYSVLDIVLMGRSTHINTFAKPKSHDYQVAMQ  111 (253)
T ss_dssp             CEEEEECCSSSSHHHHHHHHTTSSCCSEEEEEECSCEEEECSCCCCSSCCBHHHHHHGGGGGGSCTTCCCCHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCCCCcEEEEeccEEEEcCCCccCCCCCHHHHHHHhhhhhcccccCCCHHHHHHHHH
Confidence            378999999999999999998652111 00   01122221110    0011                      122345


Q ss_pred             HHHHhCCCCCc-cccCCCCHHHHH-HHHHHHhcCCeEEEEEeCCCCh------hhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          163 IMKSLMPTSSW-LKIMGKDYKSEK-TILRDYLTNKKYFTVLDDVWIE------KIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       163 i~~~l~~~~~~-~~~~~~~~~~~~-~~l~~~L~~kr~LlVLDdv~~~------~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      +++.++..... .....-+..+.+ -.|.+.|-.++-+|+||..-+.      ..+..+...+.. ..|..||++|.+..
T Consensus       112 ~l~~~~l~~~~~~~~~~LSgGq~qrv~lAraL~~~p~lllLDEPts~LD~~~~~~l~~~l~~l~~-~~g~tvi~vtHd~~  190 (253)
T 2nq2_C          112 ALDYLNLTHLAKREFTSLSGGQRQLILIARAIASECKLILLDEPTSALDLANQDIVLSLLIDLAQ-SQNMTVVFTTHQPN  190 (253)
T ss_dssp             HHHHTTCGGGTTSBGGGSCHHHHHHHHHHHHHHTTCSEEEESSSSTTSCHHHHHHHHHHHHHHHH-TSCCEEEEEESCHH
T ss_pred             HHHHcCChHHhcCChhhCCHHHHHHHHHHHHHHcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHH-hcCCEEEEEecCHH
Confidence            55555543110 011222333322 3455666677889999997653      122222222211 22566888888866


Q ss_pred             hhh
Q 040110          235 ILT  237 (348)
Q Consensus       235 v~~  237 (348)
                      .+.
T Consensus       191 ~~~  193 (253)
T 2nq2_C          191 QVV  193 (253)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            553

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=93.90  E-value=0.06  Score=51.96  Aligned_cols=89  Identities=18%  Similarity=0.176  Sum_probs=50.0

Q ss_pred             EEEEECCCCCcHHHHH-HHHhcCccccCCcc-eeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHHH----
Q 040110          114 VVAILDSRGFDKTAFA-AEIYNNNFVKFYFD-CHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKSE----  184 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA-~~v~~~~~~~~~F~-~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~~----  184 (348)
                      .++|.|.+|+|||+|| ..+.+.  .  .-+ .++++-+++.. .+.++.+++...=.......  ...+......    
T Consensus       177 R~~I~g~~g~GKT~Lal~~I~~~--~--~~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~atad~p~~~r~~a~  252 (515)
T 2r9v_A          177 RELIIGDRQTGKTAIAIDTIINQ--K--GQGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVASASDPASLQYIAP  252 (515)
T ss_dssp             BEEEEEETTSSHHHHHHHHHHTT--T--TTTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEECTTSCHHHHHHHH
T ss_pred             EEEEEcCCCCCccHHHHHHHHHh--h--cCCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEECCCCCHHHHHHHH
Confidence            4789999999999996 477776  2  234 34667777654 45566666654211111100  1111111111    


Q ss_pred             --HHHHHHHh--cCCeEEEEEeCCCC
Q 040110          185 --KTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       185 --~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                        .-.+-+++  +++.+|+++||+-.
T Consensus       253 ~~a~tiAEyfrd~G~dVLli~DslTr  278 (515)
T 2r9v_A          253 YAGCAMGEYFAYSGRDALVVYDDLSK  278 (515)
T ss_dssp             HHHHHHHHHHHTTTCEEEEEEETHHH
T ss_pred             HHHHHHHHHHHHcCCcEEEEeccHHH
Confidence              11233344  46899999999843

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=93.90  E-value=0.031  Score=50.01  Aligned_cols=23  Identities=13%  Similarity=0.070  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        48 e~~~liG~NGsGKSTLlk~l~Gl   70 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLNILNAY   70 (279)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            37899999999999999998754

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=93.89  E-value=0.031  Score=50.63  Aligned_cols=24  Identities=8%  Similarity=0.196  Sum_probs=21.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+++|+|+.|+|||||++.+..-
T Consensus       126 Ge~vaIvGpsGsGKSTLl~lL~gl  149 (305)
T 2v9p_A          126 KNCLAFIGPPNTGKSMLCNSLIHF  149 (305)
T ss_dssp             CSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHHHhhh
Confidence            347999999999999999998755

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=93.85  E-value=0.053  Score=44.58  Aligned_cols=26  Identities=12%  Similarity=0.157  Sum_probs=22.1

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....|+|+|.+|+|||||...+.+.
T Consensus        14 ~~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           14 DQEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SSCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CCceEEEEECCCCCCHHHHHHHHhcC
Confidence            34567889999999999999998866

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=93.84  E-value=0.066  Score=51.64  Aligned_cols=87  Identities=13%  Similarity=0.109  Sum_probs=48.2

Q ss_pred             EEEEECCCCCcHHHHH-HHHhcCccccCCcc-eeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCC------C---
Q 040110          114 VVAILDSRGFDKTAFA-AEIYNNNFVKFYFD-CHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMG------K---  179 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA-~~v~~~~~~~~~F~-~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~------~---  179 (348)
                      .++|.|.+|+|||+|| ..+.+..  .  -+ .++++-+++.. .+.++.+++...=.......  ...+      .   
T Consensus       165 R~~Ifg~~g~GKT~Lal~~I~~~~--~--~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~~a~  240 (507)
T 1fx0_A          165 RELIIGDRQTGKTAVATDTILNQQ--G--QNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAP  240 (507)
T ss_dssp             BCBEEESSSSSHHHHHHHHHHTCC--T--TTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHH
T ss_pred             EEEEecCCCCCccHHHHHHHHHhh--c--CCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHHHHH
Confidence            3678999999999996 5777762  2  34 35667777654 34455555543211110000  0000      1   


Q ss_pred             -CHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 040110          180 -DYKSEKTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       180 -~~~~~~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                       ..-...++++.  +++.+||++||+-.
T Consensus       241 ~~a~tiAEyfrd--~G~dVLli~Dsltr  266 (507)
T 1fx0_A          241 YTGAALAEYFMY--RERHTLIIYDDLSK  266 (507)
T ss_dssp             HHHHHHHHHHHH--TTCEEEEEEECHHH
T ss_pred             HHHHHHHHHHHH--cCCcEEEEEecHHH
Confidence             11122333433  57999999999854

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=93.84  E-value=0.042  Score=43.98  Aligned_cols=24  Identities=4%  Similarity=0.138  Sum_probs=20.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .--|.++|.+|+|||||...+.+.
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            345789999999999999999865

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=93.74  E-value=0.094  Score=53.78  Aligned_cols=97  Identities=16%  Similarity=0.218  Sum_probs=55.4

Q ss_pred             cccccccccccHHHHHhhcCCCC-------CCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS-------GLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYN  155 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~-------~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  155 (348)
                      .+.|.+...   +.|.+.+.-+-       ..+-...+-+.++|++|+|||.||+++++.  ....|     +.++    
T Consensus       478 diggl~~~k---~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e--~~~~f-----~~v~----  543 (806)
T 3cf2_A          478 DIGGLEDVK---RELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE--CQANF-----ISIK----  543 (806)
T ss_dssp             TCCSCHHHH---HHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHT--TTCEE-----EECC----
T ss_pred             HhCCHHHHH---HHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHH--hCCce-----EEec----
Confidence            566777777   66666654210       112233444678999999999999999988  33322     2222    


Q ss_pred             HHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCC
Q 040110          156 FKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       156 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                      ..+    ++...         -..+...+...+...-+..+++|.+|+++.
T Consensus       544 ~~~----l~s~~---------vGese~~vr~lF~~Ar~~~P~IifiDEiDs  581 (806)
T 3cf2_A          544 GPE----LLTMW---------FGESEANVREIFDKARQAAPCVLFFDELDS  581 (806)
T ss_dssp             HHH----HHTTT---------CSSCHHHHHHHHHHHHTTCSEEEECSCGGG
T ss_pred             cch----hhccc---------cchHHHHHHHHHHHHHHcCCceeechhhhH
Confidence            111    11111         112333333333334355789999999863

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=93.68  E-value=0.091  Score=44.92  Aligned_cols=24  Identities=13%  Similarity=0.090  Sum_probs=21.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -..|.|.|+.|+||||+++.+.+.
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~   29 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAER   29 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHH
Confidence            357889999999999999999876

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=93.66  E-value=0.031  Score=49.72  Aligned_cols=24  Identities=21%  Similarity=0.299  Sum_probs=20.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.++.|+|.+|+|||||+..++..
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~~   53 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAAQ   53 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH
Confidence            348899999999999999998754

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=93.66  E-value=0.06  Score=47.71  Aligned_cols=35  Identities=11%  Similarity=0.040  Sum_probs=26.0

Q ss_pred             HHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           97 LHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        97 l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +..+|.    ...+....+.++|++|+|||.+|.++++.
T Consensus        93 l~~~l~----~~~~~~n~~~l~GppgtGKt~~a~ala~~  127 (267)
T 1u0j_A           93 FLGWAT----KKFGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             HHHHHT----TCSTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHh----CCCCCCcEEEEECCCCCCHHHHHHHHHhh
Confidence            555555    22133456889999999999999999875

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=93.66  E-value=0.041  Score=54.76  Aligned_cols=42  Identities=10%  Similarity=0.191  Sum_probs=34.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+.    .+    ..+.|+|++|+||||||+.++..
T Consensus        42 ~i~G~~~~l---~~l~~~i~----~g----~~vll~Gp~GtGKTtlar~ia~~   83 (604)
T 3k1j_A           42 QVIGQEHAV---EVIKTAAN----QK----RHVLLIGEPGTGKSMLGQAMAEL   83 (604)
T ss_dssp             HCCSCHHHH---HHHHHHHH----TT----CCEEEECCTTSSHHHHHHHHHHT
T ss_pred             eEECchhhH---hhcccccc----CC----CEEEEEeCCCCCHHHHHHHHhcc
Confidence            689988888   77777776    11    36889999999999999999887

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=93.64  E-value=0.036  Score=44.10  Aligned_cols=23  Identities=17%  Similarity=0.443  Sum_probs=20.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -|.++|.+|+|||||...+....
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            47899999999999999997663

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=93.64  E-value=0.042  Score=45.16  Aligned_cols=26  Identities=12%  Similarity=0.156  Sum_probs=21.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|+|+|.+|+|||||...+.+..
T Consensus         6 ~~~ki~v~G~~~vGKSsli~~l~~~~   31 (184)
T 1m7b_A            6 VKCKIVVVGDSQCGKTALLHVFAKDC   31 (184)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEEECCCCCCHHHHHHHHhcCC
Confidence            34567899999999999999998763

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=93.63  E-value=0.12  Score=43.45  Aligned_cols=50  Identities=8%  Similarity=-0.077  Sum_probs=31.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMK  165 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~  165 (348)
                      .|+|=|.-|+||||.++.+++.  .+..--.++...-.......+.++.++.
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~--L~~~g~~v~~treP~~t~~~~~ir~~l~   51 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQY--LEKRGKKVILKREPGGTETGEKIRKILL   51 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH--HHHCCCcEEEEECCCCCcHHHHHHHHhh
Confidence            4678899999999999999887  3332223344433333444455555553

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=93.62  E-value=0.036  Score=52.91  Aligned_cols=50  Identities=16%  Similarity=0.193  Sum_probs=32.2

Q ss_pred             cccccccccccHHHHHhhcCC-------CCC-CCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP-------SSG-LGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~-------~~~-~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+..       ... ......+-+.++|++|+||||+|+.++..
T Consensus        16 ~IvGqe~ak---~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~   73 (444)
T 1g41_A           16 HIIGQADAK---RAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL   73 (444)
T ss_dssp             TCCSCHHHH---HHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             HhCCHHHHH---HHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHH
Confidence            567777766   666544410       000 01112344778999999999999999877

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=93.61  E-value=0.038  Score=52.65  Aligned_cols=25  Identities=24%  Similarity=0.340  Sum_probs=21.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+|+|+|.+|+||||++..++..
T Consensus        98 ~~~vI~ivG~~GvGKTTla~~La~~  122 (432)
T 2v3c_C           98 KQNVILLVGIQGSGKTTTAAKLARY  122 (432)
T ss_dssp             SCCCEEEECCSSSSTTHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4568999999999999999988765

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=93.58  E-value=0.042  Score=49.03  Aligned_cols=24  Identities=17%  Similarity=0.221  Sum_probs=20.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|+|.|-||+||||+|..++..
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~~   25 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVAA   25 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHHH
Confidence            468888999999999999888765

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=93.58  E-value=0.035  Score=49.39  Aligned_cols=22  Identities=9%  Similarity=0.463  Sum_probs=19.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|+|+.|+|||||.+.++..
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~   25 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKS   25 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5789999999999999998754

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=93.54  E-value=0.041  Score=51.42  Aligned_cols=25  Identities=16%  Similarity=0.053  Sum_probs=22.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|+|++|+|||||++.+...
T Consensus       168 ~~~~i~l~G~~GsGKSTl~~~l~~~  192 (377)
T 1svm_A          168 KKRYWLFKGPIDSGKTTLAAALLEL  192 (377)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhh
Confidence            4458999999999999999999864

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=93.53  E-value=0.055  Score=44.51  Aligned_cols=27  Identities=19%  Similarity=0.413  Sum_probs=22.5

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .....|+|+|.+|+|||||...+.+..
T Consensus        21 ~~~~~i~v~G~~~~GKSsli~~l~~~~   47 (195)
T 3pqc_A           21 PLKGEVAFVGRSNVGKSSLLNALFNRK   47 (195)
T ss_dssp             CTTCEEEEEEBTTSSHHHHHHHHHTSC
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHcCc
Confidence            344568899999999999999998763

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=93.52  E-value=0.057  Score=43.57  Aligned_cols=24  Identities=25%  Similarity=0.286  Sum_probs=20.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..-|+|+|.+|+|||||...+.+.
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEEECCCCccHHHHHHHHhcC
Confidence            345789999999999999998765

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=93.52  E-value=0.058  Score=48.74  Aligned_cols=31  Identities=13%  Similarity=0.221  Sum_probs=26.1

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|.+.+.         -.+++++|+.|+|||||.+.+. .
T Consensus       157 ~~L~~~l~---------G~i~~l~G~sG~GKSTLln~l~-~  187 (302)
T 2yv5_A          157 DELVDYLE---------GFICILAGPSGVGKSSILSRLT-G  187 (302)
T ss_dssp             HHHHHHTT---------TCEEEEECSTTSSHHHHHHHHH-S
T ss_pred             HHHHhhcc---------CcEEEEECCCCCCHHHHHHHHH-H
Confidence            77777766         1378999999999999999998 6

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=93.51  E-value=0.047  Score=45.23  Aligned_cols=28  Identities=14%  Similarity=0.090  Sum_probs=22.7

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ......|.|+|.+|+|||||...+.+..
T Consensus        14 ~~~~~ki~v~G~~~~GKSsl~~~l~~~~   41 (199)
T 4bas_A           14 SKTKLQVVMCGLDNSGKTTIINQVKPAQ   41 (199)
T ss_dssp             --CEEEEEEECCTTSCHHHHHHHHSCCC
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            4556678899999999999999988764

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=93.48  E-value=0.06  Score=43.19  Aligned_cols=25  Identities=20%  Similarity=0.209  Sum_probs=21.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .--|+++|.+|+|||||...+.+..
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCENK   30 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCC
Confidence            3457899999999999999988653

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=93.43  E-value=0.047  Score=47.36  Aligned_cols=24  Identities=13%  Similarity=0.162  Sum_probs=21.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|.|.|..|+||||+++.+...
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~   25 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHH
Confidence            357899999999999999999876

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.42  E-value=0.058  Score=43.97  Aligned_cols=25  Identities=20%  Similarity=0.154  Sum_probs=21.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|+|+|.+|+|||||...+...
T Consensus        17 ~~~~i~v~G~~~~GKssli~~l~~~   41 (183)
T 1moz_A           17 KELRILILGLDGAGKTTILYRLQIG   41 (183)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             CccEEEEECCCCCCHHHHHHHHhcC
Confidence            4556889999999999999998754

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=93.42  E-value=0.033  Score=49.12  Aligned_cols=26  Identities=12%  Similarity=0.082  Sum_probs=22.5

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....|.|.|..|+||||+|+.+...
T Consensus        22 ~~~~~I~ieG~~GsGKST~~~~L~~~   47 (263)
T 1p5z_B           22 TRIKKISIEGNIAAGKSTFVNILKQL   47 (263)
T ss_dssp             -CCEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHh
Confidence            45678999999999999999998876

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=93.42  E-value=0.044  Score=45.15  Aligned_cols=24  Identities=17%  Similarity=0.398  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..|+++|.+|+|||||+..+....
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            357889999999999999998663

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=93.41  E-value=0.045  Score=48.13  Aligned_cols=23  Identities=22%  Similarity=0.315  Sum_probs=20.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|+|.|-||+||||+|..++..
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~   24 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSG   24 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHH
T ss_pred             cEEEEecCCCCcHHHHHHHHHHH
Confidence            57888899999999999888765

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=93.39  E-value=0.041  Score=52.67  Aligned_cols=104  Identities=12%  Similarity=0.083  Sum_probs=57.2

Q ss_pred             HHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc--ceeEEEEeCCCC-CHHHHHHHHHHHhCCCCC
Q 040110           96 NLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF--DCHAWVRVSNFY-NFKRILDDIMKSLMPTSS  172 (348)
Q Consensus        96 ~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F--~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~  172 (348)
                      +.++.|.+-    ..+- .++|.|.+|+|||+|+.++++.....+.-  +.++++-+++.. .+.+++.++...=.....
T Consensus       141 r~ID~l~pi----grGQ-r~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~~g~m~rt  215 (469)
T 2c61_A          141 STIDGTNTL----VRGQ-KLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERA  215 (469)
T ss_dssp             HHHHTTSCC----BTTC-BCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHHHSGGGGE
T ss_pred             Eeeeeeecc----ccCC-EEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHhccCccce
Confidence            456666532    1122 36778999999999999998874332211  256666666553 456677776653111111


Q ss_pred             c--cccCCCCHHH------HHHHHHHHhc---CCeEEEEEeCC
Q 040110          173 W--LKIMGKDYKS------EKTILRDYLT---NKKYFTVLDDV  204 (348)
Q Consensus       173 ~--~~~~~~~~~~------~~~~l~~~L~---~kr~LlVLDdv  204 (348)
                      .  ....+.....      ..-.+.++++   ++.+||++||+
T Consensus       216 vvV~~tsd~p~~~r~~~~~~a~tiAEyfrdd~G~dVLl~~Dsl  258 (469)
T 2c61_A          216 VVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDI  258 (469)
T ss_dssp             EEEEEETTSCHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECH
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEeCH
Confidence            0  0111222211      1122344443   68999999997

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=93.38  E-value=0.051  Score=44.91  Aligned_cols=26  Identities=15%  Similarity=0.250  Sum_probs=22.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....|+|+|.+|+|||||...+.+.
T Consensus        21 ~~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           21 GGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34567889999999999999999866

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=93.35  E-value=0.062  Score=43.53  Aligned_cols=27  Identities=11%  Similarity=0.277  Sum_probs=22.4

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ....-|+|+|.+|+|||||...+.+..
T Consensus         7 ~~~~~i~v~G~~~~GKssli~~l~~~~   33 (181)
T 2fn4_A            7 SETHKLVVVGGGGVGKSALTIQFIQSY   33 (181)
T ss_dssp             SCEEEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhCc
Confidence            345568899999999999999988763

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=93.35  E-value=0.047  Score=43.53  Aligned_cols=24  Identities=21%  Similarity=0.360  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .-|+++|.+|+|||||...+.+..
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~~   28 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCc
Confidence            457899999999999999998663

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=93.34  E-value=0.033  Score=50.55  Aligned_cols=24  Identities=13%  Similarity=0.267  Sum_probs=21.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+++|+|+.|+|||||++.+..-
T Consensus        80 Ge~vaivG~sGsGKSTLl~ll~gl  103 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRLLFRF  103 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHHHTTS
T ss_pred             CCEEEEECCCCchHHHHHHHHHcC
Confidence            347999999999999999998764

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.29  E-value=0.055  Score=45.72  Aligned_cols=27  Identities=11%  Similarity=0.172  Sum_probs=22.5

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .....|.++|.+|+|||||...+.+..
T Consensus        10 ~~~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           10 SYQPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCCCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            344568899999999999999998763

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=93.27  E-value=0.073  Score=42.72  Aligned_cols=24  Identities=21%  Similarity=0.177  Sum_probs=20.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|+++|.+|+|||||...+...
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            456789999999999999999765

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=93.27  E-value=0.21  Score=48.11  Aligned_cols=87  Identities=15%  Similarity=0.147  Sum_probs=49.7

Q ss_pred             EEEEECCCCCcHHHHH-HHHhcCccccCCcc-eeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHH------
Q 040110          114 VVAILDSRGFDKTAFA-AEIYNNNFVKFYFD-CHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYK------  182 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA-~~v~~~~~~~~~F~-~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~------  182 (348)
                      .++|.|..|+|||+|| ..+.|.  .  +-+ .++++-+++.. .+.++..++...=.......  ...+....      
T Consensus       164 R~~Ifg~~g~GKT~l~l~~I~n~--~--~~dv~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tvvV~atad~p~~~r~~a~  239 (513)
T 3oaa_A          164 RELIIGDRQTGKTALAIDAIINQ--R--DSGIKCIYVAIGQKASTISNVVRKLEEHGALANTIVVVATASESAALQYLAP  239 (513)
T ss_dssp             BCEEEESSSSSHHHHHHHHHHTT--S--SSSCEEEEEEESCCHHHHHHHHHHHHHHSCSTTEEEEEECTTSCHHHHHHHH
T ss_pred             EEEeecCCCCCcchHHHHHHHhh--c--cCCceEEEEEecCChHHHHHHHHHHhhcCcccceEEEEECCCCChHHHHHHH
Confidence            3678999999999996 466665  1  223 35677777664 45566666554321211110  11111111      


Q ss_pred             ----HHHHHHHHHhcCCeEEEEEeCCCC
Q 040110          183 ----SEKTILRDYLTNKKYFTVLDDVWI  206 (348)
Q Consensus       183 ----~~~~~l~~~L~~kr~LlVLDdv~~  206 (348)
                          ...++++.  +++.+||++||+-.
T Consensus       240 ~~a~tiAEyfrd--~G~dVLli~Dsltr  265 (513)
T 3oaa_A          240 YAGCAMGEYFRD--RGEDALIIYDDLSK  265 (513)
T ss_dssp             HHHHHHHHHHHH--TTCEEEEEEETHHH
T ss_pred             HHHHHHHHHHHh--cCCCEEEEecChHH
Confidence                12233332  57899999999853

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=93.20  E-value=0.054  Score=43.45  Aligned_cols=22  Identities=18%  Similarity=0.366  Sum_probs=19.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|+++|.+|+|||||...+.+.
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            5 RVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4779999999999999999865

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=93.17  E-value=0.045  Score=49.84  Aligned_cols=25  Identities=24%  Similarity=0.239  Sum_probs=22.5

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|+|+.|.|||||.+.+...
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~   27 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNE   27 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhh
Confidence            4679999999999999999999865

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=93.16  E-value=0.096  Score=45.15  Aligned_cols=56  Identities=9%  Similarity=0.004  Sum_probs=33.7

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMK  165 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~  165 (348)
                      .....|.|.|+.|+||||+++.+.+.......+++.....-.......+.+++++.
T Consensus        19 ~~~~~i~~~G~~g~GKst~~~~l~~~l~~~~g~~v~~~treP~~t~~g~~ir~~l~   74 (223)
T 3ld9_A           19 PGSMFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVVLTREPGGTLLNESVRNLLF   74 (223)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHHHHHHHCGGGEEEEESSCSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhhccCceeeEeeeCCCCChHHHHHHHHHh
Confidence            34568889999999999999999887322123443332222223233444555554

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=93.16  E-value=0.054  Score=43.14  Aligned_cols=23  Identities=26%  Similarity=0.433  Sum_probs=19.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -|+++|.+|+|||||...+.+..
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~~   27 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            57899999999999999987653

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=93.14  E-value=0.045  Score=50.74  Aligned_cols=124  Identities=10%  Similarity=0.078  Sum_probs=65.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccC---Cc----------------ceeEEEEeCC----CCCH-------------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKF---YF----------------DCHAWVRVSN----FYNF-------------  156 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~---~F----------------~~~~wv~~~~----~~~~-------------  156 (348)
                      .+++|+|+.|+|||||.+.++.-.....   .|                ..+.+|.-..    ..++             
T Consensus        31 e~~~llGpsGsGKSTLLr~iaGl~~p~~G~I~i~G~~i~~~~~~~~~~~r~ig~vfQ~~~l~p~ltV~eni~~~l~~~~~  110 (359)
T 3fvq_A           31 EILFIIGASGCGKTTLLRCLAGFEQPDSGEISLSGKTIFSKNTNLPVRERRLGYLVQEGVLFPHLTVYRNIAYGLGNGKG  110 (359)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTSSCCSEEEEEETTEEEESSSCBCCGGGSCCEEECTTCCCCTTSCHHHHHHTTSTTSSC
T ss_pred             CEEEEECCCCchHHHHHHHHhcCCCCCCcEEEECCEECcccccccchhhCCEEEEeCCCcCCCCCCHHHHHHHHHHHcCC
Confidence            4789999999999999999976421100   00                1122221110    0111             


Q ss_pred             -----HHHHHHHHHHhCCCCCcc-ccCCCCHHHHH-HHHHHHhcCCeEEEEEeCCCCh------hh-HHHHHhhCCCCCC
Q 040110          157 -----KRILDDIMKSLMPTSSWL-KIMGKDYKSEK-TILRDYLTNKKYFTVLDDVWIE------KI-WDDLREALPDNQI  222 (348)
Q Consensus       157 -----~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~-~~l~~~L~~kr~LlVLDdv~~~------~~-~~~l~~~l~~~~~  222 (348)
                           .+-..++++.++...... .....+-.+.+ -.|.+.|-.++-+|+||.--+.      .. ++.+.....  ..
T Consensus       111 ~~~~~~~~v~~~l~~~gL~~~~~r~~~~LSGGq~QRValArAL~~~P~lLLLDEPts~LD~~~r~~l~~~l~~~~~--~~  188 (359)
T 3fvq_A          111 RTAQERQRIEAMLELTGISELAGRYPHELSGGQQQRAALARALAPDPELILLDEPFSALDEQLRRQIREDMIAALR--AN  188 (359)
T ss_dssp             CSHHHHHHHHHHHHHHTCGGGTTSCGGGSCHHHHHHHHHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHHH--HT
T ss_pred             ChHHHHHHHHHHHHHcCCchHhcCChhhCCHHHHHHHHHHHHHHcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHH--hC
Confidence                 123445666666532110 12223333333 3466677788889999997653      11 222322221  23


Q ss_pred             CcEEEEEeCChhhhhh
Q 040110          223 GSRALITVGPHNILTS  238 (348)
Q Consensus       223 gskIlvTTR~~~v~~~  238 (348)
                      |..||++|-+...+..
T Consensus       189 g~tvi~vTHd~~ea~~  204 (359)
T 3fvq_A          189 GKSAVFVSHDREEALQ  204 (359)
T ss_dssp             TCEEEEECCCHHHHHH
T ss_pred             CCEEEEEeCCHHHHHH
Confidence            6678888888766554

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.12  E-value=0.053  Score=43.36  Aligned_cols=23  Identities=13%  Similarity=0.296  Sum_probs=19.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -|.++|.+|+|||||...+.+..
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            47789999999999999988663

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=93.12  E-value=0.037  Score=52.75  Aligned_cols=105  Identities=11%  Similarity=0.128  Sum_probs=56.4

Q ss_pred             HHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCcccc--------CCcc-eeEEEEeCCCC-CHHHHHHHHHH
Q 040110           96 NLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVK--------FYFD-CHAWVRVSNFY-NFKRILDDIMK  165 (348)
Q Consensus        96 ~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~--------~~F~-~~~wv~~~~~~-~~~~~~~~i~~  165 (348)
                      +.++.|.+-    ..+- .++|.|.+|+|||+|+.++.+.....        ++=+ .++++-+++.. .+.++..++..
T Consensus       136 raID~l~pi----grGQ-r~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~  210 (464)
T 3gqb_B          136 STIDVMNTL----VRGQ-KLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFER  210 (464)
T ss_dssp             HHHHTTSCC----BTTC-BCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHH
T ss_pred             eeeeccccc----ccCC-EEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhh
Confidence            555666632    1222 36788999999999999998874431        1112 45666666543 45566666544


Q ss_pred             HhCCCCCc--cccCCCC-HHHH-----HHHHHHHhc---CCeEEEEEeCCC
Q 040110          166 SLMPTSSW--LKIMGKD-YKSE-----KTILRDYLT---NKKYFTVLDDVW  205 (348)
Q Consensus       166 ~l~~~~~~--~~~~~~~-~~~~-----~~~l~~~L~---~kr~LlVLDdv~  205 (348)
                      .=......  ....+.. ....     .-.+.++++   ++.+||++||+-
T Consensus       211 ~g~~~rtvvv~~t~d~p~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~DdlT  261 (464)
T 3gqb_B          211 TGALSRSVLFLNKADDPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMT  261 (464)
T ss_dssp             TSGGGGEEEEEEETTSCTHHHHHHHHHHHHHHHHHHHTTCCEEEEEEETHH
T ss_pred             cccccceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence            21011000  0111111 1111     123444543   689999999984

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=93.12  E-value=0.053  Score=43.30  Aligned_cols=22  Identities=23%  Similarity=0.424  Sum_probs=19.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|+++|.+|+|||||...+.+.
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999999865

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=93.10  E-value=0.055  Score=43.34  Aligned_cols=24  Identities=17%  Similarity=0.292  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      --|+++|.+|+|||||...+.+..
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            357899999999999999998763

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=93.09  E-value=0.077  Score=43.75  Aligned_cols=25  Identities=16%  Similarity=0.161  Sum_probs=20.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..--|+|+|.+|+|||||...+.+.
T Consensus        19 ~~~ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           19 PELKVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             CEEEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CeeEEEEECCCCCCHHHHHHHHhcC
Confidence            3446789999999999999887765

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=93.09  E-value=0.066  Score=43.39  Aligned_cols=26  Identities=27%  Similarity=0.322  Sum_probs=21.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|+|+|.+|+|||||...+.+..
T Consensus         7 ~~~~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A            7 NILKVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHhCc
Confidence            44568899999999999999987653

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=93.08  E-value=0.071  Score=44.38  Aligned_cols=27  Identities=19%  Similarity=0.276  Sum_probs=22.1

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ....-|+|+|.+|+|||||...+....
T Consensus        12 ~~~~ki~v~G~~~~GKSsli~~l~~~~   38 (206)
T 2bov_A           12 LALHKVIMVGSGGVGKSALTLQFMYDE   38 (206)
T ss_dssp             CCEEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CceEEEEEECCCCCCHHHHHHHHHhCC
Confidence            344568899999999999999987653

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=93.05  E-value=0.051  Score=44.32  Aligned_cols=23  Identities=13%  Similarity=0.118  Sum_probs=20.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..|+|+|.+|+|||||...+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            35789999999999999999865

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=93.03  E-value=0.054  Score=50.32  Aligned_cols=125  Identities=6%  Similarity=-0.006  Sum_probs=66.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccC---Cc-----------------ceeEEEEeCC----CCCHHH----------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKF---YF-----------------DCHAWVRVSN----FYNFKR----------  158 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~---~F-----------------~~~~wv~~~~----~~~~~~----------  158 (348)
                      .+++|+|+.|+|||||.+.+..-.....   .|                 ..+.+|.-..    ..++.+          
T Consensus        55 ei~~IiGpnGaGKSTLlr~i~GL~~p~~G~I~i~G~~i~~~~~~~~~~~r~~Ig~v~Q~~~l~~~~TV~env~~~~~~~~  134 (366)
T 3tui_C           55 QIYGVIGASGAGKSTLIRCVNLLERPTEGSVLVDGQELTTLSESELTKARRQIGMIFQHFNLLSSRTVFGNVALPLELDN  134 (366)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSCCSEEEEEETTEECSSCCHHHHHHHHTTEEEECSSCCCCTTSCHHHHHHHHHHHSC
T ss_pred             CEEEEEcCCCchHHHHHHHHhcCCCCCceEEEECCEECCcCCHHHHHHHhCcEEEEeCCCccCCCCCHHHHHHHHHHhcC
Confidence            4899999999999999999875421110   00                 0122332111    112221          


Q ss_pred             --------HHHHHHHHhCCCCCcc-ccCCCCHHHH-HHHHHHHhcCCeEEEEEeCCCCh------hhHHHHHhhCCCCCC
Q 040110          159 --------ILDDIMKSLMPTSSWL-KIMGKDYKSE-KTILRDYLTNKKYFTVLDDVWIE------KIWDDLREALPDNQI  222 (348)
Q Consensus       159 --------~~~~i~~~l~~~~~~~-~~~~~~~~~~-~~~l~~~L~~kr~LlVLDdv~~~------~~~~~l~~~l~~~~~  222 (348)
                              -..++++.++...... ....-+-.+. .-.|.+.|..++-+|+||..-+.      ...-.+...+. ...
T Consensus       135 ~~~~~~~~~v~~lL~~vgL~~~~~~~~~~LSGGqkQRVaIArAL~~~P~lLLlDEPTs~LD~~~~~~i~~lL~~l~-~~~  213 (366)
T 3tui_C          135 TPKDEVKRRVTELLSLVGLGDKHDSYPSNLSGGQKQRVAIARALASNPKVLLCDQATSALDPATTRSILELLKDIN-RRL  213 (366)
T ss_dssp             CCHHHHHHHHHHHHHHHTCGGGTTCCTTTSCHHHHHHHHHHHHTTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHH-HHS
T ss_pred             CCHHHHHHHHHHHHHHcCCchHhcCChhhCCHHHHHHHHHHHHHhcCCCEEEEECCCccCCHHHHHHHHHHHHHHH-HhC
Confidence                    2344555555532110 1222333333 33466777888889999997653      12222222221 123


Q ss_pred             CcEEEEEeCChhhhhh
Q 040110          223 GSRALITVGPHNILTS  238 (348)
Q Consensus       223 gskIlvTTR~~~v~~~  238 (348)
                      |..||++|-+-..+..
T Consensus       214 g~Tii~vTHdl~~~~~  229 (366)
T 3tui_C          214 GLTILLITHEMDVVKR  229 (366)
T ss_dssp             CCEEEEEESCHHHHHH
T ss_pred             CCEEEEEecCHHHHHH
Confidence            6678888888776654

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=93.02  E-value=0.046  Score=43.76  Aligned_cols=22  Identities=27%  Similarity=0.271  Sum_probs=19.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|+++|.+|+|||||...+.+.
T Consensus         4 ki~~vG~~~~GKSsli~~l~~~   25 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGGV   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCC
T ss_pred             EEEEECCCCCCHHHHHHHHcCc
Confidence            4779999999999999998754

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.01  E-value=0.054  Score=50.19  Aligned_cols=23  Identities=26%  Similarity=0.271  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        42 e~~~llGpnGsGKSTLLr~iaGl   64 (355)
T 1z47_A           42 EMVGLLGPSGSGKTTILRLIAGL   64 (355)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            47999999999999999998754

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=93.00  E-value=0.071  Score=42.74  Aligned_cols=22  Identities=18%  Similarity=0.259  Sum_probs=19.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|+|+|.+|+|||||...+...
T Consensus         4 ki~ivG~~~~GKSsli~~l~~~   25 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFGGL   25 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHhc
Confidence            4789999999999999998643

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=92.98  E-value=0.077  Score=45.82  Aligned_cols=107  Identities=16%  Similarity=0.145  Sum_probs=54.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc------cccCCCCHHHHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW------LKIMGKDYKSEKTI  187 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~------~~~~~~~~~~~~~~  187 (348)
                      .|.+.|.||+||||+|..+...... ..++. ..+.+...-+....  .++..+......      ......+....   
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~-~G~~V-~v~d~D~q~~~~~~--al~~gl~~~~~~~~~~~~~~~~e~~l~~~---   80 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLR-QGVRV-MAGVVETHGRAETE--ALLNGLPQQPLLRTEYRGMTLEEMDLDAL---   80 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHH-TTCCE-EEEECCCTTCHHHH--HHHTTSCBCCCEEEEETTEEEEECCHHHH---
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHH-CCCCE-EEEEeCCCCChhHH--HHhcCccccCcceeecCCcccccccHHHH---
Confidence            4667899999999999888876322 23443 33444333232211  112222211000      00112333332   


Q ss_pred             HHHHhcCCeEEEEEeCCCCh--------hhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          188 LRDYLTNKKYFTVLDDVWIE--------KIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       188 l~~~L~~kr~LlVLDdv~~~--------~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                          +..+.=++|+|++-..        .-|.++...++   .|..|++|+.-.+
T Consensus        81 ----L~~~pdlvIVDElG~~~~~~~r~~~~~qDV~~~l~---sgidVitT~Nlqh  128 (228)
T 2r8r_A           81 ----LKAAPSLVLVDELAHTNAPGSRHTKRWQDIQELLA---AGIDVYTTVNVQH  128 (228)
T ss_dssp             ----HHHCCSEEEESCTTCBCCTTCSSSBHHHHHHHHHH---TTCEEEEEEEGGG
T ss_pred             ----HhcCCCEEEEeCCCCCCcccchhHHHHHHHHHHHc---CCCCEEEEccccc
Confidence                2235668999976431        35666655433   2556887776443

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=92.97  E-value=0.048  Score=49.05  Aligned_cols=23  Identities=26%  Similarity=0.358  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        65 e~~~i~G~NGsGKSTLlk~l~Gl   87 (290)
T 2bbs_A           65 QLLAVAGSTGAGKTSLLMMIMGE   87 (290)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcC
Confidence            48999999999999999999866

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=92.96  E-value=0.054  Score=50.25  Aligned_cols=24  Identities=21%  Similarity=0.246  Sum_probs=21.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...++|+|..|+|||||++.+...
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl  193 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAV  193 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHH
Confidence            467899999999999999998765

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=92.94  E-value=0.056  Score=50.51  Aligned_cols=23  Identities=17%  Similarity=0.226  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        30 e~~~llGpsGsGKSTLLr~iaGl   52 (381)
T 3rlf_A           30 EFVVFVGPSGCGKSTLLRMIAGL   52 (381)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CEEEEEcCCCchHHHHHHHHHcC
Confidence            47899999999999999999764

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=92.93  E-value=0.06  Score=43.61  Aligned_cols=27  Identities=15%  Similarity=0.228  Sum_probs=22.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      +...-|+|+|.+|+|||||...+.+..
T Consensus         7 ~~~~~i~v~G~~~~GKssl~~~l~~~~   33 (181)
T 3tw8_B            7 DHLFKLLIIGDSGVGKSSLLLRFADNT   33 (181)
T ss_dssp             CEEEEEEEECCTTSCHHHHHHHHCSCC
T ss_pred             CcceEEEEECCCCCCHHHHHHHHhcCC
Confidence            344567899999999999999987653

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=92.87  E-value=0.11  Score=42.38  Aligned_cols=26  Identities=12%  Similarity=0.319  Sum_probs=21.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|.|+|.+|+|||||...+.+..
T Consensus        17 ~~~ki~v~G~~~~GKSsl~~~l~~~~   42 (183)
T 3kkq_A           17 PTYKLVVVGDGGVGKSALTIQFFQKI   42 (183)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhCC
Confidence            34567899999999999999988663

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=92.86  E-value=0.074  Score=43.81  Aligned_cols=25  Identities=8%  Similarity=0.134  Sum_probs=21.3

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...-|+|+|.+|+|||||...+...
T Consensus        19 ~~~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           19 RIFKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHcC
Confidence            3456889999999999999998765

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=92.86  E-value=0.058  Score=50.05  Aligned_cols=23  Identities=26%  Similarity=0.248  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl   52 (359)
T 2yyz_A           30 EFVALLGPSGCGKTTTLLMLAGI   52 (359)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEEcCCCchHHHHHHHHHCC
Confidence            47899999999999999999754

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=92.85  E-value=0.061  Score=50.57  Aligned_cols=23  Identities=17%  Similarity=0.411  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|.|.|+.|+||||||..++..
T Consensus         3 ~~i~i~GptgsGKttla~~La~~   25 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQK   25 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHHH
Confidence            57899999999999999998754

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=92.84  E-value=0.094  Score=42.39  Aligned_cols=24  Identities=13%  Similarity=0.176  Sum_probs=20.5

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .--|+|+|.+|+|||||...+.+.
T Consensus         6 ~~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            6 QLKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHGG
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhC
Confidence            345789999999999999998765

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=92.84  E-value=0.064  Score=48.55  Aligned_cols=28  Identities=14%  Similarity=0.201  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          108 GQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       108 ~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+....|+|+|.+|+|||||..++...
T Consensus         6 ~~~~~g~v~ivG~~nvGKSTLin~l~g~   33 (308)
T 3iev_A            6 HHMKVGYVAIVGKPNVGKSTLLNNLLGT   33 (308)
T ss_dssp             -CCEEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCCCCEEEEECCCCCcHHHHHHHHhCC
Confidence            3566789999999999999999998865

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=92.83  E-value=0.066  Score=44.95  Aligned_cols=26  Identities=12%  Similarity=0.115  Sum_probs=20.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..--|+++|.+|+|||||...+.+..
T Consensus        29 ~~~ki~vvG~~~~GKSsLi~~l~~~~   54 (204)
T 4gzl_A           29 QAIKCVVVGDGAVGKTCLLISYTTNA   54 (204)
T ss_dssp             -CEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             CeEEEEEECcCCCCHHHHHHHHHhCC
Confidence            34457899999999999999887653

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=92.82  E-value=0.06  Score=50.01  Aligned_cols=23  Identities=22%  Similarity=0.270  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl   52 (362)
T 2it1_A           30 EFMALLGPSGSGKSTLLYTIAGI   52 (362)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCchHHHHHHHHhcC
Confidence            47899999999999999999764

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=92.82  E-value=0.06  Score=44.26  Aligned_cols=21  Identities=24%  Similarity=0.322  Sum_probs=19.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhc
Q 040110          114 VVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      +.+|+|..|+|||||+.+++-
T Consensus        28 ~~~i~G~NGsGKStll~ai~~   48 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILF   48 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHH
Confidence            788999999999999999864

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=92.78  E-value=0.077  Score=43.49  Aligned_cols=26  Identities=15%  Similarity=0.086  Sum_probs=21.7

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +...-|+|+|.+|+|||||...+.+.
T Consensus         9 ~~~~ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A            9 DYLIKFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             SEEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceeEEEEEECCCCCCHHHHHHHHhcC
Confidence            33456789999999999999999865

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=92.77  E-value=0.067  Score=43.26  Aligned_cols=25  Identities=20%  Similarity=0.276  Sum_probs=21.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...-|+|+|.+|+|||||...+.+.
T Consensus         6 ~~~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            6 SLFKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceeEEEEECCCCCCHHHHHHHHHcC
Confidence            3446789999999999999999765

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=92.75  E-value=0.065  Score=42.84  Aligned_cols=23  Identities=9%  Similarity=0.193  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .-|+++|.+|+|||||...+...
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999998865

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=92.75  E-value=0.062  Score=50.10  Aligned_cols=23  Identities=22%  Similarity=0.215  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        38 e~~~llGpnGsGKSTLLr~iaGl   60 (372)
T 1v43_A           38 EFLVLLGPSGCGKTTTLRMIAGL   60 (372)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCChHHHHHHHHHcC
Confidence            48899999999999999998754

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=92.74  E-value=0.061  Score=50.17  Aligned_cols=23  Identities=22%  Similarity=0.199  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl   52 (372)
T 1g29_1           30 EFMILLGPSGCGKTTTLRMIAGL   52 (372)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCcHHHHHHHHHHcC
Confidence            47899999999999999999764

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=92.73  E-value=0.076  Score=42.91  Aligned_cols=26  Identities=12%  Similarity=0.137  Sum_probs=22.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|.|+|.+|+|||||...+.+..
T Consensus        14 ~~~~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           14 YIFKYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             cceEEEEECCCCCCHHHHHHHHHcCC
Confidence            34568899999999999999998664

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=92.72  E-value=0.082  Score=43.19  Aligned_cols=23  Identities=17%  Similarity=0.453  Sum_probs=20.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -|+|+|.+|+|||||...+.+..
T Consensus         6 ki~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            6 KLVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            57799999999999999998664

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=92.68  E-value=0.064  Score=42.78  Aligned_cols=21  Identities=10%  Similarity=0.088  Sum_probs=18.8

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |+++|.+|+|||||...+.+.
T Consensus         3 i~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            679999999999999998754

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=92.66  E-value=0.088  Score=45.02  Aligned_cols=26  Identities=12%  Similarity=0.286  Sum_probs=22.4

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .....|+|+|.+|+|||||...+...
T Consensus        27 ~~~~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           27 PHKKTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             TTSEEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            44567889999999999999999866

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=92.65  E-value=0.063  Score=46.52  Aligned_cols=25  Identities=24%  Similarity=0.225  Sum_probs=20.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....++|.|++|+||||+|+.+...
T Consensus         7 ~~~~~~~~G~pGsGKsT~a~~L~~~   31 (230)
T 3gmt_A            7 HHMRLILLGAPGAGKGTQANFIKEK   31 (230)
T ss_dssp             --CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cccceeeECCCCCCHHHHHHHHHHH
Confidence            3446899999999999999999876

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=92.65  E-value=0.074  Score=47.99  Aligned_cols=32  Identities=16%  Similarity=0.261  Sum_probs=26.5

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++.+.+.         -.+++|+|++|+|||||.+.+...
T Consensus       161 ~~lf~~l~---------geiv~l~G~sG~GKSTll~~l~g~  192 (301)
T 1u0l_A          161 EELKEYLK---------GKISTMAGLSGVGKSSLLNAINPG  192 (301)
T ss_dssp             HHHHHHHS---------SSEEEEECSTTSSHHHHHHHHSTT
T ss_pred             HHHHHHhc---------CCeEEEECCCCCcHHHHHHHhccc
Confidence            66777666         137899999999999999999876

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=92.62  E-value=0.056  Score=45.89  Aligned_cols=23  Identities=13%  Similarity=0.146  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|+|.|+.|+||||+++.+...
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~   26 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASE   26 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            36899999999999999998765

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=92.62  E-value=0.078  Score=48.95  Aligned_cols=25  Identities=16%  Similarity=0.084  Sum_probs=22.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++|+|.+|+|||||...+...
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~~   97 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGKM   97 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHH
Confidence            4678999999999999999998753

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=92.59  E-value=0.046  Score=45.90  Aligned_cols=25  Identities=20%  Similarity=0.112  Sum_probs=21.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .-..++|+|..|+|||||.+.+...
T Consensus        25 ~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           25 TGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3457899999999999999988765

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=92.59  E-value=0.084  Score=45.60  Aligned_cols=27  Identities=15%  Similarity=0.257  Sum_probs=22.4

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .....|+|+|.+|+|||||...+....
T Consensus        27 ~~~~~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           27 NSQLRIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             -CEEEEEEECCTTSSHHHHHHHHHTSC
T ss_pred             CCceEEEEECCCCCCHHHHHHHHcCCC
Confidence            345678899999999999999998764

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=92.59  E-value=0.084  Score=43.55  Aligned_cols=26  Identities=19%  Similarity=0.247  Sum_probs=21.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|+|+|.+|+|||||...+.+..
T Consensus        24 ~~~ki~v~G~~~~GKSsLi~~l~~~~   49 (193)
T 2oil_A           24 FVFKVVLIGESGVGKTNLLSRFTRNE   49 (193)
T ss_dssp             EEEEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             cceEEEEECcCCCCHHHHHHHHhcCC
Confidence            34567899999999999999988653

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=92.57  E-value=0.068  Score=43.97  Aligned_cols=24  Identities=17%  Similarity=0.036  Sum_probs=19.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..-|.|+|.+|+|||||.+.+.+.
T Consensus        14 ~~ki~vvG~~~~GKssL~~~l~~~   37 (198)
T 3t1o_A           14 NFKIVYYGPGLSGKTTNLKWIYSK   37 (198)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHT
T ss_pred             ccEEEEECCCCCCHHHHHHHHHhh
Confidence            345789999999999999877654

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=92.56  E-value=0.2  Score=48.28  Aligned_cols=93  Identities=13%  Similarity=0.133  Sum_probs=51.1

Q ss_pred             EEEEECCCCCcHHHHH-HHHhcCccc----cCCcc-eeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHHH
Q 040110          114 VVAILDSRGFDKTAFA-AEIYNNNFV----KFYFD-CHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKSE  184 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA-~~v~~~~~~----~~~F~-~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~~  184 (348)
                      .++|.|.+|+|||+|| ..+.|....    .++-+ .++++-+++.. .+.++.+++...=.......  ...+......
T Consensus       164 R~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r  243 (510)
T 2ck3_A          164 RELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQ  243 (510)
T ss_dssp             BCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHHH
T ss_pred             EEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCCcccceEEEECCCCCHHHH
Confidence            3678999999999995 566666321    12234 46677777664 45566666654211111110  1111111111


Q ss_pred             ------HHHHHHHh--cCCeEEEEEeCCCC
Q 040110          185 ------KTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       185 ------~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                            .-.+-+++  .++.+||++||+-.
T Consensus       244 ~~a~~~a~tiAEyfrd~G~dVLli~Dsltr  273 (510)
T 2ck3_A          244 YLAPYSGCSMGEYFRDNGKHALIIYDDLSK  273 (510)
T ss_dssp             HHHHHHHHHHHHHHHTTTCEEEEEEETHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCcEEEEEcCHHH
Confidence                  11233334  46899999999853

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=92.56  E-value=0.12  Score=53.87  Aligned_cols=21  Identities=10%  Similarity=0.036  Sum_probs=19.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEI  132 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v  132 (348)
                      -.+++|+|+.|.||||+.+.+
T Consensus       662 g~i~~ItGpNGsGKSTlLr~i  682 (934)
T 3thx_A          662 QMFHIITGPNMGGKSTYIRQT  682 (934)
T ss_dssp             BCEEEEECCTTSSHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            468999999999999999988

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=92.55  E-value=0.085  Score=42.93  Aligned_cols=25  Identities=20%  Similarity=0.320  Sum_probs=21.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..-|.|+|.+|+|||||...+.+..
T Consensus        18 ~~ki~v~G~~~~GKSsli~~l~~~~   42 (187)
T 2a9k_A           18 LHKVIMVGSGGVGKSALTLQFMYDE   42 (187)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhhCC
Confidence            4567899999999999999998653

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=92.55  E-value=0.078  Score=51.78  Aligned_cols=25  Identities=12%  Similarity=0.182  Sum_probs=21.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+|.++|++|+||||+|+.+...
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~   58 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRY   58 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4568899999999999999999765

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=92.55  E-value=0.12  Score=46.09  Aligned_cols=42  Identities=7%  Similarity=0.149  Sum_probs=28.2

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      +++.+.|.............|+|+|.+|+|||||...+....
T Consensus         9 ~~l~~~l~~~~~~~~~~~~~i~vvG~~~~GKSSLln~l~g~~   50 (299)
T 2aka_B            9 NRLQDAFSAIGQNADLDLPQIAVVGGQSAGKSSVLENFVGRD   50 (299)
T ss_dssp             HHHHHHHTTSCCCTTCCCCEEEEEEBTTSCHHHHHHHHHTSC
T ss_pred             HHHHHHHHhcCCCCCCCCCeEEEEeCCCCCHHHHHHHHHCCC
Confidence            444444442211223345578999999999999999998764

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=92.54  E-value=0.11  Score=42.94  Aligned_cols=25  Identities=12%  Similarity=0.197  Sum_probs=21.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..-|.|+|.+|+|||||...+.+..
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~~   45 (191)
T 2a5j_A           21 LFKYIIIGDTGVGKSCLLLQFTDKR   45 (191)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcCC
Confidence            4457899999999999999988653

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=92.54  E-value=0.053  Score=50.09  Aligned_cols=125  Identities=16%  Similarity=0.075  Sum_probs=64.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccC---Ccc------------eeEEEEeC----CCCCHHH---------------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKF---YFD------------CHAWVRVS----NFYNFKR---------------  158 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~---~F~------------~~~wv~~~----~~~~~~~---------------  158 (348)
                      .+++|+|+.|+|||||.+.++.-.....   .|+            .+.++.-.    ...++.+               
T Consensus        27 e~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~~~g~~i~~~~~~~r~ig~v~Q~~~l~~~ltv~enl~~~~~~~~~~~~~  106 (348)
T 3d31_A           27 EYFVILGPTGAGKTLFLELIAGFHVPDSGRILLDGKDVTDLSPEKHDIAFVYQNYSLFPHMNVKKNLEFGMRMKKIKDPK  106 (348)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTSSCCSEEEEEETTEECTTSCHHHHTCEEECTTCCCCTTSCHHHHHHHHHHHHCCCCHH
T ss_pred             CEEEEECCCCccHHHHHHHHHcCCCCCCcEEEECCEECCCCchhhCcEEEEecCcccCCCCCHHHHHHHHHHHcCCCHHH
Confidence            4799999999999999999976522110   010            12222111    1112221               


Q ss_pred             HHHHHHHHhCCCCCcc-ccCCCCHHHHH-HHHHHHhcCCeEEEEEeCCCCh------hhHHHHHhhCCCCCCCcEEEEEe
Q 040110          159 ILDDIMKSLMPTSSWL-KIMGKDYKSEK-TILRDYLTNKKYFTVLDDVWIE------KIWDDLREALPDNQIGSRALITV  230 (348)
Q Consensus       159 ~~~~i~~~l~~~~~~~-~~~~~~~~~~~-~~l~~~L~~kr~LlVLDdv~~~------~~~~~l~~~l~~~~~gskIlvTT  230 (348)
                      -..++++.++...... .....+-.+.+ -.|.+.|-.++-+|+||.--+.      ..+..+...+.. ..|..||++|
T Consensus       107 ~v~~~l~~~~L~~~~~~~~~~LSgGq~QRvalAraL~~~P~lLLLDEP~s~LD~~~~~~l~~~l~~l~~-~~g~tii~vT  185 (348)
T 3d31_A          107 RVLDTARDLKIEHLLDRNPLTLSGGEQQRVALARALVTNPKILLLDEPLSALDPRTQENAREMLSVLHK-KNKLTVLHIT  185 (348)
T ss_dssp             HHHHHHHHTTCTTTTTSCGGGSCHHHHHHHHHHHHTTSCCSEEEEESSSTTSCHHHHHHHHHHHHHHHH-HTTCEEEEEE
T ss_pred             HHHHHHHHcCCchHhcCChhhCCHHHHHHHHHHHHHHcCCCEEEEECccccCCHHHHHHHHHHHHHHHH-hcCCEEEEEe
Confidence            2345566665532110 12223333333 3466777788889999997653      112222222211 1255688888


Q ss_pred             CChhhhhh
Q 040110          231 GPHNILTS  238 (348)
Q Consensus       231 R~~~v~~~  238 (348)
                      .+...+..
T Consensus       186 Hd~~~~~~  193 (348)
T 3d31_A          186 HDQTEARI  193 (348)
T ss_dssp             SCHHHHHH
T ss_pred             CCHHHHHH
Confidence            88665543

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=92.53  E-value=0.06  Score=44.13  Aligned_cols=23  Identities=4%  Similarity=0.147  Sum_probs=20.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -|+|+|.+|+|||||...+.+..
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~~   25 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGKK   25 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCcC
Confidence            47799999999999999988763

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=92.52  E-value=0.056  Score=43.90  Aligned_cols=23  Identities=9%  Similarity=0.148  Sum_probs=20.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      --|+++|.+|+|||||...+.+.
T Consensus         8 ~ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            8 LRLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEEECCGGGCHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            45779999999999999998865

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=92.48  E-value=0.071  Score=44.35  Aligned_cols=24  Identities=8%  Similarity=0.279  Sum_probs=20.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..-|.++|.+|+|||||...+.+.
T Consensus        20 ~~ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           20 KPRILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhc
Confidence            345779999999999999987765

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=92.47  E-value=0.08  Score=42.34  Aligned_cols=23  Identities=9%  Similarity=0.307  Sum_probs=20.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .-|+|+|.+|+|||||...+.+.
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            35789999999999999998765

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=92.45  E-value=0.089  Score=48.32  Aligned_cols=24  Identities=17%  Similarity=0.120  Sum_probs=21.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      ...+++|+|.+|+|||||.+.+..
T Consensus        54 ~g~~v~i~G~~GaGKSTLl~~l~g   77 (337)
T 2qm8_A           54 RAIRVGITGVPGVGKSTTIDALGS   77 (337)
T ss_dssp             CSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            456899999999999999999874

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=92.44  E-value=0.074  Score=43.33  Aligned_cols=23  Identities=13%  Similarity=0.146  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      --|+++|.+|+|||||...+.+.
T Consensus         6 ~~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            6 IKCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999998765

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=92.42  E-value=0.092  Score=43.33  Aligned_cols=25  Identities=28%  Similarity=0.428  Sum_probs=20.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .--|.|+|.+|+|||||...+.+..
T Consensus        21 ~~ki~vvG~~~vGKTsLi~~l~~~~   45 (187)
T 3c5c_A           21 EVNLAILGRRGAGKSALTVKFLTKR   45 (187)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             eEEEEEECCCCCcHHHHHHHHHhCC
Confidence            3457899999999999999987653

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=92.40  E-value=0.077  Score=43.08  Aligned_cols=25  Identities=12%  Similarity=0.308  Sum_probs=21.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..-|.++|.+|+|||||...+....
T Consensus        12 ~~ki~v~G~~~~GKSsli~~l~~~~   36 (181)
T 2efe_B           12 NAKLVLLGDVGAGKSSLVLRFVKDQ   36 (181)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCC
Confidence            3457899999999999999987653

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=92.38  E-value=0.095  Score=43.47  Aligned_cols=25  Identities=8%  Similarity=0.046  Sum_probs=21.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...-|+|+|.+|+|||||...+...
T Consensus        28 ~~~ki~v~G~~~vGKSsLi~~l~~~   52 (192)
T 2b6h_A           28 KQMRILMVGLDAAGKTTILYKLKLG   52 (192)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHCSS
T ss_pred             CccEEEEECCCCCCHHHHHHHHHhC
Confidence            3446889999999999999998754

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=92.36  E-value=0.069  Score=44.29  Aligned_cols=23  Identities=17%  Similarity=0.164  Sum_probs=20.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..|+++|.+|+|||||...+.+.
T Consensus        24 ~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           24 GKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            36789999999999999999865

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=92.36  E-value=0.075  Score=44.42  Aligned_cols=24  Identities=13%  Similarity=0.149  Sum_probs=20.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|+++|.+|+|||||...+.+.
T Consensus        25 ~~ki~lvG~~~vGKSsLi~~l~~~   48 (198)
T 1f6b_A           25 TGKLVFLGLDNAGKTTLLHMLKDD   48 (198)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            345789999999999999998764

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=92.34  E-value=0.097  Score=45.26  Aligned_cols=24  Identities=13%  Similarity=0.094  Sum_probs=18.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -..|.|-|+.|+||||+++.+.+.
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~   48 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDR   48 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            347889999999999999999877

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.33  E-value=0.1  Score=42.90  Aligned_cols=25  Identities=20%  Similarity=0.123  Sum_probs=21.3

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|+|+|.+|+|||||...+.+.
T Consensus        15 ~~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A           15 QEHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CccEEEEECCCCCCHHHHHHHHhcC
Confidence            3456789999999999999999854

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=92.33  E-value=0.13  Score=42.40  Aligned_cols=26  Identities=8%  Similarity=0.181  Sum_probs=21.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|.|+|..|+|||||...+.+..
T Consensus        15 ~~~ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           15 YLFKLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcCC
Confidence            34567899999999999999998764

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=92.32  E-value=0.077  Score=44.25  Aligned_cols=24  Identities=17%  Similarity=0.195  Sum_probs=20.3

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      ....|+|+|.+|+|||||...+.+
T Consensus        22 ~~~ki~vvG~~~vGKSsLi~~l~~   45 (195)
T 3cbq_A           22 GIFKVMLVGESGVGKSTLAGTFGG   45 (195)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHTCC
T ss_pred             cEEEEEEECCCCCCHHHHHHHHHh
Confidence            445688999999999999999853

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=92.32  E-value=0.079  Score=43.06  Aligned_cols=23  Identities=13%  Similarity=0.098  Sum_probs=20.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .-|+|+|.+|+|||||...+.+.
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            35779999999999999998866

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=92.32  E-value=0.095  Score=43.67  Aligned_cols=26  Identities=27%  Similarity=0.325  Sum_probs=21.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ....|+|+|.+|+|||||...+.+..
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~~~   32 (207)
T 1vg8_A            7 VLLKVIILGDSGVGKTSLMNQYVNKK   32 (207)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcCC
Confidence            44568899999999999999987653

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=92.32  E-value=0.086  Score=42.88  Aligned_cols=25  Identities=20%  Similarity=0.349  Sum_probs=21.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...|+|+|.+|+|||||...+.+..
T Consensus         6 ~~ki~~~G~~~~GKSsli~~l~~~~   30 (181)
T 3t5g_A            6 SRKIAILGYRSVGKSSLTIQFVEGQ   30 (181)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcCC
Confidence            4567899999999999999998553

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=92.29  E-value=0.13  Score=43.91  Aligned_cols=52  Identities=12%  Similarity=0.035  Sum_probs=32.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMK  165 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~  165 (348)
                      ..|.+-|+.|+||||+++.+...... ..+..+.+..-.....+.+.+++++.
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l~~-~~~~~v~~~rep~~t~~g~~ir~~l~   55 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETLEQ-LGIRDMVFTREPGGTQLAEKLRSLLL   55 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHH-TTCCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH-cCCCcceeeeCCCCCHHHHHHHHHHh
Confidence            37889999999999999999877322 23333344333333334555566554

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.28  E-value=0.08  Score=43.92  Aligned_cols=25  Identities=20%  Similarity=0.352  Sum_probs=21.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..-|+|+|.+|+|||||...+.+..
T Consensus        28 ~~ki~v~G~~~vGKSsli~~l~~~~   52 (196)
T 2atv_A           28 EVKLAIFGRAGVGKSALVVRFLTKR   52 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCC
Confidence            3457899999999999999988663

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=92.28  E-value=0.093  Score=42.84  Aligned_cols=26  Identities=8%  Similarity=0.140  Sum_probs=21.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|.|+|.+|+|||||...+.+..
T Consensus         9 ~~~ki~v~G~~~~GKSsli~~l~~~~   34 (186)
T 2bme_A            9 FLFKFLVIGNAGTGKSCLLHQFIEKK   34 (186)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             cceEEEEECCCCCCHHHHHHHHHcCC
Confidence            34567899999999999999988653

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=92.28  E-value=0.046  Score=54.36  Aligned_cols=51  Identities=14%  Similarity=0.034  Sum_probs=34.0

Q ss_pred             CcccccccccccHHHHHhhcCCCCCC--CC---CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           82 DALLGLQSKIINLRNLHQRLPPSSGL--GQ---PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        82 ~~~vGr~~~~~~~~~l~~~L~~~~~~--~~---~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.++|.+...   +.+.-.|......  .+   .+..-+.++|++|+|||+||+.+++.
T Consensus       295 ~~I~G~e~vk---~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~  350 (595)
T 3f9v_A          295 PSIYGHWELK---EALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRV  350 (595)
T ss_dssp             STTSCCHHHH---HHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTT
T ss_pred             chhcChHHHH---HHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHh
Confidence            3789999877   7776666511000  00   01113678999999999999998876

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=92.27  E-value=0.072  Score=43.02  Aligned_cols=23  Identities=13%  Similarity=0.225  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .-|+|+|..|+|||||...+.+.
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            45788999999999999998755

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=92.26  E-value=0.12  Score=42.54  Aligned_cols=25  Identities=8%  Similarity=0.193  Sum_probs=21.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .--|+|+|.+|+|||||...+....
T Consensus         7 ~~ki~v~G~~~~GKSsli~~l~~~~   31 (208)
T 3clv_A            7 SYKTVLLGESSVGKSSIVLRLTKDT   31 (208)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCc
Confidence            4457899999999999999998763

>3ch4_B Pmkase, phosphomevalonate kinase; parallel beta-sheet with the strand order 23145, walker A motif, cholesterol biosynthesis, lipid synthesis; 1.76A {Homo sapiens}

Probab=92.25  E-value=0.1  Score=44.20  Aligned_cols=99  Identities=13%  Similarity=0.030  Sum_probs=53.1

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH-HHHHhCCCCCcc---ccCCC----C
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD-IMKSLMPTSSWL---KIMGK----D  180 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~-i~~~l~~~~~~~---~~~~~----~  180 (348)
                      .....+|+|+|++|+||+|+|..+.+.  ..  |....-+      .+.+.+++ .+...+......   .....    .
T Consensus         8 ~~~~~II~itGk~~SGKd~va~~l~~~--~g--~~~~~vv------~msD~iK~~~a~~~gl~~~~~l~~~~ykE~~R~~   77 (202)
T 3ch4_B            8 GAPRLVLLFSGKRKSGKDFVTEALQSR--LG--ADVCAVL------RLSGPLKEQYAQEHGLNFQRLLDTSTYKEAFRKD   77 (202)
T ss_dssp             CCCSEEEEEEECTTSSHHHHHHHHHHH--HC--TTTEEEE------CTHHHHHHHHHHTTTCCCC-------CCSSHHHH
T ss_pred             cCCCEEEEEECCCCCChHHHHHHHHHH--cC--CCCceEE------EccHHHHHHHHHHcCCCchhhcchhhhHHHHHHH
Confidence            346679999999999999999988653  11  1111111      44455553 455554432110   00000    1


Q ss_pred             HHHHHHHHHH---------HhcC-CeEEEEEeCCCChhhHHHHHhhC
Q 040110          181 YKSEKTILRD---------YLTN-KKYFTVLDDVWIEKIWDDLREAL  217 (348)
Q Consensus       181 ~~~~~~~l~~---------~L~~-kr~LlVLDdv~~~~~~~~l~~~l  217 (348)
                      +......+++         .+.. ..-.+|+|||....+.+.|...+
T Consensus        78 m~~~g~~~R~~d~~~~~~~~~~~~~~~~vII~dvR~~~Ev~~fr~~~  124 (202)
T 3ch4_B           78 MIRWGEEKRQADPGFFCRKIVEGISQPIWLVSDTRRVSDIQWFREAY  124 (202)
T ss_dssp             HHHHHHHHHHHCTTTTHHHHSBTCCCSEEEECCCCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCchHHHHHHHHhcCCCcEEEeCCCCHHHHHHHHHhC
Confidence            1111111111         1111 12278999999999999888765

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=92.21  E-value=0.05  Score=50.40  Aligned_cols=23  Identities=30%  Similarity=0.291  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        32 e~~~llGpnGsGKSTLLr~iaGl   54 (353)
T 1oxx_K           32 ERFGILGPSGAGKTTFMRIIAGL   54 (353)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            47999999999999999998754

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=92.20  E-value=0.091  Score=48.99  Aligned_cols=111  Identities=14%  Similarity=0.129  Sum_probs=59.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeE-EEEeCCCCCHHHHHHHHHHHhCCCCC-ccc-cCCCCHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHA-WVRVSNFYNFKRILDDIMKSLMPTSS-WLK-IMGKDYKSEKTI  187 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~-wv~~~~~~~~~~~~~~i~~~l~~~~~-~~~-~~~~~~~~~~~~  187 (348)
                      .-.+++|+|+.|+|||||++.+...  +.......+ ++.  .+...         .+..... .+. .-..+...+...
T Consensus       135 ~g~~i~ivG~~GsGKTTll~~l~~~--~~~~~~g~I~~~e--~~~e~---------~~~~~~~~v~Q~~~g~~~~~~~~~  201 (372)
T 2ewv_A          135 KMGLILVTGPTGSGKSTTIASMIDY--INQTKSYHIITIE--DPIEY---------VFKHKKSIVNQREVGEDTKSFADA  201 (372)
T ss_dssp             SSEEEEEECSSSSSHHHHHHHHHHH--HHHHSCCEEEEEE--SSCCS---------CCCCSSSEEEEEEBTTTBSCSHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhh--cCcCCCcEEEEec--ccHhh---------hhccCceEEEeeecCCCHHHHHHH
Confidence            4468999999999999999998765  221112222 222  11110         0000000 000 000011223456


Q ss_pred             HHHHhcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhh
Q 040110          188 LRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILT  237 (348)
Q Consensus       188 l~~~L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~  237 (348)
                      +...|...+-+|++|.+.+.+....+....   ..|..|+.|+-..++..
T Consensus       202 l~~~L~~~pd~illdE~~d~e~~~~~l~~~---~~g~~vi~t~H~~~~~~  248 (372)
T 2ewv_A          202 LRAALREDPDVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNTAID  248 (372)
T ss_dssp             HHHHTTSCCSEEEESCCCSHHHHHHHHHHH---TTTCEEEECCCCCSHHH
T ss_pred             HHHHhhhCcCEEEECCCCCHHHHHHHHHHH---hcCCEEEEEECcchHHH
Confidence            777777777889999997665554433332   23556888887766443

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=92.17  E-value=0.091  Score=48.29  Aligned_cols=26  Identities=12%  Similarity=0.087  Sum_probs=22.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+++|+|.+|+|||||+..+...
T Consensus        54 ~~~~~i~i~G~~g~GKSTl~~~l~~~   79 (341)
T 2p67_A           54 GNTLRLGVTGTPGAGKSTFLEAFGML   79 (341)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CCCEEEEEEcCCCCCHHHHHHHHHHH
Confidence            35678999999999999999998654

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=92.17  E-value=0.13  Score=44.68  Aligned_cols=52  Identities=12%  Similarity=-0.008  Sum_probs=32.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIM  164 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~  164 (348)
                      ..+|.|.|+.|+||||+++.+...... ..++.+....-.......+.+++++
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l~~-~~~~~~~~~rep~~t~~g~~ir~~l   78 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETLQQ-NGIDHITRTREPGGTLLAEKLRALV   78 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHHHH-TTCCCEEEEESSCSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh-cCCCeeeeecCCCCCHHHHHHHHHH
Confidence            357889999999999999999877322 3455344443333323334444444

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.16  E-value=0.1  Score=42.22  Aligned_cols=26  Identities=15%  Similarity=0.231  Sum_probs=21.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|+++|.+|+|||||...+.+..
T Consensus         9 ~~~~i~v~G~~~~GKssli~~l~~~~   34 (180)
T 2g6b_A            9 VAFKVMLVGDSGVGKTCLLVRFKDGA   34 (180)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             cceEEEEECcCCCCHHHHHHHHHhCC
Confidence            34467899999999999999987654

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=92.09  E-value=0.24  Score=42.01  Aligned_cols=49  Identities=16%  Similarity=0.201  Sum_probs=30.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIM  164 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~  164 (348)
                      ..|+|-|.-|+||||+++.+.+.  ....++.+ ...-.......+.+++++
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~--L~~~~~v~-~~~eP~~t~~g~~ir~~l   51 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHR--LVKDYDVI-MTREPGGVPTGEEIRKIV   51 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH--HTTTSCEE-EEESSTTCHHHHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHHHHHH--HHCCCCEE-EeeCCCCChHHHHHHHHH
Confidence            36888999999999999999887  44444432 222222333344444444

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=92.09  E-value=0.11  Score=42.73  Aligned_cols=25  Identities=12%  Similarity=0.200  Sum_probs=21.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..-|+|+|.+|+|||||...+.+..
T Consensus        22 ~~ki~vvG~~~~GKSsli~~l~~~~   46 (189)
T 2gf9_A           22 MFKLLLIGNSSVGKTSFLFRYADDS   46 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcCC
Confidence            4567899999999999999988663

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=92.08  E-value=0.075  Score=49.87  Aligned_cols=23  Identities=17%  Similarity=0.262  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        48 e~~~llGpsGsGKSTLLr~iaGl   70 (390)
T 3gd7_A           48 QRVGLLGRTGSGKSTLLSAFLRL   70 (390)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCChHHHHHHHHhCC
Confidence            47999999999999999999754

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=92.02  E-value=0.26  Score=54.46  Aligned_cols=90  Identities=13%  Similarity=0.041  Sum_probs=62.9

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTI  187 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~  187 (348)
                      -+.-++|-|+|+.|+||||||.++...  ....=..++|+......+..-     ++.++.+.... -.....-++.+..
T Consensus      1428 ~prg~~iei~g~~~sGkttl~~~~~a~--~~~~g~~~~~i~~e~~~~~~~-----~~~~Gv~~~~l~~~~p~~~e~~l~~ 1500 (1706)
T 3cmw_A         1428 LPMGRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEI 1500 (1706)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEECTTSCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHH
T ss_pred             CCCCCEEEEEcCCCCCHHHHHHHHHHH--HHhcCCeEEEEecCCCCCHHH-----HHHcCCCHHHeEEeCCCcHHHHHHH
Confidence            345578999999999999999998865  222224678888888877654     77877765432 1223344666777


Q ss_pred             HHHHhcC-CeEEEEEeCCC
Q 040110          188 LRDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       188 l~~~L~~-kr~LlVLDdv~  205 (348)
                      +...++. .--++|+|.|.
T Consensus      1501 ~~~~~~s~~~~~vvvDsv~ 1519 (1706)
T 3cmw_A         1501 CDALARSGAVDVIVVDSVA 1519 (1706)
T ss_dssp             HHHHHHHTCCSEEEESCST
T ss_pred             HHHHHHcCCCCEEEEccHH
Confidence            7777754 56788999985

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=91.98  E-value=0.12  Score=42.70  Aligned_cols=25  Identities=12%  Similarity=0.279  Sum_probs=21.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...-|+|+|.+|+|||||...+...
T Consensus         7 ~~~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            7 NDYRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CeeEEEEECCCCCcHHHHHHHHHcC
Confidence            3446789999999999999999764

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=91.98  E-value=0.11  Score=42.40  Aligned_cols=26  Identities=12%  Similarity=0.119  Sum_probs=22.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ....|+++|.+|+|||||...+.+..
T Consensus        17 ~~~~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           17 RELRLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHTTCC
T ss_pred             CeeEEEEECCCCCCHHHHHHHHhcCC
Confidence            44568899999999999999998764

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=91.97  E-value=0.092  Score=43.93  Aligned_cols=25  Identities=8%  Similarity=0.068  Sum_probs=21.3

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...-|+|+|.+|+|||||...+.+.
T Consensus        28 ~~~ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           28 FLFKLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHhhC
Confidence            3456889999999999999998765

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=91.97  E-value=0.086  Score=43.85  Aligned_cols=23  Identities=17%  Similarity=0.255  Sum_probs=19.7

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      ..-|+|+|.+|+|||||...+..
T Consensus         6 ~~kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            6 YYRVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHhc
Confidence            34578999999999999998874

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=91.96  E-value=0.093  Score=44.15  Aligned_cols=25  Identities=12%  Similarity=0.114  Sum_probs=20.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...|.|+|.+|+|||||...+.+..
T Consensus         7 ~~ki~vvG~~~~GKTsli~~l~~~~   31 (214)
T 2fh5_B            7 QRAVLFVGLCDSGKTLLFVRLLTGQ   31 (214)
T ss_dssp             -CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3467899999999999999998663

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=91.94  E-value=0.1  Score=47.05  Aligned_cols=25  Identities=12%  Similarity=0.256  Sum_probs=21.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|+|+|.+|+|||||...+...
T Consensus         7 r~~~VaIvG~~nvGKSTLln~L~g~   31 (301)
T 1ega_A            7 YCGFIAIVGRPNVGKSTLLNKLLGQ   31 (301)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHCC
Confidence            3458999999999999999999765

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=91.91  E-value=0.097  Score=43.74  Aligned_cols=42  Identities=19%  Similarity=0.107  Sum_probs=27.2

Q ss_pred             EEEEEE-CCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCH
Q 040110          113 SVVAIL-DSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNF  156 (348)
Q Consensus       113 ~vi~I~-G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  156 (348)
                      ++|+|+ +-||+||||+|..++.....+ .. .++-+......+.
T Consensus         2 ~vi~v~s~kgG~GKTt~a~~la~~la~~-g~-~vlliD~D~~~~~   44 (206)
T 4dzz_A            2 KVISFLNPKGGSGKTTAVINIATALSRS-GY-NIAVVDTDPQMSL   44 (206)
T ss_dssp             EEEEECCSSTTSSHHHHHHHHHHHHHHT-TC-CEEEEECCTTCHH
T ss_pred             eEEEEEeCCCCccHHHHHHHHHHHHHHC-CC-eEEEEECCCCCCH
Confidence            578888 579999999999887663221 11 3455555544443

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=91.89  E-value=0.045  Score=51.79  Aligned_cols=24  Identities=21%  Similarity=0.277  Sum_probs=21.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      ...+++|+|..|+|||||.+.+..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhC
Confidence            456899999999999999999987

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=91.88  E-value=0.093  Score=43.37  Aligned_cols=25  Identities=8%  Similarity=0.146  Sum_probs=21.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .--|.++|.+|+|||||...+.+..
T Consensus        23 ~~ki~~vG~~~~GKSsl~~~l~~~~   47 (194)
T 3reg_A           23 ALKIVVVGDGAVGKTCLLLAFSKGE   47 (194)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eeEEEEECcCCCCHHHHHHHHhcCC
Confidence            3457899999999999999998764

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=91.88  E-value=0.094  Score=43.21  Aligned_cols=25  Identities=16%  Similarity=0.161  Sum_probs=21.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..-|+|+|.+|+|||||...+.+..
T Consensus        22 ~~ki~v~G~~~~GKSsli~~l~~~~   46 (188)
T 1zd9_A           22 EMELTLVGLQYSGKTTFVNVIASGQ   46 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             ccEEEEECCCCCCHHHHHHHHHcCC
Confidence            3457899999999999999998653

>3t34_A Dynamin-related protein 1A, linker, dynamin-relat 1A; dynamin-like protein 1A, GTPase, membrane fission, motor Pro; HET: GDP; 2.40A {Arabidopsis thaliana} PDB: 3t35_A*

Probab=91.87  E-value=1.3  Score=40.71  Aligned_cols=25  Identities=12%  Similarity=0.258  Sum_probs=22.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|+|+|..|+|||||...+...
T Consensus        33 ~lp~I~vvG~~~sGKSSLln~l~g~   57 (360)
T 3t34_A           33 SLPAIAVVGGQSSGKSSVLESIVGK   57 (360)
T ss_dssp             CCCEEEEECBTTSSHHHHHHHHHTS
T ss_pred             cCCEEEEECCCCCcHHHHHHHHhCC
Confidence            4558999999999999999999875

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=91.86  E-value=0.086  Score=43.62  Aligned_cols=25  Identities=16%  Similarity=0.352  Sum_probs=21.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .--|+|+|.+|+|||||...+.+..
T Consensus        23 ~~ki~vvG~~~~GKSsli~~l~~~~   47 (192)
T 2fg5_A           23 ELKVCLLGDTGVGKSSIVCRFVQDH   47 (192)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHCC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcCC
Confidence            4467899999999999999998663

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=91.85  E-value=0.16  Score=46.79  Aligned_cols=27  Identities=11%  Similarity=0.113  Sum_probs=21.7

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+++.+.|.||+||||+|..++..
T Consensus        15 ~~~~~i~~~~gkGGvGKTt~a~~lA~~   41 (348)
T 3io3_A           15 HDSLKWIFVGGKGGVGKTTTSSSVAVQ   41 (348)
T ss_dssp             CTTCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHH
Confidence            345678888999999999999887643

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=91.83  E-value=0.12  Score=42.89  Aligned_cols=26  Identities=15%  Similarity=0.200  Sum_probs=21.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|+|+|.+|+|||||...+.+..
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~~~   32 (203)
T 1zbd_A            7 YMFKILIIGNSSVGKTSFLFRYADDS   32 (203)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTCC
T ss_pred             eeeEEEEECCCCCCHHHHHHHHhcCC
Confidence            34567899999999999999988663

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=91.82  E-value=0.53  Score=45.94  Aligned_cols=46  Identities=15%  Similarity=0.169  Sum_probs=33.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCC-HHHHHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYN-FKRILDDI  163 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~-~~~~~~~i  163 (348)
                      .++|.|..|+|||+|+.++.+..    +-+.++++-+++... +.+++.++
T Consensus       229 r~~I~g~~g~GKT~L~~~ia~~~----~~~~~V~~~iGER~~Ev~e~~~~~  275 (588)
T 3mfy_A          229 TAAIPGPAGSGKTVTQHQLAKWS----DAQVVIYIGCGERGNEMTDVLEEF  275 (588)
T ss_dssp             EEEECSCCSHHHHHHHHHHHHHS----SCSEEEEEECCSSSSHHHHHHHHT
T ss_pred             eEEeecCCCCCHHHHHHHHHhcc----CCCEEEEEEecccHHHHHHHHHHH
Confidence            57899999999999999988752    224677888877654 44555554

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=91.80  E-value=0.086  Score=43.95  Aligned_cols=26  Identities=27%  Similarity=0.290  Sum_probs=21.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|+|+|.+|+|||||...+.+..
T Consensus        23 ~~~ki~vvG~~~~GKSsli~~l~~~~   48 (201)
T 3oes_A           23 RYRKVVILGYRCVGKTSLAHQFVEGE   48 (201)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             CcEEEEEECCCCcCHHHHHHHHHhCC
Confidence            34567899999999999999998764

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=91.79  E-value=0.17  Score=49.98  Aligned_cols=26  Identities=12%  Similarity=0.005  Sum_probs=22.6

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+|.|.|++|+||||+|+.+...
T Consensus       394 q~~~~I~l~GlsGSGKSTiA~~La~~  419 (573)
T 1m8p_A          394 TQGFTIFLTGYMNSGKDAIARALQVT  419 (573)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccceEEEeecCCCCCHHHHHHHHHHH
Confidence            34568899999999999999999876

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=91.79  E-value=0.091  Score=51.05  Aligned_cols=26  Identities=4%  Similarity=0.052  Sum_probs=22.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...+|.+.|++|+||||+|+.+....
T Consensus       394 ~~~~I~l~GlsGsGKSTIa~~La~~L  419 (511)
T 1g8f_A          394 QGFSIVLGNSLTVSREQLSIALLSTF  419 (511)
T ss_dssp             CCEEEEECTTCCSCHHHHHHHHHHHH
T ss_pred             cceEEEecccCCCCHHHHHHHHHHHH
Confidence            34688899999999999999999883

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A

Probab=91.79  E-value=0.1  Score=45.84  Aligned_cols=43  Identities=12%  Similarity=-0.017  Sum_probs=28.5

Q ss_pred             CCcEEEEEE-CCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCC
Q 040110          110 PTHSVVAIL-DSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYN  155 (348)
Q Consensus       110 ~~~~vi~I~-G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  155 (348)
                      ...++|+|+ +-||+||||+|..++.... + .. .++-+......+
T Consensus        25 ~~~~vI~v~s~kGGvGKTT~a~~LA~~la-~-g~-~VlliD~D~~~~   68 (267)
T 3k9g_A           25 KKPKIITIASIKGGVGKSTSAIILATLLS-K-NN-KVLLIDMDTQAS   68 (267)
T ss_dssp             -CCEEEEECCSSSSSCHHHHHHHHHHHHT-T-TS-CEEEEEECTTCH
T ss_pred             CCCeEEEEEeCCCCchHHHHHHHHHHHHH-C-CC-CEEEEECCCCCC
Confidence            456788886 4699999999999887744 2 22 344555544433

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=91.79  E-value=0.1  Score=50.11  Aligned_cols=25  Identities=8%  Similarity=0.134  Sum_probs=21.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+|.++|++|+||||+++.+...
T Consensus        38 ~~~~IvlvGlpGsGKSTia~~La~~   62 (469)
T 1bif_A           38 CPTLIVMVGLPARGKTYISKKLTRY   62 (469)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHH
Confidence            3457889999999999999999865

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=91.76  E-value=0.095  Score=42.82  Aligned_cols=25  Identities=20%  Similarity=0.123  Sum_probs=20.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|.|+|..|+|||||...+.+.
T Consensus        20 ~~~~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           20 QEHKVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             -CEEEEEEEETTSSHHHHHHHHHTT
T ss_pred             ceeEEEEECCCCCCHHHHHHHHhcC
Confidence            3446789999999999999999865

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=91.75  E-value=0.12  Score=42.98  Aligned_cols=26  Identities=12%  Similarity=0.248  Sum_probs=21.1

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....-|+|+|.+|+|||||...+...
T Consensus        26 ~~~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           26 QKAYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             --CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CCCeEEEEECcCCCCHHHHHHHHHhC
Confidence            34556889999999999999999765

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=91.73  E-value=0.1  Score=42.95  Aligned_cols=24  Identities=13%  Similarity=0.302  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .-|+|+|.+|+|||||...+.+..
T Consensus        16 ~~i~v~G~~~~GKssli~~l~~~~   39 (195)
T 1x3s_A           16 LKILIIGESGVGKSSLLLRFTDDT   39 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            467899999999999999998663

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=91.73  E-value=0.07  Score=48.18  Aligned_cols=22  Identities=9%  Similarity=0.404  Sum_probs=18.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|+|+|.+|+|||||.+.++..
T Consensus        20 ~I~lvG~nG~GKSTLl~~L~g~   41 (301)
T 2qnr_A           20 TLMVVGESGLGKSTLINSLFLT   41 (301)
T ss_dssp             EEEEEEETTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3589999999999999998753

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=91.70  E-value=0.09  Score=44.19  Aligned_cols=25  Identities=12%  Similarity=0.211  Sum_probs=21.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...-|+|+|.+|+|||||...+.+.
T Consensus        25 ~~~ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           25 FLFKIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHHhC
Confidence            3456789999999999999998765

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=91.68  E-value=0.089  Score=48.57  Aligned_cols=23  Identities=22%  Similarity=0.390  Sum_probs=21.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|..|+|||||.+.+.+.
T Consensus        72 q~~gIiG~nGaGKTTLl~~I~g~   94 (347)
T 2obl_A           72 QRIGIFAGSGVGKSTLLGMICNG   94 (347)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            37999999999999999999987

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=91.68  E-value=0.11  Score=44.75  Aligned_cols=25  Identities=16%  Similarity=0.170  Sum_probs=20.4

Q ss_pred             CcEEEEEEC-CCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILD-SRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G-~gGvGKTtLA~~v~~~  135 (348)
                      ..++|+|++ -||+||||+|..++..
T Consensus         3 ~~~vI~v~s~kGGvGKTt~a~~LA~~   28 (245)
T 3ea0_A            3 AKRVFGFVSAKGGDGGSCIAANFAFA   28 (245)
T ss_dssp             CCEEEEEEESSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcchHHHHHHHHHH
Confidence            457888875 6999999999988766

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=91.65  E-value=0.13  Score=43.78  Aligned_cols=23  Identities=17%  Similarity=0.255  Sum_probs=19.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      ..-|+|+|.+|+|||||...+..
T Consensus        37 ~~kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           37 YYRVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            34688999999999999999874

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=91.63  E-value=0.075  Score=49.31  Aligned_cols=23  Identities=17%  Similarity=0.345  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.+...
T Consensus       176 ~~i~ivG~sGsGKSTll~~l~~~  198 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMKALMQE  198 (361)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc
Confidence            47899999999999999999876

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=91.62  E-value=0.11  Score=43.70  Aligned_cols=25  Identities=12%  Similarity=0.162  Sum_probs=21.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..-|+|+|.+|+|||||...+....
T Consensus        28 ~~ki~vvG~~~vGKSsLi~~l~~~~   52 (205)
T 1gwn_A           28 KCKIVVVGDSQCGKTALLHVFAKDC   52 (205)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcCC
Confidence            3467899999999999999998763

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=91.62  E-value=0.2  Score=45.87  Aligned_cols=26  Identities=12%  Similarity=0.077  Sum_probs=21.1

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++.+.|-||+||||+|..++..
T Consensus        14 ~~~~i~~~sgkGGvGKTt~a~~lA~~   39 (334)
T 3iqw_A           14 RSLRWIFVGGKGGVGKTTTSCSLAIQ   39 (334)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCccHHHHHHHHHHH
Confidence            34567778899999999999887654

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=91.60  E-value=0.07  Score=52.43  Aligned_cols=24  Identities=17%  Similarity=0.120  Sum_probs=21.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+++|+|+.|+|||||++.+...
T Consensus       369 G~iI~LiG~sGSGKSTLar~La~~  392 (552)
T 3cr8_A          369 GFTVFFTGLSGAGKSTLARALAAR  392 (552)
T ss_dssp             CEEEEEEESSCHHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCChHHHHHHHHHHh
Confidence            368999999999999999999877

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=91.55  E-value=0.095  Score=44.29  Aligned_cols=23  Identities=17%  Similarity=0.153  Sum_probs=21.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|+|.|+.|+||||+++.++..
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~   29 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEH   29 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHH
Confidence            48999999999999999999887

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=91.55  E-value=0.13  Score=42.74  Aligned_cols=26  Identities=12%  Similarity=0.156  Sum_probs=20.1

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|.|+|.+|+|||||...+.+..
T Consensus        19 ~~~ki~~~G~~~~GKssl~~~l~~~~   44 (201)
T 2q3h_A           19 RGVKCVLVGDGAVGKTSLVVSYTTNG   44 (201)
T ss_dssp             -CEEEEEECSTTSSHHHHHHHHHC--
T ss_pred             cceEEEEECCCCCCHHHHHHHHHhCC
Confidence            34467899999999999999988653

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=91.54  E-value=0.11  Score=48.21  Aligned_cols=22  Identities=9%  Similarity=0.221  Sum_probs=20.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|+|++|+|||||.+.+...
T Consensus       217 ~~~lvG~sG~GKSTLln~L~g~  238 (358)
T 2rcn_A          217 ISIFAGQSGVGKSSLLNALLGL  238 (358)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCccHHHHHHHHhcc
Confidence            7899999999999999999876

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=91.49  E-value=0.14  Score=47.68  Aligned_cols=27  Identities=22%  Similarity=0.186  Sum_probs=22.6

Q ss_pred             CCCcEEEEEEC-CCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILD-SRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G-~gGvGKTtLA~~v~~~  135 (348)
                      ....++|+|+| -||+||||+|..++..
T Consensus       140 ~~~~kvIav~s~KGGvGKTT~a~nLA~~  167 (373)
T 3fkq_A          140 NDKSSVVIFTSPCGGVGTSTVAAACAIA  167 (373)
T ss_dssp             TTSCEEEEEECSSTTSSHHHHHHHHHHH
T ss_pred             CCCceEEEEECCCCCChHHHHHHHHHHH
Confidence            45678999985 8999999999888765

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=91.47  E-value=0.13  Score=45.52  Aligned_cols=24  Identities=17%  Similarity=0.173  Sum_probs=21.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|+++|.+|+|||||...+...
T Consensus         3 ~~~i~lvG~~g~GKTTL~n~l~g~   26 (271)
T 3k53_A            3 LKTVALVGNPNVGKTTIFNALTGL   26 (271)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHTT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCC
Confidence            356899999999999999998765

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=91.47  E-value=0.097  Score=43.71  Aligned_cols=25  Identities=16%  Similarity=0.193  Sum_probs=20.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...-|+|+|.+|+|||||...+.+.
T Consensus        24 ~~~ki~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           24 FLFKFLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHC-
T ss_pred             cceEEEEECcCCCCHHHHHHHHHhC
Confidence            3456789999999999999998765

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=91.47  E-value=0.18  Score=42.14  Aligned_cols=26  Identities=8%  Similarity=0.273  Sum_probs=21.3

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|+|+|.+|+|||||...+....
T Consensus        19 ~~~~i~v~G~~~~GKSsli~~l~~~~   44 (213)
T 3cph_A           19 SIMKILLIGDSGVGKSCLLVRFVEDK   44 (213)
T ss_dssp             -CEEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             cceEEEEECCCCCCHHHHHHHHHhCC
Confidence            34567899999999999999988653

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=91.46  E-value=0.1  Score=43.09  Aligned_cols=22  Identities=14%  Similarity=0.214  Sum_probs=19.5

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -+.|.|.+|+||||||..+...
T Consensus        18 gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           18 GVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHc
Confidence            5678999999999999998765

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=91.46  E-value=0.095  Score=43.26  Aligned_cols=24  Identities=17%  Similarity=0.213  Sum_probs=20.5

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .--|+|+|.+|+|||||...+.+.
T Consensus        23 ~~ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           23 MFKLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEECCCCcCHHHHHHHHhcC
Confidence            345789999999999999998865

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=91.44  E-value=0.16  Score=52.79  Aligned_cols=23  Identities=13%  Similarity=0.192  Sum_probs=20.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHh
Q 040110          111 THSVVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~  133 (348)
                      .-.+++|+|+.|.|||||.+.+.
T Consensus       672 ~g~i~~ItGPNGaGKSTlLr~i~  694 (918)
T 3thx_B          672 SERVMIITGPNMGGKSSYIKQVA  694 (918)
T ss_dssp             SCCEEEEESCCCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCchHHHHHHHH
Confidence            34689999999999999999875

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=91.36  E-value=0.12  Score=42.85  Aligned_cols=25  Identities=28%  Similarity=0.437  Sum_probs=20.0

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..-|.|+|..|+|||||...+.+..
T Consensus        26 ~~ki~vvG~~~~GKSsLi~~l~~~~   50 (192)
T 2il1_A           26 KLQVIIIGSRGVGKTSLMERFTDDT   50 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHCC--
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcCC
Confidence            3457899999999999999987653

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=91.32  E-value=0.1  Score=44.09  Aligned_cols=24  Identities=17%  Similarity=0.239  Sum_probs=20.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..-|+|+|.+|+|||||...+.+.
T Consensus        34 ~~ki~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           34 SVKVVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHC-
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            346789999999999999998765

>2h57_A ADP-ribosylation factor-like protein 6; GTP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GTP; 2.00A {Homo sapiens}

Probab=91.31  E-value=0.1  Score=43.02  Aligned_cols=25  Identities=20%  Similarity=0.133  Sum_probs=21.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...|+|+|.+|+|||||...+.+..
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           21 EVHVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             CEEEEEEECTTSSHHHHHHHTSCGG
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcCC
Confidence            4467899999999999999987664

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=91.31  E-value=0.1  Score=43.55  Aligned_cols=26  Identities=8%  Similarity=0.190  Sum_probs=21.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...-|+|+|.+|+|||||...+.+..
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~~~   32 (206)
T 2bcg_Y            7 YLFKLLLIGNSGVGKSCLLLRFSDDT   32 (206)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHHCC
T ss_pred             cceEEEEECCCCCCHHHHHHHHhcCC
Confidence            34567899999999999999987653

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=91.31  E-value=0.1  Score=49.55  Aligned_cols=21  Identities=14%  Similarity=0.474  Sum_probs=19.5

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|+|..|+|||||.+.++..
T Consensus        45 vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            899999999999999999764

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=91.31  E-value=0.084  Score=48.36  Aligned_cols=107  Identities=14%  Similarity=0.087  Sum_probs=57.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHh
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL  192 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L  192 (348)
                      .+++|+|+.|+|||||++.+..-  +.. -...+.+.-.........    -+.+.      -... .-......+...|
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~--~~~-~~g~i~i~~~~e~~~~~~----~~~i~------~~~g-gg~~~r~~la~aL  237 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEF--IPK-EERIISIEDTEEIVFKHH----KNYTQ------LFFG-GNITSADCLKSCL  237 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGG--SCT-TSCEEEEESSCCCCCSSC----SSEEE------EECB-TTBCHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC--CcC-CCcEEEECCeeccccccc----hhEEE------EEeC-CChhHHHHHHHHh
Confidence            37899999999999999999876  222 234444432111110000    00000      0000 1123345567778


Q ss_pred             cCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhh
Q 040110          193 TNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNIL  236 (348)
Q Consensus       193 ~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~  236 (348)
                      ..++=+|+||.+.+.+.++.+.. +.. + +.-+|+||...+..
T Consensus       238 ~~~p~ilildE~~~~e~~~~l~~-~~~-g-~~tvi~t~H~~~~~  278 (330)
T 2pt7_A          238 RMRPDRIILGELRSSEAYDFYNV-LCS-G-HKGTLTTLHAGSSE  278 (330)
T ss_dssp             TSCCSEEEECCCCSTHHHHHHHH-HHT-T-CCCEEEEEECSSHH
T ss_pred             hhCCCEEEEcCCChHHHHHHHHH-Hhc-C-CCEEEEEEcccHHH
Confidence            88888999999987655554433 322 1 22266666655543

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=91.29  E-value=0.083  Score=44.73  Aligned_cols=26  Identities=12%  Similarity=0.137  Sum_probs=22.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ....|+|+|..|+|||||...+....
T Consensus        28 ~~~~i~v~G~~~~GKSslin~l~~~~   53 (223)
T 4dhe_A           28 VQPEIAFAGRSNAGKSTAINVLCNQK   53 (223)
T ss_dssp             CSCEEEEEESCHHHHHHHHHHHTTCS
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhCCC
Confidence            45578899999999999999998764

>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE; 1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A

Probab=91.26  E-value=0.14  Score=44.76  Aligned_cols=26  Identities=15%  Similarity=0.261  Sum_probs=22.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ....|+|+|.+|+|||||...+....
T Consensus        21 ~~~~I~lvG~~g~GKStl~n~l~~~~   46 (260)
T 2xtp_A           21 SELRIILVGKTGTGKSAAGNSILRKQ   46 (260)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHTSC
T ss_pred             CceEEEEECCCCCCHHHHHHHHhCCC
Confidence            45678899999999999999997653

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=91.23  E-value=0.11  Score=42.86  Aligned_cols=24  Identities=13%  Similarity=0.138  Sum_probs=20.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..-|+++|.+|+|||||...+.+.
T Consensus        18 ~~ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           18 MLKCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            346789999999999999999866

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=91.17  E-value=0.11  Score=43.52  Aligned_cols=24  Identities=8%  Similarity=0.167  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .-|+|+|.+|+|||||...+....
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~~   49 (207)
T 2fv8_A           26 KKLVVVGDGACGKTCLLIVFSKDE   49 (207)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             cEEEEECcCCCCHHHHHHHHhcCC
Confidence            357899999999999999998753

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=91.13  E-value=0.13  Score=43.32  Aligned_cols=24  Identities=25%  Similarity=0.270  Sum_probs=20.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        25 ~~ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           25 LIKLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEEEESCTTSSHHHHHHHHHCS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            346789999999999999998865

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=91.13  E-value=0.19  Score=43.14  Aligned_cols=39  Identities=18%  Similarity=-0.009  Sum_probs=25.2

Q ss_pred             EEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCC
Q 040110          115 VAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYN  155 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  155 (348)
                      |+|.|-||+||||+|..++....... . .++-|......+
T Consensus         3 I~vs~kGGvGKTt~a~~LA~~la~~g-~-~VlliD~D~~~~   41 (254)
T 3kjh_A            3 LAVAGKGGVGKTTVAAGLIKIMASDY-D-KIYAVDGDPDSC   41 (254)
T ss_dssp             EEEECSSSHHHHHHHHHHHHHHTTTC-S-CEEEEEECTTSC
T ss_pred             EEEecCCCCCHHHHHHHHHHHHHHCC-C-eEEEEeCCCCcC
Confidence            56689999999999999877632222 2 344455443333

>3b1v_A Ferrous iron uptake transporter protein B; G protein, iron transport, GTPase, transmembrane, potassium; HET: GGM; 1.85A {Streptococcus thermophilus} PDB: 3b1w_A* 3lx5_A* 3lx8_A* 3ss8_A* 3b1z_A 3b1y_A* 3b1x_A* 3tah_A*

Probab=91.10  E-value=0.2  Score=44.43  Aligned_cols=24  Identities=17%  Similarity=0.200  Sum_probs=21.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|+++|.+|+|||||...+...
T Consensus         3 ~~kI~lvG~~nvGKSTL~n~L~g~   26 (272)
T 3b1v_A            3 MTEIALIGNPNSGKTSLFNLITGH   26 (272)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHCC
Confidence            346889999999999999999865

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=91.09  E-value=0.15  Score=50.84  Aligned_cols=25  Identities=16%  Similarity=0.114  Sum_probs=22.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+|.+.|++|+||||+|+.+...
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~   75 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEY   75 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            4568899999999999999999876

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=91.09  E-value=0.13  Score=44.35  Aligned_cols=49  Identities=18%  Similarity=0.263  Sum_probs=29.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDI  163 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i  163 (348)
                      -.++.|.|.+|+|||+||.+++.+...+ .-..+++++..  .+...+...+
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~-~~~~v~~~s~E--~~~~~~~~~~   78 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEE-YGEPGVFVTLE--ERARDLRREM   78 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHH-HCCCEEEEESS--SCHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHh-cCCCceeeccc--CCHHHHHHHH
Confidence            3478899999999999998876431111 11245555543  3444554443

>1jwy_B Dynamin A GTPase domain; dynamin, GTPase, GDP, myosin, fusion-protein, hydrolase; HET: BGC ADP GDP; 2.30A {Dictyostelium discoideum} SCOP: c.37.1.8 PDB: 1jx2_B*

Probab=91.09  E-value=0.24  Score=44.44  Aligned_cols=28  Identities=11%  Similarity=0.187  Sum_probs=23.6

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ......|+|+|..|+|||||..++....
T Consensus        21 ~~~~~~I~vvG~~~~GKSTlln~l~g~~   48 (315)
T 1jwy_B           21 PLDLPQIVVVGSQSSGKSSVLENIVGRD   48 (315)
T ss_dssp             TTCCCEEEEEECSSSSHHHHHHHHHTSC
T ss_pred             CCCCCeEEEEcCCCCCHHHHHHHHHCCC
Confidence            3456689999999999999999997663

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=91.07  E-value=0.12  Score=48.86  Aligned_cols=25  Identities=12%  Similarity=0.193  Sum_probs=22.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .-.+++|+|+.|+|||||.+.+...
T Consensus       166 ~ggii~I~GpnGSGKTTlL~allg~  190 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTLYAGLQE  190 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHhh
Confidence            4468999999999999999998765

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=91.03  E-value=0.22  Score=42.60  Aligned_cols=23  Identities=17%  Similarity=0.190  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..|.+-|+.|+||||+++.+.+.
T Consensus         6 ~~i~~eG~~g~GKst~~~~l~~~   28 (216)
T 3tmk_A            6 KLILIEGLDRTGKTTQCNILYKK   28 (216)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47889999999999999999887

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=91.01  E-value=0.09  Score=50.48  Aligned_cols=23  Identities=17%  Similarity=0.232  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.++.-
T Consensus       139 e~v~IvGpnGsGKSTLlr~L~Gl  161 (460)
T 2npi_A          139 PRVVIVGGSQTGKTSLSRTLCSY  161 (460)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCc
Confidence            36899999999999999998765

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=91.00  E-value=0.13  Score=44.01  Aligned_cols=22  Identities=14%  Similarity=0.277  Sum_probs=19.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|+|.+|+|||+|...+.++
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCcCHHHHHHHHHhC
Confidence            4678999999999999998765

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=91.00  E-value=0.13  Score=52.45  Aligned_cols=50  Identities=14%  Similarity=0.245  Sum_probs=35.2

Q ss_pred             cccccccccccHHHHHhhcCCC-CC--CCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS-SG--LGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~-~~--~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+... .+  ........+.++|++|+|||++|+.+++.
T Consensus       459 ~v~g~~~~~---~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~  511 (758)
T 1r6b_X          459 LVFGQDKAI---EALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA  511 (758)
T ss_dssp             TSCSCHHHH---HHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             hccCHHHHH---HHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHH
Confidence            477888877   7766655311 00  11233457889999999999999999887

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=90.98  E-value=0.13  Score=43.55  Aligned_cols=25  Identities=12%  Similarity=0.143  Sum_probs=20.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .--|.|+|.+|+|||||...+.+..
T Consensus        27 ~~ki~vvG~~~vGKSsL~~~l~~~~   51 (214)
T 3q3j_B           27 RCKLVLVGDVQCGKTAMLQVLAKDC   51 (214)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcCC
Confidence            3457799999999999999987653

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=90.93  E-value=0.095  Score=42.71  Aligned_cols=25  Identities=12%  Similarity=0.142  Sum_probs=10.5

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...-|+|+|.+|+|||||...+.+.
T Consensus         7 ~~~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            7 YLFKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEEEECCCCC------------
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            3456889999999999999988755

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=90.88  E-value=0.12  Score=43.06  Aligned_cols=24  Identities=13%  Similarity=0.177  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCc
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .-|+|+|.+|+|||||...+....
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~~   49 (201)
T 2gco_A           26 KKLVIVGDGACGKTCLLIVFSKDQ   49 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCc
Confidence            357899999999999999998653

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=90.82  E-value=0.17  Score=43.18  Aligned_cols=27  Identities=15%  Similarity=0.105  Sum_probs=22.8

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ......|+++|.-|+||||+++.+...
T Consensus         6 ~~~~~~iglTGgigsGKStv~~~l~~~   32 (210)
T 4i1u_A            6 HHHMYAIGLTGGIGSGKTTVADLFAAR   32 (210)
T ss_dssp             CCSCCEEEEECCTTSCHHHHHHHHHHT
T ss_pred             ccceeEEEEECCCCCCHHHHHHHHHHC
Confidence            345678999999999999999987653

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=90.77  E-value=0.12  Score=49.26  Aligned_cols=23  Identities=9%  Similarity=0.221  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|..|+|||||++.+.+.
T Consensus       158 q~~~IvG~sGsGKSTLl~~Iag~  180 (438)
T 2dpy_A          158 QRMGLFAGSGVGKSVLLGMMARY  180 (438)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcc
Confidence            37899999999999999999887

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=90.73  E-value=0.65  Score=45.47  Aligned_cols=59  Identities=14%  Similarity=0.160  Sum_probs=38.5

Q ss_pred             HHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHH
Q 040110           96 NLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDI  163 (348)
Q Consensus        96 ~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i  163 (348)
                      ++++.|.+-    ..+ ..++|.|..|+|||+|+.++.+..    +-+.++++-++... .+.+++.++
T Consensus       221 rvID~l~Pi----grG-qr~~Ifgg~g~GKT~L~~~ia~~~----~~~v~V~~~iGER~~Ev~e~~~~~  280 (600)
T 3vr4_A          221 RVIDTFFPV----TKG-GAAAVPGPFGAGKTVVQHQIAKWS----DVDLVVYVGCGERGNEMTDVVNEF  280 (600)
T ss_dssp             HHHHHHSCC----BTT-CEEEEECCTTSCHHHHHHHHHHHS----SCSEEEEEEEEECHHHHHHHHHHT
T ss_pred             hhhhccCCc----cCC-CEEeeecCCCccHHHHHHHHHhcc----CCCEEEEEEecccHHHHHHHHHHH
Confidence            555666522    122 257899999999999999998762    22467777777653 344444443

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=90.72  E-value=0.13  Score=50.45  Aligned_cols=23  Identities=30%  Similarity=0.563  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.++.-
T Consensus       295 ei~~i~G~nGsGKSTLl~~l~Gl  317 (538)
T 3ozx_A          295 EIIGILGPNGIGKTTFARILVGE  317 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            37899999999999999999875

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=90.69  E-value=0.34  Score=44.01  Aligned_cols=24  Identities=25%  Similarity=0.133  Sum_probs=18.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++...|.||+||||+|..++..
T Consensus        14 ~~i~v~sgKGGvGKTTvA~~LA~~   37 (324)
T 3zq6_A           14 TTFVFIGGKGGVGKTTISAATALW   37 (324)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCchHHHHHHHHHHH
Confidence            445556689999999999887644

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=90.66  E-value=0.13  Score=48.81  Aligned_cols=22  Identities=9%  Similarity=0.437  Sum_probs=19.7

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |+|+|.+|+|||||...++...
T Consensus        34 I~lvG~sGaGKSTLln~L~g~~   55 (418)
T 2qag_C           34 LMVVGESGLGKSTLINSLFLTD   55 (418)
T ss_dssp             EEEECCTTSSHHHHHHHHTTCC
T ss_pred             EEEECCCCCcHHHHHHHHhCCC
Confidence            5999999999999999998653

>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote initiative, RSGI, structural genomics, hydrolase; HET: GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8 d.52.3.1

Probab=90.63  E-value=0.17  Score=45.66  Aligned_cols=25  Identities=16%  Similarity=0.236  Sum_probs=21.8

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|+|+|.+|+|||||..++...
T Consensus         6 ~~g~V~ivG~~nvGKSTLln~l~g~   30 (301)
T 1wf3_A            6 YSGFVAIVGKPNVGKSTLLNNLLGV   30 (301)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3457899999999999999999865

>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, N subunit, ABC-type ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus ducreyi} PDB: 3euk_A*

Probab=90.61  E-value=0.14  Score=49.30  Aligned_cols=23  Identities=17%  Similarity=0.174  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.+..-
T Consensus        30 e~~~liG~nGsGKSTLl~~l~Gl   52 (483)
T 3euj_A           30 LVTTLSGGNGAGKSTTMAGFVTA   52 (483)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHhcC
Confidence            68999999999999999998754

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=90.57  E-value=0.21  Score=39.98  Aligned_cols=22  Identities=18%  Similarity=0.336  Sum_probs=19.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHh
Q 040110          112 HSVVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~  133 (348)
                      ..+.+|+|+.|.||||+..+++
T Consensus        23 ~g~~~I~G~NGsGKStil~Ai~   44 (149)
T 1f2t_A           23 EGINLIIGQNGSGKSSLLDAIL   44 (149)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHH
Confidence            4578899999999999998875

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=90.51  E-value=0.13  Score=42.71  Aligned_cols=21  Identities=10%  Similarity=0.177  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.|+|.+|+||||+|.++...
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~   22 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD   22 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCCcHHHHHHHHHhc
Confidence            678999999999999998855

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=90.50  E-value=0.16  Score=44.88  Aligned_cols=26  Identities=12%  Similarity=0.265  Sum_probs=22.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ....|+++|.+|+|||||...+....
T Consensus        38 ~~~~I~vvG~~g~GKSSLin~l~~~~   63 (270)
T 1h65_A           38 NSLTILVMGKGGVGKSSTVNSIIGER   63 (270)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHhCCC
Confidence            34568899999999999999998764

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=90.45  E-value=0.15  Score=50.04  Aligned_cols=23  Identities=22%  Similarity=0.273  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.+..-
T Consensus        48 e~~~LvG~NGaGKSTLlk~l~Gl   70 (538)
T 1yqt_A           48 MVVGIVGPNGTGKSTAVKILAGQ   70 (538)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            47999999999999999999864

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=90.39  E-value=0.15  Score=49.97  Aligned_cols=125  Identities=14%  Similarity=0.060  Sum_probs=63.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCcccc-CC--cc-eeEEEEeCC----CCCHHHHHHH--------------HHHHhCCC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVK-FY--FD-CHAWVRVSN----FYNFKRILDD--------------IMKSLMPT  170 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~-~~--F~-~~~wv~~~~----~~~~~~~~~~--------------i~~~l~~~  170 (348)
                      .+++|+|+.|+|||||++.++.-.... ..  +. .+.++.-..    ..++.+++..              ++..++..
T Consensus       313 e~~~i~G~NGsGKSTLlk~l~Gl~~p~~G~i~~~~~i~~v~Q~~~~~~~~tv~~~~~~~~~~~~~~~~~~~~~l~~~~l~  392 (538)
T 1yqt_A          313 EVIGIVGPNGIGKTTFVKMLAGVEEPTEGKIEWDLTVAYKPQYIKADYEGTVYELLSKIDASKLNSNFYKTELLKPLGII  392 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSCCSBCCCCCCCCEEEECSSCCCCCSSBHHHHHHHHHHHHHTCHHHHHHTTTTTTCG
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCCCCeEEEECceEEEEecCCcCCCCCcHHHHHHhhhccCCCHHHHHHHHHHHcCCh
Confidence            478999999999999999998753211 11  12 233332211    1233333222              12222221


Q ss_pred             CCc-cccCCCCHHHHH-HHHHHHhcCCeEEEEEeCCCCh------hhHHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          171 SSW-LKIMGKDYKSEK-TILRDYLTNKKYFTVLDDVWIE------KIWDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       171 ~~~-~~~~~~~~~~~~-~~l~~~L~~kr~LlVLDdv~~~------~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      ... .....-+-.+.+ -.|.+.|..+.-+|+||.--+.      ..+..+...+.. ..|..||++|-+...+..
T Consensus       393 ~~~~~~~~~LSGGe~qrv~lAraL~~~p~lLlLDEPt~~LD~~~~~~i~~~l~~l~~-~~g~tvi~vsHd~~~~~~  467 (538)
T 1yqt_A          393 DLYDREVNELSGGELQRVAIAATLLRDADIYLLDEPSAYLDVEQRLAVSRAIRHLME-KNEKTALVVEHDVLMIDY  467 (538)
T ss_dssp             GGTTSBGGGCCHHHHHHHHHHHHHTSCCSEEEEECTTTTCCHHHHHHHHHHHHHHHH-HHTCEEEEECSCHHHHHH
T ss_pred             hhhcCChhhCCHHHHHHHHHHHHHHhCCCEEEEeCCcccCCHHHHHHHHHHHHHHHH-hCCCEEEEEeCCHHHHHH
Confidence            000 012223333333 3466677788889999997653      122222222211 124457888887665553

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	348
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	4e-11

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score = 60.6 bits (146), Expect = 4e-11
 Identities = 19/135 (14%), Positives = 38/135 (28%), Gaps = 14/135 (10%)

Query: 113 SVVAILDSRGFDKTAFAAEIYNNNF--VKFYFDCHAWVRVSNFYNFKRILDDIMKSLM-- 168
             + +    G  K+  A++  + +   +   +D   W++ S               LM  
Sbjct: 45  FFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLK 104

Query: 169 ----PTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGS 224
                 +            ++ I    +       V DDV  E+     +E         
Sbjct: 105 SEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQEL------RL 158

Query: 225 RALITVGPHNILTSI 239
           R L+T     I  + 
Sbjct: 159 RCLVTTRDVEISNAA 173

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	348
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.74
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.38
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.34
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.23
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.22
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.16
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.15
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.14
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.08
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.06
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.92
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.76
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	97.74
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.7
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.69
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.66
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.62
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.61
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.61
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.41
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.31
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.29
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.27
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.21
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.17
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.11
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.04
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.02
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.02
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.01
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.01
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.98
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.97
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	96.95
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.88
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.83
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.83
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.8
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.79
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.77
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.76
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.73
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.72
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.72
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.72
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.72
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.72
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.7
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.69
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.68
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.67
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.65
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.63
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.63
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.59
d1okkd2	207	GTPase domain of the signal recognition particle r	96.53
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.53
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.44
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.34
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.33
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.33
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.29
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.27
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.26
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.17
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	95.99
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.98
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.96
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	95.9
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	95.82
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.82
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	95.81
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.75
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	95.74
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	95.7
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	95.68
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	95.67
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	95.65
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	95.64
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.63
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.61
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	95.59
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.59
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.56
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.49
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.48
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.48
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.41
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	95.38
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	95.29
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	95.29
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	95.21
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	95.21
d1xpua3	289	Transcription termination factor Rho, ATPase domai	95.09
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.83
d1g2912	240	Maltose transport protein MalK, N-terminal domain	94.76
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	94.71
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	94.69
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	94.69
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.69
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.69
d2awna2	232	Maltose transport protein MalK, N-terminal domain	94.68
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	94.65
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	94.62
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	94.61
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	94.61
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.56
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.52
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	94.5
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	94.5
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.49
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	94.47
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	94.45
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.43
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	94.41
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	94.4
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	94.38
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.34
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	94.25
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.22
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.22
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.16
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	94.13
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	94.12
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	94.08
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	94.07
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	94.02
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	93.96
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	93.95
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.91
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	93.86
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	93.84
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	93.84
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.8
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	93.79
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	93.68
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	93.67
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.66
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	93.65
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	93.64
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	93.63
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.63
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	93.62
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	93.56
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	93.56
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	93.54
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	93.53
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	93.53
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.49
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	93.48
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	93.44
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	93.44
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	93.4
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	93.38
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	93.37
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	93.35
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.34
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	93.3
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	93.28
d1nrjb_	209	Signal recognition particle receptor beta-subunit	93.27
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	93.25
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	93.24
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	93.21
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	93.2
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	93.19
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	93.17
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.16
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	93.15
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	93.15
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	93.14
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	93.14
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	93.14
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	93.12
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	93.06
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	92.99
d2fh5b1	207	Signal recognition particle receptor beta-subunit	92.99
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	92.9
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	92.88
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	92.84
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	92.84
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	92.82
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	92.81
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	92.81
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	92.8
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	92.76
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	92.75
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	92.72
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.67
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.67
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	92.65
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	92.63
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	92.58
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	92.57
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	92.53
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	92.52
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	92.5
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	92.39
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	92.38
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	92.3
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	92.26
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	92.23
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	92.17
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	92.12
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	92.01
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	91.95
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	91.79
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	91.64
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	91.63
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	91.52
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	91.32
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	91.07
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	90.85
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	90.78
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	90.76
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	90.75
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	90.74
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	90.61
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	90.21
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	90.14
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	89.93
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	89.66
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	89.54
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.25
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	88.94
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	88.91
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	88.44
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	88.18
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	87.19
d1tuea_	205	Replication protein E1 helicase domain {Human papi	86.91
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	86.58
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	86.04
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	85.55
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	84.97
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	84.68
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	84.27
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	83.98
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	83.81
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	83.64
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	83.22
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	82.91
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	82.19
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	81.48

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=100.00  E-value=2e-35  Score=267.67  Aligned_cols=208  Identities=13%  Similarity=0.036  Sum_probs=162.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCcc--ccCCcceeEEEEeCCCCCHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNF--VKFYFDCHAWVRVSNFYNFKRIL  160 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~--~~~~F~~~~wv~~~~~~~~~~~~  160 (348)
                      .++||+.++   ++|+++|..   ..+...++|+|+||||+||||||+++|++..  ...+|++++|+++++.++...+.
T Consensus        21 ~~~gR~~~~---~~i~~~L~~---~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~   94 (277)
T d2a5yb3          21 TCYIREYHV---DRVIKKLDE---MCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFD   94 (277)
T ss_dssp             CSCCCHHHH---HHHHHHHHH---HTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHH
T ss_pred             ceeCcHHHH---HHHHHHHHh---ccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHH
Confidence            789999999   999999972   2345678999999999999999999998753  67789999999999998877666


Q ss_pred             HHHHH---HhCCCCCc--c-ccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          161 DDIMK---SLMPTSSW--L-KIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       161 ~~i~~---~l~~~~~~--~-~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      ..+..   .++.....  + .....+.......+.+.|.++|+|+||||||+..+|..+..      .||+||||||+..
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~~------~~srilvTTR~~~  168 (277)
T d2a5yb3          95 LFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQE------LRLRCLVTTRDVE  168 (277)
T ss_dssp             HHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHHH------TTCEEEEEESBGG
T ss_pred             HHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhhhhhhcc------cCceEEEEeehHH
Confidence            55544   33332111  0 11223334445567888999999999999999998887653      3799999999999


Q ss_pred             hhhh-------cccC-------------------------------CCCc-CCCC-cccccCccccCCHHHHHHHHHHhC
Q 040110          235 ILTS-------IELE-------------------------------NGEK-NRHD-SALVGGPLIRIKHETWQFFILHYG  274 (348)
Q Consensus       235 v~~~-------~~l~-------------------------------~~~C-~Lp~-~~~ig~~L~~~~~~~w~~~~~~~~  274 (348)
                      ++..       |+++                               .+.| |+|+ ++++|+.|+.++.+.|....+.+.
T Consensus       169 v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k~~~~~~~~~~~L~  248 (277)
T d2a5yb3         169 ISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLE  248 (277)
T ss_dssp             GGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHHHHHHHHHH
T ss_pred             HHHhcCCCCceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCCCHHHHHHHHHHhccCCHHHHHHHHHHHh
Confidence            9886       4444                               3567 9999 999999999888899999888875


Q ss_pred             CCCCCCCCCCcchhccc-cccCCCChhHHHHHhHh
Q 040110          275 STPLENETEGPSVGLKL-VSLSELPFPLIVCCLYF  308 (348)
Q Consensus       275 ~~~~~~~~~~~~i~~~l-~s~~~Lp~~lk~cf~y~  308 (348)
                      ..      .+..+...+ +||++||+++|+||.++
T Consensus       249 ~~------~~~~v~~il~~sY~~L~~~lk~c~~~l  277 (277)
T d2a5yb3         249 SR------GLVGVECITPYSYKSLAMALQRCVEVL  277 (277)
T ss_dssp             HH------CSSTTCCCSSSSSSSHHHHHHHHHHTS
T ss_pred             cC------cHHHHHHHHHHHHhcccHHHHHHHHhC
Confidence            43      124464556 99999999999999874

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.74  E-value=1.3e-08  Score=88.57  Aligned_cols=123  Identities=18%  Similarity=0.127  Sum_probs=86.0

Q ss_pred             cccccCcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcc-eeEEEEeCCCCC
Q 040110           77 TEEICDALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD-CHAWVRVSNFYN  155 (348)
Q Consensus        77 ~~~~~~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~-~~~wv~~~~~~~  155 (348)
                      |.+.++.++||+.++   +.|.++|...-.......+.+.|+|++|+|||++|+.+++.  ....+. ..+++.......
T Consensus        11 ~~y~p~~l~~Re~ei---~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~--l~~~~~~~~~~~~~~~~~~   85 (276)
T d1fnna2          11 PSYVPKRLPHREQQL---QQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWEL--YKDKTTARFVYINGFIYRN   85 (276)
T ss_dssp             TTCCCSCCTTCHHHH---HHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHH--HTTSCCCEEEEEETTTCCS
T ss_pred             CCCCCCCCCCHHHHH---HHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHH--HhcccCCcEEEecchhhhh
Confidence            344555899999999   99999885210012344567889999999999999999988  444333 345777777788


Q ss_pred             HHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcC--CeEEEEEeCCCCh
Q 040110          156 FKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTN--KKYFTVLDDVWIE  207 (348)
Q Consensus       156 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~--kr~LlVLDdv~~~  207 (348)
                      .......+...++....   ........+...+.+.+..  ...++++|++++.
T Consensus        86 ~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~  136 (276)
T d1fnna2          86 FTAIIGEIARSLNIPFP---RRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL  136 (276)
T ss_dssp             HHHHHHHHHHHTTCCCC---SSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS
T ss_pred             hhhhhhhhHHhhhhhhh---hhccchhHHHHHHHHHHhhcccccccchhHHHHh
Confidence            88899999988876642   2344556666666666533  5677778877653

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.38  E-value=1.3e-07  Score=82.09  Aligned_cols=41  Identities=15%  Similarity=0.165  Sum_probs=35.1

Q ss_pred             CcccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           82 DALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        82 ~~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.||||++++   ++|.+..          .+++.|+|++|+|||+|++++.+.
T Consensus        12 ~~f~GR~~el---~~l~~~~----------~~~i~i~G~~G~GKTsLl~~~~~~   52 (283)
T d2fnaa2          12 KDFFDREKEI---EKLKGLR----------APITLVLGLRRTGKSSIIKIGINE   52 (283)
T ss_dssp             GGSCCCHHHH---HHHHHTC----------SSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             hhCCChHHHH---HHHHhcc----------CCEEEEEcCCCCcHHHHHHHHHHH
Confidence            4999999999   9988732          246889999999999999999876

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.34  E-value=6e-07  Score=78.12  Aligned_cols=122  Identities=19%  Similarity=0.084  Sum_probs=80.8

Q ss_pred             ccccCcccccccccccHHHHHhhcCCC--CCC-CCCCcEEEEEECCCCCcHHHHHHHHhcCccc----cCCcceeEEEEe
Q 040110           78 EEICDALLGLQSKIINLRNLHQRLPPS--SGL-GQPTHSVVAILDSRGFDKTAFAAEIYNNNFV----KFYFDCHAWVRV  150 (348)
Q Consensus        78 ~~~~~~~vGr~~~~~~~~~l~~~L~~~--~~~-~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~----~~~F~~~~wv~~  150 (348)
                      .+.++.++||+.+.   ++|.++|...  .+. ......++.++|++|+|||++++.+++....    ........++..
T Consensus        12 ~~~P~~~~~Re~e~---~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~   88 (287)
T d1w5sa2          12 NYIPPELRVRRGEA---EALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNA   88 (287)
T ss_dssp             TCCCSSCSSSCHHH---HHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEG
T ss_pred             ccCCCCCCCHHHHH---HHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeecc
Confidence            34445899999999   9998876311  011 1222334567899999999999999877211    111124557777


Q ss_pred             CCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhc--CCeEEEEEeCCC
Q 040110          151 SNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT--NKKYFTVLDDVW  205 (348)
Q Consensus       151 ~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVLDdv~  205 (348)
                      ............+...++....   ............+.....  +...++++|.+.
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d  142 (287)
T d1w5sa2          89 FNAPNLYTILSLIVRQTGYPIQ---VRGAPALDILKALVDNLYVENHYLLVILDEFQ  142 (287)
T ss_dssp             GGCCSHHHHHHHHHHHHTCCCC---CTTCCHHHHHHHHHHHHHHHTCEEEEEEESTH
T ss_pred             ccccchhhHHHHHhhhcccccc---cccchHHHHHHHHHHHHHhccCccccceeEEE
Confidence            7777888888888888876542   234566666666666653  457788888774

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.23  E-value=5.5e-07  Score=76.39  Aligned_cols=123  Identities=11%  Similarity=0.079  Sum_probs=70.2

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDD  162 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  162 (348)
                      ++||.+..+   +.|.+++.    .  .....+.++|++|+||||+|+.+++............-.+.+...+.......
T Consensus        15 divg~~~~~---~~L~~~i~----~--~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~   85 (227)
T d1sxjc2          15 EVYGQNEVI---TTVRKFVD----E--GKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQ   85 (227)
T ss_dssp             GCCSCHHHH---HHHHHHHH----T--TCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTH
T ss_pred             HccCcHHHH---HHHHHHHH----c--CCCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecc
Confidence            799999999   99999987    2  22323668999999999999999876221111112222333333333222111


Q ss_pred             HHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCCh
Q 040110          163 IMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPH  233 (348)
Q Consensus       163 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~  233 (348)
                      +.......                   ....+++-++|+|++...  .....+...+......++++++|...
T Consensus        86 ~~~~~~~~-------------------~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~  139 (227)
T d1sxjc2          86 IKDFASTR-------------------QIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYA  139 (227)
T ss_dssp             HHHHHHBC-------------------CSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             hhhccccc-------------------cccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcH
Confidence            11111110                   011234568889999754  34455555554445577777777653

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.22  E-value=4.1e-07  Score=77.52  Aligned_cols=132  Identities=11%  Similarity=0.014  Sum_probs=72.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCC-cceeEEEEeCCCCCHHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFY-FDCHAWVRVSNFYNFKRILD  161 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~-F~~~~wv~~~~~~~~~~~~~  161 (348)
                      +++|.+...   +.|.+++..      .....+.++|++|+||||+|+.+++....... ......+..+.......+..
T Consensus        13 diig~~~~~---~~l~~~i~~------~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (237)
T d1sxjd2          13 EVTAQDHAV---TVLKKTLKS------ANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVRE   83 (237)
T ss_dssp             TCCSCCTTH---HHHHHHTTC------TTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTT
T ss_pred             HccCcHHHH---HHHHHHHHc------CCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHH
Confidence            789999999   999999982      22333679999999999999999876211111 11233344444444443333


Q ss_pred             HHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCC
Q 040110          162 DIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGP  232 (348)
Q Consensus       162 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~  232 (348)
                      .+-.......     .....    ..+......+.-++|+|++...  .....+...+......+++++||.+
T Consensus        84 ~~~~~~~~~~-----~~~~~----~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~  147 (237)
T d1sxjd2          84 KVKNFARLTV-----SKPSK----HDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNY  147 (237)
T ss_dssp             HHHHHHHSCC-----CCCCT----THHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             HHHHHhhhhh-----hhhhH----HHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccc
Confidence            2222211110     00111    1122233344557899998753  3444444444333445666666554

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.16  E-value=6.2e-06  Score=71.62  Aligned_cols=129  Identities=16%  Similarity=0.169  Sum_probs=78.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc---cccCCc-ceeEEE-EeCCCCCHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN---FVKFYF-DCHAWV-RVSNFYNFK  157 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~---~~~~~F-~~~~wv-~~~~~~~~~  157 (348)
                      .++||++++   +++++.|.      .....-+.++|.+|+|||+++..++...   .+.... ...+|. +++.-    
T Consensus        19 ~~igRd~Ei---~~l~~iL~------r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~l----   85 (268)
T d1r6bx2          19 PLIGREKEL---ERAIQVLC------RRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSL----   85 (268)
T ss_dssp             CCCSCHHHH---HHHHHHHT------SSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC------
T ss_pred             cccChHHHH---HHHHHHHh------cCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechH----
Confidence            489999999   99999998      2222345589999999999998887652   122222 244553 22211    


Q ss_pred             HHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHh-cCCeEEEEEeCCCCh----------hhHHHHHhhCCCCCCCcEE
Q 040110          158 RILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL-TNKKYFTVLDDVWIE----------KIWDDLREALPDNQIGSRA  226 (348)
Q Consensus       158 ~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~LlVLDdv~~~----------~~~~~l~~~l~~~~~gskI  226 (348)
                               +.+     .....+.++....+.+.+ +.++.+|++|++...          .+...+..+....+ .-++
T Consensus        86 ---------iag-----~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg-~i~v  150 (268)
T d1r6bx2          86 ---------LAG-----TKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSG-KIRV  150 (268)
T ss_dssp             ----------CC-----CCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSC-CCEE
T ss_pred             ---------hcc-----CccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHhCC-CCeE
Confidence                     011     111234555555555555 446799999997542          23445555444433 4578


Q ss_pred             EEEeCChhhhhhc
Q 040110          227 LITVGPHNILTSI  239 (348)
Q Consensus       227 lvTTR~~~v~~~~  239 (348)
                      |.||......+.+
T Consensus       151 IgatT~eey~~~~  163 (268)
T d1r6bx2         151 IGSTTYQEFSNIF  163 (268)
T ss_dssp             EEEECHHHHHCCC
T ss_pred             EEeCCHHHHHHHH
Confidence            8888877776653

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.15  E-value=9.1e-07  Score=74.96  Aligned_cols=122  Identities=13%  Similarity=0.053  Sum_probs=70.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCc-c-eeEEEEeCCCCCHHHHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF-D-CHAWVRVSNFYNFKRIL  160 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F-~-~~~wv~~~~~~~~~~~~  160 (348)
                      +++|.+...   +.|.+++.      .....-+.++|++|+||||+|+.+++.  +...+ . ..+-++.+...+...+.
T Consensus        16 d~ig~~~~~---~~L~~~~~------~~~~~~~ll~Gp~G~GKTt~a~~la~~--l~~~~~~~~~~~~n~~~~~~~~~i~   84 (224)
T d1sxjb2          16 DIVGNKETI---DRLQQIAK------DGNMPHMIISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNASDDRGIDVVR   84 (224)
T ss_dssp             GCCSCTHHH---HHHHHHHH------SCCCCCEEEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTTSCCSHHHHH
T ss_pred             HhcCCHHHH---HHHHHHHH------cCCCCeEEEECCCCCCchhhHHHHHHH--HhccccccccccccccccCCceehh
Confidence            799999999   99999998      222333668999999999999998876  22221 1 23334444444444433


Q ss_pred             HHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCCh
Q 040110          161 DDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPH  233 (348)
Q Consensus       161 ~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~  233 (348)
                      ..+.........    .              ...+.-++|+|++...  .....+...+......+++++||.+.
T Consensus        85 ~~~~~~~~~~~~----~--------------~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~  141 (224)
T d1sxjb2          85 NQIKHFAQKKLH----L--------------PPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  141 (224)
T ss_dssp             THHHHHHHBCCC----C--------------CTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             hHHHHHHHhhcc----C--------------CCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCch
Confidence            333222211100    0              0135568889998754  33333433333334456666666553

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.14  E-value=2e-06  Score=73.76  Aligned_cols=45  Identities=11%  Similarity=0.048  Sum_probs=35.7

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+...   +.|.+++..    .. ...-+.++|++|+||||+|+.+++.
T Consensus        12 diig~~~~~---~~L~~~~~~----~~-~~~~lll~Gp~G~GKTt~~~~la~~   56 (252)
T d1sxje2          12 ALSHNEELT---NFLKSLSDQ----PR-DLPHLLLYGPNGTGKKTRCMALLES   56 (252)
T ss_dssp             GCCSCHHHH---HHHHTTTTC----TT-CCCCEEEECSTTSSHHHHHHTHHHH
T ss_pred             HccCcHHHH---HHHHHHHHc----CC-CCCeEEEECCCCCCHHHHHHHHHHh
Confidence            799999999   888888872    22 2223669999999999999998875

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.08  E-value=8.9e-07  Score=75.32  Aligned_cols=44  Identities=14%  Similarity=0.235  Sum_probs=37.5

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+...   +.|..++.      ......+.++|++|+||||+|+.+++.
T Consensus        25 diig~~~~~---~~l~~~i~------~~~~~~lll~Gp~G~GKTtla~~iak~   68 (231)
T d1iqpa2          25 DIVGQEHIV---KRLKHYVK------TGSMPHLLFAGPPGVGKTTAALALARE   68 (231)
T ss_dssp             TCCSCHHHH---HHHHHHHH------HTCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             HccCcHHHH---HHHHHHHH------cCCCCeEEEECCCCCcHHHHHHHHHHH
Confidence            799999999   99999997      233445779999999999999999876

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.06  E-value=9.2e-06  Score=69.37  Aligned_cols=45  Identities=24%  Similarity=0.397  Sum_probs=36.0

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+...   +.|.+++.    .+. -+..+.++|++|+||||+|..+++.
T Consensus        13 dlig~~~~~---~~L~~~i~----~~~-~~~~~Ll~Gp~G~GKtt~a~~~~~~   57 (239)
T d1njfa_          13 DVVGQEHVL---TALANGLS----LGR-IHHAYLFSGTRGVGKTSIARLLAKG   57 (239)
T ss_dssp             GSCSCHHHH---HHHHHHHH----TTC-CCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HccChHHHH---HHHHHHHH----cCC-CCeeEEEECCCCCcHHHHHHHHHHH
Confidence            789999999   99999887    222 2335678999999999999988655

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.92  E-value=5.6e-06  Score=69.61  Aligned_cols=99  Identities=13%  Similarity=0.032  Sum_probs=60.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLT  193 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~  193 (348)
                      .+.|+|++|+|||.|++++++.  .......++++      +..++...+...+...         ...+...    .++
T Consensus        38 ~l~l~G~~G~GKTHLl~A~~~~--~~~~~~~~~~~------~~~~~~~~~~~~~~~~---------~~~~~~~----~~~   96 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLLQAAGNE--AKKRGYRVIYS------SADDFAQAMVEHLKKG---------TINEFRN----MYK   96 (213)
T ss_dssp             SEEEECSSSSSHHHHHHHHHHH--HHHTTCCEEEE------EHHHHHHHHHHHHHHT---------CHHHHHH----HHH
T ss_pred             cEEEECCCCCcHHHHHHHHHHH--hccCccceEEe------chHHHHHHHHHHHHcc---------chhhHHH----HHh
Confidence            3679999999999999999988  44444455666      3445555555555332         1222222    222


Q ss_pred             CCeEEEEEeCCCCh---hhHHHHHhhCCC--CCCCcEEEEEeCChh
Q 040110          194 NKKYFTVLDDVWIE---KIWDDLREALPD--NQIGSRALITVGPHN  234 (348)
Q Consensus       194 ~kr~LlVLDdv~~~---~~~~~l~~~l~~--~~~gskIlvTTR~~~  234 (348)
                       .--+|+|||+...   ..|+...-.+-+  ...|.+||+||+...
T Consensus        97 -~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p  141 (213)
T d1l8qa2          97 -SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHP  141 (213)
T ss_dssp             -TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCG
T ss_pred             -hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcc
Confidence             3568899999743   345442222211  235778999998753

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.76  E-value=2.9e-05  Score=63.76  Aligned_cols=44  Identities=23%  Similarity=0.336  Sum_probs=35.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++||++++   +++.+.|.      .....-+.++|.+|+|||+++..++.+
T Consensus        23 ~~igRd~Ei---~~l~~iL~------r~~k~n~lLvG~pGVGKTalv~~LA~r   66 (195)
T d1jbka_          23 PVIGRDEEI---RRTIQVLQ------RRTKNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CCCSCHHHH---HHHHHHHT------SSSSCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcCcHHHH---HHHHHHHh------ccCCCCeEEEecCCcccHHHHHHHHHH
Confidence            588999999   99999998      222234568999999999999888765

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=97.74  E-value=3e-05  Score=66.91  Aligned_cols=96  Identities=17%  Similarity=0.193  Sum_probs=54.1

Q ss_pred             cccccccccccHHHHH---hhcCCCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCH
Q 040110           83 ALLGLQSKIINLRNLH---QRLPPSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNF  156 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~---~~L~~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  156 (348)
                      +++|.++..   ++|.   .++..+.   .-+...++-+.++|++|+|||++|+.+++.  ...+   .+-++.+.-.+ 
T Consensus        13 Di~Gl~~~k---~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~--~~~~---~~~i~~~~l~~-   83 (256)
T d1lv7a_          13 DVAGCDEAK---EEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE--AKVP---FFTISGSDFVE-   83 (256)
T ss_dssp             GSCSCHHHH---HHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHH--HTCC---EEEECSCSSTT-
T ss_pred             HHhchHHHH---HHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHH--cCCC---EEEEEhHHhhh-
Confidence            678888877   5554   4433111   112234566779999999999999999976  3322   12222221111 


Q ss_pred             HHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcCCeEEEEEeCCC
Q 040110          157 KRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTNKKYFTVLDDVW  205 (348)
Q Consensus       157 ~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVLDdv~  205 (348)
                                        .........+...+...-+..+++|++||++
T Consensus        84 ------------------~~~g~~~~~l~~~f~~A~~~~P~il~iDeiD  114 (256)
T d1lv7a_          84 ------------------MFVGVGASRVRDMFEQAKKAAPCIIFIDEID  114 (256)
T ss_dssp             ------------------SCCCCCHHHHHHHHHHHHTTCSEEEEETTHH
T ss_pred             ------------------cchhHHHHHHHHHHHHHHHcCCEEEEEEChh
Confidence                              0111233344444444445678899999985

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.70  E-value=1.5e-05  Score=68.10  Aligned_cols=68  Identities=13%  Similarity=0.077  Sum_probs=46.6

Q ss_pred             cccccccccccHHHHHhhcCC-----------CCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP-----------SSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVS  151 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~-----------~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~  151 (348)
                      +++|.+..+   ++|.++|..           ....+....+.+.++|++|+||||+|+.+++.  ..   -..++++.+
T Consensus        15 dlig~~~~~---~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~--~~---~~~~~~~~~   86 (253)
T d1sxja2          15 QVCGNKGSV---MKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE--LG---YDILEQNAS   86 (253)
T ss_dssp             GCCSCHHHH---HHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHH--TT---CEEEEECTT
T ss_pred             HhcCCHHHH---HHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHH--HH---hhhhccccc
Confidence            799999999   999888741           01112334557889999999999999999987  22   134556555


Q ss_pred             CCCCHHH
Q 040110          152 NFYNFKR  158 (348)
Q Consensus       152 ~~~~~~~  158 (348)
                      ...+...
T Consensus        87 ~~~~~~~   93 (253)
T d1sxja2          87 DVRSKTL   93 (253)
T ss_dssp             SCCCHHH
T ss_pred             cchhhHH
Confidence            5544433

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.69  E-value=3.1e-05  Score=70.75  Aligned_cols=125  Identities=12%  Similarity=0.120  Sum_probs=63.9

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcCc---cc-cCCcceeEE-EEeCCCCCHH
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNNN---FV-KFYFDCHAW-VRVSNFYNFK  157 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~---~~-~~~F~~~~w-v~~~~~~~~~  157 (348)
                      .++||+.++   +++++.|.    ....+.  +.++|.+|||||+++..++.+.   .+ ..-.+..+| ++++.=    
T Consensus        23 ~~~gr~~ei---~~~~~~L~----r~~k~n--~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l----   89 (387)
T d1qvra2          23 PVIGRDEEI---RRVIQILL----RRTKNN--PVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSL----   89 (387)
T ss_dssp             CCCSCHHHH---HHHHHHHH----CSSCCC--CEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-------
T ss_pred             CCcCcHHHH---HHHHHHHh----cCCCCC--CeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhh----
Confidence            488999999   99999997    222222  3468999999999886655431   12 222344555 333211    


Q ss_pred             HHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHh-cC-CeEEEEEeCCCCh---------hhH-HHHHhhCCCCCCCcE
Q 040110          158 RILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYL-TN-KKYFTVLDDVWIE---------KIW-DDLREALPDNQIGSR  225 (348)
Q Consensus       158 ~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L-~~-kr~LlVLDdv~~~---------~~~-~~l~~~l~~~~~gsk  225 (348)
                            +....        .....++....+...+ .. .+++|++|++...         .+. +-|+++|..+.  -+
T Consensus        90 ------~ag~~--------~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg~--~~  153 (387)
T d1qvra2          90 ------LAGAK--------YRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALARGE--LR  153 (387)
T ss_dssp             ----------------------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHHTTC--CC
T ss_pred             ------hcccC--------cchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhCCC--cc
Confidence                  11110        1123444444444444 33 4799999999643         122 33344443332  35


Q ss_pred             EEEEeCChhhh
Q 040110          226 ALITVGPHNIL  236 (348)
Q Consensus       226 IlvTTR~~~v~  236 (348)
                      +|-+|-.....
T Consensus       154 ~I~~tT~~ey~  164 (387)
T d1qvra2         154 LIGATTLDEYR  164 (387)
T ss_dssp             EEEEECHHHHH
T ss_pred             eeeecCHHHHH
Confidence            66655555543

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=97.66  E-value=5.5e-05  Score=64.79  Aligned_cols=50  Identities=14%  Similarity=0.102  Sum_probs=33.1

Q ss_pred             cccccccccccHHHHHhhcCC----CCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----SSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|..+.+   +.+++-+..    .......+.+-|.++|++|+|||++|+++++.
T Consensus        10 ~~i~~~~~i---~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~   63 (246)
T d1d2na_          10 GIIKWGDPV---TRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEE   63 (246)
T ss_dssp             CCCCCSHHH---HHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCcCcCHHH---HHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhc
Confidence            677777666   555443320    00112234566789999999999999999987

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.62  E-value=5.4e-05  Score=65.27  Aligned_cols=50  Identities=14%  Similarity=0.248  Sum_probs=35.3

Q ss_pred             cccccccccccHHHHHhhc----CCC---CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRL----PPS---SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L----~~~---~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+..+   ++|.+.+    ..+   ...+-...+-+.++|++|+|||++|+++++.
T Consensus         5 dv~G~~~~k---~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~   61 (258)
T d1e32a2           5 DVGGCRKQL---AQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE   61 (258)
T ss_dssp             GCCSCSHHH---HHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhccHHHHH---HHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHH
Confidence            578888888   7777653    211   0012233455779999999999999999987

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.61  E-value=0.00017  Score=59.92  Aligned_cols=41  Identities=7%  Similarity=0.025  Sum_probs=29.5

Q ss_pred             CCeEEEEEeCCCCh--hhHHHHHhhCCCCCCCcEEEEEeCChh
Q 040110          194 NKKYFTVLDDVWIE--KIWDDLREALPDNQIGSRALITVGPHN  234 (348)
Q Consensus       194 ~kr~LlVLDdv~~~--~~~~~l~~~l~~~~~gskIlvTTR~~~  234 (348)
                      +++-++|+|+++..  ...+.++..+-.....+.+|.||++.+
T Consensus       107 ~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~  149 (207)
T d1a5ta2         107 GGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPE  149 (207)
T ss_dssp             SSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGG
T ss_pred             CccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChh
Confidence            45679999999753  556777777766566788777777654

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=97.61  E-value=1.6e-05  Score=68.24  Aligned_cols=53  Identities=19%  Similarity=0.266  Sum_probs=34.3

Q ss_pred             cccccccccccHHHHHhhcCCCC---CCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSS---GLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~---~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.++.+..+++++..+..++   ..+...++-+.++|++|+|||+||+.+++.
T Consensus        10 di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~   65 (247)
T d1ixza_          10 DVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   65 (247)
T ss_dssp             GCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHH
Confidence            78898888722233333332110   012233456789999999999999999986

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=97.41  E-value=5.8e-05  Score=63.96  Aligned_cols=49  Identities=16%  Similarity=0.236  Sum_probs=35.8

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++||.+..+   ++|..++.... .....++-+.++|++|+||||+|+.+++.
T Consensus        10 divGq~~~~---~~L~~~i~~~~-~~~~~~~~~Ll~GPpG~GKTtla~~la~~   58 (239)
T d1ixsb2          10 EYIGQERLK---QKLRVYLEAAK-ARKEPLEHLLLFGPPGLGKTTLAHVIAHE   58 (239)
T ss_dssp             GSCSCHHHH---HHHHHHHHHHT-TSSSCCCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             HhCCHHHHH---HHHHHHHHHHH-hcCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            789999888   77777764110 11223344668999999999999999877

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=97.31  E-value=0.00052  Score=56.88  Aligned_cols=92  Identities=10%  Similarity=-0.049  Sum_probs=54.0

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCH--HHHHHHHHHHhCCCCCccccCCCCHHHHHH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNF--KRILDDIMKSLMPTSSWLKIMGKDYKSEKT  186 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~--~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~  186 (348)
                      ...+.|+.++|+.|+||||.+-.++.... ++  ...+.+.....+..  .+-++...+.++.+... .....+......
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~-~~--g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~-~~~~~d~~~~l~   81 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFE-QQ--GKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIA-QHTGADSASVIF   81 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHH-TT--TCCEEEECCCTTCHHHHHHHHHHHHHTTCCEEC-CSTTCCHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHH-HC--CCcEEEEecccccccchhhhhhhhhhcCCcccc-cccCCCHHHHHH
Confidence            45678999999999999997777776532 22  23455444555554  56677888888776332 223344444444


Q ss_pred             HHHHHhcC-CeEEEEEeCC
Q 040110          187 ILRDYLTN-KKYFTVLDDV  204 (348)
Q Consensus       187 ~l~~~L~~-kr~LlVLDdv  204 (348)
                      ......+. ..=++++|=.
T Consensus        82 ~~~~~a~~~~~d~ilIDTa  100 (211)
T d2qy9a2          82 DAIQAAKARNIDVLIADTA  100 (211)
T ss_dssp             HHHHHHHHTTCSEEEECCC
T ss_pred             HHHHHHHHcCCCEEEeccC
Confidence            33333222 2235555654

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.29  E-value=0.0006  Score=56.03  Aligned_cols=106  Identities=8%  Similarity=-0.046  Sum_probs=61.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCcc--ccCCcceeEEEEeC-CCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNF--VKFYFDCHAWVRVS-NFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTI  187 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~--~~~~F~~~~wv~~~-~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  187 (348)
                      ....+.++|.+|+||||+|..+.+...  ...|- ..+++... ....+.++ +++.+.+.....               
T Consensus        14 ~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~-D~~~i~~~~~~I~Id~I-R~i~~~~~~~~~---------------   76 (198)
T d2gnoa2          14 EGISILINGEDLSYPREVSLELPEYVEKFPPKAS-DVLEIDPEGENIGIDDI-RTIKDFLNYSPE---------------   76 (198)
T ss_dssp             SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTT-TEEEECCSSSCBCHHHH-HHHHHHHTSCCS---------------
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHhccccCCC-CEEEEeCCcCCCCHHHH-HHHHHHHhhCcc---------------
Confidence            466788999999999999999887521  11222 34444322 22233333 234444433211               


Q ss_pred             HHHHhcCCeEEEEEeCCCC--hhhHHHHHhhCCCCCCCcEEEEEeCCh-hhhhh
Q 040110          188 LRDYLTNKKYFTVLDDVWI--EKIWDDLREALPDNQIGSRALITVGPH-NILTS  238 (348)
Q Consensus       188 l~~~L~~kr~LlVLDdv~~--~~~~~~l~~~l~~~~~gskIlvTTR~~-~v~~~  238 (348)
                           .+++-++|+|++..  ....+.++..+-.-..++.++++|.+. .+...
T Consensus        77 -----~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~T  125 (198)
T d2gnoa2          77 -----LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPT  125 (198)
T ss_dssp             -----SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHH
T ss_pred             -----cCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHH
Confidence                 24556888999975  366777777765444566666665554 44443

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.27  E-value=0.00045  Score=55.44  Aligned_cols=27  Identities=26%  Similarity=0.341  Sum_probs=23.3

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.+.+|.++|++|+||||+|+.+...
T Consensus        11 ~~~p~liil~G~pGsGKST~a~~l~~~   37 (172)
T d1yj5a2          11 SPNPEVVVAVGFPGAGKSTFIQEHLVS   37 (172)
T ss_dssp             CSSCCEEEEECCTTSSHHHHHHHHTGG
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHh
Confidence            456779999999999999999988654

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.21  E-value=9e-05  Score=64.10  Aligned_cols=50  Identities=24%  Similarity=0.276  Sum_probs=36.4

Q ss_pred             cccccccccccHHHHHhhcCC----C---CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPP----S---SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~----~---~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++|.+..+   ++|.+.+..    +   ...+-...+-+.++|++|+|||+||+++++.
T Consensus         8 di~G~~~~k---~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~   64 (265)
T d1r7ra3           8 DIGGLEDVK---RELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE   64 (265)
T ss_dssp             SCSSSSCCC---CHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHH
T ss_pred             HhcCHHHHH---HHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHH
Confidence            678999998   777766521    0   0112334556779999999999999999988

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.17  E-value=9.5e-05  Score=59.22  Aligned_cols=24  Identities=21%  Similarity=0.246  Sum_probs=22.2

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|+|.|++|+||||||+.+...
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~   30 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAV   30 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            578999999999999999999876

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=97.11  E-value=7.2e-05  Score=58.61  Aligned_cols=22  Identities=9%  Similarity=0.249  Sum_probs=20.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.++|++|+||||+|+.++..
T Consensus         4 ~I~l~G~~GsGKSTvak~La~~   25 (169)
T d1kaga_           4 NIFLVGPMGAGKSTIGRQLAQQ   25 (169)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5778899999999999999987

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=97.04  E-value=0.00015  Score=57.41  Aligned_cols=23  Identities=17%  Similarity=0.229  Sum_probs=21.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +|++|+|..|+|||||+.++.+.
T Consensus         3 Pvi~itG~~GSGKTTL~~~L~~~   25 (170)
T d1np6a_           3 PLLAFAAWSGTGKTTLLKKLIPA   25 (170)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHH
Confidence            58999999999999999999876

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=97.02  E-value=0.00017  Score=56.04  Aligned_cols=23  Identities=17%  Similarity=0.372  Sum_probs=20.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|.|.|++|+||||||+.+...
T Consensus         3 klIii~G~pGsGKTTla~~L~~~   25 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAK   25 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            47889999999999999988654

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=97.02  E-value=6.8e-05  Score=63.40  Aligned_cols=49  Identities=18%  Similarity=0.264  Sum_probs=36.3

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++||.+..+   +.|..++.... ......+-+.++|++|+||||+|+.+++.
T Consensus        10 divGqe~~~---~~l~~~i~~~~-~~~~~~~~~L~~GPpGtGKT~lA~~la~~   58 (238)
T d1in4a2          10 EFIGQENVK---KKLSLALEAAK-MRGEVLDHVLLAGPPGLGKTTLAHIIASE   58 (238)
T ss_dssp             GCCSCHHHH---HHHHHHHHHHH-HHTCCCCCEEEESSTTSSHHHHHHHHHHH
T ss_pred             HcCChHHHH---HHHHHHHHHHH-hcCCCCCeEEEECCCCCcHHHHHHHHHhc
Confidence            799999999   88888874110 01122334668999999999999999887

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=97.01  E-value=0.00017  Score=56.96  Aligned_cols=23  Identities=13%  Similarity=0.205  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|.|.|++|+||||+|+.+...
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~   25 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQ   25 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57889999999999999999865

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.01  E-value=0.00023  Score=56.59  Aligned_cols=24  Identities=13%  Similarity=0.004  Sum_probs=21.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+|.|+|++|+||||+|+.+...
T Consensus         6 g~~I~l~G~~GsGKTTia~~La~~   29 (183)
T d1m8pa3           6 GFTIFLTGYMNSGKDAIARALQVT   29 (183)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            357889999999999999999877

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.98  E-value=0.00023  Score=57.66  Aligned_cols=27  Identities=19%  Similarity=0.147  Sum_probs=24.0

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+.-+|+|.|.+|+||||||+++...
T Consensus        19 ~~~~~iIgI~G~~GSGKSTla~~L~~~   45 (198)
T d1rz3a_          19 TAGRLVLGIDGLSRSGKTTLANQLSQT   45 (198)
T ss_dssp             CSSSEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            456779999999999999999999876

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.97  E-value=0.0016  Score=55.97  Aligned_cols=91  Identities=16%  Similarity=0.081  Sum_probs=63.7

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTI  187 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~  187 (348)
                      -+.-+++-|.|.+|+||||||.+++.......  ..++|+.....++.+.     +++++.+.+.. -......++..+.
T Consensus        57 ~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g--~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~  129 (269)
T d1mo6a1          57 LPRGRVIEIYGPESSGKTTVALHAVANAQAAG--GVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEI  129 (269)
T ss_dssp             BCSSSEEEEECSSSSSHHHHHHHHHHHHHHTT--CEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHH
T ss_pred             cccceeEEEecCCCcHHHHHHHHHHHHHhcCC--CEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHH
Confidence            34556889999999999999988876632222  3688999888888653     56667654321 2234567777777


Q ss_pred             HHHHhcC-CeEEEEEeCCCC
Q 040110          188 LRDYLTN-KKYFTVLDDVWI  206 (348)
Q Consensus       188 l~~~L~~-kr~LlVLDdv~~  206 (348)
                      +...++. +.-|+|+|.+-.
T Consensus       130 ~~~l~~~~~~~liIiDSi~a  149 (269)
T d1mo6a1         130 ADMLIRSGALDIVVIDSVAA  149 (269)
T ss_dssp             HHHHHHTTCEEEEEEECSTT
T ss_pred             HHHHHhcCCCCEEEEecccc
Confidence            6666654 578999999854

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.95  E-value=0.001  Score=56.51  Aligned_cols=45  Identities=16%  Similarity=0.149  Sum_probs=30.5

Q ss_pred             ccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           84 LLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        84 ~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |||....+   +++.+.+...   ...+.. |.|.|..|+|||++|+.++..
T Consensus         2 ~v~~S~~~---~~~~~~~~~~---a~~~~p-vlI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2           2 YVFESPKM---KEILEKIKKI---SCAECP-VLITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             CCCCSHHH---HHHHHHHHHH---TTCCSC-EEEECSTTSSHHHHHHHHHHH
T ss_pred             eEecCHHH---HHHHHHHHHH---hCCCCC-EEEECCCCcCHHHHHHHHHHh
Confidence            67766666   6666655411   112222 578999999999999999764

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=96.88  E-value=0.0011  Score=56.91  Aligned_cols=88  Identities=13%  Similarity=0.022  Sum_probs=60.2

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTILR  189 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l~  189 (348)
                      .-+++-|+|.+|+||||||.+++...  ...=..++|++....++..     .++.++.+.+.. -....+.++..+.+.
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~~--q~~g~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~  125 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAAA--QREGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  125 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHH--HHTTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHH--HcCCCEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHHH
Confidence            44588899999999999999988773  2222357899888888864     456677653321 122345666777666


Q ss_pred             HHhcC-CeEEEEEeCCC
Q 040110          190 DYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       190 ~~L~~-kr~LlVLDdv~  205 (348)
                      ...+. ..-|+|+|.+-
T Consensus       126 ~l~~~~~~~liViDSi~  142 (263)
T d1u94a1         126 ALARSGAVDVIVVDSVA  142 (263)
T ss_dssp             HHHHHTCCSEEEEECGG
T ss_pred             HHHhcCCCCEEEEECcc
Confidence            66643 45689999984

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.83  E-value=0.00041  Score=54.86  Aligned_cols=26  Identities=23%  Similarity=0.415  Sum_probs=23.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+++.|.|++|+||||+|+.+...
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~   29 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQ   29 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            45678889999999999999999876

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=96.83  E-value=0.00026  Score=55.99  Aligned_cols=22  Identities=18%  Similarity=0.350  Sum_probs=19.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|++|+||||+|+.+...
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~   27 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASK   27 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4669999999999999999876

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.80  E-value=0.00024  Score=56.63  Aligned_cols=23  Identities=17%  Similarity=0.157  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.|.|+|++|+|||||+++++..
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~   24 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH
Confidence            45889999999999999999866

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=96.79  E-value=0.0018  Score=55.58  Aligned_cols=89  Identities=15%  Similarity=0.079  Sum_probs=63.7

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWL-KIMGKDYKSEKTIL  188 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~l  188 (348)
                      +.-+++-|+|.+|+|||+||.+++.......  ..++|+.....++..     +++.++.+.+.. -....+.++..+.+
T Consensus        55 p~g~itei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~  127 (268)
T d1xp8a1          55 PRGRITEIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIM  127 (268)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHH
T ss_pred             cCceEEEEecCCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHH
Confidence            3456889999999999999998876632222  357899988888874     677787764431 22345677777777


Q ss_pred             HHHhcC-CeEEEEEeCCC
Q 040110          189 RDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       189 ~~~L~~-kr~LlVLDdv~  205 (348)
                      ...++. ..-|+|+|.+-
T Consensus       128 ~~l~~~~~~~liIiDSi~  145 (268)
T d1xp8a1         128 ELLVRSGAIDVVVVDSVA  145 (268)
T ss_dssp             HHHHTTTCCSEEEEECTT
T ss_pred             HHHHhcCCCcEEEEeccc
Confidence            766654 46799999984

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=96.77  E-value=0.00035  Score=55.34  Aligned_cols=24  Identities=4%  Similarity=0.061  Sum_probs=21.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.|.|++|+||||+|+.+.+.
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~   26 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSV   26 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999887

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.76  E-value=0.00022  Score=57.80  Aligned_cols=24  Identities=17%  Similarity=0.122  Sum_probs=21.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -.+|.++|++|+||||+|+.+...
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~   42 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEY   42 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            357789999999999999999876

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=96.73  E-value=0.00059  Score=58.19  Aligned_cols=27  Identities=15%  Similarity=0.258  Sum_probs=23.5

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.++.|.++|++|+||||||+.+++.
T Consensus        29 ~~~P~~ilL~GpPGtGKT~la~~la~~   55 (273)
T d1gvnb_          29 VESPTAFLLGGQPGSGKTSLRSAIFEE   55 (273)
T ss_dssp             CSSCEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            345677889999999999999999987

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.72  E-value=0.00041  Score=56.83  Aligned_cols=24  Identities=8%  Similarity=0.147  Sum_probs=21.5

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.+|.++|.+|+||||+|+++++.
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~   25 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRY   25 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999999876

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=96.72  E-value=0.00048  Score=60.91  Aligned_cols=50  Identities=16%  Similarity=0.203  Sum_probs=35.1

Q ss_pred             cccccccccccHHHHHhhcCCC---CCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLPPS---SGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~---~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+...   -...+....++.++|+.|+|||.+|+.+++.
T Consensus        24 ~v~GQ~~ai---~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~   76 (315)
T d1qvra3          24 RVVGQDEAI---RAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT   76 (315)
T ss_dssp             HSCSCHHHH---HHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHH
T ss_pred             eEeCHHHHH---HHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHH
Confidence            578888777   6665544210   0122344557889999999999999998876

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=96.72  E-value=0.0037  Score=51.47  Aligned_cols=59  Identities=12%  Similarity=-0.087  Sum_probs=38.6

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC--CHHHHHHHHHHHhCCCC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY--NFKRILDDIMKSLMPTS  171 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~--~~~~~~~~i~~~l~~~~  171 (348)
                      ...+|+.++|+.|+||||.+..++..... +.. .+..+++ ..+  ...+.++...+.++.+.
T Consensus         8 ~~~~vi~lvGp~GvGKTTTiaKLA~~~~~-~g~-kV~lit~-Dt~R~gA~eQL~~~a~~l~v~~   68 (207)
T d1ls1a2           8 KDRNLWFLVGLQGSGKTTTAAKLALYYKG-KGR-RPLLVAA-DTQRPAAREQLRLLGEKVGVPV   68 (207)
T ss_dssp             CSSEEEEEECCTTTTHHHHHHHHHHHHHH-TTC-CEEEEEC-CSSCHHHHHHHHHHHHHHTCCE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHH-CCC-cEEEEec-ccccchHHHHHHHHHHhcCCcc
Confidence            34678999999999999977777665332 222 3444444 333  34466777788877753

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.72  E-value=0.0005  Score=56.01  Aligned_cols=27  Identities=19%  Similarity=0.262  Sum_probs=24.3

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+..++|.|.|++|+||||+|+.++.+
T Consensus         5 ~~~~~iI~i~GppGSGKsT~a~~La~~   31 (196)
T d1ukza_           5 PDQVSVIFVLGGPGAGKGTQCEKLVKD   31 (196)
T ss_dssp             TTTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            456889999999999999999999876

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=96.72  E-value=0.00047  Score=56.06  Aligned_cols=26  Identities=27%  Similarity=0.318  Sum_probs=23.3

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+.+|.|+|++|+||||+|+.++++
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~~   29 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            45679999999999999999999876

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=96.70  E-value=0.00049  Score=54.48  Aligned_cols=25  Identities=24%  Similarity=0.211  Sum_probs=21.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|.|.|++|+||||+|+.++..
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            3446789999999999999999876

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.69  E-value=0.00051  Score=54.40  Aligned_cols=24  Identities=17%  Similarity=0.236  Sum_probs=21.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -++|.|.|++|+||||+|+.+.+.
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~   27 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANL   27 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999876

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.68  E-value=0.0022  Score=52.99  Aligned_cols=60  Identities=12%  Similarity=0.024  Sum_probs=34.0

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPT  170 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~  170 (348)
                      ...+.|+.++|+.|+||||.+-.++..... +.. .+..+++... ..-.+-++..++.++.+
T Consensus         9 ~k~p~vi~lvGptGvGKTTTiAKLA~~~~~-~g~-kV~lit~Dt~R~ga~eQL~~~a~~l~v~   69 (211)
T d1j8yf2           9 DKIPYVIMLVGVQGTGKATTAGKLAYFYKK-KGF-KVGLVGADVYRPAALEQLQQLGQQIGVP   69 (211)
T ss_dssp             SSSSEEEEEECSCCC----HHHHHHHHHHH-TTC-CEEEEECCCSSHHHHHHHHHHHHHHTCC
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHH-CCC-ceEEEEeeccccchhHHHHHhccccCcc
Confidence            457889999999999999976666655332 222 3455554322 23345566666666665

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.67  E-value=0.0033  Score=51.92  Aligned_cols=92  Identities=13%  Similarity=0.008  Sum_probs=51.8

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC-CCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF-YNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTI  187 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  187 (348)
                      ...+.|+.++|+.|+||||.+-.++.... .+. ..+..+++... ....+-++..++.++.+... ..+..+.......
T Consensus         8 ~~~p~vi~lvGptGvGKTTTiAKLAa~~~-~~~-~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~~-~~~~~d~~~~~~~   84 (213)
T d1vmaa2           8 PEPPFVIMVVGVNGTGKTTSCGKLAKMFV-DEG-KSVVLAAADTFRAAAIEQLKIWGERVGATVIS-HSEGADPAAVAFD   84 (213)
T ss_dssp             SSSCEEEEEECCTTSSHHHHHHHHHHHHH-HTT-CCEEEEEECTTCHHHHHHHHHHHHHHTCEEEC-CSTTCCHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHH-HCC-CceEEEeecccccchhHHHHHHhhhcCccccc-cCCCCcHHHHHHH
Confidence            45678999999999999997666665532 222 24555555432 23456677777777765322 2223344443333


Q ss_pred             HHHH--hcCCeEEEEEeCC
Q 040110          188 LRDY--LTNKKYFTVLDDV  204 (348)
Q Consensus       188 l~~~--L~~kr~LlVLDdv  204 (348)
                      ....  .++.. ++++|=.
T Consensus        85 ~~~~~~~~~~d-~ilIDTa  102 (213)
T d1vmaa2          85 AVAHALARNKD-VVIIDTA  102 (213)
T ss_dssp             HHHHHHHTTCS-EEEEEEC
T ss_pred             HHHHHHHcCCC-EEEEecc
Confidence            2222  23333 5555654

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.65  E-value=0.00035  Score=55.47  Aligned_cols=21  Identities=10%  Similarity=0.216  Sum_probs=18.4

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|++|+||||+++.++..
T Consensus         4 IvliG~~G~GKSTig~~La~~   24 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKA   24 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            345699999999999999977

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.63  E-value=0.00048  Score=54.54  Aligned_cols=24  Identities=13%  Similarity=0.102  Sum_probs=21.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++++|+|..|+|||||+.++...
T Consensus         1 Mkii~I~G~~gSGKTTli~~l~~~   24 (165)
T d1xjca_           1 MNVWQVVGYKHSGKTTLMEKWVAA   24 (165)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHH
Confidence            368999999999999999999876

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.63  E-value=0.00048  Score=54.98  Aligned_cols=23  Identities=22%  Similarity=0.253  Sum_probs=21.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|+|.|+.|+||||+++.+...
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~   24 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDN   24 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999876

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.59  E-value=0.0024  Score=53.41  Aligned_cols=91  Identities=11%  Similarity=0.006  Sum_probs=57.0

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCc-----------cccCC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSW-----------LKIMG  178 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----------~~~~~  178 (348)
                      +.-.++.|+|.+|+|||+||.+++.+  .......++|++....  ...+. ..+..++.....           .....
T Consensus        24 ~~gsl~li~G~pGsGKT~l~~qia~~--~~~~~~~~~~is~e~~--~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (242)
T d1tf7a2          24 FKDSIILATGATGTGKTLLVSRFVEN--ACANKERAILFAYEES--RAQLL-RNAYSWGMDFEEMERQNLLKIVCAYPES   98 (242)
T ss_dssp             ESSCEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEESSSC--HHHHH-HHHHTTSCCHHHHHHTTSEEECCCCGGG
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHH--HHHhccccceeeccCC--HHHHH-HHHHHcCCChHHHhhcCceEEEEeecch
Confidence            34568889999999999999999888  5555667788876433  33322 223333332111           01223


Q ss_pred             CCHHHHHHHHHHHhcC-CeEEEEEeCCC
Q 040110          179 KDYKSEKTILRDYLTN-KKYFTVLDDVW  205 (348)
Q Consensus       179 ~~~~~~~~~l~~~L~~-kr~LlVLDdv~  205 (348)
                      ....+....+...+.. +.-++|+|++.
T Consensus        99 ~~~~~~~~~i~~~i~~~~~~~vviDs~~  126 (242)
T d1tf7a2          99 AGLEDHLQIIKSEINDFKPARIAIDSLS  126 (242)
T ss_dssp             SCHHHHHHHHHHHHHTTCCSEEEEECHH
T ss_pred             hhHHHHHHHHHHHHHhcCCceeeeecch
Confidence            4566667777766644 56788889864

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=96.53  E-value=0.0029  Score=52.08  Aligned_cols=59  Identities=17%  Similarity=0.012  Sum_probs=41.0

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCC-CCCHHHHHHHHHHHhCCC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSN-FYNFKRILDDIMKSLMPT  170 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~-~~~~~~~~~~i~~~l~~~  170 (348)
                      +..+++.++|+.|+||||.+-.++.....+ . ..+..++... .....+-++..++.++.+
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~~~~~-g-~kV~lit~Dt~R~gA~eQL~~~a~~l~i~   63 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRYYQNL-G-KKVMFCAGDTFRAAGGTQLSEWGKRLSIP   63 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHHHHTT-T-CCEEEECCCCSSTTHHHHHHHHHHHHTCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC-C-CcEEEEEeccccccchhhHhhcccccCce
Confidence            355789999999999999777777653322 2 2455665543 356667788888888775

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=96.53  E-value=0.00042  Score=54.85  Aligned_cols=21  Identities=14%  Similarity=0.306  Sum_probs=19.3

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|+||+|+||||+++.++..
T Consensus         3 I~liG~~GsGKsTi~k~La~~   23 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKD   23 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            667899999999999999988

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.44  E-value=0.0007  Score=53.86  Aligned_cols=21  Identities=24%  Similarity=0.390  Sum_probs=19.4

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |+|+|++|+|||||++.+...
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~   23 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHhc
Confidence            789999999999999999875

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=96.34  E-value=0.00073  Score=53.76  Aligned_cols=21  Identities=19%  Similarity=0.363  Sum_probs=19.1

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|++|+||||+|+.+++.
T Consensus         5 Iil~G~~GsGKSTia~~LA~~   25 (170)
T d1e6ca_           5 IFMVGARGCGMTTVGRELARA   25 (170)
T ss_dssp             EEEESCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            557899999999999999877

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.33  E-value=0.0011  Score=54.73  Aligned_cols=24  Identities=13%  Similarity=0.158  Sum_probs=21.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +-+|+|.|..|+||||||+.+...
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~   25 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQL   25 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998776

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.33  E-value=0.0011  Score=53.81  Aligned_cols=24  Identities=29%  Similarity=0.285  Sum_probs=21.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.+|.|.|++|+||||+|+.+++.
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~   24 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEK   24 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999999999876

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=96.29  E-value=0.0067  Score=52.97  Aligned_cols=83  Identities=14%  Similarity=0.151  Sum_probs=49.1

Q ss_pred             CCCCcEEEEEECCCCCcHHHHHHHHhcCccccCCcc--eeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHH
Q 040110          108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFD--CHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEK  185 (348)
Q Consensus       108 ~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~  185 (348)
                      ....+-+|+|.|.+|+||||+|+.+...  ....+.  .+.-++...-+-..+.+..  +.+.... . .+...|.+.+.
T Consensus        76 ~~k~P~iIGIaG~sgSGKSTla~~L~~l--L~~~~~~~~v~~Is~D~F~~~~~~l~~--~~~~~~~-g-~Pes~D~~~L~  149 (308)
T d1sq5a_          76 GQRIPYIISIAGSVAVGKSTTARVLQAL--LSRWPEHRRVELITTDGFLHPNQVLKE--RGLMKKK-G-FPESYDMHRLV  149 (308)
T ss_dssp             -CCCCEEEEEEECTTSSHHHHHHHHHHH--HTTSTTCCCEEEEEGGGGBCCHHHHHH--HTCTTCT-T-SGGGBCHHHHH
T ss_pred             CCCCCEEEEEeCCCCCCCcHHHHHHHHH--HhhhcCCCceEEEeeeeeECCchHHHH--hcCCccC-C-chHhhhHHHHH
Confidence            3456789999999999999999998876  443332  2333444333322222221  1221111 1 33456888888


Q ss_pred             HHHHHHhcCCe
Q 040110          186 TILRDYLTNKK  196 (348)
Q Consensus       186 ~~l~~~L~~kr  196 (348)
                      ..|....+++.
T Consensus       150 ~~L~~lk~g~~  160 (308)
T d1sq5a_         150 KFVSDLKSGVP  160 (308)
T ss_dssp             HHHHHHTTTCS
T ss_pred             HHHHHHHcCCC
Confidence            88888776653

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=96.27  E-value=0.0011  Score=53.02  Aligned_cols=24  Identities=13%  Similarity=0.151  Sum_probs=21.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.|.|++|+||||+++.+...
T Consensus         1 mkiivi~G~~GsGKTT~~~~La~~   24 (194)
T d1nksa_           1 MKIGIVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            368889999999999999999876

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=96.26  E-value=0.00088  Score=55.25  Aligned_cols=41  Identities=12%  Similarity=0.203  Sum_probs=30.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKS  166 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~  166 (348)
                      +||+|.|++|+||||+|+.+.++  ..  |   .++      +..+++++++..
T Consensus         4 piI~I~GppGSGKgT~ak~La~~--~g--l---~~i------StGdLlR~~a~~   44 (225)
T d1ckea_           4 PVITIDGPSGAGKGTLCKAMAEA--LQ--W---HLL------DSGAIYRVLALA   44 (225)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH--HT--C---EEE------EHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--hC--C---cEE------CHHHHHHHHHHH
Confidence            48999999999999999999988  21  1   112      456777776653

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=96.17  E-value=0.0016  Score=52.62  Aligned_cols=25  Identities=24%  Similarity=0.263  Sum_probs=21.2

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++++| |.|++|+||||+|+.++..
T Consensus         2 ~~~rii-l~G~pGSGKsT~a~~La~~   26 (190)
T d1ak2a1           2 KGVRAV-LLGPPGAGKGTQAPKLAKN   26 (190)
T ss_dssp             CCCEEE-EECCTTSSHHHHHHHHHHH
T ss_pred             CccEEE-EECCCCCCHHHHHHHHHHH
Confidence            356666 7899999999999999876

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=95.99  E-value=0.0022  Score=54.99  Aligned_cols=35  Identities=23%  Similarity=0.387  Sum_probs=27.5

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+.+.+.      ..+.++|.+.|-||+||||+|..+...
T Consensus         9 ~~~~~~~~------~~~~~iii~sGKGGVGKTT~a~nLA~~   43 (279)
T d1ihua2           9 SALVDDIA------RNEHGLIMLMGKGGVGKTTMAAAIAVR   43 (279)
T ss_dssp             HHHHHHHH------TTSCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHhh------cCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            55666665      567899999999999999987766544

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=95.98  E-value=0.002  Score=52.00  Aligned_cols=24  Identities=21%  Similarity=0.252  Sum_probs=20.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      .+-+|+|+|+.|+||||+|..+-.
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~~   25 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLRS   25 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467899999999999999998743

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=95.96  E-value=0.0018  Score=55.34  Aligned_cols=25  Identities=20%  Similarity=0.232  Sum_probs=21.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .+.|+|+|-||+||||+|..+....
T Consensus         1 mr~Iai~gKGGvGKTT~a~nLA~~L   25 (269)
T d1cp2a_           1 MRQVAIYGKGGIGKSTTTQNLTSGL   25 (269)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCcCCHHHHHHHHHHHH
Confidence            3689999999999999998887663

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=95.90  E-value=0.0016  Score=53.71  Aligned_cols=42  Identities=12%  Similarity=0.052  Sum_probs=30.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLM  168 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~  168 (348)
                      +|+|-|++|+||||+|+.+..+..+       .++      +...+++.++....
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~lg~-------~~i------stGdl~R~~a~~~~   46 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDFGF-------TYL------DTGAMYRAATYMAL   46 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHHCC-------EEE------EHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCC-------cEE------CHHHHHHHHHHHHH
Confidence            6889999999999999999887211       122      45667776665443

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.82  E-value=0.0021  Score=51.22  Aligned_cols=21  Identities=19%  Similarity=0.240  Sum_probs=19.2

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|.|++|+||||+|+.++..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAA   23 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            669999999999999999876

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=95.82  E-value=0.0018  Score=52.19  Aligned_cols=22  Identities=18%  Similarity=0.033  Sum_probs=19.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|++|+||||+|+.+++.
T Consensus         5 ~I~i~GppGsGKsT~a~~La~~   26 (189)
T d1zaka1           5 KVMISGAPASGKGTQCELIKTK   26 (189)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4669999999999999999877

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=95.81  E-value=0.0022  Score=51.98  Aligned_cols=25  Identities=12%  Similarity=0.248  Sum_probs=22.3

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++|.|.|++|+||||+|+.+...
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~   31 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQK   31 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999999999999876

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=95.75  E-value=0.0031  Score=51.06  Aligned_cols=22  Identities=23%  Similarity=0.320  Sum_probs=19.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|.|.|++|+||||+|+.++.+
T Consensus         8 rIiliG~PGSGKtT~a~~La~~   29 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKH   29 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4557899999999999999876

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=95.74  E-value=0.0032  Score=51.89  Aligned_cols=26  Identities=12%  Similarity=0.106  Sum_probs=22.7

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....+|-+.|++|+||||||+.+...
T Consensus        22 ~kg~vIwltGlsGsGKTTia~~L~~~   47 (208)
T d1m7ga_          22 QRGLTIWLTGLSASGKSTLAVELEHQ   47 (208)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35568999999999999999999866

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.70  E-value=0.0032  Score=50.31  Aligned_cols=24  Identities=17%  Similarity=0.275  Sum_probs=20.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++++ |.|++|+||||+|+.++..
T Consensus         2 ~mrIv-l~G~pGSGKtT~a~~La~~   25 (180)
T d1akya1           2 SIRMV-LIGPPGAGKGTQAPNLQER   25 (180)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHHH
T ss_pred             ceEEE-EECCCCCCHHHHHHHHHHH
Confidence            34544 7799999999999999876

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.68  E-value=0.0026  Score=50.79  Aligned_cols=21  Identities=24%  Similarity=0.305  Sum_probs=19.3

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|.|++|+||||+|+.++..
T Consensus         3 I~i~G~pGsGKsT~a~~La~~   23 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAEK   23 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            668899999999999999877

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.67  E-value=0.0046  Score=53.05  Aligned_cols=92  Identities=12%  Similarity=0.165  Sum_probs=55.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCC----c----cccCCCCHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSS----W----LKIMGKDYKSE  184 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~----~----~~~~~~~~~~~  184 (348)
                      .++|.|..|+|||+|+..+.++... .+=+.++++-+++.. .+.++.+++.+.--....    .    ....+......
T Consensus        70 r~~If~~~g~GKt~l~~~i~~~~~~-~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~tvvv~~~s~~~~~~r  148 (276)
T d2jdid3          70 KIGLFGGAGVGKTVLIMELINNVAK-AHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGAR  148 (276)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHTT-TCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSCHHHH
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHHHh-hCCCeEEEEEeccChHHHHHHHHHHHhcCccccccccceEEEEEECCCCCHHHH
Confidence            3889999999999999999876211 222467788777664 566777777664211100    0    01112222211


Q ss_pred             ------HHHHHHHhc---CCeEEEEEeCCCC
Q 040110          185 ------KTILRDYLT---NKKYFTVLDDVWI  206 (348)
Q Consensus       185 ------~~~l~~~L~---~kr~LlVLDdv~~  206 (348)
                            .-.+.++++   ++++|+++||+-.
T Consensus       149 ~~~~~~a~~iAEyf~~~~G~~VLv~~Dsltr  179 (276)
T d2jdid3         149 ARVALTGLTVAEYFRDQEGQDVLLFIDNIFR  179 (276)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSCEEEEEECTHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCeEEEEEcchhH
Confidence                  113445553   6899999999944

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=95.65  E-value=0.0022  Score=51.30  Aligned_cols=21  Identities=19%  Similarity=0.279  Sum_probs=19.4

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|.|++|+||||+|+.++.+
T Consensus         3 I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEK   23 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            668999999999999999987

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=95.64  E-value=0.002  Score=56.56  Aligned_cols=24  Identities=17%  Similarity=0.257  Sum_probs=20.8

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+-+.++|++|+|||.||+++++.
T Consensus        49 ~~~iLl~GPpG~GKT~lAkalA~~   72 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIARRLAKL   72 (309)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHhhc
Confidence            345668999999999999999976

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.63  E-value=0.0032  Score=50.75  Aligned_cols=21  Identities=14%  Similarity=0.403  Sum_probs=19.4

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|+|++|+|||||++.+.+.
T Consensus         4 Ivl~GpsG~GK~tl~~~L~~~   24 (186)
T d1gkya_           4 IVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            679999999999999999876

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.61  E-value=0.0033  Score=50.74  Aligned_cols=27  Identities=19%  Similarity=0.115  Sum_probs=23.2

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+.+|+|-|.-|+||||+++.+.+.
T Consensus         6 ~~kp~~I~ieG~~GsGKTTl~~~L~~~   32 (197)
T d2vp4a1           6 GTQPFTVLIEGNIGSGKTTYLNHFEKY   32 (197)
T ss_dssp             TCCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            345668999999999999999998765

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=95.59  E-value=0.012  Score=51.50  Aligned_cols=24  Identities=13%  Similarity=0.138  Sum_probs=20.6

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++.++|++|+|||.||+.++..
T Consensus       123 ~g~~l~~G~pG~GKT~la~ala~~  146 (321)
T d1w44a_         123 SGMVIVTGKGNSGKTPLVHALGEA  146 (321)
T ss_dssp             SEEEEEECSSSSCHHHHHHHHHHH
T ss_pred             CceEEEECCCCccHHHHHHHHHHH
Confidence            345666899999999999999987

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=95.59  E-value=0.0033  Score=55.54  Aligned_cols=37  Identities=11%  Similarity=0.013  Sum_probs=28.1

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++++.+.    ....+..+|+|+|++|+|||||...+...
T Consensus        41 ~~ll~~~~----~~~~~~~~IgitG~pGaGKSTLi~~l~~~   77 (327)
T d2p67a1          41 TQLLDAIM----PYCGNTLRLGVTGTPGAGKSTFLEAFGML   77 (327)
T ss_dssp             HHHHHHHG----GGCSCSEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             HHHHHHhh----hccCCceEEEeeCCCCCCHHHHHHHHHHH
Confidence            34555554    22456789999999999999999988765

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.56  E-value=0.0031  Score=50.45  Aligned_cols=23  Identities=13%  Similarity=0.183  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++|.|+|++|+|||||++.+...
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~   25 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRER   25 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            36789999999999999998765

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=95.49  E-value=0.0041  Score=54.86  Aligned_cols=37  Identities=16%  Similarity=0.084  Sum_probs=28.1

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++++.+.    ....+..+|+|.|++|+|||||..++...
T Consensus        38 ~~~~~~~~----~~~~~~~~igitG~pGaGKSTli~~l~~~   74 (323)
T d2qm8a1          38 RDLIDAVL----PQTGRAIRVGITGVPGVGKSTTIDALGSL   74 (323)
T ss_dssp             HHHHHHHG----GGCCCSEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHHHHhh----hccCCceEEeeeCCCCCCHHHHHHHHHHH
Confidence            44555554    23456789999999999999999888754

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.48  E-value=0.0024  Score=51.77  Aligned_cols=21  Identities=14%  Similarity=0.403  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|+|++|+|||||++.+...
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~~   23 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQE   23 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            669999999999999998766

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.48  E-value=0.015  Score=50.09  Aligned_cols=84  Identities=14%  Similarity=0.146  Sum_probs=48.3

Q ss_pred             CCCCcEEEEEECCCCCcHHHHHHHHhcCccccCC--cc-eeEEEEeCCCCCHHHHHHHHHHHhCCC----CCccccCCCC
Q 040110          108 GQPTHSVVAILDSRGFDKTAFAAEIYNNNFVKFY--FD-CHAWVRVSNFYNFKRILDDIMKSLMPT----SSWLKIMGKD  180 (348)
Q Consensus       108 ~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~--F~-~~~wv~~~~~~~~~~~~~~i~~~l~~~----~~~~~~~~~~  180 (348)
                      +...+-+|+|.|..|+||||||..+...  +...  +. .+.-+++..-+-..+-...+.+....+    ... .+...|
T Consensus        23 ~~~~P~iIGi~G~qGSGKSTl~~~l~~~--L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~~~~~pl~~~RG-~PgThD   99 (286)
T d1odfa_          23 GNKCPLFIFFSGPQGSGKSFTSIQIYNH--LMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRG-LPGTHD   99 (286)
T ss_dssp             TCCSCEEEEEECCTTSSHHHHHHHHHHH--HHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCGGGSSSC-STTSBC
T ss_pred             CCCCCEEEEeECCCCCCHHHHHHHHHHH--HHHHhCCCcceEeeccCCCCCCHHHHHHHhhhccccccceecC-CCcchh
Confidence            3456779999999999999999988766  3222  22 344555554433233233444433111    000 234457


Q ss_pred             HHHHHHHHHHHhcC
Q 040110          181 YKSEKTILRDYLTN  194 (348)
Q Consensus       181 ~~~~~~~l~~~L~~  194 (348)
                      ...+.+.+....++
T Consensus       100 ~~ll~~~l~~l~~~  113 (286)
T d1odfa_         100 MKLLQEVLNTIFNN  113 (286)
T ss_dssp             HHHHHHHHHHHTC-
T ss_pred             HHHHHHHHHHHHhh
Confidence            77777777776654

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.41  E-value=0.0033  Score=50.44  Aligned_cols=23  Identities=9%  Similarity=0.330  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.|.|+|++|+|||||++.+...
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~   26 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITK   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHh
Confidence            46888999999999999998865

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=95.38  E-value=0.0042  Score=53.56  Aligned_cols=24  Identities=17%  Similarity=0.221  Sum_probs=20.5

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.|+|.|-||+||||+|..+...
T Consensus         2 Mr~IaisgKGGVGKTT~a~NLA~~   25 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNLVAA   25 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHH
Confidence            567889999999999988887655

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=95.29  E-value=0.0055  Score=53.79  Aligned_cols=50  Identities=14%  Similarity=0.237  Sum_probs=36.4

Q ss_pred             cccccccccccHHHHHhhcC---CCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           83 ALLGLQSKIINLRNLHQRLP---PSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~---~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++|.+..+   +.+...+.   ..-...+....++.++|+.|+|||.||+.++.-
T Consensus        23 ~viGQ~~a~---~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~   75 (315)
T d1r6bx3          23 LVFGQDKAI---EALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA   75 (315)
T ss_dssp             TSCSCHHHH---HHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eecChHHHH---HHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhh
Confidence            688988888   77766552   000122445567889999999999999999876

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=95.29  E-value=0.0067  Score=52.03  Aligned_cols=25  Identities=12%  Similarity=0.094  Sum_probs=20.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .++++.+.|-||+||||+|..++..
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~~   31 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAIR   31 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCcChHHHHHHHHHHH
Confidence            4668888999999999988776554

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.21  E-value=0.0035  Score=49.90  Aligned_cols=21  Identities=19%  Similarity=0.126  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|.|++|+||||+|+.++.+
T Consensus         3 I~i~G~pGSGKsT~~~~La~~   23 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEK   23 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            568999999999999999876

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=95.21  E-value=0.018  Score=49.24  Aligned_cols=98  Identities=12%  Similarity=0.128  Sum_probs=53.2

Q ss_pred             EEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCC-CHHHHHHHHHHHhCCCCCc--cccCCC------CHHHHH
Q 040110          115 VAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFY-NFKRILDDIMKSLMPTSSW--LKIMGK------DYKSEK  185 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~--~~~~~~------~~~~~~  185 (348)
                      ++|+|..|+|||+|+..+...  ...+-..++++-++... ...++..++...=......  ....+.      -.....
T Consensus        70 ~~Ifg~~g~GKt~l~~~~~~~--~~~~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~~~a  147 (276)
T d1fx0a3          70 ELIIGDRQTGKTAVATDTILN--QQGQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPYTG  147 (276)
T ss_dssp             CBEEESSSSSHHHHHHHHHHT--CCTTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHHHH
T ss_pred             EeeccCCCCChHHHHHHHHhh--hcccCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHHHHHH
Confidence            678999999999999876555  34444567777776654 3334444443321110000  001111      111222


Q ss_pred             HHHHHHh--cCCeEEEEEeCCCCh-hhHHHHH
Q 040110          186 TILRDYL--TNKKYFTVLDDVWIE-KIWDDLR  214 (348)
Q Consensus       186 ~~l~~~L--~~kr~LlVLDdv~~~-~~~~~l~  214 (348)
                      -.+.+++  .+++.|+++||+-.. ..+.++.
T Consensus       148 ~tiAEyfrd~G~~Vlll~Dsltr~A~A~rEis  179 (276)
T d1fx0a3         148 AALAEYFMYRERHTLIIYDDLSKQAQAYRQMS  179 (276)
T ss_dssp             HHHHHHHHHTTCEEEEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCceeEEeeccHHHHHHHHHHH
Confidence            3344444  468999999999543 3344443

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=95.09  E-value=0.0075  Score=51.97  Aligned_cols=36  Identities=14%  Similarity=0.063  Sum_probs=27.2

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -++++.|.+-    ..+- .++|.|..|+|||+|+..+.+.
T Consensus        31 ~r~ID~l~Pi----grGQ-r~~I~g~~g~GKT~l~~~i~~~   66 (289)
T d1xpua3          31 ARVLDLASPI----GRGQ-RGLIVAPPKAGKTMLLQNIAQS   66 (289)
T ss_dssp             HHHHHHHSCC----BTTC-EEEEEECSSSSHHHHHHHHHHH
T ss_pred             ceeeeecccc----cCCC-eeeEeCCCCCCHHHHHHHHHHH
Confidence            4677777732    2222 4789999999999999999876

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.83  E-value=0.007  Score=50.49  Aligned_cols=50  Identities=16%  Similarity=0.146  Sum_probs=32.6

Q ss_pred             HHHHHHhcCCeEEEEEeCCCCh-------hhHHHHHhhCCCCCCCcEEEEEeCChhhhh
Q 040110          186 TILRDYLTNKKYFTVLDDVWIE-------KIWDDLREALPDNQIGSRALITVGPHNILT  237 (348)
Q Consensus       186 ~~l~~~L~~kr~LlVLDdv~~~-------~~~~~l~~~l~~~~~gskIlvTTR~~~v~~  237 (348)
                      -.|.+.|..++-+|++|..-..       ..++.+... . ...|..||++|.+..++.
T Consensus       154 vaIAraL~~~P~lLllDEPTs~LD~~~~~~i~~~l~~l-~-~~~g~tii~vTHd~~~a~  210 (230)
T d1l2ta_         154 VAIARALANNPPIILADQPTGALDSKTGEKIMQLLKKL-N-EEDGKTVVVVTHDINVAR  210 (230)
T ss_dssp             HHHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHH-H-HTTCCEEEEECSCHHHHT
T ss_pred             HHHHhhhhcCCCEEEecCCccccCHHHHHHHHHHHHHH-H-HhhCCEEEEECCCHHHHH
Confidence            3467777888899999997543       223333322 1 234677888888888774

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=94.76  E-value=0.008  Score=50.48  Aligned_cols=124  Identities=14%  Similarity=0.054  Sum_probs=65.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCcccc---------------CC--c----ceeEEEEeC----CCCCHH----------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVK---------------FY--F----DCHAWVRVS----NFYNFK----------  157 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~---------------~~--F----~~~~wv~~~----~~~~~~----------  157 (348)
                      .+++|+|+.|+|||||++.++.-..-.               ..  +    ..+.+|.-.    ...++.          
T Consensus        30 e~~~liG~sGaGKSTll~~i~gl~~p~sG~I~~~g~~i~~~~~~~~~~~~~r~ig~v~Q~~~L~~~ltV~eni~~~~~~~  109 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLR  109 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSSCCSEEEEEETTEEEEEGGGTEECCGGGSSEEEECSCCCCCTTSCHHHHHHHHHHHT
T ss_pred             CEEEEECCCCChHHHHHHHHhcCCCCCCCEEEECCEEecccchhhhcccccccceecccchhhcchhhhhHhhhhhHHHc
Confidence            389999999999999999997542210               00  0    112232111    111221          


Q ss_pred             --------HHHHHHHHHhCCCCCcc-ccCCCCHHHH-HHHHHHHhcCCeEEEEEeCCCCh-------hhHHHHHhhCCCC
Q 040110          158 --------RILDDIMKSLMPTSSWL-KIMGKDYKSE-KTILRDYLTNKKYFTVLDDVWIE-------KIWDDLREALPDN  220 (348)
Q Consensus       158 --------~~~~~i~~~l~~~~~~~-~~~~~~~~~~-~~~l~~~L~~kr~LlVLDdv~~~-------~~~~~l~~~l~~~  220 (348)
                              +-..++++.++...... ....-+-.+. .-.|.+.|..++-+|+||.--..       .-|+.+....  .
T Consensus       110 ~~~~~e~~~~v~~~l~~~~l~~~~~~~p~~LSGGqkQRv~IAraL~~~P~iLllDEPt~~LD~~~~~~i~~~l~~l~--~  187 (240)
T d1g2912         110 KVPRQEIDQRVREVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQ--R  187 (240)
T ss_dssp             TCCHHHHHHHHHHHHHHHTCGGGTTCCGGGSCHHHHHHHHHHHHHHTCCSEEEEECTTTTSCHHHHHHHHHHHHHHH--H
T ss_pred             CCCHHHHHHHHHHHHHHcCChhHhcCChhhCCHHHHHHHHHHHHHhcCCCEEEecCCCcccCHHHHHHHHHHHHHHH--h
Confidence                    22445555555432110 1112233332 33467778888999999987543       2223232211  1


Q ss_pred             CCCcEEEEEeCChhhhhh
Q 040110          221 QIGSRALITVGPHNILTS  238 (348)
Q Consensus       221 ~~gskIlvTTR~~~v~~~  238 (348)
                      ..|..||++|.+-..+..
T Consensus       188 ~~g~tvi~vTHd~~~~~~  205 (240)
T d1g2912         188 QLGVTTIYVTHDQVEAMT  205 (240)
T ss_dssp             HHTCEEEEEESCHHHHHH
T ss_pred             ccCCEEEEEcCCHHHHHH
Confidence            126778999988776654

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.71  E-value=0.017  Score=47.57  Aligned_cols=47  Identities=6%  Similarity=0.071  Sum_probs=32.6

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCc----ceeEEEEeCCCCCH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYF----DCHAWVRVSNFYNF  156 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F----~~~~wv~~~~~~~~  156 (348)
                      +.-+++-|.|.+|+||||||.++.........+    ...+|+.....++.
T Consensus        32 ~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~   82 (251)
T d1szpa2          32 ETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRP   82 (251)
T ss_dssp             ESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCG
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHH
Confidence            345588899999999999999987653222222    35777776666553

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=94.69  E-value=0.0072  Score=50.76  Aligned_cols=124  Identities=9%  Similarity=0.072  Sum_probs=66.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccC---Ccc-----------------eeEEEEeCC----CC--------------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKF---YFD-----------------CHAWVRVSN----FY--------------  154 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~---~F~-----------------~~~wv~~~~----~~--------------  154 (348)
                      .+++|+|+.|+|||||++.++.-.+...   .|+                 .+.+|.-..    ..              
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~Gl~~p~sG~I~~~g~~i~~~~~~~~~~~rr~ig~VfQ~~~l~~~~tv~eni~~~l~~~~  111 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLIRCVNLLERPTEGSVLVDGQELTTLSESELTKARRQIGMIFQHFNLLSSRTVFGNVALPLELDN  111 (240)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTTSSCCSEEEEEETTEEECTTCHHHHHHHHHHEEECCSSCCCCTTSBHHHHHHHHHHTTT
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCccccCCceEEcCeEeeeCChhhhhhhhccccccccccccCCCccHHHHHHHHHHHcC
Confidence            4899999999999999999865422110   000                 011221000    00              


Q ss_pred             ----CHHHHHHHHHHHhCCCCCcc-ccCCCCHHHHH-HHHHHHhcCCeEEEEEeCCCCh-------hhHHHHHhhCCCCC
Q 040110          155 ----NFKRILDDIMKSLMPTSSWL-KIMGKDYKSEK-TILRDYLTNKKYFTVLDDVWIE-------KIWDDLREALPDNQ  221 (348)
Q Consensus       155 ----~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~-~~l~~~L~~kr~LlVLDdv~~~-------~~~~~l~~~l~~~~  221 (348)
                          ...+...++++.++...... .....+-.+.+ -.|.+.|..++-+|++|.--..       ..++.+.. +. ..
T Consensus       112 ~~~~~~~~~v~~~L~~vgL~~~~~~~~~~LSGG~~QRvaiAraL~~~P~lLllDEPt~~LD~~~~~~i~~~l~~-l~-~~  189 (240)
T d3dhwc1         112 TPKDEVKRRVTELLSLVGLGDKHDSYPSNLSGGQKQRVAIARALASNPKVLLCDEATSALDPATTRSILELLKD-IN-RR  189 (240)
T ss_dssp             CCTTHHHHHHHHHHHHHSTTTTTSSCBSCCCHHHHHHHHHHHHHHTCCSEEEEESGGGSSCHHHHHHHHHHHHH-HH-HH
T ss_pred             CCHHHHHHHHHHHHHHcCCchhhhCChhhCCHHHHHHHHHhhhhccCCCeEEeccccccCCHHHhhHHHHHHHH-HH-hc
Confidence                12233456666665542210 12223333333 3466777888999999986432       22222222 11 12


Q ss_pred             CCcEEEEEeCChhhhhh
Q 040110          222 IGSRALITVGPHNILTS  238 (348)
Q Consensus       222 ~gskIlvTTR~~~v~~~  238 (348)
                      .|..||++|.+-..+..
T Consensus       190 ~g~tvi~vTHdl~~~~~  206 (240)
T d3dhwc1         190 LGLTILLITHEMDVVKR  206 (240)
T ss_dssp             HCCEEEEEBSCHHHHHH
T ss_pred             cCCEEEEEcCCHHHHHH
Confidence            26779999999877765

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=94.69  E-value=0.0081  Score=49.80  Aligned_cols=22  Identities=23%  Similarity=0.353  Sum_probs=20.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ||+|.|+.|+|||||..++.++
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~   23 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRY   23 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Confidence            7899999999999999998754

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.69  E-value=0.0068  Score=49.50  Aligned_cols=23  Identities=26%  Similarity=0.332  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        28 ei~~l~G~NGsGKSTLl~~i~gl   50 (200)
T d1sgwa_          28 NVVNFHGPNGIGKTTLLKTISTY   50 (200)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCChHHHHHHHHhcc
Confidence            37899999999999999999865

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=94.69  E-value=0.0081  Score=48.33  Aligned_cols=27  Identities=15%  Similarity=0.262  Sum_probs=23.4

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++.+.|+|+|.+|+|||||...+.+.
T Consensus        20 ~~~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          20 EGGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CSCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHhcCC
Confidence            456668999999999999999999864

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.68  E-value=0.0087  Score=49.95  Aligned_cols=124  Identities=10%  Similarity=0.056  Sum_probs=59.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCcccc---------------CCcceeEEE----------EeCCC------------CC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVK---------------FYFDCHAWV----------RVSNF------------YN  155 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~---------------~~F~~~~wv----------~~~~~------------~~  155 (348)
                      .+++|+|+.|+|||||.+.++.-.+..               ..-..+.+|          ++-.+            ..
T Consensus        27 ei~~liGpsGsGKSTLl~~i~Gl~~p~sG~I~i~g~~i~~~~~~~r~ig~v~Q~~~l~~~~tv~eni~~~~~~~~~~~~~  106 (232)
T d2awna2          27 EFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEV  106 (232)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSCCSEEEEEESSSCCTTSCGGGTCEEEECSSCCC---------------------CH
T ss_pred             CEEEEECCCCChHHHHHHHHhcCCCCCCCEEEECCEECCCCchhhceeeeeccccccccchhHHHHHHHHHHHcCCCHHH
Confidence            489999999999999999986432110               000011111          11111            01


Q ss_pred             HHHHHHHHHHHhCCCCCcc-ccCCCCHH-HHHHHHHHHhcCCeEEEEEeCCCCh-------hhHHHHHhhCCCCCCCcEE
Q 040110          156 FKRILDDIMKSLMPTSSWL-KIMGKDYK-SEKTILRDYLTNKKYFTVLDDVWIE-------KIWDDLREALPDNQIGSRA  226 (348)
Q Consensus       156 ~~~~~~~i~~~l~~~~~~~-~~~~~~~~-~~~~~l~~~L~~kr~LlVLDdv~~~-------~~~~~l~~~l~~~~~gskI  226 (348)
                      ..+-..++++.++...... ....-+-. ...-.|.+.|-.++-+|+||..-+.       .-++.+....  ...|..|
T Consensus       107 ~~~~v~~~l~~~~l~~~~~~~~~~LSGGqkQRvaiAraL~~~P~illlDEPts~LD~~~~~~i~~~l~~l~--~~~g~ti  184 (232)
T d2awna2         107 INQRVNQVAEVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH--KRLGRTM  184 (232)
T ss_dssp             HHHHHHHHHHHC---------------------CHHHHHHTCCSEEEEESTTTTSCHHHHHHHHHHHHHHH--HHSCCEE
T ss_pred             HHHHHHHHHHhCCChhhhhCChhhCCHHHHHHHHHHHHHhcCCCEEEEcCCCCCCCHHHHHHHHHHHHHHH--HhcCCEE
Confidence            2233456666665542210 00111111 1122355666778889999997543       2233333221  1236778


Q ss_pred             EEEeCChhhhhh
Q 040110          227 LITVGPHNILTS  238 (348)
Q Consensus       227 lvTTR~~~v~~~  238 (348)
                      |++|-+-..+..
T Consensus       185 i~vTHd~~~a~~  196 (232)
T d2awna2         185 IYVTHDQVEAMT  196 (232)
T ss_dssp             EEEESCHHHHHH
T ss_pred             EEEeCCHHHHHH
Confidence            888888776655

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.65  E-value=0.0083  Score=50.99  Aligned_cols=23  Identities=30%  Similarity=0.362  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.+..-
T Consensus        29 Ei~~iiG~sGsGKSTLl~~i~Gl   51 (258)
T d1b0ua_          29 DVISIIGSSGSGKSTFLRCINFL   51 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHHcC
Confidence            48999999999999999999764

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=94.62  E-value=0.029  Score=46.48  Aligned_cols=50  Identities=18%  Similarity=0.232  Sum_probs=34.5

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCcccc----CCcceeEEEEeCCCCCHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVK----FYFDCHAWVRVSNFYNFKRI  159 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~----~~F~~~~wv~~~~~~~~~~~  159 (348)
                      +.-+++.|.|.+|+||||||.++..+....    ......+|+......+...+
T Consensus        34 p~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (254)
T d1pzna2          34 ETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI   87 (254)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH
T ss_pred             cCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHH
Confidence            455688999999999999999887552111    12345778877777665443

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=94.61  E-value=0.0086  Score=50.35  Aligned_cols=23  Identities=22%  Similarity=0.303  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++|+|..|+|||||++.+..-
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~gl   52 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQRF   52 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc
Confidence            47999999999999999998765

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=94.61  E-value=0.0051  Score=53.12  Aligned_cols=83  Identities=12%  Similarity=0.133  Sum_probs=40.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCC--CCHHHHHHHHHH---HhCCCCCccccCCCCHHHHH
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNF--YNFKRILDDIMK---SLMPTSSWLKIMGKDYKSEK  185 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~--~~~~~~~~~i~~---~l~~~~~~~~~~~~~~~~~~  185 (348)
                      .+.+|+|.|.+|+||||+|+.+.+.... .... .+.++...-  ++-.++-..+..   .-.....-.+.+..+.+.+.
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~-~~v~-~~iI~~Dsfyr~~R~~~~~~~~~~~~~~~~~~~~~~P~A~d~dlL~   80 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRR-EGVK-AVSIEGDAFHRFNRADMKAELDRRYAAGDATFSHFSYEANELKELE   80 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHH-HTCC-EEEEEGGGGBSCCHHHHHHHHHHHHHHTCTTCSTTSGGGBCHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhh-cCCC-eEEEeCCCCCccchhhhhhhhhhhhhhhccCCCCCCcccccHHHHH
Confidence            4569999999999999999987665211 1111 223333322  233322222221   11111100034556777777


Q ss_pred             HHHHHHhcCC
Q 040110          186 TILRDYLTNK  195 (348)
Q Consensus       186 ~~l~~~L~~k  195 (348)
                      ..++.+.+++
T Consensus        81 ~~l~~L~~g~   90 (288)
T d1a7ja_          81 RVFREYGETG   90 (288)
T ss_dssp             HHHHHHHHHS
T ss_pred             HHHHHHHCCC
Confidence            7777766554

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.56  E-value=0.0081  Score=50.91  Aligned_cols=23  Identities=26%  Similarity=0.297  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.+..-
T Consensus        42 e~iaivG~sGsGKSTLl~ll~gl   64 (253)
T d3b60a1          42 KTVALVGRSGSGKSTIASLITRF   64 (253)
T ss_dssp             CEEEEEECTTSSHHHHHHHHTTT
T ss_pred             CEEEEECCCCChHHHHHHHHhcc
Confidence            47999999999999999998654

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=94.52  E-value=0.01  Score=49.78  Aligned_cols=124  Identities=7%  Similarity=0.008  Sum_probs=66.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCcccc------------C--Cc-ceeEEEEeC-------------------CCCC---
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVK------------F--YF-DCHAWVRVS-------------------NFYN---  155 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~------------~--~F-~~~~wv~~~-------------------~~~~---  155 (348)
                      .+++|+|+.|.|||||.+.+..-.+..            .  .. ..+.++.-.                   ...+   
T Consensus        33 e~~~liGpsGaGKSTLl~~i~Gl~~p~sG~I~i~g~~i~~~~~~~r~ig~v~Q~~~l~~~ltv~enl~~~~~~~~~~~~~  112 (239)
T d1v43a3          33 EFLVLLGPSGCGKTTTLRMIAGLEEPTEGRIYFGDRDVTYLPPKDRNISMVFQSYAVWPHMTVYENIAFPLKIKKFPKDE  112 (239)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSCCSEEEEEETTEECTTSCGGGGTEEEEEC------CCCHHHHHHTTCC--CCCHHH
T ss_pred             CEEEEECCCCChHHHHHHHHHcCCCCCCCEEEEcceecccCCcccceEEEEeechhhcccchHHHHHHHHHHHcCCCHHH
Confidence            479999999999999999986542110            0  00 011122110                   0111   


Q ss_pred             HHHHHHHHHHHhCCCCCcc-ccCCC-CHHHHHHHHHHHhcCCeEEEEEeCCCCh-------hhHHHHHhhCCCCCCCcEE
Q 040110          156 FKRILDDIMKSLMPTSSWL-KIMGK-DYKSEKTILRDYLTNKKYFTVLDDVWIE-------KIWDDLREALPDNQIGSRA  226 (348)
Q Consensus       156 ~~~~~~~i~~~l~~~~~~~-~~~~~-~~~~~~~~l~~~L~~kr~LlVLDdv~~~-------~~~~~l~~~l~~~~~gskI  226 (348)
                      ..+...++++.++...... ....- .-....-.|.+.|..++-+|+||.--..       ..|+.+... .. ..|..|
T Consensus       113 ~~~~~~~~l~~~~l~~~~~~~~~~LSGGq~QRvaiAraL~~~P~iLllDEPts~LD~~~~~~i~~ll~~l-~~-~~g~ti  190 (239)
T d1v43a3         113 IDKRVRWAAELLQIEELLNRYPAQLSGGQRQRVAVARAIVVEPDVLLMDEPLSNLDAKLRVAMRAEIKKL-QQ-KLKVTT  190 (239)
T ss_dssp             HHHHHHHHHHHTTCGGGTTSCTTTCCSSCHHHHHHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHH-HH-HHTCEE
T ss_pred             HHHHHHHHHHHcCChhhhcCChhhCCHHHHHHHHHHhhhccCCCceeecCCcccCCHHHHHHHHHHHHHH-HH-hcCCeE
Confidence            1233455666666542210 11111 1122334567777888999999987543       222333221 11 126679


Q ss_pred             EEEeCChhhhhh
Q 040110          227 LITVGPHNILTS  238 (348)
Q Consensus       227 lvTTR~~~v~~~  238 (348)
                      |++|-+-..+..
T Consensus       191 i~vTHd~~~a~~  202 (239)
T d1v43a3         191 IYVTHDQVEAMT  202 (239)
T ss_dssp             EEEESCHHHHHH
T ss_pred             EEEeCCHHHHHH
Confidence            999998877665

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.50  E-value=0.0094  Score=50.45  Aligned_cols=23  Identities=30%  Similarity=0.358  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.+..-
T Consensus        41 e~vaivG~sGsGKSTLl~li~gl   63 (251)
T d1jj7a_          41 EVTALVGPNGSGKSTVAALLQNL   63 (251)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcc
Confidence            47999999999999999998754

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.50  E-value=0.0096  Score=48.73  Aligned_cols=22  Identities=9%  Similarity=0.246  Sum_probs=19.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ++.|+|++|+|||||.+.+...
T Consensus         4 livi~GPSG~GK~tl~~~L~~~   25 (205)
T d1s96a_           4 LYIVSAPSGAGKSSLIQALLKT   25 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhh
Confidence            6779999999999999998865

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=94.49  E-value=0.008  Score=46.14  Aligned_cols=21  Identities=10%  Similarity=0.088  Sum_probs=18.6

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|+|.+|+|||||..++..+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            568999999999999998755

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.47  E-value=0.011  Score=49.23  Aligned_cols=25  Identities=12%  Similarity=0.141  Sum_probs=22.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +++.|+|-|+-|+||||+++.+.+.
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~~   25 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4678999999999999999999876

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=94.45  E-value=0.011  Score=49.79  Aligned_cols=24  Identities=17%  Similarity=0.185  Sum_probs=20.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -..++|+|+.|+|||||++.+..-
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~gl   51 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLERF   51 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            458999999999999999998643

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=94.43  E-value=0.01  Score=45.76  Aligned_cols=22  Identities=23%  Similarity=0.252  Sum_probs=19.7

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |+|+|.+|+|||||..++.+..
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            6799999999999999987764

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.41  E-value=0.012  Score=48.38  Aligned_cols=38  Identities=13%  Similarity=0.012  Sum_probs=26.8

Q ss_pred             cEEEEEE-CCCCCcHHHHHHHHhcCccccCCcceeEEEEeC
Q 040110          112 HSVVAIL-DSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVS  151 (348)
Q Consensus       112 ~~vi~I~-G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~  151 (348)
                      .++|+|+ |-||+||||+|..++...  .+.-..++.+...
T Consensus         1 ~kvIav~s~KGGvGKTtia~nlA~~l--a~~g~~VlliD~D   39 (232)
T d1hyqa_           1 VRTITVASGKGGTGKTTITANLGVAL--AQLGHDVTIVDAD   39 (232)
T ss_dssp             CEEEEEEESSSCSCHHHHHHHHHHHH--HHTTCCEEEEECC
T ss_pred             CEEEEEECCCCCChHHHHHHHHHHHH--HhCCCCEEEEeCC
Confidence            4788888 789999999999887663  2222246666553

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.40  E-value=0.0078  Score=49.89  Aligned_cols=24  Identities=13%  Similarity=0.090  Sum_probs=21.9

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+.|+|-|+-|+||||+|+.+.+.
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~   25 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQL   25 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999998876

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.38  E-value=0.011  Score=49.45  Aligned_cols=121  Identities=13%  Similarity=0.032  Sum_probs=66.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEE----------------eCCC------CC---------------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVR----------------VSNF------YN---------------  155 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~----------------~~~~------~~---------------  155 (348)
                      .+++|+|+.|+|||||.+.++.-...   -.+.+++.                +.+.      .+               
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~~p---~~G~I~~~G~~i~~~~~~~r~ig~v~Q~~~l~~~ltV~enl~~~l~~~~~~  101 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIVKP---DRGEVRLNGADITPLPPERRGIGFVPQDYALFPHLSVYRNIAYGLRNVERV  101 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSCC---SEEEEEETTEECTTSCTTTSCCBCCCSSCCCCTTSCHHHHHHTTCTTSCHH
T ss_pred             EEEEEECCCCChHHHHHHHHHcCCCC---CceEEEECCEECCcCCHHHcCceeeccchhhcccchhhHhhhhhhcccCHH
Confidence            37889999999999999999765211   11122210                0111      11               


Q ss_pred             -HHHHHHHHHHHhCCCCCcc-ccCCCCHHHH-HHHHHHHhcCCeEEEEEeCCCCh-------hhHHHHHhhCCCCCCCcE
Q 040110          156 -FKRILDDIMKSLMPTSSWL-KIMGKDYKSE-KTILRDYLTNKKYFTVLDDVWIE-------KIWDDLREALPDNQIGSR  225 (348)
Q Consensus       156 -~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~-~~~l~~~L~~kr~LlVLDdv~~~-------~~~~~l~~~l~~~~~gsk  225 (348)
                       ..+-..++++.++...... ....-+-.+. .-.|.+.|-.++-+|+||.--..       ..++.+... . ...|..
T Consensus       102 ~~~~~v~~~l~~~gl~~~~~~~~~~LSGG~kQRvaiAral~~~P~illlDEPts~LD~~~~~~i~~~i~~l-~-~~~g~t  179 (240)
T d2onka1         102 ERDRRVREMAEKLGIAHLLDRKPARLSGGERQRVALARALVIQPRLLLLDEPLSAVDLKTKGVLMEELRFV-Q-REFDVP  179 (240)
T ss_dssp             HHHHHHHHHHHTTTCTTTTTCCGGGSCHHHHHHHHHHHHHTTCCSSBEEESTTSSCCHHHHHHHHHHHHHH-H-HHHTCC
T ss_pred             HHHHHHHHHHHhcCcHhhhhCChhhCCHHHHHHHHHHHHHhccCCceEecCccccCCHHHHHHHHHHHHHH-H-HhcCCe
Confidence             1234566677776643220 1122233222 23467777888999999987542       223333222 1 112556


Q ss_pred             EEEEeCChhhhhh
Q 040110          226 ALITVGPHNILTS  238 (348)
Q Consensus       226 IlvTTR~~~v~~~  238 (348)
                      ||++|.+...+..
T Consensus       180 vi~vtHd~~~~~~  192 (240)
T d2onka1         180 ILHVTHDLIEAAM  192 (240)
T ss_dssp             EEEEESCHHHHHH
T ss_pred             EEEEeCCHHHHHH
Confidence            8888888665554

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=94.34  E-value=0.011  Score=48.26  Aligned_cols=20  Identities=25%  Similarity=0.313  Sum_probs=18.3

Q ss_pred             EEEEECCCCCcHHHHHHHHh
Q 040110          114 VVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~  133 (348)
                      +|+|+|+.|+||||+|+.+-
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            89999999999999998764

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=94.25  E-value=0.0081  Score=53.73  Aligned_cols=27  Identities=19%  Similarity=0.119  Sum_probs=23.7

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+..+.+.++|++|+|||++|..+++.
T Consensus       151 ~~~~~~~~~~g~~~~gk~~~~~~~~~~  177 (362)
T d1svma_         151 IPKKRYWLFKGPIDSGKTTLAAALLEL  177 (362)
T ss_dssp             CTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcCeEEEECCCCCCHHHHHHHHHHH
Confidence            445568899999999999999999987

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.22  E-value=0.015  Score=45.18  Aligned_cols=21  Identities=5%  Similarity=0.226  Sum_probs=18.6

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999988765

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=94.22  E-value=0.019  Score=45.01  Aligned_cols=25  Identities=12%  Similarity=0.150  Sum_probs=20.6

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+ -|.++|.+|+|||||..++...
T Consensus        15 ~~~-kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          15 QEV-RILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             SCE-EEEEEESTTSSHHHHHHHHCCS
T ss_pred             CEE-EEEEECCCCCCHHHHHHHHhcC
Confidence            344 4679999999999999998765

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=94.16  E-value=0.013  Score=47.78  Aligned_cols=21  Identities=24%  Similarity=0.229  Sum_probs=18.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHh
Q 040110          113 SVVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~  133 (348)
                      .+|||+|..|+||||+|+.+-
T Consensus         3 ~iIgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            479999999999999998764

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=94.13  E-value=0.01  Score=49.35  Aligned_cols=124  Identities=16%  Similarity=0.065  Sum_probs=64.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccC-----------Ccc----eeEEEEeC----CCCCHH---------------H
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKF-----------YFD----CHAWVRVS----NFYNFK---------------R  158 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~-----------~F~----~~~wv~~~----~~~~~~---------------~  158 (348)
                      .+++|+|+.|+|||||.+.+..-.....           ..+    .+.+|.-.    ...++.               +
T Consensus        27 e~~~liGpsGaGKSTll~~l~Gl~~p~sG~I~~~G~~i~~~~~~~r~ig~v~Q~~~l~~~~tV~enl~~~~~~~~~~~~~  106 (229)
T d3d31a2          27 EYFVILGPTGAGKTLFLELIAGFHVPDSGRILLDGKDVTDLSPEKHDIAFVYQNYSLFPHMNVKKNLEFGMRMKKIKDPK  106 (229)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTSSCCSEEEEEETTEECTTSCHHHHTCEEECTTCCCCTTSCHHHHHHHHHHHHCCCCHH
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCcCCCCCEEEEccEeccccchhHhcceeeccccccCccccHHHHHHHHHhhccccHHH
Confidence            3899999999999999999975421110           000    11111100    011222               2


Q ss_pred             HHHHHHHHhCCCCCcc-ccCCCCHHH-HHHHHHHHhcCCeEEEEEeCCCCh-------hhHHHHHhhCCCCCCCcEEEEE
Q 040110          159 ILDDIMKSLMPTSSWL-KIMGKDYKS-EKTILRDYLTNKKYFTVLDDVWIE-------KIWDDLREALPDNQIGSRALIT  229 (348)
Q Consensus       159 ~~~~i~~~l~~~~~~~-~~~~~~~~~-~~~~l~~~L~~kr~LlVLDdv~~~-------~~~~~l~~~l~~~~~gskIlvT  229 (348)
                      -..++++.++...... ....-+-.+ ..-.|.+.|-.++-+|+||.--..       ..++.+.. +.. ..|..||++
T Consensus       107 ~~~~~l~~~~l~~~~~~~~~~LSGG~~QRvaiAraL~~~P~iLllDEPts~LD~~~~~~i~~~l~~-l~~-~~g~tii~v  184 (229)
T d3d31a2         107 RVLDTARDLKIEHLLDRNPLTLSGGEQQRVALARALVTNPKILLLDEPLSALDPRTQENAREMLSV-LHK-KNKLTVLHI  184 (229)
T ss_dssp             HHHHHHHHTTCTTTTTSCGGGSCHHHHHHHHHHHHTTSCCSEEEEESSSTTSCHHHHHHHHHHHHH-HHH-HTTCEEEEE
T ss_pred             HHHHHHHHhcchhhHhCChhhCCHHHhcchhhhhhhhccCCceeecCCCcCCCHHHHHHHHHHHHH-HHh-cCCcEEEEE
Confidence            2444555555432210 111222222 233467778888999999987543       12222222 111 236678888


Q ss_pred             eCChhhhhh
Q 040110          230 VGPHNILTS  238 (348)
Q Consensus       230 TR~~~v~~~  238 (348)
                      |-+...+..
T Consensus       185 tHd~~~~~~  193 (229)
T d3d31a2         185 THDQTEARI  193 (229)
T ss_dssp             ESCHHHHHH
T ss_pred             cCCHHHHHH
Confidence            888776554

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.12  E-value=0.014  Score=45.43  Aligned_cols=21  Identities=10%  Similarity=0.268  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|.+|+|||||..++.+.
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999998865

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.08  E-value=0.012  Score=50.60  Aligned_cols=23  Identities=30%  Similarity=0.351  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|+|||||++.+..-
T Consensus        63 e~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          63 EMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCChHHHHHHHHhCC
Confidence            47999999999999999999865

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.07  E-value=0.11  Score=42.68  Aligned_cols=49  Identities=6%  Similarity=-0.000  Sum_probs=34.9

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcCcc----ccCCcceeEEEEeCCCCCHH
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNNNF----VKFYFDCHAWVRVSNFYNFK  157 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~~----~~~~F~~~~wv~~~~~~~~~  157 (348)
                      =+.-+++.|.|.+|+|||++|.+++.+..    ....+..+.|+.....+...
T Consensus        34 ip~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (258)
T d1v5wa_          34 IESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPD   86 (258)
T ss_dssp             BCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHH
T ss_pred             CcCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHH
Confidence            44566899999999999999999875421    22334567788777666644

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.02  E-value=0.012  Score=47.36  Aligned_cols=25  Identities=16%  Similarity=0.134  Sum_probs=21.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .-.++.|.|.+|+|||+||.+++.+
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~   46 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVT   46 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHH
Confidence            3458889999999999999998765

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.96  E-value=0.015  Score=45.74  Aligned_cols=21  Identities=14%  Similarity=0.330  Sum_probs=18.8

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|.+|+|||||+.++.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            668999999999999998766

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=93.95  E-value=0.0059  Score=53.83  Aligned_cols=43  Identities=19%  Similarity=0.217  Sum_probs=29.6

Q ss_pred             cccccccccccHHHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhc
Q 040110           83 ALLGLQSKIINLRNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus        83 ~~vGr~~~~~~~~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      .++|.+..+   ..|.-.+.      ..+..-+.+.|.+|+||||||+.+..
T Consensus         8 ~I~Gq~~~k---ral~laa~------~~~~h~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_           8 AIVGQEDMK---LALLLTAV------DPGIGGVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             GSCSCHHHH---HHHHHHHH------CGGGCCEEEECCGGGCTTHHHHHHHH
T ss_pred             hccCcHHHH---HHHHHHHh------ccCCCeEEEECCCCccHHHHHHHHHH
Confidence            789998777   65443222      01112367899999999999998853

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.91  E-value=0.02  Score=44.70  Aligned_cols=22  Identities=18%  Similarity=0.404  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |.++|.+|+|||||...+.++.
T Consensus         5 i~viG~~~vGKTsLi~r~~~~~   26 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKGT   26 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTCC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            5689999999999999887653

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.86  E-value=0.019  Score=45.23  Aligned_cols=25  Identities=16%  Similarity=0.236  Sum_probs=21.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|+|+|.+|+|||||...+.+.
T Consensus         4 ~~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           4 YSGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3457999999999999999999865

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=93.84  E-value=0.018  Score=45.13  Aligned_cols=22  Identities=14%  Similarity=0.256  Sum_probs=19.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|+|+|.+|+|||||..++...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5889999999999999998754

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.84  E-value=0.019  Score=44.98  Aligned_cols=25  Identities=12%  Similarity=0.256  Sum_probs=22.0

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ....|+|+|.+|+|||||..++.+.
T Consensus         4 ~~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           4 YCGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cccEEEEECCCCCCHHHHHHHHhCC
Confidence            4567899999999999999999864

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=93.80  E-value=0.016  Score=44.97  Aligned_cols=21  Identities=14%  Similarity=0.173  Sum_probs=18.7

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.|+|.+|+|||||...+.+.
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            669999999999999998765

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.79  E-value=0.017  Score=45.06  Aligned_cols=22  Identities=14%  Similarity=0.253  Sum_probs=19.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|+|.+|+|||+|+.++.+.
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999998765

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.68  E-value=0.023  Score=44.29  Aligned_cols=22  Identities=18%  Similarity=0.376  Sum_probs=19.3

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |.|+|.+|+|||||..++.++.
T Consensus         7 i~lvG~~~vGKTsli~rl~~~~   28 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVEDS   28 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6689999999999999988654

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.67  E-value=0.018  Score=45.04  Aligned_cols=22  Identities=18%  Similarity=0.314  Sum_probs=19.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.++|.+|+|||||...+.++
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3779999999999999988755

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=93.66  E-value=0.011  Score=49.54  Aligned_cols=125  Identities=14%  Similarity=0.068  Sum_probs=65.8

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccC-------------------Cc-ceeEEEEeCC----CCC-------------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKF-------------------YF-DCHAWVRVSN----FYN-------------  155 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~-------------------~F-~~~~wv~~~~----~~~-------------  155 (348)
                      .+++|+|+.|+|||||.+.+..-.....                   .. ..+-+|.-..    ..+             
T Consensus        32 e~~~iiG~sGsGKSTll~~i~gl~~p~~G~I~~~g~~i~~~~~~~~~~~rr~ig~vfQ~~~L~p~ltv~eni~~~l~~~~  111 (242)
T d1oxxk2          32 ERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMK  111 (242)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTSSCCSEEEEEETTEEEEETTEESSCGGGSCEEEEETTSCCCTTSCHHHHHHGGGTTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHHcCcCCCCceEEECCEEeecCchhhcchhhccceEEeccccccccccHHHHhhhhhHhhc
Confidence            4899999999999999999865421100                   00 0122221110    011             


Q ss_pred             -----HHHHHHHHHHHhCCCCCcc-ccCCCCHHHH-HHHHHHHhcCCeEEEEEeCCCCh------hhHHHHHhhCCCCCC
Q 040110          156 -----FKRILDDIMKSLMPTSSWL-KIMGKDYKSE-KTILRDYLTNKKYFTVLDDVWIE------KIWDDLREALPDNQI  222 (348)
Q Consensus       156 -----~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~-~~~l~~~L~~kr~LlVLDdv~~~------~~~~~l~~~l~~~~~  222 (348)
                           ..+-..++++.++...... .+..-+-.+. .-.|.+.|..++-+|++|..-..      .+...+...+.. ..
T Consensus       112 ~~~~~~~~~v~~~l~~~gL~~~~~~~p~~LSGGqkQRvaiARaL~~~P~llllDEPt~~LD~~~~~~i~~~i~~l~~-~~  190 (242)
T d1oxxk2         112 MSKEEIRKRVEEVAKILDIHHVLNHFPRELSGAQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQS-RL  190 (242)
T ss_dssp             CCHHHHHHHHHHHHHHTTCGGGTTSCGGGSCHHHHHHHHHHHHHTTCCSEEEEESTTTTSCGGGHHHHHHHHHHHHH-HH
T ss_pred             CCHHHHHHHHHHHHhhcChHhhhhCChhhCCHHHHhHHHHHhHHhhcccceeecCCccCCCHHHHHHHHHHHHHHHh-cc
Confidence                 1233456666666532110 1122233333 33477778889999999986432      222222222211 12


Q ss_pred             CcEEEEEeCChhhhhh
Q 040110          223 GSRALITVGPHNILTS  238 (348)
Q Consensus       223 gskIlvTTR~~~v~~~  238 (348)
                      |..||++|.+...+..
T Consensus       191 g~tvi~vTHd~~~~~~  206 (242)
T d1oxxk2         191 GVTLLVVSHDPADIFA  206 (242)
T ss_dssp             CCEEEEEESCHHHHHH
T ss_pred             CCEEEEEECCHHHHHH
Confidence            5678888888666554

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=93.65  E-value=0.018  Score=46.48  Aligned_cols=22  Identities=18%  Similarity=0.299  Sum_probs=19.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|+|-|+-|+||||+++.+.+.
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~   23 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGA   23 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999998876

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=93.64  E-value=0.02  Score=47.48  Aligned_cols=24  Identities=17%  Similarity=0.120  Sum_probs=21.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.+|+|+|..|+||||+|+.+.+.
T Consensus         1 M~iIgiTG~igSGKsTva~~l~e~   24 (241)
T d1deka_           1 MKLIFLSGVKRSGKDTTADFIMSN   24 (241)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHh
Confidence            368999999999999999998654

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.63  E-value=0.019  Score=45.56  Aligned_cols=22  Identities=27%  Similarity=0.350  Sum_probs=19.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3678999999999999998865

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.63  E-value=0.023  Score=44.47  Aligned_cols=21  Identities=33%  Similarity=0.472  Sum_probs=18.8

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|.+|+|||||...+.+.
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            679999999999999998765

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=93.62  E-value=0.018  Score=48.32  Aligned_cols=23  Identities=22%  Similarity=0.320  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|.|||||.+.+..-
T Consensus        33 ei~~liGpnGaGKSTl~~~i~Gl   55 (240)
T d1ji0a_          33 QIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            38999999999999999999754

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.56  E-value=0.025  Score=44.01  Aligned_cols=23  Identities=26%  Similarity=0.433  Sum_probs=19.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -|.++|.+|+|||+|..++.++.
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~~   27 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            36789999999999999987653

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=93.56  E-value=0.019  Score=48.07  Aligned_cols=123  Identities=10%  Similarity=-0.013  Sum_probs=66.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCcccc------------CCc----ceeEEEEeCC----CCCHH---------------
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVK------------FYF----DCHAWVRVSN----FYNFK---------------  157 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~------------~~F----~~~~wv~~~~----~~~~~---------------  157 (348)
                      .+++|+|+.|.|||||.+.+..-....            +.-    ..+.++.-..    ..++.               
T Consensus        29 ei~glvG~nGaGKSTLl~~l~G~~~p~~G~i~i~G~~i~~~~~~~~~~i~~vpq~~~~~~~ltv~e~l~~~~~~~~~~~~  108 (238)
T d1vpla_          29 EIFGLIGPNGAGKTTTLRIISTLIKPSSGIVTVFGKNVVEEPHEVRKLISYLPEEAGAYRNMQGIEYLRFVAGFYASSSS  108 (238)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSCCSEEEEEETTEETTTCHHHHHTTEEEECTTCCCCTTSBHHHHHHHHHHHHCCCHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCCCCEEEECcEecccChHHHHhhEeEeeeccccCCCccHHHHHHHHHHhcCCCHH
Confidence            489999999999999999987552211            000    1122332211    11222               


Q ss_pred             ---HHHHHHHHHhCCCCCcc-ccCCCCHHHH-HHHHHHHhcCCeEEEEEeCCCCh-------hhHHHHHhhCCCCCCCcE
Q 040110          158 ---RILDDIMKSLMPTSSWL-KIMGKDYKSE-KTILRDYLTNKKYFTVLDDVWIE-------KIWDDLREALPDNQIGSR  225 (348)
Q Consensus       158 ---~~~~~i~~~l~~~~~~~-~~~~~~~~~~-~~~l~~~L~~kr~LlVLDdv~~~-------~~~~~l~~~l~~~~~gsk  225 (348)
                         +....++..++...... .....+-.+. .-.+...|..++=+|+||..-..       .-|+.+. .+.  ..|..
T Consensus       109 ~~~~~~~~~l~~~~l~~~~~~~~~~lSgG~~qrv~iA~al~~~p~illLDEPt~gLD~~~~~~i~~~i~-~~~--~~g~t  185 (238)
T d1vpla_         109 EIEEMVERATEIAGLGEKIKDRVSTYSKGMVRKLLIARALMVNPRLAILDEPTSGLDVLNAREVRKILK-QAS--QEGLT  185 (238)
T ss_dssp             HHHHHHHHHHHHHCCGGGGGSBGGGCCHHHHHHHHHHHHHTTCCSEEEEESTTTTCCHHHHHHHHHHHH-HHH--HTTCE
T ss_pred             HHHHHHHHHHHhCCCHHHHhhhhhhCCHHHHHHHHHHHHHhcCCCEEEecCCCCCCCHHHHHHHHHHHH-HHH--hcCCE
Confidence               23344444444321110 1122233332 23566777888889999997653       2223232 222  23667


Q ss_pred             EEEEeCChhhhhh
Q 040110          226 ALITVGPHNILTS  238 (348)
Q Consensus       226 IlvTTR~~~v~~~  238 (348)
                      ||+||.+-..+..
T Consensus       186 ii~~tH~l~~~~~  198 (238)
T d1vpla_         186 ILVSSHNMLEVEF  198 (238)
T ss_dssp             EEEEECCHHHHTT
T ss_pred             EEEEeCCHHHHHH
Confidence            8999988777665

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.54  E-value=0.021  Score=44.68  Aligned_cols=22  Identities=27%  Similarity=0.271  Sum_probs=19.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.++|.+|+|||+|+..+.+.
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCcCHHHHHHHHhCC
Confidence            3678999999999999998765

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.53  E-value=0.022  Score=44.09  Aligned_cols=22  Identities=14%  Similarity=0.317  Sum_probs=19.2

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |.++|.+|+|||+|+.++.++.
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~~   24 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYDS   24 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999987653

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.53  E-value=0.025  Score=44.14  Aligned_cols=22  Identities=23%  Similarity=0.434  Sum_probs=19.3

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |.++|.+|+|||+|...+.++.
T Consensus         5 i~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            5689999999999999988764

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=93.49  E-value=0.032  Score=43.48  Aligned_cols=34  Identities=18%  Similarity=0.199  Sum_probs=25.2

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+..++.      ....+ |.|+|.+|+|||||..++...
T Consensus         5 ~~~~~~~~------~k~~k-I~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1           5 TRIWRLFN------HQEHK-VIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             HHHHHHHT------TSCEE-EEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHHHhC------CCeEE-EEEECCCCCCHHHHHHHHhcC
Confidence            45555555      33454 668999999999999998765

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.48  E-value=0.019  Score=48.53  Aligned_cols=23  Identities=22%  Similarity=0.261  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|.|||||++.+..-
T Consensus        31 ei~~liG~nGaGKSTLl~~i~Gl   53 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITGF   53 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHHCC
Confidence            38999999999999999999765

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.44  E-value=0.021  Score=43.57  Aligned_cols=22  Identities=18%  Similarity=0.166  Sum_probs=19.5

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|+++|.+|+|||||...+.+.
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3779999999999999998765

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.44  E-value=0.019  Score=45.01  Aligned_cols=22  Identities=14%  Similarity=0.344  Sum_probs=19.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.++|.+|+|||||...+.+.
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4678999999999999998865

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.40  E-value=0.029  Score=43.60  Aligned_cols=22  Identities=23%  Similarity=0.270  Sum_probs=19.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|+|.+|+|||+|..++.+.
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999998765

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=93.38  E-value=0.068  Score=45.68  Aligned_cols=93  Identities=12%  Similarity=0.104  Sum_probs=47.5

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccc-----cCCcc-eeEEEEeCCCC-CHHHHHHHHHHHhCCCCCcc--ccCCCCHHHH
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFV-----KFYFD-CHAWVRVSNFY-NFKRILDDIMKSLMPTSSWL--KIMGKDYKSE  184 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~-----~~~F~-~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~~  184 (348)
                      .++|.|.+|+|||+|+..+......     ...-. .++++-++... .+.++...+...-.......  ..........
T Consensus        70 r~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~tvvv~~ts~~~~~~r  149 (285)
T d2jdia3          70 RELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQ  149 (285)
T ss_dssp             BCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHHH
T ss_pred             EEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhcccccccceEEEEECCCCCHHHH
Confidence            3678999999999998877654211     11111 34566666554 34455555443321110000  1111111111


Q ss_pred             ------HHHHHHHh--cCCeEEEEEeCCCC
Q 040110          185 ------KTILRDYL--TNKKYFTVLDDVWI  206 (348)
Q Consensus       185 ------~~~l~~~L--~~kr~LlVLDdv~~  206 (348)
                            .-.+.+++  ++|++|+++||+-.
T Consensus       150 ~~~~~~a~tiAEyfrd~G~~VLll~Dsltr  179 (285)
T d2jdia3         150 YLAPYSGCSMGEYFRDNGKHALIIYDDLSK  179 (285)
T ss_dssp             HHHHHHHHHHHHHHHHTTCEEEEEEETHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCcEEEEEcChHH
Confidence                  11233333  57999999999844

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.37  E-value=0.022  Score=44.57  Aligned_cols=23  Identities=9%  Similarity=0.244  Sum_probs=19.5

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -|.++|.+|+|||||+.++.+..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~~   30 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            36789999999999999987653

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=93.35  E-value=0.027  Score=44.45  Aligned_cols=36  Identities=17%  Similarity=0.140  Sum_probs=25.4

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..+.+.|.    ......+ |.++|.+|+|||||..++.+.
T Consensus         5 ~~~~~~l~----~~~k~~K-I~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_           5 SSMFDKLW----GSNKELR-ILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             HHHHGGGT----TCSSCEE-EEEEEETTSSHHHHHHHTCCS
T ss_pred             HHHHHHHh----CCCceEE-EEEECCCCCCHHHHHHHHhcC
Confidence            44555555    2334455 559999999999999998654

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.34  E-value=0.036  Score=44.90  Aligned_cols=51  Identities=12%  Similarity=0.080  Sum_probs=30.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCccccC-CcceeEEEEeCCCCCHHHHHHHHHH
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVKF-YFDCHAWVRVSNFYNFKRILDDIMK  165 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~F~~~~wv~~~~~~~~~~~~~~i~~  165 (348)
                      +.|+|-|+-|+||||+++.+.+.  ... .+..+++..-.......+.+++...
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~--L~~~g~~~~~~~~ep~~~~~g~~i~~~~~   54 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVET--LEQLGIRDMVFTREPGGTQLAEKLRSLLL   54 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHH--HHHTTCCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--HHhCCCCeEEEecCCCCccchhhhHHHHh
Confidence            36888999999999999998876  322 2334444332222233444444443

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=93.30  E-value=0.022  Score=44.57  Aligned_cols=23  Identities=13%  Similarity=0.160  Sum_probs=19.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .-|.++|.+|+|||||..++...
T Consensus        14 ~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          14 GKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            34679999999999999998655

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.28  E-value=0.025  Score=46.44  Aligned_cols=23  Identities=22%  Similarity=0.368  Sum_probs=19.9

Q ss_pred             EEEEEE-CCCCCcHHHHHHHHhcC
Q 040110          113 SVVAIL-DSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~-G~gGvGKTtLA~~v~~~  135 (348)
                      ++|+|+ +-||+||||+|..++..
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~   26 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVA   26 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHH
Confidence            589999 56999999999998766

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.27  E-value=0.023  Score=45.71  Aligned_cols=22  Identities=14%  Similarity=0.196  Sum_probs=20.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|+|+|.+|+|||||...+.+.
T Consensus         5 ~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           5 SIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            6889999999999999999765

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.25  E-value=0.022  Score=47.05  Aligned_cols=25  Identities=24%  Similarity=0.239  Sum_probs=22.3

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +..|..|.|.-|.|||||.+++.+.
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            5678899999999999999998875

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.24  E-value=0.026  Score=43.86  Aligned_cols=23  Identities=22%  Similarity=0.372  Sum_probs=19.6

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .-|.|+|.+|+|||||...+.+.
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            34678999999999999998765

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.21  E-value=0.02  Score=46.76  Aligned_cols=23  Identities=4%  Similarity=0.124  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..|+|-|+-|+||||+++.+.+.
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~   26 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEA   26 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            46888999999999999999887

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=93.20  E-value=0.053  Score=44.37  Aligned_cols=57  Identities=11%  Similarity=0.028  Sum_probs=35.5

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCccccCC--------------cceeEEEEeCCCCCHHHHHHHHHHHhC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVKFY--------------FDCHAWVRVSNFYNFKRILDDIMKSLM  168 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~--------------F~~~~wv~~~~~~~~~~~~~~i~~~l~  168 (348)
                      .-.++.|.|.+|+|||++|.+++.+......              -..+.|++.....+.. ....+...+.
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~e~~~~~~-~~~~~~~~~~  103 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPE-RIMQMAEHAG  103 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHH-HHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEeecccchhcCceEEEEEecCCcCHH-HHHHHHhhcc
Confidence            4468889999999999999998765322111              1235677766555533 3334444443

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=93.19  E-value=0.21  Score=41.84  Aligned_cols=51  Identities=10%  Similarity=0.062  Sum_probs=32.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHh
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSL  167 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l  167 (348)
                      ++.|.|.+|+||||++.++..+......+. +++++.  +-+..++...++...
T Consensus        37 l~vi~G~~G~GKT~~~~~la~~~a~~~g~~-v~~~s~--E~~~~~~~~r~~~~~   87 (277)
T d1cr2a_          37 VIMVTSGSGMGKSTFVRQQALQWGTAMGKK-VGLAML--EESVEETAEDLIGLH   87 (277)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTSCCC-EEEEES--SSCHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHhhhhhcccc-eeEeee--ccchhhHHhHHHHHh
Confidence            677899999999999999876532333443 444443  344555555554433

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.17  E-value=0.032  Score=43.71  Aligned_cols=22  Identities=14%  Similarity=0.363  Sum_probs=19.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|+|.+|+|||+|...+.+.
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4669999999999999988765

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.16  E-value=0.028  Score=43.91  Aligned_cols=22  Identities=14%  Similarity=0.359  Sum_probs=19.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.++|.+|+|||+|...+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4678999999999999988765

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.15  E-value=0.031  Score=43.48  Aligned_cols=22  Identities=23%  Similarity=0.407  Sum_probs=19.2

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |.++|.+|+|||+|..++....
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~   27 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            6789999999999999987663

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.15  E-value=0.028  Score=43.72  Aligned_cols=22  Identities=18%  Similarity=0.489  Sum_probs=19.4

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |.++|.+|+|||||..++.++.
T Consensus         6 i~viG~~~vGKTsli~~l~~~~   27 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            6789999999999999988753

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.14  E-value=0.025  Score=44.48  Aligned_cols=22  Identities=18%  Similarity=0.373  Sum_probs=19.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.++|..|+|||||+..+.+.
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4779999999999999988765

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.14  E-value=0.022  Score=44.66  Aligned_cols=22  Identities=9%  Similarity=0.258  Sum_probs=19.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.++|.+|+|||||+.++...
T Consensus         7 KI~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999988654

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.14  E-value=0.015  Score=49.30  Aligned_cols=23  Identities=22%  Similarity=0.151  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ..++|+|..|+|||||++.+..-
T Consensus        45 e~vaivG~sGsGKSTLl~ll~gl   67 (255)
T d2hyda1          45 ETVAFVGMSGGGKSTLINLIPRF   67 (255)
T ss_dssp             CEEEEECSTTSSHHHHHTTTTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHHhc
Confidence            47899999999999999988643

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.12  E-value=0.018  Score=45.53  Aligned_cols=21  Identities=14%  Similarity=0.218  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |+|+|.+|+|||||...+.+.
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999998754

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.06  E-value=0.023  Score=44.16  Aligned_cols=21  Identities=10%  Similarity=0.385  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|.+|+|||||..++.+.
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999998765

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.99  E-value=0.036  Score=43.21  Aligned_cols=22  Identities=18%  Similarity=0.332  Sum_probs=19.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|+|.+|+|||+|+.++.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988665

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.99  E-value=0.027  Score=45.50  Aligned_cols=22  Identities=14%  Similarity=0.104  Sum_probs=19.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|+|+|.+|+|||||..++.+.
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5889999999999999998765

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.90  E-value=0.31  Score=40.08  Aligned_cols=108  Identities=12%  Similarity=0.065  Sum_probs=55.6

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCcccc-------------CCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNNFVK-------------FYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIM  177 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~-------------~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~  177 (348)
                      ..+++.|+|+...||||+.+.+.-..-..             ..|+ .++..++..-++..-.                 
T Consensus        40 ~~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d-~I~~~~~~~d~~~~~~-----------------  101 (234)
T d1wb9a2          40 QRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPID-RIFTRVGAADDLASGR-----------------  101 (234)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCC-EEEEEEC--------------------------
T ss_pred             CceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccch-hheeEEccCcccccch-----------------
Confidence            34678899999999999999875331111             1232 3344443332221100                 


Q ss_pred             CCCHHHHHHHHHHHh--cCCeEEEEEeCCCCh----hh---HHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          178 GKDYKSEKTILRDYL--TNKKYFTVLDDVWIE----KI---WDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       178 ~~~~~~~~~~l~~~L--~~kr~LlVLDdv~~~----~~---~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                       .....-...+.+.+  .+++.|+++|.+-..    +-   ...+...+.. ..++.+++||-...+...
T Consensus       102 -S~F~~E~~~~~~il~~~~~~sLvliDE~~~gT~~~eg~~l~~a~l~~l~~-~~~~~~i~tTH~~~l~~~  169 (234)
T d1wb9a2         102 -STFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLAN-KIKALTLFATHYFELTQL  169 (234)
T ss_dssp             ---CHHHHHHHHHHHHHCCTTEEEEEESCCCCSSSSHHHHHHHHHHHHHHH-TTCCEEEEECSCGGGGGH
T ss_pred             -hHHHHHHHHHHHHHHhcccccEEeecccccCCChhhhhHHHHHhhhhhhc-cccceEEEecchHHHhhh
Confidence             01111122233333  357889999999753    11   1122222221 235789999998877664

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=92.88  E-value=0.022  Score=47.42  Aligned_cols=23  Identities=13%  Similarity=0.313  Sum_probs=20.3

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+++|+|+.|.|||||.+.+..-
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~Gl   48 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAGM   48 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            37999999999999999998753

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.84  E-value=0.031  Score=44.75  Aligned_cols=22  Identities=9%  Similarity=0.317  Sum_probs=19.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|+|.+|+|||||...+.+.
T Consensus         8 KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhhC
Confidence            3678999999999999998765

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.84  E-value=0.042  Score=43.37  Aligned_cols=23  Identities=13%  Similarity=0.167  Sum_probs=19.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -|.|+|.+|+|||+|..++..+.
T Consensus         7 KivviG~~~vGKTsli~~~~~~~   29 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTNA   29 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            46789999999999999887653

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=92.82  E-value=0.021  Score=45.30  Aligned_cols=22  Identities=9%  Similarity=0.149  Sum_probs=19.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|+|+|.+++|||||..++.+.
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~~   24 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSSA   24 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEEE
T ss_pred             eEEEECCCCCCHHHHHHHHhCC
Confidence            3899999999999999998654

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.81  E-value=0.036  Score=43.12  Aligned_cols=21  Identities=14%  Similarity=0.316  Sum_probs=18.5

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|..|+|||+|..++.+.
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999988765

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=92.81  E-value=0.025  Score=50.43  Aligned_cols=24  Identities=21%  Similarity=0.322  Sum_probs=20.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...+..+|+.|+|||.||+.++..
T Consensus        68 ~~niLfiGPTGvGKTElAk~LA~~   91 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMAQTLAKH   91 (364)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcceeeeCCCCccHHHHHHHHHhh
Confidence            445778899999999999999765

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=92.80  E-value=0.31  Score=35.96  Aligned_cols=54  Identities=11%  Similarity=-0.004  Sum_probs=35.4

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMP  169 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~  169 (348)
                      +..++..|+++.|.|||+++..++..      ....+.+.+....-..+..+.+.+.+..
T Consensus         6 ~~~~~~ll~apTGsGKT~~~~~~~~~------~~~~vli~~P~~~l~~q~~~~~~~~~~~   59 (136)
T d1a1va1           6 QSFQVAHLHAPTGSGKSTKVPAAYAA------QGYKVLVLNPSVAATLGFGAYMSKAHGV   59 (136)
T ss_dssp             SSCEEEEEECCTTSCTTTHHHHHHHT------TTCCEEEEESCHHHHHHHHHHHHHHHSC
T ss_pred             cCCCEEEEEeCCCCCHHHHHHHHHHH------cCCcEEEEcChHHHHHHHHHHHHHHhhc
Confidence            45677888999999999988766644      1234556565554455555555555543

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=92.76  E-value=0.042  Score=45.35  Aligned_cols=32  Identities=16%  Similarity=0.265  Sum_probs=25.7

Q ss_pred             HHHHhhcCCCCCCCCCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110           95 RNLHQRLPPSSGLGQPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus        95 ~~l~~~L~~~~~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.|.++|.      .   ++..++|.+|+|||||..++..+
T Consensus        87 ~~L~~~l~------~---kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          87 EELKEYLK------G---KISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             HHHHHHHS------S---SEEEEECSTTSSHHHHHHHHSTT
T ss_pred             hhHHHHhc------C---CeEEEECCCCCCHHHHHHhhcch
Confidence            67777776      1   25678999999999999999765

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=92.75  E-value=0.038  Score=43.08  Aligned_cols=23  Identities=22%  Similarity=0.378  Sum_probs=19.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -|.++|.+|+|||||..++.+..
T Consensus         6 KivlvG~~~vGKTsli~~~~~~~   28 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            46789999999999999987653

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=92.72  E-value=0.026  Score=44.45  Aligned_cols=22  Identities=5%  Similarity=0.141  Sum_probs=19.8

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .|+|+|.+|+|||||..++.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999865

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.67  E-value=0.028  Score=44.19  Aligned_cols=23  Identities=13%  Similarity=0.128  Sum_probs=19.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -|.|+|.+|+|||+|...+.+..
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            35689999999999999887663

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=92.67  E-value=0.032  Score=43.25  Aligned_cols=21  Identities=19%  Similarity=0.226  Sum_probs=18.4

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|.+|+|||||..++...
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            568999999999999988765

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.65  E-value=0.058  Score=44.02  Aligned_cols=23  Identities=17%  Similarity=0.190  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.|+|-|+-|+||||+++.+.+.
T Consensus         4 k~I~iEG~DGsGKST~~~~L~~~   26 (214)
T d1tmka_           4 KLILIEGLDRTGKTTQCNILYKK   26 (214)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCcHHHHHHHHHHH
Confidence            47889999999999999999877

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=92.63  E-value=0.032  Score=44.11  Aligned_cols=21  Identities=33%  Similarity=0.479  Sum_probs=18.8

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999998765

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=92.58  E-value=0.03  Score=44.29  Aligned_cols=21  Identities=10%  Similarity=0.107  Sum_probs=18.0

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|.+|+|||+|..++...
T Consensus         5 ivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            568999999999999987544

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.57  E-value=0.037  Score=43.87  Aligned_cols=23  Identities=13%  Similarity=0.189  Sum_probs=19.7

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      -|.|+|.+|+|||+|..++.++.
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~~   33 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYANDA   33 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhhCC
Confidence            36789999999999999987653

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.53  E-value=0.043  Score=42.81  Aligned_cols=22  Identities=14%  Similarity=0.434  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |.++|.+|+|||+|...+.++.
T Consensus         7 i~lvG~~~vGKTsll~~~~~~~   28 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQKI   28 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5678999999999999988753

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=92.52  E-value=0.17  Score=44.04  Aligned_cols=105  Identities=13%  Similarity=0.106  Sum_probs=56.8

Q ss_pred             EEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCCCHHHHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGKDYKSEKTILRDYLTN  194 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~  194 (348)
                      +.|.|..|+||||+..++...  +.... .++-+.-.....+           ..............-...+.++..|+.
T Consensus       169 ili~G~tgSGKTT~l~al~~~--i~~~~-rivtiEd~~El~l-----------~~~~~~~~~~~~~~~~~~~ll~~~lR~  234 (323)
T d1g6oa_         169 VIVCGGTGSGKTTYIKSIMEF--IPKEE-RIISIEDTEEIVF-----------KHHKNYTQLFFGGNITSADCLKSCLRM  234 (323)
T ss_dssp             EEEEESTTSSHHHHHHHHGGG--SCTTC-CEEEEESSCCCCC-----------SSCSSEEEEECBTTBCHHHHHHHHTTS
T ss_pred             EEEEeeccccchHHHHHHhhh--ccccc-ceeeccchhhhhc-----------ccccccceeccccchhHHHHHHHHhcc
Confidence            678999999999999999876  32221 1221211111110           000000000000111344567778888


Q ss_pred             CeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhh
Q 040110          195 KKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNIL  236 (348)
Q Consensus       195 kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~  236 (348)
                      ..=.+|+..+.+.+.++.+ .....+..|  ++.|....+..
T Consensus       235 ~pd~iivgEiR~~ea~~~l-~a~~tGh~g--~~tT~Ha~s~~  273 (323)
T d1g6oa_         235 RPDRIILGELRSSEAYDFY-NVLCSGHKG--TLTTLHAGSSE  273 (323)
T ss_dssp             CCSEEEESCCCSTHHHHHH-HHHHTTCSC--EEEEECCSSHH
T ss_pred             CCCcccCCccCchhHHHHH-HHHHhcCCc--EEEEECCCCHH
Confidence            8888999999988777654 444444445  45555444433

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.50  E-value=0.031  Score=44.56  Aligned_cols=18  Identities=17%  Similarity=0.377  Sum_probs=16.6

Q ss_pred             EEEECCCCCcHHHHHHHH
Q 040110          115 VAILDSRGFDKTAFAAEI  132 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v  132 (348)
                      |.++|.+|+|||||..++
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            568999999999999988

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.39  E-value=0.047  Score=42.81  Aligned_cols=22  Identities=14%  Similarity=0.386  Sum_probs=19.1

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |.++|.+|+|||||..++.+..
T Consensus        10 i~vvG~~~vGKTsli~~l~~~~   31 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDDT   31 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6799999999999999987653

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.38  E-value=0.042  Score=42.96  Aligned_cols=22  Identities=23%  Similarity=0.362  Sum_probs=19.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.++|.+|+|||||...+.+.
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4779999999999999887765

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.30  E-value=0.039  Score=43.19  Aligned_cols=22  Identities=18%  Similarity=0.296  Sum_probs=18.9

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.++|.+|+|||+|+..+...
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~~   26 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAGV   26 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4678999999999999988654

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=92.26  E-value=0.028  Score=44.07  Aligned_cols=27  Identities=19%  Similarity=0.097  Sum_probs=22.4

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+....|+|+|.+++|||||..++...
T Consensus        13 ~~~~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          13 SDTGIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             CSCSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CccCCEEEEECCCCCCHHHHHHHHhCC
Confidence            445667899999999999999988654

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.23  E-value=0.043  Score=43.29  Aligned_cols=22  Identities=14%  Similarity=0.199  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |.++|..|+|||+|...+.+..
T Consensus         5 ivliG~~~vGKTsli~r~~~~~   26 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKDC   26 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5689999999999999887753

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=92.17  E-value=0.072  Score=41.85  Aligned_cols=24  Identities=25%  Similarity=0.296  Sum_probs=20.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .. -|+|+|..|+|||||..++.+.
T Consensus         8 ~~-kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           8 AI-KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             CE-EEEEECSTTSSHHHHHHHHHTS
T ss_pred             CC-EEEEECCCCCCHHHHHHHHHCC
Confidence            44 4789999999999999998765

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=92.12  E-value=0.038  Score=42.38  Aligned_cols=21  Identities=14%  Similarity=0.178  Sum_probs=18.6

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |+++|.+|+|||||..++...
T Consensus         4 I~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            669999999999999998754

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=92.01  E-value=0.034  Score=50.85  Aligned_cols=22  Identities=18%  Similarity=0.295  Sum_probs=20.0

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      =|.++|+.|+|||.||+.++..
T Consensus        51 NILliGPTGvGKTlLAr~LAk~   72 (443)
T d1g41a_          51 NILMIGPTGVGKTEIARRLAKL   72 (443)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHH
Confidence            4778999999999999999986

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.95  E-value=0.025  Score=44.28  Aligned_cols=21  Identities=19%  Similarity=0.362  Sum_probs=17.2

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|.+|+|||+|..++.+.
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999987655

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=91.79  E-value=0.048  Score=43.19  Aligned_cols=22  Identities=27%  Similarity=0.286  Sum_probs=19.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|.|.+|+||||+|..+..+
T Consensus        16 gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          16 GVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHc
Confidence            4678999999999999998765

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.64  E-value=0.05  Score=42.86  Aligned_cols=22  Identities=9%  Similarity=0.187  Sum_probs=19.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.++|.+|+|||||...+.+.
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4678999999999999988765

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.63  E-value=0.055  Score=43.03  Aligned_cols=22  Identities=14%  Similarity=0.217  Sum_probs=18.8

Q ss_pred             EEEECCCCCcHHHHHHHHhcCc
Q 040110          115 VAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      |.++|.+|+|||+|..++.+..
T Consensus         6 vvllG~~~vGKTSli~r~~~~~   27 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTNK   27 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5689999999999998887653

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=91.52  E-value=0.033  Score=43.53  Aligned_cols=26  Identities=12%  Similarity=0.080  Sum_probs=21.0

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ...+ |.++|.+|+|||||..++.+..
T Consensus        11 k~~k-IvlvG~~~vGKTSli~rl~~~~   36 (173)
T d1e0sa_          11 KEMR-ILMLGLDAAGKTTILYKLKLGQ   36 (173)
T ss_dssp             CCEE-EEEEEETTSSHHHHHHHTTCCC
T ss_pred             CeEE-EEEECCCCCCHHHHHHHHhcCC
Confidence            3455 5589999999999999987653

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=91.32  E-value=0.053  Score=42.98  Aligned_cols=22  Identities=23%  Similarity=0.339  Sum_probs=19.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -+.|.|.+|+||||+|..+..+
T Consensus        17 gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          17 GVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHc
Confidence            4678999999999999998765

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.07  E-value=0.051  Score=43.03  Aligned_cols=21  Identities=14%  Similarity=0.199  Sum_probs=18.2

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |.++|.+|+|||+|..++...
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            568999999999999988654

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=90.85  E-value=0.059  Score=45.31  Aligned_cols=23  Identities=22%  Similarity=0.332  Sum_probs=19.1

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+..|+|.+|+||||||.+++-.
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~   52 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQ   52 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHH
Confidence            36678999999999999887644

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.78  E-value=0.038  Score=43.22  Aligned_cols=22  Identities=14%  Similarity=0.261  Sum_probs=8.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.++|.+|+|||||...+.++
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEEECCCCC------------
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999877654

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=90.76  E-value=0.062  Score=42.24  Aligned_cols=22  Identities=27%  Similarity=0.308  Sum_probs=19.1

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.|.|.+|+||||+|..+..+
T Consensus        17 gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          17 GVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHc
Confidence            4678999999999999887765

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=90.75  E-value=0.1  Score=40.44  Aligned_cols=26  Identities=15%  Similarity=0.146  Sum_probs=22.4

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      +-.+|.+.|.=|+||||+++.+++..
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~l   57 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhc
Confidence            34589999999999999999998764

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=90.74  E-value=0.061  Score=44.03  Aligned_cols=22  Identities=9%  Similarity=0.074  Sum_probs=18.4

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -|.++|.+|+|||||..++...
T Consensus         8 KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4678999999999999987543

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=90.61  E-value=0.069  Score=43.33  Aligned_cols=24  Identities=17%  Similarity=0.218  Sum_probs=19.9

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      .-.++.|.|.+|+|||+||.+++.
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~   48 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLY   48 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHH
Confidence            445788999999999999987643

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=90.21  E-value=0.076  Score=44.62  Aligned_cols=26  Identities=12%  Similarity=0.265  Sum_probs=21.7

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..-.|.++|..|+|||||...++...
T Consensus        31 ~~l~I~LvG~tg~GKSSliN~ilg~~   56 (257)
T d1h65a_          31 NSLTILVMGKGGVGKSSTVNSIIGER   56 (257)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             CCcEEEEECCCCCcHHHHHHHHhCCC
Confidence            34457799999999999999998764

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=90.14  E-value=0.08  Score=42.54  Aligned_cols=23  Identities=9%  Similarity=0.082  Sum_probs=19.2

Q ss_pred             EEEEEECCC-CCcHHHHHHHHhcC
Q 040110          113 SVVAILDSR-GFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~g-GvGKTtLA~~v~~~  135 (348)
                      +.+.|.|-| ||||||++..++.-
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~a   25 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQA   25 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHHH
Confidence            457789997 99999998887766

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=89.93  E-value=1.3  Score=35.97  Aligned_cols=105  Identities=15%  Similarity=0.126  Sum_probs=55.4

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcCcccc-------------CCcceeEEEEeCCCCCHHHHHHHHHHHhCCCCCccccCCC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNNNFVK-------------FYFDCHAWVRVSNFYNFKRILDDIMKSLMPTSSWLKIMGK  179 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~~~~~-------------~~F~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~  179 (348)
                      +++.|+|+...||||+.+.+.-..-..             ..|+ .++..++..-++..                  ...
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d-~I~~~~~~~d~~~~------------------~~S   96 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFD-GIYTRIGASDDLAG------------------GKS   96 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCS-EEEEECCC------------------------CCS
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecc-eEEEEECCCccccC------------------Ccc
Confidence            367899999999999999875331111             1233 23333333222111                  011


Q ss_pred             CHHHHHHHHHHHh--cCCeEEEEEeCCCChhh-------HHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          180 DYKSEKTILRDYL--TNKKYFTVLDDVWIEKI-------WDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       180 ~~~~~~~~l~~~L--~~kr~LlVLDdv~~~~~-------~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      ....-...++..+  .+++.|+++|.+-...+       ...+...|.  ..++.+++||-...+...
T Consensus        97 tF~~el~~~~~il~~~~~~sLvliDE~~~gT~~~eg~ala~aile~L~--~~~~~~i~tTH~~eL~~l  162 (224)
T d1ewqa2          97 TFMVEMEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEALH--ERRAYTLFATHYFELTAL  162 (224)
T ss_dssp             HHHHHHHHHHHHHHHCCTTEEEEEESTTTTSCHHHHHHHHHHHHHHHH--HHTCEEEEECCCHHHHTC
T ss_pred             HHHHhHHHHHHHhccCCCCcEEeecccccCcchhhhcchHHHHHHHHh--hcCcceEEeeechhhhhh
Confidence            1222223333333  35789999999976411       112222222  236789999988777653

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=89.66  E-value=0.12  Score=45.81  Aligned_cols=52  Identities=13%  Similarity=0.100  Sum_probs=30.3

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcCc-cccCCcceeEEEEeCCCCCHHHHHHHH
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNNN-FVKFYFDCHAWVRVSNFYNFKRILDDI  163 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~~-~~~~~F~~~~wv~~~~~~~~~~~~~~i  163 (348)
                      .++..|.|++|+||||++..+.... +....-...+.+.....-....+...+
T Consensus       163 ~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~  215 (359)
T d1w36d1         163 RRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESL  215 (359)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHH
T ss_pred             CCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHH
Confidence            3578899999999999886544331 111111245667666554444444333

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=89.54  E-value=0.03  Score=42.96  Aligned_cols=21  Identities=14%  Similarity=0.336  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHhcC
Q 040110          115 VAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~v~~~  135 (348)
                      |+++|.+|+|||||..++.+.
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999998754

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=88.94  E-value=0.18  Score=43.94  Aligned_cols=24  Identities=8%  Similarity=0.023  Sum_probs=21.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +-.|.|=|+-|+||||+++.+.+.
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~   29 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASA   29 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSG
T ss_pred             eEEEEEECCccCCHHHHHHHHHHH
Confidence            446778899999999999999987

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=88.91  E-value=0.038  Score=45.77  Aligned_cols=22  Identities=14%  Similarity=0.232  Sum_probs=18.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +..++|.+|+|||||..++..+
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC-
T ss_pred             eEEEECCCCccHHHHHHhhccH
Confidence            3457899999999999998866

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.44  E-value=0.13  Score=43.81  Aligned_cols=27  Identities=19%  Similarity=0.153  Sum_probs=24.4

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +.++.||+|+|+-++|||+|+..++..
T Consensus        29 ~~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          29 TQPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             CSBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             CCCEEEEEEECCCCCCHHHHHHHHcCC
Confidence            456899999999999999999999876

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=88.18  E-value=0.12  Score=46.31  Aligned_cols=110  Identities=10%  Similarity=0.011  Sum_probs=61.8

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcCccccCCcceeEEEEeCCCCC--HHHHHHHHHHHhCCCCCccccCCCCHHHHHHH
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNNNFVKFYFDCHAWVRVSNFYN--FKRILDDIMKSLMPTSSWLKIMGKDYKSEKTI  187 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~--~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  187 (348)
                      ....+|.|.|+.|+||||....+.+.  +...-..+  +++..+..  ...+     .+...       ...+...-...
T Consensus       156 ~~~GliLvtGpTGSGKSTTl~~~l~~--~~~~~~~i--~tiEdPiE~~~~~~-----~q~~v-------~~~~~~~~~~~  219 (401)
T d1p9ra_         156 RPHGIILVTGPTGSGKSTTLYAGLQE--LNSSERNI--LTVEDPIEFDIDGI-----GQTQV-------NPRVDMTFARG  219 (401)
T ss_dssp             SSSEEEEEECSTTSCHHHHHHHHHHH--HCCTTSCE--EEEESSCCSCCSSS-----EEEEC-------BGGGTBCHHHH
T ss_pred             hhhceEEEEcCCCCCccHHHHHHhhh--hcCCCceE--EEeccCcccccCCC-----Ceeee-------cCCcCCCHHHH
Confidence            45678999999999999998888765  22211112  23333321  0000     00000       01111234566


Q ss_pred             HHHHhcCCeEEEEEeCCCChhhHHHHHhhCCCCCCCcEEEEEeCChhhhhh
Q 040110          188 LRDYLTNKKYFTVLDDVWIEKIWDDLREALPDNQIGSRALITVGPHNILTS  238 (348)
Q Consensus       188 l~~~L~~kr~LlVLDdv~~~~~~~~l~~~l~~~~~gskIlvTTR~~~v~~~  238 (348)
                      ++..|+.-+=.|++.++.+.+........-   ..|-.|+.|-...+....
T Consensus       220 l~~~lR~dPDvi~igEiRd~~ta~~a~~aa---~tGhlV~tTlHa~~a~~~  267 (401)
T d1p9ra_         220 LRAILRQDPDVVMVGEIRDLETAQIAVQAS---LTGHLVMSTLHTNTAVGA  267 (401)
T ss_dssp             HHHHGGGCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEECCSSSHHH
T ss_pred             HHHHHhhcCCEEEecCcCChHHHHHHHHHH---hcCCeEEEEeccCchHhh
Confidence            778888888888889998875544433321   236667666666665544

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=87.19  E-value=0.27  Score=41.43  Aligned_cols=27  Identities=15%  Similarity=0.134  Sum_probs=22.8

Q ss_pred             CCCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          109 QPTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       109 ~~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+....+.++|+|+.|||+++..+.+-
T Consensus       101 ~~k~n~~~l~G~~~tGKS~f~~~i~~~  127 (267)
T d1u0ja_         101 FGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             STTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCccEEEEEEcCCCCCHHHHHHHHHHH
Confidence            355668889999999999999988765

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=86.91  E-value=0.18  Score=40.62  Aligned_cols=26  Identities=12%  Similarity=0.216  Sum_probs=22.1

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhcC
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      +....+.++|+++.|||++|..+.+-
T Consensus        51 PKkn~i~~~GP~~TGKS~f~~sl~~~   76 (205)
T d1tuea_          51 PKKNCLVFCGPANTGKSYFGMSFIHF   76 (205)
T ss_dssp             TTCSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             CCceEEEEECCCCccHHHHHHHHHHH
Confidence            45578889999999999999887655

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=86.58  E-value=0.16  Score=43.00  Aligned_cols=25  Identities=16%  Similarity=0.056  Sum_probs=21.6

Q ss_pred             CCcEEEEEECCCCCcHHHHHHHHhc
Q 040110          110 PTHSVVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       110 ~~~~vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      .+.|-|+|+|-+|.|||||+.++..
T Consensus         4 ~~iRni~i~gh~~~GKTtL~e~ll~   28 (276)
T d2bv3a2           4 KRLRNIGIAAHIDAGKTTTTERILY   28 (276)
T ss_dssp             GGEEEEEEEECTTSCHHHHHHHHHH
T ss_pred             hhceEEEEEeCCCCCHHHHHHHHHH
Confidence            4567899999999999999988853

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=86.04  E-value=0.18  Score=43.91  Aligned_cols=24  Identities=21%  Similarity=0.068  Sum_probs=20.1

Q ss_pred             cEEEEEECCCCCcHHHHHHHHhcC
Q 040110          112 HSVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      ...|.|=|.-|+||||+++.+.+.
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~~   27 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVAL   27 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC-
T ss_pred             ceEEEEECCcCCCHHHHHHHHHHH
Confidence            345888999999999999999765

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=84.97  E-value=0.29  Score=42.54  Aligned_cols=23  Identities=22%  Similarity=0.221  Sum_probs=20.3

Q ss_pred             EEEEECCCCCcHHHHHHHHhcCc
Q 040110          114 VVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      .|.|=|.-|+||||+++.+.+..
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l   29 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHF   29 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47788999999999999998873

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=84.68  E-value=0.23  Score=38.74  Aligned_cols=21  Identities=14%  Similarity=0.202  Sum_probs=19.2

Q ss_pred             EEEEECCCCCcHHHHHHHHhc
Q 040110          114 VVAILDSRGFDKTAFAAEIYN  134 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~  134 (348)
                      -|+|+|...+|||||..++..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            489999999999999999875

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=84.27  E-value=0.28  Score=41.31  Aligned_cols=22  Identities=23%  Similarity=0.348  Sum_probs=19.4

Q ss_pred             cEEEEEECCCCCcHHHHHHHHh
Q 040110          112 HSVVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       112 ~~vi~I~G~gGvGKTtLA~~v~  133 (348)
                      .|-|+|+|-.|.|||||+.++.
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll   23 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALL   23 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHH
Confidence            3678999999999999999874

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=83.98  E-value=0.23  Score=41.97  Aligned_cols=16  Identities=25%  Similarity=0.299  Sum_probs=13.3

Q ss_pred             EEEECCCCCcHHHHHH
Q 040110          115 VAILDSRGFDKTAFAA  130 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~  130 (348)
                      +.|.|.+|+||||.+.
T Consensus        17 ~lI~g~aGTGKTt~l~   32 (306)
T d1uaaa1          17 CLVLAGAGSGKTRVIT   32 (306)
T ss_dssp             EEECCCTTSCHHHHHH
T ss_pred             EEEEeeCCccHHHHHH
Confidence            5688999999998653

>d1jala1 c.37.1.8 (A:1-278) YchF GTP-binding protein N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=83.81  E-value=0.31  Score=41.03  Aligned_cols=22  Identities=9%  Similarity=0.129  Sum_probs=19.6

Q ss_pred             EEEEECCCCCcHHHHHHHHhcC
Q 040110          114 VVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      -++|+|++.+|||||-.++-+.
T Consensus         4 ~~GivG~Pn~GKSTlf~~lt~~   25 (278)
T d1jala1           4 KCGIVGLPNVGKSTLFNALTKA   25 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHCC
Confidence            4899999999999999988755

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=83.64  E-value=0.24  Score=42.22  Aligned_cols=17  Identities=24%  Similarity=0.311  Sum_probs=13.8

Q ss_pred             EEEECCCCCcHHHHHHH
Q 040110          115 VAILDSRGFDKTAFAAE  131 (348)
Q Consensus       115 i~I~G~gGvGKTtLA~~  131 (348)
                      +.|.|.+|+||||.+.+
T Consensus        27 ~lV~g~aGSGKTt~l~~   43 (318)
T d1pjra1          27 LLIMAGAGSGKTRVLTH   43 (318)
T ss_dssp             EEEEECTTSCHHHHHHH
T ss_pred             EEEEecCCccHHHHHHH
Confidence            55789999999986644

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=83.22  E-value=0.32  Score=39.62  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCcHHHHHHHHhcC
Q 040110          113 SVVAILDSRGFDKTAFAAEIYNN  135 (348)
Q Consensus       113 ~vi~I~G~gGvGKTtLA~~v~~~  135 (348)
                      .+|+|+|-...|||||..++...
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~~   28 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRGS   28 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHhh
Confidence            46999999999999999888643

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=82.91  E-value=0.12  Score=40.41  Aligned_cols=20  Identities=20%  Similarity=0.245  Sum_probs=17.3

Q ss_pred             EEEEECCCCCcHHHHHHHHh
Q 040110          114 VVAILDSRGFDKTAFAAEIY  133 (348)
Q Consensus       114 vi~I~G~gGvGKTtLA~~v~  133 (348)
                      +..|+|+.|+||||+..++.
T Consensus        26 ~tvi~G~NGsGKStil~Ai~   45 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFV   45 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            45679999999999999885

>d1puja_ c.37.1.8 (A:) Probable GTPase YlqF {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase YlqF
species: Bacillus subtilis [TaxId: 1423]

Probab=81.48  E-value=0.69  Score=38.72  Aligned_cols=26  Identities=12%  Similarity=0.150  Sum_probs=22.3

Q ss_pred             CcEEEEEECCCCCcHHHHHHHHhcCc
Q 040110          111 THSVVAILDSRGFDKTAFAAEIYNNN  136 (348)
Q Consensus       111 ~~~vi~I~G~gGvGKTtLA~~v~~~~  136 (348)
                      ..-.++|+|++.+|||||...+.+..
T Consensus       111 ~~~~v~vvG~PNvGKSsliN~L~~~~  136 (273)
T d1puja_         111 RAIRALIIGIPNVGKSTLINRLAKKN  136 (273)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             CceEEEEEecCccchhhhhhhhhccc
Confidence            44568999999999999999998763