Citrus Sinensis ID: 045329

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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-------350-------360-------370-------380-------390-------400----
Protein Sequence
MLRLISRAAAAAAALSKQRNDTVLTSTSILIHQFFYSTKTQTKSSKKKQDDNKKSSKSKSKSSDANSLSAPAAAQADSADDLESVRARARRLAEDDRNPSLDVGPNHRPLFTKTTSLSLLTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSFARTCHMFQ
Secondary Structure (PSIPRED)
ccccccHHHHHHHHHHccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccEEEEcHHHHHHHccccccHHHHHHHHcccccEEEEcHHHHHHHHHHHHHHccccccccccccccEEEEEccccccHHHHHHHHHHHHHHccEEEEEccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHccccccHHHHHHHHHHHHHHcccccEEEEEEccccccccccccccccccccccccccccHHHHHHHHHHcccccccEEEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHcccccHHHcccccccccccHcHHccccccHHHHccccccccccccccccccccccHHHcccccHHcccccHcHHHHHHHHHccccccccccccccccccccccccccHHHccHHccccEEEccHHHHHHHccccccHHHHHHHHHcccccEEEcHHHHHHHHHHHHHHHHHHccccccccccEEEEEccccccHHHHHHHHHHHHHHcccEEEEcccHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccHHHHHHHccccHHHHHHHHHHHHHHHHccccccEEEEEcccHHHcccccccccccccccccccHHHHHHHHHHHHHHHccccccEEEEEEEEccccccccccc
Coil and Loop (DISEMBL)
MLRLISRAAAAAAALSKqrndtvltsTSILIHQFFystktqtksskkkqddnkksskskskssdanslsapaaaqadsadDLESVRARARRLaeddrnpsldvgpnhrplftkttslslltrkdactyfKFSEDELNAmlpeglptgmlgefkDSMRYALLVRQSFLDIRDNFrrivdpslqstngpkirkqivldgplccgksITLAMLVHWAREEGWLVLyvprgrewthggyfyknpqtglwdtplqAENVLKDFIKYNeshlrelpcqildpiplgegagvgllkgvdskeisegstLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIdqynnwftfseyeepvtirstrpVHARELAMVNAFRSMMHNDMMVGAFShstavgsfARTCHMFQ
Flexible Loop (DISEMBL)
MLRLISRAAAAAAalskqrndtvLTSTSILIHQffystktqtksskkkqddnkksskskskssdanslsapaaaqadsaddlESVRARARrlaeddrnpsldvgpnhrplftkttslslltRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRivdpslqstngpkirkQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSFARTCHMFQ
Low Complexity Region (SEG)
MLRLISRaaaaaaaLSKQRNDTVLTSTSILIHQFFYstktqtksskkkqddnkksskskskssdanslsapaaaqadsaddLESVrararrlaEDDRNPSLDVGPNHRPlftkttslslltRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSFARTCHMFQ
Disordered region (IsUnstruct)
*********************TVLTSTSILIHQFFYS************************************************************************LFTKTTSLSLLTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSFARTC****
Disordered Region (DISOPRED)
*************************************************************************************************************************RKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVD**L****GPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGV**************STLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAV***********
Disordered Region (DISEMBL)
********************DTVLTSTSILIHQFFYST***********************************************RARARRLAEDDRNPSLDVGPNHRPLFTKTTSLSLLTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSFARTCHMFQ
Disordered Region (DISPRO)
MLR**SRAAAAAA******N*TVLTSTSILI**FFY*****************************************************************************TTSLSLLTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSF********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLRLISRAAAAAAALSKQRNDTVLTSTSILIHQFFYSTKTQTKSSKKKQDDNKKSSKSKSKSSDANSLSAPAAAQADSADDLESVRARARRLAEDDRNPSLDVGPNHRPLFTKTTSLSLLTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSFARTCHMFQ
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	404	2.2.26 [Sep-21-2011]
P51398	398	28S ribosomal protein S29	yes	no	0.606	0.615	0.25	2e-13
P82922	397	28S ribosomal protein S29	yes	no	0.576	0.586	0.250	5e-12
Q9ER88	391	28S ribosomal protein S29	yes	no	0.603	0.624	0.249	2e-10

>sp|P51398|RT29_HUMAN 28S ribosomal protein S29, mitochondrial OS=Homo sapiens GN=DAP3 PE=1 SV=1

 Score = 77.0 bits (188), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/284 (25%), Positives = 126/284 (44%), Gaps = 39/284 (13%)

Query: 128 YFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP 187
           ++  S  +L  + P GLP   + + K      L+VR+  L++    +        S   P
Sbjct: 67  HYNISPQDLETVFPHGLPPRFVMQVKTFSEACLMVRKPALELLHYLKNT------SFAYP 120

Query: 188 KIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG--GYFYKNPQTGLW 245
            IR   +L G    GK+++L  ++H+  ++ WL+L++P    W          +     +
Sbjct: 121 AIR--YLLYGEKGTGKTLSLCHVIHFCAKQDWLILHIPDAHLWVKNCRDLLQSSYNKQRF 178

Query: 246 DTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEIS--EGSTLF 303
           D PL+A   LK+F   NE  L ++  Q                K V +K  S  +GS L 
Sbjct: 179 DQPLEASTWLKNFKTTNERFLNQIKVQ---------------EKYVWNKRESTEKGSPLG 223

Query: 304 DLVQMGINQMHA---SVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRST 360
           ++V+ GI ++     +VG+V++  K  S +    +L+A+D  N  +  +  +        
Sbjct: 224 EVVEQGITRVRNATDAVGIVLKELKRQSSLGMFHLLVAVDGINALWGRTTLKR----EDK 279

Query: 361 RPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSFARTCHMFQ 404
            P+   ELA+V+  R MM ND   GA      V + ++T  +F+
Sbjct: 280 SPIAPEELALVHNLRKMMKNDWHGGAI-----VSALSQTGSLFK 318

Involved in mediating interferon-gamma-induced cell death.
Homo sapiens (taxid: 9606)

>sp|P82922|RT29_BOVIN 28S ribosomal protein S29, mitochondrial OS=Bos taurus GN=DAP3 PE=1 SV=3

 Score = 72.8 bits (177), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 67/267 (25%), Positives = 117/267 (43%), Gaps = 34/267 (12%)

Query: 128 YFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP 187
           ++  S  EL  + P GLP   + + K      L+VR+  L++           L++TN  
Sbjct: 66  HYNISIQELKTVFPHGLPPRFVMQVKTFNEACLMVRKPALELLH--------YLKNTNFA 117

Query: 188 KIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG--GYFYKNPQTGLW 245
               + VL G    GK+++L  ++H+  ++ WL+L++P    W                +
Sbjct: 118 HPAVRYVLYGEKGTGKTLSLCHIIHFCAKQDWLILHIPDAHLWVKNCRDLLQSTYNKQRF 177

Query: 246 DTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEIS--EGSTLF 303
           D PL+A   LK+F   NE  L ++  Q                K V +K  S  +GS L 
Sbjct: 178 DQPLEASIWLKNFKTANERFLSQIKVQD---------------KYVWNKRESTEKGSPLA 222

Query: 304 DLVQMGINQMHA---SVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRST 360
           ++V+ GI ++     +VG+V++  K  S +    +L+A+D  N  +  +  +        
Sbjct: 223 EVVEQGIMRVRNATDAVGIVLKELKRQSSLGVFRLLVAVDGVNALWGRTTLKR----EDK 278

Query: 361 RPVHARELAMVNAFRSMMHNDMMVGAF 387
            P+   ELA++   R M+ ND   GA 
Sbjct: 279 SPITPEELALIYNLRKMVKNDWQGGAI 305

Involved in mediating interferon-gamma-induced cell death.

Bos taurus (taxid: 9913)

>sp|Q9ER88|RT29_MOUSE 28S ribosomal protein S29, mitochondrial OS=Mus musculus GN=Dap3 PE=2 SV=1

 Score = 67.4 bits (163), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 71/285 (24%), Positives = 124/285 (43%), Gaps = 41/285 (14%)

Query: 128 YFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP 187
           ++     +L  + P GLP   + + K      L+VR+  L++           L++TN  
Sbjct: 60  HYSIPLQDLKTVFPHGLPPRYMMQVKTFGEACLMVRKPALELLG--------YLKNTNFA 111

Query: 188 KIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGG--YFYKNPQTGLW 245
               + +L G    GK+++L   VH+     WL+L++P    W                +
Sbjct: 112 HPAVRYLLYGEKGTGKTLSLCHAVHFCARHDWLILHIPDAHLWVKNCRELLQSTHNKQRF 171

Query: 246 DTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEIS--EGSTLF 303
           D PL+A   LK+F   NE  L ++  Q                K V +K  S  +GS L 
Sbjct: 172 DQPLEASTWLKNFKTTNERFLSQIKVQE---------------KYVWNKRESTEKGSPLG 216

Query: 304 DLVQMGINQMHA---SVGVVVRLRKELSLVKDIPVLIAIDQYNN-WFTFSEYEEPVTIRS 359
           ++V+ G+ ++     +VGVV++  K  S +    +L+A+D  N  W   +  +E  T+  
Sbjct: 217 EVVEQGLTRVRNATDAVGVVLKELKAQSALGLFHLLVAVDGVNALWGRTTLKKEDRTL-- 274

Query: 360 TRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSFARTCHMFQ 404
              +   EL++V+  R M+ ND   GA      V S ++T  +F+
Sbjct: 275 ---IAPEELSLVHNLRKMVKNDWHGGAI-----VLSLSQTGSLFK 311

Involved in mediating interferon-gamma-induced cell death.

Mus musculus (taxid: 10090)

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	404
449455118	454	PREDICTED: uncharacterized protein LOC10	0.950	0.845	0.675	1e-150
255586314	465	conserved hypothetical protein [Ricinus	0.948	0.823	0.649	1e-146
225434411	457	PREDICTED: 28S ribosomal protein S29, mi	0.846	0.748	0.718	1e-143
356565942	437	PREDICTED: uncharacterized protein LOC10	0.799	0.739	0.726	1e-141
356539682	436	PREDICTED: 28S ribosomal protein S29, mi	0.769	0.713	0.741	1e-141
357458023	446	28S ribosomal protein S29 [Medicago trun	0.928	0.840	0.625	1e-139
15219396	480	mitochondrial 28S ribosomal protein S29-	0.849	0.714	0.676	1e-133
297850088	480	hypothetical protein ARALYDRAFT_471887 [	0.965	0.812	0.594	1e-132
224124712	325	predicted protein [Populus trichocarpa]	0.641	0.796	0.823	1e-127
449464748	445	PREDICTED: uncharacterized protein LOC10	0.928	0.842	0.615	1e-126

>gi|449455118|ref|XP_004145300.1| PREDICTED: uncharacterized protein LOC101220451 [Cucumis sativus]

 Score =  537 bits (1383), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 268/397 (67%), Positives = 310/397 (78%), Gaps = 13/397 (3%)

Query: 2   LRLISRAAAAAAA--LSKQRNDTVLTSTSILIHQFFYSTKTQTKSSKKKQDDNKKSSKSK 59
           +R I RA AAA+    S +    +L+ TS       YS KT TKS  KK     K  KS+
Sbjct: 1   MRSILRATAAASKHHFSNRNPSPILSLTS------NYSAKT-TKSPVKK----GKKGKSE 49

Query: 60  SKSSDANSLSAPAAAQADSADDLESVRARARRLAEDDRNPSLDVGPNHRPLFTKTTSLSL 119
           + +   +  SAPAAA  D    L   + RARRLA ++ + SLDVGPN RPLFT  +SLS 
Sbjct: 50  ADAKAGDDPSAPAAASNDLDAALSDDKIRARRLAAEENDTSLDVGPNGRPLFTSASSLSQ 109

Query: 120 LTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDP 179
           LTRKDA TYFK + + LN +LPEGLP GM+ EF++S+R A+LVRQSFLD+RDNFRR+VDP
Sbjct: 110 LTRKDAGTYFKLNMEGLNEVLPEGLPMGMVKEFEESIRSAVLVRQSFLDLRDNFRRVVDP 169

Query: 180 SLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKN 239
           SL S  G KIRKQIVLDGP+ CGKSI LAMLV WAREEGWLVLYVP GR WTHGG+F+KN
Sbjct: 170 SLLSPAGSKIRKQIVLDGPVNCGKSIALAMLVQWAREEGWLVLYVPSGRRWTHGGFFFKN 229

Query: 240 PQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEG 299
           PQTGLWDTP+QAE+VL+DF+KYNE+ LR+LPCQI +PIPLGEGAGVG+ KG DS  + EG
Sbjct: 230 PQTGLWDTPVQAEDVLRDFVKYNETQLRQLPCQISEPIPLGEGAGVGMAKGADSMRMPEG 289

Query: 300 STLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRS 359
           STL+DL+  GI   H +VGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVT+RS
Sbjct: 290 STLYDLIDTGIKHTHVAVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTVRS 349

Query: 360 TRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSF 396
           TRP+HARELAMV AFRSMMH+DMMVGAFSHSTAVG  
Sbjct: 350 TRPIHARELAMVKAFRSMMHDDMMVGAFSHSTAVGKL 386

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255586314|ref|XP_002533808.1| conserved hypothetical protein [Ricinus communis] gi|223526262|gb|EEF28577.1| conserved hypothetical protein [Ricinus communis]

 Score =  524 bits (1350), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 269/414 (64%), Positives = 310/414 (74%), Gaps = 31/414 (7%)

Query: 1   MLRLISRAAAAAAALSKQRNDTVLTSTSILIHQ-----FFYSTKTQTKSSKKKQDDNKKS 55
           MLRLI RAA        Q+  + + S S L  Q      +YS+K  TK +KK    N + 
Sbjct: 1   MLRLIVRAALRKP----QKPSSPIPSVSSLYDQNNHLCSYYSSKP-TKPNKK----NVQK 51

Query: 56  SKSKSKSSDANSLSAPAAAQADSADDLESVRARARRLAEDDRNPSLDVGPNHRPLFTKTT 115
           SK K  S +      PA A    A   +    RA RLAE++  PSLDVGPN RPLFT T+
Sbjct: 52  SKPKKPSEE------PATANDLEASLFDDGATRAHRLAEEENVPSLDVGPNGRPLFTSTS 105

Query: 116 SLSLLTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRR 175
           SLS LTRKD+CTYFKFSE+ LN  LPEGLP G++ EF++SMR A+LVRQSFLD+RDNFRR
Sbjct: 106 SLSQLTRKDSCTYFKFSEEGLNERLPEGLPMGLVKEFEESMRRAVLVRQSFLDLRDNFRR 165

Query: 176 IVDPSLQSTNG--PKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG 233
           IVDP L S+NG  PK+RKQIVLDGP+ CGKSITLAMLVHWAREEGWLV YVP GR+WTHG
Sbjct: 166 IVDPPLSSSNGKGPKVRKQIVLDGPVSCGKSITLAMLVHWAREEGWLVFYVPTGRDWTHG 225

Query: 234 GYFYKNPQTGLWDTPLQAENVLK---------DFIKYNESHLRELPCQILDPIPLGEGAG 284
           G+FYKNP+TGLWDTP+ A ++LK          F+KYNE HL+ LPC ILDP+PLGEGAG
Sbjct: 226 GFFYKNPETGLWDTPVHAGSILKARILNLFTSSFLKYNELHLKRLPCHILDPVPLGEGAG 285

Query: 285 VGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNN 344
           VG +KGV S  I EGSTL+DL+Q+GI   HA+VG VVRLRKELSLV D+PVL AIDQYNN
Sbjct: 286 VGWMKGVQSMPIPEGSTLYDLIQIGIKHTHAAVGTVVRLRKELSLVTDVPVLFAIDQYNN 345

Query: 345 WFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSFAR 398
           WFTFSEYEEPVTIRS RP+HARELA VNAFRSMMH+DMMVGAFSHSTAVG   +
Sbjct: 346 WFTFSEYEEPVTIRSCRPIHARELATVNAFRSMMHDDMMVGAFSHSTAVGKLRK 399

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225434411|ref|XP_002271596.1| PREDICTED: 28S ribosomal protein S29, mitochondrial [Vitis vinifera] gi|297745805|emb|CBI15861.3| unnamed protein product [Vitis vinifera]

 Score =  513 bits (1321), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 248/345 (71%), Positives = 289/345 (83%), Gaps = 3/345 (0%)

Query: 54  KSSKSKSKSSDANSLSAPAAAQADSADDLESVRARARRLAEDDRNPSLDVGPNHRPLFTK 113
           K+ K+KSK  DA S  A AAA  D   DL    AR RRLAEDD++PSLDVGPN R LFT 
Sbjct: 46  KAKKAKSKP-DAKSEEASAAAADDGLSDLLDEEARDRRLAEDDKDPSLDVGPNGRALFTS 104

Query: 114 TTSLSLLTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNF 173
            T++S L+RKD CTY KFS + LNA+LPEGL  GM+ EF++S R ALLVR+SFLD+RDNF
Sbjct: 105 ATTISQLSRKDTCTYMKFSTEGLNAVLPEGLTAGMVKEFEESRRSALLVRRSFLDLRDNF 164

Query: 174 RRIVDPSLQSTNG--PKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWT 231
           RRIVDP L+S++G  PK+ KQI+LDGP+  GKSI LAMLVHWAR+EGWLV YVPRGR+WT
Sbjct: 165 RRIVDPPLRSSDGKGPKVLKQIILDGPVSSGKSIALAMLVHWARDEGWLVFYVPRGRDWT 224

Query: 232 HGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGV 291
           HGG+FYKNPQTG WDTP+QA N+L+DF+K NESHL++L CQI DPIPLGEGAGVG +KGV
Sbjct: 225 HGGFFYKNPQTGFWDTPVQAANILQDFLKRNESHLKQLTCQISDPIPLGEGAGVGWMKGV 284

Query: 292 DSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEY 351
           DS  + EGSTL+DLVQ G++  HA+VGVVVRLRKELSLVKDIPVLIA+DQYN+WFTF+EY
Sbjct: 285 DSMAMPEGSTLYDLVQTGMSHTHAAVGVVVRLRKELSLVKDIPVLIAVDQYNSWFTFTEY 344

Query: 352 EEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSF 396
           EE VT+RS RP+HA+ELA VNAFRSMMHNDMMVGAFSHSTAVG  
Sbjct: 345 EEAVTVRSCRPIHAKELATVNAFRSMMHNDMMVGAFSHSTAVGKL 389

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356565942|ref|XP_003551194.1| PREDICTED: uncharacterized protein LOC100786442 [Glycine max]

 Score =  508 bits (1309), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 239/329 (72%), Positives = 276/329 (83%), Gaps = 6/329 (1%)

Query: 72  AAAQADSADDLESVRARARRLAEDDRNPSLDVGPNHRPLFTKTTSLSLLTRKDACTYFKF 131
           AAA     DD E    R R+L  DD+NPSLDVGP  RPLF+   SLS L+R D CTYFK 
Sbjct: 47  AAAAVALFDDQE----RRRQLDADDKNPSLDVGPKGRPLFSAVPSLSHLSRNDVCTYFKL 102

Query: 132 SEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP--KI 189
           ++D LN +LPEGLP GM+ EF+DS+R ALLVRQSFLD+RDNFRR+VDP + S+NG   K+
Sbjct: 103 TKDALNKVLPEGLPMGMVDEFQDSLRTALLVRQSFLDLRDNFRRVVDPPMWSSNGKGVKV 162

Query: 190 RKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPL 249
           RKQ+VLDGP+ CGKSI LAMLV WAREEGWLVLYVP+G++WTHGG+FYK+PQTGLWDTP+
Sbjct: 163 RKQVVLDGPVSCGKSIVLAMLVQWAREEGWLVLYVPKGKDWTHGGFFYKHPQTGLWDTPV 222

Query: 250 QAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMG 309
           QAENVLKDF+KYNES+L+E+PCQI DPI LGEGAGVG LK VDS  I EG+ L++LV+ G
Sbjct: 223 QAENVLKDFLKYNESYLKEMPCQIFDPILLGEGAGVGWLKDVDSLAIPEGTNLYELVKAG 282

Query: 310 INQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELA 369
           I Q HA+VGVVVRLRKELSLVKD PVLIA+DQYNNWFTFSEYEEPVTIRS RP+HAREL 
Sbjct: 283 IEQTHAAVGVVVRLRKELSLVKDRPVLIAVDQYNNWFTFSEYEEPVTIRSCRPIHARELT 342

Query: 370 MVNAFRSMMHNDMMVGAFSHSTAVGSFAR 398
           MV AFRSM+H+DMMVGAFSHSTAVG   +
Sbjct: 343 MVKAFRSMVHDDMMVGAFSHSTAVGKLRK 371

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539682|ref|XP_003538324.1| PREDICTED: 28S ribosomal protein S29, mitochondrial-like [Glycine max]

 Score =  507 bits (1305), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 232/313 (74%), Positives = 271/313 (86%), Gaps = 2/313 (0%)

Query: 88  RARRLAEDDRNPSLDVGPNHRPLFTKTTSLSLLTRKDACTYFKFSEDELNAMLPEGLPTG 147
           R R+L  DD+NPSLDVGPN RPLF+   S S L+R D CTYFK ++D LN +LPEGLP G
Sbjct: 58  RRRQLDADDKNPSLDVGPNGRPLFSAAPSFSHLSRNDVCTYFKLTKDALNKVLPEGLPVG 117

Query: 148 MLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP--KIRKQIVLDGPLCCGKSI 205
           M+ EF+DS+R ALLVRQSFLD+RDNFRR+VDP + S+NG   K+RKQ+VLDGP+ CGKSI
Sbjct: 118 MVNEFQDSLRTALLVRQSFLDLRDNFRRVVDPPMWSSNGKGVKVRKQVVLDGPVSCGKSI 177

Query: 206 TLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESH 265
            LAMLV WAREEGWLVLYVP+G++WTHGG+FYK+PQTGLWDTP+QAE+VLKDF+KYNES+
Sbjct: 178 ALAMLVQWAREEGWLVLYVPKGKDWTHGGFFYKHPQTGLWDTPVQAEDVLKDFLKYNESY 237

Query: 266 LRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRK 325
           L+E+PCQI DPI LGEGAGVG LK VDS  I EG+ L++LV+ GI Q HA++GVVVRLRK
Sbjct: 238 LKEMPCQIFDPILLGEGAGVGWLKDVDSLAIPEGTNLYELVKTGIEQTHAAIGVVVRLRK 297

Query: 326 ELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVG 385
           ELSLVKD PVLIA+DQYNNWFTFSEYEEPVTIRS RP+HARELAMV AFRSM+H+DMMVG
Sbjct: 298 ELSLVKDRPVLIAVDQYNNWFTFSEYEEPVTIRSCRPIHARELAMVKAFRSMVHDDMMVG 357

Query: 386 AFSHSTAVGSFAR 398
           AFSHSTAVG   +
Sbjct: 358 AFSHSTAVGKLRK 370

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357458023|ref|XP_003599292.1| 28S ribosomal protein S29 [Medicago truncatula] gi|355488340|gb|AES69543.1| 28S ribosomal protein S29 [Medicago truncatula]

 Score =  501 bits (1290), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 252/403 (62%), Positives = 304/403 (75%), Gaps = 28/403 (6%)

Query: 1   MLRLISRAAAAAAALSKQRNDTVLTSTSILIHQFFYSTKTQTKSSKKKQDDNKKSSKSKS 60
           MLR I++ AA       + + + + + +  I    YS+K+ +K +K      K +SK+  
Sbjct: 1   MLRHITKTAA-------KNHYSFIRNITPTISSLNYSSKSPSKPTKP----TKPTSKT-- 47

Query: 61  KSSDANSLSAPAAAQADSADDLESVRARARRLAEDDRNPSLDVGPNHRPLFTKTTSLSLL 120
                     PA   A +AD     + R R L  D++NPSL+VGPN R LFT +TSLS L
Sbjct: 48  ----------PATTTAATADIFFDEQERLRNLTADEKNPSLNVGPNGRRLFTSSTSLSKL 97

Query: 121 TRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPS 180
           T  D CTYF  +++ L+A+LPEGLP GM  EFKDSMR AL+VRQSFLD+RDNF+R+VDP 
Sbjct: 98  TNNDICTYFNLTKEGLDAVLPEGLPIGMEKEFKDSMRTALMVRQSFLDLRDNFKRVVDPR 157

Query: 181 LQSTNGP--KIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYK 238
           + S +G   K+RKQ+VLDGP+ CGKSI LAMLV WAREEGWLVLYVP  +EWTHGG+FYK
Sbjct: 158 MWSPHGKGVKVRKQVVLDGPVSCGKSIALAMLVQWAREEGWLVLYVPSAKEWTHGGFFYK 217

Query: 239 NPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISE 298
           +PQTGLWDTP+QAENVLKDF+KYNES+L+ELPCQI DPIPLGEGAGVG LK VDS  I E
Sbjct: 218 HPQTGLWDTPVQAENVLKDFLKYNESYLKELPCQIFDPIPLGEGAGVGWLKDVDSMAIPE 277

Query: 299 GSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQ---YNNWFTFSEYEEPV 355
           G+ L++LV+ GI Q HA+VGVVVRLRKELSLVK++PVLIAIDQ   YNNWFTFSEYEEPV
Sbjct: 278 GTMLYELVKTGIEQTHAAVGVVVRLRKELSLVKNMPVLIAIDQVRNYNNWFTFSEYEEPV 337

Query: 356 TIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSFAR 398
           TIRS RP+HA+EL MV AFRSMMH+DMMVGAFSHSTAVG   +
Sbjct: 338 TIRSCRPIHAKELTMVKAFRSMMHDDMMVGAFSHSTAVGKLRK 380

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15219396|ref|NP_173131.1| mitochondrial 28S ribosomal protein S29-like protein [Arabidopsis thaliana] gi|17064866|gb|AAL32587.1| Unknown protein [Arabidopsis thaliana] gi|20259906|gb|AAM13300.1| unknown protein [Arabidopsis thaliana] gi|332191391|gb|AEE29512.1| mitochondrial 28S ribosomal protein S29-like protein [Arabidopsis thaliana]

 Score =  481 bits (1238), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 236/349 (67%), Positives = 274/349 (78%), Gaps = 6/349 (1%)

Query: 54  KSSKSKSKSSDANSLSAPAAA-QADSADDLESVRARARRLAEDDRNPSLDVGPNHRPLFT 112
           +  KSK K  D  +  A      A   DDLE+   RA+RLA+D++ PSLDVGPN RPLFT
Sbjct: 68  EGKKSKPKGGDPGAAGAEEGEFGAAGGDDLEA--GRAKRLADDEKIPSLDVGPNGRPLFT 125

Query: 113 -KTTSLSLLTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRD 171
            K T+LS LT KD  +YFKF E  L A+LPEGL +G+  EF +S R ALLVR+S+L +RD
Sbjct: 126 PKDTTLSQLTHKDIGSYFKFDEAALKAVLPEGLASGIEDEFNESWRPALLVRKSYLALRD 185

Query: 172 NFRRIVDPSLQSTN--GPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGRE 229
           NFRRI DP +  ++  G K++KQIVLDGP+ CGKSI LAMLVHWAR+EGWLVLY P+GR+
Sbjct: 186 NFRRIADPPMWPSDSKGVKLQKQIVLDGPVKCGKSIALAMLVHWARDEGWLVLYAPKGRD 245

Query: 230 WTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLK 289
           WTHGGYFYKNP TG WDTPLQAEN+LKDF+K+NES LREL C+I DPI LGEGAGVG LK
Sbjct: 246 WTHGGYFYKNPHTGFWDTPLQAENILKDFVKFNESRLRELRCKIHDPIVLGEGAGVGYLK 305

Query: 290 GVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFS 349
           G D+  I E STL+DLVQMGI   HA+V VVVRLRKELS+VKD+PVLI IDQYN+WFTFS
Sbjct: 306 GADAMPIPEDSTLYDLVQMGIKSTHAAVNVVVRLRKELSVVKDVPVLIVIDQYNSWFTFS 365

Query: 350 EYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSFAR 398
           E+EEPVT RS RP+HAREL  VNAFRSMMH DMMVGAFSHSTAVG   +
Sbjct: 366 EFEEPVTPRSCRPIHARELTTVNAFRSMMHEDMMVGAFSHSTAVGKLRK 414

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297850088|ref|XP_002892925.1| hypothetical protein ARALYDRAFT_471887 [Arabidopsis lyrata subsp. lyrata] gi|297338767|gb|EFH69184.1| hypothetical protein ARALYDRAFT_471887 [Arabidopsis lyrata subsp. lyrata]

 Score =  479 bits (1233), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 251/422 (59%), Positives = 300/422 (71%), Gaps = 32/422 (7%)

Query: 1   MLRLISRAAAAAAALSKQR---NDTVL-----TSTSI------LIHQFFYSTKTQTKSSK 46
           M + + R AA    L++     NDTV      TS ++      L H     + +++  S 
Sbjct: 1   MWKFVGRLAAGNVKLNRMSSILNDTVCHFSAPTSAAVGTLFPSLDHVHRSFSSSKSTKSS 60

Query: 47  KKQDDNKKSSKSKSKSSDANSLSAPAAAQAD-------SADDLESVRARARRLAEDDRNP 99
             +    +  KSK K  D      P AA AD         DDLE+   RA+RLA+D++ P
Sbjct: 61  ITKTKKAEGKKSKPKGGD------PGAAGADDGEFGAAGGDDLEA--GRAKRLADDEKIP 112

Query: 100 SLDVGPNHRPLFT-KTTSLSLLTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRY 158
           SLDVGPN RPLFT K T+LS L+ KD  +YFKF E  L A+LPEGL +G+  EF +S R 
Sbjct: 113 SLDVGPNGRPLFTPKDTTLSQLSHKDIGSYFKFDEAALKAVLPEGLASGIEDEFNESWRP 172

Query: 159 ALLVRQSFLDIRDNFRRIVDPSLQSTNGP--KIRKQIVLDGPLCCGKSITLAMLVHWARE 216
           ALLVR++FL +RDNF RI DP +  ++G   K++KQIVLDGP+ CGKSI LAMLVHWAR+
Sbjct: 173 ALLVRKNFLALRDNFSRIADPPMWPSDGKGVKLKKQIVLDGPVKCGKSIALAMLVHWARD 232

Query: 217 EGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDP 276
           EGWLVLY P+GR+WTHGGYFYKNP TG WDTPLQAEN+LKDF+K+NES LREL C+I DP
Sbjct: 233 EGWLVLYAPKGRDWTHGGYFYKNPHTGFWDTPLQAENILKDFVKFNESRLRELRCKIHDP 292

Query: 277 IPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVL 336
           I LGEGAGVG LKG D+  I E STL+DLVQMGI   HA+V VVVRLRKELS+VKD+PVL
Sbjct: 293 IVLGEGAGVGYLKGADTMPIPEDSTLYDLVQMGIKSTHAAVNVVVRLRKELSVVKDVPVL 352

Query: 337 IAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSF 396
           I IDQYN+WFTFSE+EEPVT RS RP+HAREL  VNAFRSMMH DMMVGAFSHSTAVG  
Sbjct: 353 IVIDQYNSWFTFSEFEEPVTPRSCRPIHARELTTVNAFRSMMHEDMMVGAFSHSTAVGKL 412

Query: 397 AR 398
            +
Sbjct: 413 RK 414

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124712|ref|XP_002319403.1| predicted protein [Populus trichocarpa] gi|222857779|gb|EEE95326.1| predicted protein [Populus trichocarpa]

 Score =  461 bits (1186), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 214/260 (82%), Positives = 234/260 (90%), Gaps = 1/260 (0%)

Query: 139 MLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGP 198
           MLPEGLP GM+ EF++SMR ALLVRQSFLD+RDNFRRIVDP L S++G K+RKQIVLDGP
Sbjct: 1   MLPEGLPMGMVKEFEESMRSALLVRQSFLDLRDNFRRIVDPPLLSSDG-KVRKQIVLDGP 59

Query: 199 LCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDF 258
             CGKSITLAMLVHWAREEGWLV YVPRGREWTHGGYFYKNP TGLWDTP+QAEN LKDF
Sbjct: 60  SNCGKSITLAMLVHWAREEGWLVFYVPRGREWTHGGYFYKNPITGLWDTPIQAENALKDF 119

Query: 259 IKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVG 318
           +KYNES L++LPC I DP+PLGEGAG+GLLKGVDS  + E STL+DLVQ+GI Q HA+VG
Sbjct: 120 VKYNESLLKQLPCHIFDPVPLGEGAGIGLLKGVDSVPVPESSTLYDLVQIGIKQTHAAVG 179

Query: 319 VVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMM 378
           VV+RLRKELSLVKDIPVL AIDQYNNWFTFSEYEEPVT+RS RPVHARELAMVNAFRSMM
Sbjct: 180 VVLRLRKELSLVKDIPVLFAIDQYNNWFTFSEYEEPVTMRSCRPVHARELAMVNAFRSMM 239

Query: 379 HNDMMVGAFSHSTAVGSFAR 398
           HN MMVGAFSHSTAVG   +
Sbjct: 240 HNSMMVGAFSHSTAVGKLRK 259

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464748|ref|XP_004150091.1| PREDICTED: uncharacterized protein LOC101212097 [Cucumis sativus]

 Score =  458 bits (1178), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 245/398 (61%), Positives = 290/398 (72%), Gaps = 23/398 (5%)

Query: 1   MLRLISRAAAAAAA--LSKQRNDTVLTSTSILIHQFFYSTKTQTKSSKKKQDDNKKSSKS 58
           MLR I RA +AA+   +  +    +L+ TS       YS KT TKS  KK     K  KS
Sbjct: 1   MLRSILRATSAASKHHICNRNPAPILSLTS------NYSAKT-TKSPVKK----GKKGKS 49

Query: 59  KSKSSDANSLSAPAAAQADSADDLESVRARARRLAEDDRNPSLDVGPNHRPLFTKTTSLS 118
           ++ +   +  SA AAA  D    L   + RARRLA ++ + SLDVGPN RPLFT  +SLS
Sbjct: 50  EADAKAGDDPSASAAASDDLDAALSDDKIRARRLAAEENDTSLDVGPNGRPLFTSASSLS 109

Query: 119 LLTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVD 178
            LTRKDA TYFK++ + LN +LPEGLP GM+ EF++S+R A+LVRQSFLD+RDNFRR+VD
Sbjct: 110 QLTRKDAGTYFKYNMEGLNEVLPEGLPMGMVKEFEESIRSAVLVRQSFLDLRDNFRRVVD 169

Query: 179 PSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYK 238
           PSL S  G KIRKQIVLDGP+ CGKSI LAMLV WAREEGWLVLYVP GR WTHGG+F+K
Sbjct: 170 PSLLSPAGSKIRKQIVLDGPVNCGKSIALAMLVQWAREEGWLVLYVPSGRRWTHGGFFFK 229

Query: 239 NPQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISE 298
           N QTGLWDTP+QAE+VL+DF+KYNE  LR+LPCQI +PIPLGEGAGVG+ KG DS  + E
Sbjct: 230 NHQTGLWDTPVQAEDVLRDFLKYNEIQLRQLPCQIYEPIPLGEGAGVGMAKGADSMRMPE 289

Query: 299 GSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEYEEPVTIR 358
           GSTL+DL+  GI   H +VGVVVRLRKELSLVKDIPVLIAIDQYNN+F F +    ++  
Sbjct: 290 GSTLYDLIDTGIKHTHVAVGVVVRLRKELSLVKDIPVLIAIDQYNNYFFFFQSMMRIS-- 347

Query: 359 STRPVHARELAMVNAFRSMMHNDMMVGAFSHSTAVGSF 396
                    L  V AFRSMMH+DMMVGAFSHSTAVG  
Sbjct: 348 --------NLWQVKAFRSMMHDDMMVGAFSHSTAVGKL 377

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	404
TAIR|locus:2015631	480	AT1G16870 "AT1G16870" [Arabido	0.754	0.635	0.685	2.9e-112
DICTYBASE|DDB_G0281699	403	DDB_G0281699 "28S ribosomal pr	0.351	0.352	0.316	1.5e-11
UNIPROTKB|P51398	398	DAP3 "28S ribosomal protein S2	0.594	0.603	0.267	2.5e-11
UNIPROTKB|H9L0M5	398	H9L0M5 "Uncharacterized protei	0.576	0.585	0.271	4.3e-11
UNIPROTKB|I3LS10	398	LOC100625274 "Uncharacterized	0.571	0.580	0.262	9.5e-11
UNIPROTKB|F1RLM4	424	LOC100625274 "Uncharacterized	0.571	0.544	0.262	1.1e-10
UNIPROTKB|P82922	397	DAP3 "28S ribosomal protein S2	0.576	0.586	0.256	1.2e-10
UNIPROTKB|F1P6P0	393	DAP3 "Uncharacterized protein"	0.579	0.595	0.259	2.7e-10
RGD|1305339	391	Dap3 "death associated protein	0.611	0.631	0.262	2.2e-09
ZFIN|ZDB-GENE-051129-2	402	dap3 "death associated protein	0.576	0.579	0.270	3.1e-09

TAIR|locus:2015631 AT1G16870 "AT1G16870" [Arabidopsis thaliana (taxid:3702)]

 Score = 1108 (395.1 bits), Expect = 2.9e-112, P = 2.9e-112
 Identities = 211/308 (68%), Positives = 243/308 (78%)

Query:    94 EDDRNPSLDVGPNHRPXXX-XXXXXXXXXRKDACTYFKFSEDELNAMLPEGLPTGMLGEF 152
             +D++ PSLDVGPN RP              KD  +YFKF E  L A+LPEGL +G+  EF
Sbjct:   107 DDEKIPSLDVGPNGRPLFTPKDTTLSQLTHKDIGSYFKFDEAALKAVLPEGLASGIEDEF 166

Query:   153 KDSMRYALLVRQSFLDIRDNFRRIVDPSL--QSTNGPKIRKQIVLDGPLCCGKSITLAML 210
              +S R ALLVR+S+L +RDNFRRI DP +    + G K++KQIVLDGP+ CGKSI LAML
Sbjct:   167 NESWRPALLVRKSYLALRDNFRRIADPPMWPSDSKGVKLQKQIVLDGPVKCGKSIALAML 226

Query:   211 VHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHLRELP 270
             VHWAR+EGWLVLY P+GR+WTHGGYFYKNP TG WDTPLQAEN+LKDF+K+NES LREL 
Sbjct:   227 VHWARDEGWLVLYAPKGRDWTHGGYFYKNPHTGFWDTPLQAENILKDFVKFNESRLRELR 286

Query:   271 CQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLV 330
             C+I DPI LGEGAGVG LKG D+  I E STL+DLVQMGI   HA+V VVVRLRKELS+V
Sbjct:   287 CKIHDPIVLGEGAGVGYLKGADAMPIPEDSTLYDLVQMGIKSTHAAVNVVVRLRKELSVV 346

Query:   331 KDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMHNDMMVGAFSHS 390
             KD+PVLI IDQYN+WFTFSE+EEPVT RS RP+HAREL  VNAFRSMMH DMMVGAFSHS
Sbjct:   347 KDVPVLIVIDQYNSWFTFSEFEEPVTPRSCRPIHARELTTVNAFRSMMHEDMMVGAFSHS 406

Query:   391 TAVGSFAR 398
             TAVG   +
Sbjct:   407 TAVGKLRK 414

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0006164 "purine nucleotide biosynthetic process" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

DICTYBASE|DDB_G0281699 DDB_G0281699 "28S ribosomal protein S29, mitochondrial" [Dictyostelium discoideum (taxid:44689)]

 Score = 182 (69.1 bits), Expect = 1.5e-11, P = 1.5e-11
 Identities = 51/161 (31%), Positives = 83/161 (51%)

Query:   194 VLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGG---YFYKNPQTGLWDTPLQ 250
             VLDG    GKSI+LA +  WA+++ WLV+Y+P    + + G   +F  NP   L+     
Sbjct:   145 VLDGVAGSGKSISLAQVAFWAQQQDWLVVYIPNASSFINRGALTHFNINPL--LFAQNNL 202

Query:   251 AENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGI 310
               N +K F++ N + LRE+  +    I   E  G          E S   TLFDL+    
Sbjct:   203 CFNFIKQFVEVNHAKLREIKLKTKFKI---ESTGW---------ESSPNKTLFDLLSS-- 248

Query:   311 NQMHASVGVVVRLRKELSLVKDIPVLIAIDQYNNWFTFSEY 351
              +  +S  +    ++EL+ + + PVL+AID +N+++  S+Y
Sbjct:   249 TKYDSSSEIFYHFKRELNTIHEFPVLVAIDGFNHFYRPSDY 289

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|P51398 DAP3 "28S ribosomal protein S29, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 180 (68.4 bits), Expect = 2.5e-11, P = 2.5e-11
 Identities = 74/277 (26%), Positives = 125/277 (45%)

Query:   128 YFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP 187
             ++  S  +L  + P GLP   + + K      L+VR+  L++    +        S   P
Sbjct:    67 HYNISPQDLETVFPHGLPPRFVMQVKTFSEACLMVRKPALELLHYLKNT------SFAYP 120

Query:   188 KIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG--GYFYKNPQTGLW 245
              IR   +L G    GK+++L  ++H+  ++ WL+L++P    W          +     +
Sbjct:   121 AIR--YLLYGEKGTGKTLSLCHVIHFCAKQDWLILHIPDAHLWVKNCRDLLQSSYNKQRF 178

Query:   246 DTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGV-DSKEISE-GSTLF 303
             D PL+A   LK+F   NE  L ++  Q        E       K V + +E +E GS L 
Sbjct:   179 DQPLEASTWLKNFKTTNERFLNQIKVQ--------E-------KYVWNKRESTEKGSPLG 223

Query:   304 DLVQMGINQMHAS---VGVVVRLRKELSLVKDIPVLIAIDQYNN-WFTFSEYEEPVTIRS 359
             ++V+ GI ++  +   VG+V++  K  S +    +L+A+D  N  W   +   E  +   
Sbjct:   224 EVVEQGITRVRNATDAVGIVLKELKRQSSLGMFHLLVAVDGINALWGRTTLKREDKS--- 280

Query:   360 TRPVHARELAMVNAFRSMMHNDMMVGAF-SHSTAVGS 395
               P+   ELA+V+  R MM ND   GA  S  +  GS
Sbjct:   281 --PIAPEELALVHNLRKMMKNDWHGGAIVSALSQTGS 315

GO:0005761 "mitochondrial ribosome" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0008637 "apoptotic mitochondrial changes" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005739 "mitochondrion" evidence=IDA

GO:0097190 "apoptotic signaling pathway" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|H9L0M5 H9L0M5 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 178 (67.7 bits), Expect = 4.3e-11, P = 4.3e-11
 Identities = 72/265 (27%), Positives = 121/265 (45%)

Query:   128 YFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP 187
             ++    +E+ A+ P GLP     + K      ++VR+  L++   F  + + +      P
Sbjct:    67 HYSIPLEEVKAVFPHGLPYRFQQQIKTFQEACVMVRKPALEL---FTYLKNSNFAH---P 120

Query:   188 KIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG--GYFYKNPQTGLW 245
              +R   V+ G    GK++TL  +VH+   +GWLVL++P    W          +      
Sbjct:   121 VVR--YVIYGERGTGKTMTLCHVVHFCARQGWLVLHIPDAHLWVKNCKELMQSSYNKERL 178

Query:   246 DTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDL 305
             D PLQA   L++F   NE  L+E+  Q       G+          DS E  +G  L ++
Sbjct:   179 DQPLQASFWLRNFRTTNEHFLKEIKTQ--QKYVWGKR---------DSTE--QGRPLGEV 225

Query:   306 VQMGINQM-HAS--VGVVVRLRKELSLVKDIPVLIAIDQYNN-WFTFSEYEEPVTIRSTR 361
             V+ G+ ++ +AS  VGVV++  K+   +    VL+A+D  N  W   +  +E  +     
Sbjct:   226 VEQGLTRVKNASDAVGVVLKEIKQQCCLGSFRVLVAVDGVNALWGRTTLKKEDKS----- 280

Query:   362 PVHARELAMVNAFRSMMHNDMMVGA 386
             PV   EL +V   R M+ N+   GA
Sbjct:   281 PVSPEELTLVYNLRKMVMNNWSGGA 305

GO:0005761 "mitochondrial ribosome" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0008637 "apoptotic mitochondrial changes" evidence=IEA

UNIPROTKB|I3LS10 LOC100625274 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 175 (66.7 bits), Expect = 9.5e-11, P = 9.5e-11
 Identities = 70/267 (26%), Positives = 120/267 (44%)

Query:   128 YFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP 187
             ++  S  EL  + P GLP     + K      L+VR+  L++           L++TN  
Sbjct:    67 HYNISLQELKTVFPHGLPPRFAMQVKTFNEACLMVRKPALELLHY--------LKNTNFA 118

Query:   188 KIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG--GYFYKNPQTGLW 245
                 + VL G    GK+++L  ++H+  ++ WL+L++P    W          N     +
Sbjct:   119 HPAVRYVLYGEKGTGKTLSLCHILHFCAKQNWLILHIPDAHIWVKNCRDLLQSNYNKQRF 178

Query:   246 DTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGV-DSKEISE-GSTLF 303
             D PL+A   LK+F   NE  L ++  Q        E       K V + +E +E G  L 
Sbjct:   179 DQPLEASTWLKNFKTANEHFLSQIKVQ--------E-------KYVWNKRESTEKGRPLG 223

Query:   304 DLVQMGINQMHAS---VGVVVRLRKELSLVKDIPVLIAIDQYNN-WFTFSEYEEPVTIRS 359
             ++V+ GI ++  +   VG+V++  K  S +    +L+A+D  N  W   +   E  +   
Sbjct:   224 EVVEQGIMRVRNATDAVGIVLKELKRQSSLGIFHLLVAVDGVNALWGRTTLKREDKS--- 280

Query:   360 TRPVHARELAMVNAFRSMMHNDMMVGA 386
               P+   ELA+++  R M+ ND   GA
Sbjct:   281 --PIAPEELALIHNLRKMVKNDWQGGA 305

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005761 "mitochondrial ribosome" evidence=IEA

UNIPROTKB|F1RLM4 LOC100625274 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 175 (66.7 bits), Expect = 1.1e-10, P = 1.1e-10
 Identities = 70/267 (26%), Positives = 120/267 (44%)

Query:   128 YFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP 187
             ++  S  EL  + P GLP     + K      L+VR+  L++           L++TN  
Sbjct:    93 HYNISLQELKTVFPHGLPPRFAMQVKTFNEACLMVRKPALELLHY--------LKNTNFA 144

Query:   188 KIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG--GYFYKNPQTGLW 245
                 + VL G    GK+++L  ++H+  ++ WL+L++P    W          N     +
Sbjct:   145 HPAVRYVLYGEKGTGKTLSLCHILHFCAKQNWLILHIPDAHIWVKNCRDLLQSNYNKQRF 204

Query:   246 DTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGV-DSKEISE-GSTLF 303
             D PL+A   LK+F   NE  L ++  Q        E       K V + +E +E G  L 
Sbjct:   205 DQPLEASTWLKNFKTANEHFLSQIKVQ--------E-------KYVWNKRESTEKGRPLG 249

Query:   304 DLVQMGINQMHAS---VGVVVRLRKELSLVKDIPVLIAIDQYNN-WFTFSEYEEPVTIRS 359
             ++V+ GI ++  +   VG+V++  K  S +    +L+A+D  N  W   +   E  +   
Sbjct:   250 EVVEQGIMRVRNATDAVGIVLKELKRQSSLGIFHLLVAVDGVNALWGRTTLKREDKS--- 306

Query:   360 TRPVHARELAMVNAFRSMMHNDMMVGA 386
               P+   ELA+++  R M+ ND   GA
Sbjct:   307 --PIAPEELALIHNLRKMVKNDWQGGA 331

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005761 "mitochondrial ribosome" evidence=IEA

UNIPROTKB|P82922 DAP3 "28S ribosomal protein S29, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 174 (66.3 bits), Expect = 1.2e-10, P = 1.2e-10
 Identities = 68/265 (25%), Positives = 118/265 (44%)

Query:   128 YFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP 187
             ++  S  EL  + P GLP   + + K      L+VR+  L++           L++TN  
Sbjct:    66 HYNISIQELKTVFPHGLPPRFVMQVKTFNEACLMVRKPALELLHY--------LKNTNFA 117

Query:   188 KIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG--GYFYKNPQTGLW 245
                 + VL G    GK+++L  ++H+  ++ WL+L++P    W                +
Sbjct:   118 HPAVRYVLYGEKGTGKTLSLCHIIHFCAKQDWLILHIPDAHLWVKNCRDLLQSTYNKQRF 177

Query:   246 DTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDL 305
             D PL+A   LK+F   NE  L ++  Q  D     +          +S E  +GS L ++
Sbjct:   178 DQPLEASIWLKNFKTANERFLSQIKVQ--DKYVWNKR---------ESTE--KGSPLAEV 224

Query:   306 VQMGINQMHAS---VGVVVRLRKELSLVKDIPVLIAIDQYNN-WFTFSEYEEPVTIRSTR 361
             V+ GI ++  +   VG+V++  K  S +    +L+A+D  N  W   +   E  +     
Sbjct:   225 VEQGIMRVRNATDAVGIVLKELKRQSSLGVFRLLVAVDGVNALWGRTTLKREDKS----- 279

Query:   362 PVHARELAMVNAFRSMMHNDMMVGA 386
             P+   ELA++   R M+ ND   GA
Sbjct:   280 PITPEELALIYNLRKMVKNDWQGGA 304

GO:0005739 "mitochondrion" evidence=ISS

GO:0008637 "apoptotic mitochondrial changes" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0005761 "mitochondrial ribosome" evidence=IEA

UNIPROTKB|F1P6P0 DAP3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 171 (65.3 bits), Expect = 2.7e-10, P = 2.7e-10
 Identities = 70/270 (25%), Positives = 123/270 (45%)

Query:   125 ACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQST 184
             A  ++     +L  + P+GLP   + + K      L+VR+  L++           L++T
Sbjct:    59 AALHYHIPLQDLKTVFPQGLPPRFIMQVKTFNEACLMVRKPALELLHY--------LKNT 110

Query:   185 NGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG--GYFYKNPQT 242
             N      + VL G    GK+++L  +VH+  ++ WL+L++P    W     G    +   
Sbjct:   111 NFAHPAVRYVLYGEKGTGKTLSLCHVVHFCAKQDWLILHIPDAHLWVKNCRGLLQSSYNK 170

Query:   243 GLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGV-DSKEISE-GS 300
               +D P++A   LK+F   NE  L ++  Q        E       K V + +E +E GS
Sbjct:   171 QRFDQPVEASIWLKNFKTANERFLSQIKVQ--------E-------KYVWNKRESTEKGS 215

Query:   301 TLFDLVQMGINQMHAS---VGVVVRLRKELSLVKDIPVLIAIDQYNN-WFTFSEYEEPVT 356
              L  +V+ G+ ++  +   VG+V++  K  S +    +L+A+D  N  W   S   E  +
Sbjct:   216 PLGAVVEQGLTRVRNATDAVGIVLKELKNQSCLGAFHLLVAVDGVNALWGRTSLKREDKS 275

Query:   357 IRSTRPVHARELAMVNAFRSMMHNDMMVGA 386
             +     +   ELA+V + R M+ ND   GA
Sbjct:   276 L-----IAPEELALVCSLRKMVRNDWHGGA 300

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005761 "mitochondrial ribosome" evidence=IEA

RGD|1305339 Dap3 "death associated protein 3" [Rattus norvegicus (taxid:10116)]

 Score = 163 (62.4 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 75/286 (26%), Positives = 126/286 (44%)

Query:   128 YFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP 187
             ++     +L  + P GLP     + K      L+VR+  L++           L++TN  
Sbjct:    60 HYSIPPQDLKTVFPHGLPPRYAMQVKTFGEACLMVRKPALELLGY--------LKNTNFA 111

Query:   188 KIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTH--GGYFYKNPQTGLW 245
                 + +L G    GK+++L   VH+  +  WL+L++P    W    G           +
Sbjct:   112 HPAVRYLLYGEKGTGKTLSLCHAVHFCAKSDWLILHIPDAHLWVKNCGELLQSTYNKQRF 171

Query:   246 DTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGV-DSKEISE-GSTLF 303
             D PL+A   LK+F   NE  L ++  Q        E       K V + +E +E GS L 
Sbjct:   172 DQPLEASTWLKNFKTTNERFLGQIKVQ--------E-------KYVWNKRESTEKGSPLG 216

Query:   304 DLVQMGINQMHAS---VGVVVRLRKELSLVKDIPVLIAIDQYNN-WFTFSEYEEPVTIRS 359
             ++V+ G+ ++  +   VGVV++  K  S +    +L+A+D  N  W   +   E  T+  
Sbjct:   217 EVVEQGLTRVRNATDAVGVVLKELKTQSSLGLFHLLVAVDGVNALWGRTTLKREDRTL-- 274

Query:   360 TRPVHARELAMVNAFRSMMHNDMMVGAFSHSTA-VGSF--ARTCHM 402
                +   ELA+V   R M+ ND   GA   S +  GS   +RT ++
Sbjct:   275 ---IAPEELALVRNLRKMVKNDWHGGAIVLSLSQTGSLFKSRTAYL 317

GO:0005634 "nucleus" evidence=ISO

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=ISO

GO:0005759 "mitochondrial matrix" evidence=ISO

GO:0005761 "mitochondrial ribosome" evidence=IEA

GO:0008637 "apoptotic mitochondrial changes" evidence=IEA;ISO

GO:0015935 "small ribosomal subunit" evidence=IEA

ZFIN|ZDB-GENE-051129-2 dap3 "death associated protein 3" [Danio rerio (taxid:7955)]

 Score = 162 (62.1 bits), Expect = 3.1e-09, P = 3.1e-09
 Identities = 73/270 (27%), Positives = 115/270 (42%)

Query:   128 YFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP 187
             Y+      +  + P GLP     + K      ++VR + L++    ++         N P
Sbjct:    66 YYTLPPTHIQKLFPHGLPPRFQMQVKTFNEGCVMVRPAALELISYLKKA------DYNKP 119

Query:   188 KIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG-GYFYKNPQTGL-W 245
              +R   VL G    GKSI+L   +H+   +GWL+L+VP    W         +    L +
Sbjct:   120 PLR--YVLYGQTGSGKSISLCHTLHYCYTQGWLILHVPDAHLWVKNCKEMLPSTYNPLRF 177

Query:   246 DTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDL 305
             D P+QA   LKDF   NE  L ++               V   +  +S E  EG TL +L
Sbjct:   178 DQPVQATQWLKDFKITNEHFLSKIKTT---------RRYVWTKR--ESTE--EGRTLGEL 224

Query:   306 VQMGINQMHAS---VGVVVR-LRKELSLVKD----IPVLIAIDQYNN-WFTFSEYEEPVT 356
             +  G+N+M +S   VG V+R LR +     +      + +A+D  N  W   +  +E  T
Sbjct:   225 IDQGVNRMKSSSDVVGAVLRELRLQAGATTEGEEVFKLAVAVDGVNALWGNTTLKKEDRT 284

Query:   357 IRSTRPVHARELAMVNAFRSMMHNDMMVGA 386
             +    P    EL +++  R MM  D   GA
Sbjct:   285 M--CEP---EELTLIHNLRKMMKTDWRGGA 309

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0005761 "mitochondrial ribosome" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0001666 "response to hypoxia" evidence=IDA

---

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	404
pfam10236	274	pfam10236, DAP3, Mitochondrial ribosomal death-ass	3e-54
cd01673	193	cd01673, dNK, Deoxyribonucleoside kinase (dNK) cat	7e-04

>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein 3

 Score =  180 bits (459), Expect = 3e-54
 Identities = 68/238 (28%), Positives = 106/238 (44%), Gaps = 30/238 (12%)

Query: 160 LLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGW 219
           LLVR+  L++    +          +   +R   VL G    GKS+ LA  + +A  +GW
Sbjct: 1   LLVREETLELTKKLKE------ADASKKVVR--FVLTGERGSGKSVLLAQAMAYAFTQGW 52

Query: 220 LVLYVPRGREWTHGGYFYKN--PQTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPI 277
           +VL+VP   +W +G   Y       GL+D P+ A   L+  +K NE  L++L  ++    
Sbjct: 53  IVLHVPEAEDWVNGTTDYAPDPGNPGLYDQPMYAAAWLQKILKANEEVLKKL--KLSKDY 110

Query: 278 PLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLV-KDIPVL 336
              +            +    GSTL DL  +GIN   ++  V   + KEL    K  PVL
Sbjct: 111 KWLKR-----------ESTPAGSTLLDLASLGINDPKSAWDVFQAVWKELKAQSKAPPVL 159

Query: 337 IAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSM--MHNDMMVGAFSHSTA 392
           +A+D +N  F  S+Y  P      +P+H  +L +V  F  +    ND   G    + A
Sbjct: 160 VAVDGFNALFGPSDYRTP----DFKPIHPHDLTLVRLFLDLLSGKNDFPNGGVVTALA 213

This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29). Length = 274

>gnl|CDD|238836 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs)

 Score = 40.3 bits (95), Expect = 7e-04
 Identities = 26/89 (29%), Positives = 40/89 (44%), Gaps = 12/89 (13%)

Query: 193 IVLDGPLCCGKSITLA-MLVHWAREEGWLVLYVPRGREWTHGGY---FYKNPQTGLWDTP 248
           IV++G +  GKS TLA  L   A   G+ V+  P   +     +   FY++P+   W  P
Sbjct: 2   IVVEGNIGAGKS-TLAKEL---AEHLGYEVVPEPVEPDVEGNPFLEKFYEDPK--RWAFP 55

Query: 249 LQAENVLKDFIKYNE--SHLRELPCQILD 275
            Q   +L    +Y +   HL      IL+
Sbjct: 56  FQLYFLLSRLKQYKDALEHLSTGQGVILE 84

This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA. Length = 193

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	404
KOG3928	461	consensus Mitochondrial ribosome small subunit com	100.0
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	100.0
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	97.16
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.14
PF05729	166	NACHT: NACHT domain	96.79
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.68
PF13245	76	AAA_19: Part of AAA domain	96.64
PF13173	128	AAA_14: AAA domain	96.62
PRK06851	367	hypothetical protein; Provisional	96.53
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.5
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.49
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.37
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.32
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.3
PRK06835	329	DNA replication protein DnaC; Validated	96.29
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.27
PRK08084	235	DNA replication initiation factor; Provisional	96.22
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.2
smart00382	148	AAA ATPases associated with a variety of cellular	96.2
PRK12377	248	putative replication protein; Provisional	96.14
PF14516	331	AAA_35: AAA-like domain	96.14
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.04
PRK00411	394	cdc6 cell division control protein 6; Reviewed	95.98
PRK08727	233	hypothetical protein; Validated	95.85
PRK08181	269	transposase; Validated	95.84
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	95.82
PRK06921	266	hypothetical protein; Provisional	95.71
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	95.69
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	95.67
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.67
PRK06893	229	DNA replication initiation factor; Validated	95.63
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	95.53
PRK06526	254	transposase; Provisional	95.51
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.5
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.5
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.49
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.48
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	95.44
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	95.43
PRK05642	234	DNA replication initiation factor; Validated	95.41
PF00004	132	AAA: ATPase family associated with various cellula	95.4
PRK09183	259	transposase/IS protein; Provisional	95.38
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	95.35
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	95.33
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	95.3
TIGR02236	310	recomb_radA DNA repair and recombination protein R	95.3
PRK08533	230	flagellar accessory protein FlaH; Reviewed	95.3
PRK04296	190	thymidine kinase; Provisional	95.27
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.2
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	95.2
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	95.16
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	95.13
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	95.12
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	95.11
TIGR02237	209	recomb_radB DNA repair and recombination protein R	95.11
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.1
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	95.05
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.01
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.0
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	94.97
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	94.97
PRK07952	244	DNA replication protein DnaC; Validated	94.96
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	94.93
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.9
PRK08116	268	hypothetical protein; Validated	94.88
PTZ00112	1164	origin recognition complex 1 protein; Provisional	94.84
PRK00149	450	dnaA chromosomal replication initiation protein; R	94.79
PF10923	416	DUF2791: P-loop Domain of unknown function (DUF279	94.76
PRK13695	174	putative NTPase; Provisional	94.7
PRK08939	306	primosomal protein DnaI; Reviewed	94.7
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	94.69
cd01394	218	radB RadB. The archaeal protein radB shares simila	94.68
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	94.62
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	94.59
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	94.54
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	94.51
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	94.48
PRK04328	249	hypothetical protein; Provisional	94.47
PRK12422	445	chromosomal replication initiation protein; Provis	94.45
PF13479	213	AAA_24: AAA domain	94.44
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	94.33
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	94.29
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	94.22
PRK05973	237	replicative DNA helicase; Provisional	94.18
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	94.16
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	94.16
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	94.15
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	94.12
PLN03025	319	replication factor C subunit; Provisional	94.12
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	94.1
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	94.1
PRK06067	234	flagellar accessory protein FlaH; Validated	94.08
PF13476	202	AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V	94.08
PF12846	304	AAA_10: AAA-like domain	94.08
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	94.06
PRK11823	446	DNA repair protein RadA; Provisional	94.04
PRK12402	337	replication factor C small subunit 2; Reviewed	94.03
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	94.01
PRK13764	602	ATPase; Provisional	94.01
PRK14974	336	cell division protein FtsY; Provisional	93.98
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	93.97
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	93.93
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	93.87
TIGR00064	272	ftsY signal recognition particle-docking protein F	93.85
PHA03133	368	thymidine kinase; Provisional	93.82
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	93.77
cd03114	148	ArgK-like The function of this protein family is u	93.75
CHL00181	287	cbbX CbbX; Provisional	93.72
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	93.71
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	93.69
PRK06851	367	hypothetical protein; Provisional	93.69
PRK14088	440	dnaA chromosomal replication initiation protein; P	93.68
PRK00440	319	rfc replication factor C small subunit; Reviewed	93.65
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	93.65
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	93.64
PRK09519	790	recA DNA recombination protein RecA; Reviewed	93.62
PRK01184	184	hypothetical protein; Provisional	93.58
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	93.55
PF13555	62	AAA_29: P-loop containing region of AAA domain	93.54
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	93.51
COG4619	223	ABC-type uncharacterized transport system, ATPase	93.51
cd00983	325	recA RecA is a bacterial enzyme which has roles in	93.47
PRK14738	206	gmk guanylate kinase; Provisional	93.41
PRK09354	349	recA recombinase A; Provisional	93.38
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	93.38
PRK00889	175	adenylylsulfate kinase; Provisional	93.37
PRK06696	223	uridine kinase; Validated	93.33
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	93.32
PRK07261	171	topology modulation protein; Provisional	93.3
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	93.29
PHA03135	343	thymidine kinase; Provisional	93.24
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	93.2
PRK13833	323	conjugal transfer protein TrbB; Provisional	93.16
PRK07667	193	uridine kinase; Provisional	93.14
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	93.1
PRK09087	226	hypothetical protein; Validated	93.09
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	93.07
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	93.07
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	93.07
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	93.02
PF02492	178	cobW: CobW/HypB/UreG, nucleotide-binding domain; I	93.01
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	92.93
PRK14086	617	dnaA chromosomal replication initiation protein; P	92.93
PHA03138	340	thymidine kinase; Provisional	92.93
PRK14087	450	dnaA chromosomal replication initiation protein; P	92.83
PRK12608	380	transcription termination factor Rho; Provisional	92.82
KOG2859	293	consensus DNA repair protein, member of the recA/R	92.81
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	92.8
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	92.73
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	92.7
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	92.7
PRK14532	188	adenylate kinase; Provisional	92.69
TIGR00235	207	udk uridine kinase. Model contains a number of lon	92.61
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	92.61
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	92.55
PHA03134	340	thymidine kinase; Provisional	92.54
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	92.54
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	92.51
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	92.5
PRK06620	214	hypothetical protein; Validated	92.49
PRK00771	437	signal recognition particle protein Srp54; Provisi	92.48
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	92.46
PRK10416	318	signal recognition particle-docking protein FtsY;	92.4
cd01673	193	dNK Deoxyribonucleoside kinase (dNK) catalyzes the	92.39
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	92.38
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	92.35
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	92.35
cd00154	159	Rab Rab family. Rab GTPases form the largest famil	92.34
PRK08118	167	topology modulation protein; Reviewed	92.3
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	92.3
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	92.22
smart00487	201	DEXDc DEAD-like helicases superfamily.	92.22
PRK03992	389	proteasome-activating nucleotidase; Provisional	92.17
PRK14531	183	adenylate kinase; Provisional	92.16
TIGR00665	434	DnaB replicative DNA helicase. This model describe	92.1
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	92.09
PRK00279	215	adk adenylate kinase; Reviewed	92.04
PRK04301	317	radA DNA repair and recombination protein RadA; Va	92.04
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	92.02
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	92.01
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	91.9
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	91.87
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	91.85
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	91.83
PRK05541	176	adenylylsulfate kinase; Provisional	91.81
cd01861	161	Rab6 Rab6 subfamily. Rab6 is involved in microtubu	91.7
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	91.68
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	91.67
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	91.61
TIGR00376	637	DNA helicase, putative. The gene product may repre	91.61
cd01870	175	RhoA_like RhoA-like subfamily. The RhoA subfamily	91.6
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	91.55
PRK03846	198	adenylylsulfate kinase; Provisional	91.54
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	91.51
PRK14530	215	adenylate kinase; Provisional	91.51
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	91.49
KOG2749	415	consensus mRNA cleavage and polyadenylation factor	91.49
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	91.49
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	91.48
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	91.47
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	91.45
cd00157	171	Rho Rho (Ras homology) family. Members of the Rho	91.44
PTZ00035	337	Rad51 protein; Provisional	91.43
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	91.43
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	91.42
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	91.42
PRK13851	344	type IV secretion system protein VirB11; Provision	91.42
cd04129	187	Rho2 Rho2 subfamily. Rho2 is a fungal GTPase that	91.38
PTZ00202	550	tuzin; Provisional	91.36
PHA03136	378	thymidine kinase; Provisional	91.36
PRK06762	166	hypothetical protein; Provisional	91.34
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	91.34
PRK09435	332	membrane ATPase/protein kinase; Provisional	91.33
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	91.29
PRK13768	253	GTPase; Provisional	91.24
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	91.23
PRK02496	184	adk adenylate kinase; Provisional	91.22
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	91.18
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	91.15
PRK00698	205	tmk thymidylate kinase; Validated	91.13
CHL00195	489	ycf46 Ycf46; Provisional	91.13
PRK10536	262	hypothetical protein; Provisional	91.09
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	91.07
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	91.07
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	91.05
TIGR02533	486	type_II_gspE general secretory pathway protein E.	91.05
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	91.04
PRK10436	462	hypothetical protein; Provisional	91.04
PF00005	137	ABC_tran: ABC transporter This structure is on hol	91.02
PRK08233	182	hypothetical protein; Provisional	91.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	91.0
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	90.96
COG3911	183	Predicted ATPase [General function prediction only	90.96
PHA00729	226	NTP-binding motif containing protein	90.89
cd01869	166	Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in ev	90.85
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	90.83
cd04156	160	ARLTS1 ARLTS1 subfamily. ARLTS1 (Arf-like tumor su	90.82
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	90.8
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	90.77
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	90.75
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	90.72
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	90.72
PRK03839	180	putative kinase; Provisional	90.64
PRK00300	205	gmk guanylate kinase; Provisional	90.63
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	90.62
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	90.62
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	90.61
cd04136	163	Rap_like Rap-like subfamily. The Rap subfamily con	90.6
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	90.59
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	90.59
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	90.58
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	90.56
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	90.54
cd00876	160	Ras Ras family. The Ras family of the Ras superfam	90.53
PRK04841	903	transcriptional regulator MalT; Provisional	90.52
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	90.5
cd01863	161	Rab18 Rab18 subfamily. Mammalian Rab18 is implicat	90.47
cd01867	167	Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Yp	90.45
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	90.42
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	90.42
PRK10867	433	signal recognition particle protein; Provisional	90.4
cd02034	116	CooC The accessory protein CooC, which contains a	90.39
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	90.31
PRK04195	482	replication factor C large subunit; Provisional	90.31
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	90.28
cd01128	249	rho_factor Transcription termination factor rho is	90.27
PRK09302	509	circadian clock protein KaiC; Reviewed	90.25
PRK05480	209	uridine/cytidine kinase; Provisional	90.25
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	90.23
TIGR02528	142	EutP ethanolamine utilization protein, EutP. This	90.16
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	90.09
cd04145	164	M_R_Ras_like M-Ras/R-Ras-like subfamily. This subf	90.06
PRK11608	326	pspF phage shock protein operon transcriptional ac	90.03
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	90.03
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	90.02
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	90.0
cd04113	161	Rab4 Rab4 subfamily. Rab4 has been implicated in n	89.87
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	89.84
cd01876	170	YihA_EngB The YihA (EngB) subfamily. This subfamil	89.83
PRK00131	175	aroK shikimate kinase; Reviewed	89.82
PTZ00088	229	adenylate kinase 1; Provisional	89.78
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	89.78
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	89.77
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	89.73
PRK13973	213	thymidylate kinase; Provisional	89.72
PRK04040	188	adenylate kinase; Provisional	89.7
cd01868	165	Rab11_like Rab11-like. Rab11a, Rab11b, and Rab25 a	89.67
COG4778	235	PhnL ABC-type phosphonate transport system, ATPase	89.67
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	89.65
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	89.62
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	89.61
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	89.6
cd01860	163	Rab5_related Rab5-related subfamily. This subfamil	89.55
cd01866	168	Rab2 Rab2 subfamily. Rab2 is localized on cis-Golg	89.54
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	89.5
COG1100	219	GTPase SAR1 and related small G proteins [General	89.46
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	89.42
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	89.42
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	89.36
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	89.34
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	89.31
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	89.26
cd04140	165	ARHI_like ARHI subfamily. ARHI (A Ras homolog memb	89.25
cd01864	165	Rab19 Rab19 subfamily. Rab19 proteins are associat	89.24
PRK09825	176	idnK D-gluconate kinase; Provisional	89.23
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	89.22
PHA02544	316	44 clamp loader, small subunit; Provisional	89.1
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	89.04
TIGR00959	428	ffh signal recognition particle protein. This mode	89.02
PRK06217	183	hypothetical protein; Validated	88.98
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	88.98
PRK06547	172	hypothetical protein; Provisional	88.93
KOG0086	214	consensus GTPase Rab4, small G protein superfamily	88.92
cd04114	169	Rab30 Rab30 subfamily. Rab30 appears to be associa	88.91
cd04117	161	Rab15 Rab15 subfamily. Rab15 colocalizes with the	88.87
COG1119	257	ModF ABC-type molybdenum transport system, ATPase	88.85
TIGR03598	179	GTPase_YsxC ribosome biogenesis GTP-binding protei	88.81
cd04123	162	Rab21 Rab21 subfamily. The localization and functi	88.79
cd04134	189	Rho3 Rho3 subfamily. Rho3 is a member of the Rho f	88.75
PRK14528	186	adenylate kinase; Provisional	88.75
PTZ00132	215	GTP-binding nuclear protein Ran; Provisional	88.75
cd01865	165	Rab3 Rab3 subfamily. The Rab3 subfamily contains R	88.71
cd04122	166	Rab14 Rab14 subfamily. Rab14 GTPases are localized	88.7
PRK05416	288	glmZ(sRNA)-inactivating NTPase; Provisional	88.69
cd04127	180	Rab27A Rab27a subfamily. The Rab27a subfamily cons	88.68
cd04135	174	Tc10 TC10 subfamily. TC10 is a Rho family protein	88.68
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	88.68
cd04118	193	Rab24 Rab24 subfamily. Rab24 is distinct from othe	88.67
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	88.66
cd04157	162	Arl6 Arl6 subfamily. Arl6 (Arf-like 6) forms a sub	88.64
PRK14526	211	adenylate kinase; Provisional	88.64
PHA02530	300	pseT polynucleotide kinase; Provisional	88.61
PRK14527	191	adenylate kinase; Provisional	88.58
cd03240	204	ABC_Rad50 The catalytic domains of Rad50 are simil	88.57
COG3523	1188	IcmF Type VI protein secretion system component Va	88.56
cd04125	188	RabA_like RabA-like subfamily. RabA was first iden	88.55
cd03234	226	ABCG_White The White subfamily represents ABC tran	88.54
PRK14730	195	coaE dephospho-CoA kinase; Provisional	88.54
PRK14731	208	coaE dephospho-CoA kinase; Provisional	88.5
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	88.48
cd01895	174	EngA2 EngA2 subfamily. This CD represents the seco	88.47
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	88.47
PRK13342	413	recombination factor protein RarA; Reviewed	88.45
cd01858	157	NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protei	88.45
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	88.45
cd03260	227	ABC_PstB_phosphate_transporter Phosphate uptake is	88.31
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	88.3
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	88.26
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	88.24
PRK08506	472	replicative DNA helicase; Provisional	88.18
cd04106	162	Rab23_lke Rab23-like subfamily. Rab23 is a member	88.17
COG1162	301	Predicted GTPases [General function prediction onl	88.16
cd04164	157	trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein	88.15
PRK13700	732	conjugal transfer protein TraD; Provisional	88.14
cd00878	158	Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-lik	88.13
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	88.12
PRK09302	509	circadian clock protein KaiC; Reviewed	88.12
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	88.07
cd04175	164	Rap1 Rap1 subgroup. The Rap1 subgroup is part of t	88.01
cd04110	199	Rab35 Rab35 subfamily. Rab35 is one of several Rab	87.99
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	87.99
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	87.98
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	87.97
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	87.96
cd04176	163	Rap2 Rap2 subgroup. The Rap2 subgroup is part of t	87.94
PF04548	212	AIG1: AIG1 family; InterPro: IPR006703 This entry	87.94
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	87.93
cd00877	166	Ran Ran (Ras-related nuclear proteins) /TC4 subfam	87.9
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	87.89
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	87.89
PF09439	181	SRPRB: Signal recognition particle receptor beta s	87.87
cd03116	159	MobB Molybdenum is an essential trace element in t	87.86
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	87.84
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	87.83
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	87.83
PRK05428	308	HPr kinase/phosphorylase; Provisional	87.8
cd04177	168	RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the	87.78
cd04154	173	Arl2 Arl2 subfamily. Arl2 (Arf-like 2) GTPases are	87.78
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	87.77
cd04115	170	Rab33B_Rab33A Rab33B/Rab33A subfamily. Rab33B is u	87.74
cd03276	198	ABC_SMC6_euk Eukaryotic SMC6 proteins; SMC protein	87.73
cd04132	187	Rho4_like Rho4-like subfamily. Rho4 is a GTPase th	87.71
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	87.68
cd04101	164	RabL4 RabL4 (Rab-like4) subfamily. RabL4s are nove	87.65
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	87.63
PF00071	162	Ras: Ras family; InterPro: IPR001806 Small GTPases	87.63
PLN02200	234	adenylate kinase family protein	87.63
PRK13949	169	shikimate kinase; Provisional	87.61
cd00879	190	Sar1 Sar1 subfamily. Sar1 is an essential componen	87.61
cd04112	191	Rab26 Rab26 subfamily. First identified in rat pan	87.6
PRK06761	282	hypothetical protein; Provisional	87.6
PRK14737	186	gmk guanylate kinase; Provisional	87.57
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	87.57
PRK07933	213	thymidylate kinase; Validated	87.57
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	87.54
cd01852	196	AIG1 AIG1 (avrRpt2-induced gene 1). This represent	87.49
PRK00454	196	engB GTP-binding protein YsxC; Reviewed	87.48
cd03269	210	ABC_putative_ATPase This subfamily is involved in	87.46
cd01853	249	Toc34_like Toc34-like (Translocon at the Outer-env	87.46
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	87.46
cd04107	201	Rab32_Rab38 Rab38/Rab32 subfamily. Rab32 and Rab38	87.45
PRK04196	460	V-type ATP synthase subunit B; Provisional	87.42
TIGR03348	1169	VI_IcmF type VI secretion protein IcmF. Members of	87.41
cd04116	170	Rab9 Rab9 subfamily. Rab9 is found in late endosom	87.38
cd04141	172	Rit_Rin_Ric Rit/Rin/Ric subfamily. Rit (Ras-like p	87.38
TIGR00157	245	ribosome small subunit-dependent GTPase A. The Aqu	87.33
cd02026	273	PRK Phosphoribulokinase (PRK) is an enzyme involve	87.32
PRK14242	253	phosphate transporter ATP-binding protein; Provisi	87.32
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	87.3
PRK05595	444	replicative DNA helicase; Provisional	87.26
cd01918	149	HprK_C HprK/P, the bifunctional histidine-containi	87.23
cd04103	158	Centaurin_gamma Centaurin gamma. The centaurins (a	87.22
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	87.17
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	87.16
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	87.11
cd03275	247	ABC_SMC1_euk Eukaryotic SMC1 proteins; SMC protein	87.09
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	87.08
cd01874	175	Cdc42 Cdc42 subfamily. Cdc42 is an essential GTPas	87.08
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	87.0
cd04104	197	p47_IIGP_like p47 (47-kDa) family. The p47 GTPase	86.99
smart00174	174	RHO Rho (Ras homology) subfamily of Ras-like small	86.99
cd01897	168	NOG NOG1 is a nucleolar GTP-binding protein presen	86.97
cd04151	158	Arl1 Arl1 subfamily. Arl1 (Arf-like 1) localizes t	86.96
PRK14235	267	phosphate transporter ATP-binding protein; Provisi	86.93
TIGR01042	591	V-ATPase_V1_A V-type (H+)-ATPase V1, A subunit. Th	86.92
PRK10744	260	pstB phosphate transporter ATP-binding protein; Pr	86.92
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	86.92
PRK15177	213	Vi polysaccharide export ATP-binding protein VexC;	86.89
PHA02774	613	E1; Provisional	86.86
PRK00081	194	coaE dephospho-CoA kinase; Reviewed	86.85
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	86.84
cd03224	222	ABC_TM1139_LivF_branched LivF (TM1139) is part of	86.83
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	86.8
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	86.77
COG0593	408	DnaA ATPase involved in DNA replication initiation	86.75
PRK14238	271	phosphate transporter ATP-binding protein; Provisi	86.72
cd03219	236	ABC_Mj1267_LivG_branched The Mj1267/LivG ABC trans	86.7
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	86.7
PRK14274	259	phosphate ABC transporter ATP-binding protein; Pro	86.6
cd03270	226	ABC_UvrA_I The excision repair protein UvrA domain	86.57
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	86.53
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	86.51
PRK05748	448	replicative DNA helicase; Provisional	86.49
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	86.47
PRK14248	268	phosphate ABC transporter ATP-binding protein; Pro	86.43
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	86.42
COG4136	213	ABC-type uncharacterized transport system, ATPase	86.38
cd03257	228	ABC_NikE_OppD_transporters The ABC transporter sub	86.37
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	86.36
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	86.35
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	86.34
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	86.33
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	86.32
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	86.31
cd04146	165	RERG_RasL11_like RERG/RasL11-like subfamily. RERG	86.31
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	86.31
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	86.3
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	86.28
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	86.27
PRK14240	250	phosphate transporter ATP-binding protein; Provisi	86.26
cd04108	170	Rab36_Rab34 Rab34/Rab36 subfamily. Rab34, found pr	86.25
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	86.24
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	86.23
TIGR00101	199	ureG urease accessory protein UreG. This model rep	86.22
TIGR02323	253	CP_lyasePhnK phosphonate C-P lyase system protein	86.18
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	86.17
PHA02244	383	ATPase-like protein	86.17
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	86.12
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	86.11
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	86.11
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	86.1
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	86.08
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	86.08
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	86.08
cd01892	169	Miro2 Miro2 subfamily. Miro (mitochondrial Rho) pr	86.08
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	86.07
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	86.06
cd04153	174	Arl5_Arl8 Arl5/Arl8 subfamily. Arl5 (Arf-like 5) a	86.06
PLN03108	210	Rab family protein; Provisional	86.03
cd03254	229	ABCC_Glucan_exporter_like Glucan exporter ATP-bind	86.02
TIGR00767	415	rho transcription termination factor Rho. Members	86.0
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	85.97
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	85.96
cd04111	211	Rab39 Rab39 subfamily. Found in eukaryotes, Rab39	85.96
cd03246	173	ABCC_Protease_Secretion This family represents the	85.95
PRK13765	637	ATP-dependent protease Lon; Provisional	85.95
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	85.94
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	85.92
cd04158	169	ARD1 ARD1 subfamily. ARD1 (ADP-ribosylation factor	85.9
cd03298	211	ABC_ThiQ_thiamine_transporter ABC-type thiamine tr	85.88
TIGR03410	230	urea_trans_UrtE urea ABC transporter, ATP-binding	85.88
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	85.87
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	85.85
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	85.81
PRK14241	258	phosphate transporter ATP-binding protein; Provisi	85.79
TIGR01978	243	sufC FeS assembly ATPase SufC. SufC is part of the	85.78
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	85.77
cd01898	170	Obg Obg subfamily. The Obg nucleotide binding prot	85.76
cd00881	189	GTP_translation_factor GTP translation factor fami	85.76
COG3842	352	PotA ABC-type spermidine/putrescine transport syst	85.75

>KOG3928 consensus Mitochondrial ribosome small subunit component, mediator of apoptosis DAP3 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=2.7e-67  Score=527.97  Aligned_cols=344  Identities=30%  Similarity=0.416  Sum_probs=300.8

Q ss_pred             ChhHHHHHHHHHhhh------------ccCCCcc--eeeccccccceee-eeccccCCcccccccccccC--CCCCCCCC
Q 045329            1 MLRLISRAAAAAAAL------------SKQRNDT--VLTSTSILIHQFF-YSTKTQTKSSKKKQDDNKKS--SKSKSKSS   63 (404)
Q Consensus         1 ~~~~~~~~~~~~~~~------------~~~~~~~--~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~--~~~~~~~~   63 (404)
                      ||+.|.+.++.+...            |+..+..  +.+.|++..|+|. +|++..+++++.++   |+.  +.+++.+.
T Consensus         1 m~k~~~~~~~~i~~~~r~s~il~ntvch~~~~~~~~~~~~f~s~~~~ht~rs~~~~~~ss~~k~---K~~~~~~s~i~~~   77 (461)
T KOG3928|consen    1 MYKNIYICILYIYINFRTSRILINTVCHVVIRMLRMSTSRFISQRLFHTARSLQAAKPSSKGKT---KGISNKSSSISRY   77 (461)
T ss_pred             CCcccceehhhhhhhhhhhHhhcCcccccccchhhhhhccccccceeeeccccccCCCCccccc---ccccccccccccC
Confidence            777777777766554            3333322  7889999999999 88888888888777   333  33444444


Q ss_pred             CCcccccccccccCccchhHHHHHHhhhcccCCCCCCcccCCCCccccccCCCccccCccccceeEEeCHHHHHhhccCC
Q 045329           64 DANSLSAPAAAQADSADDLESVRARARRLAEDDRNPSLDVGPNHRPLFTKTTSLSLLTRKDACTYFKFSEDELNAMLPEG  143 (404)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ht~~~vGk~y~~p~e~~k~l~~~G  143 (404)
                      +|+..             ++.  +|..+..++...+.+++|+++|+++.+  +|..|+.+++|++|+||++++++++++|
T Consensus        78 ~p~~~-------------lh~--g~~~~ns~~~~~~~~~~~e~~~~l~~p--~p~~~ssk~~gk~~~i~~~~lk~l~~~G  140 (461)
T KOG3928|consen   78 SPARQ-------------LHP--GRLSRNSTAATIHTLQLGENARPLSLP--IPNFHSSKTEGKVFKISEEQLKQLNPLG  140 (461)
T ss_pred             Chhhe-------------ech--hhcccccccccccccccCccccccccC--CccccccccccceeecCHHHHHhhccCC
Confidence            55443             333  688999999999999999999999999  7999999999999999999999999999


Q ss_pred             CCcchhhhccccCceeEEEchhHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          144 LPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       144 Lp~~~~kqfe~f~~p~~LVRk~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      +|.++.+||++|.+||+|||++++|+.++ ++..|+.     .|.  .||||||++|||||++|+|++|||+.|+|||||
T Consensus       141 ~p~~~~~q~~tf~ea~lLVRkpalel~~~-~r~~d~~-----~P~--~r~vL~Ge~GtGKSiaL~qa~h~a~~~~wlIlh  212 (461)
T KOG3928|consen  141 LPFKKSQQFKTFTEAVLLVRKPALELLLY-KRLVDPM-----HPV--KRFVLDGEPGTGKSIALAQAVHYAADQKWLILH  212 (461)
T ss_pred             CchHHHHHHHhhhcchheechHHHHHHHH-hhhcccc-----Ccc--eEEEEeCCCCCchhhHHHHHHHHHhcCCeEEEE
Confidence            99999999999999999999999999999 4555642     455  579999999999999999999999999999999


Q ss_pred             ecCcccccccCee--ecCCCCCCccCHHHHHHHHHHHHHHhHHHHh-cCCcccccCCCCCCCCccccccCCCccccCCCC
Q 045329          224 VPRGREWTHGGYF--YKNPQTGLWDTPLQAENVLKDFIKYNESHLR-ELPCQILDPIPLGEGAGVGLLKGVDSKEISEGS  300 (404)
Q Consensus       224 IP~a~~wvng~~~--y~~~~~g~ydQP~~A~~~Lk~fl~~N~~~Lk-kLkls~~~~~~lge~~~~~w~K~~d~~~~p~g~  300 (404)
                      ||+|+.|+||..+  |.+...|+||||++|+.||++|+++|++.|+ +|+++++          |+|+++   +.+++|+
T Consensus       213 ip~a~~w~~~~~~~~y~~~~kg~~dqP~~a~~~L~~fkk~N~~~L~~~lkt~~~----------yvwsk~---e~t~kG~  279 (461)
T KOG3928|consen  213 IPYAELWTNGRKDYSYDSDLKGLWDQPLYAKKILKNFKKTNEPALKKQLKTSKD----------YVWSKR---ESTLKGK  279 (461)
T ss_pred             CCcHHHhhhccccccccccccccccChhHHHHHHHHHHhhccHHHHHHhccccc----------eeeccc---CCccCCC
Confidence            9999999999654  4456789999999999999999999999999 7877764          779987   6789999


Q ss_pred             CHHHHHHhhcccccchHHHHHHHHHHHhc---CCCCcEEEEEeCcccccCcCCcCCcccCCCCccccCCccchHHHHHhh
Q 045329          301 TLFDLVQMGINQMHASVGVVVRLRKELSL---VKDIPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSM  377 (404)
Q Consensus       301 tL~DLv~~Gi~~~~~A~~v~~aLl~EL~~---q~~~PVLvAVD~~Nalf~~S~Y~dp~~~r~~k~I~~~eLtLv~~f~~l  377 (404)
                      +|.+|++.||.+...|.+++++|++||+.   ++++||||||||||+||+.|.|++.    ++++|+|.+|+|+++++++
T Consensus       280 pl~ei~e~gI~~i~~a~~~vg~llrelk~~s~~~~~kVLvaID~~n~l~~~T~~k~~----~~~~v~P~dl~li~~~~~~  355 (461)
T KOG3928|consen  280 PLVEIVETGIASIKNAPDAVGILLRELKRLSVQSKVKVLVAIDNFNSLFTVTAYKSE----DNKPVTPLDLTLIHLLRDI  355 (461)
T ss_pred             cchhhHHhhhhhhccchHHHHHHHHHHHHhhhhcCccEEEEEcCcchheeeeeeecc----ccCcCCchhhhHHHHHHHH
Confidence            99999999999999999999999999987   7899999999999999999999988    8999999999999999999


Q ss_pred             hcCCceeEEEec
Q 045329          378 MHNDMMVGAFSH  389 (404)
Q Consensus       378 l~~dw~~GAis~  389 (404)
                      ++|||.+|+|.+
T Consensus       356 i~ndwt~g~vi~  367 (461)
T KOG3928|consen  356 ISNDWTFGSVIM  367 (461)
T ss_pred             HhcccccceEEE
Confidence            999998876655

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=1.3e-54  Score=429.70  Aligned_cols=214  Identities=36%  Similarity=0.609  Sum_probs=192.8

Q ss_pred             EEEchhHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccccCeeecC
Q 045329          160 LLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKN  239 (404)
Q Consensus       160 ~LVRk~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvng~~~y~~  239 (404)
                      +|||++|+||+++|++. +.     +++.  +||||+|++|||||++|+|++|||+++||||||||+++.|++++++|.+
T Consensus         1 ~lvR~~t~el~~~l~~~-~~-----~~~~--~r~vL~G~~GsGKS~~L~q~~~~A~~~~wiVl~vp~a~~~~~~~~~~~~   72 (309)
T PF10236_consen    1 SLVRKPTLELINKLKEA-DK-----SSKN--NRYVLTGERGSGKSVLLAQAVHYARENGWIVLYVPSAQDWVNGTTDYAP   72 (309)
T ss_pred             CccchHHHHHHHHHHHh-cc-----cCCc--eEEEEECCCCCCHHHHHHHHHHHHHhCCEEEEEcCCHHHHhhCCeeEee
Confidence            58999999999999976 22     1233  5799999999999999999999999999999999999999999998865


Q ss_pred             -C-CCCCccCHHHHHHHHHHHHHHhHHHHhcCCcccccCCCCCCCCccccccCCCccccCCCCCHHHHHHhhcccccchH
Q 045329          240 -P-QTGLWDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASV  317 (404)
Q Consensus       240 -~-~~g~ydQP~~A~~~Lk~fl~~N~~~LkkLkls~~~~~~lge~~~~~w~K~~d~~~~p~g~tL~DLv~~Gi~~~~~A~  317 (404)
                       + ++|+||||++|++||++|+++|+++|++|+++++          |.|.+.   +.+++|+||+||+++|++++++|+
T Consensus        73 ~~~~~~~~~qP~~a~~~L~~~~~~N~~~L~~i~~s~~----------~~~~~~---~~~~~g~tL~dLv~~g~~~~~~a~  139 (309)
T PF10236_consen   73 SPYNPGLYDQPMYAAKWLKKFLKANEELLKKIKLSKD----------YKWSKR---ESTPKGSTLLDLVEQGINDPKYAW  139 (309)
T ss_pred             CCCCCCeeecHHHHHHHHHHHHHHhHHHHHhcccccc----------cccccc---ccCCCCCCHHHHHHhhcccchhHH
Confidence             4 8999999999999999999999999999999887          446654   678999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCC-CcEEEEEeCcccccCcCCcCCcccCCCCccccCCccchHHHHHhhhc--CCceeEEE---eccc
Q 045329          318 GVVVRLRKELSLVKD-IPVLIAIDQYNNWFTFSEYEEPVTIRSTRPVHARELAMVNAFRSMMH--NDMMVGAF---SHST  391 (404)
Q Consensus       318 ~v~~aLl~EL~~q~~-~PVLvAVD~~Nalf~~S~Y~dp~~~r~~k~I~~~eLtLv~~f~~ll~--~dw~~GAi---s~s~  391 (404)
                      +||++||+||++|++ +||||||||||+||+.|+|+++    ++++|||++|+|+++|+++++  .+|.+|++   ..++
T Consensus       140 ~~~~~l~~EL~~~~~~~PVL~avD~~n~l~~~S~Y~~~----~~~~I~~~~L~l~~~f~~~~s~~~~~~nG~~v~~l~~t  215 (309)
T PF10236_consen  140 DVFQALIRELKAQSKRPPVLVAVDGFNALFGPSAYRDP----DFKPIHPHDLTLVRLFLDLLSGKRDFKNGAVVTALAAT  215 (309)
T ss_pred             HHHHHHHHHHHhcccCCceEEEehhhHHhhCCccccCC----CCccccHHHhhHHHHHHHHhcCccccCCCeEEEEEecc
Confidence            999999999999998 9999999999999999999999    889999999999999999955  56999998   4566


Q ss_pred             ccccCcc
Q 045329          392 AVGSFAR  398 (404)
Q Consensus       392 ~v~k~~~  398 (404)
                      +....|.
T Consensus       216 ~~~~~~~  222 (309)
T PF10236_consen  216 SVSNAPK  222 (309)
T ss_pred             ccccccC
Confidence            6555444

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>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=97.16  E-value=0.00059  Score=62.41  Aligned_cols=35  Identities=31%  Similarity=0.545  Sum_probs=27.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      .++|+|++|+|||.+|.+++......+..++|+-.
T Consensus        22 ~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~   56 (234)
T PF01637_consen   22 HILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDF   56 (234)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCC
T ss_pred             EEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEec
Confidence            48999999999999999999988766775555543

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

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

Probab=97.14  E-value=0.00077  Score=60.08  Aligned_cols=35  Identities=26%  Similarity=0.344  Sum_probs=26.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -++|+|++|+|||++|..++..+...+++++++..
T Consensus        26 ~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~   60 (185)
T PF13191_consen   26 NLLLTGESGSGKTSLLRALLDRLAERGGYVISINC   60 (185)
T ss_dssp             -EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEE
Confidence            48999999999999999999988887766776643

>PF05729 NACHT: NACHT domain

Probab=96.79  E-value=0.002  Score=56.00  Aligned_cols=27  Identities=30%  Similarity=0.288  Sum_probs=22.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      -++|+|++|+|||++|.+++..-..++
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~~   28 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEEE   28 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcC
Confidence            379999999999999999887655554

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.68  E-value=0.0038  Score=58.06  Aligned_cols=34  Identities=32%  Similarity=0.334  Sum_probs=29.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|+|++|||||+++.++..++.+.+.-++|+.
T Consensus        40 ~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~   73 (226)
T TIGR03420        40 FLYLWGESGSGKSHLLQAACAAAEERGKSAIYLP   73 (226)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEe
Confidence            4899999999999999999999887776666664

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.

>PF13245 AAA_19: Part of AAA domain

Probab=96.64  E-value=0.0032  Score=50.57  Aligned_cols=32  Identities=34%  Similarity=0.385  Sum_probs=25.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhC----CeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREE----GWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~n----gWIVL~I  224 (404)
                      ++|.|++|||||+++.+++.+...+    +.=|+.+
T Consensus        13 ~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~   48 (76)
T PF13245_consen   13 FVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVL   48 (76)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEE
Confidence            6779999999999999999988754    5555554

>PF13173 AAA_14: AAA domain

Probab=96.62  E-value=0.0026  Score=54.91  Aligned_cols=34  Identities=32%  Similarity=0.360  Sum_probs=25.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH-hCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR-EEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL~I  224 (404)
                      +-++|+|+||||||++|.|+...-. .++++.+.+
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~   37 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYINF   37 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceeecc
Confidence            3489999999999999999987654 344444443

>PRK06851 hypothetical protein; Provisional

Probab=96.53  E-value=0.0049  Score=63.49  Aligned_cols=38  Identities=29%  Similarity=0.330  Sum_probs=34.4

Q ss_pred             ceeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          190 RKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       190 r~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      .++|+|.|++|+|||++|.++...|.++|+-|.+...+
T Consensus       214 ~~~~~i~G~pG~GKstl~~~i~~~a~~~G~~v~~~hC~  251 (367)
T PRK06851        214 KNRYFLKGRPGTGKSTMLKKIAKAAEERGFDVEVYHCG  251 (367)
T ss_pred             ceEEEEeCCCCCcHHHHHHHHHHHHHhCCCeEEEEeCC
Confidence            36799999999999999999999999999998887654

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.50  E-value=0.025  Score=53.12  Aligned_cols=27  Identities=15%  Similarity=0.026  Sum_probs=23.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      .-+.|+|++|||||+++.|+...+...
T Consensus        20 ~i~~i~G~~GsGKT~l~~~l~~~~~~~   46 (235)
T cd01123          20 SITEIFGEFGSGKTQLCHQLAVTVQLP   46 (235)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHeeCc
Confidence            458999999999999999998776543

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 .

>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=96.49  E-value=0.0036  Score=51.97  Aligned_cols=36  Identities=25%  Similarity=0.318  Sum_probs=28.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|++|||||+++..+.......+.-|+++..
T Consensus        20 ~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~   55 (151)
T cd00009          20 KNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNA   55 (151)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEeh
Confidence            348999999999999988888877666666666643

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.

>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=96.37  E-value=0.0032  Score=57.75  Aligned_cols=29  Identities=24%  Similarity=0.439  Sum_probs=24.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWL  220 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWI  220 (404)
                      +++|||++|+||||+|..++.....+|.-
T Consensus         1 ~i~iTG~pG~GKTTll~k~i~~l~~~~~~   29 (168)
T PF03266_consen    1 HIFITGPPGVGKTTLLKKVIEELKKKGLP   29 (168)
T ss_dssp             EEEEES-TTSSHHHHHHHHHHHHHHTCGG
T ss_pred             CEEEECcCCCCHHHHHHHHHHHhhccCCc
Confidence            48999999999999999999999766543

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.

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=96.32  E-value=0.0049  Score=56.27  Aligned_cols=22  Identities=32%  Similarity=0.511  Sum_probs=20.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .++.|++|||||++++.+++.+
T Consensus        20 ~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   20 TLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCChHHHHHHHHHHh
Confidence            7999999999999999999988

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.30  E-value=0.0059  Score=52.45  Aligned_cols=34  Identities=29%  Similarity=0.317  Sum_probs=29.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      ++|+|++|+|||+++.++...+..+|--|+|+.-
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~   35 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDI   35 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEEC
Confidence            6899999999999999999998877777777754

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.29  E-value=0.0079  Score=61.01  Aligned_cols=93  Identities=14%  Similarity=0.215  Sum_probs=58.5

Q ss_pred             EeCHHHHHhhccC-CCCcchhhh-ccccCce----------eEEEchhHHHHHHHHHHhcCCCccCCCCCccceeEEEEC
Q 045329          130 KFSEDELNAMLPE-GLPTGMLGE-FKDSMRY----------ALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDG  197 (404)
Q Consensus       130 ~~p~e~~k~l~~~-GLp~~~~kq-fe~f~~p----------~~LVRk~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G  197 (404)
                      .+-...++.++.. |++..+.+. |+.|.--          ..--|+....+++..++.++. + ..   .. ..++|+|
T Consensus       117 C~~q~~i~~~~~~S~i~~~~~~~~F~nf~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~f~~~-f-~~---~~-~~Lll~G  190 (329)
T PRK06835        117 CYKQKLINLYYKQSNLKEILKEENFSNFNLNYYSDEKDDDEPLSPRKNMEKILEKCKNFIEN-F-DK---NN-ENLLFYG  190 (329)
T ss_pred             chhHHHHHHHHHHcCCchHHHhCChhhCCccccCccccccCCCCHHHHHHHHHHHHHHHHHH-H-hc---cC-CcEEEEC
Confidence            3345566666655 888776665 6766422          113455544444433333221 1 01   11 3499999


Q ss_pred             CCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          198 PLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       198 ~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      +.|+|||.++.-+...+..+|.-|+|++...
T Consensus       191 ~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~  221 (329)
T PRK06835        191 NTGTGKTFLSNCIAKELLDRGKSVIYRTADE  221 (329)
T ss_pred             CCCCcHHHHHHHHHHHHHHCCCeEEEEEHHH
Confidence            9999999988888888888899999987643

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.27  E-value=0.0053  Score=57.73  Aligned_cols=37  Identities=27%  Similarity=0.172  Sum_probs=32.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      -++|+|++|||||.++..+.+.+...|+-+++|....
T Consensus        44 ~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~~   80 (227)
T PRK08903         44 FFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAAS   80 (227)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehHH
Confidence            4899999999999999999988888899888886643

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.22  E-value=0.006  Score=58.44  Aligned_cols=36  Identities=28%  Similarity=0.184  Sum_probs=30.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      .++|+|++|||||.++..+.+.+..+|.=|+|++-.
T Consensus        47 ~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~   82 (235)
T PRK08084         47 YIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLD   82 (235)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHH
Confidence            489999999999999998888888888877777653

>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=96.20  E-value=0.0063  Score=54.73  Aligned_cols=32  Identities=25%  Similarity=0.206  Sum_probs=28.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|.|++|||||++..|+++.+.++|==|+|+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~   33 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYV   33 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            68999999999999999999888887777777

A related protein is found in archaea.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.20  E-value=0.0046  Score=50.57  Aligned_cols=28  Identities=25%  Similarity=0.312  Sum_probs=24.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      ..++|.|++|||||+++..+.......+
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~   30 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPG   30 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCC
Confidence            3589999999999999999988777765

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.

>PRK12377 putative replication protein; Provisional

Probab=96.14  E-value=0.011  Score=57.65  Aligned_cols=36  Identities=22%  Similarity=0.199  Sum_probs=31.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      .++|+|++|||||.++.-+...+.++|.-|++++-.
T Consensus       103 ~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~  138 (248)
T PRK12377        103 NFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVP  138 (248)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHH
Confidence            489999999999999999999998889888887554

>PF14516 AAA_35: AAA-like domain

Probab=96.14  E-value=0.082  Score=53.38  Aligned_cols=32  Identities=25%  Similarity=0.487  Sum_probs=30.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.|.|+|.+|||++|.+++..+.++|..+++|
T Consensus        34 ~~I~apRq~GKTSll~~l~~~l~~~~~~~v~i   65 (331)
T PF14516_consen   34 IRIKAPRQMGKTSLLLRLLERLQQQGYRCVYI   65 (331)
T ss_pred             EEEECcccCCHHHHHHHHHHHHHHCCCEEEEE
Confidence            79999999999999999999999999999998

>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=96.04  E-value=0.0098  Score=49.87  Aligned_cols=31  Identities=29%  Similarity=0.446  Sum_probs=26.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      |+|.|++||||||+..++...-   |+.++++-+
T Consensus         2 I~I~G~~gsGKST~a~~La~~~---~~~~i~~d~   32 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERL---GFPVISMDD   32 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH---TCEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH---CCeEEEecc
Confidence            8999999999999998886633   888888766

...

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=95.98  E-value=0.018  Score=58.40  Aligned_cols=60  Identities=18%  Similarity=0.266  Sum_probs=41.5

Q ss_pred             eEEEch-hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEecC
Q 045329          159 ALLVRQ-SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVPR  226 (404)
Q Consensus       159 ~~LVRk-~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP~  226 (404)
                      .+.-|+ +..+|...|...+..     ..+   ..++|+|++|+|||+++..+.......  ++.++||..
T Consensus        31 ~l~~Re~e~~~l~~~l~~~~~~-----~~~---~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~   93 (394)
T PRK00411         31 NLPHREEQIEELAFALRPALRG-----SRP---LNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINC   93 (394)
T ss_pred             CCCCHHHHHHHHHHHHHHHhCC-----CCC---CeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEEC
Confidence            344566 456666666554321     122   238999999999999999999887665  477888754

>PRK08727 hypothetical protein; Validated

Probab=95.85  E-value=0.011  Score=56.69  Aligned_cols=35  Identities=29%  Similarity=0.368  Sum_probs=31.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -++|+|+.|||||.++.-+.+.+.++|--|+|+|-
T Consensus        43 ~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~   77 (233)
T PRK08727         43 WLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPL   77 (233)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeH
Confidence            48999999999999999888888889988889874

>PRK08181 transposase; Validated

Probab=95.84  E-value=0.009  Score=58.98  Aligned_cols=35  Identities=34%  Similarity=0.445  Sum_probs=31.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      .++|+|++|||||.+++-+...|.++|+-|+|++-
T Consensus       108 nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~  142 (269)
T PRK08181        108 NLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRT  142 (269)
T ss_pred             eEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeH
Confidence            38999999999999999999899999999988864

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=95.82  E-value=0.01  Score=61.04  Aligned_cols=36  Identities=22%  Similarity=0.245  Sum_probs=30.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP~  226 (404)
                      +.++|+|++|+|||.++..+.+.+.++  +|-|+|++.
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~  174 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSS  174 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEH
Confidence            348999999999999998777777766  899999964

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).

>PRK06921 hypothetical protein; Provisional

Probab=95.71  E-value=0.026  Score=55.50  Aligned_cols=37  Identities=30%  Similarity=0.286  Sum_probs=32.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEecCc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVPRG  227 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP~a  227 (404)
                      ..++|+|++|+|||.++.-+...+.++ |.-|+|++..
T Consensus       118 ~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~  155 (266)
T PRK06921        118 NSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFV  155 (266)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHH
Confidence            359999999999999998888888777 9999999853

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=95.69  E-value=0.14  Score=47.44  Aligned_cols=71  Identities=17%  Similarity=0.200  Sum_probs=42.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC---CeEEEEecCcccccccCeeecC-CC-C--CCccCHHHHHHHHHHHHHHhHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE---GWLVLYVPRGREWTHGGYFYKN-PQ-T--GLWDTPLQAENVLKDFIKYNES  264 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n---gWIVL~IP~a~~wvng~~~y~~-~~-~--g~ydQP~~A~~~Lk~fl~~N~~  264 (404)
                      .+++.|..|||||++|..++..+...   +-+-|||=++..-  +-..|.+ +. .  -.-..+..+.++|+.+...-+.
T Consensus        40 h~li~G~tgsGKS~~l~~ll~~l~~~~~p~~~~l~iiD~k~~--~l~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~em~~  117 (205)
T PF01580_consen   40 HLLIAGATGSGKSTLLRTLLLSLALTYSPDDVQLYIIDPKGS--DLAPLADLPHVAAVAVATDPEEILRLLEELVEEMER  117 (205)
T ss_dssp             SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSS--CCGGGTT-TTBSS-S-B-SHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEcCCCCCccHHHHHHHHHHHHHhcCCccEEEEEcCCcc--ccchhhhhhhhccccccccHHHHHHHHHHHHHHHHH
Confidence            58999999999999999888876662   5555666554421  0011222 11 1  1456888999998887664443

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=95.67  E-value=0.036  Score=59.76  Aligned_cols=126  Identities=16%  Similarity=0.119  Sum_probs=69.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccccCeeecCC-------CCCCccC--HHHHHHHHHHHHHHh
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNP-------QTGLWDT--PLQAENVLKDFIKYN  262 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvng~~~y~~~-------~~g~ydQ--P~~A~~~Lk~fl~~N  262 (404)
                      -.+|+||.||||||++-=   .|.+.|      +...+|.|+..+-.++       .-+.+++  -.....+|....+.|
T Consensus       112 iLLltGPsGcGKSTtvkv---Lskelg------~~~~Ew~Npi~~~~~~~~h~~t~~~~~~~~s~L~~fesFler~~kyg  182 (634)
T KOG1970|consen  112 ILLLTGPSGCGKSTTVKV---LSKELG------YQLIEWSNPINLKEPENLHNETSFLMFPYQSQLAVFESFLLRATKYG  182 (634)
T ss_pred             EEEEeCCCCCCchhHHHH---HHHhhC------ceeeeecCCccccccccccccchhcccchhhHHHHHHHHHHHHHhhc
Confidence            378999999999999732   344444      4456787775532221       1122233  233345666665555


Q ss_pred             HHHHhcCCcccccCCCCCCCCccccccCCCccccCCCCCHHHHHHhhcccccchHHHHHHHHHHHhcCCCCcEEEEEeCc
Q 045329          263 ESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSLVKDIPVLIAIDQY  342 (404)
Q Consensus       263 ~~~LkkLkls~~~~~~lge~~~~~w~K~~d~~~~p~g~tL~DLv~~Gi~~~~~A~~v~~aLl~EL~~q~~~PVLvAVD~~  342 (404)
                      .-.+.......+.++.                 +     +.||=++--.  + +...|+.+++++..-+.+|++|.|=+.
T Consensus       183 ~l~~~g~~~~~~~~li-----------------L-----veDLPn~~~~--d-~~~~f~evL~~y~s~g~~PlIf~iTd~  237 (634)
T KOG1970|consen  183 SLQMSGDDLRTDKKLI-----------------L-----VEDLPNQFYR--D-DSETFREVLRLYVSIGRCPLIFIITDS  237 (634)
T ss_pred             hhhhcccccccCceEE-----------------E-----eeccchhhhh--h-hHHHHHHHHHHHHhcCCCcEEEEEecc
Confidence            4333333322221111                 0     0111111111  1 466789999999999999999999888


Q ss_pred             ccccCcCCc
Q 045329          343 NNWFTFSEY  351 (404)
Q Consensus       343 Nalf~~S~Y  351 (404)
                      +.-.....|
T Consensus       238 ~~~g~nnq~  246 (634)
T KOG1970|consen  238 LSNGNNNQD  246 (634)
T ss_pred             ccCCCcchh
Confidence            775443334

>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=95.67  E-value=0.014  Score=50.36  Aligned_cols=33  Identities=18%  Similarity=0.206  Sum_probs=24.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      ++|+|++|||||.+..++.+.. ...+++++++.
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~-~~~~~~i~~~~   34 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALL-GRPVIRINCSS   34 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHH-TCEEEEEE-TT
T ss_pred             EEEECCCCCCHHHHHHHHHHHh-hcceEEEEecc
Confidence            7999999999999887766655 55566665544

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=95.63  E-value=0.014  Score=55.56  Aligned_cols=36  Identities=19%  Similarity=0.178  Sum_probs=29.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|++|||||.++.-+.+.+.++|-=|+|++-
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~   75 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPL   75 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeH
Confidence            347999999999999998888887777656667664

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

Probab=95.53  E-value=0.034  Score=54.51  Aligned_cols=37  Identities=22%  Similarity=0.295  Sum_probs=32.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      +.++|+|++|||||.++-.++.....+|-=+|.|+..
T Consensus        53 nnvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k~   89 (249)
T PF05673_consen   53 NNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSKE   89 (249)
T ss_pred             cceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECHH
Confidence            3499999999999999999999888899888888764

>PRK06526 transposase; Provisional

Probab=95.51  E-value=0.011  Score=57.89  Aligned_cols=33  Identities=30%  Similarity=0.324  Sum_probs=29.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|++|||||.+++.+...|..+|+-|+++
T Consensus       100 nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~  132 (254)
T PRK06526        100 NVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFA  132 (254)
T ss_pred             eEEEEeCCCCchHHHHHHHHHHHHHCCCchhhh
Confidence            489999999999999999999998889887775

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.50  E-value=0.016  Score=54.67  Aligned_cols=35  Identities=17%  Similarity=0.197  Sum_probs=30.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP~  226 (404)
                      -++|.|++|+|||+++.|++..+..+ |+=|+|+.-
T Consensus        15 l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~   50 (242)
T cd00984          15 LIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSL   50 (242)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeC
Confidence            38999999999999999988877666 999999863

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.

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

Probab=95.50  E-value=0.042  Score=53.64  Aligned_cols=37  Identities=24%  Similarity=0.303  Sum_probs=32.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      ..++|+|++|+|||.+++-+.+.+...||=|++++-+
T Consensus       106 ~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~  142 (254)
T COG1484         106 ENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAP  142 (254)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHH
Confidence            3499999999999999998888888889999999765

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.49  E-value=0.017  Score=56.23  Aligned_cols=34  Identities=26%  Similarity=0.298  Sum_probs=30.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|||||++..|+...+.++|.=|+||.
T Consensus        38 ~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis   71 (259)
T TIGR03878        38 VINITGVSDTGKSLMVEQFAVTQASRGNPVLFVT   71 (259)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEE
Confidence            3899999999999999999888777899888884

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=95.48  E-value=0.018  Score=55.38  Aligned_cols=34  Identities=21%  Similarity=0.085  Sum_probs=29.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP  225 (404)
                      -++|.|++|+|||+++.|+...+..+ ||-|+||.
T Consensus        32 ~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS   66 (271)
T cd01122          32 LIILTAGTGVGKTTFLREYALDLITQHGVRVGTIS   66 (271)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEE
Confidence            38999999999999999988876555 99999985

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.44  E-value=0.012  Score=61.84  Aligned_cols=45  Identities=22%  Similarity=0.215  Sum_probs=29.9

Q ss_pred             hHHHHHHHHHHhcCCCccCCC-CCccceeEEEECCCCCcHHHHHHH
Q 045329          165 SFLDIRDNFRRIVDPSLQSTN-GPKIRKQIVLDGPLCCGKSITLAM  209 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std-~~~~r~r~vL~G~rGsGKS~~L~q  209 (404)
                      --.+|++.|...+....|=.. +.+=+++|+||||+|||||++.+-
T Consensus       209 ~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPPGTGKSS~IaA  254 (457)
T KOG0743|consen  209 LKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPPGTGKSSFIAA  254 (457)
T ss_pred             HHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCCCCCHHHHHHH
Confidence            355677777665443221111 455567899999999999998753

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.43  E-value=0.017  Score=58.32  Aligned_cols=42  Identities=29%  Similarity=0.480  Sum_probs=36.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh-CCeEEEEecCccccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE-EGWLVLYVPRGREWTHG  233 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~-ngWIVL~IP~a~~wvng  233 (404)
                      =++++|+.||||||+|+-.+.|--+ ..--||.|-++-++++.
T Consensus       127 LILVTGpTGSGKSTTlAamId~iN~~~~~HIlTIEDPIE~vh~  169 (353)
T COG2805         127 LILVTGPTGSGKSTTLAAMIDYINKHKAKHILTIEDPIEYVHE  169 (353)
T ss_pred             eEEEeCCCCCcHHHHHHHHHHHHhccCCcceEEecCchHhhhc
Confidence            3899999999999999999998665 48889999999998754

>PRK05642 DNA replication initiation factor; Validated

Probab=95.41  E-value=0.02  Score=54.84  Aligned_cols=36  Identities=25%  Similarity=0.225  Sum_probs=28.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      .++|+|++|||||.+|.-+.+.+..+|--|+|++-.
T Consensus        47 ~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~~   82 (234)
T PRK05642         47 LIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLA   82 (234)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeHH
Confidence            489999999999999766666566667778888753

>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=95.40  E-value=0.016  Score=48.63  Aligned_cols=22  Identities=32%  Similarity=0.527  Sum_probs=19.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      ++|+|++|||||++...+..+.
T Consensus         1 ill~G~~G~GKT~l~~~la~~l   22 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL   22 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT
T ss_pred             CEEECcCCCCeeHHHHHHHhhc
Confidence            5899999999999988777765

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 ....

>PRK09183 transposase/IS protein; Provisional

Probab=95.38  E-value=0.02  Score=55.89  Aligned_cols=34  Identities=32%  Similarity=0.270  Sum_probs=30.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .++|+|++|||||++++.+.+.|..+|.=|+|++
T Consensus       104 ~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~  137 (259)
T PRK09183        104 NIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTT  137 (259)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            3899999999999999999888888898888875

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

Probab=95.35  E-value=0.17  Score=52.24  Aligned_cols=50  Identities=20%  Similarity=0.303  Sum_probs=34.3

Q ss_pred             EEEch-hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          160 LLVRQ-SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       160 ~LVRk-~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      +--|+ +-.++...|..++..     ..|.+   ++++|++|||||+++..++.-..+.
T Consensus        19 l~~Re~ei~~l~~~l~~~~~~-----~~p~n---~~iyG~~GTGKT~~~~~v~~~l~~~   69 (366)
T COG1474          19 LPHREEEINQLASFLAPALRG-----ERPSN---IIIYGPTGTGKTATVKFVMEELEES   69 (366)
T ss_pred             ccccHHHHHHHHHHHHHHhcC-----CCCcc---EEEECCCCCCHhHHHHHHHHHHHhh
Confidence            44555 455566666655442     13443   8999999999999999888876643

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=95.33  E-value=0.026  Score=50.29  Aligned_cols=34  Identities=21%  Similarity=0.374  Sum_probs=28.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +++.+.|.+|||||+++..++.++.++||=|.+|
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~~~g~~v~~i   34 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELKRRGYRVAVI   34 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhHcCCceEEE
Confidence            3589999999999999999999999999988766

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

Probab=95.30  E-value=0.023  Score=48.02  Aligned_cols=24  Identities=25%  Similarity=0.401  Sum_probs=19.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -++|+|++|+|||+++.++.....
T Consensus         6 ~~~i~G~~G~GKT~~~~~~~~~~~   29 (131)
T PF13401_consen    6 ILVISGPPGSGKTTLIKRLARQLN   29 (131)
T ss_dssp             -EEEEE-TTSSHHHHHHHHHHHHH
T ss_pred             ccEEEcCCCCCHHHHHHHHHHHhH
Confidence            389999999999999999888654

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=95.30  E-value=0.067  Score=53.03  Aligned_cols=33  Identities=18%  Similarity=0.198  Sum_probs=26.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHh-------CCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWARE-------EGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~-------ngWIVL~IP~  226 (404)
                      +.|+|++|||||+++.|+...|..       +| -|+||--
T Consensus        98 ~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~-~~~yi~t  137 (310)
T TIGR02236        98 TEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGG-KAVYIDT  137 (310)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCcccCCCcc-eEEEEEC
Confidence            689999999999999999776652       34 6777743

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=95.30  E-value=0.023  Score=54.46  Aligned_cols=34  Identities=32%  Similarity=0.399  Sum_probs=30.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|||||++..|+++-..++|+-++||.
T Consensus        26 ~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~   59 (230)
T PRK08533         26 LILIEGDESTGKSILSQRLAYGFLQNGYSVSYVS   59 (230)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            4899999999999999999887778898888885

>PRK04296 thymidine kinase; Provisional

Probab=95.27  E-value=0.027  Score=52.27  Aligned_cols=32  Identities=28%  Similarity=0.238  Sum_probs=28.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .+++|+.|+|||++|.+.+..+...|.-|+++
T Consensus         5 ~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~   36 (190)
T PRK04296          5 EFIYGAMNSGKSTELLQRAYNYEERGMKVLVF   36 (190)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            68999999999999999999887778777766

>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=95.20  E-value=0.029  Score=50.45  Aligned_cols=33  Identities=36%  Similarity=0.434  Sum_probs=28.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +++.|++|+|||++...+.....++|.-|+.|.
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~   35 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVA   35 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            689999999999999999988878887666664

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.

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

Probab=95.20  E-value=0.024  Score=52.86  Aligned_cols=35  Identities=23%  Similarity=0.179  Sum_probs=29.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC------eEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG------WLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng------WIVL~IP~  226 (404)
                      -+.|+|++|||||+++.|++..+..++      .-|+||--
T Consensus        21 v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~   61 (226)
T cd01393          21 ITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDT   61 (226)
T ss_pred             EEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEec
Confidence            489999999999999999998887776      77777643

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.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=95.16  E-value=0.029  Score=52.71  Aligned_cols=34  Identities=21%  Similarity=0.251  Sum_probs=31.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|+|||++..|+++.+.++|.-|+||.
T Consensus        18 ~~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~s   51 (224)
T TIGR03880        18 VIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYIS   51 (224)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            4899999999999999999999988999999984

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=95.13  E-value=0.053  Score=54.31  Aligned_cols=60  Identities=18%  Similarity=0.324  Sum_probs=38.5

Q ss_pred             EEEch-hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHh--CC----eEEEEecCc
Q 045329          160 LLVRQ-SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWARE--EG----WLVLYVPRG  227 (404)
Q Consensus       160 ~LVRk-~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~--ng----WIVL~IP~a  227 (404)
                      +.-|+ +..+|...|+...+.     ..+   ..++|+|++|||||+++..+.....+  .+    |.++||.-.
T Consensus        17 l~gRe~e~~~l~~~l~~~~~~-----~~~---~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~   83 (365)
T TIGR02928        17 IVHRDEQIEELAKALRPILRG-----SRP---SNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQ   83 (365)
T ss_pred             CCCcHHHHHHHHHHHHHHHcC-----CCC---CcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECC
Confidence            44577 445666666654331     112   24899999999999999887765432  22    777777643

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.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=95.12  E-value=0.025  Score=50.49  Aligned_cols=32  Identities=28%  Similarity=0.466  Sum_probs=22.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGRE  229 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~  229 (404)
                      |++|+|..|||||+++.++..+    |+.++  |..-.
T Consensus         1 rI~i~G~~stGKTTL~~~L~~~----g~~~v--~E~ar   32 (163)
T PF13521_consen    1 RIVITGGPSTGKTTLIEALAAR----GYPVV--PEYAR   32 (163)
T ss_dssp             -EEEE--TTSHHHHHHHHHHHH----T-EEE----TTH
T ss_pred             CEEEECCCCCCHHHHHHHHHHc----CCeEE--eecHH
Confidence            5899999999999999998877    88866  55443

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=95.11  E-value=0.027  Score=54.38  Aligned_cols=35  Identities=31%  Similarity=0.435  Sum_probs=32.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .-++++|++|||||+...|.+.-..+.|+-|+||.
T Consensus        24 ~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs   58 (260)
T COG0467          24 SVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVS   58 (260)
T ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEE
Confidence            45999999999999999999998888899999993

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=95.11  E-value=0.033  Score=51.54  Aligned_cols=35  Identities=26%  Similarity=0.314  Sum_probs=29.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -+.|+|++|||||++..|+...+..+|-=|+||.-
T Consensus        14 i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~   48 (209)
T TIGR02237        14 ITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDT   48 (209)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEC
Confidence            48999999999999999998888777777777643

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

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.10  E-value=0.06  Score=53.20  Aligned_cols=89  Identities=21%  Similarity=0.185  Sum_probs=48.8

Q ss_pred             HHHHhhccCCCCcchhhhc-cccCc--eeEEEchhHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHH
Q 045329          134 DELNAMLPEGLPTGMLGEF-KDSMR--YALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       134 e~~k~l~~~GLp~~~~kqf-e~f~~--p~~LVRk~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qa  210 (404)
                      +-++.|...|++..+.+++ +...+  +.-.++   ..+.+.|.+.+....+..+-......++|.|+.|+|||++++.+
T Consensus       138 ~l~~~L~~~gv~~~la~~L~~~l~~~~~~~~~~---~~~~~~l~~~l~~~~~~~~~~~~~~vi~~vGptGvGKTTt~~kL  214 (282)
T TIGR03499       138 KLLERLLRAGVSPELARELLEKLPERADAEDAW---RWLREALEKMLPVKPEEDEILEQGGVIALVGPTGVGKTTTLAKL  214 (282)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHhhccCCHHHHH---HHHHHHHHHHhccCCccccccCCCeEEEEECCCCCCHHHHHHHH
Confidence            3455667778888777776 22221  001111   22333343333211001000011135889999999999999999


Q ss_pred             HHHHHhC-C-eEEEEec
Q 045329          211 VHWAREE-G-WLVLYVP  225 (404)
Q Consensus       211 v~~A~~n-g-WIVL~IP  225 (404)
                      ..++..+ | +=|..|.
T Consensus       215 a~~~~~~~g~~~V~li~  231 (282)
T TIGR03499       215 AARFVLEHGNKKVALIT  231 (282)
T ss_pred             HHHHHHHcCCCeEEEEE
Confidence            9988765 4 6666663

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=95.05  E-value=0.034  Score=52.23  Aligned_cols=34  Identities=26%  Similarity=0.289  Sum_probs=30.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -+.|+|++|+|||+++.|++..+..+|.=|+||.
T Consensus        25 i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~   58 (225)
T PRK09361         25 ITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYID   58 (225)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            3799999999999999999988888888888884

>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=95.01  E-value=0.027  Score=51.81  Aligned_cols=56  Identities=18%  Similarity=0.201  Sum_probs=39.7

Q ss_pred             hhhhccccCceeEEEchhHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHH
Q 045329          148 MLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       148 ~~kqfe~f~~p~~LVRk~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      +.++++.++-+.+.+...+-+-++.|++.+.         .  +.++|.|+.|+|||++++.++-.+
T Consensus         4 ~~~~y~~~gy~v~~~S~~~~~g~~~l~~~l~---------~--k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen    4 LLEQYEKLGYPVFFISAKTGEGIEELKELLK---------G--KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             HHHHHHHTTSEEEE-BTTTTTTHHHHHHHHT---------T--SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             HHHHHHHcCCcEEEEeCCCCcCHHHHHHHhc---------C--CEEEEECCCCCCHHHHHHHHHhhc
Confidence            4455667777788877655566666665542         1  248999999999999999988753

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.

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

Probab=95.00  E-value=0.033  Score=51.41  Aligned_cols=36  Identities=25%  Similarity=0.452  Sum_probs=30.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      .++|+|++|+|||.+.+-+...|..+|--|+|+...
T Consensus        49 ~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~   84 (178)
T PF01695_consen   49 NLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITAS   84 (178)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHH
T ss_pred             EEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecC
Confidence            499999999999999999988899999999999755

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.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=94.97  E-value=0.026  Score=58.97  Aligned_cols=33  Identities=33%  Similarity=0.434  Sum_probs=29.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      ++|-|++|.||||+|+|+.+-..+++ =||||.-
T Consensus        96 iLIgGdPGIGKSTLLLQva~~lA~~~-~vLYVsG  128 (456)
T COG1066          96 ILIGGDPGIGKSTLLLQVAARLAKRG-KVLYVSG  128 (456)
T ss_pred             EEEccCCCCCHHHHHHHHHHHHHhcC-cEEEEeC
Confidence            78999999999999999999777777 9999964

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

Probab=94.97  E-value=0.027  Score=53.82  Aligned_cols=32  Identities=19%  Similarity=0.266  Sum_probs=24.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      -++|+|++|+|||+++.++.......+.++.+
T Consensus        45 ~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~   76 (269)
T TIGR03015        45 FILITGEVGAGKTTLIRNLLKRLDQERVVAAK   76 (269)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCCCeEEee
Confidence            38999999999999999887765544444433

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=94.96  E-value=0.034  Score=54.16  Aligned_cols=34  Identities=21%  Similarity=0.203  Sum_probs=30.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .++|+|++|||||.+++.+..++..+|--|++++
T Consensus       101 ~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it  134 (244)
T PRK07952        101 SFIFSGKPGTGKNHLAAAICNELLLRGKSVLIIT  134 (244)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            5999999999999999999999988887777773

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=94.93  E-value=0.15  Score=50.77  Aligned_cols=50  Identities=22%  Similarity=0.278  Sum_probs=40.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccccCeeecCCCCCCccCHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDF  258 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvng~~~y~~~~~g~ydQP~~A~~~Lk~f  258 (404)
                      +=++|+.|||||++.+|++..|...|=.++||---..+                -|.++.++...+
T Consensus        63 tEiyG~~gsGKT~lal~~~~~aq~~g~~a~fIDtE~~l----------------~p~r~~~l~~~~  112 (279)
T COG0468          63 TEIYGPESSGKTTLALQLVANAQKPGGKAAFIDTEHAL----------------DPERAKQLGVDL  112 (279)
T ss_pred             EEEecCCCcchhhHHHHHHHHhhcCCCeEEEEeCCCCC----------------CHHHHHHHHHhh
Confidence            44899999999999999999999999888887543333                377777777765

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=94.90  E-value=0.039  Score=51.86  Aligned_cols=34  Identities=24%  Similarity=0.268  Sum_probs=29.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|||||+++.|++..+.++|.=|+||.
T Consensus        22 ~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is   55 (229)
T TIGR03881        22 FVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVT   55 (229)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEE
Confidence            4899999999999999998877767888777774

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.

>PRK08116 hypothetical protein; Validated

Probab=94.88  E-value=0.038  Score=54.27  Aligned_cols=34  Identities=26%  Similarity=0.343  Sum_probs=29.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .++|+|++|||||.++..+.+...++|--|++++
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~  149 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIEKGVPVIFVN  149 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            4999999999999999988888888787777775

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=94.84  E-value=0.31  Score=55.82  Aligned_cols=49  Identities=16%  Similarity=0.260  Sum_probs=34.2

Q ss_pred             eeEEEch-hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHH
Q 045329          158 YALLVRQ-SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       158 p~~LVRk-~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ..+.-|+ +..+|...|..++...     ++.  +-++|+|++|||||++...++.-
T Consensus       755 D~LPhREeEIeeLasfL~paIkgs-----gpn--nvLYIyG~PGTGKTATVK~VLrE  804 (1164)
T PTZ00112        755 KYLPCREKEIKEVHGFLESGIKQS-----GSN--QILYISGMPGTGKTATVYSVIQL  804 (1164)
T ss_pred             CcCCChHHHHHHHHHHHHHHHhcC-----CCC--ceEEEECCCCCCHHHHHHHHHHH
Confidence            3455777 6777778887765421     222  22569999999999999888654

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=94.79  E-value=0.036  Score=57.99  Aligned_cols=37  Identities=22%  Similarity=0.307  Sum_probs=30.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEecCc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVPRG  227 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP~a  227 (404)
                      +.++|+|++|||||.++.-+...+.++  +.-|+|++..
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~  187 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSE  187 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHH
Confidence            348999999999999998888888777  6778898653

>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria

Probab=94.76  E-value=0.068  Score=56.06  Aligned_cols=59  Identities=22%  Similarity=0.336  Sum_probs=43.6

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe-cCcccccc
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV-PRGREWTH  232 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I-P~a~~wvn  232 (404)
                      ..-.|.+.|+.+.+.      +...   -++.|+-|||||.+|..+...|+++|++|.+| =++....+
T Consensus        33 e~~~l~~~l~~v~~G------~s~~---kfi~G~YGsGKTf~l~~i~~~A~~~~fvvs~v~ls~e~~lh   92 (416)
T PF10923_consen   33 EIEALDRDLDRVADG------GSSF---KFIRGEYGSGKTFFLRLIRERALEKGFVVSEVDLSPERPLH   92 (416)
T ss_pred             HHHHHHHHHHHHhCC------CCeE---EEEEeCCCCcHHHHHHHHHHHHHHcCCEEEEEecCCCcccc
Confidence            445666667666432      3343   37789999999999999999999999999998 22244555

Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.

>PRK13695 putative NTPase; Provisional

Probab=94.70  E-value=0.054  Score=48.96  Aligned_cols=30  Identities=30%  Similarity=0.521  Sum_probs=24.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLV  221 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIV  221 (404)
                      +++|+|+.|||||++|.++.......|.-+
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~~~G~~~   31 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLKEEGYKV   31 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeE
Confidence            489999999999999999888766556543

>PRK08939 primosomal protein DnaI; Reviewed

Probab=94.70  E-value=0.04  Score=55.31  Aligned_cols=34  Identities=26%  Similarity=0.281  Sum_probs=29.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.++|+|+.|+|||.+++-+.+.+.++|+=|+++
T Consensus       157 ~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~  190 (306)
T PRK08939        157 KGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLL  190 (306)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            4699999999999999999998888888766655

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=94.69  E-value=0.056  Score=44.23  Aligned_cols=26  Identities=15%  Similarity=0.304  Sum_probs=22.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      .++|.|+.|+|||+++..++.+....
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~~   27 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDS   27 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHhc
Confidence            37999999999999999999888754

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>cd01394 radB RadB

Probab=94.68  E-value=0.048  Score=50.86  Aligned_cols=33  Identities=24%  Similarity=0.229  Sum_probs=28.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|+|++|||||++..|+...+..+|-=|+||
T Consensus        21 i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi   53 (218)
T cd01394          21 VTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYI   53 (218)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEE
Confidence            388999999999999999998887777777777

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

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=94.62  E-value=0.042  Score=49.81  Aligned_cols=24  Identities=21%  Similarity=0.224  Sum_probs=20.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -.+|.|++|+|||+++.|++....
T Consensus        34 l~~i~g~~g~GKT~~~~~l~~~~~   57 (193)
T PF13481_consen   34 LTLIAGPPGSGKTTLALQLAAALA   57 (193)
T ss_dssp             EEEEEECSTSSHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHH
Confidence            389999999999999999877443

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=94.59  E-value=0.086  Score=54.16  Aligned_cols=52  Identities=15%  Similarity=0.330  Sum_probs=34.7

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEe
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYV  224 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~I  224 (404)
                      +-.+|-..+++.+-.      ++.  +.++|.||||||||+++.+++.-+.++  +.++++.
T Consensus        32 ~~~~l~~~lkqt~~~------gEs--nsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~L   85 (408)
T KOG2228|consen   32 EQKHLSELLKQTILH------GES--NSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRL   85 (408)
T ss_pred             HHHHHHHHHHHHHHh------cCC--CceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEE
Confidence            344555555554322      233  248999999999999999999885544  5555554

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=94.54  E-value=0.05  Score=50.79  Aligned_cols=32  Identities=31%  Similarity=0.359  Sum_probs=26.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .+|.|++|||||++|..+......+|+-|+.+
T Consensus        21 ~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~   52 (196)
T PF13604_consen   21 SVLQGPAGTGKTTLLKALAEALEAAGKRVIGL   52 (196)
T ss_dssp             EEEEESTTSTHHHHHHHHHHHHHHTT--EEEE
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            78899999999999999988888877666655

>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=94.51  E-value=0.063  Score=48.21  Aligned_cols=36  Identities=22%  Similarity=0.354  Sum_probs=30.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      ++|.|..||||||++..+..+-...|+-|+.+..+.
T Consensus         3 I~ieG~~GsGKtT~~~~L~~~l~~~g~~v~~~~~~~   38 (200)
T cd01672           3 IVFEGIDGAGKTTLIELLAERLEARGYEVVLTREPG   38 (200)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCC
Confidence            789999999999999999888778888887776554

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=94.48  E-value=0.052  Score=51.41  Aligned_cols=33  Identities=27%  Similarity=0.342  Sum_probs=26.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHH--HhCCeEEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWA--REEGWLVLY  223 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A--~~ngWIVL~  223 (404)
                      ++++|+|+.|+|||++|.++..-+  .+.||.|..
T Consensus        30 ~~~~itGpNg~GKStlLk~i~~~~~la~~G~~v~a   64 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPA   64 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHHHHHHHHhCCCeeEc
Confidence            469999999999999999987433  467897753

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

>PRK04328 hypothetical protein; Provisional

Probab=94.47  E-value=0.05  Score=52.63  Aligned_cols=34  Identities=26%  Similarity=0.257  Sum_probs=30.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|||||++..|.+..+..+|.-++||.
T Consensus        25 ~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis   58 (249)
T PRK04328         25 VVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVA   58 (249)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            3889999999999999999988888899888884

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=94.45  E-value=0.045  Score=57.74  Aligned_cols=36  Identities=39%  Similarity=0.481  Sum_probs=31.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|++|+|||.++..+.+...++|.-|+|++.
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~  177 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRS  177 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeH
Confidence            358999999999999988888888888999999975

>PF13479 AAA_24: AAA domain

Probab=94.44  E-value=0.07  Score=50.32  Aligned_cols=33  Identities=27%  Similarity=0.341  Sum_probs=28.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREW  230 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~w  230 (404)
                      +++|+|++|+|||+++..+      .+.++|.+-.....
T Consensus         5 ~~lIyG~~G~GKTt~a~~~------~k~l~id~E~g~~~   37 (213)
T PF13479_consen    5 KILIYGPPGSGKTTLAASL------PKPLFIDTENGSDS   37 (213)
T ss_pred             EEEEECCCCCCHHHHHHhC------CCeEEEEeCCCccc
Confidence            5999999999999999888      88999988666443

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=94.33  E-value=0.053  Score=55.94  Aligned_cols=33  Identities=33%  Similarity=0.404  Sum_probs=29.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++|.|++|+|||+++.|+.+....+|.=|+||.
T Consensus        85 vLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs  117 (372)
T cd01121          85 ILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVS  117 (372)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            799999999999999999988777777888884

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=94.29  E-value=0.06  Score=51.44  Aligned_cols=34  Identities=26%  Similarity=0.266  Sum_probs=29.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|||||++..|++..+..+|==++||.
T Consensus        23 ~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs   56 (237)
T TIGR03877        23 VVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVA   56 (237)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEE
Confidence            4899999999999999999988778887777774

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.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.22  E-value=0.059  Score=57.52  Aligned_cols=43  Identities=21%  Similarity=0.265  Sum_probs=37.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccccC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGG  234 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvng~  234 (404)
                      =++++||.|||||++|-.++.+.....--|+.|-++-++...+
T Consensus       260 liLvTGPTGSGKTTTLY~~L~~ln~~~~nI~TiEDPVE~~~~g  302 (500)
T COG2804         260 LILVTGPTGSGKTTTLYAALSELNTPERNIITIEDPVEYQLPG  302 (500)
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEeeCCeeeecCC
Confidence            3899999999999999999999998777799999998876544

>PRK05973 replicative DNA helicase; Provisional

Probab=94.18  E-value=0.065  Score=52.14  Aligned_cols=34  Identities=18%  Similarity=0.140  Sum_probs=30.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|+|||++..|++..+..+|-=|+|+.
T Consensus        66 l~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfS   99 (237)
T PRK05973         66 LVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFT   99 (237)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            3899999999999999999998888888787773

>TIGR02012 tigrfam_recA protein RecA

Probab=94.16  E-value=0.061  Score=54.59  Aligned_cols=33  Identities=21%  Similarity=0.282  Sum_probs=29.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -+.|+|++|||||++..|++..+..+|=-|+||
T Consensus        57 iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yI   89 (321)
T TIGR02012        57 IIEIYGPESSGKTTLALHAIAEAQKAGGTAAFI   89 (321)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            378999999999999999999888887777788

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.

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=94.16  E-value=0.1  Score=51.10  Aligned_cols=40  Identities=23%  Similarity=0.238  Sum_probs=32.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWT  231 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wv  231 (404)
                      -+++.|+.|||||++|..++.+-...+.-|+.|-++.++.
T Consensus        82 lilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~  121 (264)
T cd01129          82 IILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQ  121 (264)
T ss_pred             EEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceec
Confidence            3899999999999999988877655677788887776654

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.

>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=94.15  E-value=0.065  Score=50.96  Aligned_cols=35  Identities=29%  Similarity=0.414  Sum_probs=26.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh--CCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE--EGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~--ngWIVL~IP~  226 (404)
                      -++|+|+.|+|||-+|..+.+.+.+  .+--|+|++.
T Consensus        36 ~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~   72 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSA   72 (219)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEH
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHhccccccceeecH
Confidence            4899999999999987777776664  3667778764

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.

>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=94.12  E-value=0.068  Score=50.19  Aligned_cols=33  Identities=33%  Similarity=0.419  Sum_probs=28.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++|.|+.|+|||++++-+.+|...+|+=|.-|.
T Consensus         4 i~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis   36 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIAKLAARLKLKGKKVALIS   36 (196)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE
T ss_pred             EEEECCCCCchHhHHHHHHHHHhhccccceeec
Confidence            789999999999999999999998899888874

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 ....

>PLN03025 replication factor C subunit; Provisional

Probab=94.12  E-value=0.078  Score=52.92  Aligned_cols=29  Identities=24%  Similarity=0.445  Sum_probs=22.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGW  219 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngW  219 (404)
                      +.++|+|++|||||+++..+.......+|
T Consensus        35 ~~lll~Gp~G~GKTtla~~la~~l~~~~~   63 (319)
T PLN03025         35 PNLILSGPPGTGKTTSILALAHELLGPNY   63 (319)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHhcccC
Confidence            35899999999999998877776654443

>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=94.10  E-value=0.053  Score=44.96  Aligned_cols=23  Identities=26%  Similarity=0.231  Sum_probs=20.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      |+++.|++|||||+++.+++.--
T Consensus         1 kI~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    1 KIVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CEEEECcCCCCHHHHHHHHhcCC
Confidence            58999999999999999888644

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.

>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=94.10  E-value=0.065  Score=45.98  Aligned_cols=32  Identities=34%  Similarity=0.358  Sum_probs=24.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      ++|.|++|||||++..++   +...++.++.....
T Consensus         2 ii~~G~pgsGKSt~a~~l---~~~~~~~~i~~D~~   33 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRL---AKRLGAVVISQDEI   33 (143)
T ss_dssp             EEEEESTTSSHHHHHHHH---HHHSTEEEEEHHHH
T ss_pred             EEEECCCCCCHHHHHHHH---HHHCCCEEEeHHHH
Confidence            689999999999996554   55566777766553

...

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=94.08  E-value=0.077  Score=50.25  Aligned_cols=35  Identities=26%  Similarity=0.290  Sum_probs=30.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -++|.|++|||||++.+|+++-+..+|-=|+|+.-
T Consensus        27 ~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~   61 (234)
T PRK06067         27 LILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITT   61 (234)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEc
Confidence            38999999999999999998877778888888854

>PF13476 AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V_A 3QG5_B 3QF7_A 3THO_A

Probab=94.08  E-value=0.045  Score=49.00  Aligned_cols=22  Identities=36%  Similarity=0.448  Sum_probs=19.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      .||+|+.|+|||++| .++.||.
T Consensus        22 ~vi~G~Ng~GKStil-~ai~~~L   43 (202)
T PF13476_consen   22 NVIYGPNGSGKSTIL-EAIRYAL   43 (202)
T ss_dssp             EEEEESTTSSHHHHH-HHHHHHH
T ss_pred             EEEECCCCCCHHHHH-HHHHHHH
Confidence            699999999999999 7778877

>PF12846 AAA_10: AAA-like domain

Probab=94.08  E-value=0.075  Score=50.64  Aligned_cols=39  Identities=18%  Similarity=0.195  Sum_probs=31.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREW  230 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~w  230 (404)
                      ..++.|..|||||+++..++..+...|.-|+.|.--.+|
T Consensus         3 h~~i~G~tGsGKT~~~~~l~~~~~~~g~~~~i~D~~g~~   41 (304)
T PF12846_consen    3 HTLILGKTGSGKTTLLKNLLEQLIRRGPRVVIFDPKGDY   41 (304)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHHHHcCCCEEEEcCCchH
Confidence            479999999999999999999888888877777433343

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=94.06  E-value=0.058  Score=50.67  Aligned_cols=34  Identities=26%  Similarity=0.396  Sum_probs=27.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP  225 (404)
                      -++|.|++|||||++..|.+..+.++ |==|+||.
T Consensus        21 ~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs   55 (226)
T PF06745_consen   21 VVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVS   55 (226)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEE
T ss_pred             EEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEE
Confidence            38999999999999999999887777 77777773

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 ....

>PRK11823 DNA repair protein RadA; Provisional

Probab=94.04  E-value=0.067  Score=56.38  Aligned_cols=34  Identities=29%  Similarity=0.353  Sum_probs=29.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|+|||+++.|+.+.+.++|-=|+||.
T Consensus        82 ~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs  115 (446)
T PRK11823         82 VVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVS  115 (446)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            3799999999999999999887767787888875

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=94.03  E-value=0.078  Score=52.22  Aligned_cols=28  Identities=21%  Similarity=0.501  Sum_probs=23.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGW  219 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngW  219 (404)
                      .++|+|++|||||+++..+.......+|
T Consensus        38 ~lll~Gp~GtGKT~la~~~~~~l~~~~~   65 (337)
T PRK12402         38 HLLVQGPPGSGKTAAVRALARELYGDPW   65 (337)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhcCccc
Confidence            4899999999999999888777665554

>cd01131 PilT Pilus retraction ATPase PilT

Probab=94.01  E-value=0.094  Score=48.88  Aligned_cols=39  Identities=26%  Similarity=0.481  Sum_probs=27.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEecCccccc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVPRGREWT  231 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP~a~~wv  231 (404)
                      ++|.|+.||||||+|..++.+-..+ +.-|+.+-++.++.
T Consensus         4 ilI~GptGSGKTTll~~ll~~~~~~~~~~i~t~e~~~E~~   43 (198)
T cd01131           4 VLVTGPTGSGKSTTLAAMIDYINKNKTHHILTIEDPIEFV   43 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhhhcCCcEEEEEcCCcccc
Confidence            7999999999999998877776543 33444454444443

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.

>PRK13764 ATPase; Provisional

Probab=94.01  E-value=0.079  Score=58.00  Aligned_cols=42  Identities=21%  Similarity=0.272  Sum_probs=36.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTH  232 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvn  232 (404)
                      ..++++|++||||||+|..++.+.-.++-+|+.|=++.++..
T Consensus       258 ~~ILIsG~TGSGKTTll~AL~~~i~~~~riV~TiEDp~El~~  299 (602)
T PRK13764        258 EGILIAGAPGAGKSTFAQALAEFYADMGKIVKTMESPRDLQV  299 (602)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhhCCCEEEEECCCccccC
Confidence            359999999999999999988888888999989988888754

>PRK14974 cell division protein FtsY; Provisional

Probab=93.98  E-value=0.073  Score=54.30  Aligned_cols=33  Identities=30%  Similarity=0.441  Sum_probs=29.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .+++.|++|+||||+++.+.++...+|+-|+.+
T Consensus       142 vi~~~G~~GvGKTTtiakLA~~l~~~g~~V~li  174 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIA  174 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            589999999999999999999999888866554

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=93.97  E-value=0.099  Score=50.51  Aligned_cols=40  Identities=23%  Similarity=0.291  Sum_probs=31.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREW  230 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~w  230 (404)
                      ..+++.|+.|||||++|..++.+.-..++-|+.|=+..++
T Consensus       128 ~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~  167 (270)
T PF00437_consen  128 GNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPEL  167 (270)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S
T ss_pred             eEEEEECCCccccchHHHHHhhhccccccceEEeccccce
Confidence            4599999999999999999988776665777777665554

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=93.93  E-value=0.081  Score=47.13  Aligned_cols=32  Identities=28%  Similarity=0.184  Sum_probs=27.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|.|.+|||||++...+..+-...||-++++
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i   33 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVL   33 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            68999999999999999999887888766665

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>TIGR00750 lao LAO/AO transport system ATPase

Probab=93.87  E-value=0.092  Score=52.18  Aligned_cols=34  Identities=26%  Similarity=0.280  Sum_probs=29.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..+.|.|++|||||+++..+..+....|+-|..|
T Consensus        35 ~~i~i~G~~G~GKttl~~~l~~~~~~~~~~v~~i   68 (300)
T TIGR00750        35 HRVGITGTPGAGKSTLLEALGMELRRRGLKVAVI   68 (300)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            4589999999999999999999988888766554

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=93.85  E-value=0.094  Score=51.74  Aligned_cols=34  Identities=29%  Similarity=0.351  Sum_probs=29.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .-+++.|+.|+|||++++.+..+..++|+=|+-|
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li  106 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLA  106 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEE
Confidence            3488899999999999999999888888877666

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.

>PHA03133 thymidine kinase; Provisional

Probab=93.82  E-value=0.061  Score=55.39  Aligned_cols=38  Identities=32%  Similarity=0.460  Sum_probs=30.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH-hCCeEEEEecCcccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR-EEGWLVLYVPRGREW  230 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL~IP~a~~w  230 (404)
                      -|++|+|+-|+||||++.++..-.- ..+  |+|||++-.+
T Consensus        41 ~rvYlDG~~GvGKTTt~~~l~~a~~~~~~--vl~~pEPM~Y   79 (368)
T PHA03133         41 LRIYVDGPHGLGKTTTAAALAAALGRRDD--IEYVPEPMAY   79 (368)
T ss_pred             EEEEEeCCCcCCHHHHHHHHHHhhCCCCC--eEEecCcHHH
Confidence            4799999999999999988777543 234  9999998654

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=93.77  E-value=0.081  Score=51.91  Aligned_cols=33  Identities=33%  Similarity=0.432  Sum_probs=29.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC---CeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE---GWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n---gWIVL~I  224 (404)
                      -+-|+|+.|||||+.|.++..+-..+   +++++++
T Consensus        22 ~IgL~G~WGsGKSs~l~~l~~~L~~~~~~~~~~i~f   57 (325)
T PF07693_consen   22 VIGLYGEWGSGKSSFLNMLKEELKEDNKEKYIFIYF   57 (325)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhcccccceeeEEE
Confidence            38999999999999999999988777   7888887

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>cd03114 ArgK-like The function of this protein family is unkown

Probab=93.75  E-value=0.11  Score=46.60  Aligned_cols=32  Identities=28%  Similarity=0.286  Sum_probs=26.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.+.|+.|||||+++.++..+..++|+=|+.+
T Consensus         2 i~~~G~~GsGKTt~~~~l~~~~~~~g~~v~ii   33 (148)
T cd03114           2 IGITGVPGAGKSTLIDALITALRARGKRVAVL   33 (148)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            67889999999999999999888877655443

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>CHL00181 cbbX CbbX; Provisional

Probab=93.72  E-value=0.082  Score=52.49  Aligned_cols=29  Identities=14%  Similarity=0.280  Sum_probs=25.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWL  220 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWI  220 (404)
                      .++|+|++|||||++...+...+...|.+
T Consensus        61 ~ill~G~pGtGKT~lAr~la~~~~~~g~~   89 (287)
T CHL00181         61 HMSFTGSPGTGKTTVALKMADILYKLGYI   89 (287)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCC
Confidence            48999999999999999998888776654

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=93.71  E-value=0.088  Score=48.99  Aligned_cols=31  Identities=26%  Similarity=0.400  Sum_probs=27.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLV  221 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIV  221 (404)
                      .++.++|++|+|||+++.-+....+++|+=|
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L~~~g~kv   36 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKLREKGYKV   36 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHHHhcCcee
Confidence            5799999999999999999999999886555

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=93.69  E-value=0.14  Score=39.93  Aligned_cols=33  Identities=30%  Similarity=0.278  Sum_probs=28.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +++.|..|+|||++..++..+..+.|-=|+.+.
T Consensus         2 ~~~~g~~G~Gktt~~~~l~~~l~~~g~~v~~~~   34 (99)
T cd01983           2 IVVTGKGGVGKTTLAANLAAALAKRGKRVLLID   34 (99)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEC
Confidence            578899999999999999998888887777766

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PRK06851 hypothetical protein; Provisional

Probab=93.69  E-value=0.1  Score=53.89  Aligned_cols=34  Identities=24%  Similarity=0.304  Sum_probs=29.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +-|+|+|.+|+|||+++.++.....+.||-|-++
T Consensus        31 ~~~il~G~pGtGKStl~~~i~~~~~~~g~~Ve~~   64 (367)
T PRK06851         31 RIFILKGGPGTGKSTLMKKIGEEFLEKGYDVEFL   64 (367)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            4599999999999999999999888889886655

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=93.68  E-value=0.084  Score=55.51  Aligned_cols=35  Identities=17%  Similarity=0.343  Sum_probs=28.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP~  226 (404)
                      .++|+|++|||||.++..+.+.+.++  +.-|+|++.
T Consensus       132 ~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088        132 PLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             eEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence            48999999999999887777766654  567888864

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=93.65  E-value=0.11  Score=50.55  Aligned_cols=28  Identities=25%  Similarity=0.473  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGW  219 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngW  219 (404)
                      .++|+|++|||||+++..+.......+|
T Consensus        40 ~~ll~G~~G~GKt~~~~~l~~~l~~~~~   67 (319)
T PRK00440         40 HLLFAGPPGTGKTTAALALARELYGEDW   67 (319)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCcc
Confidence            4899999999999999888777665555

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=93.65  E-value=0.28  Score=47.93  Aligned_cols=23  Identities=17%  Similarity=0.060  Sum_probs=20.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      +=|+|++|||||-++.|+...+.
T Consensus        41 tEi~G~~gsGKTql~l~l~~~~~   63 (256)
T PF08423_consen   41 TEIVGESGSGKTQLCLQLAVNVQ   63 (256)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEEecccccchHHHHHHHHhh
Confidence            56899999999999999987764

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 ....

>TIGR00416 sms DNA repair protein RadA

Probab=93.64  E-value=0.08  Score=56.00  Aligned_cols=33  Identities=30%  Similarity=0.347  Sum_probs=28.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++|.|++|+|||+++.|+...+..+|-=|+||.
T Consensus        97 ilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs  129 (454)
T TIGR00416        97 ILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVS  129 (454)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            899999999999999999887777766677774

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)).

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=93.62  E-value=0.28  Score=55.29  Aligned_cols=35  Identities=23%  Similarity=0.298  Sum_probs=28.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -+.|+|+.|||||++++|++.-|...|=-|+||--
T Consensus        62 iteI~G~~GsGKTtLal~~~~~a~~~G~~v~yId~   96 (790)
T PRK09519         62 VIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDA   96 (790)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECC
Confidence            37899999999999999998888777666666643

>PRK01184 hypothetical protein; Provisional

Probab=93.58  E-value=0.08  Score=48.04  Aligned_cols=31  Identities=29%  Similarity=0.173  Sum_probs=24.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      .++|+|++||||||+ +.   +|.+.|+-++...+
T Consensus         3 ~i~l~G~~GsGKsT~-a~---~~~~~g~~~i~~~d   33 (184)
T PRK01184          3 IIGVVGMPGSGKGEF-SK---IAREMGIPVVVMGD   33 (184)
T ss_pred             EEEEECCCCCCHHHH-HH---HHHHcCCcEEEhhH
Confidence            489999999999995 44   47778988877743

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=93.55  E-value=0.093  Score=55.71  Aligned_cols=34  Identities=15%  Similarity=0.174  Sum_probs=30.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|+|||+++.|.++.+.++|==|+||.
T Consensus       265 ~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s  298 (484)
T TIGR02655       265 IILATGATGTGKTLLVSKFLENACANKERAILFA  298 (484)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            3899999999999999999999988887778773

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.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=93.54  E-value=0.054  Score=42.30  Aligned_cols=16  Identities=38%  Similarity=0.565  Sum_probs=14.9

Q ss_pred             EEEECCCCCcHHHHHH
Q 045329          193 IVLDGPLCCGKSITLA  208 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~  208 (404)
                      .+|+|+.|+|||++|-
T Consensus        26 tli~G~nGsGKSTllD   41 (62)
T PF13555_consen   26 TLITGPNGSGKSTLLD   41 (62)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            8999999999999984

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=93.51  E-value=0.1  Score=53.35  Aligned_cols=97  Identities=14%  Similarity=0.118  Sum_probs=52.9

Q ss_pred             cccCCCccccCccccceeEEeCHHHHHhhccC---CCCcchhhhccccCceeEEEchhHHHHHHHHHHhcCCCccCCCCC
Q 045329          111 FTKTTSLSLLTRKDACTYFKFSEDELNAMLPE---GLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP  187 (404)
Q Consensus       111 ~~~~~~~~~ht~~~vGk~y~~p~e~~k~l~~~---GLp~~~~kqfe~f~~p~~LVRk~tleLi~~L~~~~d~~~~std~~  187 (404)
                      |.+..+....+..++.++..++++...++...   -++..+..-.+.+.+.....|=+|=  +..|.+.+...      -
T Consensus        52 ~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~~~~~~~~ta~~~~~~~~~~~~isTG--~~~LD~lLgGG------i  123 (344)
T PLN03187         52 IYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEKLLNQGFITGSDALLKRKSVVRITTG--SQALDELLGGG------I  123 (344)
T ss_pred             CCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHhhcccCCcHHHHHhhhccCceecCC--cHhHHhhcCCC------C
Confidence            56666778888888888888888887775432   1222221111222111111111100  11233333321      1


Q ss_pred             ccceeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          188 KIRKQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       188 ~~r~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      ....=+.|+|++|||||.+..|+...+.
T Consensus       124 ~~G~ItEI~G~~GsGKTql~lqlav~~q  151 (344)
T PLN03187        124 ETRCITEAFGEFRSGKTQLAHTLCVTTQ  151 (344)
T ss_pred             CCCeEEEEecCCCCChhHHHHHHHHHHh
Confidence            1112367999999999999999877664

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=93.51  E-value=0.057  Score=50.91  Aligned_cols=23  Identities=35%  Similarity=0.642  Sum_probs=19.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -++.|+||.|||||++|-++...
T Consensus        30 e~iaitGPSG~GKStllk~va~L   52 (223)
T COG4619          30 EFIAITGPSGCGKSTLLKIVASL   52 (223)
T ss_pred             ceEEEeCCCCccHHHHHHHHHhc
Confidence            35899999999999999887654

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

Probab=93.47  E-value=0.095  Score=53.31  Aligned_cols=34  Identities=24%  Similarity=0.272  Sum_probs=29.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -+.|+|++|||||++..|++..+..+|=.++||-
T Consensus        57 iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId   90 (325)
T cd00983          57 IIEIYGPESSGKTTLALHAIAEAQKLGGTVAFID   90 (325)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEC
Confidence            3779999999999999999988877776677774

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK14738 gmk guanylate kinase; Provisional

Probab=93.41  E-value=0.084  Score=49.52  Aligned_cols=28  Identities=29%  Similarity=0.395  Sum_probs=21.6

Q ss_pred             CCccceeEEEECCCCCcHHHHHHHHHHH
Q 045329          186 GPKIRKQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       186 ~~~~r~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+...+.+||.|+.|||||+++.++...
T Consensus         9 ~~~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738          9 KPAKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCCCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            3444456899999999999998887543

>PRK09354 recA recombinase A; Provisional

Probab=93.38  E-value=0.1  Score=53.59  Aligned_cols=35  Identities=17%  Similarity=0.246  Sum_probs=30.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -+.|+|+.|||||++.+|++.-|..+|=.++||--
T Consensus        62 IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~   96 (349)
T PRK09354         62 IVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDA   96 (349)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECC
Confidence            36799999999999999999988888877788844

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=93.38  E-value=0.11  Score=51.51  Aligned_cols=29  Identities=14%  Similarity=0.278  Sum_probs=24.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWL  220 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWI  220 (404)
                      .++|+|++|||||++...+..++...|++
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~~g~~   88 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHRLGYV   88 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCc
Confidence            59999999999999988877777776654

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.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=93.37  E-value=0.13  Score=46.34  Aligned_cols=33  Identities=24%  Similarity=0.291  Sum_probs=28.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|.+|||||++..++.......|+=|++|
T Consensus         6 ~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~i   38 (175)
T PRK00889          6 TVWFTGLSGAGKTTIARALAEKLREAGYPVEVL   38 (175)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            389999999999999999998887777655555

>PRK06696 uridine kinase; Validated

Probab=93.33  E-value=0.26  Score=46.60  Aligned_cols=35  Identities=20%  Similarity=0.285  Sum_probs=27.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ..+.|+|..||||||+..++...-...|.-|++++
T Consensus        23 ~iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~   57 (223)
T PRK06696         23 LRVAIDGITASGKTTFADELAEEIKKRGRPVIRAS   57 (223)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEec
Confidence            45899999999999999888776656676666554

>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=93.32  E-value=0.056  Score=45.05  Aligned_cols=22  Identities=23%  Similarity=0.184  Sum_probs=19.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      ++|.|.+|||||+++..+...-
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            5899999999999998887764

...

>PRK07261 topology modulation protein; Provisional

Probab=93.30  E-value=0.09  Score=47.94  Aligned_cols=30  Identities=27%  Similarity=0.191  Sum_probs=23.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      |++|.|.+||||||+..++..   .-|.-++++
T Consensus         2 ri~i~G~~GsGKSTla~~l~~---~~~~~~i~~   31 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQ---HYNCPVLHL   31 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHH---HhCCCeEec
Confidence            699999999999999988643   335555554

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=93.29  E-value=0.18  Score=50.41  Aligned_cols=39  Identities=21%  Similarity=0.178  Sum_probs=31.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEecCcccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVPRGREW  230 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP~a~~w  230 (404)
                      .+++.|+.|||||++|..++.+...+  ++-|+.|=+..++
T Consensus       134 ~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       134 NILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhh
Confidence            48999999999999999988876654  6777787776664

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.

>PHA03135 thymidine kinase; Provisional

Probab=93.24  E-value=0.099  Score=53.52  Aligned_cols=39  Identities=28%  Similarity=0.397  Sum_probs=29.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREW  230 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~w  230 (404)
                      -|+.|+|.-|+|||+++.++..... +|=-|+|||++-.+
T Consensus        11 ~rIYlDG~~GvGKTT~~~~l~~~~~-~~~~vl~vpEPM~Y   49 (343)
T PHA03135         11 IRVYLDGPFGIGKTSMLNEMPDHSP-DGVPVLKVFEPMKY   49 (343)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhcC-CCCceEEecCcHHH
Confidence            5799999999999999966666443 33338999987653

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=93.20  E-value=0.081  Score=44.13  Aligned_cols=21  Identities=38%  Similarity=0.431  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|.+|+|||+++.++..
T Consensus         3 ki~~~G~~~~GKstl~~~l~~   23 (161)
T TIGR00231         3 KIVIVGDPNVGKSTLLNRLLG   23 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            699999999999999988764

This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=93.16  E-value=0.27  Score=49.98  Aligned_cols=39  Identities=15%  Similarity=0.111  Sum_probs=29.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH--hCCeEEEEecCcccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR--EEGWLVLYVPRGREW  230 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~--~ngWIVL~IP~a~~w  230 (404)
                      .+++.|+.|||||++|..++.+..  -.++-|+-|=+..++
T Consensus       146 nilI~G~tGSGKTTll~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        146 NIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhcCCCCceEEEecCCccc
Confidence            489999999999999988887653  235666777666654

>PRK07667 uridine kinase; Provisional

Probab=93.14  E-value=0.31  Score=45.15  Aligned_cols=37  Identities=19%  Similarity=0.181  Sum_probs=29.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEecCc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVPRG  227 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP~a  227 (404)
                      ..+-|+|..|||||++...+...-...  ++.+++.++-
T Consensus        18 ~iIgI~G~~gsGKStla~~L~~~l~~~~~~~~~i~~Dd~   56 (193)
T PRK07667         18 FILGIDGLSRSGKTTFVANLKENMKQEGIPFHIFHIDDY   56 (193)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEEcCcc
Confidence            458899999999999987777765554  4788888763

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=93.10  E-value=0.12  Score=43.43  Aligned_cols=23  Identities=30%  Similarity=0.188  Sum_probs=19.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      +.|+|++|+|||++...+.....
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~   23 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLL   23 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHH
Confidence            47999999999999998776554

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

>PRK09087 hypothetical protein; Validated

Probab=93.09  E-value=0.11  Score=49.83  Aligned_cols=31  Identities=26%  Similarity=0.482  Sum_probs=22.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|+.|||||.+|.   .||...+..  ||+.
T Consensus        45 ~~l~l~G~~GsGKThLl~---~~~~~~~~~--~i~~   75 (226)
T PRK09087         45 PVVVLAGPVGSGKTHLAS---IWREKSDAL--LIHP   75 (226)
T ss_pred             CeEEEECCCCCCHHHHHH---HHHHhcCCE--EecH
Confidence            348999999999999987   455444544  6655

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=93.07  E-value=0.12  Score=45.06  Aligned_cols=28  Identities=29%  Similarity=0.166  Sum_probs=22.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      ++|+|.+|||||++..++...   .||.++.
T Consensus         2 i~l~G~~GsGKST~a~~l~~~---~~~~~i~   29 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAER---LGAPFID   29 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhh---cCCEEEe
Confidence            689999999999998886543   5777664

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>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=93.07  E-value=0.13  Score=50.00  Aligned_cols=31  Identities=23%  Similarity=0.327  Sum_probs=21.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      ..++|+||+|+|| |+|+++++.-...+..++
T Consensus        51 ~h~lf~GPPG~GK-TTLA~IIA~e~~~~~~~~   81 (233)
T PF05496_consen   51 DHMLFYGPPGLGK-TTLARIIANELGVNFKIT   81 (233)
T ss_dssp             -EEEEESSTTSSH-HHHHHHHHHHCT--EEEE
T ss_pred             ceEEEECCCccch-hHHHHHHHhccCCCeEec
Confidence            4589999999999 567888887766555433

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.

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=93.07  E-value=0.16  Score=45.96  Aligned_cols=33  Identities=24%  Similarity=0.402  Sum_probs=29.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +.+.|..|||||+++..++.....+||=|-.|=
T Consensus         2 i~i~G~~gsGKTtl~~~l~~~l~~~G~~V~viK   34 (155)
T TIGR00176         2 LQIVGPKNSGKTTLIERLVKALKARGYRVATIK   34 (155)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEe
Confidence            578899999999999999999988898777663

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.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=93.02  E-value=0.097  Score=46.47  Aligned_cols=28  Identities=32%  Similarity=0.305  Sum_probs=20.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      ++|.|++|||||++...+....   |+.++.
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l---~~~~v~   28 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL---GAKFIE   28 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc---CCeEEe
Confidence            4789999999998877665443   566654

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.

>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt

Probab=93.01  E-value=0.11  Score=47.62  Aligned_cols=36  Identities=25%  Similarity=0.292  Sum_probs=27.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHH-HHHhCCeEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVH-WAREEGWLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~-~A~~ngWIVL~IP~a  227 (404)
                      -++++|--|||||++|.|++. ......|.||--.-+
T Consensus         2 v~ii~GfLGsGKTTli~~ll~~~~~~~~~~vI~ne~g   38 (178)
T PF02492_consen    2 VIIITGFLGSGKTTLINHLLKRNRQGERVAVIVNEFG   38 (178)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTTTS-EEEEECSTT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhcCCceeEEEEcccc
Confidence            379999999999999999995 445567777754444

Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.

>cd04155 Arl3 Arl3 subfamily

Probab=92.93  E-value=0.13  Score=45.31  Aligned_cols=22  Identities=27%  Similarity=0.321  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|+.|||||+++.++..
T Consensus        15 ~~v~i~G~~g~GKStLl~~l~~   36 (173)
T cd04155          15 PRILILGLDNAGKTTILKQLAS   36 (173)
T ss_pred             cEEEEEccCCCCHHHHHHHHhc
Confidence            5699999999999999998864

Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=92.93  E-value=0.13  Score=56.49  Aligned_cols=36  Identities=31%  Similarity=0.398  Sum_probs=31.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh--CCeEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE--EGWLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~--ngWIVL~IP~a  227 (404)
                      -++|+|+.|||||.+|.-+.+++.+  .|.-|+|++..
T Consensus       316 pL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitae  353 (617)
T PRK14086        316 PLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSE  353 (617)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHH
Confidence            4899999999999999998888875  48999999874

>PHA03138 thymidine kinase; Provisional

Probab=92.93  E-value=0.12  Score=52.85  Aligned_cols=38  Identities=18%  Similarity=0.249  Sum_probs=27.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      .|+.|+|.-|+|||+++.+.+++....+=-|++||++-
T Consensus        13 ~riYleG~~GvGKTT~~~~~l~~~~~~~~~vl~vpEPm   50 (340)
T PHA03138         13 LRIYLDGAFGIGKTTAAEAFLHGFAINPNRIFFIGEPL   50 (340)
T ss_pred             EEEEEECCCCcCHHhHHHHHHHhhhcCCCceEEeeCch
Confidence            67999999999999999877776554432244555543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=92.83  E-value=0.13  Score=54.20  Aligned_cols=36  Identities=17%  Similarity=0.196  Sum_probs=27.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH--hCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR--EEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~--~ngWIVL~IP~  226 (404)
                      +.++|+|+.|+|||.+|.-+.++..  ..|.-|+|++.
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~  179 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSG  179 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence            4589999999999987754444443  34788889876

>PRK12608 transcription termination factor Rho; Provisional

Probab=92.82  E-value=0.17  Score=52.57  Aligned_cols=37  Identities=16%  Similarity=0.263  Sum_probs=27.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCC----eEEEEecCc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEG----WLVLYVPRG  227 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ng----WIVL~IP~a  227 (404)
                      .|.+|.|++|||||++|.++......+.    .++++|.+.
T Consensus       134 QR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER  174 (380)
T PRK12608        134 QRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDER  174 (380)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEecCC
Confidence            3689999999999999999777554442    466667554

>KOG2859 consensus DNA repair protein, member of the recA/RAD51 family [Replication, recombination and repair]

Probab=92.81  E-value=0.33  Score=47.39  Aligned_cols=114  Identities=18%  Similarity=0.299  Sum_probs=69.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHh------CCeEEEEecCcccccccCeeecCCCCCCccCHHHHHHHHHHHHHHhHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWARE------EGWLVLYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKDFIKYNESHL  266 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~------ngWIVL~IP~a~~wvng~~~y~~~~~g~ydQP~~A~~~Lk~fl~~N~~~L  266 (404)
                      +=++|+-|||||..|-|+++.|..      -+|.|+.|.--.               .||--..++.+=.+++++|   +
T Consensus        41 vEi~Gp~~sgKt~vL~ql~a~CilPk~~GGl~~~VLfidld~---------------~fd~lrL~~~l~hrL~q~~---~  102 (293)
T KOG2859|consen   41 VEISGPGNSGKTLVLQQLVAHCILPKKFGGLQWSVLFIDLDH---------------KFDRLRLAKSLRHRLKQYS---V  102 (293)
T ss_pred             EEEeCCCCccHHHHHHHHHHHeecccccCCceeEEEEEeccc---------------cccHHHHHHHHHHHHHHhh---h
Confidence            679999999999999999999973      367887774332               3454455555555555555   1


Q ss_pred             hcCCcccccCCCCCCCCccccccCCCccccCCCCCHHHHHHhhcccccc-----hHHHHHHHHHHHhc-CCCC-cEEEEE
Q 045329          267 RELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHA-----SVGVVVRLRKELSL-VKDI-PVLIAI  339 (404)
Q Consensus       267 kkLkls~~~~~~lge~~~~~w~K~~d~~~~p~g~tL~DLv~~Gi~~~~~-----A~~v~~aLl~EL~~-q~~~-PVLvAV  339 (404)
                      .+...                      .+.|....+.||+...+.+-.+     +.+++.-|+.-=.. +..+ =.|+++
T Consensus       103 ~e~~~----------------------~~c~te~~~eEi~~~Cm~Rf~~v~C~~s~~ll~sL~~l~y~i~~~p~~cll~~  160 (293)
T KOG2859|consen  103 GEVIA----------------------AKCPTEEQLEEIAGECMSRFRFVNCFASDDLLTSLIDLRYAIINDPGICLLAM  160 (293)
T ss_pred             hhhhh----------------------hcCCcHhHHHHHHHHHHhhEEEEEeeccHHHHHHHHHHHHHHhcCCceeEEee
Confidence            11100                      1223345788898887776432     22222222211111 3333 369999


Q ss_pred             eCccccc
Q 045329          340 DQYNNWF  346 (404)
Q Consensus       340 D~~Nalf  346 (404)
                      |.+.+|+
T Consensus       161 DslsaFy  167 (293)
T KOG2859|consen  161 DSLSAFY  167 (293)
T ss_pred             cchhhhe
Confidence            9999998

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=92.80  E-value=0.18  Score=45.84  Aligned_cols=35  Identities=29%  Similarity=0.444  Sum_probs=28.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -++|.|..||||||....+..+-...|+-|+.++.
T Consensus         5 ~IvieG~~GsGKsT~~~~L~~~l~~~g~~v~~~~~   39 (195)
T TIGR00041         5 FIVIEGIDGAGKTTQANLLKKLLQENGYDVLFTRE   39 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            38999999999999999988877777866665543

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.

>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=92.73  E-value=0.14  Score=46.35  Aligned_cols=32  Identities=25%  Similarity=0.291  Sum_probs=24.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      |++|.|++|||||++..++..   .-|+.++.+.+
T Consensus         1 ~I~i~G~pGsGKst~a~~La~---~~~~~~i~~~~   32 (194)
T cd01428           1 RILLLGPPGSGKGTQAERLAK---KYGLPHISTGD   32 (194)
T ss_pred             CEEEECCCCCCHHHHHHHHHH---HcCCeEEECcH
Confidence            489999999999988766644   34777776543

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=92.70  E-value=0.14  Score=45.92  Aligned_cols=31  Identities=26%  Similarity=0.246  Sum_probs=23.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.++|.|++|||||+++..+....   |+.++..
T Consensus         4 ~ii~i~G~~GsGKsTl~~~l~~~~---g~~~~~~   34 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQCEKIVEKY---GFTHLST   34 (188)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh---CCcEEeH
Confidence            358999999999999998876542   6655544

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=92.70  E-value=0.12  Score=50.09  Aligned_cols=28  Identities=18%  Similarity=0.270  Sum_probs=21.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      ..++|+|++|||||++...+.......|
T Consensus        43 ~~vll~GppGtGKTtlA~~ia~~l~~~~   70 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVARILGKLFKEMN   70 (261)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHhcC
Confidence            4589999999999998877766544444

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.

>PRK14532 adenylate kinase; Provisional

Probab=92.69  E-value=0.15  Score=46.43  Aligned_cols=31  Identities=29%  Similarity=0.433  Sum_probs=24.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +++|.|++|||||++...+   |..-||..+...
T Consensus         2 ~i~~~G~pGsGKsT~a~~l---a~~~g~~~is~~   32 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRL---VEERGMVQLSTG   32 (188)
T ss_pred             EEEEECCCCCCHHHHHHHH---HHHcCCeEEeCc
Confidence            4899999999999986666   456688777653

>TIGR00235 udk uridine kinase

Probab=92.61  E-value=0.14  Score=47.80  Aligned_cols=33  Identities=12%  Similarity=0.078  Sum_probs=24.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .+.|.|+.||||||++.++.......++.+++.
T Consensus         8 vi~I~G~sGsGKSTl~~~l~~~l~~~~~~~i~~   40 (207)
T TIGR00235         8 IIGIGGGSGSGKTTVARKIYEQLGKLEIVIISQ   40 (207)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcccCCeEecc
Confidence            478999999999999888876543344555543

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>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=92.61  E-value=0.11  Score=51.36  Aligned_cols=35  Identities=20%  Similarity=0.344  Sum_probs=27.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -++|.|+.|||||+++.+.+.-=....|++..++-
T Consensus        35 pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~   69 (272)
T PF12775_consen   35 PVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINF   69 (272)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES
T ss_pred             cEEEECCCCCchhHHHHhhhccCCccccceeEeec
Confidence            48999999999999999987533345677766643

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=92.55  E-value=0.13  Score=52.07  Aligned_cols=33  Identities=33%  Similarity=0.416  Sum_probs=26.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH--HhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA--REEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A--~~ngWIVL~I  224 (404)
                      -+++.|.+|||||+++.+++...  ...+.-++++
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l   37 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKELQNSEEGKKVLYL   37 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHhhccccCCceEEE
Confidence            38999999999999999999987  4555555544

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PHA03134 thymidine kinase; Provisional

Probab=92.54  E-value=0.14  Score=52.47  Aligned_cols=39  Identities=33%  Similarity=0.405  Sum_probs=30.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREW  230 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~w  230 (404)
                      -|++|+|.-|+||||++.++++.+. .|==|+|||++-.+
T Consensus        14 ~rvYlDG~~GvGKTT~~~~l~~~~~-~~~~vl~~pEPM~Y   52 (340)
T PHA03134         14 VRIYLDGAYGIGKSTTGRVMASAAS-GGGPTLYFPEPMAY   52 (340)
T ss_pred             EEEEEeCCCcCCHHHHHHHHHHhcc-CCCceEEecCcHHH
Confidence            4799999999999999976666544 33348999988654

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=92.54  E-value=0.41  Score=48.32  Aligned_cols=97  Identities=15%  Similarity=0.216  Sum_probs=50.2

Q ss_pred             cccCCCccccCccccceeEEeCHHHHHhhccCC---CCcchhhhccccCceeEEEchhHHHHHHHHHHhcCCCccCCCCC
Q 045329          111 FTKTTSLSLLTRKDACTYFKFSEDELNAMLPEG---LPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP  187 (404)
Q Consensus       111 ~~~~~~~~~ht~~~vGk~y~~p~e~~k~l~~~G---Lp~~~~kqfe~f~~p~~LVRk~tleLi~~L~~~~d~~~~std~~  187 (404)
                      |.+..|....+..++.+...++++...++...-   .+..+..-.++..+.....|=+|-  +..|.+.+...     -+
T Consensus        22 ~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~~~~~~~~ta~~~~~~~~~~~~isTG--~~~LD~lLgGG-----i~   94 (313)
T TIGR02238        22 ICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKIINPGFITAFEISQKRKKVLKITTG--SQALDGILGGG-----IE   94 (313)
T ss_pred             CCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHhhhcccCccHHHHHHhhccCceeCCC--CHHHHHHhCCC-----Cc
Confidence            445556677777888888888888887775431   111111111111111111111110  12233333321     11


Q ss_pred             ccceeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          188 KIRKQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       188 ~~r~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      . ..=+.|+|++|||||.++.|+...+.
T Consensus        95 ~-G~iteI~G~~GsGKTql~lqla~~~~  121 (313)
T TIGR02238        95 S-MSITEVFGEFRCGKTQLSHTLCVTAQ  121 (313)
T ss_pred             C-CeEEEEECCCCCCcCHHHHHHHHHHh
Confidence            1 12367999999999999999876554

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.

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=92.51  E-value=0.42  Score=41.96  Aligned_cols=26  Identities=23%  Similarity=0.403  Sum_probs=22.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHh
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWARE  216 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~  216 (404)
                      ++++|.++.|||||.+++.++.....
T Consensus        26 ~~~ll~~~tGsGKT~~~~~~~~~l~~   51 (184)
T PF04851_consen   26 RRVLLNAPTGSGKTIIALALILELAR   51 (184)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCcChhhhhhhhcccc
Confidence            46999999999999999987776655

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=92.50  E-value=0.11  Score=50.42  Aligned_cols=34  Identities=29%  Similarity=0.393  Sum_probs=31.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      ++|+|.+|||||+.-.+++.--++++|-|+++-.
T Consensus         4 iIlTGyPgsGKTtfakeLak~L~~~i~~vi~l~k   37 (261)
T COG4088           4 IILTGYPGSGKTTFAKELAKELRQEIWRVIHLEK   37 (261)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHhhhhccccch
Confidence            7999999999999999999999999999999865

>PRK06620 hypothetical protein; Validated

Probab=92.49  E-value=0.13  Score=48.82  Aligned_cols=18  Identities=22%  Similarity=0.455  Sum_probs=16.0

Q ss_pred             eeEEEECCCCCcHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLA  208 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~  208 (404)
                      +.++|+|++|||||.+|.
T Consensus        45 ~~l~l~Gp~G~GKThLl~   62 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTK   62 (214)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            348999999999999886

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=92.48  E-value=0.17  Score=53.48  Aligned_cols=34  Identities=32%  Similarity=0.380  Sum_probs=30.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .++++|..|||||++++.+..+..++||=|+.|.
T Consensus        97 vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~  130 (437)
T PRK00771         97 TIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVA  130 (437)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEec
Confidence            4899999999999999999999999999888774

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=92.46  E-value=0.16  Score=45.77  Aligned_cols=31  Identities=23%  Similarity=0.235  Sum_probs=23.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      ++|.|++|||||++-.++.   ..-|+.+|...+
T Consensus         2 i~i~G~pGsGKst~a~~la---~~~~~~~is~~d   32 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIV---ENFGFTHLSAGD   32 (183)
T ss_pred             EEEECCCCCCHHHHHHHHH---HHcCCeEEECCh
Confidence            7899999999999877653   345877776643

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.

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=92.40  E-value=0.19  Score=50.84  Aligned_cols=34  Identities=29%  Similarity=0.316  Sum_probs=29.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..+.|.|++|+||||++..+..+....|+=|+-+
T Consensus       115 ~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li  148 (318)
T PRK10416        115 FVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLA  148 (318)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEE
Confidence            3488999999999999999999988888766555

>cd01673 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs)

Probab=92.39  E-value=0.12  Score=47.25  Aligned_cols=31  Identities=32%  Similarity=0.431  Sum_probs=26.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +++.|..|||||+++..+..+   .|+.++..|.
T Consensus         2 I~ieG~~GsGKSTl~~~L~~~---~~~~~~~Ep~   32 (193)
T cd01673           2 IVVEGNIGAGKSTLAKELAEH---LGYEVVPEPV   32 (193)
T ss_pred             EEEECCCCCCHHHHHHHHHHH---hCCccccccc
Confidence            789999999999999888776   4787776664

This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.

>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=92.38  E-value=0.26  Score=45.19  Aligned_cols=52  Identities=10%  Similarity=0.229  Sum_probs=34.2

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHH-h-CCeEEEEecC
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAR-E-EGWLVLYVPR  226 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~-~-ngWIVL~IP~  226 (404)
                      ...++++.+++++..       +   ..++|+|++||||+.+...++.+.. . ..+|.++-..
T Consensus         7 ~m~~~~~~~~~~a~~-------~---~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~   60 (168)
T PF00158_consen    7 AMKRLREQAKRAASS-------D---LPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAA   60 (168)
T ss_dssp             HHHHHHHHHHHHTTS-------T---S-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTT
T ss_pred             HHHHHHHHHHHHhCC-------C---CCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhh
Confidence            456777777776421       1   2389999999999987655555443 2 3577777654

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 ....

>smart00763 AAA_PrkA PrkA AAA domain

Probab=92.35  E-value=0.21  Score=51.59  Aligned_cols=58  Identities=14%  Similarity=0.111  Sum_probs=34.9

Q ss_pred             hccccCceeEEEchhHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHH
Q 045329          151 EFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       151 qfe~f~~p~~LVRk~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .+..|..-..=..+.-.+|+++++.....      ....++-++|.|++|||||++...+....
T Consensus        45 ~y~~F~~~~~G~~~~i~~lv~~l~~~a~g------~~~~r~il~L~GPPGsGKStla~~La~~l  102 (361)
T smart00763       45 RYRFFDHDFFGMEEAIERFVNYFKSAAQG------LEERKQILYLLGPVGGGKSSLVECLKRGL  102 (361)
T ss_pred             eccccchhccCcHHHHHHHHHHHHHHHhc------CCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            34444322333444567788888765321      11222447999999999999877665543

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

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=92.35  E-value=0.12  Score=46.63  Aligned_cols=22  Identities=27%  Similarity=0.261  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .++|.|+.|||||+++.++...
T Consensus         3 ~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         3 LIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4899999999999999887554

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.

>cd00154 Rab Rab family

Probab=92.34  E-value=0.12  Score=43.51  Aligned_cols=20  Identities=40%  Similarity=0.428  Sum_probs=18.2

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      |+++.|.+|+|||+++.++.
T Consensus         2 ~i~~~G~~~~GKStl~~~l~   21 (159)
T cd00154           2 KIVLIGDSGVGKTSLLLRFV   21 (159)
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            48999999999999999875

Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di

>PRK08118 topology modulation protein; Reviewed

Probab=92.30  E-value=0.11  Score=47.23  Aligned_cols=22  Identities=36%  Similarity=0.321  Sum_probs=17.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +|++|.|++||||||+..++..
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~   23 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGE   23 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            3699999999999987665543

>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=92.30  E-value=0.15  Score=39.57  Aligned_cols=22  Identities=27%  Similarity=0.258  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      +.|.|.+|||||++...+...-
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6889999999999998877764

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=92.22  E-value=0.34  Score=47.17  Aligned_cols=32  Identities=19%  Similarity=0.288  Sum_probs=23.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|++|||||++..++. .+....++.++.
T Consensus        23 ~vLL~G~~GtGKT~lA~~la-~~lg~~~~~i~~   54 (262)
T TIGR02640        23 PVHLRGPAGTGKTTLAMHVA-RKRDRPVMLING   54 (262)
T ss_pred             eEEEEcCCCCCHHHHHHHHH-HHhCCCEEEEeC
Confidence            48999999999999876554 455556666654

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).

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=92.22  E-value=0.19  Score=43.71  Aligned_cols=27  Identities=22%  Similarity=0.382  Sum_probs=23.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      .+++.|+.|||||+++..++.++..++
T Consensus        26 ~~~i~~~~GsGKT~~~~~~~~~~~~~~   52 (201)
T smart00487       26 DVILAAPTGSGKTLAALLPALEALKRG   52 (201)
T ss_pred             cEEEECCCCCchhHHHHHHHHHHhccc
Confidence            489999999999999998888877653

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=92.17  E-value=0.17  Score=52.32  Aligned_cols=31  Identities=23%  Similarity=0.381  Sum_probs=20.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      +.++|+|++|||||++.. +++......|+.+
T Consensus       166 ~gvLL~GppGtGKT~lAk-aia~~~~~~~i~v  196 (389)
T PRK03992        166 KGVLLYGPPGTGKTLLAK-AVAHETNATFIRV  196 (389)
T ss_pred             CceEEECCCCCChHHHHH-HHHHHhCCCEEEe
Confidence            459999999999998754 4444433344443

>PRK14531 adenylate kinase; Provisional

Probab=92.16  E-value=0.15  Score=46.74  Aligned_cols=30  Identities=27%  Similarity=0.362  Sum_probs=22.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      .|+++.|++|||||++-..+..   .-|+..|.
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~---~~g~~~is   32 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCA---AHGLRHLS   32 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH---HhCCCeEe
Confidence            4699999999999998666543   34655444

>TIGR00665 DnaB replicative DNA helicase

Probab=92.10  E-value=0.18  Score=52.32  Aligned_cols=33  Identities=24%  Similarity=0.245  Sum_probs=28.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHH-HHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHW-AREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~-A~~ngWIVL~IP  225 (404)
                      ++|.|.+|+|||+++.|++.. |..+|+-|+|+.
T Consensus       198 ~vi~g~pg~GKT~~~l~~a~~~a~~~g~~vl~~S  231 (434)
T TIGR00665       198 IILAARPSMGKTAFALNIAENAAIKEGKPVAFFS  231 (434)
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHhCCCeEEEEe
Confidence            899999999999999999876 456799888883

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []

Probab=92.09  E-value=0.15  Score=47.36  Aligned_cols=35  Identities=23%  Similarity=0.199  Sum_probs=24.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      ++|-|++|||||+++.++..--...|.++|.-..-
T Consensus        18 ~i~aG~~GsGKSt~~~~~~~~~~~~~~v~i~~D~~   52 (199)
T PF06414_consen   18 IIIAGQPGSGKSTLARQLLEEFGGGGIVVIDADEF   52 (199)
T ss_dssp             EEEES-TTSTTHHHHHHHHHHT-TT-SEEE-GGGG
T ss_pred             EEEeCCCCCCHHHHHHHhhhhccCCCeEEEehHHH
Confidence            78889999999999999877433678888874443

It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.

>PRK00279 adk adenylate kinase; Reviewed

Probab=92.04  E-value=0.19  Score=47.15  Aligned_cols=32  Identities=22%  Similarity=0.324  Sum_probs=25.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      |++|.|++|||||++-..+   |..-||..+.+.+
T Consensus         2 ~I~v~G~pGsGKsT~a~~l---a~~~~~~~is~~d   33 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFI---AEKYGIPHISTGD   33 (215)
T ss_pred             EEEEECCCCCCHHHHHHHH---HHHhCCcEEECCc
Confidence            5999999999999875544   5556888887644

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=92.04  E-value=0.18  Score=50.42  Aligned_cols=34  Identities=15%  Similarity=0.083  Sum_probs=26.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCe------EEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGW------LVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngW------IVL~IP  225 (404)
                      -+.|+|++|||||++..|+...|...+.      -|+||-
T Consensus       104 vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~  143 (317)
T PRK04301        104 ITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYID  143 (317)
T ss_pred             EEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEe
Confidence            3789999999999999999887754322      566664

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.02  E-value=0.21  Score=52.15  Aligned_cols=34  Identities=26%  Similarity=0.241  Sum_probs=29.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .-++|.|+.|||||++++.+.+++..+|.=|..|
T Consensus       207 ~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lI  240 (407)
T PRK12726        207 RIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFI  240 (407)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            3478999999999999999999988888666555

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=92.01  E-value=0.16  Score=50.87  Aligned_cols=28  Identities=29%  Similarity=0.419  Sum_probs=20.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .++|+|++|||||+++..+   |.+-||-+.
T Consensus        53 ~~ll~GppG~GKT~la~~i---a~~l~~~~~   80 (328)
T PRK00080         53 HVLLYGPPGLGKTTLANII---ANEMGVNIR   80 (328)
T ss_pred             cEEEECCCCccHHHHHHHH---HHHhCCCeE
Confidence            5899999999999998754   444455433

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=91.90  E-value=0.46  Score=48.11  Aligned_cols=40  Identities=15%  Similarity=0.174  Sum_probs=27.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH--hCCeEEEEecCcccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR--EEGWLVLYVPRGREW  230 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~--~ngWIVL~IP~a~~w  230 (404)
                      ..+++.|+.|||||++|..++.+-.  ..+.-|+.|-+..++
T Consensus       149 ~~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        149 RNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEEEcCCCcc
Confidence            3489999999999999887776532  234445555555444

>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=91.87  E-value=0.14  Score=42.68  Aligned_cols=20  Identities=25%  Similarity=0.355  Sum_probs=18.7

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      |++|.|.+|+|||+++..+.
T Consensus         1 ~V~iiG~~~~GKSTlin~l~   20 (116)
T PF01926_consen    1 RVAIIGRPNVGKSTLINALT   20 (116)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHh
Confidence            58999999999999999998

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 ....

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=91.85  E-value=0.14  Score=50.11  Aligned_cols=32  Identities=16%  Similarity=0.168  Sum_probs=22.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|++|||||+++..+.+.. ..++.+++.
T Consensus        32 ~~ll~Gp~G~GKT~la~~ia~~~-~~~~~~~~~   63 (305)
T TIGR00635        32 HLLLYGPPGLGKTTLAHIIANEM-GVNLKITSG   63 (305)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh-CCCEEEecc
Confidence            48999999999998887665433 234555543

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.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=91.83  E-value=0.31  Score=44.76  Aligned_cols=24  Identities=25%  Similarity=0.430  Sum_probs=20.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      .++|.|+.|||||++|..++.+-.
T Consensus        27 ~i~I~G~tGSGKTTll~aL~~~i~   50 (186)
T cd01130          27 NILISGGTGSGKTTLLNALLAFIP   50 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhcC
Confidence            489999999999999987766543

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.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=91.81  E-value=0.26  Score=44.47  Aligned_cols=32  Identities=22%  Similarity=0.213  Sum_probs=23.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|.|..|||||++...+...-..++.-++++
T Consensus        10 I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~   41 (176)
T PRK05541         10 IWITGLAGSGKTTIAKALYERLKLKYSNVIYL   41 (176)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            89999999999999988777665543333333

>cd01861 Rab6 Rab6 subfamily

Probab=91.70  E-value=0.16  Score=43.92  Aligned_cols=21  Identities=19%  Similarity=0.352  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|++|||||+++.+++.
T Consensus         2 ki~liG~~~~GKSsli~~l~~   22 (161)
T cd01861           2 KLVFLGDQSVGKTSIITRFMY   22 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999998864

Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate

>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=91.68  E-value=0.26  Score=48.79  Aligned_cols=36  Identities=28%  Similarity=0.439  Sum_probs=28.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      +||+|-+|||||+.-.++..+..+.+|=|.+|.+..
T Consensus         4 iil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~~~~   39 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKKYLEEKGKEVVIISDDS   39 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THH
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEcccc
Confidence            799999999999999999999999999999998543

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=91.67  E-value=0.13  Score=52.67  Aligned_cols=31  Identities=35%  Similarity=0.585  Sum_probs=23.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      -++|-||.||||||+|.-+.-.=. ..|-|.|
T Consensus        31 f~vllGPSGcGKSTlLr~IAGLe~~~~G~I~i   62 (338)
T COG3839          31 FVVLLGPSGCGKSTLLRMIAGLEEPTSGEILI   62 (338)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            489999999999999987765432 5566655

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase

Probab=91.61  E-value=0.048  Score=50.90  Aligned_cols=37  Identities=22%  Similarity=0.235  Sum_probs=25.4

Q ss_pred             EEECCCCCcHHHHHHHHHHHHHhCCe--EEEEecCcccc
Q 045329          194 VLDGPLCCGKSITLAMLVHWAREEGW--LVLYVPRGREW  230 (404)
Q Consensus       194 vL~G~rGsGKS~~L~qav~~A~~ngW--IVL~IP~a~~w  230 (404)
                      ||+++||.|||++|..+++.+...|-  |+|.-|+..+.
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~~~~I~vtAP~~~~~   39 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKGKIRILVTAPSPENV   39 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-----EEEE-SS--S-
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhcCceEEEecCCHHHH
Confidence            68999999999999999999888876  77777876553

This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.

>TIGR00376 DNA helicase, putative

Probab=91.61  E-value=0.2  Score=55.15  Aligned_cols=33  Identities=30%  Similarity=0.412  Sum_probs=27.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|++|||||+++..++..+.++|--|+..
T Consensus       175 ~~lI~GpPGTGKT~t~~~ii~~~~~~g~~VLv~  207 (637)
T TIGR00376       175 LFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVT  207 (637)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            489999999999999999999888776655544

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>cd01870 RhoA_like RhoA-like subfamily

Probab=91.60  E-value=0.17  Score=44.67  Aligned_cols=22  Identities=32%  Similarity=0.600  Sum_probs=18.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++++.|+.|||||+++.+...
T Consensus         2 ~ki~iiG~~~~GKTsl~~~~~~   23 (175)
T cd01870           2 KKLVIVGDGACGKTCLLIVFSK   23 (175)
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999976654

The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. RhoA and RhoC are observed only in geranyl

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=91.55  E-value=0.26  Score=50.03  Aligned_cols=41  Identities=27%  Similarity=0.477  Sum_probs=31.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEecCcccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVPRGREWTH  232 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP~a~~wvn  232 (404)
                      -+++.|+.||||||+|..++.+.... +--|+.+-++.++..
T Consensus       124 ~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEdp~E~~~  165 (343)
T TIGR01420       124 LILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDPIEYVH  165 (343)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcCChhhhc
Confidence            38999999999999998888765532 446777777666653

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.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=91.54  E-value=0.26  Score=45.68  Aligned_cols=33  Identities=21%  Similarity=0.141  Sum_probs=25.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|+|..|||||++...+...-...|+-++++
T Consensus        26 ~i~i~G~~GsGKSTla~~l~~~l~~~~~~~~~l   58 (198)
T PRK03846         26 VLWFTGLSGSGKSTVAGALEEALHELGVSTYLL   58 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCCEEEE
Confidence            389999999999998877777666666544444

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=91.51  E-value=0.16  Score=47.19  Aligned_cols=21  Identities=38%  Similarity=0.643  Sum_probs=18.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++|+|+.|+|||++|.++.
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            359999999999999999866

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 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, a

>PRK14530 adenylate kinase; Provisional

Probab=91.51  E-value=0.23  Score=46.51  Aligned_cols=30  Identities=27%  Similarity=0.219  Sum_probs=22.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      ++++|.|++|||||++...+.   ..-|+..+.
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La---~~~~~~~i~   33 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLA---EEFGVEHVT   33 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHH---HHhCCeEEe
Confidence            469999999999999887773   334665443

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=91.49  E-value=0.3  Score=50.52  Aligned_cols=41  Identities=17%  Similarity=0.099  Sum_probs=32.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEecCcccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVPRGREWTH  232 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP~a~~wvn  232 (404)
                      -+++.|+.|||||++|..++.+-.++  +.-|+.|=++.++..
T Consensus       151 lilI~G~TGSGKTT~l~al~~~i~~~~~~~~IvtiEdp~E~~~  193 (372)
T TIGR02525       151 LGLICGETGSGKSTLAASIYQHCGETYPDRKIVTYEDPIEYIL  193 (372)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEecCchhcc
Confidence            38999999999999999988877543  456777777766643

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>KOG2749 consensus mRNA cleavage and polyadenylation factor IA/II complex, subunit CLP1 [RNA processing and modification]

Probab=91.49  E-value=0.3  Score=50.44  Aligned_cols=35  Identities=29%  Similarity=0.492  Sum_probs=33.1

Q ss_pred             ceeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          190 RKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       190 r~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -+|+++.|+.-||||++.--+..||.++||=.+|+
T Consensus       103 GPrv~vVGp~d~GKsTl~r~L~nyavk~gr~Plfv  137 (415)
T KOG2749|consen  103 GPRVMVVGPTDVGKSTLCRILLNYAVKQGRRPLFV  137 (415)
T ss_pred             CCEEEEECCCccchHHHHHHHHHHHHHcCCcceEE
Confidence            37899999999999999999999999999999887

>cd04137 RheB Rheb (Ras Homolog Enriched in Brain) subfamily

Probab=91.49  E-value=0.18  Score=44.88  Aligned_cols=21  Identities=29%  Similarity=0.368  Sum_probs=19.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|.+|+|||+++.++.
T Consensus         2 ~kv~l~G~~g~GKTtl~~~~~   22 (180)
T cd04137           2 RKIAVLGSRSVGKSSLTVQFV   22 (180)
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            469999999999999998877

Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that le

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=91.48  E-value=0.15  Score=49.51  Aligned_cols=32  Identities=25%  Similarity=0.369  Sum_probs=23.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh-CCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE-EGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~-ngWIVL~  223 (404)
                      -+.|.|+.||||||+|+-+-....- .|-+.+.
T Consensus        33 ~vaI~GpSGSGKSTLLniig~ld~pt~G~v~i~   65 (226)
T COG1136          33 FVAIVGPSGSGKSTLLNLLGGLDKPTSGEVLIN   65 (226)
T ss_pred             EEEEECCCCCCHHHHHHHHhcccCCCCceEEEC
Confidence            3899999999999999877665543 3544444

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=91.47  E-value=0.17  Score=44.18  Aligned_cols=39  Identities=18%  Similarity=0.365  Sum_probs=25.6

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHH
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      ...++.+.+++....     +.     -++|+|++||||+.+. +++|..
T Consensus         6 ~~~~l~~~l~~~a~~-----~~-----pvli~GE~GtGK~~~A-~~lh~~   44 (138)
T PF14532_consen    6 AMRRLRRQLERLAKS-----SS-----PVLITGEPGTGKSLLA-RALHRY   44 (138)
T ss_dssp             HHHHHHHHHHHHHCS-----SS------EEEECCTTSSHHHHH-HCCHHT
T ss_pred             HHHHHHHHHHHHhCC-----CC-----cEEEEcCCCCCHHHHH-HHHHhh
Confidence            345677777766321     11     2899999999999954 455543

>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily

Probab=91.45  E-value=0.19  Score=43.15  Aligned_cols=21  Identities=29%  Similarity=0.354  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++-|.+|||||+++.+++.
T Consensus         3 ki~iiG~~~vGKTsl~~~~~~   23 (162)
T cd04138           3 KLVVVGAGGVGKSALTIQLIQ   23 (162)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            589999999999999988874

H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.

>cd00157 Rho Rho (Ras homology) family

Probab=91.44  E-value=0.18  Score=43.95  Aligned_cols=22  Identities=27%  Similarity=0.247  Sum_probs=19.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ++++.|++|||||+++.+++..
T Consensus         2 ki~i~G~~~~GKSsli~~l~~~   23 (171)
T cd00157           2 KIVVVGDGAVGKTCLLISYTTG   23 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999988754

Members of the Rho family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho protein

>PTZ00035 Rad51 protein; Provisional

Probab=91.43  E-value=0.097  Score=53.25  Aligned_cols=97  Identities=15%  Similarity=0.191  Sum_probs=53.3

Q ss_pred             cccCCCccccCccccceeEEeCHHHHHhhccC---CCCcchhhhccccCceeEEEchhHHHHHHHHHHhcCCCccCCCCC
Q 045329          111 FTKTTSLSLLTRKDACTYFKFSEDELNAMLPE---GLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP  187 (404)
Q Consensus       111 ~~~~~~~~~ht~~~vGk~y~~p~e~~k~l~~~---GLp~~~~kqfe~f~~p~~LVRk~tleLi~~L~~~~d~~~~std~~  187 (404)
                      |.+..+....+..++.+...++.+...++...   -++..+..-.+...+.....|=+|=  +..|.+.+....     +
T Consensus        44 ~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~~~~~~~ta~~~~~~~~~~~~isTG--~~~LD~lLgGGi-----~  116 (337)
T PTZ00035         44 ICTVESVAYATKKDLCNIKGISEAKVEKIKEAASKLVPMGFISATEYLEARKNIIRITTG--STQLDKLLGGGI-----E  116 (337)
T ss_pred             CCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHhcccCCCCHHHHHHhhccCccccCC--cHHHHHHhCCCC-----C
Confidence            55666778888888888888888876666432   1111111111122111111111110  222344433221     1


Q ss_pred             ccceeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          188 KIRKQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       188 ~~r~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      . ..-+.|+|++|||||+++.|+...+.
T Consensus       117 ~-G~iteI~G~~GsGKT~l~~~l~~~~q  143 (337)
T PTZ00035        117 T-GSITELFGEFRTGKTQLCHTLCVTCQ  143 (337)
T ss_pred             C-CeEEEEECCCCCchhHHHHHHHHHhc
Confidence            1 12378999999999999998876664

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=91.43  E-value=0.26  Score=47.21  Aligned_cols=32  Identities=28%  Similarity=0.234  Sum_probs=26.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|.|.+|||||+...++..+....|+=|+++
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~~~~v~~i   33 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIIL   33 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCceEEE
Confidence            69999999999999999998877666644454

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.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=91.42  E-value=0.26  Score=45.32  Aligned_cols=33  Identities=12%  Similarity=0.138  Sum_probs=23.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +.|.|+.||||||+...+...-...+..|++..
T Consensus         2 igi~G~~GsGKSTl~~~l~~~l~~~~~~v~~~D   34 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIEQLGNPKVVIISQD   34 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCCeEEEEec
Confidence            578999999999999888765422234555544

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.

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=91.42  E-value=0.15  Score=47.83  Aligned_cols=23  Identities=26%  Similarity=0.245  Sum_probs=19.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      -++|+|+.|||||++|.++....
T Consensus        27 ~~~ltGpNg~GKSTllr~i~~~~   49 (199)
T cd03283          27 GILITGSNMSGKSTFLRTIGVNV   49 (199)
T ss_pred             EEEEECCCCCChHHHHHHHHHHH
Confidence            48999999999999998876543

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

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=91.42  E-value=0.23  Score=50.78  Aligned_cols=39  Identities=18%  Similarity=0.219  Sum_probs=26.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREW  230 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~w  230 (404)
                      ..+++.|+.|||||++|.-++.+--.+. -++.|=+..++
T Consensus       163 ~nilI~G~tGSGKTTll~aLl~~i~~~~-rivtiEd~~El  201 (344)
T PRK13851        163 LTMLLCGPTGSGKTTMSKTLISAIPPQE-RLITIEDTLEL  201 (344)
T ss_pred             CeEEEECCCCccHHHHHHHHHcccCCCC-CEEEECCCccc
Confidence            3499999999999999988776543322 23344444443

>cd04129 Rho2 Rho2 subfamily

Probab=91.38  E-value=0.18  Score=45.76  Aligned_cols=21  Identities=29%  Similarity=0.646  Sum_probs=19.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|+.|+|||+++.+++
T Consensus         2 ~Ki~ivG~~g~GKStLl~~l~   22 (187)
T cd04129           2 RKLVIVGDGACGKTSLLSVFT   22 (187)
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            469999999999999998886

Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).

>PTZ00202 tuzin; Provisional

Probab=91.36  E-value=0.17  Score=54.00  Aligned_cols=33  Identities=24%  Similarity=0.189  Sum_probs=27.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      -.+|+|+.|||||+++.+++.++.    .+.++++..
T Consensus       288 ivvLtG~~G~GKTTLlR~~~~~l~----~~qL~vNpr  320 (550)
T PTZ00202        288 IVVFTGFRGCGKSSLCRSAVRKEG----MPAVFVDVR  320 (550)
T ss_pred             EEEEECCCCCCHHHHHHHHHhcCC----ceEEEECCC
Confidence            478999999999999999997664    557777665

>PHA03136 thymidine kinase; Provisional

Probab=91.36  E-value=0.2  Score=51.91  Aligned_cols=36  Identities=31%  Similarity=0.458  Sum_probs=29.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeE--EEEecCccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWL--VLYVPRGRE  229 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWI--VL~IP~a~~  229 (404)
                      .|+.|+|.-|+||||++.++...   .+|.  |++||++-.
T Consensus        37 ~rvyieG~~gvGKTT~~~~l~~~---~~~~~~vl~v~EPm~   74 (378)
T PHA03136         37 VLLYLDGPFGTGKTTTAKLLMEM---PDTLAARLYLAEPMA   74 (378)
T ss_pred             EEEEEECCCcCCHHHHHHHHHhc---cccCCCeeeecCchH
Confidence            57999999999999999887762   5665  888888754

>PRK06762 hypothetical protein; Provisional

Probab=91.34  E-value=0.28  Score=43.59  Aligned_cols=30  Identities=23%  Similarity=0.305  Sum_probs=22.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      ++|+|.+|||||++-..+.... ..+++++.
T Consensus         5 i~i~G~~GsGKST~A~~L~~~l-~~~~~~i~   34 (166)
T PRK06762          5 IIIRGNSGSGKTTIAKQLQERL-GRGTLLVS   34 (166)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh-CCCeEEec
Confidence            8999999999999877665443 23666653

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=91.34  E-value=0.16  Score=44.33  Aligned_cols=20  Identities=25%  Similarity=0.272  Sum_probs=18.4

Q ss_pred             EEEECCCCCcHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++|.|.+|||||+++.++..
T Consensus         2 i~~vG~~~~GKstLi~~l~~   21 (167)
T cd04160           2 VLILGLDNAGKTTFLEQLKT   21 (167)
T ss_pred             EEEEecCCCCHHHHHHHHhh
Confidence            78999999999999999865

Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=91.33  E-value=0.31  Score=49.71  Aligned_cols=32  Identities=28%  Similarity=0.220  Sum_probs=27.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      ..+-|+|.+|+|||+++..++.+....||=|.
T Consensus        57 ~~igi~G~~GaGKSTl~~~l~~~l~~~g~~v~   88 (332)
T PRK09435         57 LRIGITGVPGVGKSTFIEALGMHLIEQGHKVA   88 (332)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCeEE
Confidence            45899999999999999999999988887433

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=91.29  E-value=0.22  Score=46.15  Aligned_cols=31  Identities=23%  Similarity=0.167  Sum_probs=20.6

Q ss_pred             EEEECCCCCcHHHHHHHH-HHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAML-VHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qa-v~~A~~ngWIVL~  223 (404)
                      ++++|.+|+|||....+. +.-|.+.|+.|+.
T Consensus         3 ~~~~G~pGsGKS~~av~~~i~~~l~~gr~V~t   34 (193)
T PF05707_consen    3 YLITGKPGSGKSYYAVSYVIIPALKKGRPVYT   34 (193)
T ss_dssp             EEEE--TTSSHHHHHHHHHHH-GGGS---EEE
T ss_pred             EEEEcCCCCcHhHHHHHHHHHHHHhCCCEEEE
Confidence            689999999999988777 6667777877665

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PRK13768 GTPase; Provisional

Probab=91.24  E-value=0.27  Score=47.73  Aligned_cols=33  Identities=27%  Similarity=0.441  Sum_probs=26.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -+++.|+.|||||++..++..+...+|-=|+.|
T Consensus         4 ~i~v~G~~G~GKTt~~~~~~~~l~~~g~~v~~i   36 (253)
T PRK13768          4 IVFFLGTAGSGKTTLTKALSDWLEEQGYDVAIV   36 (253)
T ss_pred             EEEEECCCCccHHHHHHHHHHHHHhcCCceEEE
Confidence            378999999999999999999988776543333

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=91.23  E-value=0.2  Score=43.56  Aligned_cols=21  Identities=29%  Similarity=0.311  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|++|+|||+++.+++.
T Consensus         2 ki~v~G~~~~GKTsli~~~~~   22 (164)
T smart00173        2 KLVVLGSGGVGKSALTIQFVQ   22 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999998874

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>PRK02496 adk adenylate kinase; Provisional

Probab=91.22  E-value=0.21  Score=45.32  Aligned_cols=33  Identities=15%  Similarity=0.188  Sum_probs=23.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      .|++|.|++|||||++...+...   -|+.++.+.+
T Consensus         2 ~~i~i~G~pGsGKst~a~~la~~---~~~~~i~~~~   34 (184)
T PRK02496          2 TRLIFLGPPGAGKGTQAVVLAEH---LHIPHISTGD   34 (184)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH---hCCcEEEhHH
Confidence            36999999999999988776432   3665555433

>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=91.18  E-value=0.18  Score=46.86  Aligned_cols=23  Identities=26%  Similarity=0.325  Sum_probs=20.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+++|+|+.|+|||++|.++..-
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~~   52 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGLA   52 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHHH
Confidence            46999999999999999888743

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

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=91.15  E-value=0.32  Score=53.33  Aligned_cols=38  Identities=21%  Similarity=0.269  Sum_probs=29.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC-eEEEEecCccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG-WLVLYVPRGRE  229 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng-WIVL~IP~a~~  229 (404)
                      .++|+|++|||||+++..+....-.+. ..++|+|++..
T Consensus        39 ~~ll~G~pG~GKT~la~~la~~l~~~~~~~~~~~~n~~~   77 (608)
T TIGR00764        39 NVLLIGEPGVGKSMLAKAMAELLPDEELEDILVYPNPED   77 (608)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHcCchhheeEEEEeCCCC
Confidence            489999999999998877766554444 56779998844

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK00698 tmk thymidylate kinase; Validated

Probab=91.13  E-value=0.32  Score=44.33  Aligned_cols=35  Identities=23%  Similarity=0.330  Sum_probs=26.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC--eEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG--WLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng--WIVL~IP~  226 (404)
                      -++|.|..|||||+++..+..+....|  +++...|.
T Consensus         5 ~I~ieG~~gsGKsT~~~~L~~~l~~~~~~~~~~~~p~   41 (205)
T PRK00698          5 FITIEGIDGAGKSTQIELLKELLEQQGRDVVFTREPG   41 (205)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCceeEeeCCC
Confidence            489999999999999998888766654  34444454

>CHL00195 ycf46 Ycf46; Provisional

Probab=91.13  E-value=0.23  Score=53.11  Aligned_cols=23  Identities=26%  Similarity=0.280  Sum_probs=17.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      +.++|+|++|||||.+. .+++.-
T Consensus       260 kGILL~GPpGTGKTllA-kaiA~e  282 (489)
T CHL00195        260 RGLLLVGIQGTGKSLTA-KAIAND  282 (489)
T ss_pred             ceEEEECCCCCcHHHHH-HHHHHH
Confidence            56999999999999554 555443

>PRK10536 hypothetical protein; Provisional

Probab=91.09  E-value=0.34  Score=47.97  Aligned_cols=35  Identities=26%  Similarity=0.199  Sum_probs=27.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH-hCCeEEEEecCc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR-EEGWLVLYVPRG  227 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL~IP~a  227 (404)
                      ++++|+.|||||++...+...+. ....-.++|.++
T Consensus        77 V~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP  112 (262)
T PRK10536         77 IFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRP  112 (262)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCC
Confidence            89999999999999988888766 444555666554

>TIGR03263 guanyl_kin guanylate kinase

Probab=91.07  E-value=0.19  Score=45.22  Aligned_cols=21  Identities=38%  Similarity=0.575  Sum_probs=18.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++|.|+.|||||+++..+..
T Consensus         3 ii~l~G~~GsGKsTl~~~L~~   23 (180)
T TIGR03263         3 LIVISGPSGVGKSTLVKALLE   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            489999999999998877776

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.

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=91.07  E-value=0.32  Score=46.80  Aligned_cols=34  Identities=24%  Similarity=0.244  Sum_probs=29.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP~  226 (404)
                      ++|-|.+|+|||+++.|+...+..+ |.=|+|+.-
T Consensus        22 ~vi~a~pg~GKT~~~l~ia~~~a~~~~~~vly~Sl   56 (259)
T PF03796_consen   22 TVIAARPGVGKTAFALQIALNAALNGGYPVLYFSL   56 (259)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTSSEEEEEES
T ss_pred             EEEEecccCCchHHHHHHHHHHHHhcCCeEEEEcC
Confidence            8999999999999999999877766 688888854

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. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=91.05  E-value=0.26  Score=51.03  Aligned_cols=33  Identities=27%  Similarity=0.308  Sum_probs=28.9

Q ss_pred             EEEECCCCCcHHHHHHHHHH-HHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVH-WAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~-~A~~ngWIVL~IP  225 (404)
                      ++|.|.+|+|||+++.+++. .|..+|+=|+++.
T Consensus       197 iviag~pg~GKT~~al~ia~~~a~~~g~~v~~fS  230 (421)
T TIGR03600       197 IVIGARPSMGKTTLALNIAENVALREGKPVLFFS  230 (421)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            89999999999999999985 4568899888885

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=91.05  E-value=0.21  Score=53.35  Aligned_cols=40  Identities=25%  Similarity=0.289  Sum_probs=31.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTH  232 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvn  232 (404)
                      ++++|+.|||||++|..++.+--..+--|+.|-++-++..
T Consensus       245 ilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDpvE~~~  284 (486)
T TIGR02533       245 ILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVEYQI  284 (486)
T ss_pred             EEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCCeeeec
Confidence            7999999999999998777765445566788877666543

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=91.04  E-value=0.18  Score=46.25  Aligned_cols=21  Identities=43%  Similarity=0.431  Sum_probs=18.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++|.|+.||||||++..+..
T Consensus         4 ~i~l~G~sGsGKsTl~~~l~~   24 (186)
T PRK10078          4 LIWLMGPSGSGKDSLLAALRQ   24 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            389999999999999998843

>PRK10436 hypothetical protein; Provisional

Probab=91.04  E-value=0.28  Score=52.17  Aligned_cols=41  Identities=22%  Similarity=0.201  Sum_probs=32.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTH  232 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvn  232 (404)
                      -++++|+.||||||+|..++.+....+--|+.|=++-++..
T Consensus       220 liLvtGpTGSGKTTtL~a~l~~~~~~~~~i~TiEDPvE~~l  260 (462)
T PRK10436        220 LILVTGPTGSGKTVTLYSALQTLNTAQINICSVEDPVEIPL  260 (462)
T ss_pred             eEEEECCCCCChHHHHHHHHHhhCCCCCEEEEecCCccccC
Confidence            38999999999999998888886555555777777766543

>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=91.02  E-value=0.18  Score=43.04  Aligned_cols=31  Identities=26%  Similarity=0.399  Sum_probs=22.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.-. ..|-|.+
T Consensus        13 ~~~i~G~nGsGKStLl~~l~g~~~~~~G~i~~   44 (137)
T PF00005_consen   13 IVAIVGPNGSGKSTLLKALAGLLPPDSGSILI   44 (137)
T ss_dssp             EEEEEESTTSSHHHHHHHHTTSSHESEEEEEE
T ss_pred             EEEEEccCCCccccceeeeccccccccccccc
Confidence            489999999999999976655433 4465544

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 ....

>PRK08233 hypothetical protein; Provisional

Probab=91.00  E-value=0.21  Score=44.63  Aligned_cols=32  Identities=22%  Similarity=0.173  Sum_probs=23.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -+.|.|.+||||||+..++...-  .+.-|+++.
T Consensus         5 iI~I~G~~GsGKtTla~~L~~~l--~~~~~~~~d   36 (182)
T PRK08233          5 IITIAAVSGGGKTTLTERLTHKL--KNSKALYFD   36 (182)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC--CCCceEEEC
Confidence            37889999999999998887642  234555553

>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=91.00  E-value=0.52  Score=45.22  Aligned_cols=25  Identities=16%  Similarity=0.114  Sum_probs=21.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      ..+.|+|..|+|||++..++.+...
T Consensus        20 ~~v~I~G~~G~GKT~LA~~~~~~~~   44 (287)
T PF00931_consen   20 RVVAIVGMGGIGKTTLARQVARDLR   44 (287)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHCHHH
T ss_pred             EEEEEEcCCcCCcceeeeecccccc
Confidence            5699999999999999999887644

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.

>cd04163 Era Era subfamily

Probab=90.96  E-value=0.22  Score=42.28  Aligned_cols=22  Identities=32%  Similarity=0.306  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++++.|+.|+|||+++.++..
T Consensus         4 ~~i~~~G~~g~GKttl~~~l~~   25 (168)
T cd04163           4 GFVAIVGRPNVGKSTLLNALVG   25 (168)
T ss_pred             eEEEEECCCCCCHHHHHHHHhC
Confidence            4599999999999999999763

Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.

>COG3911 Predicted ATPase [General function prediction only]

Probab=90.96  E-value=0.2  Score=46.30  Aligned_cols=31  Identities=29%  Similarity=0.432  Sum_probs=23.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++|||+|-+|+|||++|+-+-    +.|+.++..+
T Consensus        10 ~~fIltGgpGaGKTtLL~aLa----~~Gfatvee~   40 (183)
T COG3911          10 KRFILTGGPGAGKTTLLAALA----RAGFATVEEA   40 (183)
T ss_pred             eEEEEeCCCCCcHHHHHHHHH----HcCceeeccc
Confidence            479999999999999997542    3566666554

>PHA00729 NTP-binding motif containing protein

Probab=90.89  E-value=0.34  Score=47.00  Aligned_cols=23  Identities=17%  Similarity=0.089  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .++|+|.+|||||++...+...+
T Consensus        19 nIlItG~pGvGKT~LA~aLa~~l   41 (226)
T PHA00729         19 SAVIFGKQGSGKTTYALKVARDV   41 (226)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            49999999999999877766654

>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily

Probab=90.85  E-value=0.21  Score=43.74  Aligned_cols=21  Identities=29%  Similarity=0.340  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|++|||||+++.+++.
T Consensus         4 ki~i~G~~~vGKSsli~~~~~   24 (166)
T cd01869           4 KLLLIGDSGVGKSCLLLRFAD   24 (166)
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999988864

Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to t

>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=90.83  E-value=0.18  Score=46.63  Aligned_cols=19  Identities=26%  Similarity=0.225  Sum_probs=17.0

Q ss_pred             eEEEECCCCCcHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qa  210 (404)
                      ++.|.|+.||||||+|.-+
T Consensus        23 ~~~l~G~nG~GKSTLl~~i   41 (176)
T cd03238          23 LVVVTGVSGSGKSTLVNEG   41 (176)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5899999999999999754

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.

>cd04156 ARLTS1 ARLTS1 subfamily

Probab=90.82  E-value=0.2  Score=43.42  Aligned_cols=21  Identities=43%  Similarity=0.434  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|.|.+|||||+++..+..
T Consensus         1 ~i~i~G~~~~GKTsl~~~~~~   21 (160)
T cd04156           1 QVLLLGLDSAGKSTLLYKLKH   21 (160)
T ss_pred             CEEEEcCCCCCHHHHHHHHhc
Confidence            489999999999999988864

ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in h

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=90.80  E-value=0.23  Score=42.78  Aligned_cols=21  Identities=19%  Similarity=0.238  Sum_probs=19.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|.+|+|||+++.++++
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~   22 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMY   22 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999998884

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

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=90.77  E-value=0.34  Score=50.98  Aligned_cols=34  Identities=29%  Similarity=0.338  Sum_probs=28.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..++|.|+.||||||+++.+..+...+|.=|..|
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI  275 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFI  275 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEE
Confidence            3589999999999999999988888888655544

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=90.75  E-value=0.23  Score=42.84  Aligned_cols=20  Identities=20%  Similarity=0.255  Sum_probs=17.9

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++.|++|||||+++.++.
T Consensus         2 ki~~vG~~~vGKTsli~~l~   21 (168)
T cd04119           2 KVISMGNSGVGKSCIIKRYC   21 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            48999999999999998775

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=90.72  E-value=0.41  Score=43.56  Aligned_cols=33  Identities=27%  Similarity=0.256  Sum_probs=25.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|.+|||||++...+...-...|+-++++
T Consensus        20 ~i~i~G~~GsGKstla~~l~~~l~~~~~~~~~l   52 (184)
T TIGR00455        20 VIWLTGLSGSGKSTIANALEKKLESKGYRVYVL   52 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            489999999999998888887766677544444

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=90.72  E-value=0.46  Score=48.31  Aligned_cols=39  Identities=18%  Similarity=0.152  Sum_probs=30.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWT  231 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wv  231 (404)
                      .+++.|+.|||||++|.-++.+. -.++-|+.|-+..++.
T Consensus       162 nili~G~tgSGKTTll~aL~~~i-p~~~ri~tiEd~~El~  200 (332)
T PRK13900        162 NIIISGGTSTGKTTFTNAALREI-PAIERLITVEDAREIV  200 (332)
T ss_pred             cEEEECCCCCCHHHHHHHHHhhC-CCCCeEEEecCCCccc
Confidence            49999999999999997776654 4567788887776664

>PRK03839 putative kinase; Provisional

Probab=90.64  E-value=0.23  Score=44.99  Aligned_cols=32  Identities=22%  Similarity=0.332  Sum_probs=23.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +++|.|.+||||||+..++   |..-|+-++.+-+
T Consensus         2 ~I~l~G~pGsGKsT~~~~L---a~~~~~~~id~d~   33 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLL---AEKLGYEYVDLTE   33 (180)
T ss_pred             EEEEECCCCCCHHHHHHHH---HHHhCCcEEehhh
Confidence            4899999999999976554   3444676666543

>PRK00300 gmk guanylate kinase; Provisional

Probab=90.63  E-value=0.23  Score=45.71  Aligned_cols=22  Identities=41%  Similarity=0.551  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -++|.|+.|||||+++..+...
T Consensus         7 ~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          7 LIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             EEEEECCCCCCHHHHHHHHHhh
Confidence            3899999999999988887765

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=90.62  E-value=0.22  Score=43.78  Aligned_cols=21  Identities=48%  Similarity=0.571  Sum_probs=18.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ++|.|+.|||||+++..++..
T Consensus         2 i~i~GpsGsGKstl~~~L~~~   22 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEE   22 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhc
Confidence            688999999999988887764

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.

>smart00175 RAB Rab subfamily of small GTPases

Probab=90.62  E-value=0.24  Score=42.79  Aligned_cols=20  Identities=35%  Similarity=0.416  Sum_probs=18.2

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++.|++|||||+++..+.
T Consensus         2 kv~v~G~~~~GKTtli~~l~   21 (164)
T smart00175        2 KIILIGDSGVGKSSLLSRFT   21 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            48999999999999998875

Rab GTPases are implicated in vesicle trafficking.

>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=90.61  E-value=0.31  Score=41.95  Aligned_cols=20  Identities=20%  Similarity=0.292  Sum_probs=18.1

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      .++|.|+.|||||++|..+.
T Consensus        17 ~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          17 GVLITGDSGIGKTELALELI   36 (107)
T ss_pred             EEEEEcCCCCCHHHHHHHhh
Confidence            48999999999999998875

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

>cd04136 Rap_like Rap-like subfamily

Probab=90.60  E-value=0.25  Score=42.75  Aligned_cols=21  Identities=29%  Similarity=0.330  Sum_probs=18.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|.+|+|||+++.+.+.
T Consensus         3 ki~i~G~~~vGKTsl~~~~~~   23 (163)
T cd04136           3 KVVVLGSGGVGKSALTVQFVQ   23 (163)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            589999999999999887763

The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres.

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=90.59  E-value=0.25  Score=47.38  Aligned_cols=34  Identities=26%  Similarity=0.344  Sum_probs=26.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCC------eEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEG------WLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ng------WIVL~IP~  226 (404)
                      +++.|.+|||||++|.+-+.|...++      .+|+.+.+
T Consensus        16 ~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~   55 (315)
T PF00580_consen   16 LLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTN   55 (315)
T ss_dssp             EEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSH
T ss_pred             EEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCH
Confidence            78889999999999999998876544      66666544

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>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=90.59  E-value=0.4  Score=46.90  Aligned_cols=34  Identities=24%  Similarity=0.439  Sum_probs=25.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP  225 (404)
                      |.++-|++|||||+++..++.+-... .-|++--|
T Consensus        15 r~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t~   49 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLITP   49 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhcccCCEEEEEec
Confidence            58999999999999999998764432 45554444

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

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=90.58  E-value=0.3  Score=47.09  Aligned_cols=31  Identities=26%  Similarity=0.234  Sum_probs=25.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      ..++|+|++|+|||++..++     ....+++....
T Consensus        13 ~~~liyG~~G~GKtt~a~~~-----~~~~~~~~~d~   43 (220)
T TIGR01618        13 NMYLIYGKPGTGKTSTIKYL-----PGKTLVLSFDM   43 (220)
T ss_pred             cEEEEECCCCCCHHHHHHhc-----CCCCEEEeccc
Confidence            45999999999999998876     35688887755

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=90.56  E-value=0.33  Score=51.25  Aligned_cols=33  Identities=24%  Similarity=0.304  Sum_probs=28.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|..||||||+++.+.+|...+|+=|+-|
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV  134 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLV  134 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEE
Confidence            488999999999999999999998888755544

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.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=90.54  E-value=0.31  Score=49.81  Aligned_cols=33  Identities=27%  Similarity=0.499  Sum_probs=28.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|+.|||||+++..+.++++..+=.|+..
T Consensus        24 ~~fv~G~~GtGKs~l~~~i~~~~~~~~~~~~~~   56 (364)
T PF05970_consen   24 NFFVTGPAGTGKSFLIKAIIDYLRSRGKKVLVT   56 (364)
T ss_pred             EEEEEcCCCCChhHHHHHHHHHhccccceEEEe
Confidence            489999999999999999999998875555544

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>cd00876 Ras Ras family

Probab=90.53  E-value=0.23  Score=42.51  Aligned_cols=20  Identities=30%  Similarity=0.321  Sum_probs=18.0

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++.|++|||||+++..+.
T Consensus         1 ki~i~G~~~~GKTsli~~l~   20 (160)
T cd00876           1 KVVVLGAGGVGKSAITIQFV   20 (160)
T ss_pred             CEEEECCCCCCHHHHHHHHH
Confidence            37999999999999998886

The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of m

>PRK04841 transcriptional regulator MalT; Provisional

Probab=90.52  E-value=1.4  Score=49.21  Aligned_cols=28  Identities=25%  Similarity=0.324  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHhcCCCCcEEEEEeCccccc
Q 045329          318 GVVVRLRKELSLVKDIPVLIAIDQYNNWF  346 (404)
Q Consensus       318 ~v~~aLl~EL~~q~~~PVLvAVD~~Nalf  346 (404)
                      ..+..++.+|... .-|++|+|||+..+-
T Consensus       107 ~~~~~~~~~l~~~-~~~~~lvlDD~h~~~  134 (903)
T PRK04841        107 SLFAQLFIELADW-HQPLYLVIDDYHLIT  134 (903)
T ss_pred             HHHHHHHHHHhcC-CCCEEEEEeCcCcCC
Confidence            4566777888653 679999999997664

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.50  E-value=0.39  Score=49.06  Aligned_cols=22  Identities=23%  Similarity=0.294  Sum_probs=17.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -|+|+|++|+|||++...+...
T Consensus        40 ~~L~~Gp~G~GKTtla~~la~~   61 (363)
T PRK14961         40 AWLLSGTRGVGKTTIARLLAKS   61 (363)
T ss_pred             EEEEecCCCCCHHHHHHHHHHH
Confidence            4899999999999877665543

>cd01863 Rab18 Rab18 subfamily

Probab=90.47  E-value=0.25  Score=42.82  Aligned_cols=20  Identities=35%  Similarity=0.356  Sum_probs=17.9

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++.|++|||||+++.++.
T Consensus         2 ki~v~G~~~~GKSsli~~l~   21 (161)
T cd01863           2 KILLIGDSGVGKSSLLLRFT   21 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            48999999999999998775

Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of mos

>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2

Probab=90.45  E-value=0.25  Score=43.62  Aligned_cols=23  Identities=26%  Similarity=0.172  Sum_probs=19.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -++++.|++|+|||+++.++...
T Consensus         4 ~ki~vvG~~~~GKSsl~~~~~~~   26 (167)
T cd01867           4 FKLLLIGDSGVGKSCLLLRFSED   26 (167)
T ss_pred             eEEEEECCCCCCHHHHHHHHhhC
Confidence            36999999999999999888643

Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhi

>TIGR01351 adk adenylate kinases

Probab=90.42  E-value=0.28  Score=45.82  Aligned_cols=32  Identities=25%  Similarity=0.301  Sum_probs=23.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      |++|.|++|||||++-.++   |..-|+.+|..-+
T Consensus         1 rI~i~G~pGsGKsT~a~~L---a~~~g~~~is~gd   32 (210)
T TIGR01351         1 RLVLLGPPGSGKGTQAKRI---AEKYGLPHISTGD   32 (210)
T ss_pred             CEEEECCCCCCHHHHHHHH---HHHcCCCeeehhH
Confidence            4899999999999986665   3445777776543

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.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=90.42  E-value=0.38  Score=50.78  Aligned_cols=33  Identities=24%  Similarity=0.231  Sum_probs=27.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH-HHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW-AREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~-A~~ngWIVL~I  224 (404)
                      .+++.|+.||||||+++++.++ ....|.-|..+
T Consensus       225 vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Li  258 (432)
T PRK12724        225 VVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLY  258 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEe
Confidence            4789999999999999999874 46778766655

>PRK10867 signal recognition particle protein; Provisional

Probab=90.40  E-value=0.34  Score=51.17  Aligned_cols=33  Identities=27%  Similarity=0.336  Sum_probs=28.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~I  224 (404)
                      -+++.|+.||||||+.+.+..|...+ |+=|+.|
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV  135 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLV  135 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEE
Confidence            48899999999999999999988877 8755555

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=90.39  E-value=0.47  Score=40.93  Aligned_cols=32  Identities=31%  Similarity=0.433  Sum_probs=25.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +++.|+.|+|||++-..+..+..++|.=|+-|
T Consensus         2 i~~~GkgG~GKTt~a~~la~~l~~~g~~V~~i   33 (116)
T cd02034           2 IAITGKGGVGKTTIAALLARYLAEKGKPVLAI   33 (116)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            78999999999999988887766666544433

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=90.31  E-value=0.32  Score=51.65  Aligned_cols=34  Identities=12%  Similarity=0.108  Sum_probs=26.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~I  224 (404)
                      .-++|.|++|||||++..|.+.-+..+ |==++||
T Consensus        22 ~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyv   56 (484)
T TIGR02655        22 RSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFV   56 (484)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEE
Confidence            349999999999999999987765444 5555555

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.

>PRK04195 replication factor C large subunit; Provisional

Probab=90.31  E-value=0.31  Score=51.67  Aligned_cols=31  Identities=35%  Similarity=0.583  Sum_probs=23.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.++|+|++|||||++...+   |.+-||-++.+
T Consensus        40 ~~lLL~GppG~GKTtla~al---a~el~~~~iel   70 (482)
T PRK04195         40 KALLLYGPPGVGKTSLAHAL---ANDYGWEVIEL   70 (482)
T ss_pred             CeEEEECCCCCCHHHHHHHH---HHHcCCCEEEE
Confidence            45999999999999887544   55557766665

>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=90.28  E-value=0.87  Score=41.85  Aligned_cols=32  Identities=25%  Similarity=0.330  Sum_probs=24.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCC--eEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEG--WLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ng--WIVL~I  224 (404)
                      +.|.|.+|||||++..++..+-...|  -.+|+.
T Consensus         2 i~i~G~sgsGKttla~~l~~~l~~~~~~~~~i~~   35 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISL   35 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEeh
Confidence            57999999999999988887755443  344544

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

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

Probab=90.27  E-value=0.29  Score=47.87  Aligned_cols=26  Identities=15%  Similarity=0.210  Sum_probs=20.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHh
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWARE  216 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~  216 (404)
                      .|++|.|++|||||+++..+......
T Consensus        17 qr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          17 QRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcccc
Confidence            36999999999999988776665543

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.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=90.25  E-value=0.31  Score=51.79  Aligned_cols=33  Identities=12%  Similarity=0.136  Sum_probs=26.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~I  224 (404)
                      -++|.|++|+|||++..|.+..+..+ |==|+||
T Consensus        33 ~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyi   66 (509)
T PRK09302         33 PTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFV   66 (509)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEE
Confidence            38999999999999999998766655 6444444

>PRK05480 uridine/cytidine kinase; Provisional

Probab=90.25  E-value=0.42  Score=44.39  Aligned_cols=34  Identities=18%  Similarity=0.111  Sum_probs=23.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..+.|.|+.||||||+...+...=....+.+++.
T Consensus         7 ~iI~I~G~sGsGKTTl~~~l~~~l~~~~~~~i~~   40 (209)
T PRK05480          7 IIIGIAGGSGSGKTTVASTIYEELGDESIAVIPQ   40 (209)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhCCCceEEEeC
Confidence            3589999999999998877665421223444444

>cd04159 Arl10_like Arl10-like subfamily

Probab=90.23  E-value=0.23  Score=41.99  Aligned_cols=21  Identities=24%  Similarity=0.257  Sum_probs=18.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ++|.|+.|||||+++.++..-
T Consensus         2 i~i~G~~~~GKssl~~~l~~~   22 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAGG   22 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHccC
Confidence            689999999999999988643

Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.

>TIGR02528 EutP ethanolamine utilization protein, EutP

Probab=90.16  E-value=0.25  Score=42.16  Aligned_cols=20  Identities=30%  Similarity=0.556  Sum_probs=18.0

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      +++|.|.+|+|||+++..++
T Consensus         2 kv~liG~~~vGKSsL~~~l~   21 (142)
T TIGR02528         2 RIMFIGSVGCGKTTLTQALQ   21 (142)
T ss_pred             eEEEECCCCCCHHHHHHHHc
Confidence            58999999999999998765

This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=90.09  E-value=0.4  Score=49.29  Aligned_cols=40  Identities=23%  Similarity=0.243  Sum_probs=28.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh---CCeEEEEecCccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE---EGWLVLYVPRGREWT  231 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~---ngWIVL~IP~a~~wv  231 (404)
                      -+++.|+.|||||++|.-++.+-..   .+=.|+.+=++.++.
T Consensus       136 lilI~GpTGSGKTTtL~aLl~~i~~~~~~~~~Ivt~EdpiE~~  178 (358)
T TIGR02524       136 IVFITGATGSGKSTLLAAIIRELAEAPDSHRKILTYEAPIEFV  178 (358)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhcCCCCcEEEEeCCCceEe
Confidence            4899999999999999887776432   233555566665554

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.

>cd04145 M_R_Ras_like M-Ras/R-Ras-like subfamily

Probab=90.06  E-value=0.3  Score=42.27  Aligned_cols=22  Identities=23%  Similarity=0.229  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ++++.|++|+|||+++..++.-
T Consensus         4 ki~i~G~~~~GKtsl~~~~~~~   25 (164)
T cd04145           4 KLVVVGGGGVGKSALTIQFIQS   25 (164)
T ss_pred             EEEEECCCCCcHHHHHHHHHhC
Confidence            5999999999999999887653

This subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an ali

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=90.03  E-value=0.58  Score=47.18  Aligned_cols=52  Identities=17%  Similarity=0.311  Sum_probs=35.2

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHH--hCCeEEEEecC
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAR--EEGWLVLYVPR  226 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~--~ngWIVL~IP~  226 (404)
                      ...++++.++++...     +.     -++|+|++||||+++...+++...  ..-|++|+-..
T Consensus        14 ~~~~~~~~i~~~a~~-----~~-----pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~   67 (326)
T PRK11608         14 SFLEVLEQVSRLAPL-----DK-----PVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAA   67 (326)
T ss_pred             HHHHHHHHHHHHhCC-----CC-----CEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCC
Confidence            566777777776321     12     289999999999987765554443  23588887654

>cd01862 Rab7 Rab7 subfamily

Probab=90.03  E-value=0.28  Score=42.76  Aligned_cols=22  Identities=18%  Similarity=0.291  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ++++.|++|||||+++..+...
T Consensus         2 ki~viG~~~~GKSsl~~~l~~~   23 (172)
T cd01862           2 KVIILGDSGVGKTSLMNQYVNK   23 (172)
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999887653

Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=90.02  E-value=0.42  Score=50.20  Aligned_cols=33  Identities=30%  Similarity=0.263  Sum_probs=26.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH--hCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR--EEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~--~ngWIVL~I  224 (404)
                      .++|.|+.|+|||++++.+.+++.  ..|.=|..|
T Consensus       223 ~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li  257 (424)
T PRK05703        223 VVALVGPTGVGKTTTLAKLAARYALLYGKKKVALI  257 (424)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEE
Confidence            589999999999999999888765  456555555

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=90.00  E-value=0.26  Score=50.08  Aligned_cols=22  Identities=32%  Similarity=0.548  Sum_probs=17.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++|+|++|||||++...+..
T Consensus       157 ~gvLL~GppGtGKT~lakaia~  178 (364)
T TIGR01242       157 KGVLLYGPPGTGKTLLAKAVAH  178 (364)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4599999999999977655543

Many proteins may score above the trusted cutoff because an internal

>cd04113 Rab4 Rab4 subfamily

Probab=89.87  E-value=0.3  Score=42.43  Aligned_cols=21  Identities=29%  Similarity=0.381  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++-|+.|+|||+++.+++.
T Consensus         2 ki~v~G~~~vGKTsli~~l~~   22 (161)
T cd04113           2 KFIIIGSSGTGKSCLLHRFVE   22 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999999863

Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to p

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=89.84  E-value=0.23  Score=46.20  Aligned_cols=22  Identities=32%  Similarity=0.333  Sum_probs=19.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      ++++|.+|||||+.+..++.-.
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~~   22 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKDR   22 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHhc
Confidence            4899999999999999888774

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>cd01876 YihA_EngB The YihA (EngB) subfamily

Probab=89.83  E-value=0.27  Score=41.96  Aligned_cols=19  Identities=32%  Similarity=0.392  Sum_probs=17.9

Q ss_pred             EEEECCCCCcHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav  211 (404)
                      ++|.|..|+|||+++..+.
T Consensus         2 i~l~G~~g~GKTtL~~~l~   20 (170)
T cd01876           2 IAFAGRSNVGKSSLINALT   20 (170)
T ss_pred             EEEEcCCCCCHHHHHHHHh
Confidence            7899999999999999887

This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=89.82  E-value=0.41  Score=42.15  Aligned_cols=30  Identities=30%  Similarity=0.331  Sum_probs=22.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|.+|||||++...+....   |+.++..
T Consensus         6 ~i~l~G~~GsGKstla~~La~~l---~~~~~d~   35 (175)
T PRK00131          6 NIVLIGFMGAGKSTIGRLLAKRL---GYDFIDT   35 (175)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh---CCCEEEC
Confidence            49999999999999976654433   6655543

>PTZ00088 adenylate kinase 1; Provisional

Probab=89.78  E-value=0.37  Score=46.43  Aligned_cols=34  Identities=24%  Similarity=0.227  Sum_probs=26.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      .|++|.|++||||||.-.++   |..-|+.++.+-+.
T Consensus         7 mrIvl~G~PGsGK~T~a~~L---a~~~g~~~is~gdl   40 (229)
T PTZ00088          7 LKIVLFGAPGVGKGTFAEIL---SKKENLKHINMGNI   40 (229)
T ss_pred             ceEEEECCCCCCHHHHHHHH---HHHhCCcEEECChH
Confidence            35999999999999877665   44558888877654

>cd04124 RabL2 RabL2 subfamily

Probab=89.78  E-value=0.31  Score=42.87  Aligned_cols=21  Identities=29%  Similarity=0.384  Sum_probs=18.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|.+|||||+++.+++.
T Consensus         2 ki~vvG~~~vGKTsli~~~~~   22 (161)
T cd04124           2 KIILLGDSAVGKSKLVERFLM   22 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999988764

RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-b

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=89.77  E-value=0.22  Score=48.85  Aligned_cols=30  Identities=27%  Similarity=0.521  Sum_probs=21.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLV  221 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIV  221 (404)
                      -+.|-|+.||||||+|.=+.-.-. ..|=|.
T Consensus        31 fvsilGpSGcGKSTLLriiAGL~~p~~G~V~   61 (248)
T COG1116          31 FVAILGPSGCGKSTLLRLIAGLEKPTSGEVL   61 (248)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCceEE
Confidence            478999999999999976655433 334433

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=89.73  E-value=0.54  Score=43.72  Aligned_cols=33  Identities=15%  Similarity=0.055  Sum_probs=27.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -+.+.|+.|||||+++..++..-...|+-|-.|
T Consensus         8 ii~ivG~sgsGKTTLi~~li~~l~~~g~~vg~I   40 (173)
T PRK10751          8 LLAIAAWSGTGKTTLLKKLIPALCARGIRPGLI   40 (173)
T ss_pred             EEEEECCCCChHHHHHHHHHHHHhhcCCeEEEE
Confidence            478999999999999999999877778655444

>PRK13973 thymidylate kinase; Provisional

Probab=89.72  E-value=0.56  Score=44.13  Aligned_cols=39  Identities=26%  Similarity=0.304  Sum_probs=33.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREW  230 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~w  230 (404)
                      =++|.|..||||||....+..|-...|.-|++.+.+..+
T Consensus         5 ~IviEG~dGsGKtTq~~~l~~~l~~~g~~~~~~~~p~~~   43 (213)
T PRK13973          5 FITFEGGEGAGKSTQIRLLAERLRAAGYDVLVTREPGGS   43 (213)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEECCCCC
Confidence            388999999999999999999998888888888666443

>PRK04040 adenylate kinase; Provisional

Probab=89.70  E-value=0.31  Score=45.38  Aligned_cols=34  Identities=18%  Similarity=0.263  Sum_probs=24.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      .++|+|.+|||||+++..+...-- .+.-+++..+
T Consensus         4 ~i~v~G~pG~GKtt~~~~l~~~l~-~~~~~~~~g~   37 (188)
T PRK04040          4 VVVVTGVPGVGKTTVLNKALEKLK-EDYKIVNFGD   37 (188)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHhc-cCCeEEecch
Confidence            589999999999999988766432 2555555433

>cd01868 Rab11_like Rab11-like

Probab=89.67  E-value=0.31  Score=42.47  Aligned_cols=20  Identities=40%  Similarity=0.405  Sum_probs=18.5

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++.|++|||||+++.++.
T Consensus         5 ki~vvG~~~~GKSsli~~l~   24 (165)
T cd01868           5 KIVLIGDSGVGKSNLLSRFT   24 (165)
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            58999999999999999886

Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP

>COG4778 PhnL ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=89.67  E-value=0.31  Score=46.16  Aligned_cols=31  Identities=35%  Similarity=0.561  Sum_probs=25.5

Q ss_pred             EEEECCCCCcHHHHHHHHHH-HHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVH-WAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~-~A~~ngWIVL~  223 (404)
                      ++|+|+.|+|||++|..+.. |.-..|-|.+-
T Consensus        40 vvL~G~SG~GKStllr~LYaNY~~d~G~I~v~   71 (235)
T COG4778          40 VVLHGPSGSGKSTLLRSLYANYLPDEGQILVR   71 (235)
T ss_pred             EEeeCCCCCcHHHHHHHHHhccCCCCceEEEE
Confidence            89999999999999988776 66667766553

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=89.65  E-value=0.39  Score=43.82  Aligned_cols=28  Identities=32%  Similarity=0.348  Sum_probs=22.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.|+|..|||||++...+..    .|..|+..
T Consensus         2 i~itG~~gsGKst~~~~l~~----~g~~~i~~   29 (179)
T cd02022           2 IGLTGGIGSGKSTVAKLLKE----LGIPVIDA   29 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHH----CCCCEEec
Confidence            68999999999999988766    47666654

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>cd01878 HflX HflX subfamily

Probab=89.62  E-value=0.27  Score=44.97  Aligned_cols=22  Identities=27%  Similarity=0.279  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|||||++|..++.
T Consensus        42 ~~I~iiG~~g~GKStLl~~l~~   63 (204)
T cd01878          42 PTVALVGYTNAGKSTLFNALTG   63 (204)
T ss_pred             CeEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999988765

A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.

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

Probab=89.61  E-value=0.29  Score=51.03  Aligned_cols=22  Identities=27%  Similarity=0.536  Sum_probs=17.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +.++|+|++|||||++...+..
T Consensus       180 kgvLL~GppGTGKT~LAkalA~  201 (398)
T PTZ00454        180 RGVLLYGPPGTGKTMLAKAVAH  201 (398)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4699999999999998755433

>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=89.60  E-value=0.6  Score=42.74  Aligned_cols=32  Identities=25%  Similarity=0.185  Sum_probs=27.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.|+|-+|||||++-..+...-+..|+=|.++
T Consensus         5 IwltGlsGsGKtTlA~~L~~~L~~~g~~~~~L   36 (156)
T PF01583_consen    5 IWLTGLSGSGKTTLARALERRLFARGIKVYLL   36 (156)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHHHHTTS-EEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCcEEEe
Confidence            78999999999988888888888889887777

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 ....

>cd01860 Rab5_related Rab5-related subfamily

Probab=89.55  E-value=0.33  Score=42.06  Aligned_cols=21  Identities=33%  Similarity=0.404  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|+.|||||+++.++..
T Consensus         3 ki~v~G~~~~GKSsli~~l~~   23 (163)
T cd01860           3 KLVLLGDSSVGKSSLVLRFVK   23 (163)
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999988764

This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence mo

>cd01866 Rab2 Rab2 subfamily

Probab=89.54  E-value=0.32  Score=42.97  Aligned_cols=20  Identities=25%  Similarity=0.316  Sum_probs=18.4

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++.|.+|+|||++|.++.
T Consensus         6 ki~vvG~~~vGKSsLl~~l~   25 (168)
T cd01866           6 KYIIIGDTGVGKSCLLLQFT   25 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            59999999999999999875

Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key featur

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=89.50  E-value=0.53  Score=50.80  Aligned_cols=27  Identities=7%  Similarity=0.100  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHhcCCCC-cEEEEEeCcc
Q 045329          317 VGVVVRLRKELSLVKDI-PVLIAIDQYN  343 (404)
Q Consensus       317 ~~v~~aLl~EL~~q~~~-PVLvAVD~~N  343 (404)
                      +..|..++++....+++ |++|.|-+.+
T Consensus       149 ~~~f~~~L~~~l~~~~~~PlV~iiSe~~  176 (519)
T PF03215_consen  149 TSRFREALRQYLRSSRCLPLVFIISETE  176 (519)
T ss_pred             HHHHHHHHHHHHHcCCCCCEEEEEeccc
Confidence            36788888998888888 9999998654

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=89.46  E-value=0.26  Score=45.25  Aligned_cols=27  Identities=33%  Similarity=0.187  Sum_probs=23.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      -++++.|..|+|||+++.+++.+-...
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~~~~~   32 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGDEFPE   32 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcCcCcc
Confidence            369999999999999999999876653

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=89.42  E-value=0.48  Score=48.54  Aligned_cols=38  Identities=32%  Similarity=0.323  Sum_probs=30.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH-hCCeEEEEecCcccc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR-EEGWLVLYVPRGREW  230 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL~IP~a~~w  230 (404)
                      .+|.|..|+|||++...+..+.. ..||-|..+..-..+
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~l~~~~g~~v~~~~~Dd~i   40 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSATLRRERGWAVAVITYDDII   40 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhccCCeEEEEcccccc
Confidence            58999999999999999988876 689988777554433

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.

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=89.42  E-value=0.19  Score=51.48  Aligned_cols=97  Identities=14%  Similarity=0.161  Sum_probs=53.4

Q ss_pred             cccCCCccccCccccceeEEeCHHHHHhhccC---CCCcchhhhccccCceeEEEchhHHHHHHHHHHhcCCCccCCCCC
Q 045329          111 FTKTTSLSLLTRKDACTYFKFSEDELNAMLPE---GLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGP  187 (404)
Q Consensus       111 ~~~~~~~~~ht~~~vGk~y~~p~e~~k~l~~~---GLp~~~~kqfe~f~~p~~LVRk~tleLi~~L~~~~d~~~~std~~  187 (404)
                      |.+..+....+..++.++..++.+...+++..   .++..+..--+.+.....+.|=+|-  +..|.+.+....     +
T Consensus        49 ~~T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~~~~~~~~~~ta~~~~~~~~~~~~i~tG--~~~LD~lL~GG~-----~  121 (342)
T PLN03186         49 IHTVESLAYAPKKDLLQIKGISEAKVEKILEAASKLVPLGFTTASQLHAQRQEIIQITTG--SRELDKILEGGI-----E  121 (342)
T ss_pred             CCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHhcccccchHHHHhhcccCcceeCCC--CHHHHHhhcCCC-----c
Confidence            56666788888889999999998877654332   2332222111122111111111110  122333332211     1


Q ss_pred             ccceeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          188 KIRKQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       188 ~~r~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      . ..-+.|+|++|||||.+..|+...+.
T Consensus       122 ~-g~i~~i~G~~g~GKT~l~~~l~~~~~  148 (342)
T PLN03186        122 T-GSITEIYGEFRTGKTQLCHTLCVTCQ  148 (342)
T ss_pred             C-ceEEEEECCCCCCccHHHHHHHHHhh
Confidence            1 12378999999999999998876654

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=89.36  E-value=0.45  Score=53.41  Aligned_cols=33  Identities=24%  Similarity=0.169  Sum_probs=29.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|+|.+|||||++|..++..+..+|+-|+.+
T Consensus       370 ~~il~G~aGTGKTtll~~i~~~~~~~g~~V~~~  402 (744)
T TIGR02768       370 IAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGA  402 (744)
T ss_pred             EEEEEecCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            479999999999999999999888888877665

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=89.34  E-value=0.48  Score=51.44  Aligned_cols=40  Identities=18%  Similarity=0.220  Sum_probs=30.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTH  232 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvn  232 (404)
                      ++++|+.||||||+|..++.+.-..+--|+.|=++-++..
T Consensus       319 ilv~G~tGSGKTTtl~a~l~~~~~~~~~i~tiEdpvE~~~  358 (564)
T TIGR02538       319 VLVTGPTGSGKTVSLYTALNILNTEEVNISTAEDPVEINL  358 (564)
T ss_pred             EEEECCCCCCHHHHHHHHHHhhCCCCceEEEecCCceecC
Confidence            7899999999999998888876444445666666655543

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=89.31  E-value=0.85  Score=46.54  Aligned_cols=39  Identities=18%  Similarity=0.245  Sum_probs=28.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWT  231 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wv  231 (404)
                      .+++.|+.|||||++|..++.+-. ...=++.|-+..++.
T Consensus       180 ~ili~G~tGsGKTTll~al~~~i~-~~~riv~iEd~~El~  218 (340)
T TIGR03819       180 AFLISGGTGSGKTTLLSALLALVA-PDERIVLVEDAAELR  218 (340)
T ss_pred             eEEEECCCCCCHHHHHHHHHccCC-CCCcEEEECCcceec
Confidence            499999999999999987776543 334455666665553

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=89.26  E-value=0.52  Score=48.92  Aligned_cols=27  Identities=33%  Similarity=0.343  Sum_probs=23.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ng  218 (404)
                      -++|.|+.|+|||++++.+.+++. ..|
T Consensus       139 ii~lvGptGvGKTTtiakLA~~~~~~~G  166 (374)
T PRK14722        139 VFALMGPTGVGKTTTTAKLAARCVMRFG  166 (374)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcC
Confidence            489999999999999999998764 445

>cd04140 ARHI_like ARHI subfamily

Probab=89.25  E-value=0.35  Score=42.52  Aligned_cols=20  Identities=30%  Similarity=0.318  Sum_probs=18.1

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++.|.+|+|||+++.+++
T Consensus         3 kv~~vG~~~vGKTsli~~~~   22 (165)
T cd04140           3 RVVVFGAGGVGKSSLVLRFV   22 (165)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            58999999999999998765

ARHI (A Ras homolog member I) is a member of the Ras family with several unique structural and functional properties. ARHI is expressed in normal human ovarian and breast tissue, but its expression is decreased or eliminated in breast and ovarian cancer. ARHI contains an N-terminal extension of 34 residues (human) that is required to retain its tumor suppressive activity. Unlike most other Ras family members, ARHI is maintained in the constitutively active (GTP-bound) state in resting cells and has modest GTPase activity. ARHI inhibits STAT3 (signal transducers and activators of transcription 3), a latent transcription factor whose abnormal activation plays a critical role in oncogenesis. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to

>cd01864 Rab19 Rab19 subfamily

Probab=89.24  E-value=0.35  Score=42.32  Aligned_cols=22  Identities=23%  Similarity=0.270  Sum_probs=19.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++++.|+.|+|||+++.++..
T Consensus         4 ~kv~vvG~~~~GKTsli~~l~~   25 (165)
T cd01864           4 FKIILIGDSNVGKTCVVQRFKS   25 (165)
T ss_pred             eEEEEECCCCCCHHHHHHHHhh
Confidence            3589999999999999998754

Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=89.23  E-value=0.33  Score=44.67  Aligned_cols=22  Identities=23%  Similarity=0.234  Sum_probs=19.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .++|.|+.|||||+++..+...
T Consensus         5 ~i~l~G~sGsGKSTl~~~la~~   26 (176)
T PRK09825          5 SYILMGVSGSGKSLIGSKIAAL   26 (176)
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            4899999999999999877664

>TIGR03689 pup_AAA proteasome ATPase

Probab=89.22  E-value=0.4  Score=51.67  Aligned_cols=22  Identities=32%  Similarity=0.667  Sum_probs=17.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++|+|++|||||++...+..
T Consensus       217 ~GILLyGPPGTGKT~LAKAlA~  238 (512)
T TIGR03689       217 KGVLLYGPPGCGKTLIAKAVAN  238 (512)
T ss_pred             cceEEECCCCCcHHHHHHHHHH
Confidence            4699999999999986544443

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.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=89.10  E-value=0.8  Score=45.04  Aligned_cols=19  Identities=16%  Similarity=0.170  Sum_probs=15.5

Q ss_pred             EEEECCCCCcHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav  211 (404)
                      ++|+|++|+|||+++..+.
T Consensus        46 lll~G~~G~GKT~la~~l~   64 (316)
T PHA02544         46 LLHSPSPGTGKTTVAKALC   64 (316)
T ss_pred             EEeeCcCCCCHHHHHHHHH
Confidence            6669999999999865553

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=89.04  E-value=0.84  Score=39.83  Aligned_cols=35  Identities=20%  Similarity=0.447  Sum_probs=25.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC---eEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG---WLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng---WIVL~IP~  226 (404)
                      .+++.|+.|+|||.+....+.....++   -+++-+|.
T Consensus        16 ~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~   53 (169)
T PF00270_consen   16 NVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPT   53 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESS
T ss_pred             CEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeec
Confidence            389999999999999987776555443   34444454

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>TIGR00959 ffh signal recognition particle protein

Probab=89.02  E-value=0.56  Score=49.44  Aligned_cols=33  Identities=30%  Similarity=0.385  Sum_probs=27.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL~I  224 (404)
                      -+++.|.+|+|||++.+.+..++. ++|.=|+.|
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV  134 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLV  134 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEE
Confidence            488999999999999999999866 567766655

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.

>PRK06217 hypothetical protein; Validated

Probab=88.98  E-value=0.39  Score=43.88  Aligned_cols=31  Identities=19%  Similarity=0.082  Sum_probs=23.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +++|.|..|||||++-.++...   -|+-+++.-
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~---l~~~~~~~D   33 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAER---LDIPHLDTD   33 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---cCCcEEEcC
Confidence            5999999999999988777653   365555543

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=88.98  E-value=0.37  Score=51.15  Aligned_cols=32  Identities=25%  Similarity=0.397  Sum_probs=21.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +.++|+|++|||||++..-+.   .+-+.-++++.
T Consensus        89 ~giLL~GppGtGKT~la~alA---~~~~~~~~~i~  120 (495)
T TIGR01241        89 KGVLLVGPPGTGKTLLAKAVA---GEAGVPFFSIS  120 (495)
T ss_pred             CcEEEECCCCCCHHHHHHHHH---HHcCCCeeecc
Confidence            459999999999999876553   33344444443

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.

>PRK06547 hypothetical protein; Provisional

Probab=88.93  E-value=0.48  Score=43.59  Aligned_cols=31  Identities=19%  Similarity=0.361  Sum_probs=23.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..++|+|..|||||++...+..-   -|+.+++.
T Consensus        16 ~~i~i~G~~GsGKTt~a~~l~~~---~~~~~~~~   46 (172)
T PRK06547         16 ITVLIDGRSGSGKTTLAGALAAR---TGFQLVHL   46 (172)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH---hCCCeecc
Confidence            45899999999999998776653   35555544

>KOG0086 consensus GTPase Rab4, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.92  E-value=0.32  Score=45.02  Aligned_cols=24  Identities=21%  Similarity=0.220  Sum_probs=21.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      ++++.|+.|+|||++|.|.+.--+
T Consensus        11 Kfl~iG~aGtGKSCLLh~Fie~kf   34 (214)
T KOG0086|consen   11 KFLVIGSAGTGKSCLLHQFIENKF   34 (214)
T ss_pred             eeEEeccCCCChhHHHHHHHHhhh
Confidence            389999999999999999987655

>cd04114 Rab30 Rab30 subfamily

Probab=88.91  E-value=0.39  Score=41.96  Aligned_cols=22  Identities=27%  Similarity=0.303  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++++.|..|||||+++.++..
T Consensus         8 ~~v~v~G~~~~GKSsli~~l~~   29 (169)
T cd04114           8 FKIVLIGNAGVGKTCLVRRFTQ   29 (169)
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999999764

Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>cd04117 Rab15 Rab15 subfamily

Probab=88.87  E-value=0.38  Score=42.38  Aligned_cols=20  Identities=25%  Similarity=0.365  Sum_probs=18.0

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++.|++|+|||+++.+.+
T Consensus         2 ki~vvG~~~~GKTsli~~~~   21 (161)
T cd04117           2 RLLLIGDSGVGKTCLLCRFT   21 (161)
T ss_pred             EEEEECcCCCCHHHHHHHHh
Confidence            48999999999999998875

Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to

>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]

Probab=88.85  E-value=0.31  Score=48.03  Aligned_cols=25  Identities=24%  Similarity=0.302  Sum_probs=21.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE  216 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~  216 (404)
                      +++|+|+.|+|||++|.-+..+=..
T Consensus        59 ~W~I~G~NGsGKTTLL~ll~~~~~p   83 (257)
T COG1119          59 HWAIVGPNGAGKTTLLSLLTGEHPP   83 (257)
T ss_pred             cEEEECCCCCCHHHHHHHHhcccCC
Confidence            5999999999999999988876443

>TIGR03598 GTPase_YsxC ribosome biogenesis GTP-binding protein YsxC/EngB

Probab=88.81  E-value=0.41  Score=43.08  Aligned_cols=22  Identities=27%  Similarity=0.374  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||++++++..
T Consensus        19 ~~i~ivG~~~~GKStlin~l~~   40 (179)
T TIGR03598        19 PEIAFAGRSNVGKSSLINALTN   40 (179)
T ss_pred             CEEEEEcCCCCCHHHHHHHHhC
Confidence            5799999999999999998764

Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes.

>cd04123 Rab21 Rab21 subfamily

Probab=88.79  E-value=0.41  Score=40.98  Aligned_cols=21  Identities=29%  Similarity=0.294  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|..|+|||+++.+++.
T Consensus         2 ki~i~G~~~~GKStli~~l~~   22 (162)
T cd04123           2 KVVLLGEGRVGKTSLVLRYVE   22 (162)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999988875

The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site

>cd04134 Rho3 Rho3 subfamily

Probab=88.75  E-value=0.38  Score=43.78  Aligned_cols=21  Identities=29%  Similarity=0.562  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|+.|||||+++.+...
T Consensus         2 kivivG~~~vGKTsli~~~~~   22 (189)
T cd04134           2 KVVVLGDGACGKTSLLNVFTR   22 (189)
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999998764

Rho3 is a member of the Rho family found only in fungi. Rho3 is believed to regulate cell polarity by interacting with the diaphanous/formin family protein For3 to control both the actin cytoskeleton and microtubules. Rho3 is also believed to have a direct role in exocytosis that is independent of its role in regulating actin polarity. The function in exocytosis may be two-pronged: first, in the transport of post-Golgi vesicles from the mother cell to the bud, mediated by myosin (Myo2); second, in the docking and fusion of vesicles to the plasma membrane, mediated by an exocyst (Exo70) protein. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.

>PRK14528 adenylate kinase; Provisional

Probab=88.75  E-value=0.43  Score=44.00  Aligned_cols=30  Identities=20%  Similarity=0.284  Sum_probs=21.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++++.|++|||||++...+.   ..-|+.++.+
T Consensus         3 ~i~i~G~pGsGKtt~a~~la---~~~~~~~is~   32 (186)
T PRK14528          3 NIIFMGPPGAGKGTQAKILC---ERLSIPQIST   32 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHH---HHhCCCeeeC
Confidence            59999999999999876653   2236555444

>PTZ00132 GTP-binding nuclear protein Ran; Provisional

Probab=88.75  E-value=0.39  Score=44.56  Aligned_cols=22  Identities=18%  Similarity=0.191  Sum_probs=18.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|+.|||||+++.+.+.
T Consensus        10 ~kv~liG~~g~GKTtLi~~~~~   31 (215)
T PTZ00132         10 FKLILVGDGGVGKTTFVKRHLT   31 (215)
T ss_pred             ceEEEECCCCCCHHHHHHHHHh
Confidence            4599999999999999976553

>cd01865 Rab3 Rab3 subfamily

Probab=88.71  E-value=0.4  Score=42.15  Aligned_cols=21  Identities=19%  Similarity=0.265  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++-|+.|+|||+++.+++.
T Consensus         3 ki~i~G~~~~GKSsli~~l~~   23 (165)
T cd01865           3 KLLIIGNSSVGKTSFLFRYAD   23 (165)
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999988764

The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promot

>cd04122 Rab14 Rab14 subfamily

Probab=88.70  E-value=0.4  Score=42.10  Aligned_cols=21  Identities=24%  Similarity=0.379  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|..|||||+++.++..
T Consensus         4 ki~iiG~~~vGKTsli~~~~~   24 (166)
T cd04122           4 KYIIIGDMGVGKSCLLHQFTE   24 (166)
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999998753

Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GT

>PRK05416 glmZ(sRNA)-inactivating NTPase; Provisional

Probab=88.69  E-value=0.47  Score=47.41  Aligned_cols=33  Identities=21%  Similarity=0.305  Sum_probs=26.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      -++|+|..|||||+++..+-    ..||.++.-+...
T Consensus         8 ~i~i~G~~GsGKtt~~~~l~----~~g~~~~d~~~~~   40 (288)
T PRK05416          8 LVIVTGLSGAGKSVALRALE----DLGYYCVDNLPPS   40 (288)
T ss_pred             EEEEECCCCCcHHHHHHHHH----HcCCeEECCcCHH
Confidence            48999999999999998873    5588887655444

>cd04127 Rab27A Rab27a subfamily

Probab=88.68  E-value=0.4  Score=42.52  Aligned_cols=23  Identities=17%  Similarity=0.056  Sum_probs=19.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -++++.|+.|||||+++.+....
T Consensus         5 ~ki~ivG~~~vGKTsli~~~~~~   27 (180)
T cd04127           5 IKFLALGDSGVGKTSFLYQYTDN   27 (180)
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            35999999999999999887653

The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated

>cd04135 Tc10 TC10 subfamily

Probab=88.68  E-value=0.41  Score=42.14  Aligned_cols=21  Identities=24%  Similarity=0.268  Sum_probs=18.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|..|+|||+++.+...
T Consensus         2 ki~i~G~~~~GKTsl~~~~~~   22 (174)
T cd04135           2 KCVVVGDGAVGKTCLLMSYAN   22 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999977654

TC10 is a Rho family protein that has been shown to induce microspike formation and neurite outgrowth in vitro. Its expression changes dramatically after peripheral nerve injury, suggesting an important role in promoting axonal outgrowth and regeneration. TC10 regulates translocation of insulin-stimulated GLUT4 in adipocytes and has also been shown to bind directly to Golgi COPI coat proteins. GTP-bound TC10 in vitro can bind numerous potential effectors. Depending on its subcellular localization and distinct functional domains, TC10 can differentially regulate two types of filamentous actin in adipocytes. TC10 mRNAs are highly expressed in three types of mouse muscle tissues: leg skeletal muscle, cardiac muscle, and uterus; they were also present in brain, with higher levels in adults than in newborns. TC10 has also been shown to play a role in regulating the expression of cystic fibrosis transmembrane conductance regulator (CFTR) through interacti

>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=88.68  E-value=0.51  Score=40.93  Aligned_cols=29  Identities=28%  Similarity=0.323  Sum_probs=22.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|.|.+|||||++...+..   .-||..+..
T Consensus         2 i~l~G~~GsGKstla~~la~---~l~~~~~~~   30 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAK---ALGLPFVDL   30 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHH---HhCCCEEEc
Confidence            79999999999999877743   337776643

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.

>cd04118 Rab24 Rab24 subfamily

Probab=88.67  E-value=0.41  Score=43.21  Aligned_cols=21  Identities=29%  Similarity=0.442  Sum_probs=19.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|..|+|||+++.+++.
T Consensus         2 ki~vvG~~~vGKSsLi~~~~~   22 (193)
T cd04118           2 KVVMLGKESVGKTSLVERYVH   22 (193)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            589999999999999999874

Rab24 is distinct from other Rabs in several ways. It exists primarily in the GTP-bound state, having a low intrinsic GTPase activity; it is not efficiently geranyl-geranylated at the C-terminus; it does not form a detectable complex with Rab GDP-dissociation inhibitors (GDIs); and it has recently been shown to undergo tyrosine phosphorylation when overexpressed in vitro. The specific function of Rab24 still remains unknown. It is found in a transport route between ER-cis-Golgi and late endocytic compartments. It is putatively involved in an autophagic pathway, possibly directing misfolded proteins in the ER to degradative pathways. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilita

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=88.66  E-value=0.63  Score=51.12  Aligned_cols=30  Identities=13%  Similarity=0.076  Sum_probs=24.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLV  221 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIV  221 (404)
                      .|+++|++|+|||++..-+..+....+|..
T Consensus        40 A~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~   69 (605)
T PRK05896         40 AYIFSGPRGIGKTSIAKIFAKAINCLNPKD   69 (605)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhcCCCCCC
Confidence            499999999999998877777666666643

>cd04157 Arl6 Arl6 subfamily

Probab=88.64  E-value=0.34  Score=41.78  Aligned_cols=21  Identities=24%  Similarity=0.268  Sum_probs=18.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|..|||||+++.++..
T Consensus         1 ~i~~vG~~~~GKTsl~~~l~~   21 (162)
T cd04157           1 NILVVGLDNSGKTTIINQLKP   21 (162)
T ss_pred             CEEEECCCCCCHHHHHHHHcc
Confidence            378999999999999988764

Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that A

>PRK14526 adenylate kinase; Provisional

Probab=88.64  E-value=0.43  Score=45.38  Aligned_cols=29  Identities=24%  Similarity=0.382  Sum_probs=20.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      +++|.|++|||||++...+.   ..-||..+.
T Consensus         2 ~i~l~G~pGsGKsT~a~~La---~~~~~~~is   30 (211)
T PRK14526          2 KLVFLGPPGSGKGTIAKILS---NELNYYHIS   30 (211)
T ss_pred             EEEEECCCCCCHHHHHHHHH---HHhCCceee
Confidence            48999999999999876654   233554443

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=88.61  E-value=0.51  Score=46.07  Aligned_cols=30  Identities=17%  Similarity=0.015  Sum_probs=23.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~I  224 (404)
                      -++|.|.+|||||++-.++..   .. +|++|..
T Consensus         4 liil~G~pGSGKSTla~~L~~---~~~~~~~l~~   34 (300)
T PHA02530          4 IILTVGVPGSGKSTWAREFAA---KNPKAVNVNR   34 (300)
T ss_pred             EEEEEcCCCCCHHHHHHHHHH---HCCCCEEEec
Confidence            388999999999998877543   33 7877754

>PRK14527 adenylate kinase; Provisional

Probab=88.58  E-value=0.35  Score=44.37  Aligned_cols=30  Identities=30%  Similarity=0.365  Sum_probs=22.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .+++.|++|||||++..++   |.+.|+..+..
T Consensus         8 ~i~i~G~pGsGKsT~a~~L---a~~~~~~~is~   37 (191)
T PRK14527          8 VVIFLGPPGAGKGTQAERL---AQELGLKKLST   37 (191)
T ss_pred             EEEEECCCCCCHHHHHHHH---HHHhCCCCCCc
Confidence            5999999999999987776   33446655443

>cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains

Probab=88.57  E-value=0.44  Score=44.67  Aligned_cols=21  Identities=19%  Similarity=0.376  Sum_probs=17.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      ++|.|+.|+|||++|. ++.||
T Consensus        25 ~~i~G~NGsGKTTLl~-ai~~~   45 (204)
T cd03240          25 TLIVGQNGAGKTTIIE-ALKYA   45 (204)
T ss_pred             EEEECCCCCCHHHHHH-HHHHH
Confidence            7999999999999995 55544

The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.

>COG3523 IcmF Type VI protein secretion system component VasK [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.56  E-value=0.56  Score=55.06  Aligned_cols=136  Identities=20%  Similarity=0.208  Sum_probs=73.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH---HHHhCCeEEEEec---CcccccccC-eeecCCCCCCccCH-----HHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH---WAREEGWLVLYVP---RGREWTHGG-YFYKNPQTGLWDTP-----LQAENVLKDFI  259 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~---~A~~ngWIVL~IP---~a~~wvng~-~~y~~~~~g~ydQP-----~~A~~~Lk~fl  259 (404)
                      =|++.|++|||||++|...-.   ++..-|=.-+-.+   +|. |--+. ..+-+ ..|+|..+     ....+|+.-+ 
T Consensus       127 Wy~viG~pgsGKTtal~~sgl~Fpl~~~~~~~~~~~~gT~~cd-wwf~deaVlID-taGry~~q~s~~~~~~~~W~~fL-  203 (1188)
T COG3523         127 WYMVIGPPGSGKTTALLNSGLQFPLAEQMGALGLAGPGTRNCD-WWFTDEAVLID-TAGRYITQDSADEVDRAEWLGFL-  203 (1188)
T ss_pred             ceEEecCCCCCcchHHhcccccCcchhhhccccccCCCCcccC-cccccceEEEc-CCcceecccCcchhhHHHHHHHH-
Confidence            389999999999999976432   2222222222222   222 32111 11112 36888888     6678887655 


Q ss_pred             HHhHHHHhcCCcccccCCCCCCCCccccccCCCccccCCCCCHHHHHHhhcccccchHHHHHHHHHHHhc--CCCCcEEE
Q 045329          260 KYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQMGINQMHASVGVVVRLRKELSL--VKDIPVLI  337 (404)
Q Consensus       260 ~~N~~~LkkLkls~~~~~~lge~~~~~w~K~~d~~~~p~g~tL~DLv~~Gi~~~~~A~~v~~aLl~EL~~--q~~~PVLv  337 (404)
                          ..|++..-.+  ++.     |+.++           .++.||...--......+.++-.=++||..  +-++||.|
T Consensus       204 ----~lLkk~R~~~--piN-----Giilt-----------lsv~~L~~~~~~~~~~~~~~LR~RL~El~~tL~~~~PVYl  261 (1188)
T COG3523         204 ----GLLKKYRRRR--PLN-----GIILT-----------LSVSDLLTADPAEREALARTLRARLQELRETLHARLPVYL  261 (1188)
T ss_pred             ----HHHHHhccCC--CCc-----eEEEE-----------EEHHHHcCCCHHHHHHHHHHHHHHHHHHHHhhccCCceEE
Confidence                4555542211  211     12221           345566543222222235567666788887  67999988


Q ss_pred             EEeCcccccCcCCcC
Q 045329          338 AIDQYNNWFTFSEYE  352 (404)
Q Consensus       338 AVD~~Nalf~~S~Y~  352 (404)
                      .+=...-+.++.+|.
T Consensus       262 ~lTk~Dll~GF~efF  276 (1188)
T COG3523         262 VLTKADLLPGFEEFF  276 (1188)
T ss_pred             EEecccccccHHHHH
Confidence            876665555555553

>cd04125 RabA_like RabA-like subfamily

Probab=88.55  E-value=0.41  Score=43.22  Aligned_cols=21  Identities=29%  Similarity=0.384  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|+.|||||+++.++..
T Consensus         2 ki~v~G~~~vGKSsli~~~~~   22 (188)
T cd04125           2 KVVIIGDYGVGKSSLLKRFTE   22 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999999874

RabA was first identified in D. discoideum, where its expression levels were compared to other Rabs in growing and developing cells. The RabA mRNA levels were below the level of detection by Northern blot analysis, suggesting a very low level of expression. The function of RabA remains unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.

>cd03234 ABCG_White The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors

Probab=88.54  E-value=0.38  Score=45.21  Aligned_cols=31  Identities=16%  Similarity=0.273  Sum_probs=24.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH----hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR----EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~----~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.-.    ..|-|.+
T Consensus        35 ~~~l~G~nGsGKSTLlk~l~G~~~~~~~~~G~i~~   69 (226)
T cd03234          35 VMAILGSSGSGKTTLLDAISGRVEGGGTTSGQILF   69 (226)
T ss_pred             EEEEECCCCCCHHHHHHHHhCccCCCCCCceEEEE
Confidence            489999999999999987776543    5676654

The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in

>PRK14730 coaE dephospho-CoA kinase; Provisional

Probab=88.54  E-value=0.6  Score=43.62  Aligned_cols=35  Identities=26%  Similarity=0.354  Sum_probs=26.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTH  232 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvn  232 (404)
                      .+.|+|..|||||++..++...   -|+.|+   ++..+.+
T Consensus         3 ~i~itG~~gsGKst~~~~l~~~---~g~~~i---~~D~~~~   37 (195)
T PRK14730          3 RIGLTGGIASGKSTVGNYLAQQ---KGIPIL---DADIYAR   37 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHHHh---hCCeEe---eCcHHHH
Confidence            5899999999999998876643   277776   4555543

>PRK14731 coaE dephospho-CoA kinase; Provisional

Probab=88.50  E-value=0.5  Score=44.45  Aligned_cols=28  Identities=21%  Similarity=0.278  Sum_probs=22.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      .+.|+|..|||||+++..+..    .|+-|+.
T Consensus         7 ~igitG~igsGKSt~~~~l~~----~g~~v~d   34 (208)
T PRK14731          7 LVGVTGGIGSGKSTVCRFLAE----MGCELFE   34 (208)
T ss_pred             EEEEECCCCCCHHHHHHHHHH----CCCeEEe
Confidence            377999999999999887664    4777766

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=88.48  E-value=0.66  Score=46.03  Aligned_cols=33  Identities=24%  Similarity=0.223  Sum_probs=29.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.+.|.+||||||++.+++....+.| -|.+|=.
T Consensus         4 i~i~G~~gSGKTTLi~~Li~~L~~~G-~V~~IKh   36 (274)
T PRK14493          4 LSIVGYKATGKTTLVERLVDRLSGRG-RVGTVKH   36 (274)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhCC-CEEEEEE
Confidence            78899999999999999999999988 6777743

>cd01895 EngA2 EngA2 subfamily

Probab=88.47  E-value=0.42  Score=41.14  Aligned_cols=22  Identities=27%  Similarity=0.277  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.+++.
T Consensus         3 ~~i~i~G~~~~GKstli~~l~~   24 (174)
T cd01895           3 IRIAIIGRPNVGKSSLVNALLG   24 (174)
T ss_pred             cEEEEEcCCCCCHHHHHHHHhC
Confidence            3599999999999999998863

This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=88.47  E-value=0.37  Score=46.75  Aligned_cols=25  Identities=32%  Similarity=0.465  Sum_probs=20.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      .+++|.|++||||||++.++--...
T Consensus        31 e~~~i~G~nGsGKSTL~~~l~GLl~   55 (235)
T COG1122          31 ERVLLIGPNGSGKSTLLKLLNGLLK   55 (235)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCcCc
Confidence            3589999999999999988765544

>PRK13342 recombination factor protein RarA; Reviewed

Probab=88.45  E-value=0.59  Score=48.52  Aligned_cols=31  Identities=19%  Similarity=0.280  Sum_probs=21.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      .++|+|++|||||++...+... ....|+.+.
T Consensus        38 ~ilL~GppGtGKTtLA~~ia~~-~~~~~~~l~   68 (413)
T PRK13342         38 SMILWGPPGTGKTTLARIIAGA-TDAPFEALS   68 (413)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH-hCCCEEEEe
Confidence            4899999999999887766433 233444443

>cd01858 NGP_1 NGP-1

Probab=88.45  E-value=0.64  Score=41.15  Aligned_cols=43  Identities=16%  Similarity=0.070  Sum_probs=27.3

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHH
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ..-+|++.+.+..+..     ......++.+.|.+|+|||++++.+..
T Consensus        82 ~~~~L~~~l~~~~~~~-----~~~~~~~v~~~G~~nvGKStliN~l~~  124 (157)
T cd01858          82 GKGSLIQLLRQFSKLH-----SDKKQISVGFIGYPNVGKSSIINTLRS  124 (157)
T ss_pred             cHHHHHHHHHHHHhhh-----ccccceEEEEEeCCCCChHHHHHHHhc
Confidence            3455666666543210     001123477999999999999999863

Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with NKXD motif) are relocated to the N terminus.

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=88.45  E-value=0.34  Score=48.40  Aligned_cols=23  Identities=22%  Similarity=0.432  Sum_probs=18.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ++++|||++||||+|+.--+.++
T Consensus       190 rgvllygppg~gktml~kava~~  212 (408)
T KOG0727|consen  190 RGVLLYGPPGTGKTMLAKAVANH  212 (408)
T ss_pred             cceEEeCCCCCcHHHHHHHHhhc
Confidence            46999999999999876544443

>cd03260 ABC_PstB_phosphate_transporter Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient

Probab=88.31  E-value=0.52  Score=44.16  Aligned_cols=31  Identities=39%  Similarity=0.564  Sum_probs=25.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH------HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA------REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A------~~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.-      ...|.|.+
T Consensus        28 ~~~i~G~nGsGKSTLl~~i~G~~~~~~~~~~~G~i~~   64 (227)
T cd03260          28 ITALIGPSGCGKSTLLRLLNRLNDLIPGAPDEGEVLL   64 (227)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhcccccCCCCCeEEEE
Confidence            48999999999999998777654      35688765

The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space. P stA and PstC are hydrophobic and they form the transmembrane portion of the Pst system. PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein. PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD).

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=88.30  E-value=1  Score=40.17  Aligned_cols=39  Identities=21%  Similarity=0.296  Sum_probs=26.8

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHH
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .|.++.+.|-+.+.+        .  .-++|.|+-|+|||++...++..
T Consensus         7 ~t~~l~~~l~~~l~~--------~--~~i~l~G~lGaGKTtl~~~l~~~   45 (133)
T TIGR00150         7 AMDKFGKAFAKPLDF--------G--TVVLLKGDLGAGKTTLVQGLLQG   45 (133)
T ss_pred             HHHHHHHHHHHhCCC--------C--CEEEEEcCCCCCHHHHHHHHHHH
Confidence            566777766654321        1  24899999999999888666553

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.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=88.26  E-value=0.32  Score=47.32  Aligned_cols=31  Identities=29%  Similarity=0.393  Sum_probs=21.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      .++|.|+.||||||+|.-+-..= ...|-|.+
T Consensus        30 vv~iiGpSGSGKSTlLRclN~LE~~~~G~I~i   61 (240)
T COG1126          30 VVVIIGPSGSGKSTLLRCLNGLEEPDSGSITV   61 (240)
T ss_pred             EEEEECCCCCCHHHHHHHHHCCcCCCCceEEE
Confidence            37999999999999997655432 23455444

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=88.24  E-value=0.63  Score=52.05  Aligned_cols=36  Identities=28%  Similarity=0.386  Sum_probs=29.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC---eEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG---WLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng---WIVL~IP~a  227 (404)
                      -.+|+|.+|||||+++..++..+...|   .|++.-|.+
T Consensus       340 ~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg  378 (720)
T TIGR01448       340 VVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTG  378 (720)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCch
Confidence            489999999999999999999887776   466666653

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PRK08506 replicative DNA helicase; Provisional

Probab=88.18  E-value=0.59  Score=49.70  Aligned_cols=33  Identities=15%  Similarity=0.112  Sum_probs=29.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +||-|.+|+|||+++++++..|..+|+=|+++.
T Consensus       195 ivIaarpg~GKT~fal~ia~~~~~~g~~V~~fS  227 (472)
T PRK08506        195 IIIAARPSMGKTTLCLNMALKALNQDKGVAFFS  227 (472)
T ss_pred             EEEEcCCCCChHHHHHHHHHHHHhcCCcEEEEe
Confidence            899999999999999999998888899888873

>cd04106 Rab23_lke Rab23-like subfamily

Probab=88.17  E-value=0.46  Score=41.08  Aligned_cols=21  Identities=24%  Similarity=0.360  Sum_probs=18.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|.+|+|||+++.++..
T Consensus         2 kv~~vG~~~~GKTsl~~~~~~   22 (162)
T cd04106           2 KVIVVGNGNVGKSSMIQRFVK   22 (162)
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999988764

Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signalling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with G

>COG1162 Predicted GTPases [General function prediction only]

Probab=88.16  E-value=0.44  Score=48.06  Aligned_cols=146  Identities=23%  Similarity=0.227  Sum_probs=74.9

Q ss_pred             hccccCceeEEEchhHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHh-CCeEEEEecCccc
Q 045329          151 EFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWARE-EGWLVLYVPRGRE  229 (404)
Q Consensus       151 qfe~f~~p~~LVRk~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~-ngWIVL~IP~a~~  229 (404)
                      ..+.++-+.+++...+-+-+..|...+..           +-.+|.|+.|+|||++++.+.--... -|=|==..-.++.
T Consensus       136 ~y~~~gy~v~~~s~~~~~~~~~l~~~l~~-----------~~svl~GqSGVGKSSLiN~L~p~~~~~t~eIS~~~~rGkH  204 (301)
T COG1162         136 EYEDIGYPVLFVSAKNGDGLEELAELLAG-----------KITVLLGQSGVGKSTLINALLPELNQKTGEISEKLGRGRH  204 (301)
T ss_pred             HHHhCCeeEEEecCcCcccHHHHHHHhcC-----------CeEEEECCCCCcHHHHHHhhCchhhhhhhhhcccCCCCCC
Confidence            34567778888884433333333333211           13699999999999999998753221 1222111111111


Q ss_pred             cc---------ccCeeecCC---CCCC-ccCHHHHHHHHHHHHHHhHHHHhcCCcccccCCCCCCCCccccccCCCcccc
Q 045329          230 WT---------HGGYFYKNP---QTGL-WDTPLQAENVLKDFIKYNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEI  296 (404)
Q Consensus       230 wv---------ng~~~y~~~---~~g~-ydQP~~A~~~Lk~fl~~N~~~LkkLkls~~~~~~lge~~~~~w~K~~d~~~~  296 (404)
                      =|         +|+.-+-.|   .-|+ ..+|.....-...|...    +.+-+-..        .          ...-
T Consensus       205 TTt~~~l~~l~~gG~iiDTPGf~~~~l~~~~~e~l~~~F~ef~~~----~~~CkFr~--------C----------~H~~  262 (301)
T COG1162         205 TTTHVELFPLPGGGWIIDTPGFRSLGLAHLEPEDLVQAFPEFAEL----ARQCKFRD--------C----------THTH  262 (301)
T ss_pred             ccceEEEEEcCCCCEEEeCCCCCccCcccCCHHHHHHHhHHHHHH----hcCCCCCC--------C----------CCCC
Confidence            11         111111111   2344 45555555444444332    22222111        0          0123


Q ss_pred             CCCCCHHHHHHhhcccccchHHHHHHHHHHHhcC
Q 045329          297 SEGSTLFDLVQMGINQMHASVGVVVRLRKELSLV  330 (404)
Q Consensus       297 p~g~tL~DLv~~Gi~~~~~A~~v~~aLl~EL~~q  330 (404)
                      ++|..+.+.++.|--.+.+ .+-...+++||..+
T Consensus       263 EPgCav~~av~~g~i~~~R-y~~Y~kll~el~~~  295 (301)
T COG1162         263 EPGCAVKAAVEEGEIAPER-YENYLKLLDELSGN  295 (301)
T ss_pred             CCCcHHHHHHHcCCCCHHH-HHHHHHHHHHHHhh
Confidence            4688888899888544333 46678899999854

>cd04164 trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes

Probab=88.15  E-value=0.47  Score=40.30  Aligned_cols=21  Identities=33%  Similarity=0.388  Sum_probs=18.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|+.|+|||+++..+..
T Consensus         3 ~i~l~G~~~~GKstli~~l~~   23 (157)
T cd04164           3 KVVIVGKPNVGKSSLLNALAG   23 (157)
T ss_pred             EEEEECCCCCCHHHHHHHHHC
Confidence            589999999999999987653

It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=88.14  E-value=0.57  Score=52.41  Aligned_cols=37  Identities=32%  Similarity=0.566  Sum_probs=30.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCe-EEEEecCc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGW-LVLYVPRG  227 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngW-IVL~IP~a  227 (404)
                      ..++|.|-.|||||++|.+++.+++..|. .|||=|.+
T Consensus       186 ~H~li~GttGSGKS~~i~~LL~~ir~RGdrAIIyD~~G  223 (732)
T PRK13700        186 QNFCLHGTVGAGKSEVIRRLANYARQRGDMVVIYDRSG  223 (732)
T ss_pred             cceEEeCCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCC
Confidence            46999999999999999999999998865 45554544

>cd00878 Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases

Probab=88.13  E-value=0.41  Score=41.45  Aligned_cols=21  Identities=29%  Similarity=0.252  Sum_probs=18.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|.+|||||+++.++..
T Consensus         1 ki~iiG~~~~GKssli~~~~~   21 (158)
T cd00878           1 RILILGLDGAGKTTILYKLKL   21 (158)
T ss_pred             CEEEEcCCCCCHHHHHHHHhc
Confidence            379999999999999888763

Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thu

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.12  E-value=0.79  Score=46.41  Aligned_cols=26  Identities=19%  Similarity=0.360  Sum_probs=21.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHh
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWARE  216 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~  216 (404)
                      +.|+|+|++|+|||++...+..+...
T Consensus        40 ~~~L~~G~~G~GKt~~a~~la~~l~~   65 (367)
T PRK14970         40 QALLFCGPRGVGKTTCARILARKINQ   65 (367)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            35999999999999888877666543

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=88.12  E-value=0.62  Score=49.57  Aligned_cols=33  Identities=21%  Similarity=0.251  Sum_probs=29.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|++|+|||+++.|+++.+..+|==|+||
T Consensus       275 ~~li~G~~G~GKT~l~~~~~~~~~~~g~~~~yi  307 (509)
T PRK09302        275 IILVSGATGTGKTLLASKFAEAACRRGERCLLF  307 (509)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEE
Confidence            478999999999999999999887777777777

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=88.07  E-value=0.6  Score=50.86  Aligned_cols=36  Identities=28%  Similarity=0.628  Sum_probs=29.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC-eEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG-WLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng-WIVL~IP~a  227 (404)
                      .+++.|..|||||+++.+++.|.+++| -+|++=|.+
T Consensus       178 h~li~G~tGsGKs~~i~~ll~~~~~~g~~~ii~D~~g  214 (566)
T TIGR02759       178 HILIHGTTGSGKSVAIRKLLRWIRQRGDRAIIYDKGC  214 (566)
T ss_pred             ceEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEECCC
Confidence            589999999999999999999998775 455555554

The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).

>cd04175 Rap1 Rap1 subgroup

Probab=88.01  E-value=0.48  Score=41.35  Aligned_cols=20  Identities=30%  Similarity=0.321  Sum_probs=17.6

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++.|.+|+|||+++..++
T Consensus         3 ki~~~G~~~~GKTsli~~~~   22 (164)
T cd04175           3 KLVVLGSGGVGKSALTVQFV   22 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            48999999999999987765

The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the n

>cd04110 Rab35 Rab35 subfamily

Probab=87.99  E-value=0.46  Score=43.70  Aligned_cols=22  Identities=23%  Similarity=0.246  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++++.|+.|+|||+++.++..
T Consensus         7 ~kivvvG~~~vGKTsli~~l~~   28 (199)
T cd04110           7 FKLLIIGDSGVGKSSLLLRFAD   28 (199)
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            3599999999999999988863

Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=87.99  E-value=0.69  Score=48.79  Aligned_cols=38  Identities=26%  Similarity=0.280  Sum_probs=27.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCccccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG  233 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvng  233 (404)
                      -+|+.||+||||+-++.+-+---+.+   ||+| +|..++..
T Consensus        19 FIvV~GPrGSGK~elV~d~~L~~r~~---vL~I-DC~~i~~a   56 (431)
T PF10443_consen   19 FIVVQGPRGSGKRELVMDHVLKDRKN---VLVI-DCDQIVKA   56 (431)
T ss_pred             EEEEECCCCCCccHHHHHHHHhCCCC---EEEE-EChHhhhc
Confidence            58999999999999985444444555   7777 45555553

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

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

Probab=87.98  E-value=0.54  Score=47.84  Aligned_cols=17  Identities=29%  Similarity=0.415  Sum_probs=15.1

Q ss_pred             eeEEEECCCCCcHHHHH
Q 045329          191 KQIVLDGPLCCGKSITL  207 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L  207 (404)
                      +.|++|||+|+|||.+.
T Consensus        58 p~~LFyGPpGTGKTSta   74 (346)
T KOG0989|consen   58 PHYLFYGPPGTGKTSTA   74 (346)
T ss_pred             ceEEeeCCCCCcHhHHH
Confidence            56999999999999875

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=87.97  E-value=0.43  Score=43.57  Aligned_cols=31  Identities=29%  Similarity=0.323  Sum_probs=23.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.-. ..|-|.+
T Consensus        20 ~~~i~G~nGsGKSTLl~~i~G~~~~~~G~i~~   51 (190)
T TIGR01166        20 VLALLGANGAGKSTLLLHLNGLLRPQSGAVLI   51 (190)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCceeEEE
Confidence            489999999999999976654422 4576654

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=87.96  E-value=0.86  Score=42.49  Aligned_cols=25  Identities=12%  Similarity=0.125  Sum_probs=22.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      +.+.|.|..|+|||+++.++++.+.
T Consensus        23 ~~i~~~G~~gsGKTTli~~l~~~~~   47 (207)
T TIGR00073        23 VVLNFMSSPGSGKTTLIEKLIDNLK   47 (207)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4589999999999999999988754

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>cd04176 Rap2 Rap2 subgroup

Probab=87.94  E-value=0.48  Score=41.22  Aligned_cols=21  Identities=29%  Similarity=0.308  Sum_probs=18.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|.+|+|||+++...+.
T Consensus         3 ki~i~G~~~vGKTsl~~~~~~   23 (163)
T cd04176           3 KVVVLGSGGVGKSALTVQFVS   23 (163)
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999866654

The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, incl

>PF04548 AIG1: AIG1 family; InterPro: IPR006703 This entry represents a domain found in Arabidopsis protein AIG1 which appears to be involved in plant resistance to bacteria

Probab=87.94  E-value=0.5  Score=44.43  Aligned_cols=20  Identities=30%  Similarity=0.293  Sum_probs=18.2

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      |+||.|+.|||||++.+.++
T Consensus         2 ~IlllG~tGsGKSs~~N~il   21 (212)
T PF04548_consen    2 RILLLGKTGSGKSSLGNSIL   21 (212)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            69999999999999988874

The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 (avrRpt2-induced gene) exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2 []. The domain is also apparently found in a number of mammalian proteins, for example the rat immune-associated nucleotide 4 protein. ; GO: 0005525 GTP binding; PDB: 3LXX_A 3BB4_A 3DEF_A 3BB3_A 2J3E_A 3V70_B 3BB1_A 1H65_B 2XTP_A 3P1J_C ....

>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=87.93  E-value=1  Score=44.81  Aligned_cols=76  Identities=22%  Similarity=0.318  Sum_probs=47.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEecCcccccccCeeecC--------CCCCCccCHHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVPRGREWTHGGYFYKN--------PQTGLWDTPLQAENVLKDFIK  260 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP~a~~wvng~~~y~~--------~~~g~ydQP~~A~~~Lk~fl~  260 (404)
                      .++=|||++|+|||+++..++.+-++.  .--||-|--..-++-| ...-+        .+++.|.-|+.++--|--+-.
T Consensus        30 ~~iGiTG~PGaGKSTli~~l~~~~~~~g~~VaVlAVDPSSp~tGG-AlLGDRiRM~~~~~d~~vfIRS~atRG~lGGls~  108 (266)
T PF03308_consen   30 HVIGITGPPGAGKSTLIDALIRELRERGKRVAVLAVDPSSPFTGG-ALLGDRIRMQELSRDPGVFIRSMATRGSLGGLSR  108 (266)
T ss_dssp             EEEEEEE-TTSSHHHHHHHHHHHHHHTT--EEEEEE-GGGGCC----SS--GGGCHHHHTSTTEEEEEE---SSHHHHHH
T ss_pred             eEEEeeCCCCCcHHHHHHHHHHHHhhcCCceEEEEECCCCCCCCC-cccccHHHhcCcCCCCCEEEeecCcCCCCCCccH
Confidence            468899999999999999999987766  4566666333344433 22111        368999999998888887766


Q ss_pred             HhHHHHh
Q 045329          261 YNESHLR  267 (404)
Q Consensus       261 ~N~~~Lk  267 (404)
                      +-.+.+.
T Consensus       109 ~t~~~v~  115 (266)
T PF03308_consen  109 ATRDAVR  115 (266)
T ss_dssp             HHHHHHH
T ss_pred             hHHHHHH
Confidence            5555444

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.

>cd00877 Ran Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases

Probab=87.90  E-value=0.48  Score=42.10  Aligned_cols=20  Identities=25%  Similarity=0.267  Sum_probs=18.0

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++.|+.|||||+++.+++
T Consensus         2 ki~vvG~~~vGKTsli~~~~   21 (166)
T cd00877           2 KLVLVGDGGTGKTTFVKRHL   21 (166)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            48999999999999998776

Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=87.89  E-value=1.1  Score=45.48  Aligned_cols=51  Identities=18%  Similarity=0.301  Sum_probs=33.0

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHh--CCeEEEEec
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWARE--EGWLVLYVP  225 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~--ngWIVL~IP  225 (404)
                      ...++++.++++..     ++.     -++|+|++||||+++...++.+...  .-+++|+-.
T Consensus         7 ~m~~~~~~~~~~a~-----~~~-----pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~   59 (329)
T TIGR02974         7 AFLEVLEQVSRLAP-----LDR-----PVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCA   59 (329)
T ss_pred             HHHHHHHHHHHHhC-----CCC-----CEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCC
Confidence            34566666766532     112     2899999999999965544444432  468888764

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

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=87.89  E-value=0.48  Score=42.88  Aligned_cols=29  Identities=34%  Similarity=0.491  Sum_probs=22.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      ++|.|.+|||||++...+..-. ...|+.+
T Consensus         5 i~l~G~~gsGKst~a~~l~~~~-~~~~~~~   33 (175)
T cd00227           5 IILNGGSSAGKSSIARALQSVL-AEPWLHF   33 (175)
T ss_pred             EEEECCCCCCHHHHHHHHHHhh-CCCcccc
Confidence            8999999999999988776553 2346544

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 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=87.87  E-value=0.51  Score=44.25  Aligned_cols=23  Identities=30%  Similarity=0.457  Sum_probs=19.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      +.++|.|+.|||||.+..++++-
T Consensus         4 ~~vlL~Gps~SGKTaLf~~L~~~   26 (181)
T PF09439_consen    4 PTVLLVGPSGSGKTALFSQLVNG   26 (181)
T ss_dssp             -EEEEE-STTSSHHHHHHHHHHS
T ss_pred             ceEEEEcCCCCCHHHHHHHHhcC
Confidence            46999999999999999998874

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 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>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=87.86  E-value=0.86  Score=41.54  Aligned_cols=32  Identities=25%  Similarity=0.216  Sum_probs=27.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.+.|..|||||+++..++......|+-|-.|
T Consensus         4 i~i~G~~gsGKTTli~~L~~~l~~~g~~V~~i   35 (159)
T cd03116           4 IGFVGYSGSGKTTLLEKLIPALSARGLRVAVI   35 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            78999999999999999999988888755444

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=87.84  E-value=0.51  Score=52.62  Aligned_cols=20  Identities=30%  Similarity=0.501  Sum_probs=16.5

Q ss_pred             eeEEEECCCCCcHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qa  210 (404)
                      +.++|+|++|||||+++..+
T Consensus       213 ~giLL~GppGtGKT~larai  232 (733)
T TIGR01243       213 KGVLLYGPPGTGKTLLAKAV  232 (733)
T ss_pred             ceEEEECCCCCChHHHHHHH
Confidence            45999999999999876544

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.

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=87.83  E-value=0.4  Score=49.66  Aligned_cols=21  Identities=38%  Similarity=0.523  Sum_probs=16.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++|||++|||||++ +-||+
T Consensus       186 KGVLLYGPPGTGKTLL-AkAVA  206 (406)
T COG1222         186 KGVLLYGPPGTGKTLL-AKAVA  206 (406)
T ss_pred             CceEeeCCCCCcHHHH-HHHHH
Confidence            4699999999999865 44444

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=87.83  E-value=0.73  Score=47.99  Aligned_cols=24  Identities=33%  Similarity=0.416  Sum_probs=21.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -+++.|+.|+||||+++.+.++..
T Consensus       176 vi~lvGptGvGKTTT~aKLA~~~~  199 (388)
T PRK12723        176 VFILVGPTGVGKTTTIAKLAAIYG  199 (388)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999988765

>PRK05428 HPr kinase/phosphorylase; Provisional

Probab=87.80  E-value=0.55  Score=47.56  Aligned_cols=63  Identities=19%  Similarity=0.155  Sum_probs=39.7

Q ss_pred             cccCceeEEEchhHHHHHHHHHHhcCCCccCCC---CC---ccceeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          153 KDSMRYALLVRQSFLDIRDNFRRIVDPSLQSTN---GP---KIRKQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       153 e~f~~p~~LVRk~tleLi~~L~~~~d~~~~std---~~---~~r~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      +..+-|.+.-..+|.++++.+...++..+....   +.   .....++|+|+.|+|||.+.+.++..++
T Consensus       103 ~~~~ipll~t~~~t~~~i~~l~~~L~~~la~~~~iHg~~v~V~G~GvLi~G~SG~GKSelALeLi~rGh  171 (308)
T PRK05428        103 KEAGIPLLRTPLSTTRLISKLTNYLDRKLAPRTSVHGVLVDIYGIGVLITGESGIGKSETALELIKRGH  171 (308)
T ss_pred             HHcCCcEEEeCCcHHHHHHHHHHHHHHHhhhcceeeeEEEEECCEEEEEEcCCCCCHHHHHHHHHHcCC
Confidence            334444444445677777777666554321110   10   0124699999999999999999988764

>cd04177 RSR1 RSR1 subgroup

Probab=87.78  E-value=0.5  Score=41.68  Aligned_cols=21  Identities=33%  Similarity=0.343  Sum_probs=18.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|.+|+|||+++.+.+.
T Consensus         3 ki~liG~~~~GKTsli~~~~~   23 (168)
T cd04177           3 KIVVLGAGGVGKSALTVQFVQ   23 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999988863

RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key featu

>cd04154 Arl2 Arl2 subfamily

Probab=87.78  E-value=0.45  Score=42.24  Aligned_cols=22  Identities=27%  Similarity=0.310  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++++.|+.|+|||+++.+++.
T Consensus        15 ~kv~ivG~~~~GKTsL~~~l~~   36 (173)
T cd04154          15 MRILILGLDNAGKTTILKKLLG   36 (173)
T ss_pred             cEEEEECCCCCCHHHHHHHHcc
Confidence            4699999999999999988763

Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.

>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=87.77  E-value=0.7  Score=44.05  Aligned_cols=23  Identities=30%  Similarity=0.375  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      +-|.|+.||||||+...+...-.
T Consensus         2 igI~G~sGSGKTTla~~L~~~l~   24 (220)
T cd02025           2 IGIAGSVAVGKSTTARVLQALLS   24 (220)
T ss_pred             EEeeCCCCCCHHHHHHHHHHHHh
Confidence            45789999999999988777654

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily

Probab=87.74  E-value=0.51  Score=41.80  Aligned_cols=21  Identities=19%  Similarity=0.216  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|+.|||||+++.+++.
T Consensus         4 ki~vvG~~~vGKTsli~~~~~   24 (170)
T cd04115           4 KIIVIGDSNVGKTCLTYRFCA   24 (170)
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            589999999999999999864

Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine

>cd03276 ABC_SMC6_euk Eukaryotic SMC6 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains

Probab=87.73  E-value=0.53  Score=43.96  Aligned_cols=23  Identities=22%  Similarity=0.118  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHh
Q 045329          193 IVLDGPLCCGKSITLAMLVHWARE  216 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~  216 (404)
                      .+|.|+.|+|||++| .++.+|..
T Consensus        24 ~~i~G~NGsGKStll-~ai~~~l~   46 (198)
T cd03276          24 NFIVGNNGSGKSAIL-TALTIGLG   46 (198)
T ss_pred             EEEECCCCCcHHHHH-HHHHHHhc
Confidence            489999999999887 66677764

Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (for

>cd04132 Rho4_like Rho4-like subfamily

Probab=87.71  E-value=0.5  Score=42.35  Aligned_cols=21  Identities=33%  Similarity=0.520  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|..|+|||+++.+++.
T Consensus         2 ki~vvG~~~vGKTsli~~l~~   22 (187)
T cd04132           2 KIVVVGDGGCGKTCLLIVYSQ   22 (187)
T ss_pred             eEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999998875

Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=87.68  E-value=1.1  Score=42.58  Aligned_cols=27  Identities=22%  Similarity=0.331  Sum_probs=21.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      .-+.|.|+.||||||+...+...-...
T Consensus        34 ~iigi~G~~GsGKTTl~~~L~~~l~~~   60 (229)
T PRK09270         34 TIVGIAGPPGAGKSTLAEFLEALLQQD   60 (229)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            358999999999999998888655543

>cd04101 RabL4 RabL4 (Rab-like4) subfamily

Probab=87.65  E-value=0.52  Score=40.94  Aligned_cols=20  Identities=20%  Similarity=0.297  Sum_probs=17.7

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      ++++.|..|||||+++..++
T Consensus         2 ki~vvG~~~~GKtsl~~~l~   21 (164)
T cd04101           2 RCAVVGDPAVGKTAFVQMFH   21 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            48999999999999997665

RabL4s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL4 lacks a prenylation site at the C-terminus. The specific function of RabL4 remains unknown.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=87.63  E-value=0.74  Score=45.98  Aligned_cols=24  Identities=33%  Similarity=0.411  Sum_probs=20.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      ..+++.|+.|||||++|..++.+-
T Consensus       145 ~~ili~G~tGsGKTTll~al~~~~  168 (308)
T TIGR02788       145 KNIIISGGTGSGKTTFLKSLVDEI  168 (308)
T ss_pred             CEEEEECCCCCCHHHHHHHHHccC
Confidence            359999999999999998777654

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.

>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases

Probab=87.63  E-value=0.52  Score=40.87  Aligned_cols=21  Identities=29%  Similarity=0.428  Sum_probs=18.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|+.|||||+++...+.
T Consensus         1 Ki~vvG~~~vGKtsl~~~~~~   21 (162)
T PF00071_consen    1 KIVVVGDSGVGKTSLINRLIN   21 (162)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHh
Confidence            389999999999999987654

This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....

>PLN02200 adenylate kinase family protein

Probab=87.63  E-value=0.71  Score=44.49  Aligned_cols=31  Identities=19%  Similarity=0.115  Sum_probs=22.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..++|.|++|||||+....+.   ..-|+..|..
T Consensus        44 ~ii~I~G~PGSGKsT~a~~La---~~~g~~his~   74 (234)
T PLN02200         44 FITFVLGGPGSGKGTQCEKIV---ETFGFKHLSA   74 (234)
T ss_pred             EEEEEECCCCCCHHHHHHHHH---HHhCCeEEEc
Confidence            458999999999999877663   3447665444

>PRK13949 shikimate kinase; Provisional

Probab=87.61  E-value=0.54  Score=42.87  Aligned_cols=30  Identities=27%  Similarity=0.297  Sum_probs=21.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +++|.|.+|||||++...+..   .-||-++..
T Consensus         3 ~I~liG~~GsGKstl~~~La~---~l~~~~id~   32 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALAR---ELGLSFIDL   32 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHH---HcCCCeecc
Confidence            589999999999998875543   335555543

>cd00879 Sar1 Sar1 subfamily

Probab=87.61  E-value=0.5  Score=42.43  Aligned_cols=22  Identities=32%  Similarity=0.357  Sum_probs=19.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|+.|||||+++.++..
T Consensus        20 ~ki~ilG~~~~GKStLi~~l~~   41 (190)
T cd00879          20 AKILFLGLDNAGKTTLLHMLKD   41 (190)
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999998753

Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.

>cd04112 Rab26 Rab26 subfamily

Probab=87.60  E-value=0.5  Score=43.01  Aligned_cols=21  Identities=24%  Similarity=0.319  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|.+|||||+++.+++.
T Consensus         2 Ki~vvG~~~vGKTSli~~~~~   22 (191)
T cd04112           2 KVMLLGDSGVGKTCLLVRFKD   22 (191)
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999988764

First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation. Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.

>PRK06761 hypothetical protein; Provisional

Probab=87.60  E-value=0.67  Score=46.33  Aligned_cols=31  Identities=32%  Similarity=0.335  Sum_probs=25.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      -++|.|++||||||++.++.......|.=|.
T Consensus         5 lIvI~G~~GsGKTTla~~L~~~L~~~g~~v~   35 (282)
T PRK06761          5 LIIIEGLPGFGKSTTAKMLNDILSQNGIEVE   35 (282)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCcCceEEE
Confidence            4899999999999999999988766555433

>PRK14737 gmk guanylate kinase; Provisional

Probab=87.57  E-value=0.49  Score=43.99  Aligned_cols=21  Identities=19%  Similarity=0.246  Sum_probs=19.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~  213 (404)
                      +||.|+.|||||++..+++..
T Consensus         7 ivl~GpsG~GK~tl~~~l~~~   27 (186)
T PRK14737          7 FIISSVAGGGKSTIIQALLEE   27 (186)
T ss_pred             EEEECCCCCCHHHHHHHHHhc
Confidence            899999999999999998763

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=87.57  E-value=0.49  Score=43.71  Aligned_cols=31  Identities=26%  Similarity=0.369  Sum_probs=23.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.-. ..|.|.+
T Consensus        28 ~~~i~G~nGsGKSTLl~~l~Gl~~p~~G~i~~   59 (205)
T cd03226          28 IIALTGKNGAGKTTLAKILAGLIKESSGSILL   59 (205)
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCceEEEE
Confidence            489999999999999987655422 4566544

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>PRK07933 thymidylate kinase; Validated

Probab=87.57  E-value=0.94  Score=42.89  Aligned_cols=35  Identities=20%  Similarity=0.119  Sum_probs=29.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      +++.|.-||||||.+..+..|-...|-=|+++..+
T Consensus         3 IviEG~dGsGKST~~~~L~~~L~~~g~~v~~~~~P   37 (213)
T PRK07933          3 IAIEGVDGAGKRTLTEALRAALEARGRSVATLAFP   37 (213)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEecC
Confidence            78999999999999999999999888666655443

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=87.54  E-value=0.47  Score=43.96  Aligned_cols=32  Identities=22%  Similarity=0.268  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH-HHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW-AREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~-A~~ngWIVL~  223 (404)
                      .+.|.|+.|||||++|.-+.-. --..|-|.+.
T Consensus        27 ~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~~~   59 (211)
T cd03264          27 MYGLLGPNGAGKTTLMRILATLTPPSSGTIRID   59 (211)
T ss_pred             cEEEECCCCCCHHHHHHHHhCCCCCCccEEEEC
Confidence            4899999999999998766543 2246776553

The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. 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. 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.

>cd01852 AIG1 AIG1 (avrRpt2-induced gene 1)

Probab=87.49  E-value=0.46  Score=43.63  Aligned_cols=21  Identities=33%  Similarity=0.376  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|.+|+|||++++.++.
T Consensus         2 ~i~lvG~~g~GKSsl~N~ilg   22 (196)
T cd01852           2 RLVLVGKTGAGKSATGNTILG   22 (196)
T ss_pred             EEEEECCCCCCHHHHHHHhhC
Confidence            589999999999999999874

This represents Arabidoposis protein AIG1 that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins).

>PRK00454 engB GTP-binding protein YsxC; Reviewed

Probab=87.48  E-value=0.56  Score=42.16  Aligned_cols=23  Identities=26%  Similarity=0.343  Sum_probs=20.2

Q ss_pred             ceeEEEECCCCCcHHHHHHHHHH
Q 045329          190 RKQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       190 r~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ..+++|.|..|+|||+++..+..
T Consensus        24 ~~~v~ivG~~~~GKSsli~~l~~   46 (196)
T PRK00454         24 GPEIAFAGRSNVGKSSLINALTN   46 (196)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhC
Confidence            46799999999999999997764

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=87.46  E-value=0.51  Score=43.68  Aligned_cols=31  Identities=26%  Similarity=0.371  Sum_probs=21.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|=|.+
T Consensus        28 ~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   59 (210)
T cd03269          28 IFGLLGPNGAGKTTTIRMILGIILPDSGEVLF   59 (210)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCceEEEE
Confidence            488999999999999877664322 3454443

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. 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. 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.

>cd01853 Toc34_like Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts)

Probab=87.46  E-value=0.9  Score=44.32  Aligned_cols=22  Identities=27%  Similarity=0.297  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|+.|+|||++++.+..
T Consensus        32 ~~IllvG~tGvGKSSliNaLlg   53 (249)
T cd01853          32 LTILVLGKTGVGKSSTINSIFG   53 (249)
T ss_pred             eEEEEECCCCCcHHHHHHHHhC
Confidence            5699999999999999988775

This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon.

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=87.46  E-value=0.52  Score=48.78  Aligned_cols=36  Identities=28%  Similarity=0.667  Sum_probs=28.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      .|..|-|+.|||||+++.|+..|+...  +|+|+--++
T Consensus       158 qr~~I~G~~G~GKT~L~~~Iak~~~~d--vvVyv~iGE  193 (369)
T cd01134         158 GTAAIPGPFGCGKTVIQQSLSKYSNSD--IVIYVGCGE  193 (369)
T ss_pred             CEEEEECCCCCChHHHHHHHHhCCCCC--EEEEEEeCC
Confidence            368999999999999999999887543  677775443

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.

>cd04107 Rab32_Rab38 Rab38/Rab32 subfamily

Probab=87.45  E-value=0.52  Score=43.27  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=19.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      +++|.|..|+|||+++.+++..
T Consensus         2 KivivG~~~vGKTsli~~l~~~   23 (201)
T cd04107           2 KVLVIGDLGVGKTSIIKRYVHG   23 (201)
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999998753

Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.

>PRK04196 V-type ATP synthase subunit B; Provisional

Probab=87.42  E-value=0.7  Score=49.18  Aligned_cols=39  Identities=10%  Similarity=0.077  Sum_probs=32.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC----CeEEEEecCccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE----GWLVLYVPRGRE  229 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n----gWIVL~IP~a~~  229 (404)
                      .|..|.|.+|+|||+++.+++.++...    +++++|+--++.
T Consensus       144 QR~gIfgg~G~GKs~L~~~ia~~~~~d~~~~~~v~V~~~iGeR  186 (460)
T PRK04196        144 QKLPIFSGSGLPHNELAAQIARQAKVLGEEENFAVVFAAMGIT  186 (460)
T ss_pred             CEEEeeCCCCCCccHHHHHHHHhhhhccCCCceEEEEEEeccc
Confidence            468999999999999999999998653    789999865544

>TIGR03348 VI_IcmF type VI secretion protein IcmF

Probab=87.41  E-value=0.43  Score=56.12  Aligned_cols=20  Identities=25%  Similarity=0.247  Sum_probs=18.0

Q ss_pred             eeEEEECCCCCcHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qa  210 (404)
                      +=|++.|++|+|||++|.+.
T Consensus       112 PWYlviG~~gsGKtt~l~~s  131 (1169)
T TIGR03348       112 PWYLVIGPPGSGKTTLLQNS  131 (1169)
T ss_pred             CCEEEECCCCCchhHHHHhC
Confidence            44999999999999999876

Members of this protein family are IcmF homologs and tend to be associated with type VI secretion systems.

>cd04116 Rab9 Rab9 subfamily

Probab=87.38  E-value=0.55  Score=41.23  Aligned_cols=22  Identities=27%  Similarity=0.273  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++++.|.+|||||+++.+++.
T Consensus         6 ~ki~vvG~~~~GKTsli~~~~~   27 (170)
T cd04116           6 LKVILLGDGGVGKSSLMNRYVT   27 (170)
T ss_pred             EEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999988763

Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47). Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs. Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CX

>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily

Probab=87.38  E-value=0.54  Score=42.20  Aligned_cols=21  Identities=29%  Similarity=0.339  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|..|||||+++.+.+.
T Consensus         4 ki~vvG~~~vGKTsL~~~~~~   24 (172)
T cd04141           4 KIVMLGAGGVGKSAVTMQFIS   24 (172)
T ss_pred             EEEEECCCCCcHHHHHHHHHh
Confidence            489999999999999988764

Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to sign

>TIGR00157 ribosome small subunit-dependent GTPase A

Probab=87.33  E-value=0.85  Score=44.18  Aligned_cols=23  Identities=26%  Similarity=0.164  Sum_probs=20.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      ..++.|++|+|||++++++.--.
T Consensus       122 ~~~~~G~sgvGKStLiN~L~~~~  144 (245)
T TIGR00157       122 ISVFAGQSGVGKSSLINALDPSV  144 (245)
T ss_pred             EEEEECCCCCCHHHHHHHHhhhh
Confidence            48999999999999999998643

The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option).

>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=87.32  E-value=0.81  Score=45.19  Aligned_cols=35  Identities=26%  Similarity=0.224  Sum_probs=27.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      +.|.|+.|||||+++..+...-...+..|+..-+-
T Consensus         2 igI~G~sGsGKSTl~~~L~~ll~~~~~~vi~~Dd~   36 (273)
T cd02026           2 IGVAGDSGCGKSTFLRRLTSLFGSDLVTVICLDDY   36 (273)
T ss_pred             EEEECCCCCCHHHHHHHHHHhhCCCceEEEECccc
Confidence            57899999999999988876655567777776533

This enzyme 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.

>PRK14242 phosphate transporter ATP-binding protein; Provisional

Probab=87.32  E-value=0.65  Score=44.33  Aligned_cols=31  Identities=42%  Similarity=0.537  Sum_probs=23.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH------HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA------REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A------~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-      -..|.|.+
T Consensus        34 ~~~i~G~nGsGKSTLl~~l~Gl~~~~~~~~~~G~i~~   70 (253)
T PRK14242         34 VTALIGPSGCGKSTFLRCLNRMNDLIPGARVEGEILL   70 (253)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhcccCCCCCCceEEEE
Confidence            48999999999999987776442      14677655

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=87.30  E-value=0.7  Score=40.76  Aligned_cols=20  Identities=30%  Similarity=0.557  Sum_probs=16.7

Q ss_pred             EEEECCCCCcHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++|+|+.|||||++...+..
T Consensus         3 I~i~G~~GSGKstia~~la~   22 (171)
T TIGR02173         3 ITISGPPGSGKTTVAKILAE   22 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            79999999999988766643

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.

>PRK05595 replicative DNA helicase; Provisional

Probab=87.26  E-value=0.73  Score=48.35  Aligned_cols=33  Identities=21%  Similarity=0.237  Sum_probs=28.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHH-HHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHW-AREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~-A~~ngWIVL~IP  225 (404)
                      +||-|.+|+|||++.+|++.+ |..+|+=|+++.
T Consensus       204 iviaarpg~GKT~~al~ia~~~a~~~g~~vl~fS  237 (444)
T PRK05595        204 ILIAARPSMGKTTFALNIAEYAALREGKSVAIFS  237 (444)
T ss_pred             EEEEecCCCChHHHHHHHHHHHHHHcCCcEEEEe
Confidence            788999999999999999875 778898888873

>cd01918 HprK_C 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

Probab=87.23  E-value=0.61  Score=42.41  Aligned_cols=23  Identities=26%  Similarity=0.339  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ..++|.|+.|+|||++...++..
T Consensus        15 ~gvLi~G~sG~GKStlal~L~~~   37 (149)
T cd01918          15 IGVLITGPSGIGKSELALELIKR   37 (149)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            46999999999999998777665

It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.

>cd04103 Centaurin_gamma Centaurin gamma

Probab=87.22  E-value=0.58  Score=41.62  Aligned_cols=21  Identities=24%  Similarity=0.303  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++-|+.|||||+++.+.+.
T Consensus         2 ki~vvG~~gvGKTsli~~~~~   22 (158)
T cd04103           2 KLGIVGNLQSGKSALVHRYLT   22 (158)
T ss_pred             EEEEECCCCCcHHHHHHHHHh
Confidence            489999999999999988764

The centaurins (alpha, beta, gamma, and delta) are large, multi-domain proteins that all contain an ArfGAP domain and ankyrin repeats, and in some cases, numerous additional domains. Centaurin gamma contains an additional GTPase domain near its N-terminus. The specific function of this GTPase domain has not been well characterized, but centaurin gamma 2 (CENTG2) may play a role in the development of autism. Centaurin gamma 1 is also called PIKE (phosphatidyl inositol (PI) 3-kinase enhancer) and centaurin gamma 2 is also known as AGAP (ArfGAP protein with a GTPase-like domain, ankyrin repeats and a Pleckstrin homology domain) or GGAP. Three isoforms of PIKE have been identified. PIKE-S (short) and PIKE-L (long) are brain-specific isoforms, with PIKE-S restricted to the nucleus and PIKE-L found in multiple cellular compartments. A third isoform, PIKE-A was identified in human glioblastoma brain cancers and has been found in various tissues.

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=87.17  E-value=0.53  Score=43.77  Aligned_cols=32  Identities=22%  Similarity=0.311  Sum_probs=24.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL~  223 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+.
T Consensus        31 ~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~~~   63 (216)
T TIGR00960        31 MVFLVGHSGAGKSTFLKLILGIEKPTRGKIRFN   63 (216)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCceEEEEC
Confidence            489999999999999877765432 45776653

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=87.16  E-value=0.66  Score=50.95  Aligned_cols=33  Identities=21%  Similarity=0.343  Sum_probs=25.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH---------hCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR---------EEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~---------~ngWIVL~I  224 (404)
                      .++|+|++|||||+++.-+...+.         ...|+.+.-
T Consensus       177 ~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~  218 (615)
T TIGR02903       177 HIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDG  218 (615)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEec
Confidence            489999999999998877665553         346888864

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.

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=87.11  E-value=0.53  Score=42.59  Aligned_cols=21  Identities=38%  Similarity=0.474  Sum_probs=17.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      +|++|.|+.|||||+++.-+.
T Consensus         2 krimliG~~g~GKTTL~q~L~   22 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTTLAQALN   22 (143)
T ss_pred             ceEEEECCCCCCHHHHHHHHc
Confidence            479999999999998875443

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>cd03275 ABC_SMC1_euk Eukaryotic SMC1 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains

Probab=87.09  E-value=0.58  Score=44.90  Aligned_cols=23  Identities=22%  Similarity=0.234  Sum_probs=18.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -.+|.|+.|||||++| .+++|+.
T Consensus        24 ~~~i~G~NGsGKStll-~ai~~~l   46 (247)
T cd03275          24 FTCIIGPNGSGKSNLM-DAISFVL   46 (247)
T ss_pred             eEEEECCCCCCHHHHH-HHHHHHh
Confidence            4799999999999888 4555554

Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (for

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=87.08  E-value=0.6  Score=44.45  Aligned_cols=20  Identities=35%  Similarity=0.270  Sum_probs=17.5

Q ss_pred             EEEECCCCCcHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+|.|+.|+|||+++.|+..
T Consensus         4 ~ll~g~~G~GKS~lal~la~   23 (239)
T cd01125           4 SALVAPGGTGKSSLLLVLAL   23 (239)
T ss_pred             eEEEcCCCCCHHHHHHHHHH
Confidence            48999999999999999843

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.

>cd01874 Cdc42 Cdc42 subfamily

Probab=87.08  E-value=0.56  Score=42.27  Aligned_cols=21  Identities=24%  Similarity=0.241  Sum_probs=19.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|..|+|||+++.+.+.
T Consensus         3 ki~vvG~~~vGKTsl~~~~~~   23 (175)
T cd01874           3 KCVVVGDGAVGKTCLLISYTT   23 (175)
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999988875

Cdc42 is an essential GTPase that belongs to the Rho family of Ras-like GTPases. These proteins act as molecular switches by responding to exogenous and/or endogenous signals and relaying those signals to activate downstream components of a biological pathway. Cdc42 transduces signals to the actin cytoskeleton to initiate and maintain polarized growth and to mitogen-activated protein morphogenesis. In the budding yeast Saccharomyces cerevisiae, Cdc42 plays an important role in multiple actin-dependent morphogenetic events such as bud emergence, mating-projection formation, and pseudohyphal growth. In mammalian cells, Cdc42 regulates a variety of actin-dependent events and induces the JNK/SAPK protein kinase cascade, which leads to the activation of transcription factors within the nucleus. Cdc42 mediates these processes through interactions with a myriad of downstream effectors, whose number and regulation we are just starting to understand. In addi

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.00  E-value=0.92  Score=48.36  Aligned_cols=22  Identities=23%  Similarity=0.398  Sum_probs=17.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .++|+|++|||||++..-+...
T Consensus        38 ~~Lf~GPpGtGKTTlA~~lA~~   59 (472)
T PRK14962         38 AYIFAGPRGTGKTTVARILAKS   59 (472)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4899999999999877555443

>cd04104 p47_IIGP_like p47 (47-kDa) family

Probab=86.99  E-value=0.6  Score=43.16  Aligned_cols=21  Identities=29%  Similarity=0.311  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|+.|+|||++++.+..
T Consensus         3 kI~i~G~~g~GKSSLin~L~g   23 (197)
T cd04104           3 NIAVTGESGAGKSSFINALRG   23 (197)
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999999875

The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protei

>smart00174 RHO Rho (Ras homology) subfamily of Ras-like small GTPases

Probab=86.99  E-value=0.46  Score=41.77  Aligned_cols=20  Identities=25%  Similarity=0.293  Sum_probs=17.4

Q ss_pred             EEEECCCCCcHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++.|++|||||+++.+...
T Consensus         1 i~i~G~~~vGKTsli~~~~~   20 (174)
T smart00174        1 LVVVGDGAVGKTCLLISYTT   20 (174)
T ss_pred             CEEECCCCCCHHHHHHHHHh
Confidence            47889999999999988765

Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.

>cd01897 NOG NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans

Probab=86.97  E-value=0.57  Score=40.87  Aligned_cols=21  Identities=29%  Similarity=0.346  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|..|+|||+++..+..
T Consensus         2 ~i~~~G~~~~GKssli~~l~~   22 (168)
T cd01897           2 TLVIAGYPNVGKSSLVNKLTR   22 (168)
T ss_pred             eEEEEcCCCCCHHHHHHHHhc
Confidence            589999999999999998753

NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function. It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins.

>cd04151 Arl1 Arl1 subfamily

Probab=86.96  E-value=0.51  Score=41.07  Aligned_cols=20  Identities=30%  Similarity=0.298  Sum_probs=18.0

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      +++|.|..|||||+++.++.
T Consensus         1 kv~lvG~~~~GKTsl~~~l~   20 (158)
T cd04151           1 RILILGLDNAGKTTILYRLQ   20 (158)
T ss_pred             CEEEECCCCCCHHHHHHHHc
Confidence            37899999999999999984

Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.

>PRK14235 phosphate transporter ATP-binding protein; Provisional

Probab=86.93  E-value=0.69  Score=44.86  Aligned_cols=31  Identities=32%  Similarity=0.412  Sum_probs=25.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH------hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR------EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~------~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-...      ..|.|.+
T Consensus        47 ~~~i~G~nGsGKSTLl~~l~Gl~~~~~~~~~~G~I~~   83 (267)
T PRK14235         47 VTAFIGPSGCGKSTFLRCLNRMNDTIDGCRVTGKITL   83 (267)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhcccccCCCCceEEEE
Confidence            489999999999999988876543      5788765

>TIGR01042 V-ATPase_V1_A V-type (H+)-ATPase V1, A subunit

Probab=86.92  E-value=0.56  Score=51.21  Aligned_cols=36  Identities=22%  Similarity=0.548  Sum_probs=29.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      .|..|-|..|||||+++.|+..||-..  ||+|+--++
T Consensus       227 qr~~I~gg~G~GKT~l~~~lak~s~aD--viVyvg~GE  262 (591)
T TIGR01042       227 GTTAIPGAFGCGKTVISQSLSKYSNSD--AIVYVGCGE  262 (591)
T ss_pred             CeEEEEcCCCcCHHHHHHHHHhccCcC--EEEEEEEee
Confidence            468999999999999999998887544  688876543

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>PRK10744 pstB phosphate transporter ATP-binding protein; Provisional

Probab=86.92  E-value=0.59  Score=45.01  Aligned_cols=31  Identities=32%  Similarity=0.461  Sum_probs=24.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH------hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR------EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~------~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-...      ..|-|.+
T Consensus        41 ~~~i~G~nGsGKSTLl~~l~Gl~~~~p~~p~~G~i~~   77 (260)
T PRK10744         41 VTAFIGPSGCGKSTLLRTFNRMYELYPEQRAEGEILL   77 (260)
T ss_pred             EEEEECCCCCCHHHHHHHHhcccccCCCCCcceEEEE
Confidence            489999999999999877765432      4687765

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=86.92  E-value=0.3  Score=49.25  Aligned_cols=95  Identities=14%  Similarity=0.162  Sum_probs=50.8

Q ss_pred             cccCCCccccCccccceeEEeCHHHHHhhccC---CCCcchhhhcccc--CceeEEEchhHHHHHHHHHHhcCCCccCCC
Q 045329          111 FTKTTSLSLLTRKDACTYFKFSEDELNAMLPE---GLPTGMLGEFKDS--MRYALLVRQSFLDIRDNFRRIVDPSLQSTN  185 (404)
Q Consensus       111 ~~~~~~~~~ht~~~vGk~y~~p~e~~k~l~~~---GLp~~~~kqfe~f--~~p~~LVRk~tleLi~~L~~~~d~~~~std  185 (404)
                      |.+..|....+..++.+++.++.+....+...   -++..+..--+.+  +....-+.--    +..|...+..      
T Consensus        22 ~~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~~~~~~~~~~t~~~l~~~~~~~~~~~tg----~~~lD~ll~g------   91 (316)
T TIGR02239        22 LHTVESVAYAPKKQLLEIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRQEVIQLTTG----SKELDKLLGG------   91 (316)
T ss_pred             CCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHhcccccccHHHHHhcccccceeCCC----CHHHHHHhcC------
Confidence            45555667777788888888888887765432   1221111111111  1111112211    1123333222      


Q ss_pred             CCccceeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          186 GPKIRKQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       186 ~~~~r~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      +-....-+.|+|++|+|||+++.|+...|.
T Consensus        92 Gi~~g~i~~i~G~~g~GKT~l~~~~~~~~~  121 (316)
T TIGR02239        92 GIETGSITEIFGEFRTGKTQLCHTLAVTCQ  121 (316)
T ss_pred             CCCCCeEEEEECCCCCCcCHHHHHHHHHHh
Confidence            111123478999999999999999877553

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).

>PRK15177 Vi polysaccharide export ATP-binding protein VexC; Provisional

Probab=86.89  E-value=0.56  Score=44.08  Aligned_cols=30  Identities=23%  Similarity=0.266  Sum_probs=24.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH-HHhCCeEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW-AREEGWLV  221 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~-A~~ngWIV  221 (404)
                      .+.|.|+.|||||++|.-+.-. .-.+|.|.
T Consensus        15 ~~~l~G~NGsGKSTLlk~i~Gl~~~~sG~i~   45 (213)
T PRK15177         15 HIGILAAPGSGKTTLTRLLCGLDAPDEGDFI   45 (213)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCccCCCCCEE
Confidence            4899999999999999877764 33568775

>PHA02774 E1; Provisional

Probab=86.86  E-value=1.7  Score=47.76  Aligned_cols=65  Identities=20%  Similarity=0.352  Sum_probs=41.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccccCeeecC---CCCCCccCH-----HHHHHHHHHHHHHh
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHGGYFYKN---PQTGLWDTP-----LQAENVLKDFIKYN  262 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvng~~~y~~---~~~g~ydQP-----~~A~~~Lk~fl~~N  262 (404)
                      +-++|+|++|+|||++-..++.+-  +|=++.+|..-..|     .+.+   .+-+++|-+     .+....|+.++..|
T Consensus       435 nciv~~GPP~TGKS~fa~sL~~~L--~G~vi~fvN~~s~F-----wLqpl~d~ki~vlDD~t~~~w~y~d~~Lrn~LdG~  507 (613)
T PHA02774        435 NCLVIYGPPDTGKSMFCMSLIKFL--KGKVISFVNSKSHF-----WLQPLADAKIALLDDATHPCWDYIDTYLRNALDGN  507 (613)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh--CCCEEEEEECcccc-----ccchhccCCEEEEecCcchHHHHHHHHHHHHcCCC
Confidence            459999999999999988888875  57777777542222     1222   233455544     44455566666555

>PRK00081 coaE dephospho-CoA kinase; Reviewed

Probab=86.85  E-value=0.8  Score=42.53  Aligned_cols=29  Identities=28%  Similarity=0.292  Sum_probs=22.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .+.|+|..|||||++...+..    -|+-|+..
T Consensus         4 ~i~ltG~~gsGKst~~~~l~~----~g~~~i~~   32 (194)
T PRK00081          4 IIGLTGGIGSGKSTVANLFAE----LGAPVIDA   32 (194)
T ss_pred             EEEEECCCCCCHHHHHHHHHH----cCCEEEEe
Confidence            489999999999999887665    36655543

>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin

Probab=86.84  E-value=0.58  Score=43.72  Aligned_cols=31  Identities=29%  Similarity=0.384  Sum_probs=23.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.-. ..|.|.+
T Consensus        28 ~~~i~G~nGsGKSTLl~~i~G~~~~~~G~i~~   59 (220)
T cd03265          28 IFGLLGPNGAGKTTTIKMLTTLLKPTSGRATV   59 (220)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCceEEEE
Confidence            489999999999999987665432 4577665

In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. 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. 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.

>cd03224 ABC_TM1139_LivF_branched LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids

Probab=86.83  E-value=0.55  Score=43.68  Aligned_cols=31  Identities=19%  Similarity=0.236  Sum_probs=22.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.-. ..|=|.+
T Consensus        28 ~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   59 (222)
T cd03224          28 IVALLGRNGAGKTTLLKTIMGLLPPRSGSIRF   59 (222)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            489999999999999976544322 3465544

The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). 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.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=86.80  E-value=0.47  Score=43.84  Aligned_cols=21  Identities=29%  Similarity=0.333  Sum_probs=17.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      +.++++|-+|+|||++-.++.
T Consensus         8 PNILvtGTPG~GKstl~~~la   28 (176)
T KOG3347|consen    8 PNILVTGTPGTGKSTLAERLA   28 (176)
T ss_pred             CCEEEeCCCCCCchhHHHHHH
Confidence            559999999999999876665

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=86.77  E-value=0.53  Score=43.25  Aligned_cols=29  Identities=28%  Similarity=0.339  Sum_probs=21.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH--hCCeEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR--EEGWLV  221 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~--~ngWIV  221 (404)
                      ++|+|+.|+|||++|.++..-..  .-|..|
T Consensus         2 ~~ltG~N~~GKst~l~~i~~~~~la~~G~~v   32 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVGLIVIMAQIGSFV   32 (185)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHHHhCCCe
Confidence            68999999999999988764332  346544

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=86.75  E-value=0.85  Score=47.89  Aligned_cols=37  Identities=22%  Similarity=0.258  Sum_probs=31.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCe--EEEEecCc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGW--LVLYVPRG  227 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngW--IVL~IP~a  227 (404)
                      +-++|+|+.|+|||-+|.-+-+++.+++=  .|+|+...
T Consensus       114 nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se  152 (408)
T COG0593         114 NPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSE  152 (408)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHH
Confidence            44999999999999999888889888766  89998664

>PRK14238 phosphate transporter ATP-binding protein; Provisional

Probab=86.72  E-value=0.66  Score=45.18  Aligned_cols=32  Identities=25%  Similarity=0.392  Sum_probs=26.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH------hCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR------EEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~------~ngWIVL~  223 (404)
                      .+.|.|+.|||||++|.-+.-...      ..|-|.+.
T Consensus        52 ~~~I~G~nGsGKSTLl~~i~Gl~~~~~~~~~~G~i~~~   89 (271)
T PRK14238         52 VTAIIGPSGCGKSTYIKTLNRMVELVPSVKTTGKILYR   89 (271)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhccCCCCCCCceeEEEC
Confidence            589999999999999988876653      66887663

>cd03219 ABC_Mj1267_LivG_branched The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine

Probab=86.70  E-value=0.54  Score=44.26  Aligned_cols=31  Identities=23%  Similarity=0.355  Sum_probs=23.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|.|.+
T Consensus        28 ~~~l~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   59 (236)
T cd03219          28 IHGLIGPNGAGKTTLFNLISGFLRPTSGSVLF   59 (236)
T ss_pred             EEEEECCCCCCHHHHHHHHcCCCCCCCceEEE
Confidence            489999999999999877654432 4677655

MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=86.70  E-value=0.68  Score=48.42  Aligned_cols=35  Identities=20%  Similarity=0.017  Sum_probs=22.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|++|||||++.. +++-...-..|++..++
T Consensus       149 lgllL~GPPGcGKTllAr-aiA~elg~~~i~vsa~e  183 (413)
T PLN00020        149 LILGIWGGKGQGKSFQCE-LVFKKMGIEPIVMSAGE  183 (413)
T ss_pred             eEEEeeCCCCCCHHHHHH-HHHHHcCCCeEEEEHHH
Confidence            458999999999997654 33333333445554443

>PRK14274 phosphate ABC transporter ATP-binding protein; Provisional

Probab=86.60  E-value=0.78  Score=44.10  Aligned_cols=31  Identities=26%  Similarity=0.316  Sum_probs=23.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH------hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR------EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~------~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-...      ..|.|.+
T Consensus        40 ~~~l~G~nGsGKSTLl~~l~G~~~~~p~~~~~G~i~~   76 (259)
T PRK14274         40 VTAIIGPSGCGKSTFIKTLNLMIQMVPNVKLTGEMNY   76 (259)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhccCCCCCCCceEEEE
Confidence            489999999999999987765432      3687765

>cd03270 ABC_UvrA_I The excision repair protein UvrA domain I; 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=86.57  E-value=0.63  Score=44.20  Aligned_cols=21  Identities=24%  Similarity=0.169  Sum_probs=17.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+.|.|+.|||||++|...+.
T Consensus        23 ~~~l~G~sGsGKSTL~~~~i~   43 (226)
T cd03270          23 LVVITGVSGSGKSSLAFDTIY   43 (226)
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            489999999999999854443

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.

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=86.53  E-value=0.7  Score=47.53  Aligned_cols=28  Identities=29%  Similarity=0.289  Sum_probs=24.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      ..++|.|++|||||++...+..++-..+
T Consensus        39 ~~vli~G~~GtGKs~~ar~~~~~l~~~~   66 (350)
T CHL00081         39 GGVMIMGDRGTGKSTTIRALVDLLPEIE   66 (350)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHHhhcC
Confidence            3599999999999999999988886544

>cd03261 ABC_Org_Solvent_Resistant ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; 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=86.51  E-value=0.6  Score=44.05  Aligned_cols=31  Identities=29%  Similarity=0.492  Sum_probs=23.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        28 ~~~l~G~nGsGKSTLl~~l~G~~~p~~G~i~~   59 (235)
T cd03261          28 ILAIIGPSGSGKSTLLRLIVGLLRPDSGEVLI   59 (235)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCceEEEE
Confidence            489999999999999887765432 4576654

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.

>PRK05748 replicative DNA helicase; Provisional

Probab=86.49  E-value=0.82  Score=47.96  Aligned_cols=33  Identities=12%  Similarity=0.071  Sum_probs=28.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHH-HhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWA-REEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL~IP  225 (404)
                      ++|-|.+|+|||++.+|++..+ ...|+-|+++.
T Consensus       206 ivIaarpg~GKT~~al~ia~~~a~~~g~~v~~fS  239 (448)
T PRK05748        206 IIVAARPSVGKTAFALNIAQNVATKTDKNVAIFS  239 (448)
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHHhCCCeEEEEe
Confidence            8999999999999999998875 46688888773

>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids

Probab=86.47  E-value=0.61  Score=43.77  Aligned_cols=31  Identities=32%  Similarity=0.500  Sum_probs=23.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        28 ~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~   59 (232)
T cd03218          28 IVGLLGPNGAGKTTTFYMIVGLVKPDSGKILL   59 (232)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCcEEEE
Confidence            489999999999999877765433 4566554

The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.

>PRK14248 phosphate ABC transporter ATP-binding protein; Provisional

Probab=86.43  E-value=0.75  Score=44.50  Aligned_cols=31  Identities=32%  Similarity=0.445  Sum_probs=24.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH------hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR------EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~------~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-...      ..|-|.+
T Consensus        49 ~~~i~G~nGsGKSTLl~~l~Gl~~~~~~~~~~G~i~~   85 (268)
T PRK14248         49 VTALIGPSGCGKSTFLRSINRMNDLIPSARSEGEILY   85 (268)
T ss_pred             EEEEECCCCCCHHHHHHHHHhcccccCCCCCceEEEE
Confidence            489999999999999987766432      5687655

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=86.42  E-value=0.59  Score=43.19  Aligned_cols=21  Identities=24%  Similarity=0.368  Sum_probs=18.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+.|.|+.|||||++|.-+.-
T Consensus        28 ~~~i~G~nGsGKSTLl~~l~G   48 (208)
T cd03268          28 IYGFLGPNGAGKTTTMKIILG   48 (208)
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999977654

Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.

>COG4136 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=86.38  E-value=0.6  Score=43.53  Aligned_cols=19  Identities=42%  Similarity=0.803  Sum_probs=16.4

Q ss_pred             EEEECCCCCcHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav  211 (404)
                      +-|.||.|||||++|+-+.
T Consensus        31 vtlMGPSGcGKSTLls~~~   49 (213)
T COG4136          31 VTLMGPSGCGKSTLLSWMI   49 (213)
T ss_pred             EEEECCCCccHHHHHHHHH
Confidence            6789999999999997554

>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE)

Probab=86.37  E-value=0.61  Score=43.48  Aligned_cols=31  Identities=19%  Similarity=0.238  Sum_probs=23.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.- -..|-|.+
T Consensus        33 ~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   64 (228)
T cd03257          33 TLGLVGESGSGKSTLARAILGLLKPTSGSIIF   64 (228)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            48999999999999887766542 34576654

The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=86.36  E-value=0.97  Score=46.67  Aligned_cols=38  Identities=26%  Similarity=0.553  Sum_probs=29.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCC-eEEEEecCcc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEG-WLVLYVPRGR  228 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ng-WIVL~IP~a~  228 (404)
                      +.+++.|..|||||+++.+++.-++.+| =.|||=|.+.
T Consensus        16 ~~~li~G~~GsGKT~~i~~ll~~~~~~g~~~iI~D~kg~   54 (386)
T PF10412_consen   16 RHILIIGATGSGKTQAIRHLLDQIRARGDRAIIYDPKGE   54 (386)
T ss_dssp             G-EEEEE-TTSSHHHHHHHHHHHHHHTT-EEEEEEETTH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHcCCEEEEEECCch
Confidence            4599999999999999999998887664 5666666653

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=86.35  E-value=1.7  Score=40.73  Aligned_cols=32  Identities=16%  Similarity=0.153  Sum_probs=24.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.|.|.+|||||++..++....  .+..+|+.-+
T Consensus         2 i~i~G~sgsGKTtla~~l~~~~--~~~~~i~~Dd   33 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQRIL--PNCCVIHQDD   33 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc--CCCeEEcccc
Confidence            5789999999999998887763  3566665543

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.

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=86.34  E-value=0.64  Score=43.00  Aligned_cols=31  Identities=26%  Similarity=0.328  Sum_probs=22.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        29 ~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   60 (214)
T cd03292          29 FVFLVGPSGAGKSTLLKLIYKEELPTSGTIRV   60 (214)
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCceEEEE
Confidence            489999999999998877665433 3455443

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=86.33  E-value=0.59  Score=43.42  Aligned_cols=31  Identities=26%  Similarity=0.307  Sum_probs=23.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.- -..|.|.+
T Consensus        32 ~~~l~G~nGsGKSTLl~~i~Gl~~~~~G~i~~   63 (218)
T cd03255          32 FVAIVGPSGSGKSTLLNILGGLDRPTSGEVRV   63 (218)
T ss_pred             EEEEEcCCCCCHHHHHHHHhCCcCCCceeEEE
Confidence            48999999999999887665443 24677655

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=86.32  E-value=0.64  Score=43.32  Aligned_cols=31  Identities=23%  Similarity=0.291  Sum_probs=23.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.-. ..|-|.+
T Consensus        33 ~~~i~G~nGsGKSTLl~~i~G~~~~~~G~i~~   64 (221)
T TIGR02211        33 IVAIVGSSGSGKSTLLHLLGGLDNPTSGEVLF   64 (221)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCcEEEE
Confidence            489999999999999987765422 4576654

This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina.

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=86.31  E-value=0.58  Score=43.41  Aligned_cols=31  Identities=23%  Similarity=0.355  Sum_probs=22.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        27 ~~~l~G~nGsGKSTLl~~l~G~~~p~~G~i~~   58 (213)
T cd03235          27 FLAIVGPNGAGKSTLLKAILGLLKPTSGSIRV   58 (213)
T ss_pred             EEEEECCCCCCHHHHHHHHcCCCCCCCCEEEE
Confidence            489999999999999987654422 3455543

This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.

>cd04146 RERG_RasL11_like RERG/RasL11-like subfamily

Probab=86.31  E-value=0.64  Score=40.67  Aligned_cols=20  Identities=25%  Similarity=0.307  Sum_probs=17.5

Q ss_pred             EEEECCCCCcHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++.|++|||||+++...+.
T Consensus         2 i~vvG~~~~GKtsli~~~~~   21 (165)
T cd04146           2 IAVLGASGVGKSALVVRFLT   21 (165)
T ss_pred             EEEECCCCCcHHHHHHHHHh
Confidence            79999999999999977653

RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tu

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=86.31  E-value=0.59  Score=50.78  Aligned_cols=42  Identities=29%  Similarity=0.455  Sum_probs=26.1

Q ss_pred             hhHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHH
Q 045329          164 QSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLA  208 (404)
Q Consensus       164 k~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~  208 (404)
                      ++-.||+++|+   |+...+.=+-+.-++++|+|++|+|||++..
T Consensus       314 ~ELeEiVefLk---dP~kftrLGGKLPKGVLLvGPPGTGKTlLAR  355 (752)
T KOG0734|consen  314 QELEEIVEFLK---DPTKFTRLGGKLPKGVLLVGPPGTGKTLLAR  355 (752)
T ss_pred             HHHHHHHHHhc---CcHHhhhccCcCCCceEEeCCCCCchhHHHH
Confidence            45667788876   3320000022333679999999999987643

>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid []

Probab=86.30  E-value=0.93  Score=44.05  Aligned_cols=35  Identities=23%  Similarity=0.334  Sum_probs=26.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREW  230 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~w  230 (404)
                      |+|.|+.|||||-+   ++..|.+.||=||..-+.+.+
T Consensus         4 ~~i~GpT~tGKt~~---ai~lA~~~g~pvI~~Driq~y   38 (233)
T PF01745_consen    4 YLIVGPTGTGKTAL---AIALAQKTGAPVISLDRIQCY   38 (233)
T ss_dssp             EEEE-STTSSHHHH---HHHHHHHH--EEEEE-SGGG-
T ss_pred             EEEECCCCCChhHH---HHHHHHHhCCCEEEecceecc
Confidence            89999999999964   788999999999999876655

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=86.28  E-value=0.65  Score=42.69  Aligned_cols=31  Identities=23%  Similarity=0.291  Sum_probs=22.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-... ..|=|.+
T Consensus        26 ~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   57 (206)
T TIGR03608        26 MYAIIGESGSGKSTLLNIIGLLEKFDSGQVYL   57 (206)
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCCeEEEE
Confidence            489999999999998876654322 3455433

A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.

>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=86.27  E-value=0.66  Score=41.82  Aligned_cols=31  Identities=23%  Similarity=0.349  Sum_probs=23.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-... ..|-|.+
T Consensus        29 ~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   60 (166)
T cd03223          29 RLLITGPSGTGKSSLFRALAGLWPWGSGRIGM   60 (166)
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCCceEEE
Confidence            589999999999999987765432 4566543

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

>PRK14240 phosphate transporter ATP-binding protein; Provisional

Probab=86.26  E-value=0.67  Score=44.16  Aligned_cols=32  Identities=38%  Similarity=0.424  Sum_probs=24.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH------hCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR------EEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~------~ngWIVL~  223 (404)
                      .+.|.|+.|||||++|.-+.-...      ..|.|.+.
T Consensus        31 ~~~i~G~nGsGKSTLl~~i~G~~~~~~~~~~~G~i~~~   68 (250)
T PRK14240         31 VTALIGPSGCGKSTFLRTLNRMNDLIPSVKIEGEVLLD   68 (250)
T ss_pred             EEEEECCCCCCHHHHHHHHhccccccCCCCCceEEEEC
Confidence            489999999999999987765432      46877664

>cd04108 Rab36_Rab34 Rab34/Rab36 subfamily

Probab=86.25  E-value=0.67  Score=41.51  Aligned_cols=21  Identities=19%  Similarity=0.460  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|..|||||+++.+.+.
T Consensus         2 ki~ivG~~~vGKTsli~~~~~   22 (170)
T cd04108           2 KVIVVGDLSVGKTCLINRFCK   22 (170)
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999998875

Rab34, found primarily in the Golgi, interacts with its effector, Rab-interacting lysosomal protein (RILP). This enables its participation in microtubular dynenin-dynactin-mediated repositioning of lysosomes from the cell periphery to the Golgi. A Rab34 (Rah) isoform that lacks the consensus GTP-binding region has been identified in mice. This isoform is associated with membrane ruffles and promotes macropinosome formation. Rab36 has been mapped to human chromosome 22q11.2, a region that is homozygously deleted in malignant rhabdoid tumors (MRTs). However, experimental assessments do not implicate Rab36 as a tumor suppressor that would enable tumor formation through a loss-of-function mechanism. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further re

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=86.24  E-value=1  Score=48.59  Aligned_cols=22  Identities=18%  Similarity=0.292  Sum_probs=17.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ..|+|+|++|||||++..-+..
T Consensus        44 ~a~Lf~Gp~G~GKTT~ArilAk   65 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARIIAK   65 (507)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            3599999999999997655544

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=86.23  E-value=0.6  Score=44.00  Aligned_cols=31  Identities=29%  Similarity=0.353  Sum_probs=23.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.- -..|-|.+
T Consensus        29 ~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   60 (241)
T cd03256          29 FVALIGPSGAGKSTLLRCLNGLVEPTSGSVLI   60 (241)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCcCCCCceEEE
Confidence            48999999999999988776543 34677655

Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. 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.

>TIGR00101 ureG urease accessory protein UreG

Probab=86.22  E-value=1.1  Score=42.03  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=20.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .+.|.|+.|||||+++..+...-
T Consensus         3 ~i~i~G~~GsGKTTll~~l~~~l   25 (199)
T TIGR00101         3 KIGVAGPVGSGKTALIEALTRAL   25 (199)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh
Confidence            48899999999999999988753

This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel.

>TIGR02323 CP_lyasePhnK phosphonate C-P lyase system protein PhnK

Probab=86.18  E-value=0.63  Score=44.41  Aligned_cols=32  Identities=25%  Similarity=0.216  Sum_probs=25.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH-HHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW-AREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~-A~~ngWIVL~  223 (404)
                      .+.|.|+.||||||+|.-+.-. .-..|.|.+.
T Consensus        31 ~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~   63 (253)
T TIGR02323        31 VLGIVGESGSGKSTLLGCLAGRLAPDHGTATYI   63 (253)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCcEEEEe
Confidence            5899999999999999876664 3456888775

Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se.

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=86.17  E-value=0.66  Score=42.82  Aligned_cols=31  Identities=23%  Similarity=0.371  Sum_probs=23.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.. -..|.|.+
T Consensus        29 ~~~l~G~nGsGKSTLl~~i~G~~~~~~G~v~~   60 (200)
T PRK13540         29 LLHLKGSNGAGKTTLLKLIAGLLNPEKGEILF   60 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCCeeEEE
Confidence            58999999999999998765543 24576554

>PHA02244 ATPase-like protein

Probab=86.17  E-value=1.7  Score=45.33  Aligned_cols=30  Identities=17%  Similarity=0.205  Sum_probs=21.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      ++|.|++|||||++..++ +++....|+.++
T Consensus       122 VLL~GppGtGKTtLA~aL-A~~lg~pfv~In  151 (383)
T PHA02244        122 VFLKGGAGSGKNHIAEQI-AEALDLDFYFMN  151 (383)
T ss_pred             EEEECCCCCCHHHHHHHH-HHHhCCCEEEEe
Confidence            899999999999987665 444444555443

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=86.12  E-value=0.57  Score=46.79  Aligned_cols=31  Identities=32%  Similarity=0.485  Sum_probs=22.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      -++|-|+.||||||+|-.+--.-. ..|-|.+
T Consensus        29 f~vliGpSGsGKTTtLkMINrLiept~G~I~i   60 (309)
T COG1125          29 FLVLIGPSGSGKTTTLKMINRLIEPTSGEILI   60 (309)
T ss_pred             EEEEECCCCCcHHHHHHHHhcccCCCCceEEE
Confidence            379999999999999988754322 3444444

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=86.11  E-value=0.67  Score=43.11  Aligned_cols=31  Identities=29%  Similarity=0.451  Sum_probs=23.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.- -..|.|.+
T Consensus        30 ~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   61 (207)
T PRK13539         30 ALVLTGPNGSGKTTLLRLIAGLLPPAAGTIKL   61 (207)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            48999999999999988776643 24677655

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=86.11  E-value=0.63  Score=43.66  Aligned_cols=31  Identities=35%  Similarity=0.370  Sum_probs=24.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-... ..|-|.+
T Consensus        38 ~~~i~G~nGsGKSTLl~~i~Gl~~p~~G~i~~   69 (228)
T PRK10584         38 TIALIGESGSGKSTLLAILAGLDDGSSGEVSL   69 (228)
T ss_pred             EEEEECCCCCCHHHHHHHHHcCCCCCCeeEEE
Confidence            489999999999999987766533 4576654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=86.10  E-value=0.7  Score=51.52  Aligned_cols=35  Identities=20%  Similarity=0.331  Sum_probs=23.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|++|||||++...+ +.....+++.+.-|+
T Consensus       488 ~giLL~GppGtGKT~lakal-A~e~~~~fi~v~~~~  522 (733)
T TIGR01243       488 KGVLLFGPPGTGKTLLAKAV-ATESGANFIAVRGPE  522 (733)
T ss_pred             ceEEEECCCCCCHHHHHHHH-HHhcCCCEEEEehHH
Confidence            45999999999998766544 444445566555443

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.

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=86.08  E-value=0.67  Score=42.86  Aligned_cols=31  Identities=26%  Similarity=0.358  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      .+.|.|+.|+||||+|.-+.-.- -..|.|.+
T Consensus        29 ~~~l~G~nGsGKSTLl~~l~G~~~~~~G~i~~   60 (211)
T cd03225          29 FVLIVGPNGSGKSTLLRLLNGLLGPTSGEVLV   60 (211)
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCCceEEE
Confidence            48999999999999987665432 24677765

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>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=86.08  E-value=1.2  Score=46.11  Aligned_cols=50  Identities=18%  Similarity=0.244  Sum_probs=35.2

Q ss_pred             EchhHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          162 VRQSFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       162 VRk~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      +.++-.+|+++|+.++..      ....++=++|.||.|+|||++...+-..-.+-
T Consensus        66 ~~~~i~~lV~~fk~AA~g------~~~~krIl~L~GPvg~GKSsl~~~Lk~~le~y  115 (358)
T PF08298_consen   66 MEETIERLVNYFKSAAQG------LEERKRILLLLGPVGGGKSSLAELLKRGLEEY  115 (358)
T ss_pred             cHHHHHHHHHHHHHHHhc------cCccceEEEEECCCCCCHHHHHHHHHHHhheE
Confidence            556677899999876432      11222347899999999999998877655443

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=86.08  E-value=0.67  Score=42.78  Aligned_cols=30  Identities=27%  Similarity=0.357  Sum_probs=24.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLV  221 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIV  221 (404)
                      .+.|.|+.|+|||++|.-+.-.. -.+|.|.
T Consensus        33 ~~~i~G~nG~GKSTLl~~i~G~~~~~~G~i~   63 (204)
T cd03250          33 LVAIVGPVGSGKSSLLSALLGELEKLSGSVS   63 (204)
T ss_pred             EEEEECCCCCCHHHHHHHHhCcCCCCCCeEE
Confidence            59999999999999998776643 3568873

This family is also known as MRP (mulrtidrug resisitance-associated protein). 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.

>cd01892 Miro2 Miro2 subfamily

Probab=86.08  E-value=0.69  Score=41.31  Aligned_cols=21  Identities=24%  Similarity=0.210  Sum_probs=18.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|..|||||+++.+.+.
T Consensus         6 kv~~vG~~~vGKTsli~~~~~   26 (169)
T cd01892           6 LCFVLGAKGSGKSALLRAFLG   26 (169)
T ss_pred             EEEEECCCCCcHHHHHHHHhC
Confidence            589999999999999988763

Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=86.07  E-value=0.92  Score=40.71  Aligned_cols=24  Identities=25%  Similarity=0.260  Sum_probs=19.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      ..+|+|+.|+|||++|.++...+.
T Consensus        23 ~~~i~G~NgsGKS~~l~~i~~~~~   46 (162)
T cd03227          23 LTIITGPNGSGKSTILDAIGLALG   46 (162)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999998554443

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.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=86.06  E-value=0.96  Score=49.20  Aligned_cols=27  Identities=33%  Similarity=0.415  Sum_probs=22.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      ..++|.|+.|+|||++++.+..++...
T Consensus       351 ~vIaLVGPtGvGKTTtaakLAa~la~~  377 (559)
T PRK12727        351 GVIALVGPTGAGKTTTIAKLAQRFAAQ  377 (559)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            358899999999999999998876554

>cd04153 Arl5_Arl8 Arl5/Arl8 subfamily

Probab=86.06  E-value=0.62  Score=41.64  Aligned_cols=22  Identities=18%  Similarity=0.264  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++++.|.+|+|||+++.++..
T Consensus        16 ~kv~~~G~~~~GKTsl~~~l~~   37 (174)
T cd04153          16 YKVIIVGLDNAGKTTILYQFLL   37 (174)
T ss_pred             cEEEEECCCCCCHHHHHHHHcc
Confidence            4699999999999999988863

Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.

>PLN03108 Rab family protein; Provisional

Probab=86.03  E-value=0.68  Score=43.15  Aligned_cols=22  Identities=23%  Similarity=0.244  Sum_probs=19.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|+.|||||+++.++..
T Consensus         7 ~kivivG~~gvGKStLi~~l~~   28 (210)
T PLN03108          7 FKYIIIGDTGVGKSCLLLQFTD   28 (210)
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            3599999999999999988764

>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein

Probab=86.02  E-value=0.66  Score=43.44  Aligned_cols=31  Identities=19%  Similarity=0.546  Sum_probs=23.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-... ..|-|.+
T Consensus        31 ~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   62 (229)
T cd03254          31 TVAIVGPTGAGKTTLINLLMRFYDPQKGQILI   62 (229)
T ss_pred             EEEEECCCCCCHHHHHHHHhcCcCCCCCEEEE
Confidence            489999999999999988865543 3465543

In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar 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.

>TIGR00767 rho transcription termination factor Rho

Probab=86.00  E-value=0.87  Score=47.90  Aligned_cols=27  Identities=15%  Similarity=0.249  Sum_probs=20.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      .+++|.|++|||||+++..+...-..+
T Consensus       169 q~~~IvG~~g~GKTtL~~~i~~~I~~n  195 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKIAQAITRN  195 (415)
T ss_pred             CEEEEECCCCCChhHHHHHHHHhhccc
Confidence            358999999999999877766544433

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

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=85.97  E-value=0.67  Score=43.74  Aligned_cols=31  Identities=23%  Similarity=0.293  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-... ..|-|.+
T Consensus        37 ~~~l~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   68 (233)
T PRK11629         37 MMAIVGSSGSGKSTLLHLLGGLDTPTSGDVIF   68 (233)
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCceEEEE
Confidence            489999999999999877765432 4576654

>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB

Probab=85.96  E-value=0.68  Score=43.08  Aligned_cols=31  Identities=26%  Similarity=0.297  Sum_probs=23.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-... ..|=|.+
T Consensus        25 ~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~   56 (214)
T cd03297          25 VTGIFGASGAGKSTLLRCIAGLEKPDGGTIVL   56 (214)
T ss_pred             eEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            489999999999999887664432 4565544

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. 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.

>cd04111 Rab39 Rab39 subfamily

Probab=85.96  E-value=0.68  Score=43.30  Aligned_cols=21  Identities=24%  Similarity=0.349  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|+.|+|||+++.+++.
T Consensus         4 KIvvvG~~~vGKTsLi~~l~~   24 (211)
T cd04111           4 RLIVIGDSTVGKSSLLKRFTE   24 (211)
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            599999999999999999874

Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.

>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=85.95  E-value=0.72  Score=41.67  Aligned_cols=31  Identities=26%  Similarity=0.413  Sum_probs=22.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-... ..|.|.+
T Consensus        30 ~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~   61 (173)
T cd03246          30 SLAIIGPSGSGKSTLARLILGLLRPTSGRVRL   61 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHhccCCCCCeEEE
Confidence            489999999999999987765432 3455443

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

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=85.95  E-value=0.83  Score=50.54  Aligned_cols=36  Identities=19%  Similarity=0.252  Sum_probs=24.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC-eEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG-WLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng-WIVL~IP~a  227 (404)
                      .++|+|++|||||++...+........ .-++++|++
T Consensus        52 ~~l~~G~~G~GKttla~~l~~~l~~~~~~~~~~~~np   88 (637)
T PRK13765         52 HVMMIGSPGTGKSMLAKAMAELLPKEELQDILVYPNP   88 (637)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHcChHhHHHheEeeCC
Confidence            599999999999998877655422221 334455553

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=85.94  E-value=0.68  Score=43.03  Aligned_cols=31  Identities=32%  Similarity=0.416  Sum_probs=22.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.- -..|=|.+
T Consensus        33 ~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~~   64 (218)
T cd03266          33 VTGLLGPNGAGKTTTLRMLAGLLEPDAGFATV   64 (218)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCcCCCCceEEE
Confidence            48999999999999997665432 24565544

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=85.92  E-value=0.69  Score=42.81  Aligned_cols=31  Identities=35%  Similarity=0.602  Sum_probs=22.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.. ...|-|.+
T Consensus        28 ~~~l~G~nGsGKSTLl~~l~G~~~~~~G~v~~   59 (213)
T cd03301          28 FVVLLGPSGCGKTTTLRMIAGLEEPTSGRIYI   59 (213)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCceEEEE
Confidence            48999999999999997766543 24465544

ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.

>cd04158 ARD1 ARD1 subfamily

Probab=85.90  E-value=0.64  Score=41.27  Aligned_cols=21  Identities=29%  Similarity=0.246  Sum_probs=18.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|.|..|||||+++..++.
T Consensus         1 ~vvlvG~~~~GKTsl~~~l~~   21 (169)
T cd04158           1 RVVTLGLDGAGKTTILFKLKQ   21 (169)
T ss_pred             CEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999988764

ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membra

>cd03298 ABC_ThiQ_thiamine_transporter ABC-type thiamine tranport system; part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP

Probab=85.88  E-value=0.69  Score=42.84  Aligned_cols=31  Identities=23%  Similarity=0.458  Sum_probs=24.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.-. ..|.|.+
T Consensus        26 ~~~l~G~nGsGKSTLl~~l~gl~~~~~G~i~~   57 (211)
T cd03298          26 ITAIVGPSGSGKSTLLNLIAGFETPQSGRVLI   57 (211)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            589999999999999977765432 4677765

Probably responsible for the translocation of thiamine across the membrane. 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. 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.

>TIGR03410 urea_trans_UrtE urea ABC transporter, ATP-binding protein UrtE

Probab=85.88  E-value=0.66  Score=43.55  Aligned_cols=31  Identities=23%  Similarity=0.214  Sum_probs=22.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|.-+.-.-. ..|=|.+
T Consensus        28 ~~~l~G~nGsGKSTLl~~l~G~~~~~~G~i~~   59 (230)
T TIGR03410        28 VTCVLGRNGVGKTTLLKTLMGLLPVKSGSIRL   59 (230)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCCEEEE
Confidence            489999999999999876654432 4566554

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=85.87  E-value=0.69  Score=43.54  Aligned_cols=31  Identities=19%  Similarity=0.220  Sum_probs=22.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        33 ~~~l~G~nGsGKSTLl~~l~G~~~~~~G~i~~   64 (233)
T cd03258          33 IFGIIGRSGAGKSTLIRCINGLERPTSGSVLV   64 (233)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            489999999999998876654432 3566554

Other members of this system include the MetP permease and the MetQ substrate binding protein. 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.

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=85.85  E-value=0.81  Score=45.12  Aligned_cols=31  Identities=26%  Similarity=0.325  Sum_probs=25.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .+.|.|+.|+|||++|.-+.-.....|.|.+
T Consensus        32 ~~~IvG~nGsGKSTLl~~L~gl~~~~G~I~i   62 (275)
T cd03289          32 RVGLLGRTGSGKSTLLSAFLRLLNTEGDIQI   62 (275)
T ss_pred             EEEEECCCCCCHHHHHHHHhhhcCCCcEEEE
Confidence            4899999999999999887766556788765

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=85.81  E-value=1.1  Score=48.18  Aligned_cols=28  Identities=32%  Similarity=0.343  Sum_probs=23.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGW  219 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngW  219 (404)
                      -+.|.|+.|+||||+++.+..+. ...|.
T Consensus       258 Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~  286 (484)
T PRK06995        258 VFALMGPTGVGKTTTTAKLAARCVMRHGA  286 (484)
T ss_pred             EEEEECCCCccHHHHHHHHHHHHHHhcCC
Confidence            38899999999999999999866 45554

>PRK14241 phosphate transporter ATP-binding protein; Provisional

Probab=85.79  E-value=0.69  Score=44.43  Aligned_cols=31  Identities=35%  Similarity=0.481  Sum_probs=25.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH------hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR------EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~------~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-.      .+|-|.+
T Consensus        32 ~~~i~G~nGsGKSTLl~~laGl~~~~~~~~~~G~I~~   68 (258)
T PRK14241         32 VTAFIGPSGCGKSTVLRTLNRMHEVIPGARVEGEVLL   68 (258)
T ss_pred             EEEEECCCCCCHHHHHHHHhccCCcccCCCcceEEEE
Confidence            489999999999999988776543      4787776

>TIGR01978 sufC FeS assembly ATPase SufC

Probab=85.78  E-value=0.68  Score=43.71  Aligned_cols=31  Identities=19%  Similarity=0.223  Sum_probs=23.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH---HHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW---AREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~---A~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.   --..|-|.+
T Consensus        28 ~~~i~G~nGsGKSTLl~~l~Gl~~~~~~~G~i~~   61 (243)
T TIGR01978        28 IHAIMGPNGSGKSTLSKTIAGHPSYEVTSGTILF   61 (243)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCCcceEEE
Confidence            4899999999999998777654   234677655

SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic (PubMed:12554644) or associated with the membrane (PubMed:11943156). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=85.77  E-value=0.72  Score=41.77  Aligned_cols=21  Identities=38%  Similarity=0.423  Sum_probs=17.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+.|.|+.|||||++|.-+.-
T Consensus        30 ~~~i~G~nGsGKStLl~~l~G   50 (178)
T cd03247          30 KIALLGRSGSGKSTLLQLLTG   50 (178)
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999998877653

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.

>cd01898 Obg Obg subfamily

Probab=85.76  E-value=0.67  Score=40.37  Aligned_cols=20  Identities=30%  Similarity=0.320  Sum_probs=18.3

Q ss_pred             EEEECCCCCcHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++|.|..|+|||+++..+..
T Consensus         3 v~ivG~~~~GKStl~~~l~~   22 (170)
T cd01898           3 VGLVGLPNAGKSTLLSAISN   22 (170)
T ss_pred             eEEECCCCCCHHHHHHHHhc
Confidence            78999999999999999864

The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain.

>cd00881 GTP_translation_factor GTP translation factor family

Probab=85.76  E-value=0.66  Score=40.88  Aligned_cols=23  Identities=17%  Similarity=0.177  Sum_probs=20.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      +++.|..|+|||+++.++.....
T Consensus         2 v~v~G~~~~GKStlln~l~~~~~   24 (189)
T cd00881           2 VGIAGHVDHGKTTLTERLLYVTG   24 (189)
T ss_pred             EEEEeCCCCCHHHHHHHHHHhcC
Confidence            78999999999999999876643

This family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function.

>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=85.75  E-value=0.59  Score=48.13  Aligned_cols=30  Identities=33%  Similarity=0.664  Sum_probs=22.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      +.|-||.||||||+|..+.-+-. ..|-|.|
T Consensus        34 ~~lLGPSGcGKTTlLR~IAGfe~p~~G~I~l   64 (352)
T COG3842          34 VTLLGPSGCGKTTLLRMIAGFEQPSSGEILL   64 (352)
T ss_pred             EEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            67999999999999988776533 3454444

---

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	404
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04

>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 = 52.9 bits (126), Expect = 1e-07
 Identities = 42/314 (13%), Positives = 84/314 (26%), Gaps = 88/314 (28%)

Query: 117 LSLLTRKDACTYFKFSEDELNAMLPEGLPTGMLGEFKDSMRYALLVRQSFLDIRDNFRRI 176
              L  K      KF E+ L           ++   K   R   ++ + +++ RD     
Sbjct: 68  FWTLLSKQEEMVQKFVEEVLRINYK-----FLMSPIKTEQRQPSMMTRMYIEQRDRLYND 122

Query: 177 VDPSLQSTNGP------KIRKQ---------IVLDGPLCCGKSITLAML----------- 210
                   N        K+R+          +++DG L  GK+  +A+            
Sbjct: 123 NQV-FAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT-WVALDVCLSYKVQCKM 180

Query: 211 ---VHWA------REEGWLV----LYVPRGREWTHGGYFYKNPQTGLWDTPLQAENVLKD 257
              + W         E  L     L       WT       N +  +       +  L+ 
Sbjct: 181 DFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHS----IQAELRR 236

Query: 258 FIK---YNESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDL-VQMGINQM 313
            +K   Y    L      +L                V + +       F+L  ++ +   
Sbjct: 237 LLKSKPYENCLL------VLL--------------NVQNAKAWNA---FNLSCKILLTTR 273

Query: 314 HASV--GVVVRLRKELSLVKDIPVLI---AIDQYNNWFTFSEYEEPVTIRSTRPVHAREL 368
              V   +       +SL      L           +      + P  + +T P     L
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR---L 330

Query: 369 AMVNAFRSMMHNDM 382
           +++      + + +
Sbjct: 331 SIIAE---SIRDGL 341

>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 = 48.3 bits (114), Expect = 3e-06
 Identities = 59/370 (15%), Positives = 98/370 (26%), Gaps = 132/370 (35%)

Query: 22  TVLTSTSILIHQFFYSTKTQTKSSKKKQDDNKKS-SKSKSKSSDANSLSAPAAAQADSAD 80
            +LT+    +  F  +  T    +    D +  + +  + KS     L            
Sbjct: 268 ILLTTRFKQVTDFLSAATT----THISLDHHSMTLTPDEVKSLLLKYLDC-------RPQ 316

Query: 81  DLESVRARARRLAEDDRNP--------SLDVGPNH-----RPLFTKTT-----SLSLLTR 122
           DL        R      NP        S+  G             K T     SL++L  
Sbjct: 317 DL-------PREVLT-TNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP 368

Query: 123 KDACTYFKFSEDELNAMLPEG--LPTGMLG------EFKDSMRYA-LLVRQSFLDIRDNF 173
            +    F      L ++ P    +PT +L          D M     L + S ++ +   
Sbjct: 369 AEYRKMFD----RL-SVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKE 423

Query: 174 RRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWLV-LY-VPRGREWT 231
             I  PS+      K+  +  L                H  R    +V  Y +P+  +  
Sbjct: 424 STISIPSIYLELKVKLENEYAL----------------H--RS---IVDHYNIPKTFDSD 462

Query: 232 HG------GYFY-------------------------------KNPQTGL-WDTPLQAEN 253
                    YFY                               K       W+      N
Sbjct: 463 DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILN 522

Query: 254 VLKDFIKY------NESHLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFDLVQ 307
            L+    Y      N+     L   ILD +P        L+    SK         DL++
Sbjct: 523 TLQQLKFYKPYICDNDPKYERLVNAILDFLP---KIEENLIC---SKYT-------DLLR 569

Query: 308 MGINQMHASV 317
           + +     ++
Sbjct: 570 IALMAEDEAI 579

>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 = 41.4 bits (96), Expect = 5e-04
 Identities = 53/349 (15%), Positives = 103/349 (29%), Gaps = 116/349 (33%)

Query: 89  ARRLAEDDRNPSL---------DVGPNHRPLFTKTTSLSLLTRKDACTYFKFSEDELNAM 139
              +  + R PS+         D   N   +F K      ++R            +L   
Sbjct: 95  MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN----VSRLQP-------YLKLRQA 143

Query: 140 LPEGLPT------GMLGEFKDSMRYALLVRQSF------------------------LDI 169
           L E  P       G+LG  K  +  AL V  S+                        L++
Sbjct: 144 LLELRPAKNVLIDGVLGSGKTWV--ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEM 201

Query: 170 RDNFRRIVDPSL-----QSTNGP--------KIRKQ----------IVLDGPLCCGKSIT 206
                  +DP+       S+N          ++R+           +VL           
Sbjct: 202 LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN--VQNAKAW 259

Query: 207 LAMLVHWAREEGWLVLYVPRGREWTH--GGYFYKNPQTGLWDTPLQAENVLKDFIKYNES 264
            A  +   +     +L   R ++ T         +         L  + V    +KY + 
Sbjct: 260 NAFNLS-CK-----ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDC 313

Query: 265 HLRELPCQILDPIPLGEGAGVGLLKGVDSKEISEGSTLFD-LVQMGINQMHASVGVVVR- 322
             ++LP ++L   P      + ++    ++ I +G   +D    +  +++   +   +  
Sbjct: 314 RPQDLPREVLTTNPR----RLSII----AESIRDGLATWDNWKHVNCDKLTTIIESSLNV 365

Query: 323 -----LRK---ELSL----VKDIP--VLIAIDQYNNWFTFSEYEEPVTI 357
                 RK    LS+       IP  +L  I     WF      + + +
Sbjct: 366 LEPAEYRKMFDRLSVFPPSAH-IPTILLSLI-----WFD-VIKSDVMVV 407

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	404
3bos_A	242	Putative DNA replication factor; P-loop containing	96.56
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.46
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	96.17
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.04
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	95.98
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	95.87
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	95.83
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	95.8
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	95.78
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	95.77
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	95.74
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	95.73
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.73
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.46
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	95.36
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	95.34
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	95.31
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.3
2qgz_A	308	Helicase loader, putative primosome component; str	95.11
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	95.09
2chg_A	226	Replication factor C small subunit; DNA-binding pr	94.99
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	94.93
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	94.88
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.88
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	94.85
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	94.79
3io5_A	333	Recombination and repair protein; storage dimer, i	94.73
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	94.73
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	94.63
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	94.61
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	94.59
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	94.53
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	94.5
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	94.5
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	94.47
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	94.46
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	94.42
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	94.4
2cvh_A	220	DNA repair and recombination protein RADB; filamen	94.4
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	94.4
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	94.39
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	94.27
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	94.24
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	94.23
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	94.22
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	94.1
1u94_A	356	RECA protein, recombinase A; homologous recombinat	94.08
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	94.03
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	93.91
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	93.91
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	93.85
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	93.83
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	93.74
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	93.72
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	93.69
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	93.66
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	93.66
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	93.66
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	93.61
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	93.55
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	93.55
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	93.55
2fna_A	357	Conserved hypothetical protein; structural genomic	93.53
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	93.52
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	93.48
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	93.48
1xp8_A	366	RECA protein, recombinase A; recombination, radior	93.44
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	93.41
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	93.32
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	93.31
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	93.29
2z43_A	324	DNA repair and recombination protein RADA; archaea	93.28
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	93.26
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	93.26
2chq_A	319	Replication factor C small subunit; DNA-binding pr	93.25
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	93.19
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	93.19
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	93.17
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	93.16
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	93.15
4a74_A	231	DNA repair and recombination protein RADA; hydrola	93.11
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	93.07
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	93.05
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	93.03
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	93.02
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	93.02
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	92.97
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	92.93
2ged_A	193	SR-beta, signal recognition particle receptor beta	92.9
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	92.9
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	92.72
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	92.69
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	92.68
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	92.68
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	92.62
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	92.59
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	92.56
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	92.54
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	92.53
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	92.51
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	92.5
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	92.47
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	92.44
2r6a_A	454	DNAB helicase, replicative helicase; replication,	92.42
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	92.42
1via_A	175	Shikimate kinase; structural genomics, transferase	92.39
1tue_A	212	Replication protein E1; helicase, replication, E1E	92.38
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	92.38
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	92.37
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	92.35
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	92.3
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	92.29
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	92.27
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	92.23
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	92.17
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	92.13
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	92.12
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	92.1
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	92.1
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	92.08
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	92.07
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	92.06
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	91.99
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	91.96
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	91.93
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	91.93
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	91.89
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	91.88
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	91.88
3co5_A	143	Putative two-component system transcriptional RES	91.87
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	91.83
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	91.82
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	91.76
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	91.75
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	91.74
2eyu_A	261	Twitching motility protein PILT; pilus retraction	91.71
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	91.68
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	91.64
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	91.61
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	91.58
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	91.48
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	91.47
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	91.41
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	91.39
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	91.37
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	91.36
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	91.32
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	91.29
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	91.23
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	91.2
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	91.18
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	91.16
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	91.11
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	91.09
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	91.08
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	91.07
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	91.03
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	91.03
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	90.98
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	90.97
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	90.94
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	90.94
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	90.91
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	90.88
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	90.86
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	90.86
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	90.86
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	90.83
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	90.81
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	90.81
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	90.81
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	90.8
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	90.78
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	90.78
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	90.73
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	90.69
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	90.68
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	90.67
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	90.67
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	90.61
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	90.6
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	90.6
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	90.57
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	90.55
2wji_A	165	Ferrous iron transport protein B homolog; membrane	90.48
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	90.46
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	90.45
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	90.41
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	90.39
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	90.35
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	90.34
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	90.34
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	90.32
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	90.3
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	90.29
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	90.26
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	90.26
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	90.25
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	90.24
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	90.23
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	90.23
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	90.22
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	90.19
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	90.16
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	90.16
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	90.09
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	90.08
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	90.03
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	89.99
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	89.99
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	89.98
2hf9_A	226	Probable hydrogenase nickel incorporation protein	89.97
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	89.95
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	89.91
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	89.89
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	89.88
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	89.86
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	89.85
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	89.79
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	89.79
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	89.76
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	89.66
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	89.66
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	89.65
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	89.65
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	89.65
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	89.61
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	89.6
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	89.51
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	89.5
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	89.49
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	89.47
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.46
1nrj_B	218	SR-beta, signal recognition particle receptor beta	89.41
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	89.31
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	89.3
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	89.29
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	89.28
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	89.27
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	89.25
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	89.23
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	89.22
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	89.18
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	89.17
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	89.17
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	89.14
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	89.12
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	89.06
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	89.06
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	89.0
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	88.94
3kta_A	182	Chromosome segregation protein SMC; structural mai	88.94
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	88.93
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	88.86
2ewv_A	372	Twitching motility protein PILT; pilus retraction	88.84
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	88.83
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	88.81
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	88.8
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	88.78
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	88.75
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	88.67
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	88.67
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	88.66
2vli_A	183	Antibiotic resistance protein; transferase, tunica	88.64
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	88.62
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	88.62
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	88.57
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	88.53
1p9r_A	418	General secretion pathway protein E; bacterial typ	88.52
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	88.49
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	88.48
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	88.48
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	88.47
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	88.47
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	88.47
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	88.46
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	88.44
2r44_A	331	Uncharacterized protein; putative ATPase, structur	88.43
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	88.43
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	88.41
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	88.3
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	88.28
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	88.23
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	88.23
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	88.23
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	88.18
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	88.16
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	88.11
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	88.05
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	88.02
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	88.01
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	87.99
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	87.99
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	87.98
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	87.97
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	87.95
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	87.82
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	87.75
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	87.7
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	87.69
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	87.68
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	87.68
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	87.68
2og2_A	359	Putative signal recognition particle receptor; nuc	87.67
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	87.61
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	87.6
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	87.55
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	87.54
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	87.54
3pvs_A	447	Replication-associated recombination protein A; ma	87.53
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	87.52
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	87.52
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	87.47
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	87.44
2fh5_B	214	SR-beta, signal recognition particle receptor beta	87.43
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	87.43
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	87.42
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	87.42
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	87.41
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	87.39
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	87.39
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	87.38
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	87.35
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	87.34
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	87.3
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	87.27
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	87.25
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	87.17
1sgw_A	214	Putative ABC transporter; structural genomics, P p	87.09
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	87.03
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	87.01
1b0u_A	262	Histidine permease; ABC transporter, transport pro	87.0
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	87.0
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	86.94
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	86.94
1ji0_A	240	ABC transporter; ATP binding protein, structural g	86.93
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	86.9
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	86.84
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	86.82
1g6h_A	257	High-affinity branched-chain amino acid transport	86.8
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	86.78
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	86.78
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	86.76
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	86.74
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	86.73
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	86.72
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	86.66
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	86.64
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	86.62
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	86.61
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	86.6
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	86.58
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	86.47
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	86.46
2xxa_A	433	Signal recognition particle protein; protein trans	86.43
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	86.43
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	86.42
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	86.41
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	86.34
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	86.31
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	86.24
3szr_A	608	Interferon-induced GTP-binding protein MX1; interf	86.23
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	86.22
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	86.04
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	85.95
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	85.87
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	85.86
2ghi_A	260	Transport protein; multidrug resistance protein, M	85.84
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	85.78
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	85.77
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	85.76
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	85.73
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	85.72
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	85.71
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	85.69
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	85.67
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	85.66
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	85.66
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	85.64
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	85.64
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	85.64
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	85.62
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	85.57
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	85.57
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	85.54
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	85.52
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	85.51
3ice_A	422	Transcription termination factor RHO; transcriptio	85.46
1of1_A	376	Thymidine kinase; transferase, antiviral drug, enz	85.42
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	85.42
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	85.38
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	85.28
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	85.26
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	85.25
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	85.25
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	85.23
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	85.18
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	85.13
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	85.02
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	84.99
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	84.99
1e2k_A	331	Thymidine kinase; transferase, antiviral drug, enz	84.99
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	84.99
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	84.98
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	84.97
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	84.97
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	84.94
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	84.91
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	84.82
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	84.8
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	84.74
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	84.72
3llu_A	196	RAS-related GTP-binding protein C; structural geno	84.59
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	84.57
3b6e_A	216	Interferon-induced helicase C domain-containing P;	84.57
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	84.57
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	84.53
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	84.51
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	84.51
3t34_A	360	Dynamin-related protein 1A, linker, dynamin-relat	84.5
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	84.49
3a1s_A	258	Iron(II) transport protein B; FEOB, iron transport	84.49
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	84.35
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	84.25
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	84.23
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	84.21
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	84.2
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	84.12
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	84.05
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	84.02
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	83.93
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	83.88
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	83.85
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	83.82
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	83.8
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	83.62
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	83.62
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	83.6
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	83.55
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	83.52
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	83.45
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	83.45
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	83.3
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	83.27
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	83.18
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	83.16
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	83.15
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	83.07
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	83.03
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	82.93
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	82.93
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	82.89
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	82.8
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	82.77
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	82.72
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	82.58
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	82.48
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	82.43
1zcb_A	362	G alpha I/13; GTP-binding, lipoprotein, membrane,	82.41
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	82.27
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	82.25
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	82.11
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	82.05
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	81.88
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	81.88
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	81.85
3t5d_A	274	Septin-7; GTP-binding protein, cytoskeleton, signa	81.83
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	81.82
3i8s_A	274	Ferrous iron transport protein B; GTPase, GPCR, ir	81.63
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	81.63
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	81.47
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	81.46
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	81.33
2x2e_A	353	Dynamin-1; nitration, hydrolase, membrane fission,	81.21
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	81.2
3qkt_A	339	DNA double-strand break repair RAD50 ATPase; RECA-	81.09
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	81.02
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	80.86
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	80.79
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	80.78
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	80.76
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	80.75
3r7w_A	307	Gtpase1, GTP-binding protein GTR1; RAG gtpases, GT	80.68
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	80.57
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	80.16
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	80.16
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	80.05
3th5_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	80.22

>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=96.56  E-value=0.003  Score=56.38  Aligned_cols=36  Identities=25%  Similarity=0.349  Sum_probs=30.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      ..++|+|++|||||+++.++...+...++-|+++..
T Consensus        53 ~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~   88 (242)
T 3bos_A           53 QAIYLWGPVKSGRTHLIHAACARANELERRSFYIPL   88 (242)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEG
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEH
Confidence            359999999999999999998888888887777754

>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=96.46  E-value=0.0014  Score=57.25  Aligned_cols=34  Identities=15%  Similarity=0.145  Sum_probs=28.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH-hCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR-EEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL~I  224 (404)
                      ..++|+|++|||||+++..+..... .+|+.|+++
T Consensus        39 ~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~   73 (180)
T 3ec2_A           39 KGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFF   73 (180)
T ss_dssp             CEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            3589999999999999999888776 678766664

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=96.17  E-value=0.0046  Score=55.48  Aligned_cols=32  Identities=25%  Similarity=0.310  Sum_probs=27.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++++|++|+|||++|.++++.+..+|.=|+.+
T Consensus         6 ~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~   37 (184)
T 2orw_A            6 TVITGPMYSGKTTELLSFVEIYKLGKKKVAVF   37 (184)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            79999999999999999999888777755554

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.04  E-value=0.0057  Score=54.18  Aligned_cols=33  Identities=24%  Similarity=0.285  Sum_probs=27.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|++|||||+++..+...+..+|.-|+++
T Consensus        56 ~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~   88 (202)
T 2w58_A           56 GLYLHGSFGVGKTYLLAAIANELAKRNVSSLIV   88 (202)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            589999999999999888888777776655554

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=95.98  E-value=0.0087  Score=50.77  Aligned_cols=25  Identities=24%  Similarity=0.177  Sum_probs=21.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE  216 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~  216 (404)
                      .++|+|++|||||+++.++......
T Consensus        45 ~~ll~G~~G~GKT~l~~~~~~~~~~   69 (195)
T 1jbk_A           45 NPVLIGEPGVGKTAIVEGLAQRIIN   69 (195)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHh
Confidence            4899999999999999888776654

>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=95.87  E-value=0.014  Score=56.09  Aligned_cols=34  Identities=24%  Similarity=0.305  Sum_probs=29.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP  225 (404)
                      .++|+|++|||||+++..+....... +|-++++.
T Consensus        46 ~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~   80 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLRKLWELYKDKTTARFVYIN   80 (389)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEe
Confidence            48999999999999998888877666 68888875

>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=95.83  E-value=0.0071  Score=56.54  Aligned_cols=33  Identities=21%  Similarity=0.251  Sum_probs=29.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++++|+.|+|||++|.|+++.+...|.-|+++
T Consensus        14 i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~   46 (223)
T 2b8t_A           14 IEFITGPMFAGKTAELIRRLHRLEYADVKYLVF   46 (223)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEE
Confidence            389999999999999999999998888777766

>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=95.80  E-value=0.0067  Score=58.03  Aligned_cols=35  Identities=26%  Similarity=0.397  Sum_probs=30.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      .++|+|++|||||+++..+......+++-++|++.
T Consensus        39 ~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~   73 (324)
T 1l8q_A           39 PIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSA   73 (324)
T ss_dssp             SEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEH
T ss_pred             eEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEH
Confidence            48999999999999998888888777888888753

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=95.78  E-value=0.0086  Score=51.01  Aligned_cols=25  Identities=20%  Similarity=0.113  Sum_probs=21.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE  216 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~  216 (404)
                      .++|+|++|||||+++..+......
T Consensus        45 ~vll~G~~G~GKT~la~~~~~~~~~   69 (187)
T 2p65_A           45 NPILLGDPGVGKTAIVEGLAIKIVQ   69 (187)
T ss_dssp             EEEEESCGGGCHHHHHHHHHHHHHT
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHh
Confidence            4899999999999999888776654

>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=95.77  E-value=0.0083  Score=53.54  Aligned_cols=34  Identities=24%  Similarity=0.199  Sum_probs=28.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|+|+.||||||++..+...-...|++++++-
T Consensus        27 ~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~~~d   60 (200)
T 3uie_A           27 VIWVTGLSGSGKSTLACALNQMLYQKGKLCYILD   60 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCceEEEec
Confidence            4899999999999999888776667899866653

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=95.74  E-value=0.01  Score=56.76  Aligned_cols=34  Identities=18%  Similarity=0.191  Sum_probs=28.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC------CeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE------GWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n------gWIVL~IP  225 (404)
                      .++|+|++|||||+++..+.......      ++.++++.
T Consensus        46 ~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~   85 (387)
T 2v1u_A           46 NALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVN   85 (387)
T ss_dssp             CEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEE
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEE
Confidence            48999999999999998888776554      78888874

>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=95.73  E-value=0.015  Score=56.04  Aligned_cols=34  Identities=18%  Similarity=0.114  Sum_probs=28.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC--------CeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE--------GWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n--------gWIVL~IP  225 (404)
                      .++|+|++|||||+++..+.......        +|-++++.
T Consensus        47 ~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~   88 (384)
T 2qby_B           47 SNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVN   88 (384)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEE
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEE
Confidence            49999999999999998888776554        88888775

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.73  E-value=0.0071  Score=54.58  Aligned_cols=33  Identities=27%  Similarity=0.295  Sum_probs=28.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHH-HHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHW-AREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~-A~~ngWIVL~IP  225 (404)
                      ++|.|++|+|||+++.|++.. |...|+-|+|+.
T Consensus        33 ~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s   66 (251)
T 2zts_A           33 VLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVT   66 (251)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeec
Confidence            899999999999999997765 566688888873

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.46  E-value=0.011  Score=53.34  Aligned_cols=34  Identities=24%  Similarity=0.255  Sum_probs=28.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|+|||+++.|++..+..+|.=|+|+.
T Consensus        25 ~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~   58 (247)
T 2dr3_A           25 VVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVA   58 (247)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            3899999999999999999887777666666663

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=95.36  E-value=0.0094  Score=51.62  Aligned_cols=35  Identities=31%  Similarity=0.211  Sum_probs=29.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      .++|+|+.|||||+++.-+...+..+|.=++|++.
T Consensus        38 ~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~   72 (149)
T 2kjq_A           38 FIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDA   72 (149)
T ss_dssp             EEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEET
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcH
Confidence            48999999999999999988888777866666653

>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=95.34  E-value=0.011  Score=56.44  Aligned_cols=34  Identities=15%  Similarity=0.303  Sum_probs=28.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC---CeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE---GWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n---gWIVL~IP  225 (404)
                      .++|+|++|||||+++..+.......   ++-++++.
T Consensus        47 ~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~   83 (386)
T 2qby_A           47 NIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYIN   83 (386)
T ss_dssp             CEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEE
Confidence            48999999999999999888766554   77777775

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=95.31  E-value=0.015  Score=49.53  Aligned_cols=26  Identities=19%  Similarity=0.257  Sum_probs=19.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      ++|+|++|||||++...+...+...+
T Consensus        27 vll~G~~GtGKt~lA~~i~~~~~~~~   52 (145)
T 3n70_A           27 VWLYGAPGTGRMTGARYLHQFGRNAQ   52 (145)
T ss_dssp             EEEESSTTSSHHHHHHHHHHSSTTTT
T ss_pred             EEEECCCCCCHHHHHHHHHHhCCccC
Confidence            89999999999977766555544333

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.30  E-value=0.012  Score=52.14  Aligned_cols=33  Identities=27%  Similarity=0.311  Sum_probs=25.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|++|||||+++.++...+..++.=|+|+
T Consensus        25 ~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~   57 (235)
T 2w0m_A           25 FIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYV   57 (235)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            389999999999999999996655444334443

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.11  E-value=0.018  Score=55.63  Aligned_cols=34  Identities=29%  Similarity=0.339  Sum_probs=28.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH-hCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR-EEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL~I  224 (404)
                      ..++|+|++|||||.++..+...+. .+|.-|+++
T Consensus       153 ~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~  187 (308)
T 2qgz_A          153 KGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLL  187 (308)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEE
Confidence            3599999999999999988888887 777766655

>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=95.09  E-value=0.015  Score=58.11  Aligned_cols=34  Identities=15%  Similarity=0.176  Sum_probs=29.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|||||+++.|++..+...|--|+||.
T Consensus        63 i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId   96 (356)
T 3hr8_A           63 IVEIFGQESSGKTTLALHAIAEAQKMGGVAAFID   96 (356)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEe
Confidence            3799999999999999999998887777777874

>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=94.99  E-value=0.015  Score=50.46  Aligned_cols=27  Identities=26%  Similarity=0.326  Sum_probs=22.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      .++|+|++|||||+++.++.......+
T Consensus        40 ~~ll~G~~G~GKT~l~~~l~~~~~~~~   66 (226)
T 2chg_A           40 HLLFSGPPGTGKTATAIALARDLFGEN   66 (226)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHHGGG
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhccc
Confidence            399999999999999988877654443

>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=94.93  E-value=0.02  Score=48.19  Aligned_cols=29  Identities=31%  Similarity=0.389  Sum_probs=24.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|++|||||++...+    ...||.++.+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L----~~~g~~~i~~   31 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL----KERGAKVIVM   31 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH----HHTTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHH----HHCCCcEEEH
Confidence            4899999999999988777    5668888875

>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=94.88  E-value=0.033  Score=54.05  Aligned_cols=34  Identities=21%  Similarity=0.224  Sum_probs=28.3

Q ss_pred             eEEE--ECCCCCcHHHHHHHHHHHHHhC------CeEEEEec
Q 045329          192 QIVL--DGPLCCGKSITLAMLVHWAREE------GWLVLYVP  225 (404)
Q Consensus       192 r~vL--~G~rGsGKS~~L~qav~~A~~n------gWIVL~IP  225 (404)
                      .++|  +|++|+|||+++.++.......      ++.++++.
T Consensus        52 ~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~   93 (412)
T 1w5s_A           52 NMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVN   93 (412)
T ss_dssp             EEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEE
T ss_pred             EEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEE
Confidence            4788  9999999999999988776553      78888886

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=94.85  E-value=0.026  Score=54.62  Aligned_cols=33  Identities=9%  Similarity=0.024  Sum_probs=29.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++|.|++|+|||+++.|+...+..+|.-|+||.
T Consensus        71 ~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~s  103 (315)
T 3bh0_A           71 VLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  103 (315)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEE
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            899999999999999999988877887777763

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=94.79  E-value=0.044  Score=53.88  Aligned_cols=56  Identities=9%  Similarity=-0.097  Sum_probs=37.8

Q ss_pred             ch-hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHhC-------CeEEEEecC
Q 045329          163 RQ-SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREE-------GWLVLYVPR  226 (404)
Q Consensus       163 Rk-~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~n-------gWIVL~IP~  226 (404)
                      |+ +..+|...|...+...     .+   +.++|+|++|||||++...++.-....       +..++||..
T Consensus        25 Re~E~~~i~~~L~~~i~~~-----~~---~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc   88 (318)
T 3te6_A           25 QVEDFTRIFLPIYDSLMSS-----QN---KLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDA   88 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHTT-----CC---CEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEET
T ss_pred             HHHHHHHHHHHHHHHhcCC-----CC---CeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEec
Confidence            44 5566666777665321     22   348999999999999998887755432       567777753

>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=94.73  E-value=0.022  Score=56.59  Aligned_cols=34  Identities=21%  Similarity=0.128  Sum_probs=28.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP  225 (404)
                      .+.|+|++|||||++++|+++-+.++  |-.|+||.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId   65 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYD   65 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEe
Confidence            58999999999999999999988765  56677764

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=94.73  E-value=0.019  Score=60.81  Aligned_cols=32  Identities=28%  Similarity=0.452  Sum_probs=27.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .+|.||+|||||+++++++.+...+|+=||-+
T Consensus       208 ~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~  239 (646)
T 4b3f_X          208 AIIHGPPGTGKTTTVVEIILQAVKQGLKVLCC  239 (646)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            79999999999999999999988887655544

>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=94.63  E-value=0.023  Score=56.18  Aligned_cols=35  Identities=23%  Similarity=0.307  Sum_probs=30.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -++|+|++|||||+++.|++..+..+|--|+||.-
T Consensus        63 iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~   97 (349)
T 2zr9_A           63 VIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDA   97 (349)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEC
Confidence            38999999999999999999988888777777754

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=94.59  E-value=0.03  Score=47.85  Aligned_cols=31  Identities=19%  Similarity=0.118  Sum_probs=25.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|.+|||||++...+...  ..||.++..
T Consensus         4 ~I~i~G~~GsGKST~a~~L~~~--~~~~~~i~~   34 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAREFIAK--NPGFYNINR   34 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH--STTEEEECH
T ss_pred             EEEEecCCCCCHHHHHHHHHhh--cCCcEEecH
Confidence            4899999999999998777652  568887764

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.53  E-value=0.026  Score=57.81  Aligned_cols=32  Identities=19%  Similarity=0.222  Sum_probs=22.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++++||||+|||||++. .+++  .+-|+-++.|.
T Consensus       216 rGvLLyGPPGTGKTllA-kAiA--~e~~~~f~~v~  247 (434)
T 4b4t_M          216 KGALMYGPPGTGKTLLA-RACA--AQTNATFLKLA  247 (434)
T ss_dssp             CEEEEESCTTSSHHHHH-HHHH--HHHTCEEEEEE
T ss_pred             CeeEEECcCCCCHHHHH-HHHH--HHhCCCEEEEe
Confidence            57999999999999774 3433  33455555553

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=94.50  E-value=0.025  Score=54.85  Aligned_cols=35  Identities=23%  Similarity=0.278  Sum_probs=24.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +.++|+|++|||||++...+...+....++.+..+
T Consensus        46 ~~iLL~GppGtGKT~la~ala~~~~~~~~~~i~~~   80 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLAKAVATEANNSTFFSISSS   80 (322)
T ss_dssp             SEEEEESSSSSCHHHHHHHHHHHTTSCEEEEEECC
T ss_pred             ceEEEECCCCccHHHHHHHHHHHcCCCcEEEEEhH
Confidence            46999999999999988766665533344444443

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=94.50  E-value=0.032  Score=48.17  Aligned_cols=34  Identities=21%  Similarity=0.133  Sum_probs=27.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .++|.|.+||||||+...+...-...|.-+.++|
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~~~   36 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDNQGINNKIIN   36 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCceEEEEE
Confidence            4899999999999999888876555676566665

>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=94.47  E-value=0.038  Score=51.12  Aligned_cols=34  Identities=12%  Similarity=0.063  Sum_probs=22.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .++|+|++|||||+++..+.......+.-+++|+
T Consensus        31 ~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~   64 (265)
T 2bjv_A           31 PVLIIGERGTGKELIASRLHYLSSRWQGPFISLN   64 (265)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEE
T ss_pred             CEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEe
Confidence            3899999999999766555555444444444443

>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=94.46  E-value=0.029  Score=52.99  Aligned_cols=33  Identities=18%  Similarity=-0.013  Sum_probs=27.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~I  224 (404)
                      -++|.|++|+|||+++.++......+ |+=|+++
T Consensus        37 ~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~   70 (296)
T 1cr0_A           37 VIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLA   70 (296)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEE
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            38999999999999999998876654 8666665

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=94.42  E-value=0.025  Score=53.31  Aligned_cols=30  Identities=20%  Similarity=0.112  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|+|++|+|||+++.++...+   +|+.+..
T Consensus        33 ~v~i~G~~G~GKT~Ll~~~~~~~---~~~~~~~   62 (350)
T 2qen_A           33 LTLLLGIRRVGKSSLLRAFLNER---PGILIDC   62 (350)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS---SEEEEEH
T ss_pred             eEEEECCCcCCHHHHHHHHHHHc---CcEEEEe
Confidence            48999999999999999987654   5555443

>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=94.40  E-value=0.021  Score=50.01  Aligned_cols=27  Identities=19%  Similarity=0.188  Sum_probs=22.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      .++|+|++|+|||+++.++.......+
T Consensus        47 ~~ll~G~~G~GKT~l~~~~~~~~~~~~   73 (250)
T 1njg_A           47 AYLFSGTRGVGKTSIARLLAKGLNCET   73 (250)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHCTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCCC
Confidence            489999999999999988876655444

>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=94.40  E-value=0.03  Score=49.52  Aligned_cols=31  Identities=26%  Similarity=0.224  Sum_probs=25.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|||||+++.|+..   ..|.=|+||.
T Consensus        22 ~~~i~G~~GsGKTtl~~~l~~---~~~~~v~~i~   52 (220)
T 2cvh_A           22 LTQVYGPYASGKTTLALQTGL---LSGKKVAYVD   52 (220)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH---HHCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHH---HcCCcEEEEE
Confidence            489999999999999999987   4455566653

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=94.40  E-value=0.037  Score=49.23  Aligned_cols=29  Identities=17%  Similarity=0.115  Sum_probs=23.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      -++|.|+.||||||++..+...-   |++++.
T Consensus        31 ~i~l~G~~GsGKSTl~~~L~~~~---g~~~i~   59 (200)
T 4eun_A           31 HVVVMGVSGSGKTTIAHGVADET---GLEFAE   59 (200)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH---CCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh---CCeEEc
Confidence            48999999999999988775433   888775

>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=94.39  E-value=0.034  Score=51.96  Aligned_cols=34  Identities=24%  Similarity=0.174  Sum_probs=29.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|.+|||||++...+..+....||.++++.
T Consensus         6 lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~   39 (260)
T 3a4m_A            6 LIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLG   39 (260)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEEC
Confidence            4899999999999999988887667899888663

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=94.27  E-value=0.038  Score=47.34  Aligned_cols=29  Identities=28%  Similarity=0.281  Sum_probs=21.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      .++|+|+.||||||++..+..   .-|+.++.
T Consensus         6 ~i~l~G~~GsGKSTl~~~La~---~l~~~~id   34 (173)
T 1kag_A            6 NIFLVGPMGAGKSTIGRQLAQ---QLNMEFYD   34 (173)
T ss_dssp             CEEEECCTTSCHHHHHHHHHH---HTTCEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHH---HhCCCEEe
Confidence            489999999999999876633   34665543

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=94.24  E-value=0.043  Score=47.47  Aligned_cols=34  Identities=21%  Similarity=0.362  Sum_probs=28.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .++|+|..||||||+...+...-...|+-|+...
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~d   35 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYR   35 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            3799999999999999888877666788877653

>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=94.23  E-value=0.037  Score=50.84  Aligned_cols=31  Identities=23%  Similarity=0.261  Sum_probs=22.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      +.++|+|++|||||+++..+.... ..+.+.+
T Consensus        50 ~g~ll~G~~G~GKTtl~~~i~~~~-~~~~i~~   80 (254)
T 1ixz_A           50 KGVLLVGPPGVGKTHLARAVAGEA-RVPFITA   80 (254)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHT-TCCEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh-CCCEEEe
Confidence            359999999999999887665544 2444433

>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=94.22  E-value=0.045  Score=47.16  Aligned_cols=30  Identities=27%  Similarity=0.068  Sum_probs=24.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|+.|||||+++..+...   -|++++..
T Consensus        10 ~i~l~G~~GsGKSTl~~~l~~~---~g~~~i~~   39 (175)
T 1knq_A           10 IYVLMGVSGSGKSAVASEVAHQ---LHAAFLDG   39 (175)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHH---HTCEEEEG
T ss_pred             EEEEEcCCCCCHHHHHHHHHHh---hCcEEEeC
Confidence            4899999999999998876543   28887764

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.10  E-value=0.037  Score=56.61  Aligned_cols=31  Identities=19%  Similarity=0.295  Sum_probs=21.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++++|+||+|||||++...+ +...  |+=++.|
T Consensus       207 rGiLL~GPPGtGKT~lakAi-A~~~--~~~~~~v  237 (428)
T 4b4t_K          207 RGVLLYGPPGTGKTMLVKAV-ANST--KAAFIRV  237 (428)
T ss_dssp             CEEEEESCTTTTHHHHHHHH-HHHH--TCEEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHH-HHHh--CCCeEEE
Confidence            57999999999999876544 3333  4444444

>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=94.08  E-value=0.04  Score=54.73  Aligned_cols=35  Identities=20%  Similarity=0.313  Sum_probs=30.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -++|+|++|||||++..|++..+..+|--|+||.-
T Consensus        65 ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~   99 (356)
T 1u94_A           65 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA   99 (356)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeC
Confidence            38999999999999999999988888877887754

>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=94.03  E-value=0.056  Score=49.23  Aligned_cols=22  Identities=32%  Similarity=0.557  Sum_probs=17.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +.++|+|++|||||+++..+..
T Consensus        40 ~~vll~G~~GtGKT~la~~la~   61 (262)
T 2qz4_A           40 KGALLLGPPGCGKTLLAKAVAT   61 (262)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4599999999999987765544

>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=93.91  E-value=0.034  Score=56.37  Aligned_cols=36  Identities=17%  Similarity=0.341  Sum_probs=28.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP~  226 (404)
                      +.++|+|++|||||+++..+......+  +.-|+|+..
T Consensus       131 ~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~  168 (440)
T 2z4s_A          131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS  168 (440)
T ss_dssp             CCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeH
Confidence            349999999999999888777766555  777777753

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=93.91  E-value=0.088  Score=50.62  Aligned_cols=31  Identities=10%  Similarity=0.189  Sum_probs=22.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL  222 (404)
                      .++|+|++|||||+++..+......+ .|+.+
T Consensus        72 ~vLl~GppGtGKT~la~~la~~l~~~~~~~~~  103 (368)
T 3uk6_A           72 AVLIAGQPGTGKTAIAMGMAQALGPDTPFTAI  103 (368)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHCSSCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcccCCcccc
Confidence            59999999999999877766665433 44443

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.85  E-value=0.041  Score=55.97  Aligned_cols=32  Identities=25%  Similarity=0.379  Sum_probs=21.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++++|+||+|||||++...+   |.+-|+=++.|.
T Consensus       183 rGvLL~GPPGTGKTllAkAi---A~e~~~~f~~v~  214 (405)
T 4b4t_J          183 KGVILYGPPGTGKTLLARAV---AHHTDCKFIRVS  214 (405)
T ss_dssp             CCEEEESCSSSSHHHHHHHH---HHHHTCEEEEEE
T ss_pred             CceEEeCCCCCCHHHHHHHH---HHhhCCCceEEE
Confidence            57999999999999875433   333355555553

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=93.83  E-value=0.056  Score=50.21  Aligned_cols=31  Identities=32%  Similarity=0.395  Sum_probs=22.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.++|+|++|||||+++..+   |..-+.-++++
T Consensus        52 ~~~ll~G~~GtGKT~la~~l---a~~~~~~~~~v   82 (285)
T 3h4m_A           52 KGILLYGPPGTGKTLLAKAV---ATETNATFIRV   82 (285)
T ss_dssp             SEEEEESSSSSSHHHHHHHH---HHHTTCEEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHH---HHHhCCCEEEE
Confidence            45999999999999887665   33345555554

>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=93.74  E-value=0.048  Score=48.99  Aligned_cols=24  Identities=17%  Similarity=0.083  Sum_probs=20.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -++|.|++|||||+++.++...+.
T Consensus        26 ~~~i~G~~GsGKTtl~~~l~~~~~   49 (243)
T 1n0w_A           26 ITEMFGEFRTGKTQICHTLAVTCQ   49 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHh
Confidence            389999999999999999887643

>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=93.72  E-value=0.07  Score=46.00  Aligned_cols=33  Identities=18%  Similarity=0.331  Sum_probs=26.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC--eEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG--WLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng--WIVL~I  224 (404)
                      .++|.|.+||||||+...+...--.+|  +.++.+
T Consensus         5 ~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~i~~   39 (192)
T 1kht_A            5 VVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVSF   39 (192)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTTCCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCcceEEEeh
Confidence            489999999999999888877555555  666654

>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=93.69  E-value=0.063  Score=46.91  Aligned_cols=29  Identities=24%  Similarity=0.301  Sum_probs=22.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      ++|.|+.||||||++..+..  ...|.+.+.
T Consensus         5 i~l~G~~GaGKSTl~~~L~~--~~~g~~~i~   33 (189)
T 2bdt_A            5 YIITGPAGVGKSTTCKRLAA--QLDNSAYIE   33 (189)
T ss_dssp             EEEECSTTSSHHHHHHHHHH--HSSSEEEEE
T ss_pred             EEEECCCCCcHHHHHHHHhc--ccCCeEEEc
Confidence            78999999999999988853  344555543

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=93.66  E-value=0.061  Score=48.84  Aligned_cols=33  Identities=24%  Similarity=0.237  Sum_probs=28.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++++|+.|+|||++|.++++-+...|.=|+-+
T Consensus        10 i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~   42 (191)
T 1xx6_A           10 VEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVF   42 (191)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            489999999999999999999988777655555

>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=93.66  E-value=0.03  Score=48.77  Aligned_cols=30  Identities=20%  Similarity=0.170  Sum_probs=22.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .++|.|++||||||++..+... ...|.|.+
T Consensus        11 ~i~l~G~~GsGKSTl~~~La~~-~~~g~i~i   40 (191)
T 1zp6_A           11 ILLLSGHPGSGKSTIAEALANL-PGVPKVHF   40 (191)
T ss_dssp             EEEEEECTTSCHHHHHHHHHTC-SSSCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHhc-cCCCeEEE
Confidence            4899999999999999887654 33455444

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=93.66  E-value=0.055  Score=50.74  Aligned_cols=28  Identities=14%  Similarity=0.252  Sum_probs=22.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGW  219 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngW  219 (404)
                      .++|+|++|||||++...+.......++
T Consensus        69 ~vll~G~~GtGKT~la~~la~~l~~~~~   96 (309)
T 3syl_A           69 HMSFTGNPGTGKTTVALKMAGLLHRLGY   96 (309)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHTTS
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCC
Confidence            4999999999999988777766665544

>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=93.61  E-value=0.081  Score=49.11  Aligned_cols=23  Identities=26%  Similarity=0.419  Sum_probs=18.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ..++|+|++|||||++...+...
T Consensus        65 ~~vLl~G~~GtGKT~la~~ia~~   87 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALAAKIAEE   87 (272)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH
Confidence            45999999999999877654443

>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=93.55  E-value=0.068  Score=46.35  Aligned_cols=33  Identities=18%  Similarity=0.160  Sum_probs=26.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|..||||||++..+..+-...|+-++.+
T Consensus         7 ~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~   39 (179)
T 2pez_A            7 TVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTL   39 (179)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEE
Confidence            489999999999999988877655578655554

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=93.55  E-value=0.058  Score=50.44  Aligned_cols=31  Identities=23%  Similarity=0.261  Sum_probs=22.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      +.++|+|++|||||+++..+.... ..+.+.+
T Consensus        74 ~gvll~Gp~GtGKTtl~~~i~~~~-~~~~i~~  104 (278)
T 1iy2_A           74 KGVLLVGPPGVGKTHLARAVAGEA-RVPFITA  104 (278)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHT-TCCEEEE
T ss_pred             CeEEEECCCcChHHHHHHHHHHHc-CCCEEEe
Confidence            359999999999999887665544 3444433

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=93.55  E-value=0.068  Score=46.66  Aligned_cols=34  Identities=24%  Similarity=0.271  Sum_probs=26.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .-++|.|..|||||++...+..+....|+-|.++
T Consensus        14 ~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~   47 (186)
T 2yvu_A           14 IVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVL   47 (186)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEe
Confidence            3489999999999999999888877666544333

>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=93.53  E-value=0.051  Score=51.19  Aligned_cols=24  Identities=17%  Similarity=0.082  Sum_probs=21.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -++|+|++|+|||+++.++...+.
T Consensus        32 ~v~i~G~~G~GKT~L~~~~~~~~~   55 (357)
T 2fna_A           32 ITLVLGLRRTGKSSIIKIGINELN   55 (357)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             cEEEECCCCCCHHHHHHHHHHhcC
Confidence            489999999999999999887653

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.52  E-value=0.055  Score=55.65  Aligned_cols=31  Identities=23%  Similarity=0.251  Sum_probs=20.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++++|+|++|||||++.. +++.  +-|+-++.|
T Consensus       217 rGvLLyGPPGTGKTlLAk-AiA~--e~~~~fi~v  247 (437)
T 4b4t_I          217 KGVILYGAPGTGKTLLAK-AVAN--QTSATFLRI  247 (437)
T ss_dssp             SEEEEESSTTTTHHHHHH-HHHH--HHTCEEEEE
T ss_pred             CCCceECCCCchHHHHHH-HHHH--HhCCCEEEE
Confidence            579999999999998644 3333  334444444

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=93.48  E-value=0.062  Score=54.80  Aligned_cols=34  Identities=9%  Similarity=-0.002  Sum_probs=30.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|.+|+|||++++|+...+..+|+=|+|+.
T Consensus       199 liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fS  232 (444)
T 3bgw_A          199 FVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  232 (444)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEEC
T ss_pred             EEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEE
Confidence            3899999999999999999998887898888884

>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=93.48  E-value=0.043  Score=48.87  Aligned_cols=23  Identities=22%  Similarity=0.384  Sum_probs=19.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      ++.|.|+.||||||+|.-+.-.-
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l   24 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999998777654

>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=93.44  E-value=0.055  Score=54.03  Aligned_cols=34  Identities=21%  Similarity=0.277  Sum_probs=29.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      ++|+|++|||||++++|++..+..+|--|+||.-
T Consensus        77 i~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~  110 (366)
T 1xp8_A           77 TEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDA  110 (366)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEEC
Confidence            7999999999999999999988888777788754

>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=93.41  E-value=0.06  Score=52.59  Aligned_cols=39  Identities=21%  Similarity=0.343  Sum_probs=32.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTH  232 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvn  232 (404)
                      .+.|.|+.||||||+|.-+.-.-  .|-|+.++|.-..+..
T Consensus       128 ~vaIvGpsGsGKSTLl~lL~gl~--~G~I~~~v~q~~~lf~  166 (305)
T 2v9p_A          128 CLAFIGPPNTGKSMLCNSLIHFL--GGSVLSFANHKSHFWL  166 (305)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHH--TCEEECGGGTTSGGGG
T ss_pred             EEEEECCCCCcHHHHHHHHhhhc--CceEEEEecCcccccc
Confidence            58999999999999998888766  8999999887544433

>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=93.32  E-value=0.058  Score=47.65  Aligned_cols=32  Identities=34%  Similarity=0.432  Sum_probs=26.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      ++.|+|..||||||++..+..    .|+.+++....
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~----~g~~~i~~d~~   34 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE----LGAYVLDADKL   34 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH----TTCEEEEHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH----CCCEEEEccHH
Confidence            489999999999999877755    38888887553

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=93.31  E-value=0.071  Score=52.80  Aligned_cols=33  Identities=15%  Similarity=0.145  Sum_probs=30.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++|.|++|+|||+++.|+...+..+|+-|+|+.
T Consensus        49 iiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fS   81 (338)
T 4a1f_A           49 VIIGARPSMGKTSLMMNMVLSALNDDRGVAVFS   81 (338)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            899999999999999999988877898888874

>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=93.29  E-value=0.062  Score=51.62  Aligned_cols=31  Identities=26%  Similarity=0.216  Sum_probs=21.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.++|+|++|||||+++..+...   .+.-+++|
T Consensus        52 ~~vLl~GppGtGKT~la~aia~~---~~~~~~~v   82 (322)
T 3eie_A           52 SGILLYGPPGTGKSYLAKAVATE---ANSTFFSV   82 (322)
T ss_dssp             CEEEEECSSSSCHHHHHHHHHHH---HTCEEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHH---HCCCEEEE
Confidence            46999999999999877655333   34444444

>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=93.28  E-value=0.053  Score=52.47  Aligned_cols=34  Identities=15%  Similarity=0.072  Sum_probs=27.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC------CeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE------GWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n------gWIVL~IP  225 (404)
                      -++|+|++|||||+++.|+...+...      |.-|+||.
T Consensus       109 i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~  148 (324)
T 2z43_A          109 MTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYID  148 (324)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEE
T ss_pred             EEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEE
Confidence            38999999999999999998876544      55666663

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.26  E-value=0.054  Score=56.09  Aligned_cols=31  Identities=29%  Similarity=0.293  Sum_probs=21.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++++|+|++|||||++. .+++.  +-|+-++.|
T Consensus       244 rGILLyGPPGTGKTlLA-kAiA~--e~~~~fi~v  274 (467)
T 4b4t_H          244 KGILLYGPPGTGKTLCA-RAVAN--RTDATFIRV  274 (467)
T ss_dssp             SEEEECSCTTSSHHHHH-HHHHH--HHTCEEEEE
T ss_pred             CceEeeCCCCCcHHHHH-HHHHh--ccCCCeEEE
Confidence            57999999999998654 44433  335555554

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=93.26  E-value=0.086  Score=53.40  Aligned_cols=35  Identities=17%  Similarity=0.403  Sum_probs=29.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCe--EEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGW--LVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngW--IVL~IP~  226 (404)
                      -++|.|++|||||+++.+++.+....|.  |++.-|.
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~a~T   83 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEALISTGETGIILAAPT   83 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEecCc
Confidence            4899999999999999999999888775  5555454

>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=93.25  E-value=0.095  Score=48.81  Aligned_cols=27  Identities=26%  Similarity=0.326  Sum_probs=21.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      .++|+|++|||||++...+.......+
T Consensus        40 ~~ll~G~~G~GKt~la~~l~~~l~~~~   66 (319)
T 2chq_A           40 HLLFSGPPGTGKTATAIALARDLFGEN   66 (319)
T ss_dssp             CEEEESSSSSSHHHHHHHHHHHHHTTC
T ss_pred             eEEEECcCCcCHHHHHHHHHHHhcCCc
Confidence            399999999999998877776654444

>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=93.19  E-value=0.061  Score=46.61  Aligned_cols=30  Identities=20%  Similarity=0.137  Sum_probs=23.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|.+||||||+...+..+   -||.++..
T Consensus         7 ~I~l~G~~GsGKST~~~~L~~~---l~~~~i~~   36 (193)
T 2rhm_A            7 LIIVTGHPATGKTTLSQALATG---LRLPLLSK   36 (193)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH---HTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---cCCeEecH
Confidence            4899999999999988777553   27877764

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=93.19  E-value=0.069  Score=47.26  Aligned_cols=30  Identities=23%  Similarity=0.200  Sum_probs=23.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|..||||||+...+...-   ||.++..
T Consensus        20 ~I~l~G~~GsGKSTla~~L~~~l---g~~~i~~   49 (202)
T 3t61_A           20 SIVVMGVSGSGKSSVGEAIAEAC---GYPFIEG   49 (202)
T ss_dssp             CEEEECSTTSCHHHHHHHHHHHH---TCCEEEG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh---CCEEEeC
Confidence            49999999999999887665432   7777653

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=93.17  E-value=0.064  Score=51.18  Aligned_cols=19  Identities=26%  Similarity=0.565  Sum_probs=17.0

Q ss_pred             eEEEECCCCCcHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qa  210 (404)
                      .++|+|++|||||+++.++
T Consensus        57 ~vll~G~~GtGKT~la~~i   75 (338)
T 3pfi_A           57 HILFSGPAGLGKTTLANII   75 (338)
T ss_dssp             CEEEECSTTSSHHHHHHHH
T ss_pred             eEEEECcCCCCHHHHHHHH
Confidence            4899999999999988776

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.16  E-value=0.054  Score=55.56  Aligned_cols=32  Identities=25%  Similarity=0.429  Sum_probs=22.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++++||||+|||||++...+..   +-|+=+++|.
T Consensus       216 rGvLL~GPPGtGKTllAkAiA~---e~~~~~~~v~  247 (437)
T 4b4t_L          216 KGVLLYGPPGTGKTLLAKAVAA---TIGANFIFSP  247 (437)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHH---HHTCEEEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHH---HhCCCEEEEe
Confidence            5799999999999987554433   3355555553

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=93.15  E-value=0.055  Score=47.48  Aligned_cols=22  Identities=23%  Similarity=0.356  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -+.|.|+.||||||++..+...
T Consensus         9 ii~l~Gp~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A            9 LFIISAPSGAGKTSLVRALVKA   30 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECcCCCCHHHHHHHHHhh
Confidence            3899999999999999887765

>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=93.11  E-value=0.064  Score=47.67  Aligned_cols=24  Identities=17%  Similarity=0.104  Sum_probs=20.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -+.|.|+.|||||+++.++.....
T Consensus        27 ~~~l~G~nGsGKSTll~~l~g~~~   50 (231)
T 4a74_A           27 ITEVFGEFGSGKTQLAHTLAVMVQ   50 (231)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            489999999999999999887543

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=93.07  E-value=0.094  Score=49.43  Aligned_cols=32  Identities=19%  Similarity=0.252  Sum_probs=27.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .++++.|+.|||||++.+++.+.+.++|.=|+
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~   38 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQLRQGVRVM   38 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCCEE
Confidence            46999999999999999999999888886443

>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=93.05  E-value=0.067  Score=47.76  Aligned_cols=30  Identities=23%  Similarity=0.206  Sum_probs=23.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +++|+|++||||||+...+.   ..-|+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~---~~~~~~~i~~   31 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIV---EKYGIPHIST   31 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHH---HHSSCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHH---HHhCCcEEeH
Confidence            48999999999999887764   3458877766

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=93.03  E-value=0.097  Score=51.61  Aligned_cols=33  Identities=21%  Similarity=0.311  Sum_probs=25.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|++|||||++...+   |...|+-+++|..
T Consensus       149 ~~vLL~GppGtGKT~la~ai---a~~~~~~~~~v~~  181 (389)
T 3vfd_A          149 RGLLLFGPPGNGKTMLAKAV---AAESNATFFNISA  181 (389)
T ss_dssp             SEEEEESSTTSCHHHHHHHH---HHHTTCEEEEECS
T ss_pred             ceEEEECCCCCCHHHHHHHH---HHhhcCcEEEeeH
Confidence            45999999999999877655   5556777777654

>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=93.02  E-value=0.07  Score=50.02  Aligned_cols=26  Identities=27%  Similarity=0.157  Sum_probs=21.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      -++|.|+.|||||+++.|+...+. .|
T Consensus        32 i~~i~G~~GsGKTtl~~~l~~~~~-~g   57 (279)
T 1nlf_A           32 VGALVSPGGAGKSMLALQLAAQIA-GG   57 (279)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH-TC
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHh-cC
Confidence            389999999999999999987543 44

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=93.02  E-value=0.077  Score=48.87  Aligned_cols=34  Identities=26%  Similarity=0.302  Sum_probs=29.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++++|+-|+|||+.|.|+++.....|-=|+++-
T Consensus        22 l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~k   55 (195)
T 1w4r_A           22 IQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIK   55 (195)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEc
Confidence            4899999999999999999999888877777764

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=92.97  E-value=0.086  Score=49.30  Aligned_cols=32  Identities=22%  Similarity=0.217  Sum_probs=22.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ..++|+|++|||||+++..+...   .+.-++++.
T Consensus        55 ~~vll~Gp~GtGKT~la~~la~~---~~~~~~~i~   86 (297)
T 3b9p_A           55 KGLLLFGPPGNGKTLLARAVATE---CSATFLNIS   86 (297)
T ss_dssp             SEEEEESSSSSCHHHHHHHHHHH---TTCEEEEEE
T ss_pred             CeEEEECcCCCCHHHHHHHHHHH---hCCCeEEee
Confidence            45999999999999987655433   344444443

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=92.93  E-value=0.072  Score=46.69  Aligned_cols=22  Identities=23%  Similarity=0.241  Sum_probs=19.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -++|.|+.||||||++..+...
T Consensus         7 ~i~i~GpsGsGKSTL~~~L~~~   28 (180)
T 1kgd_A            7 TLVLLGAHGVGRRHIKNTLITK   28 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhh
Confidence            4899999999999999888764

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=92.90  E-value=0.087  Score=45.42  Aligned_cols=22  Identities=32%  Similarity=0.597  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.++..
T Consensus        49 ~~i~vvG~~g~GKSsll~~l~~   70 (193)
T 2ged_A           49 PSIIIAGPQNSGKTSLLTLLTT   70 (193)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999988764

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=92.90  E-value=0.077  Score=47.24  Aligned_cols=30  Identities=20%  Similarity=0.177  Sum_probs=23.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +++|+|++||||||+...+..   .-|+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~---~~~~~~i~~   31 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIE---KYEIPHIST   31 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH---HHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH---HhCCcEeeH
Confidence            489999999999998877643   237777755

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=92.72  E-value=0.065  Score=51.09  Aligned_cols=22  Identities=18%  Similarity=0.130  Sum_probs=17.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ..++|+|++|||||++...+..
T Consensus        37 ~~lLl~GppGtGKT~la~aiA~   58 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQCELVFR   58 (293)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3589999999999986554433

>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=92.69  E-value=0.1  Score=51.76  Aligned_cols=40  Identities=25%  Similarity=0.407  Sum_probs=30.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEecCccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVPRGREWT  231 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP~a~~wv  231 (404)
                      -++|.|+.||||||+|.-++.+-... +-.|+.+-+...+.
T Consensus       125 ~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~  165 (356)
T 3jvv_A          125 LVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFV  165 (356)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhh
Confidence            48999999999999999888776543 66777776655543

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=92.68  E-value=0.094  Score=50.37  Aligned_cols=49  Identities=10%  Similarity=0.209  Sum_probs=29.6

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHhCC--eEEEE
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEG--WLVLY  223 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~ng--WIVL~  223 (404)
                      ...++.+.++.+..       .+   ..++|+|++|||||++...+.......+  ++.++
T Consensus        10 ~~~~~~~~~~~~a~-------~~---~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~   60 (304)
T 1ojl_A           10 AMQHLLNEIAMVAP-------SD---ATVLIHGDSGTGKELVARALHACSARSDRPLVTLN   60 (304)
T ss_dssp             HHHHHHHHHHHHCS-------TT---SCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEE
T ss_pred             HHHHHHHHHHHHhC-------CC---CcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEe
Confidence            34556666665421       11   2389999999999977655555443344  44444

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=92.68  E-value=0.077  Score=48.77  Aligned_cols=23  Identities=22%  Similarity=0.351  Sum_probs=18.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      +.++|+|++|||||+++..+...
T Consensus        46 ~~vll~G~~GtGKT~la~~la~~   68 (257)
T 1lv7_A           46 KGVLMVGPPGTGKTLLAKAIAGE   68 (257)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHHHHHHH
Confidence            45999999999999887655443

>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=92.62  E-value=0.075  Score=45.01  Aligned_cols=30  Identities=33%  Similarity=0.473  Sum_probs=21.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|.+||||||+...+...   -||.++..
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~---l~~~~i~~   32 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKE---LKYPIIKG   32 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHH---HCCCEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---hCCeeecC
Confidence            3899999999999988776432   25544433

>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=92.59  E-value=0.11  Score=49.92  Aligned_cols=27  Identities=22%  Similarity=0.337  Sum_probs=21.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      .++|+|++|||||+++..+.......+
T Consensus        48 ~~ll~Gp~G~GKTtla~~la~~l~~~~   74 (340)
T 1sxj_C           48 HLLFYGPPGTGKTSTIVALAREIYGKN   74 (340)
T ss_dssp             CEEEECSSSSSHHHHHHHHHHHHHTTS
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHcCCC
Confidence            389999999999999887766654333

>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=92.56  E-value=0.11  Score=45.48  Aligned_cols=32  Identities=28%  Similarity=0.412  Sum_probs=24.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHh-CCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWARE-EGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~-ngWIVL~IP  225 (404)
                      ..++|+|.+|||||++...+.   .. .||.++..-
T Consensus        11 ~~I~l~G~~GsGKSTv~~~La---~~l~g~~~id~d   43 (184)
T 1y63_A           11 INILITGTPGTGKTSMAEMIA---AELDGFQHLEVG   43 (184)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH---HHSTTEEEEEHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH---HhcCCCEEeeHH
Confidence            459999999999999886654   34 588887753

>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=92.54  E-value=0.087  Score=51.54  Aligned_cols=33  Identities=18%  Similarity=0.139  Sum_probs=25.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh------CCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE------EGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~------ngWIVL~I  224 (404)
                      -++|+|++|||||+++.|+...|..      .|--|+||
T Consensus       124 i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi  162 (343)
T 1v5w_A          124 ITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFI  162 (343)
T ss_dssp             EEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEE
Confidence            4799999999999999999887644      34455555

>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=92.53  E-value=0.1  Score=53.78  Aligned_cols=33  Identities=24%  Similarity=0.382  Sum_probs=25.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|++|||||+++..+.   .+-||-++++..
T Consensus        78 ~~lLL~GppGtGKTtla~~la---~~l~~~~i~in~  110 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAAHLVA---QELGYDILEQNA  110 (516)
T ss_dssp             SEEEEECSTTSSHHHHHHHHH---HHTTCEEEEECT
T ss_pred             cEEEEECCCCCCHHHHHHHHH---HHcCCCEEEEeC
Confidence            459999999999999876543   334888888854

>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=92.51  E-value=0.065  Score=54.89  Aligned_cols=34  Identities=12%  Similarity=-0.178  Sum_probs=29.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP  225 (404)
                      -++|.|++|+|||++++|+...+..+ |+=|+||.
T Consensus       244 l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s  278 (503)
T 1q57_A          244 VIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAM  278 (503)
T ss_dssp             EEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEE
T ss_pred             EEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEe
Confidence            38999999999999999998887766 88888874

>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=92.50  E-value=0.11  Score=50.80  Aligned_cols=33  Identities=24%  Similarity=0.346  Sum_probs=24.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|++|||||+++..+.   .+.++-+++|..
T Consensus       118 ~~vLl~GppGtGKT~la~aia---~~~~~~~~~i~~  150 (357)
T 3d8b_A          118 KGILLFGPPGTGKTLIGKCIA---SQSGATFFSISA  150 (357)
T ss_dssp             SEEEEESSTTSSHHHHHHHHH---HHTTCEEEEEEG
T ss_pred             ceEEEECCCCCCHHHHHHHHH---HHcCCeEEEEeh
Confidence            359999999999999887663   344666666643

>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=92.47  E-value=0.077  Score=47.00  Aligned_cols=29  Identities=17%  Similarity=0.248  Sum_probs=23.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .+.|+|+.||||||+...+..    .|+.++..
T Consensus         4 ~i~l~G~~GsGKST~~~~La~----lg~~~id~   32 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD----LGVPLVDA   32 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT----TTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH----CCCcccch
Confidence            378999999999999887754    47777653

>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=92.44  E-value=0.13  Score=46.06  Aligned_cols=34  Identities=29%  Similarity=0.273  Sum_probs=27.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.+.|.|..|||||+++..++.+-...|+=|-.|
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l~~~g~~v~~i   38 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTV   38 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhhHhcCCeeeEE
Confidence            3589999999999999999998877777644444

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=92.42  E-value=0.1  Score=52.92  Aligned_cols=34  Identities=12%  Similarity=0.032  Sum_probs=28.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh-CCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE-EGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~-ngWIVL~IP  225 (404)
                      -++|.|++|+|||+++.|+...+.. +|.-|+|+.
T Consensus       205 liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s  239 (454)
T 2r6a_A          205 LIIVAARPSVGKTAFALNIAQNVATKTNENVAIFS  239 (454)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            3899999999999999999887654 677677663

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=92.42  E-value=0.22  Score=44.27  Aligned_cols=28  Identities=29%  Similarity=0.321  Sum_probs=22.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGW  219 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngW  219 (404)
                      -+.|+|+.||||||++..+...-...|.
T Consensus        24 ~i~i~G~~GsGKstl~~~l~~~~~~~~~   51 (201)
T 1rz3_A           24 VLGIDGLSRSGKTTLANQLSQTLREQGI   51 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhcCC
Confidence            4899999999999999888776554443

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=92.39  E-value=0.093  Score=45.32  Aligned_cols=29  Identities=28%  Similarity=0.310  Sum_probs=21.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      .++|.|++|||||++...+.   ..-||.++.
T Consensus         6 ~i~i~G~~GsGKsTla~~La---~~l~~~~~d   34 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALA---KDLDLVFLD   34 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHH---HHHTCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHH---HHcCCCEEc
Confidence            48999999999999876653   334665554

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=92.38  E-value=0.12  Score=48.41  Aligned_cols=42  Identities=24%  Similarity=0.458  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHH
Q 045329          166 FLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       166 tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .++.+..|+..+..      .|. ++.++++|++|||||++...++.+.
T Consensus        41 ~~~f~~~l~~~~~~------iPk-kn~ili~GPPGtGKTt~a~ala~~l   82 (212)
T 1tue_A           41 FITFLGALKSFLKG------TPK-KNCLVFCGPANTGKSYFGMSFIHFI   82 (212)
T ss_dssp             HHHHHHHHHHHHHT------CTT-CSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhc------CCc-ccEEEEECCCCCCHHHHHHHHHHHh
Confidence            34455555554321      233 3469999999999999876665553

>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=92.38  E-value=0.086  Score=46.04  Aligned_cols=30  Identities=37%  Similarity=0.582  Sum_probs=24.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..+.|+|..|||||++...+...    |+.++..
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~~----g~~~id~   38 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRSW----GYPVLDL   38 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHT----TCCEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHC----CCEEEcc
Confidence            35899999999999998776553    8887764

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=92.37  E-value=0.13  Score=44.36  Aligned_cols=30  Identities=23%  Similarity=0.323  Sum_probs=22.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|.+||||||+...+...   -||.++..
T Consensus         6 ~I~l~G~~GsGKST~~~~La~~---l~~~~i~~   35 (186)
T 3cm0_A            6 AVIFLGPPGAGKGTQASRLAQE---LGFKKLST   35 (186)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH---HTCEEECH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---hCCeEecH
Confidence            4899999999999988776543   36665543

>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=92.35  E-value=0.055  Score=47.81  Aligned_cols=34  Identities=24%  Similarity=0.193  Sum_probs=28.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      ++|.|..||||||++..+..+-...|+-|..+..
T Consensus         3 I~i~G~~GsGKsTl~~~L~~~l~~~g~~v~~~~~   36 (214)
T 1gtv_A            3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAF   36 (214)
T ss_dssp             EEEEEEEEEEHHHHHHHHHHHHHEEEEEEEEEES
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEee
Confidence            7899999999999999988887777877766543

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=92.30  E-value=0.079  Score=50.21  Aligned_cols=23  Identities=26%  Similarity=0.550  Sum_probs=18.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ++++|+|++|||||+++..+...
T Consensus        45 ~GvlL~Gp~GtGKTtLakala~~   67 (274)
T 2x8a_A           45 AGVLLAGPPGCGKTLLAKAVANE   67 (274)
T ss_dssp             SEEEEESSTTSCHHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Confidence            35999999999999998766543

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=92.29  E-value=0.067  Score=46.68  Aligned_cols=18  Identities=33%  Similarity=0.266  Sum_probs=16.6

Q ss_pred             eEEEECCCCCcHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAM  209 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~q  209 (404)
                      -+.|.|+.||||||++..
T Consensus        11 i~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A           11 LVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            389999999999999987

>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=92.27  E-value=0.12  Score=50.57  Aligned_cols=24  Identities=33%  Similarity=0.320  Sum_probs=18.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      +.++|+|++|||||++...+...+
T Consensus        85 ~~iLL~GppGtGKT~la~ala~~~  108 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYLAKAVATEA  108 (355)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHh
Confidence            359999999999998876555443

>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=92.23  E-value=0.068  Score=54.18  Aligned_cols=32  Identities=25%  Similarity=0.250  Sum_probs=22.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.++|+|++|||||++...+...+  ++.-+++|
T Consensus       168 ~~vLL~GppGtGKT~lA~aia~~~--~~~~~~~v  199 (444)
T 2zan_A          168 RGILLFGPPGTGKSYLAKAVATEA--NNSTFFSI  199 (444)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHC--CSSEEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHc--CCCCEEEE
Confidence            469999999999998876555443  24444444

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=92.17  E-value=0.11  Score=54.75  Aligned_cols=33  Identities=30%  Similarity=0.249  Sum_probs=28.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|+|++|||||+++..++..+..+|.-|+.+
T Consensus       206 ~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~  238 (574)
T 3e1s_A          206 LVVLTGGPGTGKSTTTKAVADLAESLGLEVGLC  238 (574)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEe
Confidence            489999999999999999999888887655554

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=92.13  E-value=0.08  Score=47.76  Aligned_cols=27  Identities=22%  Similarity=0.401  Sum_probs=23.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      .+.|.|+.||||||+|.-+..+-..+|
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~~~~G   29 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVLKSSG   29 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCChHHHHHHHHHhhcccCC
Confidence            489999999999999999888766777

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=92.12  E-value=0.1  Score=43.16  Aligned_cols=22  Identities=27%  Similarity=0.386  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++++.|+.|+|||+++.++..
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~   23 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLK   23 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4689999999999999988764

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=92.10  E-value=0.17  Score=43.63  Aligned_cols=30  Identities=23%  Similarity=0.219  Sum_probs=22.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|.+||||||+...+...   -||.++..
T Consensus         5 ~I~l~G~~GsGKsT~a~~L~~~---~~~~~i~~   34 (196)
T 1tev_A            5 VVFVLGGPGAGKGTQCARIVEK---YGYTHLSA   34 (196)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH---HCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---hCCeEEeH
Confidence            4899999999999987765442   37776654

>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=92.08  E-value=0.17  Score=46.78  Aligned_cols=33  Identities=15%  Similarity=0.055  Sum_probs=25.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      .+++|.|++||||||+...+...-   |+.++.+.+
T Consensus        30 ~~I~l~G~~GsGKsT~a~~L~~~~---g~~~is~~~   62 (243)
T 3tlx_A           30 GRYIFLGAPGSGKGTQSLNLKKSH---CYCHLSTGD   62 (243)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH---CCEEEEHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh---CCeEEecHH
Confidence            469999999999999887776432   777776543

>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=92.07  E-value=0.14  Score=47.71  Aligned_cols=24  Identities=21%  Similarity=0.302  Sum_probs=20.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHh
Q 045329          193 IVLDGPLCCGKSITLAMLVHWARE  216 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~  216 (404)
                      ++|+|++|+|||+++..+......
T Consensus        45 ~ll~G~~G~GKt~la~~l~~~l~~   68 (323)
T 1sxj_B           45 MIISGMPGIGKTTSVHCLAHELLG   68 (323)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHG
T ss_pred             EEEECcCCCCHHHHHHHHHHHhcC
Confidence            999999999999988887776543

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=92.06  E-value=0.096  Score=49.02  Aligned_cols=27  Identities=19%  Similarity=0.177  Sum_probs=21.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      .++|+|++|||||++...+.......+
T Consensus        49 ~~ll~G~~GtGKt~la~~la~~~~~~~   75 (311)
T 4fcw_A           49 SFLFLGPTGVGKTELAKTLAATLFDTE   75 (311)
T ss_dssp             EEEEESCSSSSHHHHHHHHHHHHHSCG
T ss_pred             EEEEECCCCcCHHHHHHHHHHHHcCCC
Confidence            499999999999998877776655443

>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=91.99  E-value=0.15  Score=47.40  Aligned_cols=22  Identities=27%  Similarity=0.379  Sum_probs=17.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .++|+|++|||||+++..+...
T Consensus        52 ~vll~G~~GtGKT~la~~la~~   73 (310)
T 1ofh_A           52 NILMIGPTGVGKTEIARRLAKL   73 (310)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4999999999999877655443

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=91.96  E-value=0.097  Score=46.83  Aligned_cols=23  Identities=39%  Similarity=0.492  Sum_probs=20.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .++|.|+.||||||++..+...-
T Consensus         6 ~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            6 PVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            48999999999999999887754

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=91.93  E-value=0.089  Score=46.11  Aligned_cols=22  Identities=32%  Similarity=0.362  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .++|.|+.||||||++..+...
T Consensus         8 ~i~l~G~~GsGKSTl~~~L~~~   29 (207)
T 2j41_A            8 LIVLSGPSGVGKGTVRKRIFED   29 (207)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            4899999999999999887654

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=91.93  E-value=0.13  Score=45.52  Aligned_cols=30  Identities=17%  Similarity=0.154  Sum_probs=22.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|++|||||++...+...-   ||.++..
T Consensus        27 ~i~l~G~~GsGKsTl~~~La~~l---~~~~i~~   56 (199)
T 3vaa_A           27 RIFLTGYMGAGKTTLGKAFARKL---NVPFIDL   56 (199)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH---TCCEEEH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc---CCCEEcc
Confidence            59999999999999987765432   6655543

>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=91.89  E-value=0.16  Score=45.24  Aligned_cols=31  Identities=16%  Similarity=0.057  Sum_probs=25.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLV  221 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIV  221 (404)
                      +.++|.|+.|||||+++..++..-...|+-|
T Consensus         7 ~~i~i~G~sGsGKTTl~~~l~~~l~~~g~~v   37 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLLKKLIPALCARGIRP   37 (174)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHTTCCE
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhccccCCce
Confidence            3589999999999999999998765666443

>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=91.88  E-value=0.087  Score=50.18  Aligned_cols=23  Identities=26%  Similarity=0.551  Sum_probs=18.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ..++|+|++|||||+++..+...
T Consensus        50 ~~vLL~Gp~GtGKT~la~ala~~   72 (301)
T 3cf0_A           50 KGVLFYGPPGCGKTLLAKAIANE   72 (301)
T ss_dssp             SEEEEECSSSSSHHHHHHHHHHH
T ss_pred             ceEEEECCCCcCHHHHHHHHHHH
Confidence            35999999999999887655443

>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=91.88  E-value=0.15  Score=44.10  Aligned_cols=31  Identities=26%  Similarity=0.238  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .++|+|.+|||||++...+...   -|+.++...
T Consensus        13 ~i~i~G~~GsGKst~~~~l~~~---~~~~~~~~d   43 (180)
T 3iij_A           13 NILLTGTPGVGKTTLGKELASK---SGLKYINVG   43 (180)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHH---HCCEEEEHH
T ss_pred             eEEEEeCCCCCHHHHHHHHHHH---hCCeEEEHH
Confidence            4899999999999988766543   277766553

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=91.87  E-value=0.12  Score=43.74  Aligned_cols=20  Identities=10%  Similarity=0.047  Sum_probs=15.7

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      .++|+|++|||||++...+.
T Consensus        29 ~vll~G~~GtGKt~lA~~i~   48 (143)
T 3co5_A           29 PVFLTGEAGSPFETVARYFH   48 (143)
T ss_dssp             CEEEEEETTCCHHHHHGGGC
T ss_pred             cEEEECCCCccHHHHHHHHH
Confidence            38999999999997654433

>1ko7_A HPR kinase/phosphatase; protein kinase, phosphotransfer, protein phosphatase, dual activity, product, substrate, transferase, hydrolase; 1.95A {Staphylococcus xylosus} SCOP: c.98.2.1 c.91.1.2

Probab=91.83  E-value=0.18  Score=49.64  Aligned_cols=83  Identities=12%  Similarity=0.130  Sum_probs=50.5

Q ss_pred             cchhhhccccCceeEEEchhHHHHHHHHHHhcCCCccCC---CCC---ccceeEEEECCCCCcHHHHHHHHHHHHH---h
Q 045329          146 TGMLGEFKDSMRYALLVRQSFLDIRDNFRRIVDPSLQST---NGP---KIRKQIVLDGPLCCGKSITLAMLVHWAR---E  216 (404)
Q Consensus       146 ~~~~kqfe~f~~p~~LVRk~tleLi~~L~~~~d~~~~st---d~~---~~r~r~vL~G~rGsGKS~~L~qav~~A~---~  216 (404)
                      ..+.+.-+..+-|.+-...+|-+++..|...++..+...   .+.   .....++|.|+.|+|||++...++....   .
T Consensus        94 eelie~A~~~~IPVL~T~~~ts~~~~~l~~~l~~~~~~~~~~H~~~v~~~g~~vl~~G~sG~GKSt~a~~l~~~g~~lv~  173 (314)
T 1ko7_A           94 EELIEAAKEHETPLITSKIATTQLMSRLTTFLEHELARTTSLHGVLVDVYGVGVLITGDSGIGKSETALELIKRGHRLVA  173 (314)
T ss_dssp             HHHHHHHHHTTCCEEECCSCHHHHHHHHHHHHHHHTCEEEEEESEEEEETTEEEEEEESTTSSHHHHHHHHHHTTCEEEE
T ss_pred             HHHHHHHHHCCCeEEEECCchhHHHHHHHHHHHHhhccceeeeEEEEEECCEEEEEEeCCCCCHHHHHHHHHhcCCceec
Confidence            344544555566766666677777777765544211000   000   0114699999999999999999887543   3


Q ss_pred             CCeEEEEecCcc
Q 045329          217 EGWLVLYVPRGR  228 (404)
Q Consensus       217 ngWIVL~IP~a~  228 (404)
                      .+++.+..-+..
T Consensus       174 dD~~~i~~~~~~  185 (314)
T 1ko7_A          174 DDNVEIREISKD  185 (314)
T ss_dssp             SSEEEEEESSSS
T ss_pred             CCeEEEEEcCCC
Confidence            466666655443

>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=91.82  E-value=0.1  Score=45.25  Aligned_cols=31  Identities=29%  Similarity=0.144  Sum_probs=23.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .++|+|.+|||||++...+..   .-||.++..-
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~---~lg~~~id~D   34 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAK---ALGVGLLDTD   34 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHH---HHTCCEEEHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH---HcCCCEEeCc
Confidence            489999999999998766644   3377766543

>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=91.76  E-value=0.17  Score=43.49  Aligned_cols=30  Identities=27%  Similarity=0.325  Sum_probs=23.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|.+|||||++...+...   -||.++..
T Consensus         8 ~I~l~G~~GsGKsT~~~~L~~~---l~~~~i~~   37 (194)
T 1qf9_A            8 VVFVLGGPGSGKGTQCANIVRD---FGWVHLSA   37 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH---HCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---hCCeEeeH
Confidence            5899999999999987766543   37777765

>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=91.75  E-value=0.18  Score=42.95  Aligned_cols=30  Identities=20%  Similarity=0.251  Sum_probs=22.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|..|||||++...+...   -||.++..
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~---lg~~~id~   33 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARA---LGYEFVDT   33 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHH---HTCEEEEH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH---hCCcEEcc
Confidence            4899999999999988766543   26666653

>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=91.74  E-value=0.33  Score=49.80  Aligned_cols=35  Identities=26%  Similarity=0.340  Sum_probs=30.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ..+++.|..|+||||+++.+..|...+|+=|+-|.
T Consensus       101 ~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~  135 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVC  135 (443)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             eEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            35899999999999999999999888888776663

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=91.71  E-value=0.17  Score=47.82  Aligned_cols=32  Identities=25%  Similarity=0.457  Sum_probs=25.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-h-CCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-E-EGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~-ngWIVL~  223 (404)
                      -++|.|+.||||||+|.-+.-+-. . .|-|++.
T Consensus        27 ~v~i~Gp~GsGKSTll~~l~g~~~~~~~G~I~~~   60 (261)
T 2eyu_A           27 LILVTGPTGSGKSTTIASMIDYINQTKSYHIITI   60 (261)
T ss_dssp             EEEEECSTTCSHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             EEEEECCCCccHHHHHHHHHHhCCCCCCCEEEEc
Confidence            489999999999999998887654 3 6776553

>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=91.68  E-value=0.12  Score=46.34  Aligned_cols=30  Identities=20%  Similarity=0.274  Sum_probs=23.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +++|.|.+||||||....+..+-   |+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~---g~~~i~~   31 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY---GIPQIST   31 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH---CCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh---CCeEEeH
Confidence            48999999999999887776532   7777766

>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=91.64  E-value=0.11  Score=48.52  Aligned_cols=27  Identities=22%  Similarity=0.308  Sum_probs=21.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      .++|+|++|+|||+++..+.......+
T Consensus        48 ~~ll~G~~G~GKT~la~~l~~~l~~~~   74 (327)
T 1iqp_A           48 HLLFAGPPGVGKTTAALALARELFGEN   74 (327)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHHGGG
T ss_pred             eEEEECcCCCCHHHHHHHHHHHhcCCc
Confidence            499999999999999887776654333

>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=91.61  E-value=0.16  Score=45.51  Aligned_cols=31  Identities=29%  Similarity=0.194  Sum_probs=24.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCC--eEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEG--WLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ng--WIVL  222 (404)
                      -++|.|..|||||++...+..+-. ..|  ++++
T Consensus        27 ~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~   60 (211)
T 1m7g_A           27 TIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRL   60 (211)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhccccCCcEEEE
Confidence            489999999999999988877654 567  5544

>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=91.58  E-value=0.15  Score=49.52  Aligned_cols=31  Identities=19%  Similarity=0.260  Sum_probs=20.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      ..++|+|++|||||++. ++++......++.+
T Consensus        52 ~~vll~GppGtGKT~la-~~ia~~~~~~~~~~   82 (363)
T 3hws_A           52 SNILLIGPTGSGKTLLA-ETLARLLDVPFTMA   82 (363)
T ss_dssp             CCEEEECCTTSSHHHHH-HHHHHHTTCCEEEE
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHcCCCEEEe
Confidence            35999999999999855 44444433333333

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=91.48  E-value=0.16  Score=44.16  Aligned_cols=30  Identities=27%  Similarity=0.222  Sum_probs=23.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|.+|||||++...+..+-   ||.++..
T Consensus        14 ~I~l~G~~GsGKsT~a~~L~~~l---~~~~i~~   43 (199)
T 2bwj_A           14 IIFIIGGPGSGKGTQCEKLVEKY---GFTHLST   43 (199)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH---TCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh---CCeEEcH
Confidence            58999999999999887765532   6776654

>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=91.47  E-value=0.11  Score=44.47  Aligned_cols=32  Identities=34%  Similarity=0.463  Sum_probs=22.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|+|.+||||||+...+.. ....+|+.+.+
T Consensus         5 ~i~l~G~~GsGKST~a~~La~-~l~~~~~~~~~   36 (178)
T 1qhx_A            5 MIILNGGSSAGKSGIVRCLQS-VLPEPWLAFGV   36 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH-HSSSCEEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-hcCCCeEEecc
Confidence            389999999999998766543 22346766554

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=91.41  E-value=0.18  Score=47.06  Aligned_cols=34  Identities=21%  Similarity=0.122  Sum_probs=29.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++++|+-|+|||+.|.+.++-+...|.=|+-+-
T Consensus        30 l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k   63 (214)
T 2j9r_A           30 IEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFK   63 (214)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEE
Confidence            3689999999999999999999988877666653

>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=91.39  E-value=0.13  Score=49.19  Aligned_cols=23  Identities=13%  Similarity=0.053  Sum_probs=20.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      -++|+|++|||||+++.|+...+
T Consensus       100 i~~i~G~~gsGKT~la~~la~~~  122 (322)
T 2i1q_A          100 VTEFAGVFGSGKTQIMHQSCVNL  122 (322)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            38999999999999999998764

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=91.37  E-value=0.19  Score=43.98  Aligned_cols=27  Identities=26%  Similarity=0.391  Sum_probs=22.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      .++|.|.+||||||+...+...-...|
T Consensus         6 ~I~i~G~~GsGKsT~~~~L~~~l~~~g   32 (213)
T 2plr_A            6 LIAFEGIDGSGKSSQATLLKDWIELKR   32 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTTTS
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHhhcC
Confidence            589999999999999988877544444

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=91.36  E-value=0.17  Score=43.84  Aligned_cols=30  Identities=23%  Similarity=0.216  Sum_probs=23.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|.+|||||++...+..+   -||.++..
T Consensus        11 ~I~l~G~~GsGKsT~~~~La~~---l~~~~i~~   40 (196)
T 2c95_A           11 IIFVVGGPGSGKGTQCEKIVQK---YGYTHLST   40 (196)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHH---HCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---hCCeEEcH
Confidence            5999999999999988776542   37776654

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=91.32  E-value=0.14  Score=51.62  Aligned_cols=34  Identities=18%  Similarity=0.039  Sum_probs=27.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh-CCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE-EGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~-ngWIVL~IP  225 (404)
                      -++|.|++|+|||+++.|+...+.. +|.=|+|+.
T Consensus       202 l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~s  236 (444)
T 2q6t_A          202 LNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYS  236 (444)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEE
Confidence            3899999999999999998887664 577666663

>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=91.29  E-value=0.079  Score=51.24  Aligned_cols=41  Identities=20%  Similarity=0.114  Sum_probs=29.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCccccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWT  231 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wv  231 (404)
                      +-++|+|..||||||+|.++.......+|.||.--.+...+
T Consensus         5 ~v~~i~G~~GaGKTTll~~l~~~~~~~~~aVi~~d~G~i~i   45 (318)
T 1nij_A            5 AVTLLTGFLGAGKTTLLRHILNEQHGYKIAVIENEFGEVSV   45 (318)
T ss_dssp             EEEEEEESSSSSCHHHHHHHHHSCCCCCEEEECSSCCSCCE
T ss_pred             cEEEEEecCCCCHHHHHHHHHhhcCCCcEEEEEecCcccCc
Confidence            34899999999999999998876544566665433333333

>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=91.23  E-value=0.11  Score=46.59  Aligned_cols=22  Identities=32%  Similarity=0.371  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -++|.|+.|||||+++..+...
T Consensus        10 ~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A           10 LIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhh
Confidence            3899999999999999887653

>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=91.20  E-value=0.14  Score=42.47  Aligned_cols=22  Identities=23%  Similarity=0.261  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++++.|..|+|||+++.++..
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~   27 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCK   27 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECcCCCCHHHHHHHHHc
Confidence            4699999999999999998774

>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=91.18  E-value=0.14  Score=42.20  Aligned_cols=21  Identities=29%  Similarity=0.306  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|+.|+|||+++.++..
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~   25 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            599999999999999988764

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=91.16  E-value=0.23  Score=43.69  Aligned_cols=32  Identities=22%  Similarity=0.218  Sum_probs=24.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ..++|+|..|||||++...+..   .-|+.++...
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~---~~g~~~i~~d   47 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVK---DYSFVHLSAG   47 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH---HSSCEEEEHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH---HcCceEEeHH
Confidence            3589999999999998766643   3588777653

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=91.11  E-value=0.15  Score=44.11  Aligned_cols=30  Identities=20%  Similarity=0.163  Sum_probs=22.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|.+|||||++...+..   .-||.++..
T Consensus         7 ~i~l~G~~GsGKst~a~~La~---~l~~~~i~~   36 (185)
T 3trf_A            7 NIYLIGLMGAGKTSVGSQLAK---LTKRILYDS   36 (185)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH---HHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH---HhCCCEEEC
Confidence            589999999999998776643   336655543

>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=91.09  E-value=0.15  Score=42.36  Aligned_cols=21  Identities=33%  Similarity=0.426  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|..|+|||+++.+++.
T Consensus         5 ~i~v~G~~~~GKssli~~l~~   25 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            599999999999999998864

>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=91.08  E-value=0.16  Score=48.91  Aligned_cols=34  Identities=32%  Similarity=0.359  Sum_probs=28.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL~IP  225 (404)
                      .++|.|+.|+||||++..+..+.. .+|.=|+.+.
T Consensus       107 vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~  141 (296)
T 2px0_A          107 YIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFIT  141 (296)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEe
Confidence            488999999999999999988776 4787666664

>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=91.07  E-value=0.069  Score=49.19  Aligned_cols=22  Identities=23%  Similarity=0.321  Sum_probs=18.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .++|+|++|||||+++..+...
T Consensus        46 ~vll~G~~GtGKT~la~~la~~   67 (268)
T 2r62_A           46 GVLLVGPPGTGKTLLAKAVAGE   67 (268)
T ss_dssp             CCCCBCSSCSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHH
Confidence            4899999999999988766544

>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=91.03  E-value=0.13  Score=45.93  Aligned_cols=21  Identities=29%  Similarity=0.471  Sum_probs=18.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+.|+|+.||||||++..+..
T Consensus         7 ~i~i~G~~GsGKSTl~~~L~~   27 (227)
T 1cke_A            7 VITIDGPSGAGKGTLCKAMAE   27 (227)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            489999999999999877654

>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=91.03  E-value=0.18  Score=48.07  Aligned_cols=29  Identities=24%  Similarity=0.200  Sum_probs=20.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHH--HHhCCeEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHW--AREEGWLV  221 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~--A~~ngWIV  221 (404)
                      ++|+|++|+|||+++..+...  +...|.+.
T Consensus        39 ~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~   69 (354)
T 1sxj_E           39 LLLYGPNGTGKKTRCMALLESIFGPGVYRLK   69 (354)
T ss_dssp             EEEECSTTSSHHHHHHTHHHHHSCTTCCC--
T ss_pred             EEEECCCCCCHHHHHHHHHHHHcCCCCCeEE
Confidence            999999999999998776663  23345543

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=90.98  E-value=0.24  Score=47.30  Aligned_cols=31  Identities=16%  Similarity=0.206  Sum_probs=23.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      -++|.|++||||||+...+... ...+|++|.
T Consensus        35 livl~G~sGsGKSTla~~L~~~-~~~~~~~Is   65 (287)
T 1gvn_B           35 AFLLGGQPGSGKTSLRSAIFEE-TQGNVIVID   65 (287)
T ss_dssp             EEEEECCTTSCTHHHHHHHHHH-TTTCCEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHH-hCCCeEEEe
Confidence            4899999999999988776542 224676663

>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=90.97  E-value=0.2  Score=44.75  Aligned_cols=29  Identities=24%  Similarity=0.294  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|..||||||++..+..    .|+.++..
T Consensus         6 ~I~i~G~~GSGKST~~~~L~~----lg~~~id~   34 (218)
T 1vht_A            6 IVALTGGIGSGKSTVANAFAD----LGINVIDA   34 (218)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH----TTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH----cCCEEEEc
Confidence            489999999999998877643    58877764

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=90.94  E-value=0.16  Score=44.22  Aligned_cols=31  Identities=26%  Similarity=0.370  Sum_probs=23.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .++|.|..||||||+...+..+-   |+.++..|
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l---~~~~~~e~   32 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL---GYEIFKEP   32 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH---CCEEECCC
T ss_pred             EEEEECCCccCHHHHHHHHHHhc---CCcEEccc
Confidence            48999999999999988776543   55555444

>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=90.94  E-value=0.16  Score=41.99  Aligned_cols=22  Identities=18%  Similarity=0.253  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++++.|..|+|||+++.++..
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~   26 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            3699999999999999988764

>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=90.91  E-value=0.13  Score=46.03  Aligned_cols=23  Identities=35%  Similarity=0.491  Sum_probs=19.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      -+.|.|+.||||||++..+.-.-
T Consensus        22 i~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           22 VVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            37899999999999998877653

>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=90.88  E-value=0.14  Score=51.61  Aligned_cols=24  Identities=25%  Similarity=0.099  Sum_probs=20.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -++|.|++|||||+++.|+...+.
T Consensus       180 i~~I~G~sGsGKTTLl~~la~~~~  203 (400)
T 3lda_A          180 ITELFGEFRTGKSQLCHTLAVTCQ  203 (400)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEEcCCCCChHHHHHHHHHHhc
Confidence            489999999999999999876554

>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=90.86  E-value=0.14  Score=42.08  Aligned_cols=21  Identities=29%  Similarity=0.354  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|..|+|||+++.++..
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~   25 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            589999999999999988864

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=90.86  E-value=0.15  Score=42.42  Aligned_cols=22  Identities=23%  Similarity=0.217  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++++.|..|+|||+++.++..
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~   25 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVK   25 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            3599999999999999988764

>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=90.86  E-value=0.14  Score=44.78  Aligned_cols=22  Identities=32%  Similarity=0.314  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|+.|+|||++|..+..
T Consensus         6 ~kv~lvG~~g~GKSTLl~~l~~   27 (199)
T 2f9l_A            6 FKVVLIGDSGVGKSNLLSRFTR   27 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEEECcCCCCHHHHHHHHhc
Confidence            3589999999999999988765

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=90.83  E-value=0.24  Score=44.93  Aligned_cols=30  Identities=17%  Similarity=0.138  Sum_probs=23.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|.+||||||+...+..+-   |+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l---g~~~i~~   31 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY---SLAHIES   31 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH---TCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh---CCeEEch
Confidence            48999999999999887775532   6776665

>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=90.81  E-value=0.2  Score=48.64  Aligned_cols=33  Identities=24%  Similarity=0.245  Sum_probs=26.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|+.||||||++..+..+...+|.=|+.+
T Consensus       106 vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv  138 (306)
T 1vma_A          106 VIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLA  138 (306)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEE
Confidence            478999999999999999998776666544433

>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=90.81  E-value=0.18  Score=44.43  Aligned_cols=30  Identities=23%  Similarity=0.268  Sum_probs=23.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|.+|||||++...+..+   -||.++.+
T Consensus        22 ~I~l~G~~GsGKST~a~~La~~---l~~~~i~~   51 (201)
T 2cdn_A           22 RVLLLGPPGAGKGTQAVKLAEK---LGIPQIST   51 (201)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH---HTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---hCCcEEeh
Confidence            5999999999999987766543   26766655

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=90.81  E-value=0.14  Score=43.71  Aligned_cols=23  Identities=26%  Similarity=0.358  Sum_probs=19.9

Q ss_pred             ceeEEEECCCCCcHHHHHHHHHH
Q 045329          190 RKQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       190 r~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +.+++|.|..|+|||+++.+++.
T Consensus        23 ~~~i~v~G~~~~GKSsli~~l~~   45 (195)
T 3pqc_A           23 KGEVAFVGRSNVGKSSLLNALFN   45 (195)
T ss_dssp             TCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHc
Confidence            35799999999999999988753

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=90.80  E-value=1.8  Score=45.89  Aligned_cols=68  Identities=15%  Similarity=0.150  Sum_probs=41.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH-hC--CeEEEEecCcccccccCeeecC-CC--CCCccCHHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR-EE--GWLVLYVPRGREWTHGGYFYKN-PQ--TGLWDTPLQAENVLKDFIK  260 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~-~n--gWIVL~IP~a~~wvng~~~y~~-~~--~g~ydQP~~A~~~Lk~fl~  260 (404)
                      +.+++.|..|||||++|.-++.... ..  +-+-+++=++..-  +-..|.. ++  ......|..+.+.|+.+..
T Consensus       215 pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~ev~lilIDpKg~--eLs~~~~lPHl~~~Vvtd~~~a~~~L~~lv~  288 (574)
T 2iut_A          215 PHLLVAGTTGSGKSVGVNAMLLSILFKSTPSEARLIMIDPKML--ELSIYEGIPHLLCPVVTDMKEAANALRWSVA  288 (574)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECSSSH--HHHTTTTCTTBSSSCBCCHHHHHHHHHHHHH
T ss_pred             CeeEEECCCCCCHHHHHHHHHHHHHHhCCCcceEEEEeCCChh--hhHhhcCCCcccceeeCCHHHHHHHHHHHHH
Confidence            5689999999999999998776433 32  4555665454431  0011221 21  1245678888887776643

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=90.78  E-value=0.15  Score=45.36  Aligned_cols=22  Identities=23%  Similarity=0.351  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -++|.|++|||||++...+...
T Consensus        14 ~i~l~G~sGsGKsTl~~~L~~~   35 (204)
T 2qor_A           14 PLVVCGPSGVGKGTLIKKVLSE   35 (204)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            4899999999999988887654

>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=90.78  E-value=0.14  Score=48.09  Aligned_cols=23  Identities=26%  Similarity=0.380  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .++|+|++|||||+++..+....
T Consensus        40 ~vll~G~~GtGKT~la~~i~~~~   62 (324)
T 1hqc_A           40 HLLLFGPPGLGKTTLAHVIAHEL   62 (324)
T ss_dssp             CCEEECCTTCCCHHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999887665543

>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=90.73  E-value=0.16  Score=42.28  Aligned_cols=22  Identities=27%  Similarity=0.386  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++++.|..|+|||+++.++..
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~   28 (170)
T 1z08_A            7 FKVVLLGEGCVGKTSLVLRYCE   28 (170)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHc
Confidence            4699999999999999988764

>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=90.69  E-value=0.16  Score=42.69  Aligned_cols=22  Identities=27%  Similarity=0.255  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.+++.
T Consensus         8 ~~i~v~G~~~~GKSsli~~l~~   29 (177)
T 1wms_A            8 FKVILLGDGGVGKSSLMNRYVT   29 (177)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999998864

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=90.68  E-value=0.12  Score=45.74  Aligned_cols=22  Identities=23%  Similarity=0.222  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+.|+|+.||||||++..+...
T Consensus         8 ~i~i~G~~GsGKSTl~~~l~~~   29 (211)
T 3asz_A            8 VIGIAGGTASGKTTLAQALART   29 (211)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999877664

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=90.67  E-value=0.15  Score=47.64  Aligned_cols=31  Identities=32%  Similarity=0.680  Sum_probs=24.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      ++|.|++|||||++...+.   ..-|+.++..-.
T Consensus         4 i~I~G~~GSGKSTla~~La---~~~~~~~i~~D~   34 (253)
T 2ze6_A            4 HLIYGPTCSGKTDMAIQIA---QETGWPVVALDR   34 (253)
T ss_dssp             EEEECCTTSSHHHHHHHHH---HHHCCCEEECCS
T ss_pred             EEEECCCCcCHHHHHHHHH---hcCCCeEEeccH
Confidence            7999999999999877663   344788877654

>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=90.67  E-value=0.14  Score=46.89  Aligned_cols=21  Identities=24%  Similarity=0.370  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++|.|++||||||++..+..
T Consensus        29 ~i~l~G~~GsGKSTl~k~La~   49 (246)
T 2bbw_A           29 RAVILGPPGSGKGTVCQRIAQ   49 (246)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999988764

>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=90.61  E-value=0.29  Score=46.03  Aligned_cols=45  Identities=22%  Similarity=0.351  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHH
Q 045329          166 FLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       166 tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -+++++.|++.+..-  ..+ ....+++++.|.+|+|||+++..++..
T Consensus         3 ~~~~~~~l~~~~~~~--~~~-~~~~~~I~vvG~~~~GKSTlln~l~g~   47 (315)
T 1jwy_B            3 LIPVINKLQDVFNTL--GSD-PLDLPQIVVVGSQSSGKSSVLENIVGR   47 (315)
T ss_dssp             HHHHHHHHHHHTTTS--SSC-TTCCCEEEEEECSSSSHHHHHHHHHTS
T ss_pred             hHHHHHHHHHHHHHc--CCC-CCCCCeEEEEcCCCCCHHHHHHHHHCC
Confidence            467788887765321  111 122367999999999999999988753

>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=90.60  E-value=0.13  Score=44.47  Aligned_cols=21  Identities=24%  Similarity=0.425  Sum_probs=18.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|+.|||||+++..++.
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999988764

>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=90.60  E-value=0.33  Score=46.66  Aligned_cols=22  Identities=32%  Similarity=0.434  Sum_probs=17.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +.++|+|++|||||++..-+.+
T Consensus       105 n~~~l~GppgtGKt~~a~ala~  126 (267)
T 1u0j_A          105 NTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHh
Confidence            5699999999999998764443

>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=90.57  E-value=0.17  Score=42.02  Aligned_cols=22  Identities=27%  Similarity=0.274  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++++.|..|+|||+++..++.
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~   28 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVE   28 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHc
Confidence            4699999999999999998764

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=90.55  E-value=0.18  Score=42.73  Aligned_cols=29  Identities=28%  Similarity=0.275  Sum_probs=22.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      .++|+|..|||||++...+...   -||.++.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~---l~~~~i~   30 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRS---LNIPFYD   30 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHH---HTCCEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHH---hCCCEEE
Confidence            4899999999999988776553   2565554

>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=90.48  E-value=0.16  Score=42.99  Aligned_cols=21  Identities=33%  Similarity=0.340  Sum_probs=18.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|+.|+|||+++.++.
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~   24 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALT   24 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHh
Confidence            358999999999999999875

>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=90.46  E-value=0.17  Score=42.45  Aligned_cols=21  Identities=24%  Similarity=0.327  Sum_probs=18.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|.+|+|||+++.++.
T Consensus         5 ~ki~i~G~~~vGKSsl~~~l~   25 (175)
T 2nzj_A            5 YRVVLLGDPGVGKTSLASLFA   25 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEEECCCCccHHHHHHHHh
Confidence            469999999999999998775

>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=90.45  E-value=0.22  Score=46.67  Aligned_cols=31  Identities=19%  Similarity=0.185  Sum_probs=23.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|.+||||||+...+..  ...||.++..
T Consensus         4 ~I~l~G~~GsGKST~a~~L~~--~~~~~~~i~~   34 (301)
T 1ltq_A            4 IILTIGCPGSGKSTWAREFIA--KNPGFYNINR   34 (301)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH--HSTTEEEECH
T ss_pred             EEEEECCCCCCHHHHHHHHHH--hCCCcEEecc
Confidence            489999999999998877654  1248877754

>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=90.41  E-value=0.18  Score=42.42  Aligned_cols=22  Identities=18%  Similarity=0.294  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++++.|..|+|||+++.+++.
T Consensus         9 ~~i~v~G~~~~GKSsli~~l~~   30 (182)
T 1ky3_A            9 LKVIILGDSGVGKTSLMHRYVN   30 (182)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999988875

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=90.39  E-value=0.2  Score=52.87  Aligned_cols=35  Identities=23%  Similarity=0.362  Sum_probs=26.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh-CCe-EEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE-EGW-LVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~-ngW-IVL~IP~  226 (404)
                      -++|.|++|||||+++..++.+... .++ |++--|.
T Consensus       197 ~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~a~t  233 (624)
T 2gk6_A          197 LSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS  233 (624)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEEESS
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEeCc
Confidence            3799999999999999999987665 454 4343343

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=90.35  E-value=0.17  Score=43.24  Aligned_cols=21  Identities=33%  Similarity=0.340  Sum_probs=19.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|+.|+|||+++.++.
T Consensus         8 ~~i~lvG~~gvGKStL~~~l~   28 (188)
T 2wjg_A            8 YEIALIGNPNVGKSTIFNALT   28 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHh
Confidence            569999999999999999875

>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=90.34  E-value=0.18  Score=49.62  Aligned_cols=23  Identities=17%  Similarity=0.086  Sum_probs=21.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      -+.|.|++|||||+++.|+...+
T Consensus       133 i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          133 ITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999998876

>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=90.34  E-value=0.15  Score=49.26  Aligned_cols=23  Identities=22%  Similarity=0.368  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .++|+|++|||||+++.-+....
T Consensus        53 ~~ll~Gp~G~GKTTLa~~ia~~l   75 (334)
T 1in4_A           53 HVLLAGPPGLGKTTLAHIIASEL   75 (334)
T ss_dssp             CEEEESSTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHHh
Confidence            48999999999999876665543

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=90.32  E-value=0.15  Score=46.29  Aligned_cols=29  Identities=21%  Similarity=0.373  Sum_probs=23.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      -+.|.|+.||||||++..+.-.- . |-|.+
T Consensus        25 ~~~lvGpsGsGKSTLl~~L~g~~-p-G~i~~   53 (218)
T 1z6g_A           25 PLVICGPSGVGKGTLIKKLLNEF-P-NYFYF   53 (218)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHS-T-TTEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC-C-CcEEE
Confidence            38999999999999999887654 2 66655

>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=90.30  E-value=0.24  Score=48.34  Aligned_cols=20  Identities=35%  Similarity=0.556  Sum_probs=16.1

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      .++|+|++|||||++...+.
T Consensus        74 ~ill~Gp~GtGKT~la~~la   93 (376)
T 1um8_A           74 NILLIGPTGSGKTLMAQTLA   93 (376)
T ss_dssp             CEEEECCTTSSHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHH
Confidence            49999999999997665443

>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=90.29  E-value=0.2  Score=51.27  Aligned_cols=35  Identities=29%  Similarity=0.314  Sum_probs=29.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .-+++.|+.||||||+++.+..+...+|.=|+.+.
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~  132 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVA  132 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            35889999999999999999998888887776653

>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=90.26  E-value=0.16  Score=42.28  Aligned_cols=22  Identities=36%  Similarity=0.391  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++++.|..|+|||+++..+..
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~   25 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVE   25 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            3599999999999999988763

>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=90.26  E-value=0.17  Score=48.46  Aligned_cols=23  Identities=17%  Similarity=0.223  Sum_probs=19.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .|+|+|++|+|||+++..+....
T Consensus        40 ~~ll~G~~G~GKT~la~~la~~l   62 (373)
T 1jr3_A           40 AYLFSGTRGVGKTSIARLLAKGL   62 (373)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999997776554

>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=90.25  E-value=0.18  Score=42.09  Aligned_cols=20  Identities=25%  Similarity=0.282  Sum_probs=18.2

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      +++|.|.+|+|||+++..+.
T Consensus         4 ki~ivG~~~~GKSsli~~l~   23 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFG   23 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            58999999999999998875

>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=90.24  E-value=0.15  Score=46.84  Aligned_cols=22  Identities=23%  Similarity=0.324  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -++|.|+.||||||+|..+...
T Consensus        18 ii~l~GpsGsGKSTLlk~L~g~   39 (219)
T 1s96_A           18 LYIVSAPSGAGKSSLIQALLKT   39 (219)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcc
Confidence            4899999999999999887664

>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=90.23  E-value=0.17  Score=48.02  Aligned_cols=22  Identities=27%  Similarity=0.379  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      ++|+|++|||||+++..+....
T Consensus        61 ~ll~G~~G~GKT~la~~la~~l   82 (353)
T 1sxj_D           61 MLFYGPPGTGKTSTILALTKEL   82 (353)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            8999999999999887766653

>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=90.23  E-value=0.25  Score=43.49  Aligned_cols=33  Identities=30%  Similarity=0.228  Sum_probs=25.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|..||||||+...+...-...+.-|..+
T Consensus        11 ~I~l~G~~GsGKsT~~~~L~~~l~~~~~~v~~~   43 (215)
T 1nn5_A           11 LIVLEGVDRAGKSTQSRKLVEALCAAGHRAELL   43 (215)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEe
Confidence            489999999999999998877654555544333

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=90.22  E-value=0.38  Score=44.67  Aligned_cols=22  Identities=36%  Similarity=0.382  Sum_probs=19.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|.+|+|||+++..++.
T Consensus        27 ~~i~vvG~~~~GKSSLln~l~g   48 (299)
T 2aka_B           27 PQIAVVGGQSAGKSSVLENFVG   48 (299)
T ss_dssp             CEEEEEEBTTSCHHHHHHHHHT
T ss_pred             CeEEEEeCCCCCHHHHHHHHHC
Confidence            5799999999999999998863

>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=90.19  E-value=0.15  Score=44.57  Aligned_cols=22  Identities=32%  Similarity=0.314  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|+.|||||+++..+..
T Consensus        30 ~kv~lvG~~g~GKSTLl~~l~~   51 (191)
T 1oix_A           30 FKVVLIGDSGVGKSNLLSRFTR   51 (191)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHhc
Confidence            4689999999999999988764

>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=90.16  E-value=0.2  Score=42.05  Aligned_cols=22  Identities=23%  Similarity=0.312  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++++.|..|+|||+++.++..
T Consensus        16 ~~i~v~G~~~~GKSsli~~l~~   37 (179)
T 1z0f_A           16 FKYIIIGDMGVGKSCLLHQFTE   37 (179)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            5699999999999999998764

>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=90.16  E-value=0.2  Score=41.52  Aligned_cols=22  Identities=32%  Similarity=0.345  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~   28 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999988765

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=90.09  E-value=0.24  Score=44.19  Aligned_cols=28  Identities=25%  Similarity=0.266  Sum_probs=22.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      ..+.|.|+.||||||++..+...-...|
T Consensus        23 ~~v~I~G~sGsGKSTl~~~l~~~~~~~g   50 (208)
T 3c8u_A           23 QLVALSGAPGSGKSTLSNPLAAALSAQG   50 (208)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcC
Confidence            3588999999999999988877655433

>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=90.08  E-value=0.31  Score=43.63  Aligned_cols=30  Identities=27%  Similarity=0.174  Sum_probs=23.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|.+||||||+...+..+   -||.++..
T Consensus         6 ~I~l~G~~GsGKsT~a~~La~~---l~~~~i~~   35 (220)
T 1aky_A            6 RMVLIGPPGAGKGTQAPNLQER---FHAAHLAT   35 (220)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH---HCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---cCceEEeh
Confidence            5999999999999987776543   36776654

>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=90.03  E-value=0.19  Score=41.58  Aligned_cols=21  Identities=29%  Similarity=0.325  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++.|..|+|||+++..+..
T Consensus         5 ki~v~G~~~~GKssli~~l~~   25 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999988874

>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=89.99  E-value=0.2  Score=42.46  Aligned_cols=22  Identities=18%  Similarity=0.146  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        12 ~ki~v~G~~~~GKSsli~~l~~   33 (195)
T 3bc1_A           12 IKFLALGDSGVGKTSVLYQYTD   33 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999988764

>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=89.99  E-value=0.21  Score=41.68  Aligned_cols=22  Identities=27%  Similarity=0.217  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++++.|..|+|||+++.++..
T Consensus         8 ~~i~v~G~~~~GKssl~~~l~~   29 (171)
T 1upt_A            8 MRILILGLDGAGKTTILYRLQV   29 (171)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999988754

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=89.98  E-value=0.11  Score=47.02  Aligned_cols=22  Identities=32%  Similarity=0.542  Sum_probs=14.1

Q ss_pred             eEEEECCCCCcHHHHHHHHH-HH
Q 045329          192 QIVLDGPLCCGKSITLAMLV-HW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav-~~  213 (404)
                      -+.|.|+.||||||++..+. ..
T Consensus        29 ii~l~Gp~GsGKSTl~~~L~~~~   51 (231)
T 3lnc_A           29 ILVLSSPSGCGKTTVANKLLEKQ   51 (231)
T ss_dssp             EEEEECSCC----CHHHHHHC--
T ss_pred             EEEEECCCCCCHHHHHHHHHhcC
Confidence            48999999999999998876 54

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=89.97  E-value=0.27  Score=43.65  Aligned_cols=27  Identities=15%  Similarity=0.329  Sum_probs=23.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      ..++|.|..|||||+++.+++......
T Consensus        39 ~~i~ivG~~gvGKTtl~~~l~~~~~~~   65 (226)
T 2hf9_A           39 VAFDFMGAIGSGKTLLIEKLIDNLKDK   65 (226)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHTTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhccC
Confidence            468999999999999999999876554

>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=89.95  E-value=0.16  Score=43.66  Aligned_cols=22  Identities=32%  Similarity=0.427  Sum_probs=19.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.+++.
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~   45 (195)
T 1svi_A           24 PEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            5699999999999999998864

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=89.91  E-value=0.25  Score=45.08  Aligned_cols=35  Identities=17%  Similarity=0.148  Sum_probs=25.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH---hCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR---EEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~---~ngWIVL~IP  225 (404)
                      ..++|.|+.|+|||++...++....   ..+++++..-
T Consensus        17 ~gvli~G~SGaGKStlal~L~~rG~~lvaDD~v~i~~~   54 (181)
T 3tqf_A           17 MGVLITGEANIGKSELSLALIDRGHQLVCDDVIDLKQE   54 (181)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHTTCEEEESSEEEEEES
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHcCCeEecCCEEEEEEe
Confidence            4699999999999999988887432   2344444443

>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=89.89  E-value=0.22  Score=41.38  Aligned_cols=21  Identities=29%  Similarity=0.309  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|..|+|||+++.++..
T Consensus         2 ki~~~G~~~~GKssl~~~l~~   22 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKL   22 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            489999999999999988765

>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=89.88  E-value=0.19  Score=42.20  Aligned_cols=22  Identities=18%  Similarity=0.279  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..++.
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~   36 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMY   36 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999998863

>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=89.86  E-value=0.25  Score=44.98  Aligned_cols=33  Identities=21%  Similarity=0.341  Sum_probs=26.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .-+++.|..|+|||+++.++..+.. .|.=|+-|
T Consensus        15 ~i~~~~GkgGvGKTTl~~~La~~l~-~g~~v~vv   47 (262)
T 1yrb_A           15 MIVVFVGTAGSGKTTLTGEFGRYLE-DNYKVAYV   47 (262)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHT-TTSCEEEE
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHH-CCCeEEEE
Confidence            3488999999999999999988776 66444444

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=89.85  E-value=0.21  Score=42.49  Aligned_cols=22  Identities=32%  Similarity=0.295  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..++.
T Consensus         8 ~ki~v~G~~~~GKSsli~~l~~   29 (208)
T 3clv_A            8 YKTVLLGESSVGKSSIVLRLTK   29 (208)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999998875

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=89.79  E-value=0.28  Score=47.39  Aligned_cols=31  Identities=26%  Similarity=0.361  Sum_probs=25.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL  222 (404)
                      -+.|.|+.||||||++.-+..+.... |-|.+
T Consensus       102 vi~lvG~nGsGKTTll~~Lag~l~~~~g~V~l  133 (302)
T 3b9q_A          102 VIMIVGVNGGGKTTSLGKLAHRLKNEGTKVLM  133 (302)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEE
Confidence            47899999999999999998876654 44444

>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=89.79  E-value=0.45  Score=45.00  Aligned_cols=31  Identities=16%  Similarity=0.170  Sum_probs=22.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++++|++|||||++...+   |..-++=++++.
T Consensus        50 ~~L~~G~~G~GKT~la~~l---a~~l~~~~~~i~   80 (324)
T 3u61_B           50 IILHSPSPGTGKTTVAKAL---CHDVNADMMFVN   80 (324)
T ss_dssp             EEEECSSTTSSHHHHHHHH---HHHTTEEEEEEE
T ss_pred             EEEeeCcCCCCHHHHHHHH---HHHhCCCEEEEc
Confidence            3788899999999887655   344467677765

>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=89.76  E-value=0.3  Score=47.81  Aligned_cols=32  Identities=25%  Similarity=0.253  Sum_probs=25.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .+++|.|.+|+|||+++.++.......|.=|.
T Consensus        80 ~~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~  111 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIEALGMHLIERGHRVA  111 (355)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTTCCEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCceE
Confidence            46999999999999999998887665554333

>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=89.66  E-value=0.29  Score=48.03  Aligned_cols=32  Identities=31%  Similarity=0.553  Sum_probs=25.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      -+.|.|+.||||||++..+..+-...+.=|+.
T Consensus       131 vi~lvG~nGaGKTTll~~Lag~l~~~~g~V~l  162 (328)
T 3e70_C          131 VIMFVGFNGSGKTTTIAKLANWLKNHGFSVVI  162 (328)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCEEEE
Confidence            48999999999999999998877766544433

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=89.66  E-value=0.2  Score=45.27  Aligned_cols=31  Identities=16%  Similarity=0.066  Sum_probs=24.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..++|.|.+|||||++...+..   .-|+.++..
T Consensus         8 ~~I~l~G~~GsGKsT~a~~La~---~l~~~~i~~   38 (227)
T 1zd8_A            8 LRAVIMGAPGSGKGTVSSRITT---HFELKHLSS   38 (227)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH---HSSSEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH---HcCCeEEec
Confidence            3599999999999998776654   347877754

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=89.65  E-value=0.21  Score=42.02  Aligned_cols=22  Identities=23%  Similarity=0.347  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..+..
T Consensus         9 ~~i~v~G~~~~GKssl~~~l~~   30 (178)
T 2lkc_A            9 PVVTIMGHVDHGKTTLLDAIRH   30 (178)
T ss_dssp             CEEEEESCTTTTHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4699999999999999988753

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=89.65  E-value=0.23  Score=51.18  Aligned_cols=28  Identities=21%  Similarity=0.213  Sum_probs=23.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGW  219 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngW  219 (404)
                      -++|.|++|||||+++.++......+|-
T Consensus       283 i~~i~G~~GsGKSTLl~~l~g~~~~~G~  310 (525)
T 1tf7_A          283 IILATGATGTGKTLLVSRFVENACANKE  310 (525)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTTTC
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhCCC
Confidence            3899999999999999999887665664

>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=89.65  E-value=0.22  Score=41.98  Aligned_cols=22  Identities=32%  Similarity=0.415  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.++..
T Consensus        13 ~ki~v~G~~~~GKSsli~~l~~   34 (181)
T 2efe_B           13 AKLVLLGDVGAGKSSLVLRFVK   34 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHc
Confidence            4699999999999999988764

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=89.61  E-value=0.28  Score=44.09  Aligned_cols=31  Identities=19%  Similarity=0.215  Sum_probs=23.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..++|.|.+||||||....+..+-   ||.++..
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l---~~~~i~~   36 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEY---GLAHLST   36 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH---CCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh---CceEEeh
Confidence            358999999999999876665432   7877765

>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=89.60  E-value=0.21  Score=42.34  Aligned_cols=22  Identities=27%  Similarity=0.312  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~   26 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQ   26 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999988874

>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=89.51  E-value=0.18  Score=41.91  Aligned_cols=20  Identities=25%  Similarity=0.306  Sum_probs=17.9

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      +++|.|..|+|||+++..+.
T Consensus         4 ki~~vG~~~~GKSsli~~l~   23 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFG   23 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHc
Confidence            58999999999999998764

>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=89.50  E-value=0.22  Score=42.04  Aligned_cols=22  Identities=18%  Similarity=0.253  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..+..
T Consensus        19 ~ki~v~G~~~~GKSsli~~l~~   40 (187)
T 2a9k_A           19 HKVIMVGSGGVGKSALTLQFMY   40 (187)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHhh
Confidence            4699999999999999988774

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=89.49  E-value=0.31  Score=47.56  Aligned_cols=33  Identities=30%  Similarity=0.404  Sum_probs=26.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -+.+.|+.|+||||++..+..+....|.=|+.+
T Consensus       107 vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVlli  139 (320)
T 1zu4_A          107 IFMLVGVNGTGKTTSLAKMANYYAELGYKVLIA  139 (320)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            488999999999999999888766665544444

>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=89.47  E-value=0.19  Score=42.85  Aligned_cols=21  Identities=29%  Similarity=0.354  Sum_probs=18.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|..|+|||+++.++..
T Consensus         3 ki~v~G~~~~GKSsli~~l~~   23 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTG   23 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999988763

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.46  E-value=0.24  Score=59.47  Aligned_cols=36  Identities=19%  Similarity=0.297  Sum_probs=32.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      -++|+|++|||||++..|+++-|..+|+-|+||.-.
T Consensus      1429 ~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e 1464 (2050)
T 3cmu_A         1429 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE 1464 (2050)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEcc
Confidence            489999999999999999999999999999998543

>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=89.41  E-value=0.23  Score=43.73  Aligned_cols=22  Identities=32%  Similarity=0.597  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|+.|+|||+++.++..
T Consensus        13 ~~i~~~G~~g~GKTsl~~~l~~   34 (218)
T 1nrj_B           13 PSIIIAGPQNSGKTSLLTLLTT   34 (218)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            5699999999999999988765

>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=89.31  E-value=0.31  Score=50.27  Aligned_cols=32  Identities=28%  Similarity=0.484  Sum_probs=22.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ..++|+|++|||||+++..+   |.+.+.-+++|.
T Consensus       239 ~~vLL~GppGtGKT~lArai---a~~~~~~fv~vn  270 (489)
T 3hu3_A          239 RGILLYGPPGTGKTLIARAV---ANETGAFFFLIN  270 (489)
T ss_dssp             CEEEEECSTTSSHHHHHHHH---HHHCSSEEEEEE
T ss_pred             CcEEEECcCCCCHHHHHHHH---HHHhCCCEEEEE
Confidence            35999999999999876554   333355555553

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=89.30  E-value=0.23  Score=41.76  Aligned_cols=22  Identities=23%  Similarity=0.253  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.++..
T Consensus         7 ~ki~v~G~~~~GKssl~~~l~~   28 (178)
T 2hxs_A            7 LKIVVLGDGASGKTSLTTCFAQ   28 (178)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHG
T ss_pred             EEEEEECcCCCCHHHHHHHHHh
Confidence            4699999999999999988763

>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=89.29  E-value=0.32  Score=47.11  Aligned_cols=31  Identities=19%  Similarity=0.246  Sum_probs=24.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL  222 (404)
                      -+.|.|+.||||||++.-+..+-... |-|.+
T Consensus       104 vi~lvG~nGsGKTTll~~Lagll~~~~g~V~l  135 (304)
T 1rj9_A          104 VVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMF  135 (304)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHTTTCCEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhcCCEEEE
Confidence            47899999999999999988876654 44433

>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=89.28  E-value=0.15  Score=51.88  Aligned_cols=34  Identities=26%  Similarity=0.337  Sum_probs=30.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      .+++.|+.|+|||++.+.+..++..+|+=|+.|.
T Consensus       101 vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~  134 (432)
T 2v3c_C          101 VILLVGIQGSGKTTTAAKLARYIQKRGLKPALIA  134 (432)
T ss_dssp             CEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            4899999999999999999999888888777664

>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=89.27  E-value=0.087  Score=52.31  Aligned_cols=22  Identities=18%  Similarity=0.185  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -++|+|++|||||++..|+.+.
T Consensus       125 viLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          125 MVIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             EEEEECSCSSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHh
Confidence            3799999999999999998654

>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=89.25  E-value=0.2  Score=42.99  Aligned_cols=22  Identities=32%  Similarity=0.392  Sum_probs=19.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|.+|+|||+++..+..
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~   26 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAG   26 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            3599999999999999988753

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=89.23  E-value=0.25  Score=43.78  Aligned_cols=27  Identities=15%  Similarity=0.295  Sum_probs=23.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      +.++|.|..|+|||+++.+++......
T Consensus        31 ~~i~i~G~~g~GKTTl~~~l~~~~~~~   57 (221)
T 2wsm_A           31 VAVNIMGAIGSGKTLLIERTIERIGNE   57 (221)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHTTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhccC
Confidence            469999999999999999998876443

>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=89.22  E-value=0.25  Score=41.59  Aligned_cols=22  Identities=23%  Similarity=0.271  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.++..
T Consensus        11 ~~i~v~G~~~~GKssli~~l~~   32 (180)
T 2g6b_A           11 FKVMLVGDSGVGKTCLLVRFKD   32 (180)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            4699999999999999988764

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=89.18  E-value=0.23  Score=41.74  Aligned_cols=21  Identities=24%  Similarity=0.251  Sum_probs=18.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|..|+|||+++..++
T Consensus        10 ~~i~v~G~~~~GKssl~~~l~   30 (181)
T 3tw8_B           10 FKLLIIGDSGVGKSSLLLRFA   30 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHh
Confidence            569999999999999998875

>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=89.17  E-value=0.24  Score=42.09  Aligned_cols=22  Identities=23%  Similarity=0.215  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        19 ~ki~v~G~~~~GKSsl~~~l~~   40 (183)
T 3kkq_A           19 YKLVVVGDGGVGKSALTIQFFQ   40 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999988873

>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=89.17  E-value=0.25  Score=42.91  Aligned_cols=22  Identities=23%  Similarity=0.300  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|||||+++.+++.
T Consensus        21 ~ki~ivG~~~vGKSsL~~~~~~   42 (184)
T 3ihw_A           21 LKVGIVGNLSSGKSALVHRYLT   42 (184)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999988765

>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=89.14  E-value=0.23  Score=41.75  Aligned_cols=23  Identities=22%  Similarity=0.228  Sum_probs=20.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+++|.|..|+|||+++..+..-
T Consensus        10 ~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A           10 HKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            56999999999999999887754

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=89.12  E-value=0.38  Score=42.26  Aligned_cols=28  Identities=32%  Similarity=0.456  Sum_probs=22.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      ..++|+|..||||||+...+..+-...+
T Consensus        11 ~~I~l~G~~GsGKST~~~~L~~~l~~~~   38 (212)
T 2wwf_A           11 KFIVFEGLDRSGKSTQSKLLVEYLKNNN   38 (212)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHcC
Confidence            3599999999999999988877544343

>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=89.06  E-value=0.23  Score=43.44  Aligned_cols=33  Identities=21%  Similarity=0.205  Sum_probs=23.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCe--EEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGW--LVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngW--IVL~IP~  226 (404)
                      .++|.|..||||||+...+..+-  .|+  +.+..|.
T Consensus         6 ~I~l~G~~GsGKsT~~~~L~~~l--~g~~~~~~~~~~   40 (204)
T 2v54_A            6 LIVFEGLDKSGKTTQCMNIMESI--PANTIKYLNFPQ   40 (204)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHTS--CGGGEEEEESSC
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH--CCCceEEEecCC
Confidence            48999999999999988776542  345  4444443

>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=89.06  E-value=0.23  Score=42.22  Aligned_cols=22  Identities=23%  Similarity=0.279  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.++..
T Consensus        11 ~ki~v~G~~~~GKSsli~~l~~   32 (186)
T 2bme_A           11 FKFLVIGNAGTGKSCLLHQFIE   32 (186)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999998764

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=89.00  E-value=0.26  Score=44.41  Aligned_cols=23  Identities=22%  Similarity=0.049  Sum_probs=18.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -.+|+|+.|+|||++| .++.||.
T Consensus        25 ~~~I~G~NgsGKStil-~ai~~~l   47 (203)
T 3qks_A           25 INLIIGQNGSGKSSLL-DAILVGL   47 (203)
T ss_dssp             EEEEECCTTSSHHHHH-HHHHHHH
T ss_pred             eEEEEcCCCCCHHHHH-HHHHHHh
Confidence            3799999999999987 4556655

>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=88.94  E-value=0.27  Score=42.15  Aligned_cols=22  Identities=27%  Similarity=0.306  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++++.|..|+|||+++.++..
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~   43 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQ   43 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHc
Confidence            4699999999999999998874

>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=88.94  E-value=0.21  Score=43.19  Aligned_cols=22  Identities=18%  Similarity=0.105  Sum_probs=17.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      .+|+|+.|||||++|. ++.++.
T Consensus        29 ~~i~G~NGsGKStll~-ai~~~l   50 (182)
T 3kta_A           29 TAIVGANGSGKSNIGD-AILFVL   50 (182)
T ss_dssp             EEEEECTTSSHHHHHH-HHHHHT
T ss_pred             EEEECCCCCCHHHHHH-HHHHHH
Confidence            7999999999998874 566653

>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=88.93  E-value=0.25  Score=45.16  Aligned_cols=22  Identities=27%  Similarity=0.270  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -++|.|+.|||||+++..++..
T Consensus        21 ~ivl~GPSGaGKsTL~~~L~~~   42 (197)
T 3ney_A           21 TLVLIGASGVGRSHIKNALLSQ   42 (197)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECcCCCCHHHHHHHHHhh
Confidence            4899999999999999887753

>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=88.86  E-value=0.28  Score=41.47  Aligned_cols=22  Identities=23%  Similarity=0.199  Sum_probs=19.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.++..
T Consensus         6 ~~i~~~G~~~~GKssl~~~l~~   27 (186)
T 1mh1_A            6 IKCVVVGDGAVGKTCLLISYTT   27 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999988764

>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=88.84  E-value=0.39  Score=47.66  Aligned_cols=31  Identities=26%  Similarity=0.499  Sum_probs=25.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh--CCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE--EGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~--ngWIVL  222 (404)
                      -++|.|+.||||||+|.-+..+-..  .|-|++
T Consensus       138 ~i~ivG~~GsGKTTll~~l~~~~~~~~~g~I~~  170 (372)
T 2ewv_A          138 LILVTGPTGSGKSTTIASMIDYINQTKSYHIIT  170 (372)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHHHHSCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHhhcCcCCCcEEEE
Confidence            4899999999999999998886553  566644

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=88.83  E-value=0.26  Score=42.25  Aligned_cols=22  Identities=27%  Similarity=0.274  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.++..
T Consensus        17 ~ki~v~G~~~~GKSsli~~l~~   38 (196)
T 3tkl_A           17 FKLLLIGDSGVGKSCLLLRFAD   38 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHc
Confidence            4699999999999999988874

>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=88.81  E-value=0.28  Score=42.26  Aligned_cols=22  Identities=27%  Similarity=0.306  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~   47 (193)
T 2oil_A           26 FKVVLIGESGVGKTNLLSRFTR   47 (193)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHhc
Confidence            4699999999999999988765

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=88.80  E-value=0.38  Score=45.53  Aligned_cols=34  Identities=26%  Similarity=0.302  Sum_probs=29.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++++|+-|+|||+.|.+.++.+...|.=|+-+-
T Consensus        21 l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~k   54 (234)
T 2orv_A           21 IQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIK   54 (234)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEe
Confidence            4899999999999999999999988876666553

>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=88.78  E-value=0.25  Score=44.66  Aligned_cols=20  Identities=45%  Similarity=0.599  Sum_probs=18.0

Q ss_pred             EEEECCCCCcHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~  212 (404)
                      +||.||.|+||++++..++.
T Consensus         4 IVi~GPSG~GK~Tl~~~L~~   23 (186)
T 1ex7_A            4 IVISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            89999999999999987754

>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=88.75  E-value=0.15  Score=48.43  Aligned_cols=21  Identities=24%  Similarity=0.290  Sum_probs=17.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++|+|++|||||+++..+..
T Consensus        47 ~vLl~G~~GtGKT~la~~la~   67 (350)
T 1g8p_A           47 GVLVFGDRGTGKSTAVRALAA   67 (350)
T ss_dssp             CEEEECCGGGCTTHHHHHHHH
T ss_pred             eEEEECCCCccHHHHHHHHHH
Confidence            399999999999987765554

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=88.67  E-value=0.25  Score=48.82  Aligned_cols=22  Identities=32%  Similarity=0.477  Sum_probs=18.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      ++|+|+.|+|||++| -++.||.
T Consensus        26 ~~i~G~NGaGKTTll-~ai~~al   47 (365)
T 3qf7_A           26 TVVEGPNGAGKSSLF-EAISFAL   47 (365)
T ss_dssp             EEEECCTTSSHHHHH-HHHHHHH
T ss_pred             EEEECCCCCCHHHHH-HHHHHHh
Confidence            789999999999888 6666663

>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=88.67  E-value=0.22  Score=46.11  Aligned_cols=31  Identities=26%  Similarity=0.385  Sum_probs=21.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        33 ~~~iiG~nGsGKSTLl~~l~Gl~~p~~G~I~~   64 (235)
T 3tif_A           33 FVSIMGPSGSGKSTMLNIIGCLDKPTEGEVYI   64 (235)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHhcCCCCCceEEEE
Confidence            388999999999999876654322 3455544

>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=88.66  E-value=0.43  Score=48.27  Aligned_cols=23  Identities=22%  Similarity=0.384  Sum_probs=17.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      +.++|+|++|||||++...+...
T Consensus        64 ~~iLl~GppGtGKT~la~ala~~   86 (456)
T 2c9o_A           64 RAVLLAGPPGTGKTALALAIAQE   86 (456)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCcCCHHHHHHHHHHH
Confidence            35999999999999876544443

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=88.64  E-value=0.19  Score=43.17  Aligned_cols=28  Identities=25%  Similarity=0.262  Sum_probs=16.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .++|.|.+|||||++...+.   ..-|+-++
T Consensus         7 ~I~l~G~~GsGKST~a~~La---~~l~~~~i   34 (183)
T 2vli_A            7 IIWINGPFGVGKTHTAHTLH---ERLPGSFV   34 (183)
T ss_dssp             EEEEECCC----CHHHHHHH---HHSTTCEE
T ss_pred             EEEEECCCCCCHHHHHHHHH---HhcCCCEE
Confidence            48999999999999877763   33455444

>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=88.62  E-value=0.38  Score=44.27  Aligned_cols=33  Identities=21%  Similarity=0.362  Sum_probs=25.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..++|.|..||||||++..+..+-.. |+-|+..
T Consensus        27 ~~i~i~G~~GsGKsT~~~~l~~~l~~-~~~~~~~   59 (229)
T 4eaq_A           27 AFITFEGPEGSGKTTVINEVYHRLVK-DYDVIMT   59 (229)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTT-TSCEEEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhc-CCCceee
Confidence            45899999999999999888877655 6555443

>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=88.62  E-value=0.27  Score=42.48  Aligned_cols=22  Identities=18%  Similarity=0.253  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.++..
T Consensus        15 ~ki~v~G~~~~GKSsli~~l~~   36 (206)
T 2bov_A           15 HKVIMVGSGGVGKSALTLQFMY   36 (206)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999988764

>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=88.57  E-value=0.24  Score=41.95  Aligned_cols=21  Identities=29%  Similarity=0.314  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|..|+|||+++..++
T Consensus         7 ~ki~~~G~~~~GKSsli~~l~   27 (181)
T 3t5g_A            7 RKIAILGYRSVGKSSLTIQFV   27 (181)
T ss_dssp             EEEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEEECcCCCCHHHHHHHHH
Confidence            569999999999999998887

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=88.53  E-value=0.25  Score=44.31  Aligned_cols=28  Identities=11%  Similarity=0.217  Sum_probs=21.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .++|.|.+||||||+...+..+   -|+..+
T Consensus         7 ~I~l~G~~GsGKsT~~~~La~~---l~~~~i   34 (222)
T 1zak_A            7 KVMISGAPASGKGTQCELIKTK---YQLAHI   34 (222)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHH---HCCEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---hCCcee
Confidence            4999999999999988776543   355443

>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=88.52  E-value=0.32  Score=49.29  Aligned_cols=32  Identities=28%  Similarity=0.278  Sum_probs=24.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh-CCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE-EGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~-ngWIVL~  223 (404)
                      -++|.|+.||||||+|.-++.+-.. .|-|++.
T Consensus       169 ii~I~GpnGSGKTTlL~allg~l~~~~g~I~~~  201 (418)
T 1p9r_A          169 IILVTGPTGSGKSTTLYAGLQELNSSERNILTV  201 (418)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHhhcCCCCCEEEEe
Confidence            4899999999999999998877543 4555543

>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=88.49  E-value=0.27  Score=44.67  Aligned_cols=22  Identities=36%  Similarity=0.333  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..++.
T Consensus        30 ~~i~lvG~~g~GKStlin~l~g   51 (239)
T 3lxx_A           30 LRIVLVGKTGAGKSATGNSILG   51 (239)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHcC
Confidence            5799999999999999988774

>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=88.48  E-value=0.44  Score=43.64  Aligned_cols=34  Identities=32%  Similarity=0.390  Sum_probs=28.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|..||||||.+..+..+-...|.-|+...
T Consensus         8 ~i~~eG~~gsGKsT~~~~l~~~l~~~~~~v~~~~   41 (213)
T 4edh_A            8 FVTLEGPEGAGKSTNRDYLAERLRERGIEVQLTR   41 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHcCCCccccc
Confidence            4899999999999999999998887777555443

>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=88.48  E-value=0.3  Score=42.02  Aligned_cols=22  Identities=18%  Similarity=0.157  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.+++.
T Consensus        21 ~ki~v~G~~~~GKSsli~~l~~   42 (189)
T 1z06_A           21 FKIIVIGDSNVGKTCLTYRFCA   42 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999988764

>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=88.47  E-value=0.31  Score=41.16  Aligned_cols=22  Identities=23%  Similarity=0.154  Sum_probs=19.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++++.|..|+|||+++.++..
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~   30 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTS   30 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4599999999999999977763

>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=88.47  E-value=0.3  Score=42.15  Aligned_cols=22  Identities=23%  Similarity=0.244  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~   43 (191)
T 2a5j_A           22 FKYIIIGDTGVGKSCLLLQFTD   43 (191)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHhc
Confidence            4699999999999999988764

>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=88.47  E-value=0.3  Score=41.68  Aligned_cols=22  Identities=27%  Similarity=0.283  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        16 ~~i~v~G~~~~GKssli~~l~~   37 (195)
T 1x3s_A           16 LKILIIGESGVGKSSLLLRFTD   37 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999988864

>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=88.46  E-value=0.3  Score=42.38  Aligned_cols=23  Identities=17%  Similarity=0.248  Sum_probs=20.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+++|.|..|+|||+++..++..
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            9 LKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46999999999999999888653

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=88.44  E-value=0.28  Score=42.16  Aligned_cols=23  Identities=22%  Similarity=0.271  Sum_probs=20.1

Q ss_pred             ceeEEEECCCCCcHHHHHHHHHH
Q 045329          190 RKQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       190 r~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ..+++|.|..|+|||+++.+++.
T Consensus        17 ~~ki~v~G~~~~GKSsl~~~l~~   39 (199)
T 4bas_A           17 KLQVVMCGLDNSGKTTIINQVKP   39 (199)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc
Confidence            46799999999999999988753

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=88.43  E-value=0.22  Score=47.44  Aligned_cols=31  Identities=16%  Similarity=0.297  Sum_probs=20.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      .++|+|++|||||+++..+.. ......+.++
T Consensus        48 ~vll~G~pGtGKT~la~~la~-~~~~~~~~i~   78 (331)
T 2r44_A           48 HILLEGVPGLAKTLSVNTLAK-TMDLDFHRIQ   78 (331)
T ss_dssp             CEEEESCCCHHHHHHHHHHHH-HTTCCEEEEE
T ss_pred             eEEEECCCCCcHHHHHHHHHH-HhCCCeEEEe
Confidence            489999999999987765533 3333344333

>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=88.43  E-value=0.43  Score=45.22  Aligned_cols=30  Identities=23%  Similarity=0.144  Sum_probs=24.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..++|+|..||||||+...+..    .|+-|+..
T Consensus        76 ~iI~I~G~~GSGKSTva~~La~----lg~~~id~  105 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLKN----LGAYIIDS  105 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH----HTCEEEEH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH----CCCcEEeh
Confidence            3589999999999998877763    48877764

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=88.41  E-value=0.31  Score=41.57  Aligned_cols=29  Identities=31%  Similarity=0.136  Sum_probs=21.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|+|..|||||++...+..   .-||-++..
T Consensus        10 i~l~G~~GsGKSTva~~La~---~lg~~~id~   38 (168)
T 1zuh_A           10 LVLIGFMGSGKSSLAQELGL---ALKLEVLDT   38 (168)
T ss_dssp             EEEESCTTSSHHHHHHHHHH---HHTCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHH---HhCCCEEEC
Confidence            89999999999998766543   336655543

>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=88.30  E-value=0.32  Score=46.90  Aligned_cols=33  Identities=30%  Similarity=0.364  Sum_probs=27.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -+++.|+.|+|||+++..+..+...+|.=|+.+
T Consensus       100 vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~  132 (297)
T 1j8m_F          100 VIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLV  132 (297)
T ss_dssp             EEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            478899999999999999988877776655554

>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=88.28  E-value=0.29  Score=42.86  Aligned_cols=21  Identities=29%  Similarity=0.347  Sum_probs=18.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      -+++|-|.+|+|||+++.+.+
T Consensus         7 ~kv~lvG~~~vGKSsL~~~~~   27 (192)
T 2cjw_A            7 YRVVLIGEQGVGKSTLANIFA   27 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHh
Confidence            469999999999999998765

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=88.23  E-value=0.27  Score=45.51  Aligned_cols=31  Identities=16%  Similarity=0.187  Sum_probs=21.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      ..++|.|.+|||||++...+... ...+++++
T Consensus        33 ~~i~l~G~~GsGKSTla~~L~~~-l~~~~~~~   63 (253)
T 2p5t_B           33 IAILLGGQSGAGKTTIHRIKQKE-FQGNIVII   63 (253)
T ss_dssp             EEEEEESCGGGTTHHHHHHHHHH-TTTCCEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh-cCCCcEEE
Confidence            35899999999999987776543 22345544

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=88.23  E-value=0.36  Score=50.16  Aligned_cols=34  Identities=18%  Similarity=0.162  Sum_probs=23.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +.++|+|++|||||+++..+... ...+.+.+.-+
T Consensus        65 ~GvLL~GppGtGKTtLaraIa~~-~~~~~i~i~g~   98 (499)
T 2dhr_A           65 KGVLLVGPPGVGKTHLARAVAGE-ARVPFITASGS   98 (499)
T ss_dssp             SEEEEECSSSSSHHHHHHHHHHH-TTCCEEEEEGG
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH-hCCCEEEEehh
Confidence            45999999999999877555444 34566655543

>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=88.23  E-value=0.24  Score=41.83  Aligned_cols=22  Identities=18%  Similarity=0.184  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.+++.
T Consensus         8 ~ki~~vG~~~vGKTsli~~l~~   29 (178)
T 2iwr_A            8 LRLGVLGDARSGKSSLIHRFLT   29 (178)
T ss_dssp             EEEEEECCGGGCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999988765

>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=88.18  E-value=0.32  Score=41.97  Aligned_cols=22  Identities=18%  Similarity=0.317  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.++..
T Consensus        23 ~ki~v~G~~~~GKSsli~~l~~   44 (188)
T 1zd9_A           23 MELTLVGLQYSGKTTFVNVIAS   44 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999988864

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=88.16  E-value=0.27  Score=45.13  Aligned_cols=22  Identities=23%  Similarity=0.279  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+-|+|+.||||||++..+...
T Consensus        27 iigI~G~~GsGKSTl~k~L~~~   48 (245)
T 2jeo_A           27 LIGVSGGTASGKSTVCEKIMEL   48 (245)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999877653

>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=88.11  E-value=0.31  Score=41.93  Aligned_cols=22  Identities=23%  Similarity=0.221  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.++..
T Consensus        23 ~ki~vvG~~~~GKSsli~~l~~   44 (189)
T 2gf9_A           23 FKLLLIGNSSVGKTSFLFRYAD   44 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            4699999999999999988764

>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=88.05  E-value=0.29  Score=42.00  Aligned_cols=22  Identities=32%  Similarity=0.525  Sum_probs=19.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++++.|..|+|||+++.++..
T Consensus         8 ~ki~v~G~~~vGKSsli~~l~~   29 (184)
T 1m7b_A            8 CKIVVVGDSQCGKTALLHVFAK   29 (184)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999998775

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=88.02  E-value=0.47  Score=48.32  Aligned_cols=23  Identities=26%  Similarity=0.154  Sum_probs=18.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .++|+|++|||||++...+....
T Consensus       203 ~~LL~G~pG~GKT~la~~la~~l  225 (468)
T 3pxg_A          203 NPVLIGEPGVGKTAIAEGLAQQI  225 (468)
T ss_dssp             EEEEESCTTTTTHHHHHHHHHHH
T ss_pred             CeEEECCCCCCHHHHHHHHHHHH
Confidence            48999999999999776555543

>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=88.01  E-value=0.31  Score=42.02  Aligned_cols=21  Identities=33%  Similarity=0.330  Sum_probs=18.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|..|+|||+++.++.
T Consensus        17 ~ki~ivG~~~vGKSsL~~~l~   37 (181)
T 1fzq_A           17 VRILLLGLDNAGKTTLLKQLA   37 (181)
T ss_dssp             EEEEEEESTTSSHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHh
Confidence            579999999999999998765

>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=87.99  E-value=0.35  Score=52.87  Aligned_cols=35  Identities=20%  Similarity=0.181  Sum_probs=26.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh-------CCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE-------EGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~-------ngWIVL~IP~  226 (404)
                      .++|+|++|||||+++..+......       .|+-|++++-
T Consensus       193 ~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~  234 (854)
T 1qvr_A          193 NPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQM  234 (854)
T ss_dssp             CCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC
T ss_pred             ceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeeh
Confidence            4899999999999988777666543       3777777754

>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=87.99  E-value=0.28  Score=42.41  Aligned_cols=23  Identities=17%  Similarity=0.120  Sum_probs=20.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -+++|.|..|+|||+++..+..-
T Consensus        24 ~ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           24 FKLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHhcC
Confidence            46999999999999999887753

>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=87.98  E-value=0.36  Score=41.51  Aligned_cols=23  Identities=22%  Similarity=0.049  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -.+|+|+.|+|||++| .++.||.
T Consensus        25 ~~~I~G~NGsGKStil-~Ai~~~l   47 (149)
T 1f2t_A           25 INLIIGQNGSGKSSLL-DAILVGL   47 (149)
T ss_dssp             EEEEECCTTSSHHHHH-HHHHHHH
T ss_pred             eEEEECCCCCCHHHHH-HHHHHHH
Confidence            3799999999999986 4666765

>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=87.97  E-value=0.31  Score=42.28  Aligned_cols=22  Identities=23%  Similarity=0.221  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~   30 (203)
T 1zbd_A            9 FKILIIGNSSVGKTSFLFRYAD   30 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999988764

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=87.95  E-value=0.4  Score=47.00  Aligned_cols=27  Identities=26%  Similarity=0.318  Sum_probs=23.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      ..+.|.|.+|+|||++|..++.+-...
T Consensus        75 ~~v~lvG~pgaGKSTLln~L~~~~~~~  101 (349)
T 2www_A           75 FRVGLSGPPGAGKSTFIEYFGKMLTER  101 (349)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhhhc
Confidence            469999999999999999999876544

>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=87.82  E-value=0.35  Score=42.15  Aligned_cols=22  Identities=36%  Similarity=0.391  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..+..
T Consensus        21 ~~i~v~G~~~~GKSsli~~l~~   42 (213)
T 3cph_A           21 MKILLIGDSGVGKSCLLVRFVE   42 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999988763

>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=87.75  E-value=0.39  Score=46.01  Aligned_cols=31  Identities=29%  Similarity=0.340  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH---hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR---EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~---~ngWIVL  222 (404)
                      .+.|.|+.||||||++..+...-.   ..|-|.+
T Consensus        82 iigI~G~~GsGKSTl~~~L~~~l~~~~~~G~i~v  115 (308)
T 1sq5_A           82 IISIAGSVAVGKSTTARVLQALLSRWPEHRRVEL  115 (308)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhCCCCCeEEE
Confidence            488999999999999988776543   3455544

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=87.70  E-value=0.25  Score=45.41  Aligned_cols=31  Identities=29%  Similarity=0.276  Sum_probs=22.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        32 ~~~iiG~nGsGKSTLl~~l~Gl~~p~~G~i~~   63 (224)
T 2pcj_A           32 FVSIIGASGSGKSTLLYILGLLDAPTEGKVFL   63 (224)
T ss_dssp             EEEEEECTTSCHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCceEEEE
Confidence            378999999999999876654322 3465554

>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=87.69  E-value=0.38  Score=56.89  Aligned_cols=35  Identities=20%  Similarity=0.313  Sum_probs=31.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -++|+|++|||||++++|++..+..+|--|+||.-
T Consensus       385 lilI~G~pGsGKTtLaLq~a~~~~~~G~~vlyis~  419 (1706)
T 3cmw_A          385 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA  419 (1706)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEc
Confidence            38999999999999999999999888888888854

>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=87.68  E-value=0.36  Score=41.68  Aligned_cols=22  Identities=27%  Similarity=0.309  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        24 ~ki~~vG~~~~GKSsl~~~l~~   45 (194)
T 3reg_A           24 LKIVVVGDGAVGKTCLLLAFSK   45 (194)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHhc
Confidence            4699999999999999988764

>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=87.68  E-value=0.27  Score=43.49  Aligned_cols=31  Identities=19%  Similarity=0.095  Sum_probs=22.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .+.|+|+.||||||++..+...  ..++.++..
T Consensus        23 ~i~i~G~~GsGKSTl~~~L~~~--~~~~~~i~~   53 (207)
T 2qt1_A           23 IIGISGVTNSGKTTLAKNLQKH--LPNCSVISQ   53 (207)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTT--STTEEEEEG
T ss_pred             EEEEECCCCCCHHHHHHHHHHh--cCCcEEEeC
Confidence            4889999999999988766542  126666554

>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=87.68  E-value=0.31  Score=41.84  Aligned_cols=22  Identities=27%  Similarity=0.267  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.+++.
T Consensus         9 ~ki~vvG~~~~GKSsli~~l~~   30 (199)
T 2gf0_A            9 YRVVVFGAGGVGKSSLVLRFVK   30 (199)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHc
Confidence            4699999999999999998875

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=87.67  E-value=0.46  Score=47.28  Aligned_cols=31  Identities=26%  Similarity=0.361  Sum_probs=25.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL  222 (404)
                      -+.|.|+.||||||++.-+..+...+ |-|.+
T Consensus       159 vi~lvG~nGsGKTTll~~Lag~l~~~~G~V~l  190 (359)
T 2og2_A          159 VIMIVGVNGGGKTTSLGKLAHRLKNEGTKVLM  190 (359)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EEEEEcCCCChHHHHHHHHHhhccccCCEEEE
Confidence            48899999999999999998877654 44444

>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=87.61  E-value=0.36  Score=41.80  Aligned_cols=22  Identities=18%  Similarity=0.206  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.+++.
T Consensus        22 ~ki~vvG~~~vGKTsLi~~l~~   43 (187)
T 3c5c_A           22 VNLAILGRRGAGKSALTVKFLT   43 (187)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCcHHHHHHHHHh
Confidence            4699999999999999988775

>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=87.60  E-value=0.32  Score=42.16  Aligned_cols=22  Identities=27%  Similarity=0.333  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        24 ~ki~vvG~~~~GKSsli~~l~~   45 (192)
T 2fg5_A           24 LKVCLLGDTGVGKSSIVCRFVQ   45 (192)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHhc
Confidence            4699999999999999988764

>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=87.55  E-value=0.35  Score=41.15  Aligned_cols=21  Identities=33%  Similarity=0.401  Sum_probs=17.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++ +.+.
T Consensus        15 ~ki~vvG~~~~GKssL~-~~l~   35 (198)
T 3t1o_A           15 FKIVYYGPGLSGKTTNL-KWIY   35 (198)
T ss_dssp             EEEEEECSTTSSHHHHH-HHHH
T ss_pred             cEEEEECCCCCCHHHHH-HHHH
Confidence            56999999999999998 5444

>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=87.54  E-value=0.23  Score=45.21  Aligned_cols=22  Identities=18%  Similarity=0.501  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -+.|.|+.||||||++..+..+
T Consensus        22 ~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           22 TVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHhc
Confidence            4889999999999999887766

>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=87.54  E-value=0.33  Score=42.48  Aligned_cols=22  Identities=23%  Similarity=0.326  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+.|.|+.|+||||+|.-+.-.
T Consensus        35 ~v~L~G~nGaGKTTLlr~l~g~   56 (158)
T 1htw_A           35 MVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            4789999999999999877654

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=87.53  E-value=0.34  Score=49.39  Aligned_cols=21  Identities=24%  Similarity=0.435  Sum_probs=16.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++|+|++|||||+++..+..
T Consensus        52 ~vLL~GppGtGKTtlAr~ia~   72 (447)
T 3pvs_A           52 SMILWGPPGTGKTTLAEVIAR   72 (447)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHH
Confidence            499999999999887655443

>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=87.52  E-value=0.6  Score=42.39  Aligned_cols=22  Identities=18%  Similarity=0.487  Sum_probs=18.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -+++.|+.|||||+++...+.-
T Consensus        78 ~~~i~g~TGsGKTt~~~~~~~~   99 (235)
T 3llm_A           78 VVIIRGATGCGKTTQVPQFILD   99 (235)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCcHHhHHHHHhc
Confidence            3899999999999988776544

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=87.52  E-value=0.28  Score=43.51  Aligned_cols=27  Identities=22%  Similarity=0.347  Sum_probs=23.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      .+.|.|+.||||||++.-++-+-...|
T Consensus         4 ~v~IvG~SGsGKSTL~~~L~~~~~~~g   30 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTLITRMMPILRERG   30 (171)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhhcC
Confidence            478999999999999999888766554

>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=87.47  E-value=0.37  Score=41.76  Aligned_cols=22  Identities=18%  Similarity=0.261  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        29 ~ki~v~G~~~vGKSsli~~l~~   50 (196)
T 2atv_A           29 VKLAIFGRAGVGKSALVVRFLT   50 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999988765

>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=87.44  E-value=0.42  Score=52.61  Aligned_cols=20  Identities=30%  Similarity=0.516  Sum_probs=17.1

Q ss_pred             eeEEEECCCCCcHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qa  210 (404)
                      +.++|+|++|||||++...+
T Consensus       239 ~GILL~GPPGTGKT~LArai  258 (806)
T 3cf2_A          239 RGILLYGPPGTGKTLIARAV  258 (806)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            57999999999999887554

>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=87.43  E-value=0.37  Score=42.27  Aligned_cols=23  Identities=17%  Similarity=0.304  Sum_probs=20.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+++|.|..|+|||+++.+++.-
T Consensus         8 ~ki~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B            8 RAVLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46999999999999999987753

>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=87.43  E-value=0.3  Score=41.69  Aligned_cols=22  Identities=18%  Similarity=0.191  Sum_probs=19.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++++.|..|+|||+++.++..
T Consensus        19 ~~i~v~G~~~~GKssl~~~l~~   40 (186)
T 1ksh_A           19 LRLLMLGLDNAGKTTILKKFNG   40 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999988763

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=87.42  E-value=0.31  Score=45.45  Aligned_cols=31  Identities=32%  Similarity=0.468  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        26 ~~~liG~nGsGKSTLl~~l~Gl~~p~~G~i~~   57 (240)
T 2onk_A           26 YCVLLGPTGAGKSVFLELIAGIVKPDRGEVRL   57 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCceEEEE
Confidence            488999999999999987765432 3466655

>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=87.42  E-value=0.3  Score=45.32  Aligned_cols=36  Identities=36%  Similarity=0.575  Sum_probs=25.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeE-----EEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWL-----VLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWI-----VL~IP~a  227 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|     |-|+|.-
T Consensus        33 ~~~i~G~nGsGKSTLl~~l~Gl~~p~~G~I~~~g~i~~v~Q~   74 (237)
T 2cbz_A           33 LVAVVGQVGCGKSSLLSALLAEMDKVEGHVAIKGSVAYVPQQ   74 (237)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTCSEEEEEEEEECSCEEEECSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCEEEEEcCC
Confidence            489999999999999987654322 34555     3456554

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=87.41  E-value=0.42  Score=52.40  Aligned_cols=35  Identities=23%  Similarity=0.362  Sum_probs=26.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh-CCe-EEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE-EGW-LVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~-ngW-IVL~IP~  226 (404)
                      -++|.|++|||||+++..++.+... .++ |++--|.
T Consensus       373 ~~lI~GppGTGKT~ti~~~i~~l~~~~~~~ilv~a~t  409 (800)
T 2wjy_A          373 LSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS  409 (800)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTCSSCEEEEESS
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCCcEEEEcCc
Confidence            3799999999999999999987765 444 4444444

>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=87.39  E-value=0.28  Score=42.03  Aligned_cols=22  Identities=18%  Similarity=0.271  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.++..
T Consensus        22 ~~i~v~G~~~~GKSsli~~l~~   43 (181)
T 2h17_A           22 HKVIIVGLDNAGKTTILYQFSM   43 (181)
T ss_dssp             EEEEEEEETTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            5699999999999999988764

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=87.39  E-value=0.31  Score=45.18  Aligned_cols=20  Identities=35%  Similarity=0.491  Sum_probs=17.4

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+.|+|+.||||||++..+.
T Consensus        29 ~I~I~G~~GsGKSTl~k~La   48 (252)
T 4e22_A           29 VITVDGPSGAGKGTLCKALA   48 (252)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            48999999999999987664

>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=87.38  E-value=0.32  Score=41.77  Aligned_cols=21  Identities=19%  Similarity=0.305  Sum_probs=19.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|..|+|||+++.++.
T Consensus        17 ~~i~v~G~~~~GKssl~~~l~   37 (187)
T 1zj6_A           17 HKVIIVGLDNAGKTTILYQFS   37 (187)
T ss_dssp             EEEEEEESTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHh
Confidence            469999999999999998876

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=87.35  E-value=0.52  Score=49.08  Aligned_cols=34  Identities=24%  Similarity=0.427  Sum_probs=28.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..++|.|.+||||||+++.+.++...+|+=|+-|
T Consensus       102 ~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllV  135 (504)
T 2j37_W          102 NVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLI  135 (504)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            3588999999999999999999888877755444

>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=87.34  E-value=0.26  Score=41.77  Aligned_cols=21  Identities=29%  Similarity=0.248  Sum_probs=18.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|+.|+|||+++.++.
T Consensus        19 ~~i~v~G~~~~GKssli~~l~   39 (183)
T 1moz_A           19 LRILILGLDGAGKTTILYRLQ   39 (183)
T ss_dssp             EEEEEEEETTSSHHHHHHHTC
T ss_pred             cEEEEECCCCCCHHHHHHHHh
Confidence            569999999999999997654

>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=87.30  E-value=0.34  Score=42.28  Aligned_cols=22  Identities=27%  Similarity=0.255  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..+..
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~   30 (206)
T 2bcg_Y            9 FKLLLIGNSGVGKSCLLLRFSD   30 (206)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999988764

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=87.27  E-value=0.55  Score=46.12  Aligned_cols=33  Identities=24%  Similarity=0.223  Sum_probs=25.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..++.|+.|+|||+++..++......|--|+.+
T Consensus        37 ~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~   69 (392)
T 4ag6_A           37 NWTILAKPGAGKSFTAKMLLLREYMQGSRVIII   69 (392)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             ceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEE
Confidence            479999999999999999887766654444444

>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=87.25  E-value=0.39  Score=41.79  Aligned_cols=22  Identities=41%  Similarity=0.454  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..+..
T Consensus        29 ~ki~v~G~~~~GKSsli~~l~~   50 (199)
T 2p5s_A           29 YKIVLAGDAAVGKSSFLMRLCK   50 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            4699999999999999988764

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=87.17  E-value=0.55  Score=45.85  Aligned_cols=32  Identities=19%  Similarity=0.163  Sum_probs=25.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC-CeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE-GWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL  222 (404)
                      ..+.|.|++|+|||++|..+..+-... |=|.+
T Consensus        56 ~~v~i~G~~GaGKSTLl~~l~g~~~~~~g~v~i   88 (337)
T 2qm8_A           56 IRVGITGVPGVGKSTTIDALGSLLTAAGHKVAV   88 (337)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhhhhCCCEEEE
Confidence            358999999999999999998876643 43433

>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=87.09  E-value=0.32  Score=44.70  Aligned_cols=31  Identities=19%  Similarity=0.388  Sum_probs=22.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        37 ~~~iiG~NGsGKSTLlk~l~Gl~~p~~G~I~~   68 (214)
T 1sgw_A           37 VVNFHGPNGIGKTTLLKTISTYLKPLKGEIIY   68 (214)
T ss_dssp             CEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCCeEEEE
Confidence            388999999999999987654322 2355544

>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=87.03  E-value=0.34  Score=42.47  Aligned_cols=22  Identities=23%  Similarity=0.299  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.+++.
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~   47 (200)
T 2o52_A           26 FKFLVIGSAGTGKSCLLHQFIE   47 (200)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            4699999999999999998864

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=87.01  E-value=0.58  Score=49.37  Aligned_cols=35  Identities=29%  Similarity=0.285  Sum_probs=26.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh----CC-eEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE----EG-WLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~----ng-WIVL~IP~  226 (404)
                      -++|+|++|||||+++..++.....    .+ -|++--|.
T Consensus       166 ~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APT  205 (608)
T 1w36_D          166 ISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPT  205 (608)
T ss_dssp             EEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSS
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeCC
Confidence            4899999999999999998887652    34 45555565

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=87.00  E-value=0.32  Score=45.87  Aligned_cols=31  Identities=26%  Similarity=0.348  Sum_probs=22.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        34 ~~~liG~nGsGKSTLlk~l~Gl~~p~~G~i~~   65 (262)
T 1b0u_A           34 VISIIGSSGSGKSTFLRCINFLEKPSEGAIIV   65 (262)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCCcEEEE
Confidence            378999999999999987654432 3466654

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=87.00  E-value=0.43  Score=57.36  Aligned_cols=36  Identities=19%  Similarity=0.297  Sum_probs=31.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      -++|+|++|+|||++++|++..+..+|.-|+||.--
T Consensus       385 lilI~G~pGsGKTtLaLqia~~~a~~G~~vlyis~E  420 (2050)
T 3cmu_A          385 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE  420 (2050)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEcC
Confidence            389999999999999999999998888888888543

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=86.94  E-value=0.26  Score=44.96  Aligned_cols=29  Identities=17%  Similarity=0.050  Sum_probs=23.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWL  220 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWI  220 (404)
                      .+.|.|+.||||||+|.-+.-..-..|-|
T Consensus        24 ~~~liG~nGsGKSTLl~~l~Gl~p~~G~I   52 (208)
T 3b85_A           24 IVFGLGPAGSGKTYLAMAKAVQALQSKQV   52 (208)
T ss_dssp             EEEEECCTTSSTTHHHHHHHHHHHHTTSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCcCCee
Confidence            37899999999999998887773356766

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=86.94  E-value=0.34  Score=42.26  Aligned_cols=22  Identities=27%  Similarity=0.505  Sum_probs=19.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..+..
T Consensus        25 ~ki~vvG~~~~GKSsli~~l~~   46 (201)
T 3oes_A           25 RKVVILGYRCVGKTSLAHQFVE   46 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            5699999999999999988875

>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=86.93  E-value=0.33  Score=45.04  Aligned_cols=31  Identities=26%  Similarity=0.441  Sum_probs=22.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        34 ~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~   65 (240)
T 1ji0_A           34 IVTLIGANGAGKTTTLSAIAGLVRAQKGKIIF   65 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCceEEE
Confidence            478999999999999987654322 3455544

>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=86.90  E-value=0.39  Score=42.22  Aligned_cols=22  Identities=18%  Similarity=0.147  Sum_probs=19.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        26 ~ki~vvG~~~~GKSsLi~~l~~   47 (217)
T 2f7s_A           26 IKLLALGDSGVGKTTFLYRYTD   47 (217)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHhc
Confidence            4699999999999999987763

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=86.84  E-value=0.4  Score=41.52  Aligned_cols=22  Identities=23%  Similarity=0.208  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        21 ~ki~~~G~~~~GKssl~~~l~~   42 (201)
T 2q3h_A           21 VKCVLVGDGAVGKTSLVVSYTT   42 (201)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999988764

>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=86.82  E-value=0.52  Score=49.19  Aligned_cols=32  Identities=22%  Similarity=0.245  Sum_probs=25.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE-GWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~  223 (404)
                      -+.|.|+.||||||+|..+..+-... |-|.|.
T Consensus       295 VI~LVGpNGSGKTTLl~~LAgll~~~~G~V~l~  327 (503)
T 2yhs_A          295 VILMVGVNGVGKTTTIGKLARQFEQQGKSVMLA  327 (503)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCcccHHHHHHHHHHHhhhcCCeEEEe
Confidence            48899999999999999988876654 555553

>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=86.80  E-value=0.34  Score=45.46  Aligned_cols=31  Identities=23%  Similarity=0.460  Sum_probs=22.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        35 ~~~liG~nGsGKSTLlk~l~Gl~~p~~G~i~~   66 (257)
T 1g6h_A           35 VTLIIGPNGSGKSTLINVITGFLKADEGRVYF   66 (257)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCcEEEE
Confidence            478999999999999987654322 3455544

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=86.78  E-value=0.66  Score=41.72  Aligned_cols=32  Identities=25%  Similarity=0.411  Sum_probs=27.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +++-|.-||||||.+..+..|-.++|.=|+..
T Consensus         3 I~~EG~DGsGKsTq~~~L~~~L~~~g~~v~~t   34 (197)
T 3hjn_A            3 ITFEGIDGSGKSTQIQLLAQYLEKRGKKVILK   34 (197)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            68899999999999999999988887655554

>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=86.78  E-value=0.34  Score=45.00  Aligned_cols=31  Identities=26%  Similarity=0.454  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        30 ~~~i~G~nGsGKSTLl~~l~Gl~~p~~G~i~~   61 (243)
T 1mv5_A           30 IIAFAGPSGGGKSTIFSLLERFYQPTAGEITI   61 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCSBSCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCCcEEEE
Confidence            489999999999999987665432 4576655

>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=86.76  E-value=0.41  Score=46.80  Aligned_cols=23  Identities=26%  Similarity=0.323  Sum_probs=20.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .++.|.|+.||||||++..+.-.
T Consensus       171 ~k~~IvG~nGsGKSTLlk~L~gl  193 (365)
T 1lw7_A          171 KTVAILGGESSGKSVLVNKLAAV  193 (365)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            57999999999999999887765

>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=86.74  E-value=0.38  Score=41.85  Aligned_cols=22  Identities=27%  Similarity=0.341  Sum_probs=19.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.++..
T Consensus        24 ~ki~~vG~~~vGKSsli~~l~~   45 (190)
T 1m2o_B           24 GKLLFLGLDNAGKTTLLHMLKN   45 (190)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            3699999999999999987764

>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=86.73  E-value=0.34  Score=45.26  Aligned_cols=22  Identities=23%  Similarity=0.267  Sum_probs=18.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+.|.|+.||||||+|.-+.-.
T Consensus        37 ~~~i~G~nGsGKSTLl~~l~Gl   58 (247)
T 2ff7_A           37 VIGIVGRSGSGKSTLTKLIQRF   58 (247)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4889999999999999876544

>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=86.72  E-value=0.44  Score=43.25  Aligned_cols=31  Identities=26%  Similarity=0.120  Sum_probs=23.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..++|.|.+|||||++...+..+   -||.++..
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~---l~~~~i~~   47 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKN---FCVCHLAT   47 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH---HTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH---hCCceecH
Confidence            35999999999999987766543   25666654

>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=86.66  E-value=0.47  Score=56.12  Aligned_cols=34  Identities=21%  Similarity=0.328  Sum_probs=30.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|++|+|||++++|+...+..+|.-|+||.
T Consensus       734 lVlI~G~PG~GKTtLal~lA~~aa~~g~~VlyiS  767 (1706)
T 3cmw_A          734 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID  767 (1706)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             eEEEECCCCCCcHHHHHHHHHHHHHcCCCeEEEe
Confidence            3899999999999999999999888888788874

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=86.64  E-value=0.39  Score=41.65  Aligned_cols=22  Identities=18%  Similarity=0.309  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.++..
T Consensus        27 ~ki~vvG~~~~GKSsLi~~l~~   48 (192)
T 2il1_A           27 LQVIIIGSRGVGKTSLMERFTD   48 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHCC
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            5699999999999999988764

>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=86.61  E-value=0.6  Score=44.75  Aligned_cols=33  Identities=30%  Similarity=0.276  Sum_probs=25.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .+.+.|+.|+|||+++..+..+....|.=|+.+
T Consensus       100 ~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~  132 (295)
T 1ls1_A          100 LWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLV  132 (295)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            477889999999999999888766555444433

>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=86.60  E-value=0.37  Score=44.97  Aligned_cols=31  Identities=32%  Similarity=0.280  Sum_probs=23.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH---HHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW---AREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~---A~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.   .-..|-|.+
T Consensus        31 ~~~l~G~nGsGKSTLlk~l~Gl~~~~p~~G~I~~   64 (250)
T 2d2e_A           31 VHALMGPNGAGKSTLGKILAGDPEYTVERGEILL   64 (250)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTCTTCEEEEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCCceEEEE
Confidence            3789999999999999877653   223565554

>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=86.58  E-value=0.35  Score=44.52  Aligned_cols=38  Identities=18%  Similarity=0.213  Sum_probs=26.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE-----EecCccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL-----YVPRGRE  229 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL-----~IP~a~~  229 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+     |+|.-..
T Consensus        36 ~~~i~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~i~~v~q~~~   79 (229)
T 2pze_A           36 LLAVAGSTGAGKTSLLMMIMGELEPSEGKIKHSGRISFCSQFSW   79 (229)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCSEEEEEECSCEEEECSSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCcCCccEEEECCEEEEEecCCc
Confidence            488999999999999987765432 3566643     5665433

>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=86.47  E-value=0.35  Score=46.18  Aligned_cols=31  Identities=16%  Similarity=0.181  Sum_probs=22.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        36 ~~~iiGpnGsGKSTLl~~l~Gl~~p~~G~I~~   67 (275)
T 3gfo_A           36 VTAILGGNGVGKSTLFQNFNGILKPSSGRILF   67 (275)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHcCCCCCCeEEEE
Confidence            389999999999999987665332 3455544

>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=86.46  E-value=0.29  Score=42.72  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=18.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|+.|||||+++..+.
T Consensus        27 ~~v~lvG~~g~GKSTLl~~l~   47 (210)
T 1pui_A           27 IEVAFAGRSNAGKSSALNTLT   47 (210)
T ss_dssp             EEEEEEECTTSSHHHHHTTTC
T ss_pred             cEEEEECCCCCCHHHHHHHHh
Confidence            459999999999999997664

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=86.43  E-value=0.64  Score=47.28  Aligned_cols=34  Identities=26%  Similarity=0.354  Sum_probs=29.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~I  224 (404)
                      ..+++.|..|+||||+.+.+.++...+ |.=|+-|
T Consensus       101 ~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllv  135 (433)
T 2xxa_A          101 AVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVV  135 (433)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEE
Confidence            357888999999999999999988887 8877766

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=86.43  E-value=0.57  Score=45.91  Aligned_cols=24  Identities=29%  Similarity=0.318  Sum_probs=19.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -+-|.|+.||||||++..+...-.
T Consensus        94 iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            378999999999999877766543

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=86.42  E-value=0.51  Score=49.03  Aligned_cols=25  Identities=16%  Similarity=0.263  Sum_probs=22.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      +++.|.+|||||++|.+-+.|...+
T Consensus        25 ~lV~a~aGsGKT~~l~~ri~~l~~~   49 (647)
T 3lfu_A           25 LLVLAGAGSGKTRVLVHRIAWLMSV   49 (647)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHh
Confidence            7899999999999999999887765

>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=86.41  E-value=0.7  Score=41.57  Aligned_cols=30  Identities=27%  Similarity=0.230  Sum_probs=22.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      ..+.|+|..||||||+...+...   -|+-|+.
T Consensus        13 ~iIgltG~~GSGKSTva~~L~~~---lg~~vid   42 (192)
T 2grj_A           13 MVIGVTGKIGTGKSTVCEILKNK---YGAHVVN   42 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH---HCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh---cCCEEEE
Confidence            34889999999999998776553   2666655

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=86.34  E-value=0.88  Score=44.77  Aligned_cols=34  Identities=26%  Similarity=0.235  Sum_probs=27.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      .++|.|+.|||||++-..+   |..-|+.++.+-+..
T Consensus         7 ~i~i~GptGsGKTtla~~L---a~~l~~~iis~Ds~q   40 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLAMAL---ADALPCELISVDSAL   40 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHH---HHHSCEEEEEECTTT
T ss_pred             EEEEECCCCCCHHHHHHHH---HHHcCCcEEeccchh
Confidence            4899999999999976554   556789999886544

>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=86.31  E-value=0.39  Score=45.42  Aligned_cols=31  Identities=26%  Similarity=0.201  Sum_probs=22.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH---HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA---REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A---~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-   -..|=|.+
T Consensus        48 ~~~l~G~NGsGKSTLlk~l~Gl~~~~p~~G~I~~   81 (267)
T 2zu0_C           48 VHAIMGPNGSGKSTLSATLAGREDYEVTGGTVEF   81 (267)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTCTTCEEEEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCCCeEEEE
Confidence            48899999999999998776541   13465544

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=86.24  E-value=0.33  Score=45.11  Aligned_cols=22  Identities=27%  Similarity=0.295  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..+..
T Consensus        37 ~~I~lvG~~g~GKSSLin~l~~   58 (262)
T 3def_A           37 MTVLVLGKGGVGKSSTVNSLIG   58 (262)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            4699999999999999988764

>3szr_A Interferon-induced GTP-binding protein MX1; interferon-induced antiviral GTPase, membrane associated, PR binding; 3.50A {Homo sapiens} PDB: 3zys_B

Probab=86.23  E-value=0.6  Score=49.38  Aligned_cols=43  Identities=23%  Similarity=0.245  Sum_probs=28.9

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHH
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      +.+++++.|...--    +.+  -.-+.+.|.|+.|||||++|..++-.
T Consensus        26 ~ll~~id~l~~~gv----~~~--l~lp~iaIvG~nGsGKSTLL~~I~Gl   68 (608)
T 3szr_A           26 PCIDLIDSLRALGV----EQD--LALPAIAVIGDQSSGKSSVLEALSGV   68 (608)
T ss_dssp             HHHHHHHHHHHHSC----CSS--CCCCCEECCCCTTSCHHHHHHHHHSC
T ss_pred             HHHHHHHHHHhCCC----CCc--ccCCeEEEECCCCChHHHHHHHHhCC
Confidence            45677777665411    111  11256999999999999999888754

>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=86.22  E-value=0.27  Score=41.81  Aligned_cols=22  Identities=23%  Similarity=0.250  Sum_probs=10.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus         9 ~ki~v~G~~~~GKssl~~~l~~   30 (183)
T 2fu5_C            9 FKLLLIGDSGVGKTCVLFRFSE   30 (183)
T ss_dssp             EEEEEECCCCC-----------
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4699999999999999988763

>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=86.04  E-value=0.39  Score=45.12  Aligned_cols=31  Identities=29%  Similarity=0.350  Sum_probs=22.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-.-.|-|.+
T Consensus        28 ~~~liG~NGsGKSTLlk~l~Gl~~p~G~i~~   58 (249)
T 2qi9_C           28 ILHLVGPNGAGKSTLLARMAGMTSGKGSIQF   58 (249)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCEEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCCCCeEEEE
Confidence            4789999999999999876554221155544

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=85.95  E-value=0.25  Score=43.57  Aligned_cols=23  Identities=26%  Similarity=0.465  Sum_probs=19.9

Q ss_pred             ceeEEEECCCCCcHHHHHHHHHH
Q 045329          190 RKQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       190 r~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +.+++|.|..|+|||+++..++.
T Consensus        29 ~~~i~v~G~~~~GKSslin~l~~   51 (223)
T 4dhe_A           29 QPEIAFAGRSNAGKSTAINVLCN   51 (223)
T ss_dssp             SCEEEEEESCHHHHHHHHHHHTT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhC
Confidence            35799999999999999988754

>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=85.87  E-value=0.44  Score=42.24  Aligned_cols=22  Identities=27%  Similarity=0.303  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.+++.
T Consensus        27 ~ki~lvG~~~vGKSsLi~~l~~   48 (201)
T 2ew1_A           27 FKIVLIGNAGVGKTCLVRRFTQ   48 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            4699999999999999998765

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=85.86  E-value=0.5  Score=51.75  Aligned_cols=35  Identities=23%  Similarity=0.415  Sum_probs=26.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh-C-CeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE-E-GWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~-n-gWIVL~IP~  226 (404)
                      -++|.|++|||||+++.+++.+... . .-|++--|.
T Consensus       377 ~~lI~GppGTGKT~~i~~~i~~l~~~~~~~ILv~a~t  413 (802)
T 2xzl_A          377 LSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPS  413 (802)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEEcCc
Confidence            3799999999999999999887654 3 344444444

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=85.84  E-value=0.4  Score=45.12  Aligned_cols=31  Identities=26%  Similarity=0.302  Sum_probs=22.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-...|-|.+
T Consensus        48 ~~~i~G~nGsGKSTLl~~l~Gl~~~~G~I~i   78 (260)
T 2ghi_A           48 TCALVGHTGSGKSTIAKLLYRFYDAEGDIKI   78 (260)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhccCCCCeEEEE
Confidence            4899999999999999877654222455544

>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=85.78  E-value=0.4  Score=45.42  Aligned_cols=31  Identities=32%  Similarity=0.443  Sum_probs=23.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        52 i~~liG~NGsGKSTLlk~l~Gl~~p~~G~I~~   83 (263)
T 2olj_A           52 VVVVIGPSGSGKSTFLRCLNLLEDFDEGEIII   83 (263)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEEcCCCCcHHHHHHHHHcCCCCCCcEEEE
Confidence            488999999999999987665432 3466654

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=85.77  E-value=0.41  Score=45.18  Aligned_cols=31  Identities=19%  Similarity=0.293  Sum_probs=22.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        35 ~~~liG~nGsGKSTLl~~i~Gl~~p~~G~I~~   66 (266)
T 2yz2_A           35 CLLVAGNTGSGKSTLLQIVAGLIEPTSGDVLY   66 (266)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCCCCCcEEEE
Confidence            478999999999999987654322 3455543

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=85.76  E-value=0.39  Score=45.49  Aligned_cols=22  Identities=27%  Similarity=0.280  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+.|.|+.|+||||+|.-+.-.
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            3789999999999999887754

>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=85.73  E-value=0.41  Score=45.35  Aligned_cols=31  Identities=29%  Similarity=0.380  Sum_probs=23.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.- -..|-|.+
T Consensus        39 ~~~liG~nGsGKSTLl~~l~Gl~~p~~G~I~~   70 (266)
T 4g1u_C           39 MVAIIGPNGAGKSTLLRLLTGYLSPSHGECHL   70 (266)
T ss_dssp             EEEEECCTTSCHHHHHHHHTSSSCCSSCEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHhcCCCCCCcEEEE
Confidence            48899999999999998776532 24566655

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=85.72  E-value=0.71  Score=45.86  Aligned_cols=39  Identities=26%  Similarity=0.406  Sum_probs=29.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCC-eEEEEecCccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEG-WLVLYVPRGRE  229 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ng-WIVL~IP~a~~  229 (404)
                      ..+++.|..|||||+++..++..+...| -+|++=|.++.
T Consensus        54 ~h~~i~G~tGsGKs~~~~~li~~~~~~g~~viv~Dpkge~   93 (437)
T 1e9r_A           54 RHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDM   93 (437)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCCch
Confidence            3489999999999999988888777654 45555465544

>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=85.71  E-value=0.58  Score=43.78  Aligned_cols=20  Identities=35%  Similarity=0.448  Sum_probs=17.0

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+.|+|+.|||||++...+.
T Consensus        11 ~i~i~G~~GsGKsTla~~la   30 (233)
T 3r20_A           11 VVAVDGPAGTGKSSVSRGLA   30 (233)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            48999999999999876654

>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=85.69  E-value=0.39  Score=42.15  Aligned_cols=21  Identities=24%  Similarity=0.216  Sum_probs=18.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|..|+|||+++.++.
T Consensus        24 ~ki~vvG~~~vGKSsLi~~l~   44 (195)
T 3cbq_A           24 FKVMLVGESGVGKSTLAGTFG   44 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHTC
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            469999999999999998863

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=85.67  E-value=0.41  Score=45.38  Aligned_cols=31  Identities=32%  Similarity=0.387  Sum_probs=22.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        47 ~~~i~G~nGsGKSTLlk~l~Gl~~p~~G~I~~   78 (271)
T 2ixe_A           47 VTALVGPNGSGKSTVAALLQNLYQPTGGKVLL   78 (271)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCCCEEEE
Confidence            488999999999999987654422 3455544

>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=85.66  E-value=0.42  Score=42.80  Aligned_cols=22  Identities=32%  Similarity=0.486  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..++.
T Consensus        30 ~kI~vvG~~~vGKSsLin~l~~   51 (228)
T 2qu8_A           30 KTIILSGAPNVGKSSFMNIVSR   51 (228)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            5799999999999999988753

>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=85.66  E-value=0.52  Score=41.95  Aligned_cols=23  Identities=35%  Similarity=0.546  Sum_probs=20.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -+++|.|..|+|||+++.+++.-
T Consensus        28 ~ki~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           28 CKLVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            46999999999999999987753

>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=85.64  E-value=0.42  Score=43.83  Aligned_cols=22  Identities=27%  Similarity=0.315  Sum_probs=19.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..++.
T Consensus        23 ~~I~lvG~~g~GKStl~n~l~~   44 (260)
T 2xtp_A           23 LRIILVGKTGTGKSAAGNSILR   44 (260)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHhC
Confidence            5699999999999999998874

>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=85.64  E-value=0.34  Score=41.65  Aligned_cols=22  Identities=18%  Similarity=0.152  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.++..
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~   43 (190)
T 2h57_A           22 VHVLCLGLDNSGKTTIINKLKP   43 (190)
T ss_dssp             EEEEEEECTTSSHHHHHHHTSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            5699999999999999988754

>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=85.64  E-value=0.46  Score=41.72  Aligned_cols=22  Identities=32%  Similarity=0.585  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..+..
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~   47 (207)
T 2fv8_A           26 KKLVVVGDGACGKTCLLIVFSK   47 (207)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             cEEEEECcCCCCHHHHHHHHhc
Confidence            5799999999999999988764

>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=85.62  E-value=0.48  Score=42.92  Aligned_cols=21  Identities=29%  Similarity=0.347  Sum_probs=18.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      -+++|.|.+|+|||+++.+.+
T Consensus        38 ~kVvlvG~~~vGKSSLl~r~~   58 (211)
T 2g3y_A           38 YRVVLIGEQGVGKSTLANIFA   58 (211)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            469999999999999998765

>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=85.57  E-value=0.68  Score=50.93  Aligned_cols=17  Identities=35%  Similarity=0.770  Sum_probs=14.6

Q ss_pred             eeEEEECCCCCcHHHHH
Q 045329          191 KQIVLDGPLCCGKSITL  207 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L  207 (404)
                      ++++|+|++|||||++.
T Consensus       512 ~gvLl~GPPGtGKT~lA  528 (806)
T 3cf2_A          512 KGVLFYGPPGCGKTLLA  528 (806)
T ss_dssp             SCCEEESSTTSSHHHHH
T ss_pred             ceEEEecCCCCCchHHH
Confidence            56999999999998653

>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=85.57  E-value=0.51  Score=48.74  Aligned_cols=22  Identities=32%  Similarity=0.445  Sum_probs=17.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +.++|+|++|||||+++..+..
T Consensus        50 ~gvLL~GppGtGKT~Laraia~   71 (476)
T 2ce7_A           50 KGILLVGPPGTGKTLLARAVAG   71 (476)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4599999999999987765543

>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=85.54  E-value=0.45  Score=41.60  Aligned_cols=22  Identities=32%  Similarity=0.600  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++..+..
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~   47 (201)
T 2gco_A           26 KKLVIVGDGACGKTCLLIVFSK   47 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            5699999999999999987764

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=85.52  E-value=0.46  Score=43.20  Aligned_cols=17  Identities=18%  Similarity=0.427  Sum_probs=14.9

Q ss_pred             EEEECCCCCcHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAM  209 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~q  209 (404)
                      ++++|++|||||+....
T Consensus         8 ~l~tG~pGsGKT~~a~~   24 (199)
T 2r2a_A            8 CLITGTPGSGKTLKMVS   24 (199)
T ss_dssp             EEEECCTTSSHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHH
Confidence            79999999999997544

>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=85.51  E-value=0.42  Score=45.03  Aligned_cols=31  Identities=26%  Similarity=0.392  Sum_probs=22.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        43 i~~l~G~NGsGKSTLlk~l~Gl~~p~~G~I~~   74 (256)
T 1vpl_A           43 IFGLIGPNGAGKTTTLRIISTLIKPSSGIVTV   74 (256)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCceEEEE
Confidence            388999999999999987654322 3465544

>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=85.46  E-value=0.72  Score=47.14  Aligned_cols=34  Identities=12%  Similarity=0.213  Sum_probs=26.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~I  224 (404)
                      .++.|.|++|||||+++.++..+..++  +..++|+
T Consensus       175 Qr~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~~I~~  210 (422)
T 3ice_A          175 QRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVL  210 (422)
T ss_dssp             CEEEEECCSSSSHHHHHHHHHHHHHHHCTTSEEEEE
T ss_pred             cEEEEecCCCCChhHHHHHHHHHHhhcCCCeeEEEE
Confidence            368999999999999999998887653  5444444

>1of1_A Thymidine kinase; transferase, antiviral drug, enzyme- prodrug gene, DNA synthesis, ATP-binding; HET: SCT; 1.95A {Herpes simplex virus} SCOP: c.37.1.1

Probab=85.42  E-value=0.48  Score=47.67  Aligned_cols=35  Identities=26%  Similarity=0.434  Sum_probs=25.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ..++|.|.-||||||++..+..+-...|+++...|
T Consensus        50 ~fIt~EG~dGsGKTT~~~~Lae~L~~~gvv~trEP   84 (376)
T 1of1_A           50 LRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEP   84 (376)
T ss_dssp             EEEEECSSTTSSHHHHHHHHHC----CCEEEECCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhhCCEEEEeCC
Confidence            45899999999999999999888777885555454

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=85.38  E-value=0.77  Score=42.66  Aligned_cols=22  Identities=27%  Similarity=0.296  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++++.|..|+|||+++..+..
T Consensus        40 ~~I~vvG~~g~GKSSLin~l~~   61 (270)
T 1h65_A           40 LTILVMGKGGVGKSSTVNSIIG   61 (270)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHhC
Confidence            4699999999999999998774

>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=85.28  E-value=0.46  Score=42.14  Aligned_cols=22  Identities=32%  Similarity=0.516  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        35 ~ki~vvG~~~vGKSsli~~l~~   56 (214)
T 2j1l_A           35 VKVVLVGDGGCGKTSLLMVFAD   56 (214)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHHc
Confidence            4699999999999999988764

>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=85.26  E-value=0.44  Score=41.49  Aligned_cols=21  Identities=29%  Similarity=0.317  Sum_probs=18.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      -+++|.|..|+|||+++.++.
T Consensus        30 ~ki~v~G~~~vGKSsLi~~l~   50 (192)
T 2b6h_A           30 MRILMVGLDAAGKTTILYKLK   50 (192)
T ss_dssp             EEEEEEESTTSSHHHHHHHHC
T ss_pred             cEEEEECCCCCCHHHHHHHHH
Confidence            469999999999999998764

>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=85.25  E-value=0.46  Score=42.16  Aligned_cols=22  Identities=32%  Similarity=0.525  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.++..
T Consensus        29 ~ki~vvG~~~vGKSsLi~~l~~   50 (205)
T 1gwn_A           29 CKIVVVGDSQCGKTALLHVFAK   50 (205)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999998775

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=85.25  E-value=0.44  Score=44.75  Aligned_cols=36  Identities=31%  Similarity=0.471  Sum_probs=24.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeE-----EEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWL-----VLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWI-----VL~IP~a  227 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|     |-|+|.-
T Consensus        33 ~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~I~~~~~i~~v~q~   74 (253)
T 2nq2_C           33 ILAVLGQNGCGKSTLLDLLLGIHRPIQGKIEVYQSIGFVPQF   74 (253)
T ss_dssp             EEEEECCSSSSHHHHHHHHTTSSCCSEEEEEECSCEEEECSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCCcEEEEeccEEEEcCC
Confidence            478999999999999987654322 34655     4455543

>3iby_A Ferrous iron transport protein B; G protein, G domain, iron uptake, cell inner membrane, cell GTP-binding, ION transport, membrane; 2.50A {Legionella pneumophila}

Probab=85.23  E-value=0.45  Score=44.49  Aligned_cols=31  Identities=26%  Similarity=0.317  Sum_probs=22.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++++|.|.+|||||+++.++..    ....|-+.|
T Consensus         2 ~kI~lvG~~n~GKSTL~n~L~g----~~~~v~~~p   32 (256)
T 3iby_A            2 THALLIGNPNCGKTTLFNALTN----ANQRVGNWP   32 (256)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHT----TSEEEEECT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC----CCCCccCCC
Confidence            3589999999999999988743    234454444

>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=85.18  E-value=0.51  Score=40.62  Aligned_cols=22  Identities=23%  Similarity=0.225  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|..|+|||+++.++..
T Consensus        19 ~ki~v~G~~~~GKssli~~l~~   40 (194)
T 2atx_A           19 LKCVVVGDGAVGKTCLLMSYAN   40 (194)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999988774

>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=85.13  E-value=0.51  Score=41.53  Aligned_cols=22  Identities=23%  Similarity=0.199  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        31 ~ki~vvG~~~~GKSsLi~~l~~   52 (204)
T 4gzl_A           31 IKCVVVGDGAVGKTCLLISYTT   52 (204)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECcCCCCHHHHHHHHHh
Confidence            4699999999999999987764

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=85.02  E-value=0.54  Score=42.82  Aligned_cols=33  Identities=24%  Similarity=0.457  Sum_probs=25.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      .++|.|..||||||++..+..+-  +++.++..|-
T Consensus         4 ~i~~~G~~g~GKtt~~~~l~~~l--~~~~~~~Ep~   36 (241)
T 2ocp_A            4 RLSIEGNIAVGKSTFVKLLTKTY--PEWHVATEPV   36 (241)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHC--TTSEEECCCG
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc--CCCeeeecch
Confidence            48999999999999887776543  3677766554

>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=84.99  E-value=0.89  Score=43.80  Aligned_cols=24  Identities=8%  Similarity=0.152  Sum_probs=19.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      .|+|+|++|+|||++...+...-.
T Consensus        26 a~L~~G~~G~GKt~~a~~la~~l~   49 (334)
T 1a5t_A           26 ALLIQALPGMGDDALIYALSRYLL   49 (334)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             eEEEECCCCchHHHHHHHHHHHHh
Confidence            499999999999988876665543

>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=84.99  E-value=0.57  Score=42.71  Aligned_cols=22  Identities=18%  Similarity=0.279  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      =+++|-|..|+|||.++.+.+.
T Consensus        14 ~KivlvGd~~VGKTsLi~r~~~   35 (216)
T 4dkx_A           14 FKLVFLGEQSVGKTSLITRFMY   35 (216)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECcCCcCHHHHHHHHHh
Confidence            4699999999999999998764

>1e2k_A Thymidine kinase; transferase, antiviral drug, enzyme-prodrug gene therapy, sugar ring pucker; HET: TMC; 1.7A {Herpes simplex virus} SCOP: c.37.1.1 PDB: 1e2i_A* 1e2h_A* 1e2m_A* 1e2n_A* 1e2p_A* 1ki2_A* 1ki3_A* 1ki4_A* 1ki6_B* 1ki7_A* 1ki8_A* 3rdp_A* 2ki5_A* 1kim_A* 1qhi_A* 1p7c_A* 1vtk_A* 2vtk_A* 3vtk_A* 3f0t_A* ...

Probab=84.99  E-value=0.45  Score=47.01  Aligned_cols=35  Identities=26%  Similarity=0.434  Sum_probs=25.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ..++|.|.-||||||++..+..+-...|+++...|
T Consensus         5 ~fI~~EG~dGsGKTT~~~~La~~L~~~gv~~trEP   39 (331)
T 1e2k_A            5 LRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEP   39 (331)
T ss_dssp             EEEEECSCTTSSHHHHHHHHTC----CCEEEECCC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhhhCCEEEEeCC
Confidence            35899999999999999999888777885544444

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=84.99  E-value=0.5  Score=44.47  Aligned_cols=30  Identities=17%  Similarity=0.288  Sum_probs=22.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|+.||||||++..+..   .-||-++..
T Consensus        50 ~i~l~G~~GsGKSTl~~~La~---~lg~~~~d~   79 (250)
T 3nwj_A           50 SMYLVGMMGSGKTTVGKIMAR---SLGYTFFDC   79 (250)
T ss_dssp             CEEEECSTTSCHHHHHHHHHH---HHTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH---hcCCcEEeC
Confidence            489999999999999866644   236765554

>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=84.98  E-value=0.42  Score=47.68  Aligned_cols=31  Identities=26%  Similarity=0.485  Sum_probs=23.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      -+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        32 ~~~llGpsGsGKSTLLr~iaGl~~p~~G~I~i   63 (359)
T 3fvq_A           32 ILFIIGASGCGKTTLLRCLAGFEQPDSGEISL   63 (359)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCchHHHHHHHHhcCCCCCCcEEEE
Confidence            378999999999999987765432 3566654

>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=84.97  E-value=0.51  Score=43.83  Aligned_cols=22  Identities=32%  Similarity=0.341  Sum_probs=18.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ..++|.|+.|+|||++...++.
T Consensus        35 ~~ilI~GpsGsGKStLA~~La~   56 (205)
T 2qmh_A           35 LGVLITGDSGVGKSETALELVQ   56 (205)
T ss_dssp             EEEEEECCCTTTTHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            4599999999999999877654

>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=84.97  E-value=0.56  Score=40.90  Aligned_cols=21  Identities=29%  Similarity=0.464  Sum_probs=17.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+.|+|+.|||||++...+..
T Consensus         4 ~i~i~G~~GsGKst~~~~la~   24 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAA   24 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            489999999999998876644

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=84.94  E-value=0.46  Score=45.33  Aligned_cols=31  Identities=26%  Similarity=0.328  Sum_probs=23.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        49 ~~~liG~NGsGKSTLlk~l~Gl~~p~~G~I~~   80 (279)
T 2ihy_A           49 KWILYGLNGAGKTTLLNILNAYEPATSGTVNL   80 (279)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCCCCCeEEEE
Confidence            488999999999999987654422 3466655

>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=84.91  E-value=0.41  Score=42.04  Aligned_cols=21  Identities=33%  Similarity=0.363  Sum_probs=18.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|+.|+|||+++.++.
T Consensus        26 ~ki~lvG~~~vGKSsLi~~l~   46 (198)
T 1f6b_A           26 GKLVFLGLDNAGKTTLLHMLK   46 (198)
T ss_dssp             EEEEEEEETTSSHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHh
Confidence            469999999999999998875

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=84.82  E-value=0.57  Score=48.27  Aligned_cols=20  Identities=15%  Similarity=0.295  Sum_probs=18.0

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      -+.|.|+.||||||++.+++
T Consensus        41 ~~~l~G~nGsGKSTL~~~~l   60 (525)
T 1tf7_A           41 STLVSGTSGTGKTLFSIQFL   60 (525)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHH
Confidence            38999999999999999964

>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=84.80  E-value=0.48  Score=47.66  Aligned_cols=31  Identities=35%  Similarity=0.553  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      -+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        31 ~~~llGpsGsGKSTLLr~iaGl~~p~~G~I~i   62 (381)
T 3rlf_A           31 FVVFVGPSGCGKSTLLRMIAGLETITSGDLFI   62 (381)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEEcCCCchHHHHHHHHHcCCCCCCeEEEE
Confidence            378999999999999987765432 3577655

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=84.74  E-value=0.43  Score=47.00  Aligned_cols=32  Identities=19%  Similarity=0.291  Sum_probs=24.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL~  223 (404)
                      .++|.|+.||||||+|.-+..+-. ..|-|.+.
T Consensus       177 ~i~ivG~sGsGKSTll~~l~~~~~~~~g~I~ie  209 (361)
T 2gza_A          177 VIVVAGETGSGKTTLMKALMQEIPFDQRLITIE  209 (361)
T ss_dssp             CEEEEESSSSCHHHHHHHHHTTSCTTSCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHhcCCCCceEEEEC
Confidence            389999999999999988876533 45666654

>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=84.72  E-value=0.54  Score=41.25  Aligned_cols=22  Identities=23%  Similarity=0.311  Sum_probs=19.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.++..
T Consensus        30 ~ki~vvG~~~vGKSsli~~l~~   51 (201)
T 2hup_A           30 FKLVLVGDASVGKTCVVQRFKT   51 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHhh
Confidence            5699999999999999988754

>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=84.59  E-value=0.53  Score=40.96  Aligned_cols=21  Identities=29%  Similarity=0.341  Sum_probs=17.8

Q ss_pred             ceeEEEECCCCCcHHHHHHHH
Q 045329          190 RKQIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       190 r~r~vL~G~rGsGKS~~L~qa  210 (404)
                      ..+++|.|..|+|||+++..+
T Consensus        20 ~~ki~~vG~~~vGKTsLi~~l   40 (196)
T 3llu_A           20 KPRILLMGLRRSGKSSIQKVV   40 (196)
T ss_dssp             CCEEEEEESTTSSHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHH
Confidence            356999999999999998743

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=84.57  E-value=0.62  Score=41.44  Aligned_cols=22  Identities=36%  Similarity=0.327  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++..+..
T Consensus        14 ~ki~v~G~~~vGKSsli~~l~~   35 (223)
T 3cpj_B           14 FKIVLIGDSGVGKSNLLSRFTK   35 (223)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHhc
Confidence            4699999999999999988764

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=84.57  E-value=0.86  Score=39.65  Aligned_cols=24  Identities=17%  Similarity=0.145  Sum_probs=19.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      .+++.++.|+|||++...++....
T Consensus        50 ~~li~~~tGsGKT~~~~~~~~~~~   73 (216)
T 3b6e_A           50 NIIICLPTGSGKTRVAVYIAKDHL   73 (216)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHH
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH
Confidence            489999999999998877766543

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=84.57  E-value=0.51  Score=46.95  Aligned_cols=31  Identities=26%  Similarity=0.381  Sum_probs=23.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        43 ~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   74 (355)
T 1z47_A           43 MVGLLGPSGSGKTTILRLIAGLERPTKGDVWI   74 (355)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCCCCccEEEE
Confidence            378999999999999987664432 3566655

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=84.53  E-value=0.56  Score=41.03  Aligned_cols=22  Identities=23%  Similarity=0.172  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.++..
T Consensus        10 ~ki~i~G~~~~GKTsli~~l~~   31 (212)
T 2j0v_A           10 IKCVTVGDGAVGKTCMLICYTS   31 (212)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999988764

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=84.51  E-value=0.85  Score=41.78  Aligned_cols=28  Identities=25%  Similarity=0.318  Sum_probs=25.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGW  219 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngW  219 (404)
                      -+++.|..||||||.+..+..+-...|.
T Consensus         5 ~i~~eG~~gsGKsT~~~~l~~~l~~~~~   32 (213)
T 4tmk_A            5 YIVIEGLEGAGKTTARNVVVETLEQLGI   32 (213)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCC
Confidence            4899999999999999999998888886

>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=84.51  E-value=0.51  Score=46.96  Aligned_cols=31  Identities=35%  Similarity=0.538  Sum_probs=23.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        31 ~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   62 (359)
T 2yyz_A           31 FVALLGPSGCGKTTTLLMLAGIYKPTSGEIYF   62 (359)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEEcCCCchHHHHHHHHHCCCCCCccEEEE
Confidence            378999999999999987765432 3576655

>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=84.50  E-value=0.54  Score=45.80  Aligned_cols=22  Identities=32%  Similarity=0.356  Sum_probs=20.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++|.|..|||||++|..++.
T Consensus        35 p~I~vvG~~~sGKSSLln~l~g   56 (360)
T 3t34_A           35 PAIAVVGGQSSGKSSVLESIVG   56 (360)
T ss_dssp             CEEEEECBTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            5799999999999999999886

>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=84.49  E-value=0.52  Score=45.70  Aligned_cols=24  Identities=29%  Similarity=0.314  Sum_probs=19.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -+.|.|+.||||||++..+...-.
T Consensus        92 ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           92 IIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCchHHHHHHHHHhhcc
Confidence            478999999999999987766543

>3a1s_A Iron(II) transport protein B; FEOB, iron transporter, small GTPase, G protein, GDI; HET: GDP; 1.50A {Thermotoga maritima} PDB: 3a1t_A* 3a1u_A* 3a1v_A* 3a1w_A

Probab=84.49  E-value=0.61  Score=43.58  Aligned_cols=21  Identities=24%  Similarity=0.308  Sum_probs=19.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|.+|||||+++.++.
T Consensus         6 ~kI~lvG~~nvGKTsL~n~l~   26 (258)
T 3a1s_A            6 VKVALAGCPNVGKTSLFNALT   26 (258)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            469999999999999999885

>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=84.35  E-value=0.52  Score=47.04  Aligned_cols=31  Identities=32%  Similarity=0.599  Sum_probs=23.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      -+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        31 ~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   62 (372)
T 1g29_1           31 FMILLGPSGCGKTTTLRMIAGLEEPSRGQIYI   62 (372)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCcHHHHHHHHHHcCCCCCccEEEE
Confidence            378999999999999987765432 3466655

>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=84.25  E-value=0.45  Score=47.15  Aligned_cols=31  Identities=26%  Similarity=0.543  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        28 ~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~~   59 (348)
T 3d31_A           28 YFVILGPTGAGKTLFLELIAGFHVPDSGRILL   59 (348)
T ss_dssp             EEEEECCCTHHHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCccHHHHHHHHHcCCCCCCcEEEE
Confidence            378999999999999987765432 3576665

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=84.23  E-value=0.78  Score=49.27  Aligned_cols=33  Identities=15%  Similarity=0.160  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|++|||||.+...+.......+.-+++|
T Consensus       523 ~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i  555 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARALAESIFGDEESMIRI  555 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCCCcceEEE
Confidence            499999999999988776666655444333444

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=84.21  E-value=0.53  Score=46.89  Aligned_cols=31  Identities=26%  Similarity=0.309  Sum_probs=23.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        31 ~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   62 (362)
T 2it1_A           31 FMALLGPSGSGKSTLLYTIAGIYKPTSGKIYF   62 (362)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCchHHHHHHHHhcCCCCCceEEEE
Confidence            378999999999999987665432 3576665

>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=84.20  E-value=0.54  Score=43.77  Aligned_cols=21  Identities=29%  Similarity=0.385  Sum_probs=18.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|.+|||||+++..+.
T Consensus         4 ~~i~lvG~~g~GKTTL~n~l~   24 (271)
T 3k53_A            4 KTVALVGNPNVGKTTIFNALT   24 (271)
T ss_dssp             EEEEEEECSSSSHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHh
Confidence            469999999999999998874

>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=84.12  E-value=0.89  Score=44.22  Aligned_cols=28  Identities=25%  Similarity=0.237  Sum_probs=23.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      ..+.|.|++|+|||+++..+.......|
T Consensus        57 ~~i~i~G~~g~GKSTl~~~l~~~~~~~~   84 (341)
T 2p67_A           57 LRLGVTGTPGAGKSTFLEAFGMLLIREG   84 (341)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHhcC
Confidence            4589999999999999999887766544

>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=84.05  E-value=0.54  Score=46.99  Aligned_cols=31  Identities=39%  Similarity=0.640  Sum_probs=23.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        39 ~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   70 (372)
T 1v43_A           39 FLVLLGPSGCGKTTTLRMIAGLEEPTEGRIYF   70 (372)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCChHHHHHHHHHcCCCCCceEEEE
Confidence            378999999999999987665432 3576665

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=84.02  E-value=0.43  Score=48.93  Aligned_cols=33  Identities=21%  Similarity=0.249  Sum_probs=26.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHh-CC-e-EEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWARE-EG-W-LVLY  223 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~-ng-W-IVL~  223 (404)
                      .++.|.|+.||||||+|.-+.-++.. .| - |.+.
T Consensus       139 e~v~IvGpnGsGKSTLlr~L~Gl~~p~~G~~pI~vd  174 (460)
T 2npi_A          139 PRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYIN  174 (460)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHTTHHHHCCCCEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHhCcccccCCceeEEEc
Confidence            45899999999999999999888764 46 3 5554

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=83.93  E-value=0.89  Score=42.56  Aligned_cols=29  Identities=21%  Similarity=0.133  Sum_probs=23.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLV  221 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIV  221 (404)
                      .+++|+-|||||+.|.+.+..+...|--|
T Consensus        31 ~vitG~M~sGKTT~Llr~~~r~~~~g~kv   59 (219)
T 3e2i_A           31 ECITGSMFSGKSEELIRRLRRGIYAKQKV   59 (219)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTTCCE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCce
Confidence            68999999999998888887776655333

>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=83.88  E-value=0.69  Score=46.12  Aligned_cols=22  Identities=27%  Similarity=0.290  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+.|.|+.|+|||++|..+.-.
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            4899999999999999888743

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=83.85  E-value=1  Score=39.89  Aligned_cols=29  Identities=31%  Similarity=0.433  Sum_probs=20.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      .++|+|..|||||++...+.   ..-|+-++.
T Consensus         5 ~i~i~G~~gsGkst~~~~l~---~~~g~~~~~   33 (219)
T 2h92_A            5 NIALDGPAAAGKSTIAKRVA---SELSMIYVD   33 (219)
T ss_dssp             CEEEECCTTSSHHHHHHHHH---HHTTCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHH---HhcCCceec
Confidence            38999999999999876553   334555444

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=83.82  E-value=0.41  Score=41.04  Aligned_cols=21  Identities=24%  Similarity=0.210  Sum_probs=18.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .++++.|..|+|||+++.++.
T Consensus        23 ~~i~v~G~~~~GKssli~~l~   43 (189)
T 2x77_A           23 IRVLMLGLDNAGKTSILYRLH   43 (189)
T ss_dssp             EEEEEEEETTSSHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            469999999999999998763

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=83.80  E-value=0.6  Score=46.02  Aligned_cols=26  Identities=27%  Similarity=0.247  Sum_probs=22.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      ++.|.|+.||||||+|.++.-+..-.
T Consensus        73 ~~gIiG~nGaGKTTLl~~I~g~~~~~   98 (347)
T 2obl_A           73 RIGIFAGSGVGKSTLLGMICNGASAD   98 (347)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            58999999999999999888886543

>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=83.62  E-value=0.6  Score=44.75  Aligned_cols=30  Identities=27%  Similarity=0.227  Sum_probs=22.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|+|||++|..+. ... ..|-|.+
T Consensus       167 i~~l~G~sG~GKSTLln~l~-~~~~~~G~i~~  197 (302)
T 2yv5_A          167 ICILAGPSGVGKSSILSRLT-GEELRTQEVSE  197 (302)
T ss_dssp             EEEEECSTTSSHHHHHHHHH-SCCCCCSCC--
T ss_pred             EEEEECCCCCCHHHHHHHHH-HhhCccccccc
Confidence            47899999999999999988 432 3465555

>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=83.62  E-value=0.91  Score=46.21  Aligned_cols=33  Identities=30%  Similarity=0.276  Sum_probs=27.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .+++.|+.||||||++..+..+...+|.=|+.+
T Consensus       100 vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllv  132 (425)
T 2ffh_A          100 LWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLV  132 (425)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            477889999999999999998877776655554

>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=83.60  E-value=0.62  Score=48.46  Aligned_cols=32  Identities=16%  Similarity=0.244  Sum_probs=22.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|++|||||+++..+.... ....+.+.+
T Consensus       110 ~vll~Gp~GtGKTtlar~ia~~l-~~~~~~i~~  141 (543)
T 3m6a_A          110 ILCLAGPPGVGKTSLAKSIAKSL-GRKFVRISL  141 (543)
T ss_dssp             EEEEESSSSSSHHHHHHHHHHHH-TCEEEEECC
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc-CCCeEEEEe
Confidence            48999999999998776554443 334444443

>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=83.55  E-value=0.58  Score=44.74  Aligned_cols=31  Identities=16%  Similarity=0.008  Sum_probs=20.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.|||||++|..+.-... ..|-|.+
T Consensus       171 iv~l~G~sG~GKSTll~~l~g~~~~~~G~i~~  202 (301)
T 1u0l_A          171 ISTMAGLSGVGKSSLLNAINPGLKLRVSEVSE  202 (301)
T ss_dssp             EEEEECSTTSSHHHHHHHHSTTCCCC------
T ss_pred             eEEEECCCCCcHHHHHHHhcccccccccceec
Confidence            478999999999999988875433 2355554

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=83.52  E-value=0.62  Score=44.12  Aligned_cols=31  Identities=19%  Similarity=0.342  Sum_probs=22.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.--..|-|.+
T Consensus        32 ~~~i~G~NGsGKSTLlk~l~Gl~p~~G~I~~   62 (263)
T 2pjz_A           32 KVIILGPNGSGKTTLLRAISGLLPYSGNIFI   62 (263)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCCCcEEEE
Confidence            4889999999999999876543233455544

>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=83.45  E-value=0.99  Score=46.77  Aligned_cols=35  Identities=26%  Similarity=0.375  Sum_probs=27.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL~IP~  226 (404)
                      +.+|.|++|+|||+++.+++... ...+-+++++--
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~~~~~~~~i~V~~~i  188 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHNIAQEHGGISVFAGV  188 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHHHHHHTCCCEEEEEE
T ss_pred             EEEEECCCCCCccHHHHHHHhhhhhccCcEEEEeee
Confidence            58999999999999999998874 445666666533

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=83.45  E-value=0.46  Score=49.41  Aligned_cols=31  Identities=16%  Similarity=0.296  Sum_probs=23.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh-CCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE-EGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~-ngWIVL  222 (404)
                      .++|.|+.||||||+|..++.+-.. .|-|.+
T Consensus       262 ~i~I~GptGSGKTTlL~aL~~~i~~~~giiti  293 (511)
T 2oap_1          262 SAIVVGETASGKTTTLNAIMMFIPPDAKVVSI  293 (511)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGSCTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHhhCCCCCCEEEE
Confidence            3899999999999999887765432 354444

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=83.30  E-value=1.7  Score=45.40  Aligned_cols=68  Identities=12%  Similarity=0.167  Sum_probs=41.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH-HHH--hCCeEEEEecCcccccccCeeecC-CCC--CCccCHHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH-WAR--EEGWLVLYVPRGREWTHGGYFYKN-PQT--GLWDTPLQAENVLKDFIK  260 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~-~A~--~ngWIVL~IP~a~~wvng~~~y~~-~~~--g~ydQP~~A~~~Lk~fl~  260 (404)
                      +.+++.|..|||||++|..++. .+.  .-+-+-+++=++..-.-  ..|.. ++.  ...+.|..+.+.|+.+..
T Consensus       168 pHlLIaG~TGSGKSt~L~~li~sLl~~~~p~~v~l~liDpK~~el--~~~~~lPhl~~~Vvtd~~~a~~~L~~~~~  241 (512)
T 2ius_A          168 PHLLVAGTTGSGASVGVNAMILSMLYKAQPEDVRFIMIDPKMLEL--SVYEGIPHLLTEVVTDMKDAANALRWCVN  241 (512)
T ss_dssp             CSEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECCSSSGG--GGGTTCTTBSSSCBCSHHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHhCCCceEEEEEECCchhhh--hhhccCCcccceeecCHHHHHHHHHHHHH
Confidence            4689999999999999988775 333  23666666655443100  11221 221  245677777777765443

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=83.27  E-value=0.43  Score=49.55  Aligned_cols=23  Identities=26%  Similarity=0.192  Sum_probs=18.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .++|+|++|||||++...+....
T Consensus        43 ~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           43 SVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             EEEEECCSSSSHHHHHHHGGGGB
T ss_pred             eeEeecCchHHHHHHHHHHHHHH
Confidence            48999999999998776555444

>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=83.18  E-value=1  Score=42.02  Aligned_cols=29  Identities=28%  Similarity=0.373  Sum_probs=25.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWL  220 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWI  220 (404)
                      -++|.|..|||||+.+..+..+-...|.=
T Consensus        29 ~i~~eG~~GsGKsT~~~~l~~~l~~~~~~   57 (236)
T 3lv8_A           29 FIVIEGLEGAGKSTAIQVVVETLQQNGID   57 (236)
T ss_dssp             EEEEEESTTSCHHHHHHHHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCC
Confidence            48999999999999999998887777754

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*

Probab=83.16  E-value=0.65  Score=45.58  Aligned_cols=22  Identities=27%  Similarity=0.323  Sum_probs=18.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      -.+|+|+.|+|||++|- +++||
T Consensus        27 l~vi~G~NGaGKT~ile-AI~~~   48 (371)
T 3auy_A           27 IVAIIGENGSGKSSIFE-AVFFA   48 (371)
T ss_dssp             EEEEEECTTSSHHHHHH-HHHHH
T ss_pred             eEEEECCCCCCHHHHHH-HHHHH
Confidence            37999999999999974 66664

>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=83.15  E-value=0.69  Score=43.79  Aligned_cols=21  Identities=24%  Similarity=0.371  Sum_probs=18.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|.+|||||+++.++.
T Consensus         4 ~kI~lvG~~nvGKSTL~n~L~   24 (272)
T 3b1v_A            4 TEIALIGNPNSGKTSLFNLIT   24 (272)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            358999999999999999886

>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=83.07  E-value=0.82  Score=41.62  Aligned_cols=29  Identities=28%  Similarity=0.478  Sum_probs=20.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      .++|.|++||||+|.-..+.   ..-|+..|.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La---~~~g~~~is   30 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLA---KEKGFVHIS   30 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHH---HHHCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHH---HHHCCeEEc
Confidence            47899999999998655544   334665443

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=83.03  E-value=1  Score=41.39  Aligned_cols=33  Identities=15%  Similarity=0.084  Sum_probs=22.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +++|.|+.|+|||.+...++...  .+.+++-+|.
T Consensus       110 ~~ll~~~tG~GKT~~a~~~~~~~--~~~~liv~P~  142 (237)
T 2fz4_A          110 RGCIVLPTGSGKTHVAMAAINEL--STPTLIVVPT  142 (237)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHS--CSCEEEEESS
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHc--CCCEEEEeCC
Confidence            48999999999999876655432  3444444443

>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=82.93  E-value=0.56  Score=45.10  Aligned_cols=36  Identities=19%  Similarity=0.361  Sum_probs=25.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeE-----EEEecCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWL-----VLYVPRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWI-----VL~IP~a  227 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|     |-|+|.-
T Consensus        66 ~~~i~G~NGsGKSTLlk~l~Gl~~p~~G~I~~~g~i~~v~Q~  107 (290)
T 2bbs_A           66 LLAVAGSTGAGKTSLLMMIMGELEPSEGKIKHSGRISFCSQN  107 (290)
T ss_dssp             EEEEEESTTSSHHHHHHHHTTSSCEEEEEEECCSCEEEECSS
T ss_pred             EEEEECCCCCcHHHHHHHHhcCCCCCCcEEEECCEEEEEeCC
Confidence            488999999999999987665432 34555     3355554

>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=82.93  E-value=1.6  Score=41.87  Aligned_cols=25  Identities=32%  Similarity=0.389  Sum_probs=20.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE  216 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~  216 (404)
                      -+.|.|+.||||||++..+...-..
T Consensus        33 ii~I~G~sGsGKSTla~~L~~~l~~   57 (290)
T 1odf_A           33 FIFFSGPQGSGKSFTSIQIYNHLME   57 (290)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhh
Confidence            4889999999999998777765543

>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=82.89  E-value=0.48  Score=47.55  Aligned_cols=30  Identities=20%  Similarity=0.188  Sum_probs=23.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|.+|||||++...+.   ...||.+|..
T Consensus       260 lIil~G~pGSGKSTla~~L~---~~~~~~~i~~  289 (416)
T 3zvl_A          260 VVVAVGFPGAGKSTFIQEHL---VSAGYVHVNR  289 (416)
T ss_dssp             EEEEESCTTSSHHHHHHHHT---GGGTCEECCG
T ss_pred             EEEEECCCCCCHHHHHHHHH---HhcCcEEEcc
Confidence            48999999999999887654   3457877654

>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=82.80  E-value=0.58  Score=47.06  Aligned_cols=31  Identities=26%  Similarity=0.335  Sum_probs=23.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-...|-|.+
T Consensus        49 ~~~llGpsGsGKSTLLr~iaGl~~~~G~I~i   79 (390)
T 3gd7_A           49 RVGLLGRTGSGKSTLLSAFLRLLNTEGEIQI   79 (390)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTCSEEEEEEEE
T ss_pred             EEEEECCCCChHHHHHHHHhCCCCCCeEEEE
Confidence            4899999999999999877654334565555

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=82.77  E-value=0.31  Score=42.03  Aligned_cols=23  Identities=22%  Similarity=0.315  Sum_probs=5.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      -+++|.|..|+|||+++..+..-
T Consensus        21 ~~i~v~G~~~~GKssli~~l~~~   43 (208)
T 2yc2_C           21 CKVAVVGEATVGKSALISMFTSK   43 (208)
T ss_dssp             EEEEEC-----------------
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46999999999999999887754

>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=82.72  E-value=0.76  Score=42.27  Aligned_cols=21  Identities=33%  Similarity=0.363  Sum_probs=17.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+.|+|..|||||++...+..
T Consensus        24 iI~I~G~~GSGKST~a~~L~~   44 (252)
T 1uj2_A           24 LIGVSGGTASGKSSVCAKIVQ   44 (252)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            589999999999998776654

>1knx_A Probable HPR(Ser) kinase/phosphatase; HPR kinase, HPR kinase/phosphatase, HPRK/P, P-loop, walker A BOX, catabolite repression; 2.50A {Mycoplasma pneumoniae} SCOP: c.98.2.1 c.91.1.2

Probab=82.58  E-value=0.82  Score=44.86  Aligned_cols=34  Identities=21%  Similarity=0.228  Sum_probs=24.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH---hCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR---EEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~---~ngWIVL~I  224 (404)
                      ..++|.|+.|+|||++.+.++..+.   ..+++.+..
T Consensus       148 ~gvli~G~sG~GKStlal~l~~~G~~lv~DD~v~i~~  184 (312)
T 1knx_A          148 VGVLLTGRSGIGKSECALDLINKNHLFVGDDAIEIYR  184 (312)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTTTCEEEEEEEEEEEE
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHcCCEEEeCCEEEEEE
Confidence            4699999999999999888776332   234455544

>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=82.48  E-value=1.6  Score=46.70  Aligned_cols=25  Identities=20%  Similarity=0.108  Sum_probs=19.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      +.++|+|++|||||+++..+.....
T Consensus       208 ~~vlL~G~~GtGKT~la~~la~~l~  232 (758)
T 1r6b_X          208 NNPLLVGESGVGKTAIAEGLAWRIV  232 (758)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEcCCCCCHHHHHHHHHHHHH
Confidence            3489999999999998876665543

>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=82.43  E-value=0.36  Score=44.68  Aligned_cols=33  Identities=33%  Similarity=0.628  Sum_probs=25.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ..++|.|..||||||+...+..+-  .+|.++..|
T Consensus        25 ~~I~ieG~~GsGKST~~~~L~~~l--~~~~~i~ep   57 (263)
T 1p5z_B           25 KKISIEGNIAAGKSTFVNILKQLC--EDWEVVPEP   57 (263)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGC--TTEEEECCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc--CCCEEEecc
Confidence            458999999999999987776542  357776554

>1zcb_A G alpha I/13; GTP-binding, lipoprotein, membrane, transducer, signaling PR; HET: GDP; 2.00A {Mus musculus} SCOP: a.66.1.1 c.37.1.8 PDB: 3ab3_A* 3cx8_A* 3cx7_A* 3cx6_A* 1zca_A*

Probab=82.41  E-value=0.92  Score=45.00  Aligned_cols=28  Identities=25%  Similarity=0.245  Sum_probs=22.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGW  219 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngW  219 (404)
                      .|++|-|..||||||++.|+- .-+..||
T Consensus        34 ~killlG~~~SGKST~~kq~~-i~~~~~~   61 (362)
T 1zcb_A           34 VKILLLGAGESGKSTFLKQMR-IIHGQDF   61 (362)
T ss_dssp             EEEEEECSTTSSHHHHHHHHH-HHHSCCC
T ss_pred             cEEEEECCCCCcHHHHHHHHH-HHhCCCC
Confidence            579999999999999999973 2334565

>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=82.27  E-value=0.76  Score=45.99  Aligned_cols=30  Identities=23%  Similarity=0.331  Sum_probs=22.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      ..++|.|++|||||+++..+...  ..|-++.
T Consensus       170 ~~i~l~G~~GsGKSTl~~~l~~~--~~g~~~~  199 (377)
T 1svm_A          170 RYWLFKGPIDSGKTTLAAALLEL--CGGKALN  199 (377)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH--HCCEEEC
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh--cCCcEEE
Confidence            35899999999999998877653  3554443

>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=82.25  E-value=0.48  Score=46.91  Aligned_cols=31  Identities=19%  Similarity=0.298  Sum_probs=23.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        33 ~~~llGpnGsGKSTLLr~iaGl~~p~~G~I~i   64 (353)
T 1oxx_K           33 RFGILGPSGAGKTTFMRIIAGLDVPSTGELYF   64 (353)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCCCCceEEEE
Confidence            378999999999999987664432 3576655

>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=82.11  E-value=0.5  Score=46.06  Aligned_cols=32  Identities=16%  Similarity=0.315  Sum_probs=23.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL~  223 (404)
                      .++|.|+.||||||+|.-+..+-. ..|-|.+.
T Consensus       173 ~v~i~G~~GsGKTTll~~l~g~~~~~~g~i~i~  205 (330)
T 2pt7_A          173 NVIVCGGTGSGKTTYIKSIMEFIPKEERIISIE  205 (330)
T ss_dssp             CEEEEESTTSCHHHHHHHGGGGSCTTSCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCcCCCcEEEEC
Confidence            389999999999999987776532 34655553

>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=82.05  E-value=1.7  Score=42.84  Aligned_cols=37  Identities=24%  Similarity=0.230  Sum_probs=27.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREW  230 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~w  230 (404)
                      +-++|.|+.|||||++...+   |..-+..|+..-+.+.+
T Consensus        11 ~~i~i~GptgsGKt~la~~L---a~~~~~~iis~Ds~qvY   47 (316)
T 3foz_A           11 KAIFLMGPTASGKTALAIEL---RKILPVELISVDSALIY   47 (316)
T ss_dssp             EEEEEECCTTSCHHHHHHHH---HHHSCEEEEECCTTTTB
T ss_pred             cEEEEECCCccCHHHHHHHH---HHhCCCcEEeccccccc
Confidence            34899999999999987655   55678888887665443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=81.88  E-value=1.1  Score=48.10  Aligned_cols=22  Identities=27%  Similarity=0.173  Sum_probs=17.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .++|+|++|||||++...+...
T Consensus       203 ~vLL~G~pGtGKT~la~~la~~  224 (758)
T 3pxi_A          203 NPVLIGEPGVGKTAIAEGLAQQ  224 (758)
T ss_dssp             EEEEESCTTTTTHHHHHHHHHH
T ss_pred             CeEEECCCCCCHHHHHHHHHHH
Confidence            4899999999999866544433

>3gj0_A GTP-binding nuclear protein RAN; G protein, GDP, acetylation, cytoplasm, HOST- virus interaction, nucleotide-binding, nucleus, phosphoprotein; HET: GDP; 1.48A {Homo sapiens} SCOP: c.37.1.8 PDB: 3gj3_A* 3gj5_A* 3gj4_A* 3gj6_A* 3gj7_A* 3gj8_A* 1i2m_A 1a2k_C 1ibr_A* 1k5d_A* 1k5g_A* 1qbk_C* 3a6p_C* 3ch5_A* 4gmx_A* 4gpt_A* 4hat_A* 4hau_A* 4hav_A* 4haw_A* ...

Probab=81.88  E-value=0.43  Score=42.29  Aligned_cols=23  Identities=22%  Similarity=0.202  Sum_probs=19.7

Q ss_pred             ceeEEEECCCCCcHHHHHHHHHH
Q 045329          190 RKQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       190 r~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .-+++|.|..|||||+++..++.
T Consensus        15 ~~ki~v~G~~~~GKSsli~~~~~   37 (221)
T 3gj0_A           15 QFKLVLVGDGGTGKTTFVKRHLT   37 (221)
T ss_dssp             EEEEEEEECTTSSHHHHHTTBHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHc
Confidence            35799999999999999998554

>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=81.85  E-value=0.64  Score=44.55  Aligned_cols=21  Identities=24%  Similarity=0.275  Sum_probs=18.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++|.|+.|+|||++|..+..
T Consensus        20 ~I~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           20 TLMVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             EEEEEEETTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999999653

>3t5d_A Septin-7; GTP-binding protein, cytoskeleton, signaling protein; HET: GDP; 3.30A {Homo sapiens} PDB: 3tw4_A*

Probab=81.83  E-value=0.7  Score=43.14  Aligned_cols=21  Identities=24%  Similarity=0.252  Sum_probs=18.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      -+++|.|..|+|||+++..+.
T Consensus         9 ~~I~vvG~~g~GKSTLin~L~   29 (274)
T 3t5d_A            9 FTLMVVGESGLGKSTLINSLF   29 (274)
T ss_dssp             EEEEEEECTTSSHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHh
Confidence            359999999999999998864

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=81.82  E-value=0.86  Score=41.37  Aligned_cols=22  Identities=36%  Similarity=0.625  Sum_probs=18.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ..+.|+|..|||||++...+..
T Consensus        17 ~~i~i~G~~gsGKst~~~~l~~   38 (236)
T 1q3t_A           17 IQIAIDGPASSGKSTVAKIIAK   38 (236)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            3589999999999998876543

>3i8s_A Ferrous iron transport protein B; GTPase, GPCR, iron uptake, FEO, cell inner membrane, cell ME GTP-binding, ION transport, membrane; 1.80A {Escherichia coli} PDB: 3i8x_A* 3i92_A* 3hyr_A 3hyt_A* 2wic_A* 2wib_A* 2wia_A*

Probab=81.63  E-value=0.8  Score=43.00  Aligned_cols=21  Identities=29%  Similarity=0.233  Sum_probs=18.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+++|.|.+|||||+++..+.
T Consensus         4 ~~I~lvG~~n~GKSTLin~l~   24 (274)
T 3i8s_A            4 LTIGLIGNPNSGKTTLFNQLT   24 (274)
T ss_dssp             EEEEEEECTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHh
Confidence            469999999999999999874

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=81.63  E-value=0.92  Score=42.13  Aligned_cols=26  Identities=23%  Similarity=0.295  Sum_probs=19.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      -+++.|..||||||....+..+-...
T Consensus        27 ~I~~eG~~GsGKsT~~~~l~~~l~~~   52 (227)
T 3v9p_A           27 FITFEGIDGAGKTTHLQWFCDRLQER   52 (227)
T ss_dssp             EEEEECCC---CHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhh
Confidence            48999999999999999888876655

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=81.47  E-value=1.1  Score=41.22  Aligned_cols=34  Identities=21%  Similarity=0.272  Sum_probs=27.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -+++.|..|||||+....+..+-.. ...++..|.
T Consensus         7 ~i~~eG~~g~GKst~~~~l~~~l~~-~~~~~~ep~   40 (216)
T 3tmk_A            7 LILIEGLDRTGKTTQCNILYKKLQP-NCKLLKFPE   40 (216)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHCS-SEEEEESSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcc-cceEEEecC
Confidence            4899999999999999888876554 456777773

>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=81.46  E-value=1.1  Score=43.18  Aligned_cols=22  Identities=14%  Similarity=-0.007  Sum_probs=17.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +.|+++|++|+||+++...+..
T Consensus        19 ~~~Lf~Gp~G~GKtt~a~~la~   40 (305)
T 2gno_A           19 ISILINGEDLSYPREVSLELPE   40 (305)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5699999999999887655544

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=81.33  E-value=0.82  Score=46.52  Aligned_cols=25  Identities=28%  Similarity=0.408  Sum_probs=21.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE  216 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~  216 (404)
                      ++.|.|+.||||||+|..+.-+...
T Consensus       159 ~~~IvG~sGsGKSTLl~~Iag~~~~  183 (438)
T 2dpy_A          159 RMGLFAGSGVGKSVLLGMMARYTRA  183 (438)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcccCC
Confidence            5899999999999999888877643

>2x2e_A Dynamin-1; nitration, hydrolase, membrane fission, nucleotide-binding, endocytosis, motor protein; HET: GDP; 2.00A {Homo sapiens} PDB: 2x2f_A* 3zyc_A* 3zys_A

Probab=81.21  E-value=0.88  Score=44.26  Aligned_cols=22  Identities=36%  Similarity=0.382  Sum_probs=19.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++++.|.+|+|||++|..++-
T Consensus        32 ~~I~vvG~~~~GKSSLln~L~g   53 (353)
T 2x2e_A           32 PQIAVVGGQSAGKSSVLENFVG   53 (353)
T ss_dssp             CEEEEECBTTSSHHHHHHTTTT
T ss_pred             CeEEEECCCCCCHHHHHHHHhC
Confidence            5799999999999999988764

>4djt_A GTP-binding nuclear protein GSP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid, RAN family; HET: GDP; 1.80A {Encephalitozoon cuniculi}

Probab=81.20  E-value=0.75  Score=40.38  Aligned_cols=21  Identities=24%  Similarity=0.260  Sum_probs=18.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      -+++|.|..|+|||+++..++
T Consensus        12 ~ki~vvG~~~~GKSsli~~l~   32 (218)
T 4djt_A           12 YKICLIGDGGVGKTTYINRVL   32 (218)
T ss_dssp             EEEEEECCTTSSHHHHHCBCT
T ss_pred             cEEEEECCCCCCHHHHHHHHh
Confidence            469999999999999998766

>3qkt_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATP binding, DNA bindi MRE11, replication; HET: DNA ANP; 1.90A {Pyrococcus furiosus} PDB: 3qku_A* 1ii8_A 3qks_B* 3qkr_B* 1ii8_B

Probab=81.09  E-value=0.99  Score=43.71  Aligned_cols=22  Identities=23%  Similarity=0.120  Sum_probs=17.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      .+|.|+.|+|||++|- ++.||.
T Consensus        26 ~~i~G~NGsGKS~lle-Ai~~~l   47 (339)
T 3qkt_A           26 NLIIGQNGSGKSSLLD-AILVGL   47 (339)
T ss_dssp             EEEECCTTSSHHHHHH-HHHHHH
T ss_pred             EEEECCCCCCHHHHHH-HHHHHh
Confidence            6899999999999974 445544

>1mky_A Probable GTP-binding protein ENGA; GTPase, DER, KH-domain, tandem G-domains, ligand binding protein; HET: GDP; 1.90A {Thermotoga maritima} SCOP: c.37.1.8 c.37.1.8 d.52.5.1

Probab=81.02  E-value=0.88  Score=45.71  Aligned_cols=22  Identities=18%  Similarity=0.320  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|.|++|||||+++..++.
T Consensus       181 ~kvaivG~~gvGKSTLln~l~g  202 (439)
T 1mky_A          181 IKVAIVGRPNVGKSTLFNAILN  202 (439)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHT
T ss_pred             ceEEEECCCCCCHHHHHHHHhC
Confidence            4699999999999999988764

>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=80.86  E-value=0.97  Score=43.32  Aligned_cols=22  Identities=27%  Similarity=0.264  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ..++|.|.+|+|||+++.+++.
T Consensus         8 g~V~ivG~~nvGKSTLln~l~g   29 (301)
T 1wf3_A            8 GFVAIVGKPNVGKSTLLNNLLG   29 (301)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4589999999999999999874

>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=80.79  E-value=0.97  Score=49.41  Aligned_cols=33  Identities=15%  Similarity=0.148  Sum_probs=22.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|++|||||++...+.......+.-+++|
T Consensus       590 ~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i  622 (854)
T 1qvr_A          590 SFLFLGPTGVGKTELAKTLAATLFDTEEAMIRI  622 (854)
T ss_dssp             EEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEE
Confidence            599999999999986665555554444334444

>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=80.78  E-value=0.97  Score=43.16  Aligned_cols=22  Identities=32%  Similarity=0.285  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ..+.|.|.+|+|||+++..++.
T Consensus         9 ~~VaIvG~~nvGKSTLln~L~g   30 (301)
T 1ega_A            9 GFIAIVGRPNVGKSTLLNKLLG   30 (301)
T ss_dssp             EEEEEECSSSSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
Confidence            3589999999999999999874

>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown function, PSI-2, protein struct initiative; 1.60A {Pyrococcus horikoshii}

Probab=80.76  E-value=1.4  Score=41.89  Aligned_cols=35  Identities=9%  Similarity=-0.032  Sum_probs=31.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -++|.|.+|+||+++..|.+.-+.++|.-++||--
T Consensus        23 ~~li~g~p~~~~~~l~~qfl~~g~~~Ge~~~~~~~   57 (260)
T 3bs4_A           23 ILIHEEDASSRGKDILFYILSRKLKSDNLVGMFSI   57 (260)
T ss_dssp             EEEEECSGGGCHHHHHHHHHHHHHHTTCEEEEEEC
T ss_pred             EEEEEeCCCccHHHHHHHHHHHHHHCCCcEEEEEE
Confidence            47888999999998889999999999999999843

>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=80.75  E-value=1.2  Score=45.25  Aligned_cols=21  Identities=24%  Similarity=0.305  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+.|.|+.|+||||+|..+.-
T Consensus        71 ~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           71 NVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHhC
Confidence            588999999999999988775

>3r7w_A Gtpase1, GTP-binding protein GTR1; RAG gtpases, GTR1P, GTR2P, MTOR, protein transport; HET: GNP; 2.77A {Saccharomyces cerevisiae} PDB: 4arz_A*

Probab=80.68  E-value=0.95  Score=43.21  Aligned_cols=23  Identities=22%  Similarity=0.277  Sum_probs=20.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .+++|.|.+|+|||+++.+++.-
T Consensus         4 ~KI~lvG~~~vGKSSLi~~l~~~   26 (307)
T 3r7w_A            4 SKLLLMGRSGSGKSSMRSIIFSN   26 (307)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46999999999999999987653

>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=80.57  E-value=0.88  Score=45.51  Aligned_cols=31  Identities=23%  Similarity=0.224  Sum_probs=22.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      -+.|.|+.||||||+|.-+.-.-. ..|-|.+
T Consensus        56 i~~IiGpnGaGKSTLlr~i~GL~~p~~G~I~i   87 (366)
T 3tui_C           56 IYGVIGASGAGKSTLIRCVNLLERPTEGSVLV   87 (366)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEEcCCCchHHHHHHHHhcCCCCCceEEEE
Confidence            378999999999999876654432 3465554

>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=80.16  E-value=0.8  Score=44.48  Aligned_cols=31  Identities=29%  Similarity=0.484  Sum_probs=22.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-+- -..|-|.+
T Consensus        82 ~vaivG~sGsGKSTLl~ll~gl~~p~~G~I~i  113 (306)
T 3nh6_A           82 TLALVGPSGAGKSTILRLLFRFYDISSGCIRI  113 (306)
T ss_dssp             EEEEESSSCHHHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCchHHHHHHHHHcCCCCCCcEEEE
Confidence            48999999999999997665432 23455543

>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=80.16  E-value=0.96  Score=43.26  Aligned_cols=22  Identities=27%  Similarity=0.277  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ..+.|.|.+|+|||+++.+++.
T Consensus        11 g~v~ivG~~nvGKSTLin~l~g   32 (308)
T 3iev_A           11 GYVAIVGKPNVGKSTLLNNLLG   32 (308)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            4589999999999999998873

>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=80.05  E-value=0.74  Score=47.65  Aligned_cols=34  Identities=6%  Similarity=0.035  Sum_probs=28.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC----CeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE----GWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n----gWIVL~IP  225 (404)
                      |..|.|.+|+|||++|.|+..++..|    |.+++|+-
T Consensus       154 r~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~  191 (469)
T 2c61_A          154 KLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAA  191 (469)
T ss_dssp             BCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEE
Confidence            57888999999999999999988764    46777763

>3th5_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTPase, GTP binding, protein binding, signali protein; HET: GNP; 2.30A {Homo sapiens}

Probab=80.22  E-value=0.4  Score=41.82  Aligned_cols=22  Identities=23%  Similarity=0.199  Sum_probs=19.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|..|+|||+++.++..
T Consensus        31 ~ki~v~G~~~~GKSsli~~l~~   52 (204)
T 3th5_A           31 IKCVVVGDGAVGKTCLLISYTT   52 (204)
Confidence            3599999999999999987764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	404
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.14
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.82
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	96.78
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.64
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	96.52
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	96.23
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.21
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	95.92
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.79
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	95.7
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.66
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	95.66
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	95.61
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	95.52
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	95.51
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	95.45
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	95.37
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	95.32
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	95.21
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.17
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.16
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.12
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	95.07
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	94.83
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	94.81
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	94.77
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	94.74
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	94.71
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	94.67
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	94.61
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	94.6
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.42
d1ls1a2	207	GTPase domain of the signal sequence recognition p	94.42
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	94.39
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	94.39
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	94.38
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	94.37
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	94.36
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	94.36
d1vmaa2	213	GTPase domain of the signal recognition particle r	94.36
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	94.33
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	94.29
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	94.25
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	94.16
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	94.09
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	94.05
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	94.05
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.04
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.02
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	93.96
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	93.9
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	93.8
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	93.64
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	93.61
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	93.55
d1okkd2	207	GTPase domain of the signal recognition particle r	93.54
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	93.47
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	93.43
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	93.36
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	93.34
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	93.29
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.28
d2qy9a2	211	GTPase domain of the signal recognition particle r	93.2
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	93.14
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	93.13
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	93.11
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	93.1
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	93.02
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	92.97
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.94
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	92.88
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	92.78
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.71
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	92.66
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	92.65
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	92.64
d1j8yf2	211	GTPase domain of the signal sequence recognition p	92.63
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	92.53
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	92.53
d1nrjb_	209	Signal recognition particle receptor beta-subunit	92.35
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	92.18
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	92.17
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	92.07
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	91.97
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	91.81
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	91.81
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	91.79
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	91.78
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	91.77
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	91.76
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	91.71
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	91.69
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	91.67
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	91.66
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	91.64
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	91.61
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.6
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	91.56
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	91.55
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	91.55
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	91.52
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	91.5
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	91.38
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	91.37
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	91.34
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	91.33
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	91.29
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	91.19
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	91.17
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	91.08
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	91.07
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	91.04
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	90.98
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	90.94
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	90.94
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	90.88
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	90.87
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	90.82
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	90.79
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	90.77
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	90.67
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	90.56
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	90.52
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	90.5
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	90.44
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	90.4
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	90.31
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	90.27
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	90.19
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	90.19
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	90.12
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	90.11
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	90.06
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	90.02
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	89.98
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	89.96
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	89.92
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	89.92
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	89.83
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	89.78
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	89.75
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	89.66
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	89.65
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	89.58
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	89.49
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	89.48
d2fh5b1	207	Signal recognition particle receptor beta-subunit	89.47
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	89.41
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	89.4
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	89.37
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	89.36
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	89.35
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	89.27
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	89.24
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	89.2
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	89.17
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	89.12
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	88.81
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	88.7
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	88.68
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	88.63
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	88.5
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	88.47
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	88.26
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	88.23
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	88.18
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	88.11
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	88.04
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	87.92
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	87.76
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	87.74
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	87.61
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	87.59
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	87.51
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	87.36
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	87.35
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	87.32
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	87.26
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	87.22
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	87.06
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	87.02
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	86.98
d1tuea_	205	Replication protein E1 helicase domain {Human papi	86.97
d2awna2	232	Maltose transport protein MalK, N-terminal domain	86.94
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	86.93
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	86.77
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	86.66
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	86.57
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	85.87
d2akab1	299	Dynamin G domain {Rat (Rattus norvegicus) [TaxId:	85.72
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	85.59
d1xpua3	289	Transcription termination factor Rho, ATPase domai	85.47
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	85.34
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	85.26
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	85.12
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	85.09
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	85.04
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	84.86
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	84.77
d1g2912	240	Maltose transport protein MalK, N-terminal domain	84.76
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	84.72
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	84.62
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	84.52
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	84.44
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	84.42
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	84.1
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	84.1
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	83.81
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	83.7
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	83.68
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	83.56
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	83.44
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	83.36
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	83.05
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	82.73
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	82.53
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	82.39
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	82.38
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	82.07
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	80.97
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	80.83
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	80.78
d1jwyb_	306	Dynamin G domain {Dictyostelium discoideum [TaxId:	80.64
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	80.41
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	80.15
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	80.1

>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=97.14  E-value=0.00014  Score=59.90  Aligned_cols=33  Identities=21%  Similarity=0.234  Sum_probs=27.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|+|++|||||+++.+++.....+|-.|..+
T Consensus         3 ~v~ItG~~GtGKTtl~~~i~~~l~~~~~~v~~~   35 (189)
T d2i3ba1           3 HVFLTGPPGVGKTTLIHKASEVLKSSGVPVDGF   35 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHHHTTCCCEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            489999999999999999999888777555433

>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=96.82  E-value=0.00048  Score=56.51  Aligned_cols=32  Identities=16%  Similarity=0.065  Sum_probs=28.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.++|.+||||||++.+++.+...+|+-|..+
T Consensus         5 i~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~   36 (170)
T d1np6a_           5 LAFAAWSGTGKTTLLKKLIPALCARGIRPGLI   36 (170)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEe
Confidence            79999999999999999999999999865554

>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=96.78  E-value=0.0014  Score=57.13  Aligned_cols=28  Identities=14%  Similarity=0.224  Sum_probs=22.1

Q ss_pred             HHHHHHHHhcCCCCcEEEEEeCcccccC
Q 045329          320 VVRLRKELSLVKDIPVLIAIDQYNNWFT  347 (404)
Q Consensus       320 ~~aLl~EL~~q~~~PVLvAVD~~Nalf~  347 (404)
                      +..+++++....+.++++.+|++..+..
T Consensus       123 ~~~~l~~l~~~~~~~~~i~id~~~~~~~  150 (283)
T d2fnaa2         123 FANLLESFEQASKDNVIIVLDEAQELVK  150 (283)
T ss_dssp             HHHHHHHHHHTCSSCEEEEEETGGGGGG
T ss_pred             HHHHHHHHHhhcccccccccchhhhhcc
Confidence            5556677777778899999999988764

>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=96.64  E-value=0.0006  Score=59.86  Aligned_cols=34  Identities=18%  Similarity=0.186  Sum_probs=31.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|+|++|||||++++|+++.+..+|+-|+|+.
T Consensus        28 l~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is   61 (242)
T d1tf7a2          28 IILATGATGTGKTLLVSRFVENACANKERAILFA   61 (242)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhccccceee
Confidence            3899999999999999999999999999998884

>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=96.52  E-value=0.0007  Score=58.07  Aligned_cols=35  Identities=14%  Similarity=0.085  Sum_probs=29.5

Q ss_pred             eEEEECCCCCcHHHHHHHHH-HHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLV-HWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav-~~A~~ngWIVL~IP~  226 (404)
                      -++|+|++|+|||+++.|++ +.|..++|.|+|+..
T Consensus        28 ~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~   63 (242)
T d1tf7a1          28 STLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF   63 (242)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhcCCCcccccc
Confidence            48999999999999999954 467788999998743

>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=96.23  E-value=0.0034  Score=54.66  Aligned_cols=36  Identities=22%  Similarity=0.274  Sum_probs=26.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP~  226 (404)
                      +.++|+|++|||||+++..+......+ +..+++++.
T Consensus        44 ~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~   80 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYING   80 (276)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEET
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecc
Confidence            359999999999999998877766554 444444433

>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=96.21  E-value=0.0012  Score=54.87  Aligned_cols=23  Identities=22%  Similarity=0.384  Sum_probs=19.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      +++|+|++||||||+|..++..-
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l   24 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCcHHHHHHHHHHhcC
Confidence            58999999999999998877643

>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=95.92  E-value=0.0037  Score=56.56  Aligned_cols=37  Identities=22%  Similarity=0.360  Sum_probs=27.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREW  230 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~w  230 (404)
                      ..++|+|++|||||++...+   |.+-|+-++.|..+..|
T Consensus        41 ~~vLL~GppGtGKT~la~al---A~~~~~~~~~i~~~~~~   77 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALAAKI---AEESNFPFIKICSPDKM   77 (246)
T ss_dssp             EEEEEECSTTSSHHHHHHHH---HHHHTCSEEEEECGGGC
T ss_pred             eEEEEECcCCCCHHHHHHHH---hhccccccccccccccc
Confidence            46999999999998886555   44557777777555444

>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=95.79  E-value=0.002  Score=53.31  Aligned_cols=27  Identities=15%  Similarity=-0.022  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      =++|.|++|||||++++|+++.+...+
T Consensus        25 v~~i~G~~GsGKT~l~l~la~~~~~~~   51 (242)
T d1n0wa_          25 ITEMFGEFRTGKTQICHTLAVTCQLPI   51 (242)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHTTSCG
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHhh
Confidence            389999999999999999998876554

>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=95.70  E-value=0.031  Score=51.36  Aligned_cols=34  Identities=21%  Similarity=0.264  Sum_probs=30.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      =..++|+.|||||++.+|++.-|...|-.|+||-
T Consensus        59 itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiD   92 (268)
T d1xp8a1          59 ITEIYGPESGGKTTLALAIVAQAQKAGGTCAFID   92 (268)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEecCCccchHHHHHHHHHHHHhCCCEEEEEE
Confidence            3789999999999999999999999988888773

>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=95.66  E-value=0.0043  Score=55.61  Aligned_cols=33  Identities=21%  Similarity=0.178  Sum_probs=29.0

Q ss_pred             EEEECCCCCcHHHHHHHHHH-HHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVH-WAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~-~A~~ngWIVL~IP  225 (404)
                      ++|.|.+|+|||+++.|++. +|..+||=|+|+.
T Consensus        38 ~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s   71 (277)
T d1cr2a_          38 IMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAM   71 (277)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             EEEEeCCCCCHHHHHHHHHHhhhhhcccceeEee
Confidence            89999999999999999875 6778899888874

>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=95.66  E-value=0.0041  Score=55.07  Aligned_cols=36  Identities=25%  Similarity=0.386  Sum_probs=30.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      ++|+|++|||||-+|.-+.+.+..++--|+|++...
T Consensus        39 l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~   74 (213)
T d1l8qa2          39 IFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADD   74 (213)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHHhccCccceEEechHH
Confidence            899999999999988888778888888888886653

>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=95.61  E-value=0.0059  Score=53.40  Aligned_cols=24  Identities=21%  Similarity=0.358  Sum_probs=17.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      +.++|+||+|||||++.. +++-..
T Consensus        36 ~~~L~~GPpGtGKT~lA~-~la~~~   59 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAH-IIASEL   59 (238)
T ss_dssp             CCEEEESSTTSSHHHHHH-HHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH-HHHhcc
Confidence            459999999999999664 444333

>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=95.52  E-value=0.0039  Score=49.65  Aligned_cols=28  Identities=25%  Similarity=0.297  Sum_probs=19.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      .++|+|++|||||| +++.++-.  -|+-++
T Consensus         4 ~I~l~G~~GsGKST-vak~La~~--L~~~~i   31 (169)
T d1kaga_           4 NIFLVGPMGAGKST-IGRQLAQQ--LNMEFY   31 (169)
T ss_dssp             CEEEECCTTSCHHH-HHHHHHHH--TTCEEE
T ss_pred             eEEEECCCCCCHHH-HHHHHHHH--hCCCeE
Confidence            38999999999995 45555443  366554

>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=95.51  E-value=0.0091  Score=52.24  Aligned_cols=24  Identities=33%  Similarity=0.486  Sum_probs=18.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      +.++|+||+||||| +|+++++...
T Consensus        36 ~~~Ll~GPpG~GKT-tla~~la~~~   59 (239)
T d1ixsb2          36 EHLLLFGPPGLGKT-TLAHVIAHEL   59 (239)
T ss_dssp             CCEEEECCTTSCHH-HHHHHHHHHH
T ss_pred             CeEEEECCCCCCHH-HHHHHHHHHh
Confidence            45999999999998 5556665443

>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=95.45  E-value=0.0062  Score=55.15  Aligned_cols=33  Identities=27%  Similarity=0.460  Sum_probs=24.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|++|||||++...+   |.+-++-++++..
T Consensus        39 ~giLL~GppGtGKT~l~~al---a~~~~~~~~~i~~   71 (258)
T d1e32a2          39 RGILLYGPPGTGKTLIARAV---ANETGAFFFLING   71 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHH---HHHTTCEEEEECH
T ss_pred             ceeEEecCCCCCchHHHHHH---HHHhCCeEEEEEc
Confidence            46999999999999975433   3345777776643

>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=95.37  E-value=0.0049  Score=50.15  Aligned_cols=31  Identities=19%  Similarity=0.169  Sum_probs=23.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++++|.|++||||||+...+..+.   |.-++..
T Consensus         8 K~I~i~G~~GsGKTTla~~La~~~---~~~~i~~   38 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLAAVF---NTTSAWE   38 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHT---TCEEECC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh---CCCeEee
Confidence            569999999999999988766643   5544443

>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=95.32  E-value=0.0043  Score=50.53  Aligned_cols=33  Identities=24%  Similarity=0.262  Sum_probs=25.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|++||||||+...+.   ..-||-++.+-+
T Consensus         5 ~~I~i~G~pGsGKTTia~~La---~~l~~~~i~~~~   37 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELA---SKSGLKYINVGD   37 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHH---HHHCCEEEEHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH---HHHCCcEEechH
Confidence            458999999999999876653   344888776543

>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=95.21  E-value=0.0067  Score=49.61  Aligned_cols=32  Identities=22%  Similarity=0.261  Sum_probs=26.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|+|.+||||||++..+..+...+++=+..+
T Consensus         4 I~i~G~~GsGKsT~~~~L~~~l~~~~~~~~~~   35 (190)
T d1khta_           4 VVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMV   35 (190)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTTCCCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCeEEE
Confidence            89999999999999999998877776555444

>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=95.17  E-value=0.0087  Score=49.65  Aligned_cols=33  Identities=30%  Similarity=0.282  Sum_probs=29.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +-++|.+||||||++.+++.+-..+|+=|-.|-
T Consensus         4 i~I~G~~gSGKTTli~~l~~~L~~~g~~v~vik   36 (165)
T d1xjca_           4 WQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   36 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            459999999999999999999999988777763

>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=95.16  E-value=0.0076  Score=52.04  Aligned_cols=31  Identities=13%  Similarity=0.138  Sum_probs=25.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCe-EEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGW-LVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngW-IVL~  223 (404)
                      +++.|..|+||||++.++.+|....++ .|++
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~~~~~~~~ivn   34 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVN   34 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTTTSCEEEEE
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhCCeEEEEe
Confidence            689999999999999999998866544 4444

>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=95.12  E-value=0.008  Score=55.25  Aligned_cols=35  Identities=20%  Similarity=0.313  Sum_probs=31.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      =..|+|++|||||++++|++.-|..+|-.|+||-.
T Consensus        56 itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidt   90 (263)
T d1u94a1          56 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA   90 (263)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEcc
Confidence            37899999999999999999999999888887743

>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=95.07  E-value=0.0093  Score=47.95  Aligned_cols=31  Identities=19%  Similarity=0.198  Sum_probs=22.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++|+|++|||||++...++.  ...|+.++...
T Consensus         5 Iii~G~pGsGKTTla~~L~~--~~~~~~~~~~d   35 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWAREFIA--KNPGFYNINRD   35 (152)
T ss_dssp             EEEECCTTSSHHHHHHHHHH--HSTTEEEECHH
T ss_pred             EEEECCCCCCHHHHHHHHHH--hCCCCEEechH
Confidence            78999999999998776532  23466655543

>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=94.83  E-value=0.014  Score=51.03  Aligned_cols=33  Identities=27%  Similarity=0.361  Sum_probs=23.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+||+|||||+++.-   .|.+-|.=+++++.
T Consensus        53 ~~lll~GPpG~GKTt~a~~---la~~~~~~~~~~~~   85 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAHL---VAQELGYDILEQNA   85 (253)
T ss_dssp             SEEEEECSTTSSHHHHHHH---HHHHTTCEEEEECT
T ss_pred             ceEEEECCCCCCHHHHHHH---HHHHHHhhhhcccc
Confidence            4599999999999987753   34455555555544

>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=94.81  E-value=0.013  Score=51.37  Aligned_cols=31  Identities=16%  Similarity=0.171  Sum_probs=21.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      .++|+|++|||||++. ++++-...-+.+++.
T Consensus        34 ~ilL~GpPGtGKT~la-~~la~~~~~~~~~i~   64 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLR-SAIFEETQGNVIVID   64 (273)
T ss_dssp             EEEEECCTTSCTHHHH-HHHHHHTTTCCEEEC
T ss_pred             EEEEECCCCCCHHHHH-HHHHHHhhcceEEEe
Confidence            4999999999999975 444444444555553

>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=94.77  E-value=0.014  Score=50.51  Aligned_cols=23  Identities=26%  Similarity=0.410  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .++|+|++|||||+++.-+....
T Consensus        37 ~lLl~Gp~G~GKttl~~~la~~l   59 (227)
T d1sxjc2          37 HLLFYGPPGTGKTSTIVALAREI   59 (227)
T ss_dssp             CEEEECSSSSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCChhHHHHHHHHHh
Confidence            48999999999999877666543

>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=94.74  E-value=0.0099  Score=51.88  Aligned_cols=24  Identities=25%  Similarity=0.326  Sum_probs=19.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      +.++|+|++|||||++...+...-
T Consensus        34 ~~lll~Gp~G~GKTt~~~~la~~l   57 (252)
T d1sxje2          34 PHLLLYGPNGTGKKTRCMALLESI   57 (252)
T ss_dssp             CCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhh
Confidence            358999999999999886665543

>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=94.71  E-value=0.009  Score=48.15  Aligned_cols=20  Identities=35%  Similarity=0.484  Sum_probs=17.1

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      -++|+|++||||||+..++.
T Consensus         4 lI~i~G~~GsGKTTva~~L~   23 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCKRLA   23 (176)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            48999999999999976654

>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=94.67  E-value=0.0077  Score=52.61  Aligned_cols=22  Identities=18%  Similarity=0.080  Sum_probs=18.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      ++|+|++|||||+++..+....
T Consensus        49 l~l~GppGtGKT~l~~~l~~~l   70 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLAKFTVKRV   70 (287)
T ss_dssp             EECTTCCSSSHHHHHHHHHHHH
T ss_pred             EEeECCCCCCHHHHHHHHHHHH
Confidence            5678999999999998877653

>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=94.61  E-value=0.0093  Score=48.70  Aligned_cols=30  Identities=23%  Similarity=0.186  Sum_probs=22.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++|.|++||||||+...   .|.+-|+-+++++
T Consensus         7 I~l~G~~GsGKSTia~~---La~~lg~~~~~~~   36 (176)
T d1zp6a1           7 LLLSGHPGSGKSTIAEA---LANLPGVPKVHFH   36 (176)
T ss_dssp             EEEEECTTSCHHHHHHH---HHTCSSSCEEEEC
T ss_pred             EEEECCCCCCHHHHHHH---HHHHhCCCEEEec
Confidence            78999999999997543   3566677777764

>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=94.60  E-value=0.015  Score=53.04  Aligned_cols=33  Identities=18%  Similarity=0.291  Sum_probs=24.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|+|++|||||++...+..   +-|+=+++|..
T Consensus        46 ~~iLL~GppGtGKT~la~~iA~---~~~~~~~~i~~   78 (256)
T d1lv7a_          46 KGVLMVGPPGTGKTLLAKAIAG---EAKVPFFTISG   78 (256)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH---HHTCCEEEECS
T ss_pred             CeEEeeCCCCCCccHHHHHHHH---HcCCCEEEEEh
Confidence            4699999999999999665543   33666666644

>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=94.42  E-value=0.012  Score=47.14  Aligned_cols=21  Identities=29%  Similarity=0.309  Sum_probs=18.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|.|++|||||+++.++..
T Consensus         2 kivlvG~~~vGKSsLi~~l~~   22 (160)
T d1r8sa_           2 RILMVGLDAAGKTTILYKLKL   22 (160)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999988753

>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=94.42  E-value=0.016  Score=51.39  Aligned_cols=32  Identities=31%  Similarity=0.302  Sum_probs=28.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|.|+.|+||||+++-+.+|...+|+=|.-|
T Consensus        13 i~lvGp~GvGKTTTiaKLA~~~~~~g~kV~li   44 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLALYYKGKGRRPLLV   44 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            67899999999999999999999888877644

>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=94.39  E-value=0.013  Score=53.10  Aligned_cols=32  Identities=22%  Similarity=0.242  Sum_probs=24.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +.++|+|++|||||++...+.+   +-||=+++|.
T Consensus        43 ~giLl~GppGtGKT~la~aia~---~~~~~~~~i~   74 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHLARAVAG---EARVPFITAS   74 (247)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHH---HTTCCEEEEE
T ss_pred             ceEEEecCCCCChhHHHHHHHH---HcCCCEEEEE
Confidence            4599999999999998866654   4467676664

>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=94.39  E-value=0.016  Score=47.57  Aligned_cols=32  Identities=22%  Similarity=0.171  Sum_probs=26.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +||+|.+||||||+...+..+-..+|.-+..+
T Consensus         4 ivi~G~~GsGKTT~~~~La~~L~~~~~~~~~~   35 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLAKVKEILDNQGINNKII   35 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            68899999999999999988877776555444

>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=94.38  E-value=0.015  Score=47.39  Aligned_cols=21  Identities=24%  Similarity=0.382  Sum_probs=17.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      ..++|+|++||||||+...+.
T Consensus         6 ~~I~i~G~~GsGKTT~~~~La   26 (174)
T d1y63a_           6 INILITGTPGTGKTSMAEMIA   26 (174)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHH
Confidence            359999999999999876554

>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=94.37  E-value=0.013  Score=49.84  Aligned_cols=29  Identities=21%  Similarity=0.177  Sum_probs=23.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +||.|.+|||||++..++   +...||+++..
T Consensus        17 iil~G~pGsGKST~a~~l---~~~~~~~~i~~   45 (172)
T d1yj5a2          17 VVAVGFPGAGKSTFIQEH---LVSAGYVHVNR   45 (172)
T ss_dssp             EEEECCTTSSHHHHHHHH---TGGGTCEEEEH
T ss_pred             EEEECCCCCCHHHHHHHH---HHhcCCEEEch
Confidence            899999999999976544   45678887754

>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=94.36  E-value=0.017  Score=50.10  Aligned_cols=20  Identities=20%  Similarity=0.411  Sum_probs=16.0

Q ss_pred             eeEEEECCCCCcHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qa  210 (404)
                      +.++|+|++|||||++..-+
T Consensus        37 ~~~ll~Gp~G~GKTt~a~~l   56 (224)
T d1sxjb2          37 PHMIISGMPGIGKTTSVHCL   56 (224)
T ss_dssp             CCEEEECSTTSSHHHHHHHH
T ss_pred             CeEEEECCCCCCchhhHHHH
Confidence            34999999999999875433

>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=94.36  E-value=0.017  Score=46.70  Aligned_cols=31  Identities=35%  Similarity=0.485  Sum_probs=21.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|+|.+|||||++...+ +-.....|+.+..
T Consensus         6 I~l~G~~GsGKsTva~~L-~~~l~~~~~~~~~   36 (178)
T d1qhxa_           6 IILNGGSSAGKSGIVRCL-QSVLPEPWLAFGV   36 (178)
T ss_dssp             EEEECCTTSSHHHHHHHH-HHHSSSCEEEEEH
T ss_pred             EEEECCCCCCHHHHHHHH-HHHcCCCeEEeec
Confidence            889999999999776543 3333345666543

>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=94.36  E-value=0.019  Score=51.19  Aligned_cols=32  Identities=25%  Similarity=0.268  Sum_probs=27.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|.|+.|+||||+++-+.+|...+|+=|.-|
T Consensus        14 i~lvGptGvGKTTTiAKLAa~~~~~~~kV~li   45 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLA   45 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCceEEE
Confidence            78899999999999999999988887655544

>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=94.33  E-value=0.016  Score=50.25  Aligned_cols=22  Identities=23%  Similarity=0.451  Sum_probs=17.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +.++|+|++|||||++..-+..
T Consensus        46 ~~lll~Gp~G~GKTtla~~iak   67 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAALALAR   67 (231)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHH
Confidence            3499999999999987654443

>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=94.29  E-value=0.015  Score=50.15  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .++|+|++|||||+++..+..-
T Consensus        35 ~lll~Gp~G~GKTtl~~~i~~~   56 (237)
T d1sxjd2          35 HMLFYGPPGTGKTSTILALTKE   56 (237)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCChHHHHHHHHHH
Confidence            4899999999999988777654

>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=94.25  E-value=0.014  Score=50.48  Aligned_cols=26  Identities=15%  Similarity=0.054  Sum_probs=23.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      -++|+|++|||||++..|.++.+..+
T Consensus        38 ~~li~G~pGsGKT~~~lq~~~~~~~~   63 (254)
T d1pzna2          38 ITEVFGEFGSGKTQLAHTLAVMVQLP   63 (254)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTSC
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhhch
Confidence            48999999999999999999887654

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

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: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=94.16  E-value=0.0096  Score=46.59  Aligned_cols=40  Identities=18%  Similarity=0.081  Sum_probs=28.2

Q ss_pred             eeEEEECCCCCcHHHHH-HHHHHHHHhCCeEEEEecCcccc
Q 045329          191 KQIVLDGPLCCGKSITL-AMLVHWAREEGWLVLYVPRGREW  230 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L-~qav~~A~~ngWIVL~IP~a~~w  230 (404)
                      ..++|.++.|+|||... ..++.++.+.+..|+.++-...+
T Consensus         8 ~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~~~l   48 (140)
T d1yksa1           8 MTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVV   48 (140)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHH
T ss_pred             CcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecchhH
Confidence            35899999999999555 45667777777666666544333

>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=94.09  E-value=0.011  Score=50.59  Aligned_cols=25  Identities=24%  Similarity=0.060  Sum_probs=21.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE  216 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~  216 (404)
                      -++|+|++|||||++.+|+++.|..
T Consensus        36 ~~li~G~pGsGKT~l~lq~~~~~~~   60 (251)
T d1szpa2          36 ITELFGEFRTGKSQLCHTLAVTCQI   60 (251)
T ss_dssp             EEEEEESTTSSHHHHHHHHTTTTTS
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhhh
Confidence            3899999999999999999876643

>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=94.05  E-value=0.019  Score=47.58  Aligned_cols=32  Identities=19%  Similarity=0.153  Sum_probs=23.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      |++|.|++||||||....+   |..-||..+...+
T Consensus         2 ~I~i~G~pGSGKsT~a~~L---a~~~~~~~i~~~~   33 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKI---VAAYGIPHISTGD   33 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHH---HHHHCCCEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHH---HHHHCCceechhH
Confidence            5899999999999966544   3344888776543

>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=94.05  E-value=0.02  Score=51.96  Aligned_cols=32  Identities=25%  Similarity=0.420  Sum_probs=24.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +.++|+|++|||||++...+   |.+-|+=++++.
T Consensus        42 ~giLL~Gp~GtGKT~l~~al---a~~~~~~~~~~~   73 (265)
T d1r7ra3          42 KGVLFYGPPGCGKTLLAKAI---ANECQANFISIK   73 (265)
T ss_dssp             CEEEEBCCTTSSHHHHHHHH---HHHTTCEEEEEC
T ss_pred             CeEEEECCCCCcchhHHHHH---HHHhCCcEEEEE
Confidence            46999999999999988776   333466666663

>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=94.04  E-value=0.016  Score=47.20  Aligned_cols=21  Identities=33%  Similarity=0.363  Sum_probs=18.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      .|++|.|.+|||||++|.++.
T Consensus        14 ~kI~lvG~~~vGKTsLl~~l~   34 (186)
T d1f6ba_          14 GKLVFLGLDNAGKTTLLHMLK   34 (186)
T ss_dssp             EEEEEEEETTSSHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHh
Confidence            579999999999999998763

>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=94.02  E-value=0.0086  Score=51.01  Aligned_cols=35  Identities=9%  Similarity=-0.073  Sum_probs=27.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhC-CeEEEEecCc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREE-GWLVLYVPRG  227 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~n-gWIVL~IP~a  227 (404)
                      ++|.|++|+|||+++.|++..+..+ .|.+++...-
T Consensus        37 ~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~   72 (258)
T d2i1qa2          37 TEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVS   72 (258)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSC
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEeecc
Confidence            8999999999999999998876655 5555444333

>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=93.96  E-value=0.026  Score=45.86  Aligned_cols=30  Identities=27%  Similarity=0.068  Sum_probs=22.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|++||||||+...+...   -||..+..
T Consensus         8 iivl~G~~GsGKsT~a~~La~~---l~~~~~~~   37 (171)
T d1knqa_           8 IYVLMGVSGSGKSAVASEVAHQ---LHAAFLDG   37 (171)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHH---HTCEEEEG
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---hCCCeech
Confidence            3899999999999998776543   36665554

>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=93.90  E-value=0.027  Score=51.89  Aligned_cols=35  Identities=23%  Similarity=0.298  Sum_probs=31.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      =..|+|+.|||||++++|++.-|..+|-.|+||-.
T Consensus        62 i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDt   96 (269)
T d1mo6a1          62 VIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDA   96 (269)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEES
T ss_pred             eEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEEC
Confidence            37899999999999999999999999988888843

>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=93.80  E-value=0.014  Score=50.28  Aligned_cols=26  Identities=19%  Similarity=-0.010  Sum_probs=23.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      -++|.|++|||||++..|+++.|...
T Consensus        39 ~~~i~G~~GsGKT~lalq~~~~~~~~   64 (258)
T d1v5wa_          39 ITEAFGEFRTGKTQLSHTLCVTAQLP   64 (258)
T ss_dssp             EEEEECCTTCTHHHHHHHHHHHTTSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhh
Confidence            48999999999999999999987643

>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=93.64  E-value=0.034  Score=46.95  Aligned_cols=33  Identities=18%  Similarity=0.197  Sum_probs=26.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +.++|.|++||||||....+   |..-||..|...+
T Consensus         9 ~iI~i~GppGSGKsT~a~~L---a~~~g~~~is~gd   41 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQCEKL---VKDYSFVHLSAGD   41 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHH---HHHSSCEEEEHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH---HHHhCCeEEehhH
Confidence            56999999999999977666   5566998777643

>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=93.61  E-value=0.02  Score=47.43  Aligned_cols=29  Identities=31%  Similarity=0.211  Sum_probs=21.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      +|+||.|.+|||||++-..+.   ..-||-.+
T Consensus         2 p~IvliG~~G~GKSTig~~La---~~l~~~fi   30 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRRLA---KALGVGLL   30 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHHHH---HHHTCCEE
T ss_pred             CcEEEECCCCCCHHHHHHHHH---HHhCCCeE
Confidence            568999999999999765552   33366554

>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=93.55  E-value=0.045  Score=45.10  Aligned_cols=32  Identities=28%  Similarity=0.340  Sum_probs=25.2

Q ss_pred             EE-EECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IV-LDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~v-L~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +| |+|+.||||||+..++...-...+-.+..+
T Consensus        24 iIgI~G~~GSGKSTla~~L~~~l~~~~~~~~~~   56 (198)
T d1rz3a_          24 VLGIDGLSRSGKTTLANQLSQTLREQGISVCVF   56 (198)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhccccccceec
Confidence            45 999999999999999988776665444443

>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=93.54  E-value=0.029  Score=49.69  Aligned_cols=33  Identities=24%  Similarity=0.347  Sum_probs=28.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -++|.|+.|||||++++=+.+|+..+|+=|.-|
T Consensus         8 vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~li   40 (207)
T d1okkd2           8 VVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFC   40 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            378899999999999999999998888766654

>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=93.47  E-value=0.022  Score=45.16  Aligned_cols=21  Identities=29%  Similarity=0.374  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|.|++|+|||++|..++.
T Consensus         2 KI~liG~~nvGKSSLln~l~~   22 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKN   22 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999998654

>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=93.43  E-value=0.033  Score=46.81  Aligned_cols=31  Identities=26%  Similarity=0.192  Sum_probs=24.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      |+||.|++||||||.-..+.   ..-|+..|.+.
T Consensus         5 riil~G~pGSGKsT~a~~La---~~~g~~~i~~g   35 (190)
T d1ak2a1           5 RAVLLGPPGAGKGTQAPKLA---KNFCVCHLATG   35 (190)
T ss_dssp             EEEEECCTTSSHHHHHHHHH---HHHTCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHH---HHhCCeEEeHH
Confidence            69999999999999776553   34488877764

>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=93.36  E-value=0.028  Score=47.20  Aligned_cols=32  Identities=25%  Similarity=0.165  Sum_probs=25.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      |++|.|++||||||....+..   .-||..|...+
T Consensus         4 rIvl~G~pGSGKtT~a~~La~---~~g~~~i~~~d   35 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQE---RFHAAHLATGD   35 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH---HHCCEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH---HhCCceEeccc
Confidence            699999999999998877754   34888777644

>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=93.34  E-value=0.024  Score=51.20  Aligned_cols=26  Identities=15%  Similarity=0.209  Sum_probs=22.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      ++|.|.+|||||++|.+.+++...++
T Consensus        27 ~lV~g~aGSGKTt~l~~ri~~ll~~~   52 (318)
T d1pjra1          27 LLIMAGAGSGKTRVLTHRIAYLMAEK   52 (318)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTT
T ss_pred             EEEEecCCccHHHHHHHHHHHHHHcC
Confidence            78889999999999999888766543

>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=93.29  E-value=0.031  Score=47.37  Aligned_cols=32  Identities=19%  Similarity=0.201  Sum_probs=24.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      -++|.|++||||||....+   |..-||..|...+
T Consensus        10 iI~l~G~pGSGKsT~a~~L---a~~~g~~~is~g~   41 (194)
T d3adka_          10 IIFVVGGPGSGKGTQCEKI---VQKYGYTHLSTGD   41 (194)
T ss_dssp             EEEEEECTTSSHHHHHHHH---HHHTCCEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHH---HHHhCCeeEeccH
Confidence            3889999999999966544   5567998876643

>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=93.28  E-value=0.021  Score=46.88  Aligned_cols=22  Identities=18%  Similarity=0.271  Sum_probs=19.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -|++|.|.+|||||+++.+++.
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~   37 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSM   37 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4699999999999999998764

>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=93.20  E-value=0.042  Score=48.89  Aligned_cols=32  Identities=25%  Similarity=0.329  Sum_probs=26.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|.|+.|+||||+++=+.++...+|.=|.-|
T Consensus        12 i~lvGptGvGKTTTiAKLA~~~~~~g~kV~li   43 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQFEQQGKSVMLA   43 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            67899999999999999988888777655544

>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=93.14  E-value=0.042  Score=46.10  Aligned_cols=30  Identities=23%  Similarity=0.271  Sum_probs=23.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|++||||||....+..   .-||..|..
T Consensus         3 iI~i~GppGSGKsT~a~~La~---~~g~~~i~~   32 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVE---KYGYTHLSA   32 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH---HHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHH---HhCCceEcH
Confidence            589999999999998776644   338887755

>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=93.13  E-value=0.021  Score=50.86  Aligned_cols=25  Identities=8%  Similarity=-0.000  Sum_probs=21.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      ++|.|.+|||||++|.+.+.|...+
T Consensus        17 ~lI~g~aGTGKTt~l~~rv~~ll~~   41 (306)
T d1uaaa1          17 CLVLAGAGSGKTRVITNKIAHLIRG   41 (306)
T ss_dssp             EEECCCTTSCHHHHHHHHHHHHHHH
T ss_pred             EEEEeeCCccHHHHHHHHHHHHHHh
Confidence            7888999999999999988876543

>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=93.11  E-value=0.041  Score=46.28  Aligned_cols=30  Identities=30%  Similarity=0.458  Sum_probs=22.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .++|.|++||||||+...+.   ..-||+.|..
T Consensus         8 iI~i~G~pGSGKsT~a~~La---~~~g~~~i~~   37 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQCANIV---RDFGWVHLSA   37 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHH---HHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHH---HHHCCceEch
Confidence            48999999999999765553   3448887765

>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=93.10  E-value=0.021  Score=48.10  Aligned_cols=30  Identities=13%  Similarity=0.267  Sum_probs=22.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +++|.|++||||||... .+  |..-||..+.+
T Consensus         5 ~I~i~GppGsGKsT~a~-~L--a~~~~~~~is~   34 (189)
T d1zaka1           5 KVMISGAPASGKGTQCE-LI--KTKYQLAHISA   34 (189)
T ss_dssp             CEEEEESTTSSHHHHHH-HH--HHHHCCEECCH
T ss_pred             EEEEECCCCCCHHHHHH-HH--HHHHCCcEEeh
Confidence            59999999999999553 33  44458876644

>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=93.02  E-value=0.035  Score=53.44  Aligned_cols=42  Identities=26%  Similarity=0.232  Sum_probs=33.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCccccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTHG  233 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvng  233 (404)
                      -++++|+.||||||+|.-++.+.-.++-=|+.|=++-++...
T Consensus       160 liLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~~~~  201 (401)
T d1p9ra_         160 IILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFDID  201 (401)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSCCS
T ss_pred             eEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCcccccC
Confidence            489999999999999999999875544456777777776553

>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=92.97  E-value=0.028  Score=47.04  Aligned_cols=31  Identities=26%  Similarity=0.208  Sum_probs=22.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +++|.|++||||||....+.   ..-|+..+...
T Consensus         2 ~I~i~G~pGSGKsT~a~~La---~~~g~~~is~g   32 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIV---EKYGTPHISTG   32 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHH---HHHCCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHH---HHHCCceeeHH
Confidence            58999999999999654443   33488777653

>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=92.94  E-value=0.029  Score=44.89  Aligned_cols=21  Identities=29%  Similarity=0.249  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|.|.+|||||+++..++.
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~   27 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQV   27 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            599999999999999987653

>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=92.88  E-value=0.036  Score=48.94  Aligned_cols=25  Identities=28%  Similarity=0.203  Sum_probs=20.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEG  218 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ng  218 (404)
                      .+|+|++|+|||++++|+.. +..+|
T Consensus        32 ~~i~G~~G~GKS~l~l~la~-~ia~g   56 (274)
T d1nlfa_          32 GALVSPGGAGKSMLALQLAA-QIAGG   56 (274)
T ss_dssp             EEEEESTTSSHHHHHHHHHH-HHHTC
T ss_pred             EEEEeCCCCCHHHHHHHHHH-HHHcC
Confidence            68999999999999999754 33343

>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=92.78  E-value=0.04  Score=45.93  Aligned_cols=32  Identities=22%  Similarity=0.256  Sum_probs=23.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~  226 (404)
                      +++|.|++||||||.-..+...-   ||..+-+.+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~---g~~~i~~~~   33 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL---GIPQISTGE   33 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH---TCCEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH---CCceEchHH
Confidence            58999999999999655544332   887776533

>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=92.71  E-value=0.031  Score=46.49  Aligned_cols=23  Identities=35%  Similarity=0.570  Sum_probs=20.0

Q ss_pred             ceeEEEECCCCCcHHHHHHHHHH
Q 045329          190 RKQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       190 r~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |.+++|-|..|||||+++.+.+.
T Consensus         2 r~KivvvG~~~vGKTsLi~~~~~   24 (177)
T d1kmqa_           2 RKKLVIVGDGACGKTCLLIVNSK   24 (177)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEEECCCCcCHHHHHHHHHh
Confidence            45799999999999999988764

>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=92.66  E-value=0.069  Score=50.11  Aligned_cols=40  Identities=23%  Similarity=0.146  Sum_probs=30.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEecCcccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVPRGREW  230 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP~a~~w  230 (404)
                      .++=|+|++|+|||+++.+++.+.+..  .--|+.+--....
T Consensus        52 ~~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss~~   93 (323)
T d2qm8a1          52 IRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTR   93 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGGGS
T ss_pred             eEEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccccHH
Confidence            568999999999999999999887765  4455555333333

>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=92.65  E-value=0.054  Score=45.72  Aligned_cols=33  Identities=24%  Similarity=0.231  Sum_probs=27.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      ++|.|.-||||||++..+..+=...|+=|+.+.
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~~   35 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLA   35 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEe
Confidence            789999999999999999988777787555543

>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=92.64  E-value=0.051  Score=45.60  Aligned_cols=34  Identities=21%  Similarity=0.286  Sum_probs=31.3

Q ss_pred             eeEEEECCC-CCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPL-CCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~r-GsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +||+++|-- |+|||++-+.+...-.+.|.=|++|
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEE
Confidence            579999995 9999999999999988999999998

>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=92.63  E-value=0.042  Score=48.82  Aligned_cols=32  Identities=31%  Similarity=0.387  Sum_probs=22.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|.|+.|+|||++++=+.+|...+|+=|.-|
T Consensus        15 i~lvGptGvGKTTTiAKLA~~~~~~g~kV~li   46 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAYFYKKKGFKVGLV   46 (211)
T ss_dssp             EEEECSCCC----HHHHHHHHHHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCceEEE
Confidence            67799999999999999988888887655444

>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=92.53  E-value=0.037  Score=45.38  Aligned_cols=21  Identities=24%  Similarity=0.306  Sum_probs=19.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|++|||||+++.+.+.
T Consensus         4 Kv~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           4 KMVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            599999999999999998775

>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=92.53  E-value=0.051  Score=50.15  Aligned_cols=36  Identities=17%  Similarity=0.193  Sum_probs=26.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG  227 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a  227 (404)
                      ..++|+||+|||||.+.-+ ++-.....++.+..+.-
T Consensus        50 ~~iLl~GPpG~GKT~lAka-lA~~~~~~~~~i~~s~~   85 (309)
T d1ofha_          50 KNILMIGPTGVGKTEIARR-LAKLANAPFIKVEATKF   85 (309)
T ss_dssp             CCEEEECCTTSSHHHHHHH-HHHHHTCCEEEEEGGGG
T ss_pred             ceEEEECCCCCCHHHHHHH-Hhhccccchhccccccc
Confidence            3599999999999987754 55455667777766553

>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=92.35  E-value=0.039  Score=46.34  Aligned_cols=22  Identities=32%  Similarity=0.597  Sum_probs=20.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++|.|.+|+|||+++..++.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~   25 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTT   25 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            5699999999999999999975

>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=92.18  E-value=0.043  Score=45.18  Aligned_cols=21  Identities=19%  Similarity=0.341  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|.|++|||||+++.+++.
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHc
Confidence            599999999999999998764

>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=92.17  E-value=0.088  Score=49.47  Aligned_cols=34  Identities=26%  Similarity=0.231  Sum_probs=28.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCC--eEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEG--WLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ng--WIVL~I  224 (404)
                      .++=|+|++|+|||+++..++.+-+..|  --|+-+
T Consensus        55 ~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlav   90 (327)
T d2p67a1          55 LRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAV   90 (327)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             eEEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecC
Confidence            5699999999999999999998888876  345555

>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=92.07  E-value=0.038  Score=44.68  Aligned_cols=20  Identities=35%  Similarity=0.478  Sum_probs=18.2

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      +++|.|++|+|||+++.++.
T Consensus         3 kI~lvG~~nvGKSsLin~l~   22 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALA   22 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            58999999999999998876

>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=91.81  E-value=0.049  Score=45.45  Aligned_cols=21  Identities=19%  Similarity=0.360  Sum_probs=19.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|-|.+|||||+++.+++.
T Consensus         4 Kv~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           4 KVIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999998765

>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=91.81  E-value=0.043  Score=44.21  Aligned_cols=18  Identities=33%  Similarity=0.429  Sum_probs=14.6

Q ss_pred             EEEECCCCCcHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAML  210 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qa  210 (404)
                      ++|+|.+||||||+-..+
T Consensus         9 I~l~G~~GsGKTTia~~L   26 (183)
T d1m8pa3           9 IFLTGYMNSGKDAIARAL   26 (183)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            669999999999975443

>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=91.79  E-value=0.062  Score=45.80  Aligned_cols=32  Identities=13%  Similarity=0.038  Sum_probs=24.5

Q ss_pred             ceeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          190 RKQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       190 r~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      .-|++|.|++||||||.-..+.   ..-||..|.+
T Consensus         6 ~mrIiliG~PGSGKtT~a~~La---~~~g~~~is~   37 (189)
T d2ak3a1           6 LLRAAIMGAPGSGKGTVSSRIT---KHFELKHLSS   37 (189)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHH---HHBCCEEEEH
T ss_pred             ceeEEEECCCCCCHHHHHHHHH---HHHCCeEEcH
Confidence            3579999999999999866554   3458777655

>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=91.78  E-value=0.045  Score=44.88  Aligned_cols=22  Identities=27%  Similarity=0.306  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+++|-|+.|||||++|.+++.
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            4699999999999999998864

>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=91.77  E-value=0.051  Score=44.96  Aligned_cols=21  Identities=24%  Similarity=0.308  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++-|++|||||+++.+++.
T Consensus         5 KivvvG~~~vGKTsli~r~~~   25 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTD   25 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHhc
Confidence            589999999999999998764

>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=91.76  E-value=0.051  Score=44.73  Aligned_cols=21  Identities=33%  Similarity=0.414  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++-|.+|||||+++.+++.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999999875

>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=91.71  E-value=0.052  Score=44.55  Aligned_cols=21  Identities=29%  Similarity=0.456  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|.|.+|||||+++.+.+.
T Consensus         5 KivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999998763

>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=91.69  E-value=0.05  Score=44.54  Aligned_cols=20  Identities=20%  Similarity=0.375  Sum_probs=18.3

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      |++|.|++|||||+++.+++
T Consensus         4 ki~i~G~~~~GKTsLl~~l~   23 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIA   23 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            68999999999999998875

>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=91.67  E-value=0.053  Score=44.51  Aligned_cols=21  Identities=29%  Similarity=0.321  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|.+|||||+++.+++.
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999999875

>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=91.66  E-value=0.084  Score=47.34  Aligned_cols=38  Identities=21%  Similarity=0.300  Sum_probs=27.6

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHH
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ...|+...+++.        +..  ..+++|.|.+|+|||++++.++-
T Consensus        17 ~l~e~~~~l~~~--------~~~--~l~I~LvG~tg~GKSSliN~ilg   54 (257)
T d1h65a_          17 KLLELLGNLKQE--------DVN--SLTILVMGKGGVGKSSTVNSIIG   54 (257)
T ss_dssp             HHHHHHHHHHHT--------TCC--EEEEEEEESTTSSHHHHHHHHHT
T ss_pred             HHHHHHHHHhhc--------CCC--CcEEEEECCCCCcHHHHHHHHhC
Confidence            345667766653        112  24699999999999999999873

>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=91.64  E-value=0.05  Score=45.21  Aligned_cols=31  Identities=19%  Similarity=0.293  Sum_probs=23.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +++|.|++||||||....+..   .-||..+...
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~---~~~~~~i~~~   32 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIME---KYGIPQISTG   32 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH---HHCCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH---HhCCceechh
Confidence            589999999999998766543   3477766543

>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=91.61  E-value=0.028  Score=53.27  Aligned_cols=42  Identities=21%  Similarity=0.307  Sum_probs=34.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc-ccccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG-REWTH  232 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a-~~wvn  232 (404)
                      -|++|.|.-|+||||++..+..+....|.-|+++|.+ ..|.+
T Consensus         6 lrI~IEG~iGsGKSTl~~~L~~~l~~~g~~v~~~~EP~~~W~~   48 (331)
T d1osna_           6 LRIYLDGAYGIGKTTAAEEFLHHFAITPNRILLIGEPLSYWRN   48 (331)
T ss_dssp             EEEEEEESSSSCTTHHHHHHHHTTTTSGGGEEEECCCHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcCCceEEEeCchHhhhc
Confidence            4699999999999999999999887777777777776 34543

>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=91.60  E-value=0.049  Score=44.36  Aligned_cols=20  Identities=20%  Similarity=0.268  Sum_probs=18.0

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      |++|-|.+|||||+++.++.
T Consensus         4 ki~ivG~~~~GKTsLi~~l~   23 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFN   23 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHc
Confidence            59999999999999998863

>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=91.56  E-value=0.056  Score=44.29  Aligned_cols=21  Identities=29%  Similarity=0.306  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|+.|||||+++.+.+.
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~   25 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998764

>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=91.55  E-value=0.056  Score=44.40  Aligned_cols=21  Identities=33%  Similarity=0.426  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|-|.+|||||+++.+.+.
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~   25 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999998764

>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=91.55  E-value=0.056  Score=43.98  Aligned_cols=21  Identities=19%  Similarity=0.216  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|..|||||+++.+++.
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999999764

>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=91.52  E-value=0.046  Score=45.08  Aligned_cols=21  Identities=24%  Similarity=0.292  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|.+|||||++|.+.+.
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            599999999999999998875

>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=91.50  E-value=0.053  Score=44.49  Aligned_cols=21  Identities=24%  Similarity=0.260  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|..|||||+++.+.+.
T Consensus         4 Ki~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           4 RVAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999988764

>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=91.38  E-value=0.052  Score=44.50  Aligned_cols=21  Identities=29%  Similarity=0.354  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|.|+.|||||+++.+++.
T Consensus         5 Ki~viG~~~vGKTsli~~l~~   25 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999999875

>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=91.37  E-value=0.059  Score=44.43  Aligned_cols=21  Identities=19%  Similarity=0.300  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|++|||||+++.+.+.
T Consensus         4 Ki~lvG~~~vGKTsli~r~~~   24 (168)
T d2atva1           4 KLAIFGRAGVGKSALVVRFLT   24 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999998775

>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=91.34  E-value=0.033  Score=49.23  Aligned_cols=33  Identities=21%  Similarity=0.183  Sum_probs=26.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      +=++|+|--|+||||+|.+++.......|.||-
T Consensus         4 Pv~iitGFLGaGKTTll~~lL~~~~~~riaVI~   36 (222)
T d1nija1           4 AVTLLTGFLGAGKTTLLRHILNEQHGYKIAVIE   36 (222)
T ss_dssp             EEEEEEESSSSSCHHHHHHHHHSCCCCCEEEEC
T ss_pred             CEEEEeeCCCCCHHHHHHHHHhcCCCCcEEEEE
Confidence            348999999999999999998864444676663

>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=91.33  E-value=0.053  Score=44.69  Aligned_cols=21  Identities=29%  Similarity=0.370  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|.+|||||+++.+++.
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            599999999999999998764

>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=91.29  E-value=0.06  Score=44.97  Aligned_cols=22  Identities=27%  Similarity=0.323  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      ++|.|.+||||||+-.++..+=
T Consensus         5 i~l~GlpgsGKSTla~~L~~~l   26 (213)
T d1bifa1           5 IVMVGLPARGKTYISKKLTRYL   26 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7999999999999988876543

>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=91.19  E-value=0.056  Score=44.01  Aligned_cols=21  Identities=19%  Similarity=0.344  Sum_probs=18.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|-|.+|||||++|.+++.
T Consensus         2 Kv~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           2 KLVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998763

>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=91.17  E-value=0.064  Score=44.15  Aligned_cols=21  Identities=24%  Similarity=0.284  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++-|.+|||||+++.+++.
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~   27 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYAD   27 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHc
Confidence            589999999999999988764

>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=91.07  E-value=0.055  Score=51.21  Aligned_cols=40  Identities=33%  Similarity=0.421  Sum_probs=30.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc-cccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG-REWT  231 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a-~~wv  231 (404)
                      -|++|.|.-||||||++..+..+-...+ .|+++|.+ ..|.
T Consensus         7 ~rI~iEG~iGsGKSTl~~~L~~~l~~~~-~v~~~~EPm~yW~   47 (333)
T d1p6xa_           7 VRIYLDGVYGIGKSTTGRVMASAASGGS-PTLYFPEPMAYWR   47 (333)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHSGGGCSS-CEEEECCCHHHHH
T ss_pred             EEEEEECCccCCHHHHHHHHHHHhccCC-CeEEEeCchhhhc
Confidence            4799999999999999998888754443 66678876 3454

>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=91.04  E-value=0.066  Score=44.65  Aligned_cols=21  Identities=24%  Similarity=0.241  Sum_probs=19.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|.+|||||+++.+.+.
T Consensus         7 KivviG~~~vGKTsli~~~~~   27 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTT   27 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            599999999999999999875

>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=90.98  E-value=0.078  Score=42.08  Aligned_cols=31  Identities=26%  Similarity=0.365  Sum_probs=21.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ...+|.++.|+|||+.+.++   +.+.|+-|+++
T Consensus         9 ~~~ll~apTGsGKT~~~~~~---~~~~~~~vli~   39 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAA---YAAQGYKVLVL   39 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHH---HHTTTCCEEEE
T ss_pred             CEEEEEeCCCCCHHHHHHHH---HHHcCCcEEEE
Confidence            45799999999999876443   34455444444

>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=90.94  E-value=0.021  Score=46.38  Aligned_cols=22  Identities=32%  Similarity=0.214  Sum_probs=17.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      .||+|+.|||||++| .|+.||.
T Consensus        27 tvi~G~NGsGKStil-~Ai~~~L   48 (222)
T d1qhla_          27 TTLSGGNGAGKSTTM-AAFVTAL   48 (222)
T ss_dssp             HHHHSCCSHHHHHHH-HHHHHHH
T ss_pred             EEEECCCCCCHHHHH-HHHHHHh
Confidence            488999999999987 4555664

>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=90.94  E-value=0.069  Score=44.08  Aligned_cols=21  Identities=29%  Similarity=0.319  Sum_probs=19.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|.+|||||+++.+++.
T Consensus         8 KI~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            599999999999999999875

>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=90.88  E-value=0.071  Score=44.01  Aligned_cols=28  Identities=29%  Similarity=0.194  Sum_probs=20.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      ++|.|.+|||||++..-+...   -||-.+-
T Consensus         3 I~liG~~GsGKsTi~k~La~~---l~~~~~d   30 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKD---LDLVFLD   30 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH---HTCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHH---hCCCEEe
Confidence            899999999999886554332   2666554

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {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: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=90.87  E-value=0.096  Score=49.23  Aligned_cols=36  Identities=28%  Similarity=0.392  Sum_probs=27.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe-cCc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV-PRG  227 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I-P~a  227 (404)
                      .+++.|..|||||++|.+++..+...|.-|+-| |.+
T Consensus        52 H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~kg   88 (433)
T d1e9ra_          52 HLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNG   88 (433)
T ss_dssp             CEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETT
T ss_pred             eEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCCh
Confidence            489999999999999988888777765544444 443

>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=90.82  E-value=0.063  Score=44.93  Aligned_cols=20  Identities=40%  Similarity=0.629  Sum_probs=17.5

Q ss_pred             EEEECCCCCcHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++|.||.|||||+++..+..
T Consensus         5 ivl~GpsG~GK~tl~~~L~~   24 (182)
T d1znwa1           5 VVLSGPSAVGKSTVVRCLRE   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            89999999999999877654

>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=90.79  E-value=0.074  Score=43.54  Aligned_cols=21  Identities=24%  Similarity=0.379  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|-|.+|+|||+++.+++.
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTE   26 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999998764

>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=90.77  E-value=0.074  Score=44.00  Aligned_cols=22  Identities=23%  Similarity=0.288  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|.|.+|||||+++.+++.
T Consensus         7 ~Kv~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           7 HKLVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            4699999999999999988764

>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=90.67  E-value=0.14  Score=46.17  Aligned_cols=50  Identities=14%  Similarity=0.165  Sum_probs=34.2

Q ss_pred             ceeEEEchh-HHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          157 RYALLVRQS-FLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       157 ~p~~LVRk~-tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      ++.+..|+. ..+|++.|.+..|       . .. .-+.|+|..|+|||++..++...+.
T Consensus        19 ~~~~~gR~~~~~~i~~~L~~~~~-------~-~~-~~v~I~GmgGiGKTtLA~~v~~~~~   69 (277)
T d2a5yb3          19 QMTCYIREYHVDRVIKKLDEMCD-------L-DS-FFLFLHGRAGSGKSVIASQALSKSD   69 (277)
T ss_dssp             CCCSCCCHHHHHHHHHHHHHHTT-------S-SS-EEEEEECSTTSSHHHHHHHHHHHCS
T ss_pred             CCceeCcHHHHHHHHHHHHhccC-------C-Cc-eEEEEECCCCCCHHHHHHHHHHhhh
Confidence            344556884 4467777765422       1 11 2377999999999999999987653

>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=90.56  E-value=0.15  Score=44.67  Aligned_cols=22  Identities=18%  Similarity=0.252  Sum_probs=17.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      .++|+|++|+|||++..-+...
T Consensus        36 ~~Ll~Gp~G~GKtt~a~~~~~~   57 (239)
T d1njfa_          36 AYLFSGTRGVGKTSIARLLAKG   57 (239)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHH
Confidence            3899999999999976544443

>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=90.52  E-value=0.067  Score=44.28  Aligned_cols=28  Identities=25%  Similarity=0.362  Sum_probs=20.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      ++|.|.+||||||+-..+.   ..-||-.+-
T Consensus         5 Iil~G~~GsGKSTia~~LA---~~Lg~~~id   32 (170)
T d1e6ca_           5 IFMVGARGCGMTTVGRELA---RALGYEFVD   32 (170)
T ss_dssp             EEEESCTTSSHHHHHHHHH---HHHTCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHH---HHhCCCEEe
Confidence            8899999999999876554   333676553

>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=90.50  E-value=0.15  Score=48.48  Aligned_cols=31  Identities=29%  Similarity=0.430  Sum_probs=23.8

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      +.++|+||+|||||++...++.++   |+=|+.|
T Consensus       155 ~~~~~~g~~~~gk~~~~~~~~~~~---~~~~i~i  185 (362)
T d1svma_         155 RYWLFKGPIDSGKTTLAAALLELC---GGKALNV  185 (362)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH---CCEEECC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc---CCCEEEE
Confidence            569999999999999876665554   5556665

>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=90.44  E-value=0.083  Score=43.28  Aligned_cols=21  Identities=29%  Similarity=0.325  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|..|||||++|.+.+.
T Consensus         5 KivvvG~~~vGKTsli~r~~~   25 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            489999999999999998764

>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=90.40  E-value=0.083  Score=43.51  Aligned_cols=21  Identities=24%  Similarity=0.303  Sum_probs=15.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ++|+|.+||||||+-..+..+
T Consensus        22 I~L~G~pGSGKTTiAk~La~~   42 (195)
T d1x6va3          22 VWLTGLSGAGKTTVSMALEEY   42 (195)
T ss_dssp             EEEESSCHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            669999999998865544433

>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=90.31  E-value=0.07  Score=43.93  Aligned_cols=21  Identities=24%  Similarity=0.344  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|-|..|||||++|.+++.
T Consensus         7 KI~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            599999999999999998763

>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=90.27  E-value=0.092  Score=42.99  Aligned_cols=22  Identities=32%  Similarity=0.312  Sum_probs=19.2

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++++.|.+|||||+++.+++.
T Consensus        17 ~kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          17 VRILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            5699999999999999987743

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase 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: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.19  E-value=0.15  Score=46.57  Aligned_cols=31  Identities=19%  Similarity=0.374  Sum_probs=26.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      .+|.|..|||||.+-..++..|..+|.=|+.
T Consensus       107 rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~  137 (264)
T d1gm5a3         107 RLLQGDVGSGKTVVAQLAILDNYEAGFQTAF  137 (264)
T ss_dssp             CEEECCSSSSHHHHHHHHHHHHHHHTSCEEE
T ss_pred             eeeeccccccccHHHHHHHHHHHhcccceeE
Confidence            4999999999999999999999887754443

>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=90.19  E-value=0.081  Score=44.71  Aligned_cols=20  Identities=45%  Similarity=0.599  Sum_probs=18.0

Q ss_pred             EEEECCCCCcHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~  212 (404)
                      +||.|+.||||++++.+++.
T Consensus         4 Ivl~GpsG~GK~tl~~~L~~   23 (186)
T d1gkya_           4 IVISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            89999999999999988754

>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=90.12  E-value=0.091  Score=43.32  Aligned_cols=21  Identities=19%  Similarity=0.256  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|.+|||||+++.+.+.
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            599999999999999998764

>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=90.11  E-value=0.085  Score=43.90  Aligned_cols=20  Identities=20%  Similarity=0.190  Sum_probs=18.1

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      |++|-|.+|||||+++.+++
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~   26 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYT   26 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHh
Confidence            58999999999999998775

>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=90.02  E-value=0.13  Score=44.45  Aligned_cols=27  Identities=30%  Similarity=0.350  Sum_probs=21.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLV  221 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIV  221 (404)
                      ..++|.|+.|+|||++.+.++.    .||-+
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~----~g~~l   41 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQ----RGHRL   41 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH----TTCEE
T ss_pred             EEEEEEeCCCCCHHHHHHHHHH----cCCeE
Confidence            4699999999999998876553    56643

>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=89.98  E-value=0.094  Score=43.27  Aligned_cols=21  Identities=24%  Similarity=0.259  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|.+|||||++|.+.+.
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998765

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {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: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=89.96  E-value=0.23  Score=44.55  Aligned_cols=33  Identities=15%  Similarity=0.076  Sum_probs=28.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ..+|.|..|||||.+-..++..|..+|.=|+.+
T Consensus        78 ~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l  110 (233)
T d2eyqa3          78 DRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVL  110 (233)
T ss_dssp             EEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEE
T ss_pred             CeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEE
Confidence            369999999999999999999999987665554

>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=89.92  E-value=0.082  Score=44.64  Aligned_cols=22  Identities=27%  Similarity=0.255  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|-|++|||||+++.+++.
T Consensus         7 ~KivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           7 FKLLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHhh
Confidence            3589999999999999999874

>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=89.92  E-value=0.097  Score=43.26  Aligned_cols=21  Identities=33%  Similarity=0.381  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++-|.+|||||+++.+.+.
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999988765

>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=89.83  E-value=0.092  Score=43.19  Aligned_cols=20  Identities=25%  Similarity=0.306  Sum_probs=17.7

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      +++|-|.+|||||+++.++.
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~   22 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFG   22 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHh
Confidence            48999999999999998765

>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=89.78  E-value=0.055  Score=46.46  Aligned_cols=39  Identities=31%  Similarity=0.649  Sum_probs=29.1

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcccccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWTH  232 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wvn  232 (404)
                      +.++|.|.-||||||++..+..+-  +++-+..+|-. .|..
T Consensus         3 k~I~ieG~dGsGKST~~~~L~~~l--~~~~~~~e~~~-~~~~   41 (241)
T d1p5zb_           3 KKISIEGNIAAGKSTFVNILKQLC--EDWEVVPEPVA-RWCN   41 (241)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGC--TTEEEECCCHH-HHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH--hcCCCeeeeee-ecCC
Confidence            469999999999999998877653  56666666643 4544

>d1e69a_ c.37.1.12 (A:) Smc head 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: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=89.75  E-value=0.051  Score=48.56  Aligned_cols=21  Identities=29%  Similarity=0.539  Sum_probs=18.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      -+|.|+.|||||++| +|+.||
T Consensus        27 nvlvG~NgsGKS~iL-~Ai~~~   47 (308)
T d1e69a_          27 TAIVGPNGSGKSNII-DAIKWV   47 (308)
T ss_dssp             EEEECCTTTCSTHHH-HHHHHT
T ss_pred             EEEECCCCCcHHHHH-HHHHHH
Confidence            599999999999976 888886

>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=89.66  E-value=0.096  Score=43.33  Aligned_cols=20  Identities=30%  Similarity=0.400  Sum_probs=17.8

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      +++|.|.+|||||+++.+..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~   24 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFA   24 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHH
Confidence            48999999999999998764

>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=89.65  E-value=0.11  Score=45.06  Aligned_cols=27  Identities=26%  Similarity=0.289  Sum_probs=21.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLV  221 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIV  221 (404)
                      ..++|.|+.|+|||++.+.++.    +||-+
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~----~G~~l   42 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLIN----KNHLF   42 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHT----TTCEE
T ss_pred             EEEEEEcCCCCCHHHHHHHHHH----cCCce
Confidence            4699999999999999988764    45543

>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=89.58  E-value=0.059  Score=45.17  Aligned_cols=32  Identities=19%  Similarity=0.433  Sum_probs=24.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      -++|.|.-||||||++..+..+  .+++.++..|
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~--l~~~~~~~ep   42 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKY--KNDICLLTEP   42 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGG--TTTEEEECCT
T ss_pred             EEEEECCCCCCHHHHHHHHHHH--hCCcEEEEEe
Confidence            4899999999999988776543  2566666665

>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=89.49  E-value=0.098  Score=43.72  Aligned_cols=22  Identities=32%  Similarity=0.525  Sum_probs=19.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|-|..|||||.++.+.+.
T Consensus         3 ~KivliG~~~vGKTsli~r~~~   24 (179)
T d1m7ba_           3 CKIVVVGDSQCGKTALLHVFAK   24 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            4689999999999999988765

>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=89.48  E-value=0.11  Score=43.02  Aligned_cols=21  Identities=29%  Similarity=0.330  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      |++|.|.+|||||+++.+++.
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            599999999999999988764

>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=89.47  E-value=0.1  Score=44.17  Aligned_cols=21  Identities=19%  Similarity=0.354  Sum_probs=18.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++|.|++|||||++|.+++.
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~   22 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLT   22 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            389999999999999998764

>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=89.41  E-value=0.088  Score=44.14  Aligned_cols=22  Identities=32%  Similarity=0.427  Sum_probs=19.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++|.|.+|+|||+++..+..
T Consensus        24 ~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          24 PEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHhcC
Confidence            5799999999999999998863

>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=89.40  E-value=0.24  Score=44.16  Aligned_cols=50  Identities=22%  Similarity=0.412  Sum_probs=31.6

Q ss_pred             hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHH---hCCeEEEEec
Q 045329          165 SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAR---EEGWLVLYVP  225 (404)
Q Consensus       165 ~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~---~ngWIVL~IP  225 (404)
                      ...++++.+++...     ++.     -++|+|++||||+. ++.++|...   ....+++...
T Consensus         8 ~~~~~~~~~~~~a~-----~~~-----pvlI~Ge~GtGK~~-~A~~ih~~s~~~~~~~~~~~~~   60 (247)
T d1ny5a2           8 KMKEILEKIKKISC-----AEC-----PVLITGESGVGKEV-VARLIHKLSDRSKEPFVALNVA   60 (247)
T ss_dssp             HHHHHHHHHHHHTT-----CCS-----CEEEECSTTSSHHH-HHHHHHHHSTTTTSCEEEEETT
T ss_pred             HHHHHHHHHHHHhC-----CCC-----CEEEECCCCcCHHH-HHHHHHHhcCCcccccccchhh
Confidence            45667777776532     112     28999999999985 666666543   2345555543

>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=89.37  E-value=0.12  Score=44.09  Aligned_cols=28  Identities=25%  Similarity=0.318  Sum_probs=25.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGW  219 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngW  219 (404)
                      -+++.|..||||||....+..+-...|.
T Consensus         4 fIviEG~dGsGKsT~~~~L~~~L~~~g~   31 (210)
T d4tmka_           4 YIVIEGLEGAGKTTARNVVVETLEQLGI   31 (210)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCC
Confidence            3788999999999999999999888885

>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=89.36  E-value=0.08  Score=49.58  Aligned_cols=39  Identities=10%  Similarity=0.220  Sum_probs=28.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCccccc
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGREWT  231 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~~wv  231 (404)
                      .+++.|+.|||||++|..++.+. ..++-|+.|=+..++.
T Consensus       168 nili~G~tgSGKTT~l~al~~~i-~~~~rivtiEd~~El~  206 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEFI-PKEERIISIEDTEEIV  206 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGS-CTTCCEEEEESSCCCC
T ss_pred             CEEEEeeccccchHHHHHHhhhc-ccccceeeccchhhhh
Confidence            38999999999999998776654 3456666775655553

>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=89.35  E-value=0.097  Score=43.97  Aligned_cols=21  Identities=24%  Similarity=0.241  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|++|||||+++.+.+.
T Consensus         5 KvvllG~~~vGKTSli~r~~~   25 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTT   25 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998775

>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=89.27  E-value=0.11  Score=44.11  Aligned_cols=21  Identities=43%  Similarity=0.555  Sum_probs=18.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~  213 (404)
                      +||.||.||||+++..+++..
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~~   23 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQE   23 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            899999999999998887765

>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=89.24  E-value=0.099  Score=43.76  Aligned_cols=22  Identities=23%  Similarity=0.225  Sum_probs=19.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++|-|..|||||+++.+.+.
T Consensus        10 ~Ki~lvG~~~vGKTsLi~r~~~   31 (185)
T d2atxa1          10 LKCVVVGDGAVGKTCLLMSYAN   31 (185)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhh
Confidence            3599999999999999988764

>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=89.20  E-value=0.1  Score=42.50  Aligned_cols=21  Identities=38%  Similarity=0.431  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++-|.+|||||+++.+++.
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~   24 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVE   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999988753

>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=89.17  E-value=0.12  Score=42.38  Aligned_cols=21  Identities=24%  Similarity=0.336  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|++|||||+++.+.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999998764

>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=89.12  E-value=0.11  Score=42.67  Aligned_cols=20  Identities=30%  Similarity=0.414  Sum_probs=18.2

Q ss_pred             EEEECCCCCcHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++|.|++|+|||+++.++..
T Consensus         3 V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           3 VLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999998863

>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=88.81  E-value=0.092  Score=49.60  Aligned_cols=39  Identities=31%  Similarity=0.648  Sum_probs=26.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCc-cccc
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRG-REWT  231 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a-~~wv  231 (404)
                      .|++|.|.-||||||++..+..+...++  |+++|.+ ..|.
T Consensus         5 lrI~IEG~iGsGKTTl~~~La~~l~~~~--v~~~~EP~~~W~   44 (329)
T d1e2ka_           5 LRVYIDGPHGMGKTTTTQLLVALGSRDD--IVYVPEPMTYWR   44 (329)
T ss_dssp             EEEEECSCTTSSHHHHHHHHTC----CC--EEEECCCHHHHH
T ss_pred             eEEEEECCcCCCHHHHHHHHHHHhCCCC--eEEeccchhhcc
Confidence            4699999999999999988877665444  5666665 3453

>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=88.70  E-value=0.14  Score=48.42  Aligned_cols=25  Identities=28%  Similarity=0.264  Sum_probs=20.5

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      +-.+|+|++|||||+++..++....
T Consensus       164 ~~~vI~G~pGTGKTt~i~~~l~~l~  188 (359)
T d1w36d1         164 RISVISGGPGTGKTTTVAKLLAALI  188 (359)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHHHH
T ss_pred             CeEEEEcCCCCCceehHHHHHHHHH
Confidence            3489999999999999988765443

>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=88.68  E-value=0.066  Score=44.15  Aligned_cols=21  Identities=29%  Similarity=0.300  Sum_probs=18.6

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      -+++|.|.+|||||+++.+++
T Consensus        13 ~kIvlvG~~~vGKTSli~rl~   33 (173)
T d1e0sa_          13 MRILMLGLDAAGKTTILYKLK   33 (173)
T ss_dssp             EEEEEEEETTSSHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHh
Confidence            359999999999999998864

>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=88.63  E-value=0.12  Score=42.88  Aligned_cols=19  Identities=37%  Similarity=0.378  Sum_probs=17.8

Q ss_pred             eEEEECCCCCcHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qa  210 (404)
                      +++|-|..|||||++|.+.
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5899999999999999987

>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=88.50  E-value=0.12  Score=43.38  Aligned_cols=20  Identities=30%  Similarity=0.488  Sum_probs=15.9

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      =++|+|++||||||.-..++
T Consensus         5 iI~I~GppGSGKgT~ak~La   24 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMA   24 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            37899999999999765443

>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=88.47  E-value=0.13  Score=43.63  Aligned_cols=27  Identities=33%  Similarity=0.632  Sum_probs=19.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      +.|+|++||||||.-..+..   .-||.-|
T Consensus         6 IaIdGp~GsGKgT~ak~La~---~lg~~~i   32 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAK---DFGFTYL   32 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHH---HHCCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHH---HhCCcEE
Confidence            67899999999997655544   2255533

>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=88.26  E-value=0.18  Score=43.28  Aligned_cols=27  Identities=26%  Similarity=0.357  Sum_probs=21.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      +-|+|..|||||++...+    .+.|+-|+.
T Consensus         6 IgitG~igSGKStv~~~l----~~~G~~vid   32 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAF----ADLGINVID   32 (208)
T ss_dssp             EEEECCTTSCHHHHHHHH----HHTTCEEEE
T ss_pred             EEEECCCcCCHHHHHHHH----HHCCCcEEE
Confidence            347999999999987643    467988875

>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=88.23  E-value=0.14  Score=43.32  Aligned_cols=21  Identities=24%  Similarity=0.308  Sum_probs=18.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+||.||.|+||++++.+++.
T Consensus         5 ~ivl~Gpsg~GK~tl~~~L~~   25 (178)
T d1kgda_           5 TLVLLGAHGVGRRHIKNTLIT   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHH
Confidence            389999999999999987764

>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=88.18  E-value=0.14  Score=41.89  Aligned_cols=22  Identities=23%  Similarity=0.214  Sum_probs=19.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ++||-|..|||||++|.|...-
T Consensus         4 KivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            5899999999999999997653

>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=88.11  E-value=0.12  Score=46.35  Aligned_cols=20  Identities=30%  Similarity=0.434  Sum_probs=16.6

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      -+.|.|+.||||||+|.-+.
T Consensus        33 ~~~iiG~sGsGKSTLl~~i~   52 (230)
T d1l2ta_          33 FVSIMGPSGSGKSTMLNIIG   52 (230)
T ss_dssp             EEEEECSTTSSHHHHHHHHT
T ss_pred             EEEEECCCCCCcchhhHhcc
Confidence            38999999999999886443

>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=88.04  E-value=0.085  Score=43.55  Aligned_cols=21  Identities=24%  Similarity=0.314  Sum_probs=9.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|-|.+|||||++|.+++.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEEECCCCC-----------
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999988764

>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=87.92  E-value=0.15  Score=43.96  Aligned_cols=33  Identities=24%  Similarity=0.504  Sum_probs=25.3

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +.+++.|.-||||||++.++..+-  +...+.+.|
T Consensus         3 k~IviEG~~GsGKST~~~~L~~~l--~~~~i~~ep   35 (241)
T d2ocpa1           3 RRLSIEGNIAVGKSTFVKLLTKTY--PEWHVATEP   35 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHC--TTSEEECCC
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHH--hhcCCcccc
Confidence            359999999999999998888764  344455544

>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=87.76  E-value=0.25  Score=43.19  Aligned_cols=21  Identities=29%  Similarity=0.272  Sum_probs=17.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .++|.|++|+|||.+...+..
T Consensus        45 n~lLvG~pGVGKTalv~~LA~   65 (195)
T d1jbka_          45 NPVLIGEPGVGKTAIVEGLAQ   65 (195)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEecCCcccHHHHHHHHH
Confidence            489999999999998855544

>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=87.74  E-value=0.16  Score=42.44  Aligned_cols=21  Identities=19%  Similarity=0.226  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      ++++-|..|||||+++.+.+.
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~   27 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLT   27 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            599999999999999998764

>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=87.61  E-value=0.28  Score=42.23  Aligned_cols=23  Identities=9%  Similarity=0.190  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .++|+|++|+|||++...+..+-
T Consensus        26 ~lLl~Gp~G~GKtt~a~~~a~~l   48 (207)
T d1a5ta2          26 ALLIQALPGMGDDALIYALSRYL   48 (207)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHhc
Confidence            39999999999999776665543

>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=87.59  E-value=0.22  Score=44.56  Aligned_cols=32  Identities=16%  Similarity=-0.014  Sum_probs=24.4

Q ss_pred             CCCCCHHHHHHhhcccccchHHHHHHHHHHHhc
Q 045329          297 SEGSTLFDLVQMGINQMHASVGVVVRLRKELSL  329 (404)
Q Consensus       297 p~g~tL~DLv~~Gi~~~~~A~~v~~aLl~EL~~  329 (404)
                      +.|.-+.+-++.|.=...+ .+-+..+++||..
T Consensus       192 EpgCaVk~av~~g~i~~~R-y~~Y~~l~~el~~  223 (225)
T d1u0la2         192 EPECGVKEAVENGEIAESR-YENYVKMFYELLG  223 (225)
T ss_dssp             CSSCHHHHHHHHTSSCHHH-HHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHcCCCCHHH-HHHHHHHHHHHHh
Confidence            4578899999988655444 6778899999975

>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=87.51  E-value=0.098  Score=43.33  Aligned_cols=20  Identities=30%  Similarity=0.285  Sum_probs=18.0

Q ss_pred             eeEEEECCCCCcHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qa  210 (404)
                      -+++|.|.+|||||+++.++
T Consensus        18 ~KI~lvG~~~vGKTsLi~~l   37 (182)
T d1moza_          18 LRILILGLDGAGKTTILYRL   37 (182)
T ss_dssp             EEEEEEEETTSSHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            46999999999999999875

>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=87.36  E-value=0.34  Score=44.17  Aligned_cols=23  Identities=22%  Similarity=0.134  Sum_probs=19.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA  214 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A  214 (404)
                      .++|.|++|+|||.++..++..-
T Consensus        41 n~lLVG~~GvGKTalv~~la~ri   63 (268)
T d1r6bx2          41 NPLLVGESGVGKTAIAEGLAWRI   63 (268)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEECCCCCcHHHHHHHHHHHH
Confidence            48999999999999987766543

>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=87.35  E-value=0.15  Score=46.11  Aligned_cols=30  Identities=33%  Similarity=0.502  Sum_probs=21.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      +.|.|+.||||||+|..+.-.-. .+|-|.+
T Consensus        27 ~~liGpnGaGKSTll~~i~Gl~~p~~G~I~~   57 (240)
T d2onka1          27 CVLLGPTGAGKSVFLELIAGIVKPDRGEVRL   57 (240)
T ss_dssp             EEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEECCCCChHHHHHHHHHcCCCCCceEEEE
Confidence            67889999999999987765432 2344433

>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=87.32  E-value=0.078  Score=43.82  Aligned_cols=21  Identities=24%  Similarity=0.249  Sum_probs=18.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      +++|.|..|||||++|.+.+.
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~   25 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLT   25 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC-
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999988754

>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=87.26  E-value=0.17  Score=44.02  Aligned_cols=21  Identities=24%  Similarity=0.365  Sum_probs=18.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~  213 (404)
                      +||.||.|||||++...++.-
T Consensus         5 ivi~GPSG~GK~tl~~~L~~~   25 (205)
T d1s96a_           5 YIVSAPSGAGKSSLIQALLKT   25 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHhh
Confidence            899999999999999887764

>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=87.22  E-value=0.087  Score=42.80  Aligned_cols=21  Identities=29%  Similarity=0.377  Sum_probs=18.6

Q ss_pred             ceeEEEECCCCCcHHHHHHHH
Q 045329          190 RKQIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       190 r~r~vL~G~rGsGKS~~L~qa  210 (404)
                      ..+++|.|.+++|||+++..+
T Consensus        16 ~~~I~lvG~~NvGKSSL~n~L   36 (188)
T d1puia_          16 GIEVAFAGRSNAGKSSALNTL   36 (188)
T ss_dssp             SEEEEEEECTTSSHHHHHTTT
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            367999999999999999766

>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=87.06  E-value=0.25  Score=42.69  Aligned_cols=35  Identities=20%  Similarity=0.261  Sum_probs=27.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEecCcc
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVPRGR  228 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP~a~  228 (404)
                      +++.|.-||||||....+..+ .+.+..++.+|...
T Consensus         6 I~iEG~DGsGKST~~~~L~~~-L~~~~~~~~~p~~~   40 (214)
T d1tmka_           6 ILIEGLDRTGKTTQCNILYKK-LQPNCKLLKFPERS   40 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH-TTTSEEEEESSCTT
T ss_pred             EEEECCCCCcHHHHHHHHHHH-HHhCCEEEEECCCC
Confidence            899999999999998777655 34567788888643

>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=87.02  E-value=0.26  Score=42.59  Aligned_cols=32  Identities=31%  Similarity=0.252  Sum_probs=26.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++|.|..||||||....+..+-...|.=|+.+
T Consensus         6 I~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~   37 (209)
T d1nn5a_           6 IVLEGVDRAGKSTQSRKLVEALCAAGHRAELL   37 (209)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            67779999999999999999877777755544

>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=86.98  E-value=0.16  Score=44.20  Aligned_cols=31  Identities=19%  Similarity=0.388  Sum_probs=24.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-+-. ..|-|.+
T Consensus        29 i~~l~G~NGsGKSTLl~~i~gl~~p~~G~I~~   60 (200)
T d1sgwa_          29 VVNFHGPNGIGKTTLLKTISTYLKPLKGEIIY   60 (200)
T ss_dssp             CEEEECCTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCChHHHHHHHHhcccccCCCEEEE
Confidence            488999999999999988765433 5577765

>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=86.97  E-value=0.27  Score=43.50  Aligned_cols=46  Identities=24%  Similarity=0.465  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHHHHHhCCeE
Q 045329          166 FLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVHWAREEGWL  220 (404)
Q Consensus       166 tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~~A~~ngWI  220 (404)
                      .++.+..|+..+..      .|+ ++-++|+|+++||||+....+++..  .|-+
T Consensus        36 ~~~Fl~~l~~~l~~------~PK-kn~i~~~GP~~TGKS~f~~sl~~~l--~G~v   81 (205)
T d1tuea_          36 FITFLGALKSFLKG------TPK-KNCLVFCGPANTGKSYFGMSFIHFI--QGAV   81 (205)
T ss_dssp             HHHHHHHHHHHHHT------CTT-CSEEEEESCGGGCHHHHHHHHHHHH--TCEE
T ss_pred             HHHHHHHHHHHHcC------CCC-ceEEEEECCCCccHHHHHHHHHHHh--CCEE
Confidence            45555556554421      333 3569999999999999987777774  4644

>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=86.94  E-value=0.16  Score=45.54  Aligned_cols=31  Identities=35%  Similarity=0.530  Sum_probs=21.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      -+.|-|+.||||||+|..+.-.- -..|=|.+
T Consensus        28 i~~liGpsGsGKSTLl~~i~Gl~~p~sG~I~i   59 (232)
T d2awna2          28 FVVFVGPSGCGKSTLLRMIAGLETITSGDLFI   59 (232)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCChHHHHHHHHhcCCCCCCCEEEE
Confidence            38899999999999987664432 13455544

>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=86.93  E-value=0.16  Score=45.78  Aligned_cols=31  Identities=39%  Similarity=0.640  Sum_probs=22.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      -+.|.|+.||||||+|..+.-.-. .+|-|.+
T Consensus        34 ~~~liGpsGaGKSTLl~~i~Gl~~p~sG~I~i   65 (239)
T d1v43a3          34 FLVLLGPSGCGKTTTLRMIAGLEEPTEGRIYF   65 (239)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCChHHHHHHHHHcCCCCCCCEEEE
Confidence            389999999999999987765432 3455444

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {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: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=86.77  E-value=0.22  Score=41.57  Aligned_cols=34  Identities=18%  Similarity=0.303  Sum_probs=21.6

Q ss_pred             EEEECCCCCcHHHHHHHHHH-HHHhCC-eEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVH-WAREEG-WLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~-~A~~ng-WIVL~IP~  226 (404)
                      .++.++.|+|||++..-++. ++..++ .+|+-+|.
T Consensus        26 ~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~   61 (200)
T d1wp9a1          26 CLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPT   61 (200)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSS
T ss_pred             eEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCc
Confidence            68889999999986554443 334443 34444454

>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=86.66  E-value=0.29  Score=42.94  Aligned_cols=33  Identities=24%  Similarity=0.232  Sum_probs=27.5

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEEec
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLYVP  225 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~IP  225 (404)
                      +++.|+=|+||||+-+++..+..+.|.=|+.|.
T Consensus        23 ii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD   55 (279)
T d1ihua2          23 IMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTT   55 (279)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            677899999999999998776667788788773

>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=86.57  E-value=0.17  Score=41.39  Aligned_cols=19  Identities=32%  Similarity=0.415  Sum_probs=17.4

Q ss_pred             EEEECCCCCcHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav  211 (404)
                      ++|.|.+|+|||++++.+.
T Consensus         3 I~lvG~~nvGKSsLin~l~   21 (184)
T d2cxxa1           3 IIFAGRSNVGKSTLIYRLT   21 (184)
T ss_dssp             EEEEEBTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            8999999999999998875

>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=85.87  E-value=0.17  Score=45.68  Aligned_cols=21  Identities=19%  Similarity=0.074  Sum_probs=17.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+.|.|+.||||||+|..+.-
T Consensus        33 ~~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          33 IYGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             EEEEEESTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            479999999999999876644

>d2akab1 c.37.1.8 (B:6-304) Dynamin G 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: G proteins
domain: Dynamin G domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=85.72  E-value=0.5  Score=42.09  Aligned_cols=45  Identities=22%  Similarity=0.208  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHH
Q 045329          166 FLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       166 tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -+++++.|+..+..-..  +..-..+++++.|+.++|||++|.-++-
T Consensus         4 ~~~~~~~l~d~l~~lg~--~~~~~~P~ivvvG~~SsGKSsliNaLlg   48 (299)
T d2akab1           4 LIPLVNRLQDAFSAIGQ--NADLDLPQIAVVGGQSAGKSSVLENFVG   48 (299)
T ss_dssp             HHHHHHHHHHHHTTSCC--CTTCCCCEEEEEEBTTSCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCC--CCCCCCCeEEEEcCCCCCHHHHHHHHhC
Confidence            35677777543322111  1112236799999999999999998864

>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=85.59  E-value=0.23  Score=42.45  Aligned_cols=26  Identities=27%  Similarity=0.320  Sum_probs=20.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhCCeE
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREEGWL  220 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~ngWI  220 (404)
                      ..++|.|++|+|||++.+.++.    +||-
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~----~g~~   41 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIK----RGHR   41 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH----TTCE
T ss_pred             EEEEEEeCCCCCHHHHHHHHHH----cCCe
Confidence            4699999999999998766553    4664

>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=85.47  E-value=0.17  Score=46.94  Aligned_cols=27  Identities=15%  Similarity=0.192  Sum_probs=23.9

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHhC
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWAREE  217 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~n  217 (404)
                      .|..|-|++|+|||+++.+++.++..+
T Consensus        44 Qr~~I~g~~g~GKT~l~~~i~~~~~~~   70 (289)
T d1xpua3          44 QRGLIVAPPKAGKTMLLQNIAQSIAYN   70 (289)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHHHHH
T ss_pred             CeeeEeCCCCCCHHHHHHHHHHHHhhc
Confidence            368999999999999999999987654

>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=85.34  E-value=0.22  Score=40.85  Aligned_cols=22  Identities=23%  Similarity=0.197  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~  213 (404)
                      ++||-|..|||||++|.+..--
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999987443

>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=85.26  E-value=0.33  Score=41.75  Aligned_cols=30  Identities=20%  Similarity=0.216  Sum_probs=22.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      -+-|+|..||||||+...+..   ..|+.|+..
T Consensus         3 iIgiTG~igSGKsTva~~l~e---~~g~~~i~~   32 (241)
T d1deka_           3 LIFLSGVKRSGKDTTADFIMS---NYSAVKYQL   32 (241)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH---HSCEEECCT
T ss_pred             EEEEECCCCCCHHHHHHHHHH---hCCCeEEcc
Confidence            378999999999998877633   347776653

>d1w1wa_ c.37.1.12 (A:) Smc head 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: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.12  E-value=0.23  Score=45.55  Aligned_cols=22  Identities=23%  Similarity=0.320  Sum_probs=17.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAR  215 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~  215 (404)
                      -+|+|+.|||||++|- |++||.
T Consensus        28 ~~i~G~NGsGKS~ile-Ai~~~l   49 (427)
T d1w1wa_          28 TSIIGPNGSGKSNMMD-AISFVL   49 (427)
T ss_dssp             EEEECSTTSSHHHHHH-HHHHHT
T ss_pred             EEEECCCCCCHHHHHH-HHHHHh
Confidence            4899999999999885 556764

>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=85.09  E-value=0.23  Score=44.77  Aligned_cols=21  Identities=38%  Similarity=0.438  Sum_probs=18.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+.|.|+.||||||+|.-+.-
T Consensus        42 ~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          42 VTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             EEEEECSTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCcHHHHHHHHhc
Confidence            489999999999999976654

>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=85.04  E-value=0.26  Score=40.42  Aligned_cols=21  Identities=19%  Similarity=0.316  Sum_probs=18.4

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      -|+.|.|..|+|||+++.-++
T Consensus         9 ~kV~iiG~~~~GKSTLin~l~   29 (186)
T d1mkya2           9 IKVAIVGRPNVGKSTLFNAIL   29 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH
Confidence            469999999999999997764

>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=84.86  E-value=0.2  Score=45.41  Aligned_cols=20  Identities=20%  Similarity=0.282  Sum_probs=17.2

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+.|.|+.||||||+|.-+.
T Consensus        46 ~vaivG~sGsGKSTLl~ll~   65 (255)
T d2hyda1          46 TVAFVGMSGGGKSTLINLIP   65 (255)
T ss_dssp             EEEEECSTTSSHHHHHTTTT
T ss_pred             EEEEECCCCCcHHHHHHHHH
Confidence            58999999999999986544

>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=84.77  E-value=0.32  Score=44.68  Aligned_cols=34  Identities=21%  Similarity=0.296  Sum_probs=27.0

Q ss_pred             eeEEEECCCCCcHHHHHHHHHHHHHh-CCeEEEEe
Q 045329          191 KQIVLDGPLCCGKSITLAMLVHWARE-EGWLVLYV  224 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav~~A~~-ngWIVL~I  224 (404)
                      .|..|.|.+|+|||+++.+++..+.+ +.=+++|+
T Consensus        69 Qr~~If~~~g~GKt~l~~~i~~~~~~~~~~v~V~~  103 (276)
T d2jdid3          69 GKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFA  103 (276)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHTTTCSSEEEEE
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHHHHhhCCCeEEEE
Confidence            36899999999999999999987543 44466665

>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=84.76  E-value=0.24  Score=44.56  Aligned_cols=20  Identities=45%  Similarity=0.806  Sum_probs=17.0

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      .+.|.|+.||||||+|.-+.
T Consensus        31 ~~~liG~sGaGKSTll~~i~   50 (240)
T d1g2912          31 FMILLGPSGCGKTTTLRMIA   50 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHh
Confidence            48999999999999887554

>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=84.72  E-value=0.2  Score=44.81  Aligned_cols=31  Identities=26%  Similarity=0.554  Sum_probs=22.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHH-HhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWA-REEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A-~~ngWIVL  222 (404)
                      -+.|-|+.||||||+|..+.-.- -.+|=|.+
T Consensus        28 ~~~liGpsGaGKSTll~~l~Gl~~p~sG~I~~   59 (229)
T d3d31a2          28 YFVILGPTGAGKTLFLELIAGFHVPDSGRILL   59 (229)
T ss_dssp             EEEEECCCTHHHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHhcCcCCCCCEEEE
Confidence            38999999999999998776542 23455554

>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=84.62  E-value=0.22  Score=44.69  Aligned_cols=31  Identities=23%  Similarity=0.299  Sum_probs=23.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||+|.-+.-+-. ..|-|.+
T Consensus        31 ~vaIvG~sGsGKSTLl~ll~gl~~p~~G~I~i   62 (241)
T d2pmka1          31 VIGIVGRSGSGKSTLTKLIQRFYIPENGQVLI   62 (241)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCSEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHhcCCCCCCEEEE
Confidence            489999999999999877766432 3455544

>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=84.52  E-value=0.2  Score=45.29  Aligned_cols=31  Identities=23%  Similarity=0.469  Sum_probs=22.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||++.-+.-+-. .+|-|.+
T Consensus        43 ~iaivG~sGsGKSTLl~ll~gl~~p~~G~I~i   74 (253)
T d3b60a1          43 TVALVGRSGSGKSTIASLITRFYDIDEGHILM   74 (253)
T ss_dssp             EEEEEECTTSSHHHHHHHHTTTTCCSEEEEEE
T ss_pred             EEEEECCCCChHHHHHHHHhcccCCCccEEEE
Confidence            489999999999999877664332 3455443

>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=84.44  E-value=0.3  Score=40.55  Aligned_cols=27  Identities=41%  Similarity=0.533  Sum_probs=19.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      +-|+|..|||||++...+    .+.|+-|+.
T Consensus         6 IgitG~~gSGKstva~~l----~~~g~~~~~   32 (191)
T d1uf9a_           6 IGITGNIGSGKSTVAALL----RSWGYPVLD   32 (191)
T ss_dssp             EEEEECTTSCHHHHHHHH----HHTTCCEEE
T ss_pred             EEEECCCCCCHHHHHHHH----HHCCCeEEE
Confidence            458999999999986544    355776654

>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=84.42  E-value=0.31  Score=41.56  Aligned_cols=27  Identities=19%  Similarity=0.314  Sum_probs=20.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVLY  223 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~  223 (404)
                      +-|||..|||||+++..+    .+.|+-|+.
T Consensus         5 IgITG~igSGKStv~~~l----~~~G~~vid   31 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLF----TDLGVPLVD   31 (205)
T ss_dssp             EEEECSTTSCHHHHHHHH----HTTTCCEEE
T ss_pred             EEEECCCCCCHHHHHHHH----HHCCCeEEE
Confidence            447999999999976433    456877764

>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=84.10  E-value=0.43  Score=43.92  Aligned_cols=66  Identities=23%  Similarity=0.200  Sum_probs=37.6

Q ss_pred             EECCCCCcHHHHHHHHHHHHHh-----CCeEEEEecCcccccccC----------ee-e-cCCCCCCccCHHHHHHHHHH
Q 045329          195 LDGPLCCGKSITLAMLVHWARE-----EGWLVLYVPRGREWTHGG----------YF-Y-KNPQTGLWDTPLQAENVLKD  257 (404)
Q Consensus       195 L~G~rGsGKS~~L~qav~~A~~-----ngWIVL~IP~a~~wvng~----------~~-y-~~~~~g~ydQP~~A~~~Lk~  257 (404)
                      |.|..||||||+...++.+-.+     ..-+||.+-+-+ +++..          +. + .+-.+|.+|.++ +.+.|+.
T Consensus        32 i~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY-~t~~~r~~L~~~~~~~pl~~~RG~PgThD~~l-l~~~l~~  109 (286)
T d1odfa_          32 FSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFY-LTHEDQLKLNEQFKNNKLLQGRGLPGTHDMKL-LQEVLNT  109 (286)
T ss_dssp             EECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGB-CCHHHHHHHHHHTTTCGGGSSSCSTTSBCHHH-HHHHHHH
T ss_pred             eECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCC-CCHHHHHHHhhhccccccceecCCCcchhHHH-HHHHHHH
Confidence            7899999999988887766433     233455554432 22110          10 0 112489999854 4556666


Q ss_pred             HHHHh
Q 045329          258 FIKYN  262 (404)
Q Consensus       258 fl~~N  262 (404)
                      +++.+
T Consensus       110 l~~~~  114 (286)
T d1odfa_         110 IFNNN  114 (286)
T ss_dssp             HTC--
T ss_pred             HHhhc
Confidence            65544

>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=84.10  E-value=0.25  Score=45.26  Aligned_cols=21  Identities=19%  Similarity=0.414  Sum_probs=18.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~  212 (404)
                      .+.|.|+.||||||+|.-+.-
T Consensus        64 ~vaivG~nGsGKSTLl~~i~G   84 (281)
T d1r0wa_          64 MLAITGSTGSGKTSLLMLILG   84 (281)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCChHHHHHHHHhC
Confidence            488999999999999877654

>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=83.81  E-value=0.3  Score=39.61  Aligned_cols=19  Identities=37%  Similarity=0.419  Sum_probs=17.7

Q ss_pred             EEEECCCCCcHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav  211 (404)
                      ++|.|.+|+|||+++..+.
T Consensus         8 I~iiG~~nvGKSSLin~L~   26 (179)
T d1egaa1           8 IAIVGRPNVGKSTLLNKLL   26 (179)
T ss_dssp             EEEECSSSSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            7899999999999999886

>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=83.70  E-value=0.19  Score=45.41  Aligned_cols=31  Identities=19%  Similarity=0.314  Sum_probs=24.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH-HHhCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHW-AREEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~-A~~ngWIVL  222 (404)
                      .+.|.|+.||||||+|..+.-. .-..|-|.+
T Consensus        33 ~~~iiG~sGsGKSTll~~i~gl~~p~~G~I~~   64 (242)
T d1oxxk2          33 RFGILGPSGAGKTTFMRIIAGLDVPSTGELYF   64 (242)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTSSCCSEEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHcCcCCCCceEEE
Confidence            4899999999999999887764 234566554

>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=83.68  E-value=0.13  Score=47.12  Aligned_cols=20  Identities=25%  Similarity=0.318  Sum_probs=16.8

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      .++|.|++|||||+++--+.
T Consensus        30 ~vLl~G~pG~GKT~lar~~~   49 (333)
T d1g8pa_          30 GVLVFGDRGTGKSTAVRALA   49 (333)
T ss_dssp             CEEEECCGGGCTTHHHHHHH
T ss_pred             eEEEECCCCccHHHHHHHHH
Confidence            49999999999999875544

>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=83.56  E-value=0.26  Score=44.16  Aligned_cols=31  Identities=26%  Similarity=0.454  Sum_probs=22.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHH-hCCeEEE
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAR-EEGWLVL  222 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~-~ngWIVL  222 (404)
                      .+.|.|+.||||||++.-+.-.-. .+|=|.+
T Consensus        30 ~vaivG~sGsGKSTLl~ll~gl~~p~~G~I~i   61 (242)
T d1mv5a_          30 IIAFAGPSGGGKSTIFSLLERFYQPTAGEITI   61 (242)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCSBSCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhCCCCCEEEE
Confidence            589999999999988866554322 4566655

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {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: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=83.44  E-value=0.44  Score=40.14  Aligned_cols=35  Identities=23%  Similarity=0.305  Sum_probs=22.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHh-CCeEEEEecC
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWARE-EGWLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~-ngWIVL~IP~  226 (404)
                      .++|.++.|||||++..-.+.++.. .+-+|+-+|.
T Consensus        42 ~~il~apTGsGKT~~a~l~i~~~~~~~~~vl~l~P~   77 (202)
T d2p6ra3          42 NLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPL   77 (202)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CEEEEcCCCCchhHHHHHHHHHHhhccCcceeeccc
Confidence            4899999999999875555555443 3444444443

>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=83.36  E-value=0.32  Score=39.90  Aligned_cols=20  Identities=30%  Similarity=0.331  Sum_probs=17.8

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      -++|.|.+|+|||+++..+.
T Consensus         7 ~I~lvG~~~~GKSSLin~l~   26 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLL   26 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            48999999999999998764

>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=83.05  E-value=0.51  Score=41.30  Aligned_cols=33  Identities=27%  Similarity=0.222  Sum_probs=27.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHHHhCCeEEEEe
Q 045329          192 QIVLDGPLCCGKSITLAMLVHWAREEGWLVLYV  224 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav~~A~~ngWIVL~I  224 (404)
                      ++.++|+=|+|||++-+++.+...++|+=|+-|
T Consensus         3 ~Iai~gKGGvGKTT~a~nLA~~LA~~G~rVllI   35 (269)
T d1cp2a_           3 QVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVV   35 (269)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEECCCcCCHHHHHHHHHHHHHhCCCcEEEE
Confidence            477899999999999999888777788866666

>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=82.73  E-value=0.39  Score=40.58  Aligned_cols=21  Identities=33%  Similarity=0.377  Sum_probs=16.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q 045329          193 IVLDGPLCCGKSITLAMLVHW  213 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~  213 (404)
                      +-|+|+.||||||+-..+...
T Consensus         5 IgI~G~~gSGKSTla~~L~~~   25 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQL   25 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            459999999999887666554

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {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: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=82.53  E-value=0.32  Score=42.08  Aligned_cols=29  Identities=14%  Similarity=0.079  Sum_probs=21.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLV  221 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIV  221 (404)
                      +++.++.|+|||++...++.+...+|.-|
T Consensus        61 ~~i~apTGsGKT~~~~~~~~~~~~~~~rv   89 (237)
T d1gkub1          61 FAATAPTGVGKTSFGLAMSLFLALKGKRC   89 (237)
T ss_dssp             EECCCCBTSCSHHHHHHHHHHHHTTSCCE
T ss_pred             EEEEecCCChHHHHHHHHHHHHHHhcCeE
Confidence            79999999999987666655555554433

>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=82.39  E-value=0.13  Score=41.19  Aligned_cols=20  Identities=35%  Similarity=0.453  Sum_probs=18.1

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      +++|.|.+|+|||++++.+.
T Consensus         2 kI~liG~~n~GKSSLin~l~   21 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLL   21 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            58999999999999999865

>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=82.38  E-value=0.38  Score=41.52  Aligned_cols=21  Identities=24%  Similarity=0.292  Sum_probs=18.7

Q ss_pred             eeEEEECCCCCcHHHHHHHHH
Q 045329          191 KQIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       191 ~r~vL~G~rGsGKS~~L~qav  211 (404)
                      -++||-|..|+|||++|.|..
T Consensus         7 ~KilllG~~~vGKTsll~~~~   27 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMR   27 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHh
Confidence            469999999999999999874

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

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: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=82.07  E-value=0.3  Score=43.00  Aligned_cols=35  Identities=23%  Similarity=0.286  Sum_probs=23.9

Q ss_pred             eEEEECCCCCcHHH-HHHHHHHHHHhCC-eEEEEecC
Q 045329          192 QIVLDGPLCCGKSI-TLAMLVHWAREEG-WLVLYVPR  226 (404)
Q Consensus       192 r~vL~G~rGsGKS~-~L~qav~~A~~ng-WIVL~IP~  226 (404)
                      ..+|.++.|||||+ .|..++..+..+| .+++-+|.
T Consensus        11 ~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~Pt   47 (305)
T d2bmfa2          11 LTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPT   47 (305)
T ss_dssp             EEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEESS
T ss_pred             cEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEccH
Confidence            47889999999996 4556666666554 44444464

>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=80.83  E-value=0.4  Score=43.37  Aligned_cols=20  Identities=30%  Similarity=0.265  Sum_probs=16.7

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAMLV  211 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qav  211 (404)
                      -+-|.|+.||||||+|.-+.
T Consensus        30 i~~iiG~sGsGKSTLl~~i~   49 (258)
T d1b0ua_          30 VISIIGSSGSGKSTFLRCIN   49 (258)
T ss_dssp             EEEEECCTTSSHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHH
Confidence            37899999999998877654

>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=80.78  E-value=0.93  Score=42.26  Aligned_cols=33  Identities=12%  Similarity=0.103  Sum_probs=20.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhC--CeEEEEecC
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREE--GWLVLYVPR  226 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~n--gWIVL~IP~  226 (404)
                      ++|+|++|||||.+. .+++.....  ..+.+..++
T Consensus       126 ~l~~G~pG~GKT~la-~ala~~~~~~~~~~~~~~~~  160 (321)
T d1w44a_         126 VIVTGKGNSGKTPLV-HALGEALGGKDKYATVRFGE  160 (321)
T ss_dssp             EEEECSSSSCHHHHH-HHHHHHHHTTSCCEEEEBSC
T ss_pred             EEEECCCCccHHHHH-HHHHHHhcCCCCeEEEEhhH
Confidence            556999999998654 455544432  455544333

>d1jwyb_ c.37.1.8 (B:) Dynamin G domain {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: G proteins
domain: Dynamin G domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=80.64  E-value=0.94  Score=40.49  Aligned_cols=44  Identities=25%  Similarity=0.417  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHH
Q 045329          166 FLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       166 tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      -++|++.|...+.. . ..+ .-.-+++++.|..++|||++|.-++-
T Consensus         3 l~~~~n~l~d~~~~-~-~~~-~~~lP~ivVvG~~ssGKSSliNaLlG   46 (306)
T d1jwyb_           3 LIPVINKLQDVFNT-L-GSD-PLDLPQIVVVGSQSSGKSSVLENIVG   46 (306)
T ss_dssp             HHHHHHHHHHHTTT-S-SSC-TTCCCEEEEEECSSSSHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHH-h-CcC-CCCCCeEEEEeCCCCCHHHHHHHHhC
Confidence            36778887765432 1 111 11126799999999999999998874

>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=80.41  E-value=0.57  Score=44.72  Aligned_cols=39  Identities=21%  Similarity=0.156  Sum_probs=25.6

Q ss_pred             Ech-hHHHHHHHHHHhcCCCccCCCCCccceeEEEECCCCCcHHHHHHHHHH
Q 045329          162 VRQ-SFLDIRDNFRRIVDPSLQSTNGPKIRKQIVLDGPLCCGKSITLAMLVH  212 (404)
Q Consensus       162 VRk-~tleLi~~L~~~~d~~~~std~~~~r~r~vL~G~rGsGKS~~L~qav~  212 (404)
                      =|+ +.-++++.|-+.         .++   ..||.|++|+|||.++..+..
T Consensus        26 gr~~ei~~~~~~L~r~---------~k~---n~llvG~~GvGKtaiv~~la~   65 (387)
T d1qvra2          26 GRDEEIRRVIQILLRR---------TKN---NPVLIGEPGVGKTAIVEGLAQ   65 (387)
T ss_dssp             SCHHHHHHHHHHHHCS---------SCC---CCEEEECTTSCHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHhcC---------CCC---CCeEECCCCCCHHHHHHHHHH
Confidence            366 555666666431         112   269999999999999765544

>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=80.15  E-value=0.34  Score=42.89  Aligned_cols=30  Identities=30%  Similarity=0.382  Sum_probs=21.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCeEEE
Q 045329          193 IVLDGPLCCGKSITLAMLVHWAREEGWLVL  222 (404)
Q Consensus       193 ~vL~G~rGsGKS~~L~qav~~A~~ngWIVL  222 (404)
                      +-|-|+.||||||+|..+.-.-..+|=|.+
T Consensus        28 ~~iiG~nGaGKSTLl~~l~Gl~~~~G~I~~   57 (231)
T d1l7vc_          28 LHLVGPNGAGKSTLLARMAGMTSGKGSIQF   57 (231)
T ss_dssp             EECBCCTTSSHHHHHHHHHTSCCCSSEEEE
T ss_pred             EEEECCCCCcHHHHHHHHhCCCCCceEEEE
Confidence            788999999999998766432223455444

>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=80.10  E-value=0.37  Score=39.59  Aligned_cols=19  Identities=32%  Similarity=0.370  Sum_probs=17.0

Q ss_pred             eEEEECCCCCcHHHHHHHH
Q 045329          192 QIVLDGPLCCGKSITLAML  210 (404)
Q Consensus       192 r~vL~G~rGsGKS~~L~qa  210 (404)
                      .+-|.|.+++|||++++.+
T Consensus         3 ~VaiiG~~nvGKSSLin~L   21 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVV   21 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHS
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            3789999999999999875