Citrus Sinensis ID: 029028

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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
Protein Sequence
MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLCMVKKPLTTSFFNGGVGALKVTRLRIAPSSRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNTRVS
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccHHccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccEEccccccccccccccccccccccEEEcccccccHccccccEEEEEEEEEccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
maaksqivtgftmpmtpapsssssssssslcmvkkplttsffnggvgalkvtrlriapssrshcyrqgggalntRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNTRVS
Flexible Loop (DISEMBL)
maaksqivtgftmpmtpapssssssssssLCMVKKPLTTSFFNGGVGALKVTrlriapssrshcyrqgggalntRMNLFDRLARVVKSYANAilssfedpEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALkaqldqqknvvnnlvsntrvs
Low Complexity Region (SEG)
MAAKSQIVTGFTMPMTPAPssssssssssLCMVKKPLTTSFFNGGVGALKVTRLRIAPSSRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNTRVS
Disordered region (IsUnstruct)
******************************CMVKKPLTTSFFNGGVGALKVTRLRIAPSSRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVK***********************************************************************************
Disordered Region (DISOPRED)
********TGF**************************TTSFFNGGVGALK**********************NTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQ*LA*****************DWYRKAQLALQKGEEDLAREALKRRKSY************Q**NVVNN*VSNT***
Disordered Region (DISEMBL)
MAAKSQIVTGFTMPM****************MVKKPLTTSFFNGGVGALKVTRLRIAPSSRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLAS**************SEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNTRVS
Disordered Region (DISPRO)
*****Q**TGFTMPMTPA**********SLCMVKKPLTTSFFNGGVGALKVTRLRIAPSSRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSN****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLCMVKKPLTTSFFNGGVGALKVTRLRIAPSSRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASxxxxxxxxxxxxxxxxxxxxxAQLALQKGEEDLxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxTRVS
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	200	2.2.26 [Sep-21-2011]
Q03943	323	Membrane-associated 30 kD	N/A	no	0.915	0.566	0.69	5e-69
O80796	330	Membrane-associated prote	yes	no	0.97	0.587	0.66	1e-62
Q8S0J7	317	Probable membrane-associa	yes	no	0.865	0.545	0.664	4e-62
Q55707	267	Uncharacterized protein s	N/A	no	0.605	0.453	0.504	4e-27
Q9RUB7	223	Phage shock protein A hom	yes	no	0.62	0.556	0.338	5e-13
P0AFM8	222	Phage shock protein A OS=	yes	no	0.54	0.486	0.370	8e-12
P0AFM6	222	Phage shock protein A OS=	N/A	no	0.54	0.486	0.370	8e-12
P0AFM7	222	Phage shock protein A OS=	N/A	no	0.54	0.486	0.370	8e-12
P54617	227	Phage shock protein A hom	yes	no	0.465	0.409	0.353	1e-06

>sp|Q03943|IM30_PEA Membrane-associated 30 kDa protein, chloroplastic OS=Pisum sativum GN=IM30 PE=2 SV=1

 Score =  260 bits (664), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 138/200 (69%), Positives = 156/200 (78%), Gaps = 17/200 (8%)

Query: 1   MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLCMVKKPLTTSFFNG-GVGALKVTRLRIAPS 59
           M  K QI +G  +P  P   SSS        ++KKPL T+ F    V  LK   +RIA  
Sbjct: 1   MTTKFQIFSG--LPSAPLQPSSS--------LLKKPLATTLFGTRPVDTLKFRVMRIAKP 50

Query: 60  SRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMR 119
            R      GGGA+  RMNLFDR ARVVKSYANA++S+FEDPEKILEQAVLEMNDDL KMR
Sbjct: 51  VR------GGGAIGVRMNLFDRFARVVKSYANALVSTFEDPEKILEQAVLEMNDDLTKMR 104

Query: 120 QATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANAL 179
           QATAQVLASQKRLENK KAA+QASE+WYRKAQLALQKGEEDLAREALKRRKS+ADNA++L
Sbjct: 105 QATAQVLASQKRLENKYKAAQQASEEWYRKAQLALQKGEEDLAREALKRRKSFADNASSL 164

Query: 180 KAQLDQQKNVVNNLVSNTRV 199
           KAQLDQQK+VV+NLVSNTR+
Sbjct: 165 KAQLDQQKSVVDNLVSNTRL 184

Pisum sativum (taxid: 3888)

>sp|O80796|VIPP1_ARATH Membrane-associated protein VIPP1, chloroplastic OS=Arabidopsis thaliana GN=VIPP1 PE=1 SV=1

 Score =  238 bits (608), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 132/200 (66%), Positives = 157/200 (78%), Gaps = 6/200 (3%)

Query: 1   MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLCMVKK-PLTTSFFNGGVGALKVTRLRIAPS 59
           MA K+  VTG   P+ P  SSS S+SS+  C ++  PL TSFF    GAL+V  LR+A  
Sbjct: 1   MALKASPVTGLFPPLRPTASSSPSTSSNRPCSLRILPLRTSFFGNSSGALRVNVLRLACD 60

Query: 60  SRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMR 119
           +R  C   G GA    MNLF+R +RVVKSYANA++SSFEDPEKILEQ V+EMN DL KMR
Sbjct: 61  NRLRC--NGHGAT---MNLFERFSRVVKSYANALISSFEDPEKILEQTVIEMNSDLTKMR 115

Query: 120 QATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANAL 179
           QATAQVLASQK+L+NK KAA+Q+S+DWY++AQLAL KG+EDLAREALKRRKS+ADNA AL
Sbjct: 116 QATAQVLASQKQLQNKYKAAQQSSDDWYKRAQLALAKGDEDLAREALKRRKSFADNATAL 175

Query: 180 KAQLDQQKNVVNNLVSNTRV 199
           K QLDQQK VV+NLVSNTR+
Sbjct: 176 KTQLDQQKGVVDNLVSNTRL 195

Required for plastid vesicle formation and thylakoid membrane biogenesis, but not for functional assembly of thylakoid protein complexes.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8S0J7|IM30_ORYSJ Probable membrane-associated 30 kDa protein, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0895100 PE=1 SV=1

 Score =  237 bits (604), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 125/188 (66%), Positives = 146/188 (77%), Gaps = 15/188 (7%)

Query: 12  TMPMTPAPSSSSSSSSSSLCMVKKPLTTSFFNGGVGALKVTRLRIAPSSRSHCYRQGGGA 71
           ++ + P P +S+S         +  L TSF NG V +L++ ++R +  +R  C       
Sbjct: 9   SLRLAPPPPASAS-------FRRTALRTSFLNGSV-SLRLIQVRQSNVNRFKCN------ 54

Query: 72  LNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKR 131
              R NL DR +RVVKSYANA+LSSFEDPEKIL+QAVLEMNDDL KMRQATAQVLASQKR
Sbjct: 55  -GIRSNLLDRFSRVVKSYANAVLSSFEDPEKILDQAVLEMNDDLTKMRQATAQVLASQKR 113

Query: 132 LENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVN 191
           LENK KAAEQAS+DWYR+AQLALQKG+EDLAREALKRRKSYADNA++LKAQLDQQK VV 
Sbjct: 114 LENKYKAAEQASDDWYRRAQLALQKGDEDLAREALKRRKSYADNASSLKAQLDQQKGVVE 173

Query: 192 NLVSNTRV 199
           NLVSNTRV
Sbjct: 174 NLVSNTRV 181

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q55707|Y617_SYNY3 Uncharacterized protein sll0617 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=sll0617 PE=3 SV=1

 Score =  121 bits (303), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 61/121 (50%), Positives = 84/121 (69%)

Query: 76  MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
           M LFDRL RVV++  N ++S  EDPEK+LEQAV++M +DLV++RQA A+ +A +KR E +
Sbjct: 1   MGLFDRLGRVVRANLNDLVSKAEDPEKVLEQAVIDMQEDLVQLRQAVARTIAEEKRTEQR 60

Query: 136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVS 195
                Q ++ W  +A+LAL  GEE+LAREAL R+KS  D A A + QL QQ+ +  NL  
Sbjct: 61  LNQDTQEAKKWEDRAKLALTNGEENLAREALARKKSLTDTAAAYQTQLAQQRTMSENLRR 120

Query: 196 N 196
           N
Sbjct: 121 N 121

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|Q9RUB7|PSPA_DEIRA Phage shock protein A homolog OS=Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) GN=DR_1473 PE=1 SV=1

 Score = 74.3 bits (181), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 42/124 (33%), Positives = 73/124 (58%)

Query: 76  MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
           M++FDRL+R++++  N ++S  EDP KI++QA+ +M       R   A  +A   +LE +
Sbjct: 1   MSIFDRLSRLLRANVNDMISKAEDPAKIIDQALRDMRSAYADARNEVAGAMAQAAKLERE 60

Query: 136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVS 195
                + + ++ +KA+ AL+ G EDLAREAL+R +++ D A     Q   Q++ V+ L +
Sbjct: 61  AGTNSKLAAEYEKKAEEALRGGSEDLAREALRRAQNHKDLAKGFDEQRTVQQSTVDQLKT 120

Query: 196 NTRV 199
             R 
Sbjct: 121 QLRA 124

Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (taxid: 243230)

>sp|P0AFM8|PSPA_SHIFL Phage shock protein A OS=Shigella flexneri GN=pspA PE=3 SV=2

 Score = 70.5 bits (171), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 40/108 (37%), Positives = 64/108 (59%)

Query: 76  MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
           M +F R A +V +  NA+L   EDP+K++   + EM D LV++R  +A+ LA +K+L  +
Sbjct: 1   MGIFSRFADIVNANINALLEKAEDPQKLVRLMIQEMEDTLVEVRSTSARALAEKKQLTRR 60

Query: 136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQL 183
            + A     +W  KA+LAL K  EDLAR AL  ++   D   +L+ ++
Sbjct: 61  IEQASAREVEWQEKAELALLKEREDLARAALIEKQKLTDLIKSLEHEV 108

The phage shock protein (psp) operon (pspABCDE) may play a significant role in the competition for survival under nutrient-or energy-limited conditions. PspA negatively regulates expression of the pspABCDE promoter and of pspG through negative regulation of the psp-specific transcriptional activator PspF. Is also required for membrane integrity, efficient translocation and maintenance of the proton motive force.

Shigella flexneri (taxid: 623)

>sp|P0AFM6|PSPA_ECOLI Phage shock protein A OS=Escherichia coli (strain K12) GN=pspA PE=1 SV=2

 Score = 70.5 bits (171), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 40/108 (37%), Positives = 64/108 (59%)

Query: 76  MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
           M +F R A +V +  NA+L   EDP+K++   + EM D LV++R  +A+ LA +K+L  +
Sbjct: 1   MGIFSRFADIVNANINALLEKAEDPQKLVRLMIQEMEDTLVEVRSTSARALAEKKQLTRR 60

Query: 136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQL 183
            + A     +W  KA+LAL K  EDLAR AL  ++   D   +L+ ++
Sbjct: 61  IEQASAREVEWQEKAELALLKEREDLARAALIEKQKLTDLIKSLEHEV 108

The phage shock protein (psp) operon (pspABCDE) may play a significant role in the competition for survival under nutrient-or energy-limited conditions. PspA negatively regulates expression of the pspABCDE promoter and of pspG through negative regulation of the psp-specific transcriptional activator PspF. Is also required for membrane integrity, efficient translocation and maintenance of the proton motive force.

Escherichia coli (strain K12) (taxid: 83333)

>sp|P0AFM7|PSPA_ECO57 Phage shock protein A OS=Escherichia coli O157:H7 GN=pspA PE=3 SV=2

 Score = 70.5 bits (171), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 40/108 (37%), Positives = 64/108 (59%)

Query: 76  MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
           M +F R A +V +  NA+L   EDP+K++   + EM D LV++R  +A+ LA +K+L  +
Sbjct: 1   MGIFSRFADIVNANINALLEKAEDPQKLVRLMIQEMEDTLVEVRSTSARALAEKKQLTRR 60

Query: 136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQL 183
            + A     +W  KA+LAL K  EDLAR AL  ++   D   +L+ ++
Sbjct: 61  IEQASAREVEWQEKAELALLKEREDLARAALIEKQKLTDLIKSLEHEV 108

The phage shock protein (psp) operon (pspABCDE) may play a significant role in the competition for survival under nutrient-or energy-limited conditions. PspA negatively regulates expression of the pspABCDE promoter and of pspG through negative regulation of the psp-specific transcriptional activator PspF. Is also required for membrane integrity, efficient translocation and maintenance of the proton motive force.

Escherichia coli O157:H7 (taxid: 83334)

>sp|P54617|PSPA_BACSU Phage shock protein A homolog OS=Bacillus subtilis (strain 168) GN=ydjF PE=1 SV=3

 Score = 53.1 bits (126), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/99 (35%), Positives = 58/99 (58%), Gaps = 6/99 (6%)

Query: 76  MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQ---KRL 132
           M++  R   ++ +  NA+L   E+PEK+++Q +  MN DL K++  TA V+A +   KR 
Sbjct: 1   MSIIGRFKDIMSANINALLDKAENPEKMVDQYLRNMNSDLAKVKAETAAVMAEEQRAKRE 60

Query: 133 ENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKS 171
            ++C+A  +  E +  K   ALQ G E  AR+ L+R+ S
Sbjct: 61  YHECQADMEKMESYAMK---ALQAGNESDARKFLERKTS 96

Bacillus subtilis (strain 168) (taxid: 224308)

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	200
224138834	339	predicted protein [Populus trichocarpa]	0.995	0.587	0.756	2e-82
255578930	312	Membrane-associated 30 kDa protein, chlo	0.98	0.628	0.757	7e-79
147795803	465	hypothetical protein VITISV_012616 [Viti	0.975	0.419	0.725	1e-76
363807044	323	uncharacterized protein LOC100781742 [Gl	0.935	0.578	0.76	9e-76
363806682	322	uncharacterized protein LOC100818209 [Gl	0.93	0.577	0.755	1e-74
449468854	332	PREDICTED: membrane-associated 30 kDa pr	0.99	0.596	0.705	6e-71
225430912	324	PREDICTED: probable membrane-associated	0.945	0.583	0.698	1e-69
359478255	314	PREDICTED: membrane-associated 30 kDa pr	0.89	0.566	0.683	4e-69
729842	323	RecName: Full=Membrane-associated 30 kDa	0.915	0.566	0.69	3e-67
388510656	326	unknown [Lotus japonicus]	0.95	0.582	0.705	5e-67

>gi|224138834|ref|XP_002322913.1| predicted protein [Populus trichocarpa] gi|222867543|gb|EEF04674.1| predicted protein [Populus trichocarpa]

 Score =  310 bits (795), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 155/205 (75%), Positives = 176/205 (85%), Gaps = 6/205 (2%)

Query: 1   MAAKSQIVTGFTMPMTPAP-----SSSSSSSSSSLCMVKK-PLTTSFFNGGVGALKVTRL 54
           MA KSQ++TG T+PM   P     S+++ +++++LCMVK+  LTTSFFNGGV ALKV R+
Sbjct: 1   MAIKSQLITGLTLPMPHPPYTSSSSNNNGNNNTTLCMVKRRTLTTSFFNGGVEALKVARI 60

Query: 55  RIAPSSRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDD 114
           R + S+RS CYRQGGGAL T MNLFDR  RVVKSYANAI+SSFEDPEKILEQ VLEMNDD
Sbjct: 61  RTSLSTRSQCYRQGGGALGTCMNLFDRFGRVVKSYANAIISSFEDPEKILEQTVLEMNDD 120

Query: 115 LVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYAD 174
           L KMRQATAQVLASQKRLENK KAA+ ASE+WYRKAQLALQKGEEDLAREALKRRK+YAD
Sbjct: 121 LTKMRQATAQVLASQKRLENKYKAAQLASEEWYRKAQLALQKGEEDLAREALKRRKTYAD 180

Query: 175 NANALKAQLDQQKNVVNNLVSNTRV 199
           NAN+ KAQLDQQK VV NLVSNTR+
Sbjct: 181 NANSFKAQLDQQKGVVENLVSNTRL 205

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255578930|ref|XP_002530318.1| Membrane-associated 30 kDa protein, chloroplast precursor, putative [Ricinus communis] gi|223530174|gb|EEF32085.1| Membrane-associated 30 kDa protein, chloroplast precursor, putative [Ricinus communis]

 Score =  298 bits (764), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 159/210 (75%), Positives = 176/210 (83%), Gaps = 14/210 (6%)

Query: 1   MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLC----------MVKKP-LTTSFFNGGVGAL 49
           MA KSQ++TG T+P+ P P  +S+SSSS+            MVK P LTTSFFNGGV AL
Sbjct: 1   MAIKSQLITGLTLPVPPPPPHASTSSSSNCNSSSSSGNTLSMVKPPYLTTSFFNGGVKAL 60

Query: 50  KVTRLRIAPSSRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVL 109
           KVTR R   +SRSHC+  GGG L TRMNLFDR +RVVKSYANAILSSFEDPEKIL+Q VL
Sbjct: 61  KVTRTR---TSRSHCFAHGGGGLGTRMNLFDRFSRVVKSYANAILSSFEDPEKILDQTVL 117

Query: 110 EMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRR 169
           EMNDDL KMRQATAQVLASQKRLENK KAAEQASEDWYRKAQLALQKGEEDLAREALKRR
Sbjct: 118 EMNDDLTKMRQATAQVLASQKRLENKYKAAEQASEDWYRKAQLALQKGEEDLAREALKRR 177

Query: 170 KSYADNANALKAQLDQQKNVVNNLVSNTRV 199
           KSYADNA +LK+QLDQQ++VV+NLVSNTR+
Sbjct: 178 KSYADNAKSLKSQLDQQRSVVDNLVSNTRL 207

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147795803|emb|CAN69783.1| hypothetical protein VITISV_012616 [Vitis vinifera]

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 145/200 (72%), Positives = 165/200 (82%), Gaps = 5/200 (2%)

Query: 1   MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLCMVKKPLTTSFFNGGVGALKVTRLRIAPSS 60
           M   SQI+TG  MP+  AP+SS+S S   +C+V +PLT+SFFNGGV  LKV    +A S+
Sbjct: 1   MPLNSQIITG--MPLASAPASSTSDS---VCVVXQPLTSSFFNGGVRVLKVRGTXVANSN 55

Query: 61  RSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQ 120
            S C R G  AL  RM+L DR ARVVKSYANAI+SS EDPEKILEQ VLEMNDDL+KMRQ
Sbjct: 56  XSQCSRHGAAALGARMSLLDRFARVVKSYANAIISSMEDPEKILEQTVLEMNDDLIKMRQ 115

Query: 121 ATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALK 180
           ATAQVLASQKRLENK KAA+QASEDWYRKAQ AL+KG+EDLAREALKRRKSYADNA+ALK
Sbjct: 116 ATAQVLASQKRLENKYKAAQQASEDWYRKAQFALEKGDEDLAREALKRRKSYADNASALK 175

Query: 181 AQLDQQKNVVNNLVSNTRVS 200
           AQ DQQKNV+ NLVSNT++S
Sbjct: 176 AQFDQQKNVIENLVSNTQMS 195

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807044|ref|NP_001242581.1| uncharacterized protein LOC100781742 [Glycine max] gi|255641682|gb|ACU21113.1| unknown [Glycine max]

 Score =  288 bits (737), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 152/200 (76%), Positives = 165/200 (82%), Gaps = 13/200 (6%)

Query: 1   MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLCMVKKPLTTSFFNGG-VGALKVTRLRIAPS 59
           MAAK QI TG    + PAP  SSSSS+  LC++KKPLTTSFF    V  LK+  +RI   
Sbjct: 1   MAAKLQIFTG----LPPAPFQSSSSST--LCVLKKPLTTSFFGTARVEVLKLRVMRIVKP 54

Query: 60  SRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMR 119
           +R      GGGAL  RMNLFDR ARVVKSYANA+LSSFEDPEKILEQAVLEMNDDL KMR
Sbjct: 55  TR------GGGALGARMNLFDRFARVVKSYANAVLSSFEDPEKILEQAVLEMNDDLTKMR 108

Query: 120 QATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANAL 179
           QATAQVLASQKRLENK KAA+QASE+WYRKAQLALQKGEEDLAREALKRRKSYADNA++L
Sbjct: 109 QATAQVLASQKRLENKYKAAQQASEEWYRKAQLALQKGEEDLAREALKRRKSYADNASSL 168

Query: 180 KAQLDQQKNVVNNLVSNTRV 199
           KAQLDQQK VV NLVSNTR+
Sbjct: 169 KAQLDQQKTVVENLVSNTRL 188

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363806682|ref|NP_001242008.1| uncharacterized protein LOC100818209 [Glycine max] gi|255639265|gb|ACU19931.1| unknown [Glycine max]

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 151/200 (75%), Positives = 164/200 (82%), Gaps = 14/200 (7%)

Query: 1   MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLCMVKKPLTTSFFNGG-VGALKVTRLRIAPS 59
           MAAK QI TG    + PAP  SSSS+   LC++KKPLTTSFF    V  LK+  +RIA  
Sbjct: 1   MAAKLQIFTG----LPPAPFQSSSST---LCVLKKPLTTSFFGTARVEVLKLRVMRIAKP 53

Query: 60  SRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMR 119
           +R      GGGAL  RMNLFDR ARVVKSYANA+LSSFEDPEKILEQAVLEMNDDL KMR
Sbjct: 54  AR------GGGALGARMNLFDRFARVVKSYANAVLSSFEDPEKILEQAVLEMNDDLTKMR 107

Query: 120 QATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANAL 179
           QATAQVLASQKRLENK KAA+QASE+WYRKAQLALQKGEEDLAR ALKRRKSYADNA++L
Sbjct: 108 QATAQVLASQKRLENKYKAAQQASEEWYRKAQLALQKGEEDLARGALKRRKSYADNASSL 167

Query: 180 KAQLDQQKNVVNNLVSNTRV 199
           KAQLDQQK VV NLVSNTR+
Sbjct: 168 KAQLDQQKTVVENLVSNTRL 187

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468854|ref|XP_004152136.1| PREDICTED: membrane-associated 30 kDa protein, chloroplastic-like [Cucumis sativus] gi|449484741|ref|XP_004156967.1| PREDICTED: membrane-associated 30 kDa protein, chloroplastic-like [Cucumis sativus]

 Score =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 141/200 (70%), Positives = 164/200 (82%), Gaps = 2/200 (1%)

Query: 1   MAAKSQIVTGFTMPMTPAPSSSSSSSS-SSLCMVKKPLTTSFFNGGVGALKVTRLRIAPS 59
           MAA++ + TG  +  TP+ S   SSS  ++LC+  K L TSF NGG   L++TR+     
Sbjct: 1   MAAQTHVFTGLALASTPSSSFQPSSSKPATLCVASKLLRTSFLNGGGNTLQITRMNSLHL 60

Query: 60  SRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMR 119
            RSH  R+GG AL  RMNLFDR+AR+VKSYANA++SSFEDPEKILEQ VLEMNDDL KMR
Sbjct: 61  DRSHGSRRGG-ALGARMNLFDRVARLVKSYANALVSSFEDPEKILEQTVLEMNDDLTKMR 119

Query: 120 QATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANAL 179
           QATAQVLASQKRLENK K+A+QA++DWYRKAQLALQKG++DLAREALKRRKSYADNANAL
Sbjct: 120 QATAQVLASQKRLENKYKSAQQAADDWYRKAQLALQKGDDDLAREALKRRKSYADNANAL 179

Query: 180 KAQLDQQKNVVNNLVSNTRV 199
           KAQLDQQK VV NLVSNTR+
Sbjct: 180 KAQLDQQKGVVENLVSNTRL 199

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225430912|ref|XP_002276816.1| PREDICTED: probable membrane-associated 30 kDa protein, chloroplastic [Vitis vinifera] gi|297735245|emb|CBI17607.3| unnamed protein product [Vitis vinifera]

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 139/199 (69%), Positives = 156/199 (78%), Gaps = 10/199 (5%)

Query: 1   MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLCMVKKPLTTSFFNGGVGALKVTRLRIAPSS 60
           MA K  I  G ++   P  S+  S       +V   L ++FF  GVGALKV  +RIA SS
Sbjct: 1   MATKVPIGAGLSLASPPCASNVRS-------LV---LKSAFFGHGVGALKVRGIRIARSS 50

Query: 61  RSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQ 120
              C   GGGAL T+MNLFDR ARVVKSYANA+LSSFEDPEKILEQ VLEMNDDL KMRQ
Sbjct: 51  TYRCNGHGGGALGTQMNLFDRFARVVKSYANAVLSSFEDPEKILEQTVLEMNDDLTKMRQ 110

Query: 121 ATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALK 180
           ATAQVLASQK+LEN+ KAA+QASEDWY++AQLAL KG+EDLAREALKRRKSYADNA+ALK
Sbjct: 111 ATAQVLASQKQLENRYKAAQQASEDWYKRAQLALGKGDEDLAREALKRRKSYADNASALK 170

Query: 181 AQLDQQKNVVNNLVSNTRV 199
           AQLDQQK VV NLVSNTR+
Sbjct: 171 AQLDQQKTVVENLVSNTRL 189

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359478255|ref|XP_002273068.2| PREDICTED: membrane-associated 30 kDa protein, chloroplastic-like [Vitis vinifera]

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 136/199 (68%), Positives = 155/199 (77%), Gaps = 21/199 (10%)

Query: 1   MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLCMVKKPLTTSFFNGGVGALKVTRLRIAPSS 60
           M   SQI+TG  MP+  AP+SS+S S   +C+V +PLT+SFFNGG  +L           
Sbjct: 1   MPLNSQIITG--MPLASAPASSTSDS---VCVVGQPLTSSFFNGGGVSL----------- 44

Query: 61  RSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQ 120
                  G  AL  RM+L DR ARVVKSYANAI+SS EDPEKILEQ VLEMNDDL+KMRQ
Sbjct: 45  -----LHGAAALGARMSLLDRFARVVKSYANAIISSMEDPEKILEQTVLEMNDDLIKMRQ 99

Query: 121 ATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALK 180
           ATAQVLASQKRLENK KAA+QASEDWYRKAQ AL+KG+EDLAREALKRRKSYADNA+ALK
Sbjct: 100 ATAQVLASQKRLENKYKAAQQASEDWYRKAQFALEKGDEDLAREALKRRKSYADNASALK 159

Query: 181 AQLDQQKNVVNNLVSNTRV 199
           AQ DQQKNV+ NLVSNT++
Sbjct: 160 AQFDQQKNVIENLVSNTQL 178

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|729842|sp|Q03943.1|IM30_PEA RecName: Full=Membrane-associated 30 kDa protein, chloroplastic; Short=M30; Flags: Precursor gi|169107|gb|AAA53545.1| IM30 [Pisum sativum]

 Score =  260 bits (664), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 138/200 (69%), Positives = 156/200 (78%), Gaps = 17/200 (8%)

Query: 1   MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLCMVKKPLTTSFFNG-GVGALKVTRLRIAPS 59
           M  K QI +G  +P  P   SSS        ++KKPL T+ F    V  LK   +RIA  
Sbjct: 1   MTTKFQIFSG--LPSAPLQPSSS--------LLKKPLATTLFGTRPVDTLKFRVMRIAKP 50

Query: 60  SRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMR 119
            R      GGGA+  RMNLFDR ARVVKSYANA++S+FEDPEKILEQAVLEMNDDL KMR
Sbjct: 51  VR------GGGAIGVRMNLFDRFARVVKSYANALVSTFEDPEKILEQAVLEMNDDLTKMR 104

Query: 120 QATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANAL 179
           QATAQVLASQKRLENK KAA+QASE+WYRKAQLALQKGEEDLAREALKRRKS+ADNA++L
Sbjct: 105 QATAQVLASQKRLENKYKAAQQASEEWYRKAQLALQKGEEDLAREALKRRKSFADNASSL 164

Query: 180 KAQLDQQKNVVNNLVSNTRV 199
           KAQLDQQK+VV+NLVSNTR+
Sbjct: 165 KAQLDQQKSVVDNLVSNTRL 184

Source: Pisum sativum

Species: Pisum sativum

Genus: Pisum

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388510656|gb|AFK43394.1| unknown [Lotus japonicus]

 Score =  259 bits (662), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 141/200 (70%), Positives = 161/200 (80%), Gaps = 10/200 (5%)

Query: 1   MAAKSQIVTGFTMPMTPAPSSSSSSSSSSLCMVKKPLTTSFFNGG-VGALKVTRLRIAPS 59
           M+ K QI TG     +    SSS S SS+LCM+KKPLTTSF   G V  L+++ +R+   
Sbjct: 1   MSTKLQIFTGLP---STPFQSSSPSPSSTLCMLKKPLTTSFLGTGTVEVLRLSGMRVVKP 57

Query: 60  SRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMR 119
            R+   R+GG     RMNLFDR ARVVKSYANA++SSFEDPEKILEQAVLEMNDDL KMR
Sbjct: 58  VRAP--RRGGA----RMNLFDRFARVVKSYANAVISSFEDPEKILEQAVLEMNDDLTKMR 111

Query: 120 QATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANAL 179
           QATAQVLASQKR+ENK KAA+QASE+WYRKAQLALQKGEEDLAREALKRRKS+ADNA++ 
Sbjct: 112 QATAQVLASQKRMENKYKAAQQASEEWYRKAQLALQKGEEDLAREALKRRKSFADNASSS 171

Query: 180 KAQLDQQKNVVNNLVSNTRV 199
           KAQLDQQK VV NLVSNTR+
Sbjct: 172 KAQLDQQKGVVENLVSNTRL 191

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

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	200
TAIR|locus:2206290	330	PTAC4 "plastid transcriptional	0.97	0.587	0.63	5.1e-58
TIGR_CMR|CPS_3772	221	CPS_3772 "phage shock protein	0.54	0.488	0.398	6.7e-17
TIGR_CMR|SO_1807	227	SO_1807 "phage shock protein A	0.54	0.475	0.388	1.1e-16
UNIPROTKB|Q9KRG4	222	VC1678 "Phage shock protein A"	0.455	0.409	0.461	4.7e-16
TIGR_CMR|VC_1678	222	VC_1678 "phage shock protein A	0.455	0.409	0.461	4.7e-16
UNIPROTKB|P0AFM6	222	pspA [Escherichia coli K-12 (t	0.54	0.486	0.370	1.6e-15
UNIPROTKB|Q9F4H4	221	pspA "Phage shock protein A" [	0.49	0.443	0.393	8.8e-15
TIGR_CMR|CPS_4751	220	CPS_4751 "phage shock protein	0.58	0.527	0.341	1.1e-14
UNIPROTKB|Q81KD9	221	BAS4700 "Uncharacterized prote	0.59	0.533	0.271	2.9e-08
TIGR_CMR|BA_5061	221	BA_5061 "conserved hypothetica	0.59	0.533	0.271	2.9e-08

TAIR|locus:2206290 PTAC4 "plastid transcriptionally active 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 596 (214.9 bits), Expect = 5.1e-58, P = 5.1e-58
 Identities = 126/200 (63%), Positives = 149/200 (74%)

Query:     1 MAAKSQIVTGFTMPMTPAPXXXXXXXXXXLCMVK-KPLTTSFFNGGVGALKVTRLRIAPS 59
             MA K+  VTG   P+ P             C ++  PL TSFF    GAL+V  LR+A  
Sbjct:     1 MALKASPVTGLFPPLRPTASSSPSTSSNRPCSLRILPLRTSFFGNSSGALRVNVLRLACD 60

Query:    60 SRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMR 119
             +R  C   G GA    MNLF+R +RVVKSYANA++SSFEDPEKILEQ V+EMN DL KMR
Sbjct:    61 NRLRC--NGHGAT---MNLFERFSRVVKSYANALISSFEDPEKILEQTVIEMNSDLTKMR 115

Query:   120 QATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANAL 179
             QATAQVLASQK+L+NK KAA+Q+S+DWY++AQLAL KG+EDLAREALKRRKS+ADNA AL
Sbjct:   116 QATAQVLASQKQLQNKYKAAQQSSDDWYKRAQLALAKGDEDLAREALKRRKSFADNATAL 175

Query:   180 KAQLDQQKNVVNNLVSNTRV 199
             K QLDQQK VV+NLVSNTR+
Sbjct:   176 KTQLDQQKGVVDNLVSNTRL 195

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0016020 "membrane" evidence=ISS

GO:0010027 "thylakoid membrane organization" evidence=RCA;IMP

GO:0016050 "vesicle organization" evidence=IMP

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009295 "nucleoid" evidence=IDA

GO:0009508 "plastid chromosome" evidence=IDA

TIGR_CMR|CPS_3772 CPS_3772 "phage shock protein A" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 208 (78.3 bits), Expect = 6.7e-17, P = 6.7e-17
 Identities = 43/108 (39%), Positives = 64/108 (59%)

Query:    76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
             M +F R   ++ S  N +L   EDP K++   + EM D LV++R ++A+ LA +K L  +
Sbjct:     1 MGIFSRFTDIINSNINNLLDKAEDPAKMVRLIIQEMEDTLVEVRSSSAKTLADKKELARQ 60

Query:   136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQL 183
                 EQ +E W  KA+LAL K  EDLAR AL  +K  +++A AL  +L
Sbjct:    61 VSRLEQDAEQWQAKAELALSKDREDLARAALMEKKKSSESAQALVDEL 108

GO:0009271 "phage shock" evidence=ISS

TIGR_CMR|SO_1807 SO_1807 "phage shock protein A" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 42/108 (38%), Positives = 64/108 (59%)

Query:    76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
             M +F R A ++ S  +A+L   EDPEK++   + EM D LV++R  +A+VLA +K L  +
Sbjct:     1 MGIFSRFADIINSNISALLDKAEDPEKMVRLIIQEMEDTLVEVRSTSAKVLAEKKELHRR 60

Query:   136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQL 183
                 E+  +DW  KA+LAL K  EDLA+ AL  ++  A   + L  +L
Sbjct:    61 ISRVEEQVQDWQDKAELALSKDREDLAKAALVEKQKAAGLVDTLNQEL 108

GO:0009271 "phage shock" evidence=ISS

UNIPROTKB|Q9KRG4 VC1678 "Phage shock protein A" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 42/91 (46%), Positives = 57/91 (62%)

Query:    76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
             M +F R A +V S  +A+L   EDPEK++   + EM D LV++R  +A+ +A +K L  K
Sbjct:     1 MGIFSRFADIVNSNISALLDKAEDPEKMIRLIIQEMEDTLVEVRTNSAKAMADKKELARK 60

Query:   136 CKAAEQASEDWYRKAQLALQKGEEDLAREAL 166
              ++ EQ  EDW  KA LAL K  EDLAR AL
Sbjct:    61 VESIEQQLEDWQNKATLALTKQREDLARAAL 91

GO:0009271 "phage shock" evidence=ISS

TIGR_CMR|VC_1678 VC_1678 "phage shock protein A" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 42/91 (46%), Positives = 57/91 (62%)

Query:    76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
             M +F R A +V S  +A+L   EDPEK++   + EM D LV++R  +A+ +A +K L  K
Sbjct:     1 MGIFSRFADIVNSNISALLDKAEDPEKMIRLIIQEMEDTLVEVRTNSAKAMADKKELARK 60

Query:   136 CKAAEQASEDWYRKAQLALQKGEEDLAREAL 166
              ++ EQ  EDW  KA LAL K  EDLAR AL
Sbjct:    61 VESIEQQLEDWQNKATLALTKQREDLARAAL 91

GO:0009271 "phage shock" evidence=ISS

UNIPROTKB|P0AFM6 pspA [Escherichia coli K-12 (taxid:83333)]

 Score = 195 (73.7 bits), Expect = 1.6e-15, P = 1.6e-15
 Identities = 40/108 (37%), Positives = 64/108 (59%)

Query:    76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
             M +F R A +V +  NA+L   EDP+K++   + EM D LV++R  +A+ LA +K+L  +
Sbjct:     1 MGIFSRFADIVNANINALLEKAEDPQKLVRLMIQEMEDTLVEVRSTSARALAEKKQLTRR 60

Query:   136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQL 183
              + A     +W  KA+LAL K  EDLAR AL  ++   D   +L+ ++
Sbjct:    61 IEQASAREVEWQEKAELALLKEREDLARAALIEKQKLTDLIKSLEHEV 108

GO:0009408 "response to heat" evidence=IEP

GO:0009271 "phage shock" evidence=IEP

GO:0005737 "cytoplasm" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0016020 "membrane" evidence=IEA

UNIPROTKB|Q9F4H4 pspA "Phage shock protein A" [Yersinia enterocolitica (taxid:630)]

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 39/99 (39%), Positives = 62/99 (62%)

Query:    76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
             M +F R A +V +  N +L   EDP+K++   + EM D LV++R  +A+ LA +K+L  +
Sbjct:     1 MGIFSRFADIVNANINTLLDKAEDPQKLVRLMIQEMEDTLVEIRSTSARALAEKKQLLRR 60

Query:   136 CKAAEQASEDWYRKAQLALQKGEEDLAREAL-KRRKSYA 173
                 E   ++W  KA+LAL+K +EDLAR AL +++K  A
Sbjct:    61 IDHCESQQQEWQDKAELALRKDKEDLARAALIEKQKVVA 99

GO:0005515 "protein binding" evidence=IPI

TIGR_CMR|CPS_4751 CPS_4751 "phage shock protein A" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 187 (70.9 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 41/120 (34%), Positives = 67/120 (55%)

Query:    76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
             M LF R   +V +  N++L   E PEK++   + EM + LV++R   A+ +A QK L  K
Sbjct:     1 MGLFSRFTDIVNANLNSMLDKAEHPEKMIRMIIGEMEETLVEVRSTAAKNIAEQKTLARK 60

Query:   136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVS 195
              K  ++    W+ KA++AL KG EDLA+ AL ++        A   QL+++   + +L+S
Sbjct:    61 VKTTQEGVAHWHDKAEIALNKGREDLAKSALAQKHK----CQAELTQLNEENVQLTDLLS 116

GO:0009271 "phage shock" evidence=ISS

UNIPROTKB|Q81KD9 BAS4700 "Uncharacterized protein" [Bacillus anthracis (taxid:1392)]

 Score = 135 (52.6 bits), Expect = 2.9e-08, P = 2.9e-08
 Identities = 32/118 (27%), Positives = 61/118 (51%)

Query:    76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
             M++F RL  +  S   +++   EDP K+ +Q + +M  D+ +  ++ A  +A +K+ +  
Sbjct:     1 MSVFKRLRDLTMSNVYSLIEKAEDPVKMTDQYLRDMQADVQEAEKSVAAQIALEKKFKIL 60

Query:   136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNL 193
              +  E   +    +A +A+Q    DLAR AL+ +++     N  KA  +Q K   +NL
Sbjct:    61 FEEQEALVKKREEQAHMAVQASNLDLARRALEEKQNAEQKMNEYKASYEQNKAAADNL 118

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|BA_5061 BA_5061 "conserved hypothetical protein" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 135 (52.6 bits), Expect = 2.9e-08, P = 2.9e-08
 Identities = 32/118 (27%), Positives = 61/118 (51%)

Query:    76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
             M++F RL  +  S   +++   EDP K+ +Q + +M  D+ +  ++ A  +A +K+ +  
Sbjct:     1 MSVFKRLRDLTMSNVYSLIEKAEDPVKMTDQYLRDMQADVQEAEKSVAAQIALEKKFKIL 60

Query:   136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNL 193
              +  E   +    +A +A+Q    DLAR AL+ +++     N  KA  +Q K   +NL
Sbjct:    61 FEEQEALVKKREEQAHMAVQASNLDLARRALEEKQNAEQKMNEYKASYEQNKAAADNL 118


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.127   0.348    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      200       190   0.00091  110 3  10 22  0.45    32
                                                     31  0.42    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  10
  No. of states in DFA:  606 (64 KB)
  Total size of DFA:  194 KB (2111 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  30.16u 0.22s 30.38t   Elapsed:  00:00:01
  Total cpu time:  30.16u 0.22s 30.38t   Elapsed:  00:00:01
  Start:  Fri May 10 03:16:25 2013   End:  Fri May 10 03:16:26 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

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

Your Input: estExt_Genewise1_v1.C_LG_XVI3149 hypothetical protein (339 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	200
COG1842	225	COG1842, PspA, Phage shock protein A (IM30), suppr	3e-30
pfam04012	220	pfam04012, PspA_IM30, PspA/IM30 family	7e-28
TIGR02977	219	TIGR02977, phageshock_pspA, phage shock protein A	2e-27
PRK10698	222	PRK10698, PRK10698, phage shock protein PspA; Prov	2e-18

>gnl|CDD|224755 COG1842, PspA, Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]

 Score =  110 bits (277), Expect = 3e-30
 Identities = 56/112 (50%), Positives = 76/112 (67%)

Query: 76  MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
           M +F RL  +VK+  N +L   EDPEK+LEQA+ +M  +L K RQA AQ +A QK+LE K
Sbjct: 1   MGIFSRLKDLVKANINELLDKAEDPEKMLEQAIRDMESELAKARQALAQAIARQKQLERK 60

Query: 136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQK 187
            + A+  +E    KA+LALQ G EDLAREAL+ ++S  D A AL+A+L Q +
Sbjct: 61  LEEAQARAEKLEEKAELALQAGNEDLAREALEEKQSLEDLAKALEAELQQAE 112

Length = 225

>gnl|CDD|217843 pfam04012, PspA_IM30, PspA/IM30 family

 Score =  104 bits (260), Expect = 7e-28
 Identities = 51/117 (43%), Positives = 74/117 (63%)

Query: 77  NLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKC 136
            +F RL R++++  +  L   EDPEK+LEQA+ +M  +L K RQA AQV+A QK+LE K 
Sbjct: 1   GIFKRLLRLLRANIHEGLDKAEDPEKMLEQAIRDMQSELGKARQALAQVIARQKQLERKL 60

Query: 137 KAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNL 193
           +  ++ ++    KA+ AL KG E+LAREAL    +    A AL+ QL QQ++ V  L
Sbjct: 61  EEQKEQAKKLENKARAALTKGNEELAREALAEIATLEKQAEALETQLTQQRSAVEQL 117

This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma(54) containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator. Length = 220

>gnl|CDD|213755 TIGR02977, phageshock_pspA, phage shock protein A

 Score =  103 bits (258), Expect = 2e-27
 Identities = 47/110 (42%), Positives = 66/110 (60%)

Query: 76  MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
           M +F R A +V S  NA+L   EDPEK++   + EM D LV++R A+A+ +A +K LE +
Sbjct: 1   MGIFSRFADIVNSNLNALLDKAEDPEKMIRLIIQEMEDTLVEVRTASARTIADKKELERR 60

Query: 136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQ 185
               E    DW  KA+LAL KG EDLAR AL  ++   + A AL+ +L  
Sbjct: 61  VSRLEAQVADWQDKAELALSKGREDLARAALIEKQKAQELAEALERELAA 110

Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects [Cellular processes, Adaptations to atypical conditions]. Length = 219

>gnl|CDD|182657 PRK10698, PRK10698, phage shock protein PspA; Provisional

 Score = 79.8 bits (197), Expect = 2e-18
 Identities = 41/110 (37%), Positives = 66/110 (60%)

Query: 76  MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENK 135
           M +F R A +V +  NA+L   EDP+K++   + EM D LV++R  +A+ LA +K+L  +
Sbjct: 1   MGIFSRFADIVNANINALLEKAEDPQKLVRLMIQEMEDTLVEVRSTSARALAEKKQLTRR 60

Query: 136 CKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQ 185
            + AE    +W  KA+LAL+K +EDLAR AL  ++   D    L+ ++  
Sbjct: 61  IEQAEAQQVEWQEKAELALRKEKEDLARAALIEKQKLTDLIATLEHEVTL 110

Length = 222

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	200
TIGR02977	219	phageshock_pspA phage shock protein A. Members of	99.97
PRK10698	222	phage shock protein PspA; Provisional	99.97
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	99.96
COG1842	225	PspA Phage shock protein A (IM30), suppresses sigm	99.96
PF03357	171	Snf7: Snf7; InterPro: IPR005024 This is a family o	97.1
PTZ00446	191	vacuolar sorting protein SNF7-like; Provisional	97.05
KOG2910	209	consensus Uncharacterized conserved protein predic	95.51
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	95.31
KOG2911	439	consensus Uncharacterized conserved protein [Funct	95.12
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	94.16
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	94.11
KOG0963	629	consensus Transcription factor/CCAAT displacement	93.35
PRK11637	428	AmiB activator; Provisional	93.19
PTZ00464	211	SNF-7-like protein; Provisional	93.04
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	93.03
PRK08476	141	F0F1 ATP synthase subunit B'; Validated	93.02
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	92.55
PF03194	254	LUC7: LUC7 N_terminus; InterPro: IPR004882 This fa	92.41
PF11180	192	DUF2968: Protein of unknown function (DUF2968); In	92.12
PF05816	333	TelA: Toxic anion resistance protein (TelA); Inter	91.62
KOG0971	1243	consensus Microtubule-associated protein dynactin	91.62
CHL00118	156	atpG ATP synthase CF0 B' subunit; Validated	91.22
PRK11637	428	AmiB activator; Provisional	91.12
PRK09174	204	F0F1 ATP synthase subunit B'; Validated	90.83
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	90.79
PRK04863	1486	mukB cell division protein MukB; Provisional	90.77
PRK15422	79	septal ring assembly protein ZapB; Provisional	90.74
PF06637	442	PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 Th	90.54
PRK02224	880	chromosome segregation protein; Provisional	90.35
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	90.31
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	90.06
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	89.96
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	89.79
PRK13454	181	F0F1 ATP synthase subunit B'; Provisional	89.79
PRK09039	343	hypothetical protein; Validated	89.65
COG1382	119	GimC Prefoldin, chaperonin cofactor [Posttranslati	89.33
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	89.14
PF00038	312	Filament: Intermediate filament protein; InterPro:	89.1
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	88.92
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	88.9
PRK10884	206	SH3 domain-containing protein; Provisional	88.88
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	88.84
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	88.77
PRK02224	880	chromosome segregation protein; Provisional	88.6
PF05103	131	DivIVA: DivIVA protein; InterPro: IPR007793 The Ba	88.49
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	88.48
KOG3232	203	consensus Vacuolar assembly/sorting protein DID2 [	88.3
PF00769	246	ERM: Ezrin/radixin/moesin family; InterPro: IPR011	88.23
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	87.88
PRK06569	155	F0F1 ATP synthase subunit B'; Validated	87.88
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	87.87
KOG1656	221	consensus Protein involved in glucose derepression	87.76
KOG0971	1243	consensus Microtubule-associated protein dynactin	87.62
smart00685	59	DM14 Repeats in fly CG4713, worm Y37H9A.3 and huma	87.04
TIGR02977	219	phageshock_pspA phage shock protein A. Members of	87.03
PRK12704	520	phosphodiesterase; Provisional	86.97
PRK00409	782	recombination and DNA strand exchange inhibitor pr	86.86
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	86.55
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	86.47
PRK08476	141	F0F1 ATP synthase subunit B'; Validated	86.42
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	85.49
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	85.35
PRK10698	222	phage shock protein PspA; Provisional	85.13
PRK14472	175	F0F1 ATP synthase subunit B; Provisional	85.08
TIGR02473	141	flagell_FliJ flagellar export protein FliJ. Member	84.94
PRK09343	121	prefoldin subunit beta; Provisional	84.86
PRK09039	343	hypothetical protein; Validated	84.46
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	84.36
PRK14475	167	F0F1 ATP synthase subunit B; Provisional	84.21
PRK00106	535	hypothetical protein; Provisional	83.89
smart00502	127	BBC B-Box C-terminal domain. Coiled coil region C-	83.87
PF05546	207	She9_MDM33: She9 / Mdm33 family; InterPro: IPR0088	83.44
PF12128	1201	DUF3584: Protein of unknown function (DUF3584); In	83.31
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	83.27
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	83.27
PF06008	264	Laminin_I: Laminin Domain I; InterPro: IPR009254 L	83.07
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	82.92
TIGR02231	525	conserved hypothetical protein. This family consis	82.82
TIGR03545	555	conserved hypothetical protein TIGR03545. This mod	82.81
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	82.74
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	82.61
TIGR02338	110	gimC_beta prefoldin, beta subunit, archaeal. Chape	82.44
PHA02562	562	46 endonuclease subunit; Provisional	82.43
PF03148	384	Tektin: Tektin family; InterPro: IPR000435 Tektin	81.87
PRK03918	880	chromosome segregation protein; Provisional	81.82
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	81.73
KOG2391	365	consensus Vacuolar sorting protein/ubiquitin recep	81.67
PRK13428	445	F0F1 ATP synthase subunit delta; Provisional	81.53
PRK06569	155	F0F1 ATP synthase subunit B'; Validated	81.52
PRK13460	173	F0F1 ATP synthase subunit B; Provisional	81.02
PRK06231	205	F0F1 ATP synthase subunit B; Validated	80.54
TIGR01144	147	ATP_synt_b ATP synthase, F0 subunit b. This model	80.39
PRK05431	425	seryl-tRNA synthetase; Provisional	80.27
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	80.2

>TIGR02977 phageshock_pspA phage shock protein A

Probab=99.97  E-value=6.6e-30  Score=217.38  Aligned_cols=123  Identities=38%  Similarity=0.595  Sum_probs=121.3

Q ss_pred             CcHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029028           76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQ  155 (200)
Q Consensus        76 Msif~Rl~~lvra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~  155 (200)
                      ||||+||+++|+|++|+++|++|||++||+|+|+||+++|.+++++++.+++.+++++++++++...+++|+++|+.||+
T Consensus         1 M~if~Rl~~iv~a~~n~~~dk~EDP~~~l~q~irem~~~l~~ar~~lA~~~a~~k~~e~~~~~~~~~~~~~~~~A~~Al~   80 (219)
T TIGR02977         1 MGIFSRFADIVNSNLNALLDKAEDPEKMIRLIIQEMEDTLVEVRTTSARTIADKKELERRVSRLEAQVADWQEKAELALS   80 (219)
T ss_pred             CcHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029028          156 KGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNTR  198 (200)
Q Consensus       156 ~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l~  198 (200)
                      +|+||||++||.++..++..+..|+.+++.+...|++|+..|.
T Consensus        81 ~G~EdLAr~Al~~k~~~~~~~~~l~~~~~~~~~~v~~l~~~l~  123 (219)
T TIGR02977        81 KGREDLARAALIEKQKAQELAEALERELAAVEETLAKLQEDIA  123 (219)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999998875

Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.

>PRK10698 phage shock protein PspA; Provisional

Probab=99.97  E-value=8.6e-30  Score=217.80  Aligned_cols=123  Identities=33%  Similarity=0.546  Sum_probs=121.0

Q ss_pred             CcHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029028           76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQ  155 (200)
Q Consensus        76 Msif~Rl~~lvra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~  155 (200)
                      ||||+||+++|+|++|+++|++|||++||+|+|+||++++.++++++|.+++.++++++++.++...+++|+.+|+.||.
T Consensus         1 M~if~Rl~~ii~a~in~~ldkaEDP~k~l~q~i~em~~~l~~~r~alA~~~A~~k~~er~~~~~~~~~~~~e~kA~~Al~   80 (222)
T PRK10698          1 MGIFSRFADIVNANINALLEKAEDPQKLVRLMIQEMEDTLVEVRSTSARALAEKKQLTRRIEQAEAQQVEWQEKAELALR   80 (222)
T ss_pred             CCHHHHHHHHHHhHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029028          156 KGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNTR  198 (200)
Q Consensus       156 ~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l~  198 (200)
                      +|+|||||+||.+|..++..+..|+.+++.+...+++|+..+.
T Consensus        81 ~G~EdLAr~AL~~K~~~~~~~~~l~~~~~~~~~~~~~L~~~l~  123 (222)
T PRK10698         81 KEKEDLARAALIEKQKLTDLIATLEHEVTLVDETLARMKKEIG  123 (222)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999988775

>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription

Probab=99.96  E-value=3.5e-28  Score=205.45  Aligned_cols=122  Identities=48%  Similarity=0.692  Sum_probs=120.3

Q ss_pred             cHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 029028           77 NLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQK  156 (200)
Q Consensus        77 sif~Rl~~lvra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~  156 (200)
                      |||+||+++|+|++|+++|++|||++||+|+||||+++|.+++++++.+++.+++++++++++...+++|+.+|..||.+
T Consensus         1 ~lf~Rl~~~~~a~~~~~ld~~EDP~~~l~q~ird~e~~l~~a~~~~a~~~a~~~~le~~~~~~~~~~~~~~~~A~~Al~~   80 (221)
T PF04012_consen    1 GLFKRLKTLVKANINELLDKAEDPEKMLEQAIRDMEEQLRKARQALARVMANQKRLERKLDEAEEEAEKWEKQAELALAA   80 (221)
T ss_pred             CHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029028          157 GEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNTR  198 (200)
Q Consensus       157 G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l~  198 (200)
                      |+||||++||.++..+++.+..++.+++.+..++++|+..|.
T Consensus        81 g~edLAr~al~~k~~~e~~~~~l~~~~~~~~~~~~~l~~~l~  122 (221)
T PF04012_consen   81 GREDLAREALQRKADLEEQAERLEQQLDQAEAQVEKLKEQLE  122 (221)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999998875

The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].

>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]

Probab=99.96  E-value=4e-28  Score=208.15  Aligned_cols=123  Identities=47%  Similarity=0.634  Sum_probs=121.3

Q ss_pred             CcHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029028           76 MNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQ  155 (200)
Q Consensus        76 Msif~Rl~~lvra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~  155 (200)
                      ||||+||+++|++++|+++|++|||++||+|+||||+.++.++++.+|++++.+++++++|++....+++|+.+|+.||.
T Consensus         1 M~i~~r~~~~~~a~~~~~~dk~EDp~~~l~Q~ird~~~~l~~ar~~~A~~~a~~k~~e~~~~~~~~~~~k~e~~A~~Al~   80 (225)
T COG1842           1 MGIFSRLKDLVKANINELLDKAEDPEKMLEQAIRDMESELAKARQALAQAIARQKQLERKLEEAQARAEKLEEKAELALQ   80 (225)
T ss_pred             CchHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029028          156 KGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNTR  198 (200)
Q Consensus       156 ~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l~  198 (200)
                      +|+|+||+++|.+++.|++.+..++.++..+...+++|+.++.
T Consensus        81 ~g~E~LAr~al~~~~~le~~~~~~~~~~~~~~~~~~~l~~~~~  123 (225)
T COG1842          81 AGNEDLAREALEEKQSLEDLAKALEAELQQAEEQVEKLKKQLA  123 (225)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999998874

>PF03357 Snf7: Snf7; InterPro: IPR005024 This is a family of eukaryotic proteins which are variously described as either hypothetical protein, developmental protein or related to yeast SNF7

Probab=97.10  E-value=0.012  Score=47.07  Aligned_cols=76  Identities=26%  Similarity=0.352  Sum_probs=67.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 029028          121 ATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSN  196 (200)
Q Consensus       121 ~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~  196 (200)
                      ++.......++++++...++.++.+...+|..++++|+.+.|+..|.+++.++..+..+...+..++....++...
T Consensus         2 ai~~Lk~~~~~L~~~~~~le~~i~~~~~~~k~~~~~~~~~~A~~~lk~~k~~~k~~~~~~~~~~~l~~~~~~ie~a   77 (171)
T PF03357_consen    2 AILKLKKTIRRLEKQIKRLEKKIKKLEKKAKKAIKKGNKERAKIYLKRKKRLEKQLEKLLNQLSNLESVLLQIETA   77 (171)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556677888999999999999999999999999999999999999999999999999999999888887777653

The family contains human CHMP1. CHMP1 (CHromatin Modifying Protein; CHarged Multivesicular body Protein), is encoded by an alternative open reading frame in the PRSM1 gene [] and is conserved in both complex and simple eukaryotes. CHMP1 contains a predicted bipartite nuclear localisation signal and distributes as distinct forms to the cytoplasm and the nuclear matrix in all cell lines tested. Human CHMP1 is strongly implicated in multivesicular body formation. A multivesicular body is a vesicle-filled endosome that targets proteins to the interior of lysosomes. Immunocytochemistry and biochemical fractionation localise CHMP1 to early endosomes and CHMP1 physically interacts with SKD1/VPS4, a highly conserved protein directly linked to multivesicular body sorting in yeast. Similar to the action of a mutant SKD1 protein, over expression of a fusion derivative of human CHMP1 dilates endosomal compartments and disrupts the normal distribution of several endosomal markers. Genetic studies in Saccharomyces cerevisiae (Baker's yeast) further support a conserved role of CHMP1 in vesicle trafficking. Deletion of CHM1, the budding yeast homologue of CHMP1, results in defective sorting of carboxypeptidases S and Y and produces abnormal, multi-lamellar prevacuolar compartments. This phenotype classifies CHM1 as a member of the class E vacuolar protein sorting genes []. ; GO: 0015031 protein transport; PDB: 2V6X_B 2W2U_D 2GD5_D 3FRT_B 3FRV_A 4ABM_D 3EAB_H 3HTU_D.

>PTZ00446 vacuolar sorting protein SNF7-like; Provisional

Probab=97.05  E-value=0.017  Score=48.93  Aligned_cols=76  Identities=18%  Similarity=0.164  Sum_probs=62.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029028          120 QATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVS  195 (200)
Q Consensus       120 ~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~  195 (200)
                      .++.........++++...++..|++....|+..+..|+-+-|..+|.+|+.||.+++.+..++..++.++..+..
T Consensus        27 ~AIl~Lk~~~~~L~krq~~Le~kIe~e~~~Ak~~~~~~kk~~Al~~LkrKK~~E~ql~q~~~ql~nLEq~~~~iE~  102 (191)
T PTZ00446         27 KAILKNREAIDALEKKQVQVEKKIKQLEIEAKQKVEQNQMSNAKILLKRKKLYEQEIENILNNRLTLEDNMINLEN  102 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444555566677777777777777888899999999999999999999999999999999999999888764

>KOG2910 consensus Uncharacterized conserved protein predicted to be involved in protein sorting [General function prediction only]

Probab=95.51  E-value=0.34  Score=41.30  Aligned_cols=77  Identities=18%  Similarity=0.180  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          118 MRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLV  194 (200)
Q Consensus       118 ar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk  194 (200)
                      .-+++-.+..++..+.+-.+.++..++.-...|+..+..|+.|-|+.+|.+|.-++.-+.+...++-..++.+..+.
T Consensus        14 ~DrAIL~lK~QRdkl~qyqkR~e~~le~Er~~Ar~lird~rKdrAlllLKkKryQE~Ll~qt~~qL~nlEqmvsdiE   90 (209)
T KOG2910|consen   14 QDRAILSLKTQRDKLKQYQKRLEKQLEAERQLARDLIRDGRKDRALLLLKKKRYQEELLTQTDNQLINLEQMVSDIE   90 (209)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555566666666666777777777788999999999999999999999999999999999999988887764

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=95.31  E-value=0.65  Score=39.33  Aligned_cols=113  Identities=17%  Similarity=0.240  Sum_probs=83.7

Q ss_pred             HHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHH
Q 029028           82 LARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDL  161 (200)
Q Consensus        82 l~~lvra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDL  161 (200)
                      +-.-+...-..+|+++||.+.-|.|.|.-+.+++.-.+..+-........+++++.+...++.+..+.... |.+   -.
T Consensus        37 ~Lk~lq~Rq~kAL~k~e~~e~~Lpqll~~h~eEvr~Lr~~LR~~q~~~r~~~~klk~~~~el~k~~~~l~~-L~~---L~  112 (194)
T PF15619_consen   37 TLKQLQKRQEKALQKYEDTEAELPQLLQRHNEEVRVLRERLRKSQEQERELERKLKDKDEELLKTKDELKH-LKK---LS  112 (194)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH---HH
Confidence            33444455667899999999999999999999999999999999999999999999999999887766654 222   11


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029028          162 AREALKRRKSYADNANALKAQLDQQKNVVNNLVSNTR  198 (200)
Q Consensus       162 Ar~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l~  198 (200)
                      ...-|.+...+...+..++..++..+..+..|..++.
T Consensus       113 ~dknL~eReeL~~kL~~~~~~l~~~~~ki~~Lek~le  149 (194)
T PF15619_consen  113 EDKNLAEREELQRKLSQLEQKLQEKEKKIQELEKQLE  149 (194)
T ss_pred             HcCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            1123344555666666666667776666666666554

>KOG2911 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.12  E-value=0.26  Score=46.47  Aligned_cols=79  Identities=19%  Similarity=0.316  Sum_probs=69.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          115 LVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNL  193 (200)
Q Consensus       115 l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~L  193 (200)
                      +.+.-.+++.++.....+.+++..+++++++...+++.|++.|.--+|..-|.+++-.+..++..-..+.+.+....+.
T Consensus       228 it~~D~~V~~L~~~~~~L~kqie~L~qeie~~~~~~r~~~k~g~K~iA~~ylr~rk~~eK~~er~~~~l~~l~~vl~~I  306 (439)
T KOG2911|consen  228 ITEIDGSVADLIQARAKLAKQIEFLEQEIEKSKEKLRQALKEGKKQIAITYLRARKLLEKDLERKVSSLNNLETVLSQI  306 (439)
T ss_pred             CccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence            4556677888888889999999999999999999999999999999999999999999999999888887776665544

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=94.16  E-value=0.77  Score=43.91  Aligned_cols=83  Identities=12%  Similarity=0.261  Sum_probs=63.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          107 AVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQ  186 (200)
Q Consensus       107 ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~  186 (200)
                      .||.+-.++.+.|..+..++.+-+.+..+-++++++......+...||+..+.++.+    ++.++.++..+++.+++++
T Consensus        60 TlrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~----~~~ql~~~~~~~~~~l~~l  135 (472)
T TIGR03752        60 TLRTLVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTK----EIEQLKSERQQLQGLIDQL  135 (472)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHH----HHHHHHHHHHHHHHHHHHH
Confidence            456777888888999999999999999999999999999999999999887655443    4555555555666666666


Q ss_pred             HHHHHHH
Q 029028          187 KNVVNNL  193 (200)
Q Consensus       187 ~~~ve~L  193 (200)
                      ..+.+.+
T Consensus       136 ~~~l~~~  142 (472)
T TIGR03752       136 QRRLAGV  142 (472)
T ss_pred             HHHHhhc
Confidence            5555443

Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.

>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=94.11  E-value=3.4  Score=35.52  Aligned_cols=98  Identities=18%  Similarity=0.237  Sum_probs=60.2

Q ss_pred             hccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q 029028           95 SSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYAD  174 (200)
Q Consensus        95 dk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~  174 (200)
                      +.+|+-...++.-|.++++.|..+...+-..-+.......+...++..|..+..+...|     +.-|-.|-.+...++.
T Consensus       130 e~aEeR~e~~E~ki~eLE~el~~~~~~lk~lE~~~~~~~~re~~~e~~i~~L~~~lkea-----E~Rae~aE~~v~~Le~  204 (237)
T PF00261_consen  130 ERAEERAEAAESKIKELEEELKSVGNNLKSLEASEEKASEREDEYEEKIRDLEEKLKEA-----ENRAEFAERRVKKLEK  204 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhchhHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHH
Confidence            33334445555666666666666666666666666666666666666666666666655     4445556666666777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhh
Q 029028          175 NANALKAQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       175 ~a~~lq~qld~~~~~ve~Lk~~l  197 (200)
                      .+..+...+.........++..|
T Consensus       205 ~id~le~eL~~~k~~~~~~~~el  227 (237)
T PF00261_consen  205 EIDRLEDELEKEKEKYKKVQEEL  227 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777777666666666665554

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....

>KOG0963 consensus Transcription factor/CCAAT displacement protein CDP1 [Transcription]

Probab=93.35  E-value=1.8  Score=42.70  Aligned_cols=125  Identities=17%  Similarity=0.206  Sum_probs=97.3

Q ss_pred             CcccccCcHHHHHHHH-----HHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           70 GALNTRMNLFDRLARV-----VKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASE  144 (200)
Q Consensus        70 ~~~~~~Msif~Rl~~l-----vra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~  144 (200)
                      -+.-+.|+++++|..+     +-+.+-.++++..+    ..-.++++...+.+....++.....+-.+.+-...+.+.-.
T Consensus        84 ~aE~afl~vye~L~eaPDP~pll~sa~~~l~k~~~----~~~e~~~lk~~lee~~~el~~~k~qq~~v~~l~e~l~k~~~  159 (629)
T KOG0963|consen   84 FAEAAFLDVYEKLIEAPDPVPLLASAAELLNKQQK----ASEENEELKEELEEVNNELADLKTQQVTVRNLKERLRKLEQ  159 (629)
T ss_pred             hhHHHHHHHHHHHhhCCCCchHHHHHHHHhhhhhh----hhhhHHHHHHHHHHHHHHHhhhhhhHHHHHhHHHHHHHHHH
Confidence            3444678888777642     22223333334333    23346688888888888888888888888888888888888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029028          145 DWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNTR  198 (200)
Q Consensus       145 ~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l~  198 (200)
                      .....++.+..--.+.+.+..+.+.+.+.++-..++.++..++..+..|...+.
T Consensus       160 ~~~~~ie~~a~~~e~~~~q~~~e~e~~L~~~~~~~~~q~~~le~ki~~lq~a~~  213 (629)
T KOG0963|consen  160 LLEIFIENAANETEEKLEQEWAEREAGLKDEEQNLQEQLEELEKKISSLQSAIE  213 (629)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            888899988888899999999999999999999999999999999999976654

>PRK11637 AmiB activator; Provisional

Probab=93.19  E-value=2.7  Score=39.00  Aligned_cols=47  Identities=17%  Similarity=0.162  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          104 LEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKA  150 (200)
Q Consensus       104 LdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA  150 (200)
                      +++.+.+.++++.+..+.+.........++.+++.+..++...+.+.
T Consensus        45 ~~~~l~~l~~qi~~~~~~i~~~~~~~~~~~~~l~~l~~qi~~~~~~i   91 (428)
T PRK11637         45 NRDQLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAISQASRKL   91 (428)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44445555555555555555555555555555555555555554433

>PTZ00464 SNF-7-like protein; Provisional

Probab=93.04  E-value=2.3  Score=36.53  Aligned_cols=37  Identities=14%  Similarity=0.176  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029028          159 EDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVS  195 (200)
Q Consensus       159 EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~  195 (200)
                      -.-|..+|.+|+.||.+++.+..++..+++.+..+..
T Consensus        60 K~~Al~~LK~KK~~E~ql~~l~~q~~nleq~~~~ie~   96 (211)
T PTZ00464         60 KQRAMQLLQQKRMYQNQQDMMMQQQFNMDQLQFTTES   96 (211)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4577889999999999999999888888877776643

>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association []

Probab=93.03  E-value=5.9  Score=35.72  Aligned_cols=93  Identities=13%  Similarity=0.162  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKA  181 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~  181 (200)
                      ..|+..+..|+++...+...+..+-...-.+...+..+..++..++..... +...|-+--..+-.+...+...+...+.
T Consensus       152 ~~L~~~~~~L~~D~~~L~~~~~~l~~~~~~l~~~~~~L~~e~~~Lk~~~~e-~~~~D~~eL~~lr~eL~~~~~~i~~~k~  230 (325)
T PF08317_consen  152 EGLEENLELLQEDYAKLDKQLEQLDELLPKLRERKAELEEELENLKQLVEE-IESCDQEELEALRQELAEQKEEIEAKKK  230 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-hhhcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566666666666666666666666667777777777777777666554 3333333333344444444444444444


Q ss_pred             HHHHHHHHHHHHHh
Q 029028          182 QLDQQKNVVNNLVS  195 (200)
Q Consensus       182 qld~~~~~ve~Lk~  195 (200)
                      .+++++.+...++.
T Consensus       231 ~l~el~~el~~l~~  244 (325)
T PF08317_consen  231 ELAELQEELEELEE  244 (325)
T ss_pred             HHHHHHHHHHHHHH
Confidence            44444444444433

>PRK08476 F0F1 ATP synthase subunit B'; Validated

Probab=93.02  E-value=3.8  Score=32.61  Aligned_cols=13  Identities=23%  Similarity=0.148  Sum_probs=4.8

Q ss_pred             HHHHHHHHHHHHH
Q 029028          107 AVLEMNDDLVKMR  119 (200)
Q Consensus       107 ~IReme~~l~kar  119 (200)
                      ...+.++.+.+++
T Consensus        60 ~~~e~e~~l~~Ar   72 (141)
T PRK08476         60 IEHEIETILKNAR   72 (141)
T ss_pred             HHHHHHHHHHHHH
Confidence            3333333333333

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=92.55  E-value=2.9  Score=39.94  Aligned_cols=93  Identities=13%  Similarity=0.127  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          106 QAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQ  185 (200)
Q Consensus       106 Q~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~  185 (200)
                      |++.+.-............+.+.++-+|+++.+....+++|+++-.. ++.-+..|-+.-...+..+++.-+.++.++..
T Consensus       354 ~~~e~~~~e~~~l~~~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~~-~~E~n~~l~knq~vw~~kl~~~~e~~~~~~~s  432 (493)
T KOG0804|consen  354 QYYELLITEADSLKQESSDLEAEKKIVERKLQQLQTKLKKCQKELKE-EREENKKLIKNQDVWRGKLKELEEREKEALGS  432 (493)
T ss_pred             HHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444445556667777888888899999999999998877543 23333344444445555566666666666666


Q ss_pred             HHHHHHHHHhhhhc
Q 029028          186 QKNVVNNLVSNTRV  199 (200)
Q Consensus       186 ~~~~ve~Lk~~l~~  199 (200)
                      .+.++..|+.+||+
T Consensus       433 ~d~~I~dLqEQlrD  446 (493)
T KOG0804|consen  433 KDEKITDLQEQLRD  446 (493)
T ss_pred             HHHHHHHHHHHHHh
Confidence            67777777766653

>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes

Probab=92.41  E-value=1.9  Score=37.89  Aligned_cols=92  Identities=11%  Similarity=0.235  Sum_probs=74.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q 029028          100 PEKILEQAVLEMNDDLVKMRQATAQVLAS-----QKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYAD  174 (200)
Q Consensus       100 P~~mLdQ~IReme~~l~kar~~lA~v~A~-----~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~  174 (200)
                      -...|+.+|+|++..|.+++..|+.....     ......++..+..+|.+.-.+|+.+=..|+-|-|...+.+...+..
T Consensus        84 ~~~~L~~~i~d~drrI~~~k~RL~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~  163 (254)
T PF03194_consen   84 FLRYLQRLIRDCDRRIERAKERLEQTQEEQAKEADEEKAEKIDELDEKIGELLKEAEELGEEGDVDEAQKLMEEVEKLKE  163 (254)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            34889999999999999999888763322     1112678999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q 029028          175 NANALKAQLDQQKNVVN  191 (200)
Q Consensus       175 ~a~~lq~qld~~~~~ve  191 (200)
                      +...++.+++.......
T Consensus       164 ek~~le~~~~~~~~~~~  180 (254)
T PF03194_consen  164 EKEELEKELEEYRNSIE  180 (254)
T ss_pred             HHHHHHhhhhhhhhhhh
Confidence            88888886655544433

LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].

>PF11180 DUF2968: Protein of unknown function (DUF2968); InterPro: IPR021350 This family of proteins has no known function

Probab=92.12  E-value=3.6  Score=35.07  Aligned_cols=111  Identities=22%  Similarity=0.224  Sum_probs=65.9

Q ss_pred             HHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCH
Q 029028           80 DRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEE  159 (200)
Q Consensus        80 ~Rl~~lvra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~E  159 (200)
                      +.||++||..      .....|.+.....+. -..|....-.-+...|++..+++.+...+..++.++.....+-.....
T Consensus        72 k~fWRViKt~------d~~~AE~~Y~~F~~Q-t~~LA~~eirR~~LeAQka~~eR~ia~~~~ra~~LqaDl~~~~~Q~~~  144 (192)
T PF11180_consen   72 KAFWRVIKTQ------DEARAEAIYRDFAQQ-TARLADVEIRRAQLEAQKAQLERLIAESEARANRLQADLQIARQQQQQ  144 (192)
T ss_pred             CceeEeeecC------ChhhHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567766653      111223333333322 334555666666777777778888887777777777666655443332


Q ss_pred             HHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029028          160 DLA--REALKRRKSYADNANALKAQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       160 DLA--r~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l  197 (200)
                      --.  +.+-.+...++.+-...+.+|+.+..+|..|....
T Consensus       145 va~~Q~q~r~ea~aL~~e~~aaqaQL~~lQ~qv~~Lq~q~  184 (192)
T PF11180_consen  145 VAARQQQARQEAQALEAERRAAQAQLRQLQRQVRQLQRQA  184 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            222  33444556677777777777888888877777654

>PF05816 TelA: Toxic anion resistance protein (TelA); InterPro: IPR008863 This family consists of several prokaryotic TelA like proteins

Probab=91.62  E-value=9  Score=34.68  Aligned_cols=70  Identities=7%  Similarity=0.113  Sum_probs=48.7

Q ss_pred             cCcHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           75 RMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASE  144 (200)
Q Consensus        75 ~Msif~Rl~~lvra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~  144 (200)
                      .-|+|.||+.-++..+..++.+++.-..-+|..+.+++..-....+..+..-.........+.++..-|.
T Consensus        71 ~~~~l~klf~k~~~~~~~~~~ky~sv~~qId~I~~~L~~~~~~L~~d~~~L~~l~~~n~~~~~~L~~~I~  140 (333)
T PF05816_consen   71 KKGFLGKLFGKAKNSLERYFAKYQSVQSQIDKIIAELESGQDELLRDNAMLDQLYEKNWEYYQELEKYIA  140 (333)
T ss_pred             hhhHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3578888777777888888888888888888888887777777777666555555544444444444433

TelA and KlA are associated with tellurite resistance [] and plasmid fertility inhibition [].

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=91.62  E-value=19  Score=37.52  Aligned_cols=122  Identities=16%  Similarity=0.245  Sum_probs=67.6

Q ss_pred             ccCcHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH
Q 029028           74 TRMNLFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQAS---EDWYRKA  150 (200)
Q Consensus        74 ~~Msif~Rl~~lvra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i---~~we~rA  150 (200)
                      +.|++=..|+++-.--=---+.+.||-.++.+  +..|.=++.+...--.+.|..+-.|++++.+.+.++   .+|..+-
T Consensus       225 te~eLr~QvrdLtEkLetlR~kR~EDk~Kl~E--lekmkiqleqlqEfkSkim~qqa~Lqrel~raR~e~keaqe~ke~~  302 (1243)
T KOG0971|consen  225 TEEELRAQVRDLTEKLETLRLKRAEDKAKLKE--LEKMKIQLEQLQEFKSKIMEQQADLQRELKRARKEAKEAQEAKERY  302 (1243)
T ss_pred             chHHHHHHHHHHHHHHHHHHhhhhhhHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45665555554443333334566778887765  445555566666666667777777777777665544   3343333


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029028          151 QLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNTR  198 (200)
Q Consensus       151 ~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l~  198 (200)
                      ..-+.---|.. .-+--.|.-.|+.++.|+..++.+++.++.|...|.
T Consensus       303 k~emad~ad~i-EmaTldKEmAEERaesLQ~eve~lkEr~deletdlE  349 (1243)
T KOG0971|consen  303 KEEMADTADAI-EMATLDKEMAEERAESLQQEVEALKERVDELETDLE  349 (1243)
T ss_pred             HHHHHHHHHHH-HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            22221111110 112334555666777777777777777777666553

>CHL00118 atpG ATP synthase CF0 B' subunit; Validated

Probab=91.22  E-value=6.7  Score=31.52  Aligned_cols=52  Identities=17%  Similarity=0.173  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLA  153 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~A  153 (200)
                      .++++--..+.+++.++.+...++.......+.++.+.+.++.+.-+.|+..
T Consensus        49 ~~l~~R~~~I~~~l~~Ae~~~~ea~~~~~e~e~~L~~A~~ea~~ii~~A~~~  100 (156)
T CHL00118         49 KVLDERKEYIRKNLTKASEILAKANELTKQYEQELSKARKEAQLEITQSQKE  100 (156)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5566666666666666666666666666666666666666655555555544

>PRK11637 AmiB activator; Provisional

Probab=91.12  E-value=9.4  Score=35.46  Aligned_cols=58  Identities=10%  Similarity=0.152  Sum_probs=37.5

Q ss_pred             HHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           91 NAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYR  148 (200)
Q Consensus        91 n~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~  148 (200)
                      .++++.+.+-..-|.....++++++.+....++.....+..++.+..+.+..+++++.
T Consensus       169 ~~~l~~l~~~~~~L~~~k~~le~~~~~l~~~~~e~~~~k~~L~~~k~e~~~~l~~L~~  226 (428)
T PRK11637        169 QETIAELKQTREELAAQKAELEEKQSQQKTLLYEQQAQQQKLEQARNERKKTLTGLES  226 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666666666666667777777777777777777777666666665555555543

>PRK09174 F0F1 ATP synthase subunit B'; Validated

Probab=90.83  E-value=9.3  Score=32.47  Aligned_cols=52  Identities=17%  Similarity=0.127  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLA  153 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~A  153 (200)
                      .+|+.--..+.+++.++.+...++.......+.++.+.+.++.+.-..|+..
T Consensus        80 ~vLe~R~~~I~~~L~~Ae~~k~eAe~~~~~ye~~L~~Ar~eA~~Ii~~Ar~e  131 (204)
T PRK09174         80 GIIETRRDRIAQDLDQAARLKQEADAAVAAYEQELAQARAKAHSIAQAAREA  131 (204)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555555555555555555555555555555555555554444443

>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes

Probab=90.79  E-value=10  Score=38.13  Aligned_cols=105  Identities=17%  Similarity=0.313  Sum_probs=61.6

Q ss_pred             HhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHH---HHhcCCH---
Q 029028           93 ILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQ-------KRLENKCKAAEQASEDWYRKAQL---ALQKGEE---  159 (200)
Q Consensus        93 ~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~-------k~le~k~~~~~~~i~~we~rA~~---AL~~G~E---  159 (200)
                      -+......++.+...|.+++.+.+.++..+......+       ..+|+++.+....-...|.+...   +-+...+   
T Consensus       447 qis~l~~~Er~lk~eL~qlr~ene~Lq~Kl~~L~~aRq~DKq~l~~LEkrL~eE~~~R~~lEkQL~eErk~r~~ee~~aa  526 (697)
T PF09726_consen  447 QISSLTNNERSLKSELSQLRQENEQLQNKLQNLVQARQQDKQSLQQLEKRLAEERRQRASLEKQLQEERKARKEEEEKAA  526 (697)
T ss_pred             HHhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhh
Confidence            3444555556666666666666555555444444333       44555555555554444444322   1111112   


Q ss_pred             -----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029028          160 -----------DLAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       160 -----------DLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l  197 (200)
                                 +-+..+-.|+.++|.++..++.++..-++++..|+..+
T Consensus       527 r~~~~~~~~r~e~~e~~r~r~~~lE~E~~~lr~elk~kee~~~~~e~~~  575 (697)
T PF09726_consen  527 RALAQAQATRQECAESCRQRRRQLESELKKLRRELKQKEEQIRELESEL  575 (697)
T ss_pred             hccccchhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                       33333556888999999999999988888888887765

; GO: 0016021 integral to membrane

>PRK04863 mukB cell division protein MukB; Provisional

Probab=90.77  E-value=8.6  Score=41.77  Aligned_cols=76  Identities=22%  Similarity=0.241  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHHHHHHHhhccCCHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           78 LFDRLARVVKSYANAILSSFEDPE---KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLAL  154 (200)
Q Consensus        78 if~Rl~~lvra~in~~ldk~EDP~---~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL  154 (200)
                      +|+.|-....+++-+-.  +-.|+   .+++.. --.+....++++.+..+.....+++..+.++..++.+++..+..|.
T Consensus       258 lFk~lI~~~~~~~aad~--~r~~eERR~liEEA-ag~r~rk~eA~kkLe~tE~nL~rI~diL~ELe~rL~kLEkQaEkA~  334 (1486)
T PRK04863        258 LFKHLITESTNYVAADY--MRHANERRVHLEEA-LELRRELYTSRRQLAAEQYRLVEMARELAELNEAESDLEQDYQAAS  334 (1486)
T ss_pred             HHHHHhhhhhhhhHHHH--hhCHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67777777777664444  33453   777777 4577888888888889999999999989999999988888888886


Q ss_pred             hc
Q 029028          155 QK  156 (200)
Q Consensus       155 ~~  156 (200)
                      +.
T Consensus       335 ky  336 (1486)
T PRK04863        335 DH  336 (1486)
T ss_pred             HH
Confidence            65

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=90.74  E-value=5.3  Score=29.47  Aligned_cols=60  Identities=15%  Similarity=0.266  Sum_probs=54.7

Q ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 029028           97 FEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQK  156 (200)
Q Consensus        97 ~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~  156 (200)
                      +-|-+.+|...|.|++++=....+....+...+..++++...+..+-..|+.|.+.-|.+
T Consensus        16 AvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~~~WqerLr~LLGk   75 (79)
T PRK15422         16 AIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQALLGR   75 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            336789999999999999999999999999999999999999999999999998876654

>PF06637 PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 This family consists of several PV-1 (PLVAP) proteins, which seem to be specific to mammals

Probab=90.54  E-value=7.6  Score=36.53  Aligned_cols=32  Identities=19%  Similarity=0.379  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 029028          165 ALKRRKSYADNANALKAQLDQQKNVVNNLVSN  196 (200)
Q Consensus       165 AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~  196 (200)
                      ||++|..+..+-+.+..+++.-+++++.|+..
T Consensus       347 aLEEKaaLrkerd~L~keLeekkreleql~~q  378 (442)
T PF06637_consen  347 ALEEKAALRKERDSLAKELEEKKRELEQLKMQ  378 (442)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444433

PV-1 is a novel protein component of the endothelial fenestral and stomatal diaphragms []. The function of this family is unknown.

>PRK02224 chromosome segregation protein; Provisional

Probab=90.35  E-value=17  Score=36.61  Aligned_cols=36  Identities=14%  Similarity=0.198  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          112 NDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWY  147 (200)
Q Consensus       112 e~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we  147 (200)
                      ...+..++..+..+......++.++..+..++++++
T Consensus       205 ~~~l~~~~~~l~el~~~i~~~~~~~~~l~~~l~~l~  240 (880)
T PRK02224        205 HERLNGLESELAELDEEIERYEEQREQARETRDEAD  240 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444444444444444444443

>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs

Probab=90.31  E-value=7  Score=39.31  Aligned_cols=119  Identities=18%  Similarity=0.260  Sum_probs=64.6

Q ss_pred             CcHHHHHHHHHHHH-HH---HHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           76 MNLFDRLARVVKSY-AN---AILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQ  151 (200)
Q Consensus        76 Msif~Rl~~lvra~-in---~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~  151 (200)
                      -.+|.+-..+++-. +.   .+-+.++--...|...+.+--+.+.+++.....+......+..+|+++.+.-+.+.+|+.
T Consensus       538 l~lL~~a~~vlreeYi~~~~~ar~ei~~rv~~Lk~~~e~Ql~~L~~l~e~~~~l~~~ae~LaeR~e~a~d~Qe~L~~R~~  617 (717)
T PF10168_consen  538 LELLSQATKVLREEYIEKQDLAREEIQRRVKLLKQQKEQQLKELQELQEERKSLRESAEKLAERYEEAKDKQEKLMKRVD  617 (717)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34666666666644 22   122222223355666666656666667777777777777777777777777777777776


Q ss_pred             HHHhcCCH---HHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          152 LALQKGEE---DLA---REALKRRKSYADNANALKAQLDQQKNVVNNLV  194 (200)
Q Consensus       152 ~AL~~G~E---DLA---r~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk  194 (200)
                      .-+..=..   .|-   |+...+...+.+++..++..+++.+...+..+
T Consensus       618 ~vl~~l~~~~P~LS~AEr~~~~EL~~~~~~l~~l~~si~~lk~k~~~Q~  666 (717)
T PF10168_consen  618 RVLQLLNSQLPVLSEAEREFKKELERMKDQLQDLKASIEQLKKKLDYQQ  666 (717)
T ss_pred             HHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            54332211   111   33344444444455555555555444444433

It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].

>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]

Probab=90.06  E-value=6.2  Score=41.98  Aligned_cols=50  Identities=16%  Similarity=0.097  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQ  151 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~  151 (200)
                      +-.+-.|+..++.|.+++..++.+........+++.+++..++++..++.
T Consensus      1587 ~~a~~~~~~a~~~l~kv~~~t~~aE~~~~~a~q~~~eL~~~~e~lk~~~~ 1636 (1758)
T KOG0994|consen 1587 QGADRDIRLAQQLLAKVQEETAAAEKLATSATQQLGELETRMEELKHKAA 1636 (1758)
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444566666667777776666666666666666666666666665543

>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=89.96  E-value=8.2  Score=34.89  Aligned_cols=89  Identities=13%  Similarity=0.201  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKA  181 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~  181 (200)
                      .-++..+.+++.+..++.+.+..+..+...+.+++..++.+.++++..-..-...-+     .-..+..++.++...++.
T Consensus        46 ~~~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n-----~~~~~l~~~~~e~~sl~~  120 (314)
T PF04111_consen   46 EELEEELEKLEQEEEELLQELEELEKEREELDQELEELEEELEELDEEEEEYWREYN-----ELQLELIEFQEERDSLKN  120 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHH
Confidence            556666666666666666666666666666666666666666665544333222111     122344556677777888


Q ss_pred             HHHHHHHHHHHHHh
Q 029028          182 QLDQQKNVVNNLVS  195 (200)
Q Consensus       182 qld~~~~~ve~Lk~  195 (200)
                      +++....++++|++
T Consensus       121 q~~~~~~~L~~L~k  134 (314)
T PF04111_consen  121 QYEYASNQLDRLRK  134 (314)
T ss_dssp             HHHHHHHHHHCHHT
T ss_pred             HHHHHHHHHHHHHh
Confidence            88888888887764

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=89.79  E-value=5.2  Score=38.62  Aligned_cols=60  Identities=22%  Similarity=0.167  Sum_probs=35.3

Q ss_pred             HHHHhhccC-CHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           90 ANAILSSFE-DPEKILEQAVLEMNDDLVKMRQAT-AQVLASQKRLENKCKAAEQASEDWYRK  149 (200)
Q Consensus        90 in~~ldk~E-DP~~mLdQ~IReme~~l~kar~~l-A~v~A~~k~le~k~~~~~~~i~~we~r  149 (200)
                      ....++.++ +.+.++++...++++...+++... ..+...+..+++++++.+.++.+++++
T Consensus        23 a~~~l~~Ae~eAe~i~keA~~eAke~~ke~~~EaeeE~~~~R~Ele~el~~~e~rL~qrE~r   84 (514)
T TIGR03319        23 AEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQRLERR   84 (514)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444333 445777777777766666666555 455555566666665656666666555

>PRK13454 F0F1 ATP synthase subunit B'; Provisional

Probab=89.79  E-value=10  Score=31.36  Aligned_cols=51  Identities=10%  Similarity=0.179  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQL  152 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~  152 (200)
                      .+|++--..+.+++.++.....++.......+.++...+.+....-+.|+.
T Consensus        58 ~~l~~R~~~I~~~l~~Ae~~~~eA~~~~~eye~~L~~Ar~EA~~ii~~A~~  108 (181)
T PRK13454         58 AVLAERQGTITNDLAAAEELKQKAVEAEKAYNKALADARAEAQRIVAETRA  108 (181)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455544444445555555555555555555555555555555444444433

>PRK09039 hypothetical protein; Validated

Probab=89.65  E-value=11  Score=34.48  Aligned_cols=44  Identities=18%  Similarity=0.162  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          108 VLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQ  151 (200)
Q Consensus       108 IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~  151 (200)
                      +.+++++|...+....+......+|.+++..++.++..++....
T Consensus       118 ~~~l~~~L~~~k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~  161 (343)
T PRK09039        118 AGELAQELDSEKQVSARALAQVELLNQQIAALRRQLAALEAALD  161 (343)
T ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344445555555555555555555555555555444444333

>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]

Probab=89.33  E-value=9.3  Score=30.21  Aligned_cols=92  Identities=21%  Similarity=0.273  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHhcCC-------HHHHHHHHHHHHHHHHHH
Q 029028          107 AVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRK---AQLALQKGE-------EDLAREALKRRKSYADNA  176 (200)
Q Consensus       107 ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~r---A~~AL~~G~-------EDLAr~AL~rk~~~e~~a  176 (200)
                      .+.+.-.++.+....+..++.++..++.+++++....++++.-   +.-...-|+       +++-.+.=.++..++-++
T Consensus         7 ~~q~~l~q~QqLq~ql~~~~~qk~~le~qL~E~~~al~Ele~l~eD~~vYk~VG~llvk~~k~~~~~eL~er~E~Le~ri   86 (119)
T COG1382           7 EVQAQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELEKLDEDAPVYKKVGNLLVKVSKEEAVDELEERKETLELRI   86 (119)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHhhhHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence            3445556778888899999999999999999888776666543   333444444       555566666777788888


Q ss_pred             HHHHHHHHHHHHHHHHHHhhhh
Q 029028          177 NALKAQLDQQKNVVNNLVSNTR  198 (200)
Q Consensus       177 ~~lq~qld~~~~~ve~Lk~~l~  198 (200)
                      ..++.|-+..+..+++|+..|.
T Consensus        87 ~tLekQe~~l~e~l~eLq~~i~  108 (119)
T COG1382          87 KTLEKQEEKLQERLEELQSEIQ  108 (119)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            8898888888888888888775

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=89.14  E-value=5  Score=29.13  Aligned_cols=63  Identities=14%  Similarity=0.262  Sum_probs=55.1

Q ss_pred             hhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 029028           94 LSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQK  156 (200)
Q Consensus        94 ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~  156 (200)
                      +..+-|...+|.-.|.++++.-....+.+..+.-...-++++-..+..+-.-|+.+.+.-|.+
T Consensus        13 iqqAvdTI~LLQmEieELKEknn~l~~e~q~~q~~reaL~~eneqlk~e~~~WQerlrsLLGk   75 (79)
T COG3074          13 VQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALERENEQLKEEQNGWQERLRALLGK   75 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            334447789999999999999999999999999999999999999999999999999877654

>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope

Probab=89.10  E-value=15  Score=32.23  Aligned_cols=62  Identities=10%  Similarity=0.148  Sum_probs=34.1

Q ss_pred             HHHHHHHHHhhccCC----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           85 VVKSYANAILSSFED----PEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDW  146 (200)
Q Consensus        85 lvra~in~~ldk~ED----P~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~w  146 (200)
                      .+...++.+-++...    ...+++..|++++..|..+...-+.+......+..++.++..+.+..
T Consensus        29 ~Le~~i~~~~~~~~~~~~~~~~~ye~el~~lr~~id~~~~eka~l~~e~~~l~~e~~~~r~k~e~e   94 (312)
T PF00038_consen   29 RLESEIEELREKKGEEVSRIKEMYEEELRELRRQIDDLSKEKARLELEIDNLKEELEDLRRKYEEE   94 (312)
T ss_dssp             HHHHHHHH---------HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHhcccccCcccccchhhHHHHhHHhhhhHHHHhhHHhhhhhhHHHHHHHHHHHHHHH
Confidence            455555655555322    23667777777777777776666666666666666666655555544

They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....

>smart00787 Spc7 Spc7 kinetochore protein

Probab=88.92  E-value=18  Score=32.85  Aligned_cols=96  Identities=10%  Similarity=0.087  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Q 029028          101 EKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALK  180 (200)
Q Consensus       101 ~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq  180 (200)
                      ...|+..+..|+.+.....+.+..+-...-.+..++..+..++..+.+.....=..+ .+..+.+=.+......++...+
T Consensus       146 k~~L~~~~~~l~~D~~~L~~~~~~l~~~~~~l~~~~~~L~~e~~~L~~~~~e~~~~d-~~eL~~lk~~l~~~~~ei~~~~  224 (312)
T smart00787      146 KEGLDENLEGLKEDYKLLMKELELLNSIKPKLRDRKDALEEELRQLKQLEDELEDCD-PTELDRAKEKLKKLLQEIMIKV  224 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhCC-HHHHHHHHHHHHHHHHHHHHHH
Confidence            355666666677776666666666666666677777777777777665555532333 2233333345555555555555


Q ss_pred             HHHHHHHHHHHHHHhhh
Q 029028          181 AQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       181 ~qld~~~~~ve~Lk~~l  197 (200)
                      ..+++++.++..++..|
T Consensus       225 ~~l~e~~~~l~~l~~~I  241 (312)
T smart00787      225 KKLEELEEELQELESKI  241 (312)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            55555555555554444

This domain is found in cell division proteins which are required for kinetochore-spindle association.

>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]

Probab=88.90  E-value=18  Score=38.08  Aligned_cols=36  Identities=17%  Similarity=0.307  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          108 VLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQAS  143 (200)
Q Consensus       108 IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i  143 (200)
                      |.++.+.+..++....++.......++.+.+.....
T Consensus       339 i~~~r~~~~~~~re~~~~~~~~~~~~n~i~~~k~~~  374 (1074)
T KOG0250|consen  339 IEEARKDLDDLRREVNDLKEEIREIENSIRKLKKEV  374 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444443333333333333333333

>PRK10884 SH3 domain-containing protein; Provisional

Probab=88.88  E-value=10  Score=32.42  Aligned_cols=34  Identities=3%  Similarity=0.027  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029028          165 ALKRRKSYADNANALKAQLDQQKNVVNNLVSNTR  198 (200)
Q Consensus       165 AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l~  198 (200)
                      .-.+-.++.+++..++.+++.++.+.+.+++++.
T Consensus       137 L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~~~~  170 (206)
T PRK10884        137 LKEENQKLKNQLIVAQKKVDAANLQLDDKQRTII  170 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344455566666677777777777777766554

>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family

Probab=88.84  E-value=13  Score=33.46  Aligned_cols=11  Identities=27%  Similarity=0.280  Sum_probs=5.3

Q ss_pred             cCccceEEeec
Q 029028           43 NGGVGALKVTR   53 (200)
Q Consensus        43 ~~~~~~~~~~~   53 (200)
                      +|-+..+.|..
T Consensus        51 ~G~v~~i~V~e   61 (423)
T TIGR01843        51 GGIVREILVRE   61 (423)
T ss_pred             CcEEEEEEeCC
Confidence            34455555543

Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.

>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]

Probab=88.77  E-value=8.1  Score=37.77  Aligned_cols=82  Identities=16%  Similarity=0.213  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HhcCCHHHHHHH--------------HHHHHHHHHHHHH
Q 029028          115 LVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLA--LQKGEEDLAREA--------------LKRRKSYADNANA  178 (200)
Q Consensus       115 l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~A--L~~G~EDLAr~A--------------L~rk~~~e~~a~~  178 (200)
                      +..++..+..+-.....++.++..+..+++++..+-..+  ...|...-.+..              ..++..++++...
T Consensus        94 l~~ar~~l~e~~~~ra~~e~ei~kl~~e~~elr~~~~~~~k~~~~~re~~~~~~~~l~~leAe~~~~krr~~~le~e~~~  173 (546)
T KOG0977|consen   94 LATARKLLDETARERAKLEIEITKLREELKELRKKLEKAEKERRGAREKLDDYLSRLSELEAEINTLKRRIKALEDELKR  173 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence            444444555555555555555555555555544444444  222322222222              3344555555555


Q ss_pred             HHHHHHHHHHHHHHHHhh
Q 029028          179 LKAQLDQQKNVVNNLVSN  196 (200)
Q Consensus       179 lq~qld~~~~~ve~Lk~~  196 (200)
                      ++.+...+..++..++..
T Consensus       174 Lk~en~rl~~~l~~~r~~  191 (546)
T KOG0977|consen  174 LKAENSRLREELARARKQ  191 (546)
T ss_pred             HHHHhhhhHHHHHHHHHH
Confidence            555555555555555543

>PRK02224 chromosome segregation protein; Provisional

Probab=88.60  E-value=26  Score=35.30  Aligned_cols=46  Identities=7%  Similarity=0.190  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          105 EQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKA  150 (200)
Q Consensus       105 dQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA  150 (200)
                      ...+.+++..+.+++..+.........++.++..+...+.+|....
T Consensus       205 ~~~l~~~~~~l~el~~~i~~~~~~~~~l~~~l~~l~~~~~el~~~~  250 (880)
T PRK02224        205 HERLNGLESELAELDEEIERYEEQREQARETRDEADEVLEEHEERR  250 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445666666666666666666666666666666666665555543

>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []

Probab=88.49  E-value=0.14  Score=39.41  Aligned_cols=44  Identities=14%  Similarity=0.301  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          105 EQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYR  148 (200)
Q Consensus       105 dQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~  148 (200)
                      |.+|.++..++.......+........++.++..+......+.+
T Consensus        24 D~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~~~~~l~~   67 (131)
T PF05103_consen   24 DDFLDELAEELERLQRENAELKEEIEELQAQLEELREEEESLQR   67 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT-------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHH
Confidence            44444444444444444444444444444444444444333333

Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

Probab=88.48  E-value=15  Score=32.25  Aligned_cols=33  Identities=18%  Similarity=0.244  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          110 EMNDDLVKMRQATAQVLASQKRLENKCKAAEQA  142 (200)
Q Consensus       110 eme~~l~kar~~lA~v~A~~k~le~k~~~~~~~  142 (200)
                      .++..+..++..+....-...-++.++...+..
T Consensus        35 k~~~e~e~~~~~~~~~~~e~e~le~qv~~~e~e   67 (239)
T COG1579          35 KAKAELEALNKALEALEIELEDLENQVSQLESE   67 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333333333333

>KOG3232 consensus Vacuolar assembly/sorting protein DID2 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.30  E-value=15  Score=31.21  Aligned_cols=54  Identities=22%  Similarity=0.241  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 029028          118 MRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKS  171 (200)
Q Consensus       118 ar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~  171 (200)
                      ....+=......++|+++-..++++...-..++..|+++|+.|.||--++-...
T Consensus         7 le~~lf~LkF~sk~L~r~a~kceKeEK~Ek~K~kkAi~kgN~dvArIyAeNAIR   60 (203)
T KOG3232|consen    7 LENHLFDLKFTSKQLQRQAKKCEKEEKAEKAKLKKAIQKGNMDVARIYAENAIR   60 (203)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcchHHHHHHHHHHHH
Confidence            344555666677888888888888888888899999999999999865544333

>PF00769 ERM: Ezrin/radixin/moesin family; InterPro: IPR011259 The ERM family consists of three closely-related proteins, ezrin, radixin and moesin []

Probab=88.23  E-value=17  Score=31.74  Aligned_cols=53  Identities=26%  Similarity=0.352  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLAL  154 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL  154 (200)
                      .-|..-+..++++..+++..|.........|+.+...++.....++.++..|.
T Consensus         8 ~Ele~rL~q~eee~~~a~~~L~e~e~~a~~Leek~k~aeeea~~Le~k~~eae   60 (246)
T PF00769_consen    8 QELEERLRQMEEEMRRAQEALEESEETAEELEEKLKQAEEEAEELEQKRQEAE   60 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56778889999999999999999999999999999999999999888876663

Ezrin was first identified as a constituent of microvilli [], radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions [], and moesin as a heparin binding protein []. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain; an extended alpha-helical domain; and a charged C-terminal domain []. Ezrin, radixin and merlin also contain a polyproline region between the helical and C-terminal domains. The N-terminal domain is highly conserved, and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily. ERM proteins crosslink actin filaments with plasma membranes. They co-localise with CD44 at actin filament-plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains [].; GO: 0008092 cytoskeletal protein binding, 0005737 cytoplasm, 0019898 extrinsic to membrane; PDB: 2I1J_A 2I1K_A 1E5W_A 1EF1_C.

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=87.88  E-value=29  Score=34.10  Aligned_cols=29  Identities=10%  Similarity=0.248  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          165 ALKRRKSYADNANALKAQLDQQKNVVNNL  193 (200)
Q Consensus       165 AL~rk~~~e~~a~~lq~qld~~~~~ve~L  193 (200)
                      .+.++.+++.+...++.++++......++
T Consensus       260 ~~~~r~~Le~ei~~le~e~~e~~~~l~~l  288 (650)
T TIGR03185       260 LFEEREQLERQLKEIEAARKANRAQLREL  288 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33445566666666666666555555444

This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.

>PRK06569 F0F1 ATP synthase subunit B'; Validated

Probab=87.88  E-value=14  Score=30.41  Aligned_cols=38  Identities=11%  Similarity=0.167  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          109 LEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDW  146 (200)
Q Consensus       109 Reme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~w  146 (200)
                      ....+++.++.+.-.++.......+.++.+++.++...
T Consensus        44 ~~I~~~L~~Ae~~k~eAe~l~a~ye~~L~~Ar~eA~~I   81 (155)
T PRK06569         44 TNIQDNITQADTLTIEVEKLNKYYNEEIDKTNTEIDRL   81 (155)
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334444444444444444444444444444444333

>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]

Probab=87.87  E-value=21  Score=38.21  Aligned_cols=58  Identities=21%  Similarity=0.208  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHHHhcCCHH--HHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029028          140 EQASEDWYRKAQLALQKGEED--LAREALKRR----KSYADNANALKAQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       140 ~~~i~~we~rA~~AL~~G~ED--LAr~AL~rk----~~~e~~a~~lq~qld~~~~~ve~Lk~~l  197 (200)
                      .++++.-+..|+.|++.-+.|  +|+.-|.+.    ...|..+....+++.+++..++.||.+.
T Consensus      1572 L~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~kv~~~t~~aE~~~~~a~q~~~eL~~~~e~lk~~~ 1635 (1758)
T KOG0994|consen 1572 LEEADVAQGEAQDAIQGADRDIRLAQQLLAKVQEETAAAEKLATSATQQLGELETRMEELKHKA 1635 (1758)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444555556666555432  344444443    3355666666777777777777777654

>KOG1656 consensus Protein involved in glucose derepression and pre-vacuolar endosome protein sorting [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.76  E-value=13  Score=32.17  Aligned_cols=37  Identities=24%  Similarity=0.339  Sum_probs=30.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          158 EEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLV  194 (200)
Q Consensus       158 ~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk  194 (200)
                      +--.|..||.||+.||.++..+...+...+.+.+.|.
T Consensus        59 NKR~AlqaLkrKK~~E~qL~qidG~l~tie~Qr~alE   95 (221)
T KOG1656|consen   59 NKRMALQALKRKKRYEKQLAQIDGTLSTIEFQREALE   95 (221)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            5567788999999999999999988888777766554

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=87.62  E-value=9.9  Score=39.51  Aligned_cols=94  Identities=16%  Similarity=0.246  Sum_probs=65.7

Q ss_pred             HHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 029028           90 ANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRR  169 (200)
Q Consensus        90 in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk  169 (200)
                      +.+.+=++.|-..-=.|.+-.+.+.+.+-+..+..++..+.+|.++++.++..|.+++.+...||  |-|++......++
T Consensus       380 LKdalVrLRDlsA~ek~d~qK~~kelE~k~sE~~eL~r~kE~Lsr~~d~aEs~iadlkEQVDAAl--GAE~MV~qLtdkn  457 (1243)
T KOG0971|consen  380 LKDALVRLRDLSASEKQDHQKLQKELEKKNSELEELRRQKERLSRELDQAESTIADLKEQVDAAL--GAEEMVEQLTDKN  457 (1243)
T ss_pred             HHHHHHHHHhcchHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--cHHHHHHHHHhhc
Confidence            33444444444433344555566677777788888999999999999999999999999999998  4466666666666


Q ss_pred             HHHHHHHHHHHHHHHH
Q 029028          170 KSYADNANALKAQLDQ  185 (200)
Q Consensus       170 ~~~e~~a~~lq~qld~  185 (200)
                      ..+|+.+..|+..+.+
T Consensus       458 lnlEekVklLeetv~d  473 (1243)
T KOG0971|consen  458 LNLEEKVKLLEETVGD  473 (1243)
T ss_pred             cCHHHHHHHHHHHHHH
Confidence            6666666555554444

>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A

Probab=87.04  E-value=3.2  Score=28.91  Aligned_cols=44  Identities=27%  Similarity=0.379  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Q 029028          137 KAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALK  180 (200)
Q Consensus       137 ~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq  180 (200)
                      +.++...++|..-|..|...||.+-||.-+.-.+.+++.++..+
T Consensus         2 ~~L~~R~~~yk~Aa~~AK~~gd~~kAr~~~R~~K~~~~~I~~~~   45 (59)
T smart00685        2 ALLQQRQEQYKQAALQAKRAGDEEKARRHLRIAKQFDDAIKAAR   45 (59)
T ss_pred             hHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhhHHHHHHHHH
Confidence            45677888899999999999999999999999999888887665

3 and human FLJ20241.

>TIGR02977 phageshock_pspA phage shock protein A

Probab=87.03  E-value=18  Score=30.74  Aligned_cols=90  Identities=14%  Similarity=0.167  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Q 029028          104 LEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASE-----DWYRKAQLALQKGEEDLAREALKRRKSYADNANA  178 (200)
Q Consensus       104 LdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~-----~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~  178 (200)
                      ++..|.+++..+.++...--.........+......+..+.     --++-|+.||.     --.........|+.++..
T Consensus        36 m~~~l~~ar~~lA~~~a~~k~~e~~~~~~~~~~~~~~~~A~~Al~~G~EdLAr~Al~-----~k~~~~~~~~~l~~~~~~  110 (219)
T TIGR02977        36 MEDTLVEVRTTSARTIADKKELERRVSRLEAQVADWQEKAELALSKGREDLARAALI-----EKQKAQELAEALERELAA  110 (219)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH-----HHHHHHHHHHHHHHHHHH
Confidence            33355566666666655444444444444444444444443     24556777766     233445556667777777


Q ss_pred             HHHHHHHHHHHHHHHHhhhh
Q 029028          179 LKAQLDQQKNVVNNLVSNTR  198 (200)
Q Consensus       179 lq~qld~~~~~ve~Lk~~l~  198 (200)
                      ++.+++.++..+.+|+..|.
T Consensus       111 ~~~~v~~l~~~l~~L~~ki~  130 (219)
T TIGR02977       111 VEETLAKLQEDIAKLQAKLA  130 (219)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            77777777777777766654

Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.

>PRK12704 phosphodiesterase; Provisional

Probab=86.97  E-value=28  Score=33.75  Aligned_cols=51  Identities=12%  Similarity=0.175  Sum_probs=32.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           99 DPEKILEQAVLEMNDDLVKMRQAT-AQVLASQKRLENKCKAAEQASEDWYRK  149 (200)
Q Consensus        99 DP~~mLdQ~IReme~~l~kar~~l-A~v~A~~k~le~k~~~~~~~i~~we~r  149 (200)
                      +.+.++++...++++...+++... ..+...+..+++++++.+.++.+.+++
T Consensus        39 eAe~I~keA~~eAke~~ke~~leaeeE~~~~R~Ele~e~~~~e~~L~qrE~r   90 (520)
T PRK12704         39 EAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKR   90 (520)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445777777777776666666554 455555566666666666666666554

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=86.86  E-value=20  Score=36.39  Aligned_cols=56  Identities=18%  Similarity=0.318  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHH---HHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           78 LFDRLARVVKS---YANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLE  133 (200)
Q Consensus        78 if~Rl~~lvra---~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le  133 (200)
                      |..|-..++..   +++.+++++++-...+++..++++..+.++++...+.......++
T Consensus       503 ii~~A~~~~~~~~~~~~~li~~l~~~~~~~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~  561 (782)
T PRK00409        503 IIEEAKKLIGEDKEKLNELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQ  561 (782)
T ss_pred             HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45554444432   334444444444444444444444444444444444333333333

>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association []

Probab=86.55  E-value=21  Score=32.16  Aligned_cols=57  Identities=12%  Similarity=0.254  Sum_probs=33.9

Q ss_pred             HHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           91 NAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWY  147 (200)
Q Consensus        91 n~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we  147 (200)
                      +.+.+.+++-...|++-...+.+.+..+...+-.+......++.++..+++.....+
T Consensus       148 ~gl~~~L~~~~~~L~~D~~~L~~~~~~l~~~~~~l~~~~~~L~~e~~~Lk~~~~e~~  204 (325)
T PF08317_consen  148 EGLKEGLEENLELLQEDYAKLDKQLEQLDELLPKLRERKAELEEELENLKQLVEEIE  204 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            444455555556666666666666666666666666666666666666666555433

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=86.47  E-value=36  Score=34.73  Aligned_cols=10  Identities=10%  Similarity=0.388  Sum_probs=5.1

Q ss_pred             CCCcccccCC
Q 029028           60 SRSHCYRQGG   69 (200)
Q Consensus        60 ~~~~~~~~~~   69 (200)
                      .+|.++.++|
T Consensus       644 ldG~~~~~~G  653 (1164)
T TIGR02169       644 LEGELFEKSG  653 (1164)
T ss_pred             eCceeEcCCc
Confidence            3566655443

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.

>PRK08476 F0F1 ATP synthase subunit B'; Validated

Probab=86.42  E-value=15  Score=29.20  Aligned_cols=49  Identities=20%  Similarity=0.331  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKA  150 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA  150 (200)
                      .+|++-=..+.+++..+...-.++.......+..+...+.+++.+...+
T Consensus        34 ~~l~~R~~~I~~~l~~A~~~~~ea~~~~~e~e~~l~~Ar~eA~~~~~~a   82 (141)
T PRK08476         34 KFMDNRNASIKNDLEKVKTNSSDVSEIEHEIETILKNAREEANKIRQKA   82 (141)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555555555555555555555555555555555555555555554443

>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT)

Probab=85.49  E-value=16  Score=28.67  Aligned_cols=91  Identities=10%  Similarity=0.104  Sum_probs=62.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          106 QAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQ  185 (200)
Q Consensus       106 Q~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~  185 (200)
                      ...+++++.+..--..-+..+..-..++.++..+...+..+...+..|-.. -+..=..+-.++..++.++..++..++.
T Consensus        38 ~~a~~Aq~~YE~El~~Ha~~~~~L~~lr~e~~~~~~~~~~l~~~~~~a~~~-l~~~e~sw~~qk~~le~e~~~~~~r~~d  116 (132)
T PF07926_consen   38 KIAQEAQQKYERELVKHAEDIKELQQLREELQELQQEINELKAEAESAKAE-LEESEASWEEQKEQLEKELSELEQRIED  116 (132)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            334444455554445566777777888888888999999998888877443 2333345677777888888888887777


Q ss_pred             HHHHHHHHHhhh
Q 029028          186 QKNVVNNLVSNT  197 (200)
Q Consensus       186 ~~~~ve~Lk~~l  197 (200)
                      +..+=.-|-..|
T Consensus       117 L~~QN~lLh~Ql  128 (132)
T PF07926_consen  117 LNEQNKLLHDQL  128 (132)
T ss_pred             HHHHHHHHHHHH
Confidence            776665555544

These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore

>TIGR00606 rad50 rad50

Probab=85.35  E-value=19  Score=38.34  Aligned_cols=33  Identities=12%  Similarity=0.300  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029028          165 ALKRRKSYADNANALKAQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       165 AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l  197 (200)
                      .+.++.+++.+++.+...++.+...+..++..+
T Consensus       879 ~l~~r~~le~~L~el~~el~~l~~~~~~~~~~~  911 (1311)
T TIGR00606       879 NLQRRQQFEEQLVELSTEVQSLIREIKDAKEQD  911 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            667888888888888888888888777776654

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

>PRK10698 phage shock protein PspA; Provisional

Probab=85.13  E-value=23  Score=30.35  Aligned_cols=88  Identities=11%  Similarity=0.115  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Q 029028          106 QAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASE-----DWYRKAQLALQKGEEDLAREALKRRKSYADNANALK  180 (200)
Q Consensus       106 Q~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~-----~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq  180 (200)
                      ..+.+++..+.++...--.........+.........+.     --++-|+.||..-     ..+......|+.+++..+
T Consensus        38 ~~l~~~r~alA~~~A~~k~~er~~~~~~~~~~~~e~kA~~Al~~G~EdLAr~AL~~K-----~~~~~~~~~l~~~~~~~~  112 (222)
T PRK10698         38 DTLVEVRSTSARALAEKKQLTRRIEQAEAQQVEWQEKAELALRKEKEDLARAALIEK-----QKLTDLIATLEHEVTLVD  112 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHH
Confidence            333344444444443333333333344444444333333     3455666666442     335667778888888888


Q ss_pred             HHHHHHHHHHHHHHhhhh
Q 029028          181 AQLDQQKNVVNNLVSNTR  198 (200)
Q Consensus       181 ~qld~~~~~ve~Lk~~l~  198 (200)
                      .+++.++..+.+|+..|.
T Consensus       113 ~~~~~L~~~l~~L~~ki~  130 (222)
T PRK10698        113 ETLARMKKEIGELENKLS  130 (222)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            888888888888887764

>PRK14472 F0F1 ATP synthase subunit B; Provisional

Probab=85.08  E-value=19  Score=29.32  Aligned_cols=25  Identities=12%  Similarity=0.143  Sum_probs=11.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVL  126 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~  126 (200)
                      .-.++.+.+.+..+.+++......+
T Consensus        66 ~eA~~~~~e~e~~L~~a~~ea~~ii   90 (175)
T PRK14472         66 DEAEAILRKNRELLAKADAEADKII   90 (175)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444445555555554444433

>TIGR02473 flagell_FliJ flagellar export protein FliJ

Probab=84.94  E-value=15  Score=28.10  Aligned_cols=50  Identities=16%  Similarity=0.145  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 029028          108 VLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKG  157 (200)
Q Consensus       108 IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G  157 (200)
                      ++=-+....+++..++.+.+.....+.++..+......+......-...|
T Consensus         8 l~lr~~~ed~a~~~la~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~g   57 (141)
T TIGR02473         8 LDLREKEEEQAKLELAKAQAEFERLETQLQQLIKYREEYEQQALEKVGAG   57 (141)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            33445567788889999999999999999999999998888776665666

Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacgterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Sequence scoring in the gray zone between trusted and noise cutoffs include both probable FliJ proteins and components of bacterial type III secretion systems.

>PRK09343 prefoldin subunit beta; Provisional

Probab=84.86  E-value=17  Score=28.36  Aligned_cols=96  Identities=13%  Similarity=0.208  Sum_probs=67.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HH-HHHhcCCHHHHHHHHHHHHHHH
Q 029028          104 LEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRK---------AQ-LALQKGEEDLAREALKRRKSYA  173 (200)
Q Consensus       104 LdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~r---------A~-~AL~~G~EDLAr~AL~rk~~~e  173 (200)
                      |...+.+.-..+...++.+..+......++.++.+++.-.++++.-         .- .-+....+++-...-.|+..++
T Consensus         5 ~~~~~q~~~~~~q~lq~~l~~~~~q~~~le~q~~e~~~~~~EL~~L~~d~~VYk~VG~vlv~qd~~e~~~~l~~r~E~ie   84 (121)
T PRK09343          5 IPPEVQAQLAQLQQLQQQLERLLQQKSQIDLELREINKALEELEKLPDDTPIYKIVGNLLVKVDKTKVEKELKERKELLE   84 (121)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHhhHHHhhccHHHHHHHHHHHHHHHH
Confidence            4445556666777888888888888888888888877666655431         11 1233334555566666777788


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhc
Q 029028          174 DNANALKAQLDQQKNVVNNLVSNTRV  199 (200)
Q Consensus       174 ~~a~~lq~qld~~~~~ve~Lk~~l~~  199 (200)
                      ..+..++.+.+.++..+.++..+|+.
T Consensus        85 ~~ik~lekq~~~l~~~l~e~q~~l~~  110 (121)
T PRK09343         85 LRSRTLEKQEKKLREKLKELQAKINE  110 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88899999999988888888888763

>PRK09039 hypothetical protein; Validated

Probab=84.46  E-value=32  Score=31.40  Aligned_cols=29  Identities=17%  Similarity=0.325  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          109 LEMNDDLVKMRQATAQVLASQKRLENKCK  137 (200)
Q Consensus       109 Reme~~l~kar~~lA~v~A~~k~le~k~~  137 (200)
                      .++++.+.+.+..+..+.+.+.+++..+.
T Consensus        77 ~~l~~~l~~l~~~l~~a~~~r~~Le~~~~  105 (343)
T PRK09039         77 QDLQDSVANLRASLSAAEAERSRLQALLA  105 (343)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33444444444444444444444444444

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=84.36  E-value=47  Score=37.27  Aligned_cols=118  Identities=18%  Similarity=0.269  Sum_probs=85.7

Q ss_pred             cHHHHHHHHHHHHHHHHhhccCCHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           77 NLFDRLARVVKSYANAILSSFEDPE---KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLA  153 (200)
Q Consensus        77 sif~Rl~~lvra~in~~ldk~EDP~---~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~A  153 (200)
                      +-+.|....+...+.++=+.++++.   .-+.-.++.++.+....+..+..-.-....+.+++.....++.+|..+...-
T Consensus      1290 ~~~~r~~~~~~~qle~~k~qle~e~r~k~~l~~~l~~l~~e~~~l~e~leee~e~~~~l~r~lsk~~~e~~~~~~k~e~~ 1369 (1930)
T KOG0161|consen 1290 SALSRDKQALESQLEELKRQLEEETREKSALENALRQLEHELDLLREQLEEEQEAKNELERKLSKANAELAQWKKKFEEE 1369 (1930)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456666677777777766666653   6778888888889999999999999999999999999999999999999887


Q ss_pred             Hhc---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          154 LQK---GEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLV  194 (200)
Q Consensus       154 L~~---G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk  194 (200)
                      +..   +-|+.=+....+...+++.++......+.++..-..|.
T Consensus      1370 ~~~~~eelee~kk~l~~~lq~~qe~~e~~~~~~~~Lek~k~~l~ 1413 (1930)
T KOG0161|consen 1370 VLQRLEELEELKKKLQQRLQELEEQIEAANAKNASLEKAKNRLQ 1413 (1930)
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            664   34455555566666666666655555555544444443

>PRK14475 F0F1 ATP synthase subunit B; Provisional

Probab=84.21  E-value=21  Score=28.99  Aligned_cols=48  Identities=17%  Similarity=0.312  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHHhhccCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           80 DRLARVVKSYANAILSSFEDP---EKILEQAVLEMNDDLVKMRQATAQVLA  127 (200)
Q Consensus        80 ~Rl~~lvra~in~~ldk~EDP---~~mLdQ~IReme~~l~kar~~lA~v~A  127 (200)
                      +.+..++...-+.+.+.+++.   ..-.++...+++..+.+++......+.
T Consensus        33 ~pi~~~le~R~~~I~~~l~~Ae~~k~eAe~~~~~~e~~L~~A~~ea~~Ii~   83 (167)
T PRK14475         33 KALAGALDAYAAKIQAELDEAQRLREEAQALLADVKAEREEAERQAAAMLA   83 (167)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555544443333333333   355555566666666666555444443

>PRK00106 hypothetical protein; Provisional

Probab=83.89  E-value=38  Score=33.11  Aligned_cols=32  Identities=19%  Similarity=0.069  Sum_probs=15.1

Q ss_pred             HHHhhccC-CHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           91 NAILSSFE-DPEKILEQAVLEMNDDLVKMRQAT  122 (200)
Q Consensus        91 n~~ldk~E-DP~~mLdQ~IReme~~l~kar~~l  122 (200)
                      +.+++.++ +.+.++++...+.++...+++...
T Consensus        45 ~~IleeAe~eAe~I~keA~~EAke~~ke~~lEa   77 (535)
T PRK00106         45 VNLRGKAERDAEHIKKTAKRESKALKKELLLEA   77 (535)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34443333 334555555555555554444443

>smart00502 BBC B-Box C-terminal domain

Probab=83.87  E-value=15  Score=27.05  Aligned_cols=92  Identities=14%  Similarity=0.231  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHH----HHHHHHHHHHHHHHHH
Q 029028          104 LEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAR----EALKRRKSYADNANAL  179 (200)
Q Consensus       104 LdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr----~AL~rk~~~e~~a~~l  179 (200)
                      |...+.++......+...+..+......++.+.......|...-.....+|..-.+.|-.    ..-.+...+..+...+
T Consensus         5 L~~~l~~l~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~I~~~f~~l~~~L~~~e~~ll~~l~~~~~~~~~~l~~q~~~l   84 (127)
T smart00502        5 LEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQLESL   84 (127)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555555555555556666666666666666666666666555443332    2223334444444444


Q ss_pred             HHHHHHHHHHHHHHHh
Q 029028          180 KAQLDQQKNVVNNLVS  195 (200)
Q Consensus       180 q~qld~~~~~ve~Lk~  195 (200)
                      +..++.....++-.+.
T Consensus        85 ~~~l~~l~~~~~~~e~  100 (127)
T smart00502       85 TQKQEKLSHAINFTEE  100 (127)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4444444444444433

Coiled coil region C-terminal to (some) B-Box domains

>PF05546 She9_MDM33: She9 / Mdm33 family; InterPro: IPR008839 Members of this family are mitochondrial inner membrane proteins with a role in inner mitochondrial membrane organisation and biogenesis []

Probab=83.44  E-value=15  Score=31.75  Aligned_cols=94  Identities=12%  Similarity=0.203  Sum_probs=51.4

Q ss_pred             hhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHH--HHHH
Q 029028           94 LSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALK--RRKS  171 (200)
Q Consensus        94 ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~--rk~~  171 (200)
                      |+++.+-+..++..+++....+.+++.....+++.+-..+++++++-..-..|.          ..||.|..--  .-..
T Consensus        34 Ie~LK~~i~~~E~~l~~~r~~~~~aK~~Y~~ai~~Rs~sQrEvn~LLqRK~sWs----------~~DleRFT~Lyr~dH~  103 (207)
T PF05546_consen   34 IEKLKKSIEELEDELEAARQEVREAKAAYDDAIQQRSSSQREVNELLQRKHSWS----------PADLERFTELYRNDHE  103 (207)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCC----------hHHHHHHHHHHHhhhh
Confidence            344444455566666666666666666666666666666666666666544443          2444443322  2223


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029028          172 YADNANALKAQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       172 ~e~~a~~lq~qld~~~~~ve~Lk~~l  197 (200)
                      .+......+..+.+.+..++++-..|
T Consensus       104 ~e~~e~~ak~~l~~aE~~~e~~~~~L  129 (207)
T PF05546_consen  104 NEQAEEEAKEALEEAEEKVEEAFDDL  129 (207)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444555555555555555554443

The yeast Mdm33 protein assembles into an oligomeric complex in the inner membrane where it performs homotypic protein-protein interactions. It has been suggested that Mdm33 plays a distinct role, possibly involved in fission of the mitochondrial inner membrane [].

>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins

Probab=83.31  E-value=36  Score=36.13  Aligned_cols=58  Identities=14%  Similarity=0.228  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 029028          101 EKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGE  158 (200)
Q Consensus       101 ~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~  158 (200)
                      ..-++..+......+..++..+..+....++.+.++..+..+...|+.+...++..-.
T Consensus       623 ~~~~e~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  680 (1201)
T PF12128_consen  623 QEELEKQLKQINKKIEELKREITQAEQELKQAEQDLQRLKNEREQLKQEIEEAKEERK  680 (1201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555556666777777777777777777777777777777777777766655443

>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion

Probab=83.27  E-value=23  Score=28.84  Aligned_cols=35  Identities=11%  Similarity=0.191  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029028          163 REALKRRKSYADNANALKAQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       163 r~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l  197 (200)
                      ++...+..........++..++.+.+.+.++++-+
T Consensus       154 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~  188 (191)
T PF04156_consen  154 QDSREEVQELRSQLERLQENLQQLEEKIQELQELL  188 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444445555566666666666666666666544

The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].

>PF13851 GAS: Growth-arrest specific micro-tubule binding

Probab=83.27  E-value=27  Score=29.56  Aligned_cols=114  Identities=20%  Similarity=0.233  Sum_probs=81.6

Q ss_pred             HHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCH
Q 029028           80 DRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEE  159 (200)
Q Consensus        80 ~Rl~~lvra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~E  159 (200)
                      .+-+.=++.+.|++...-=+=++-|...|.+|+......++.+..+..+-+++..-+..++.+.+.++.....- .+...
T Consensus         8 e~af~~iK~YYndIT~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~~y-~kdK~   86 (201)
T PF13851_consen    8 EKAFQEIKNYYNDITLNNLELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLKNY-EKDKQ   86 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH-HHHHH
Confidence            44455566777777766556678999999999999999999999999999999999999999999888877652 22222


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029028          160 DLAREALKRRKSYADNANALKAQLDQQKNVVNNLVS  195 (200)
Q Consensus       160 DLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~  195 (200)
                      .|+ .+-.+...++.++..++-..+.+.....++..
T Consensus        87 ~L~-~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~  121 (201)
T PF13851_consen   87 SLQ-NLKARLKELEKELKDLKWEHEVLEQRFEKLEQ  121 (201)
T ss_pred             HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            222 23344455566666666666666666555543

>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells

Probab=83.07  E-value=30  Score=29.98  Aligned_cols=50  Identities=20%  Similarity=0.223  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 029028          108 VLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKG  157 (200)
Q Consensus       108 IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G  157 (200)
                      |.++...+......+......-..++.++..+...++.+..++..++..|
T Consensus        26 ~e~~~~~L~~~~~~~~~~~~~~~~~e~~l~~L~~d~~~L~~k~~~~~~~~   75 (264)
T PF06008_consen   26 IEDLTNQLRSYRSKLNPQKQQLDPLEKELESLEQDVENLQEKATKVSRKA   75 (264)
T ss_pred             HHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444443333333333344444444444444444444444444444

Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex

>TIGR01069 mutS2 MutS2 family protein

Probab=82.92  E-value=30  Score=35.07  Aligned_cols=9  Identities=0%  Similarity=0.194  Sum_probs=4.4

Q ss_pred             HHHHHHHHH
Q 029028           78 LFDRLARVV   86 (200)
Q Consensus        78 if~Rl~~lv   86 (200)
                      |.+|-..++
T Consensus       498 ii~~A~~~~  506 (771)
T TIGR01069       498 IIEQAKTFY  506 (771)
T ss_pred             HHHHHHHHH
Confidence            555544443

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>TIGR02231 conserved hypothetical protein

Probab=82.82  E-value=26  Score=33.37  Aligned_cols=30  Identities=7%  Similarity=0.144  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          107 AVLEMNDDLVKMRQATAQVLASQKRLENKC  136 (200)
Q Consensus       107 ~IReme~~l~kar~~lA~v~A~~k~le~k~  136 (200)
                      .+.++++++.+++..++.+.+....++.++
T Consensus        72 ~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~  101 (525)
T TIGR02231        72 RLAELRKQIRELEAELRDLEDRGDALKALA  101 (525)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444444

This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.

>TIGR03545 conserved hypothetical protein TIGR03545

Probab=82.81  E-value=20  Score=35.04  Aligned_cols=57  Identities=14%  Similarity=0.251  Sum_probs=27.8

Q ss_pred             hccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           95 SSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQL  152 (200)
Q Consensus        95 dk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~  152 (200)
                      ..+-||..+|++.=..-.+...++++.+......++....++- -..+++.|+++.+.
T Consensus       146 ~~lp~~~eil~~~~L~T~~~~~~~~~~~k~~~~~w~~~~~~Lp-~~~~~~~yk~~v~~  202 (555)
T TIGR03545       146 SQLPDPRALLKGEDLKTVETAEEIEKSLKAMQQKWKKRKKDLP-NKQDLEEYKKRLEA  202 (555)
T ss_pred             ccCCCHHHHhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHhcC-CchhHHHHHHHHHH
Confidence            3455888888865444444444555444444444443333332 14444444444443

This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.

>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication

Probab=82.74  E-value=6  Score=30.52  Aligned_cols=63  Identities=22%  Similarity=0.348  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHhcCCHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYR--------KAQLALQKGEEDLARE  164 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~--------rA~~AL~~G~EDLAr~  164 (200)
                      .-+++.|.++-+++.+.+..+..++-+-..|..+-..++..+.+.+.        ....-+..|.+.||+-
T Consensus        11 ~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~~~~~~~~~~~~~~~~~g~~NL~~L   81 (107)
T PF06156_consen   11 DQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQEEEEKEEKKTKKKLGEGRDNLARL   81 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccchHHHHHHH
Confidence            45788899999999999999999999999999999999999988865        3334466778888763

SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.

>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []

Probab=82.61  E-value=22  Score=28.00  Aligned_cols=41  Identities=12%  Similarity=0.259  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          106 QAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDW  146 (200)
Q Consensus       106 Q~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~w  146 (200)
                      ..||..+.++...+..++++.+.+..+..++-.+-...+.+
T Consensus        23 s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~   63 (120)
T PF12325_consen   23 SQLRRLEGELASLQEELARLEAERDELREEIVKLMEENEEL   63 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555555555555555555555554444

The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].

>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal

Probab=82.44  E-value=19  Score=27.28  Aligned_cols=92  Identities=18%  Similarity=0.273  Sum_probs=67.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---H-------HHHHhcCCHHHHHHHHHHHHHHHHHHH
Q 029028          108 VLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRK---A-------QLALQKGEEDLAREALKRRKSYADNAN  177 (200)
Q Consensus       108 IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~r---A-------~~AL~~G~EDLAr~AL~rk~~~e~~a~  177 (200)
                      +.+.-..+...++.+..+......++.++.+...-++.++.-   +       ..-+....++.-...-.++..++..+.
T Consensus         5 ~q~~~~~~q~~q~~~~~l~~q~~~le~~~~E~~~v~~eL~~l~~d~~vyk~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~   84 (110)
T TIGR02338         5 VQNQLAQLQQLQQQLQAVATQKQQVEAQLKEAEKALEELERLPDDTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVK   84 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHhchhhheecHHHHHHHHHHHHHHHHHHHH
Confidence            445556667777777777777888888887777766666542   1       122334446666777778888999999


Q ss_pred             HHHHHHHHHHHHHHHHHhhhhc
Q 029028          178 ALKAQLDQQKNVVNNLVSNTRV  199 (200)
Q Consensus       178 ~lq~qld~~~~~ve~Lk~~l~~  199 (200)
                      .++.+.+.++..+.++.++|+.
T Consensus        85 ~lek~~~~l~~~l~e~q~~l~~  106 (110)
T TIGR02338        85 TLQRQEERLREQLKELQEKIQE  106 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999988863

Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.

>PHA02562 46 endonuclease subunit; Provisional

Probab=82.43  E-value=33  Score=32.44  Aligned_cols=16  Identities=25%  Similarity=0.312  Sum_probs=6.1

Q ss_pred             HHHHHHHHHHHHHHHH
Q 029028          134 NKCKAAEQASEDWYRK  149 (200)
Q Consensus       134 ~k~~~~~~~i~~we~r  149 (200)
                      .+...++.++++++..
T Consensus       358 ~~~~~l~~ei~~l~~~  373 (562)
T PHA02562        358 DKAKKVKAAIEELQAE  373 (562)
T ss_pred             HHHHHHHHHHHHHHhh
Confidence            3333333333333333

>PF03148 Tektin: Tektin family; InterPro: IPR000435 Tektin heteropolymers form unique protofilaments of flagellar microtubules []

Probab=81.87  E-value=43  Score=30.96  Aligned_cols=119  Identities=16%  Similarity=0.218  Sum_probs=84.5

Q ss_pred             HHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----
Q 029028           78 LFDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLA----  153 (200)
Q Consensus        78 if~Rl~~lvra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~A----  153 (200)
                      +-.-+..++.-..+++-....--+..|.+-|.++++...+..-.+..++.+...+++.+..++..+.+-..-...|    
T Consensus       223 LR~~i~~~l~~~~~dl~~Q~~~vn~al~~Ri~et~~ak~~Le~ql~~~~~ei~~~e~~i~~L~~ai~~k~~~lkvaqTRL  302 (384)
T PF03148_consen  223 LREDIDSILEQTANDLRAQADAVNAALRKRIHETQEAKNELEWQLKKTLQEIAEMEKNIEDLEKAIRDKEGPLKVAQTRL  302 (384)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence            3344444444444555555444567888888888888888888888888888888888888888887777655544    


Q ss_pred             -HhcCC------HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 029028          154 -LQKGE------EDLAREAL-KRRKSYADNANALKAQLDQQKNVVNNLVSN  196 (200)
Q Consensus       154 -L~~G~------EDLAr~AL-~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~  196 (200)
                       ....+      -|-|...| .+...+.+.+..|+.++.+.+.....|...
T Consensus       303 ~~R~~RP~vElcrD~~q~~L~~Ev~~l~~~i~~L~~~L~~a~~~l~~L~~~  353 (384)
T PF03148_consen  303 ENRTQRPNVELCRDPPQYGLIEEVKELRESIEALQEKLDEAEASLQKLERT  353 (384)
T ss_pred             hhHhcCCchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             22223      25566666 688899999999999999988888877654

The proteins are predicted to form extended rods composed of 2 alpha- helical segments (~180 residues long) capable of forming coiled coils, interrupted by non-helical linkers []. The 2 segments are similar in sequence, indicating a gene duplication event. Along each tektin rod, cysteine residues occur with a periodicity of ~8nm, coincident with the axial repeat of tubulin dimers in microtubules []. It is proposed that the assembly of tektin heteropolymers produces filaments with repeats of 8, 16, 24, 32, 40, 48 and 96nm, generating the basis for the complex spatial arrangements of axonemal components [].; GO: 0000226 microtubule cytoskeleton organization, 0005874 microtubule

>PRK03918 chromosome segregation protein; Provisional

Probab=81.82  E-value=60  Score=32.54  Aligned_cols=17  Identities=24%  Similarity=0.264  Sum_probs=7.8

Q ss_pred             HHHHHHHHHHHHHHHHh
Q 029028           78 LFDRLARVVKSYANAIL   94 (200)
Q Consensus        78 if~Rl~~lvra~in~~l   94 (200)
                      +|....-+-.|.+..++
T Consensus       125 ~f~~~~~~~Qg~~~~~~  141 (880)
T PRK03918        125 VFLNAIYIRQGEIDAIL  141 (880)
T ss_pred             HhceeEEEeccchHHHh
Confidence            44333334455555554

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

Probab=81.73  E-value=36  Score=29.94  Aligned_cols=41  Identities=10%  Similarity=0.092  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          107 AVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWY  147 (200)
Q Consensus       107 ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we  147 (200)
                      .+..+.+.+......+..+.-+..+++.++.++++++++.+
T Consensus        39 e~e~~~~~~~~~~~e~e~le~qv~~~e~ei~~~r~r~~~~e   79 (239)
T COG1579          39 ELEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAE   79 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444444444444433

>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]

Probab=81.67  E-value=45  Score=31.01  Aligned_cols=110  Identities=17%  Similarity=0.184  Sum_probs=64.7

Q ss_pred             ccccccccccccCccceEEeeccc-cccCCCCcccccCCCcccccCcHHHHHHHHHHHHHHHHhhccCCH--HHHHH---
Q 029028           32 MVKKPLTTSFFNGGVGALKVTRLR-IAPSSRSHCYRQGGGALNTRMNLFDRLARVVKSYANAILSSFEDP--EKILE---  105 (200)
Q Consensus        32 ~~~~~l~~~f~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~Msif~Rl~~lvra~in~~ldk~EDP--~~mLd---  105 (200)
                      ..++|+.++.-.||+..+..-... ...+..    .|.|-.     +        |++.++++++.--+-  ++.++   
T Consensus       169 ~~~~p~p~p~~~~gas~~~~~~~d~~~~yp~----n~~~~~-----~--------irasvisa~~eklR~r~eeeme~~~  231 (365)
T KOG2391|consen  169 AYKPPLPPPPPPGGASALPYMTDDNAEPYPP----NASGKL-----V--------IRASVISAVREKLRRRREEEMERLQ  231 (365)
T ss_pred             CcCCCCCCCCCCCccccCcccCCCCCCcCCC----Cccccc-----c--------hhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            677889999999998743322111 111111    122222     1        444444433321111  12222   


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 029028          106 QAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGE  158 (200)
Q Consensus       106 Q~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~  158 (200)
                      -.+.+++.--++.+.......+....||+++..+...++=+..+.+.||.+-.
T Consensus       232 aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~~niDIL~~k~~eal~~~~  284 (365)
T KOG2391|consen  232 AEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQKNIDILKSKVREALEKAE  284 (365)
T ss_pred             HHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhc
Confidence            23344455556666677788888899999999999999999999888776543

>PRK13428 F0F1 ATP synthase subunit delta; Provisional

Probab=81.53  E-value=49  Score=31.32  Aligned_cols=50  Identities=10%  Similarity=0.194  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHHHhhccCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           79 FDRLARVVKSYANAILSSFED---PEKILEQAVLEMNDDLVKMRQATAQVLAS  128 (200)
Q Consensus        79 f~Rl~~lvra~in~~ldk~ED---P~~mLdQ~IReme~~l~kar~~lA~v~A~  128 (200)
                      |+.+..++...-..+.+.+++   -..-++....+.++.+.+++..-...+.+
T Consensus        23 ~~Pi~~~l~~R~~~I~~~L~eAe~a~~ea~~~~~~~e~~L~~Ak~ea~~Ii~~   75 (445)
T PRK13428         23 VPPVRRLMAARQDTVRQQLAESATAADRLAEADQAHTKAVEDAKAEAARVVEE   75 (445)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555554444333333333   33555555555555555555554444433

>PRK06569 F0F1 ATP synthase subunit B'; Validated

Probab=81.52  E-value=28  Score=28.61  Aligned_cols=104  Identities=11%  Similarity=0.096  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHHHHHhhccC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           78 LFDRLARVVKSYANAILSSFE---DPEKILEQAVLEMNDDLVKMRQATAQVLAS-QKRLENKCKAAEQASEDWYRKAQLA  153 (200)
Q Consensus        78 if~Rl~~lvra~in~~ldk~E---DP~~mLdQ~IReme~~l~kar~~lA~v~A~-~k~le~k~~~~~~~i~~we~rA~~A  153 (200)
                      +|.++.+++..+-..+-+.++   .-..-.+....+.++.+.+++....+...+ ..++..   +...+....+......
T Consensus        31 ~~ppI~~iLe~R~~~I~~~L~~Ae~~k~eAe~l~a~ye~~L~~Ar~eA~~I~~e~~~~~~a---~~~~~~~~~ea~L~~~  107 (155)
T PRK06569         31 ITPKAEEIFNNRQTNIQDNITQADTLTIEVEKLNKYYNEEIDKTNTEIDRLKKEKIDSLES---EFLIKKKNLEQDLKNS  107 (155)
T ss_pred             hHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Confidence            466777777665444443333   333555556666666666666666655555 333333   3344455566667777


Q ss_pred             HhcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          154 LQKGEEDLAREALKRRKSYADNANALKAQLD  184 (200)
Q Consensus       154 L~~G~EDLAr~AL~rk~~~e~~a~~lq~qld  184 (200)
                      |..|..+.=..+-.=+.++++++-.+...+.
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~~i~  138 (155)
T PRK06569        108 INQNIEDINLAAKQFRTNKSEAIIKLAVNII  138 (155)
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            7777777766666555566655555554443

>PRK13460 F0F1 ATP synthase subunit B; Provisional

Probab=81.02  E-value=28  Score=28.30  Aligned_cols=14  Identities=14%  Similarity=0.302  Sum_probs=5.1

Q ss_pred             HHHHHHHHHHHHHH
Q 029028          132 LENKCKAAEQASED  145 (200)
Q Consensus       132 le~k~~~~~~~i~~  145 (200)
                      .+.++.+.+.++..
T Consensus        73 ~e~~l~~a~~ea~~   86 (173)
T PRK13460         73 YEARLNSAKDEANA   86 (173)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333333333333

>PRK06231 F0F1 ATP synthase subunit B; Validated

Probab=80.54  E-value=34  Score=28.93  Aligned_cols=18  Identities=6%  Similarity=-0.066  Sum_probs=7.4

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 029028          104 LEQAVLEMNDDLVKMRQA  121 (200)
Q Consensus       104 LdQ~IReme~~l~kar~~  121 (200)
                      .++.+.+++..+.+++..
T Consensus        98 A~~~l~e~e~~L~~A~~e  115 (205)
T PRK06231         98 AQQLLENAKQRHENALAQ  115 (205)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            333344444444444433

>TIGR01144 ATP_synt_b ATP synthase, F0 subunit b

Probab=80.39  E-value=26  Score=27.43  Aligned_cols=49  Identities=14%  Similarity=0.224  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHHHHhhccCCHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           78 LFDRLARVVKSYANAILSSFEDPE---KILEQAVLEMNDDLVKMRQATAQVL  126 (200)
Q Consensus        78 if~Rl~~lvra~in~~ldk~EDP~---~mLdQ~IReme~~l~kar~~lA~v~  126 (200)
                      +|+.+..++...-..+.+.+++.+   .-.+....+.+..+.+++......+
T Consensus        16 ~~~pi~~~l~~R~~~I~~~l~~A~~~~~ea~~~~~e~~~~l~~A~~ea~~i~   67 (147)
T TIGR01144        16 VWPPLAKAIETRQKKIADGLASAERAKKEAALAQKKAQVILKEAKDEAQEII   67 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355555555554444444444333   3444445555555555555444444

This model describes the F1/F0 ATP synthase b subunit in bacteria only. Scoring just below the trusted cutoff are the N-terminal domains of Mycobacterial b/delta fusion proteins and a subunit from an archaeon, Methanosarcina barkeri, in which the ATP synthase homolog differs in architecture and is not experimentally confirmed. This model helps resolve b from the related b' subunit. Within the family is an example from a sodium-translocating rather than proton-translocating ATP synthase.

>PRK05431 seryl-tRNA synthetase; Provisional

Probab=80.27  E-value=33  Score=32.24  Aligned_cols=71  Identities=18%  Similarity=0.299  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          122 TAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLV  194 (200)
Q Consensus       122 lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk  194 (200)
                      +...-.+++.+..+++.++.+.....+....+.+.+.+  +.+...+.+.+.+++..+++++...+..+..+-
T Consensus        30 i~~ld~~~r~l~~~~~~lr~~rn~~sk~i~~~~~~~~~--~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~  100 (425)
T PRK05431         30 LLELDEERRELQTELEELQAERNALSKEIGQAKRKGED--AEALIAEVKELKEEIKALEAELDELEAELEELL  100 (425)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCc--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555556666666666665555554444422  233455556666777777777777666666553

>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility

Probab=80.20  E-value=34  Score=28.67  Aligned_cols=63  Identities=19%  Similarity=0.175  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          123 AQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNV  189 (200)
Q Consensus       123 A~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~  189 (200)
                      .........++.+..++...+.+|..+....-+...+.++    .+.+.+.++++.++.+..++..+
T Consensus       123 ~~l~~~i~~L~~e~~~L~~~~~~l~~~~e~~ek~~~e~~~----~~~k~~~~ei~~lk~~~~ql~~~  185 (189)
T PF10211_consen  123 QELEEEIEELEEEKEELEKQVQELKNKCEQLEKREEELRQ----EEEKKHQEEIDFLKKQNQQLKAQ  185 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444555666666666666666665554433222222    12233444455455444444433

Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains [].

---

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	200
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	5e-05

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 41.3 bits (96), Expect = 5e-05
 Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 21/90 (23%)

Query: 98  EDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKG 157
           ++PE I +           +  Q         KRL+    A++   ++W  KA+  L   
Sbjct: 82  QEPESIRKW----------REEQR--------KRLQELDAASKVMEQEWREKAKKDL--- 120

Query: 158 EEDLAREALKRRKSYADNANALKAQLDQQK 187
           EE   R++ +  K+  +N  A KA   Q  
Sbjct: 121 EEWNQRQSEQVEKNKINNRIADKAFYQQPD 150

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	200
3mq9_A	471	Bone marrow stromal antigen 2 fused to maltose-BI	97.59
4abm_A	79	Charged multivesicular BODY protein 4B; cell cycle	97.58
2gd5_A	179	Charged multivesicular BODY protein 3; CHMP3, ESCR	95.89
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	94.18
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	94.07
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	93.73
3bas_A	89	Myosin heavy chain, striated muscle/general contro	92.33
2efr_A	155	General control protein GCN4 and tropomyosin 1 Al;	92.22
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	92.2
3frt_A	218	Charged multivesicular BODY protein 3; ESCRT, ESCR	90.67
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	89.74
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	88.7
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	88.6
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	88.06
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	86.55
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	84.25
3iox_A	497	AGI/II, PA; alpha helix, PPII helix, supersandwich	83.93
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	83.7
3mq9_A	471	Bone marrow stromal antigen 2 fused to maltose-BI	82.63
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	82.37
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	82.26
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	81.5
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	81.1
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	80.75
3fpp_A	341	Macrolide-specific efflux protein MACA; hexameric	80.29

>3mq9_A Bone marrow stromal antigen 2 fused to maltose-BI periplasmic protein; HIV, antiviral protein; 2.80A {Escherichia coli}

Probab=97.59  E-value=0.0034  Score=56.65  Aligned_cols=115  Identities=14%  Similarity=0.127  Sum_probs=94.0

Q ss_pred             HHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----
Q 029028           79 FDRLARVVKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLA-----  153 (200)
Q Consensus        79 f~Rl~~lvra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~A-----  153 (200)
                      +..+.+.+...+..++..-.||+..|+....++++.|.+.+... +..-....+++++.++++...+.+.+|-.|     
T Consensus       350 ~~~~~~~~~~~~~~vl~G~~t~eeal~~~~~~i~~~l~~~~~~~-e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  428 (471)
T 3mq9_A          350 MSAFWYAVRTAVINAASGRQTVDEALKDAQTRITAARDGLRAVM-EARNVTHLLQQELTEAQKGFQDVEAQAATANHTVM  428 (471)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhhHHHH-HhhhHHHHHHHHHHHHhhhHHHHHHHhhhcchhHH
Confidence            56777888888888888888999999999999999998886655 777888889999999999999999888765     


Q ss_pred             -HhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          154 -LQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNLV  194 (200)
Q Consensus       154 -L~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk  194 (200)
                       |..-=|.---.++.+++++|.++..+..+++.+..+|++++
T Consensus       429 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  470 (471)
T 3mq9_A          429 ALMASLDAEKAQGQKKVEELEGEITTLNHKLQDASAEVERLR  470 (471)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence             33332322233667889999999999999999999998886

>4abm_A Charged multivesicular BODY protein 4B; cell cycle, protein transport, HIV-1; 1.80A {Homo sapiens}

Probab=97.58  E-value=0.0019  Score=46.31  Aligned_cols=75  Identities=20%  Similarity=0.194  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          118 MRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKAQLDQQKNVVNNL  193 (200)
Q Consensus       118 ar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~L  193 (200)
                      ...++.........++.+...++..++.-...|+..+ .++-.-|..||.+|+.||.+++.+..++..++.++..+
T Consensus         4 ~~~AI~~Lr~~~d~L~kkq~~L~~~i~~e~~~Ak~~~-~knK~~Al~aLkrKK~~E~qL~q~~~ql~~LE~q~~~i   78 (79)
T 4abm_A            4 EQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHG-TKNKRAALQALKRKKRYEKQLAQIDGTLSTIEFQREAL   78 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HcCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3456666777777888888888899999999999998 56678999999999999999999999999999998876

>2gd5_A Charged multivesicular BODY protein 3; CHMP3, ESCRT-III, protein transport; 2.80A {Homo sapiens} PDB: 3frv_A

Probab=95.89  E-value=0.22  Score=40.01  Aligned_cols=68  Identities=22%  Similarity=0.316  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029028          129 QKRLENKCKAAEQASEDWYRKAQLALQKGEED----LAREALKRRKSYADNANALKAQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       129 ~k~le~k~~~~~~~i~~we~rA~~AL~~G~ED----LAr~AL~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l  197 (200)
                      .+.+++++..++.+-.+.......|.++|+.+    +|+.++..+.. ..++-..+.+++...-.+....++.
T Consensus        23 ~r~Ldr~~~kle~~ekk~~~~Ikka~k~g~~~~aki~Ak~lvr~rk~-~~~l~~~~a~l~~v~~~lqt~~~~~   94 (179)
T 2gd5_A           23 MRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMIRSRKA-VSKLYASKAHMNSVLMGMKNQLAVL   94 (179)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455566666666666667778889999988    77777777765 5555558888888888887776644

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=94.07  E-value=2  Score=35.94  Aligned_cols=50  Identities=6%  Similarity=0.032  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQ  151 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~  151 (200)
                      .-|+..+..++..+..++..+..+....++++.++.+....+.+++.+-.
T Consensus        35 ~~le~~~~~l~~~~~~~~~~l~d~~~~~~~~e~~i~~~~~ri~~~~~~l~   84 (256)
T 3na7_A           35 DKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKMS   84 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455555666666666666666666666777777777777777776653

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=93.73  E-value=1.3  Score=31.71  Aligned_cols=67  Identities=13%  Similarity=0.286  Sum_probs=58.0

Q ss_pred             HHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 029028           86 VKSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQK  156 (200)
Q Consensus        86 vra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~  156 (200)
                      +.+.|..++    |-..+|...|.++++.-..+......+...+..+.++...+..+...|+.|...-|.+
T Consensus        11 LE~KIq~av----dtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~wq~Rl~~LLgk   77 (81)
T 2jee_A           11 LEAKVQQAI----DTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQALLGR   77 (81)
T ss_dssp             HHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345555555    5578999999999999999999999999999999999999999999999999876654

>3bas_A Myosin heavy chain, striated muscle/general control protein GCN4 chimera; alpha-helical coiled coil, disorder, salt links; 2.30A {Argopecten irradians} SCOP: h.1.26.1 PDB: 1nkn_A 3bat_A

Probab=92.33  E-value=2.2  Score=30.53  Aligned_cols=46  Identities=20%  Similarity=0.234  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          104 LEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRK  149 (200)
Q Consensus       104 LdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~r  149 (200)
                      -+-.+..+++.+.+++..+.......+.++.++..+..+..++..+
T Consensus        12 ~eeEm~~~eeel~~lke~l~k~e~~rkele~~~~~l~~ek~~L~~q   57 (89)
T 3bas_A           12 QEEEMKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDLFGS   57 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3556778999999999999999999999999999999999999888

>2efr_A General control protein GCN4 and tropomyosin 1 Al; destabilizing cluster, hydrophobic core, contractIle protein; 1.80A {Saccharomyces cerevisiae} PDB: 2efs_A 2d3e_A

Probab=92.22  E-value=3.6  Score=32.69  Aligned_cols=102  Identities=17%  Similarity=0.155  Sum_probs=65.6

Q ss_pred             HHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 029028           90 ANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRR  169 (200)
Q Consensus        90 in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk  169 (200)
                      +..=++++|+--...+..|+++++.+..+-..+-...+.......+-..++.+|..+..+...|     |.-|.+|-...
T Consensus        26 ~E~dLEraEERae~aE~k~~eLEeeL~~v~~nlKsLE~seekasqrEd~yEeqIk~L~~kLKEA-----E~RAE~AERsv  100 (155)
T 2efr_A           26 LKKLLERAEERAELSEGKSAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEA-----ETRAEFAERSV  100 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccchhhhhHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHH
Confidence            4445555666666667777777777777777777777776666667777777777777776666     34455666666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 029028          170 KSYADNANALKAQLDQQKNVVNNLVSN  196 (200)
Q Consensus       170 ~~~e~~a~~lq~qld~~~~~ve~Lk~~  196 (200)
                      ..++..++.+...+...+.....+...
T Consensus       101 ~kLEk~id~lEd~L~~~Kek~~~i~~e  127 (155)
T 2efr_A          101 TKLEKSIDDLEDELYAQKLKYKAISEE  127 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            666666666666666555544444433

>2fxo_A Myosin heavy chain, cardiac muscle beta isoform; coiled coil (dimeric, parallel), familial hypertrophic cardiomyopathy, FHC-associated mutant E924K; 2.50A {Homo sapiens} SCOP: h.1.26.1 PDB: 2fxm_A

Probab=92.20  E-value=3  Score=31.68  Aligned_cols=90  Identities=17%  Similarity=0.273  Sum_probs=62.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          104 LEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQL--ALQKGEEDLAREALKRRKSYADNANALKA  181 (200)
Q Consensus       104 LdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~--AL~~G~EDLAr~AL~rk~~~e~~a~~lq~  181 (200)
                      -+..+..+++.+.+++..+.......+.++.++..+..+..++..+...  ..-..-++.-.....++.+++..+..+..
T Consensus        11 ~e~E~~~~~eel~~lke~l~k~e~~r~ele~~~~~l~~Ek~~L~~qL~~E~~~l~e~EE~~~~L~~~k~eLe~~l~el~~   90 (129)
T 2fxo_A           11 REKEMASMKEEFTRLKEALEKSEARRKELEEKMVSLLQEKNDLQLQVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMNK   90 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456778888888888888888888888888888888888777655433  22223355555666677777777777777


Q ss_pred             HHHHHHHHHHHH
Q 029028          182 QLDQQKNVVNNL  193 (200)
Q Consensus       182 qld~~~~~ve~L  193 (200)
                      .++........|
T Consensus        91 rleeeee~~~~L  102 (129)
T 2fxo_A           91 RLEDEEEMNAEL  102 (129)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            777755544444

>3frt_A Charged multivesicular BODY protein 3; ESCRT, ESCRT-111, CHMP, IST1, coiled coil, cytoplasm, lipoprotein, membrane, myristate, phosphoprotein; 4.00A {Homo sapiens}

Probab=90.67  E-value=6.5  Score=32.70  Aligned_cols=70  Identities=17%  Similarity=0.201  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029028          128 SQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALK---RRKSYADNANALKAQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       128 ~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~---rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l  197 (200)
                      ..+.|++++..++.+-.+.....+.|.++|+-+-||-.+.   |+..+...+-..+.+++...-++....+..
T Consensus        22 ~~R~LdR~~~kle~eEkk~~~~IKkaakkg~~~~arilAkelVR~Rk~~~rl~~~kaqL~sV~~rlqt~~s~~   94 (218)
T 3frt_A           22 EMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVL   94 (218)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566777778888888888899999999999887775554   444455556666667766666665555443

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=88.70  E-value=5.4  Score=40.33  Aligned_cols=22  Identities=9%  Similarity=0.167  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 029028          167 KRRKSYADNANALKAQLDQQKN  188 (200)
Q Consensus       167 ~rk~~~e~~a~~lq~qld~~~~  188 (200)
                      .+...++++...|++|+++++.
T Consensus      1023 ~kv~~L~~e~~~L~qq~~~l~~ 1044 (1080)
T 2dfs_A         1023 QLVSELKEQNTLLKTEKEELNR 1044 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444455555554443

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=88.60  E-value=11  Score=34.32  Aligned_cols=31  Identities=13%  Similarity=0.183  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          114 DLVKMRQATAQVLASQKRLENKCKAAEQASE  144 (200)
Q Consensus       114 ~l~kar~~lA~v~A~~k~le~k~~~~~~~i~  144 (200)
                      ++.+.+..+..+.....+.++.+...+.+++
T Consensus       457 e~~~~~~~i~~l~~~~~~~~~~l~~~~~~i~  487 (597)
T 3oja_B          457 EVNELRAEVQQLTNEQIQQEQLLQGLHAEID  487 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3334444444444444444444444444443

>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B*

Probab=88.06  E-value=9  Score=35.40  Aligned_cols=21  Identities=19%  Similarity=0.336  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHh
Q 029028          175 NANALKAQLDQQKNVVNNLVS  195 (200)
Q Consensus       175 ~a~~lq~qld~~~~~ve~Lk~  195 (200)
                      .+..|+..++.+...+.+|+.
T Consensus       169 ~i~~L~~~~~~l~~ki~~l~~  189 (464)
T 1m1j_B          169 SLRVLRAVIDSLHKKIQKLEN  189 (464)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444443

>3mq7_A Bone marrow stromal antigen 2; HIV, antiviral protein; 2.28A {Homo sapiens} PDB: 3mqc_A 3mqb_A 3mkx_A 3nwh_A 2xg7_A* 2x7a_A

Probab=86.55  E-value=9.1  Score=29.18  Aligned_cols=31  Identities=16%  Similarity=0.253  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029028          167 KRRKSYADNANALKAQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       167 ~rk~~~e~~a~~lq~qld~~~~~ve~Lk~~l  197 (200)
                      .+.+.+++++..+...|......+++|++..
T Consensus        71 ~~vqeLqgEI~~Lnq~Lq~a~ae~erlr~~~  101 (121)
T 3mq7_A           71 KKVEELEGEITTLNHKLQDASAEVERLRREN  101 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3567778888888888888888888887654

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=84.25  E-value=11  Score=28.28  Aligned_cols=16  Identities=6%  Similarity=0.318  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHHHH
Q 029028          167 KRRKSYADNANALKAQ  182 (200)
Q Consensus       167 ~rk~~~e~~a~~lq~q  182 (200)
                      .+|.+++.++..++.+
T Consensus        90 ~eKe~L~~ql~~Lq~q  105 (110)
T 2v4h_A           90 EKKEYLQEQLEQLQRE  105 (110)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHH
Confidence            3344444444444443

>3iox_A AGI/II, PA; alpha helix, PPII helix, supersandwich fold, surface adhesin WALL, peptidoglycan-anchor, cell adhesion; HET: PMS; 1.80A {Streptococcus mutans} PDB: 3ipk_A* 1jmm_A

Probab=83.93  E-value=15  Score=34.29  Aligned_cols=25  Identities=16%  Similarity=0.197  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          169 RKSYADNANALKAQLDQQKNVVNNL  193 (200)
Q Consensus       169 k~~~e~~a~~lq~qld~~~~~ve~L  193 (200)
                      .++|+..+..++..++......+++
T Consensus        82 ~AeY~~kl~aYe~~~~~~~k~lae~  106 (497)
T 3iox_A           82 LADYPVKLKAYEDEQTSIKAALAEL  106 (497)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444444443

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=83.70  E-value=10  Score=34.44  Aligned_cols=20  Identities=15%  Similarity=0.202  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 029028          108 VLEMNDDLVKMRQATAQVLA  127 (200)
Q Consensus       108 IReme~~l~kar~~lA~v~A  127 (200)
                      +.+.+..+.+.+..+.....
T Consensus       458 ~~~~~~~i~~l~~~~~~~~~  477 (597)
T 3oja_B          458 VNELRAEVQQLTNEQIQQEQ  477 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444333333

>3mq9_A Bone marrow stromal antigen 2 fused to maltose-BI periplasmic protein; HIV, antiviral protein; 2.80A {Escherichia coli}

Probab=82.63  E-value=25  Score=31.07  Aligned_cols=26  Identities=4%  Similarity=0.150  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029028          172 YADNANALKAQLDQQKNVVNNLVSNT  197 (200)
Q Consensus       172 ~e~~a~~lq~qld~~~~~ve~Lk~~l  197 (200)
                      .+..+++++.++..++.+++++...+
T Consensus       441 ~~~~~~~~~~~~~~~~~~~~~~~~~~  466 (471)
T 3mq9_A          441 GQKKVEELEGEITTLNHKLQDASAEV  466 (471)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444445544444444444443

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A

Probab=82.37  E-value=12  Score=37.80  Aligned_cols=41  Identities=15%  Similarity=0.165  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          107 AVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWY  147 (200)
Q Consensus       107 ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we  147 (200)
                      .|+++++.+.+.+..+..+......++.++..++.+.++++
T Consensus       858 El~~L~~eL~el~~~L~~le~~l~ele~~l~~Le~e~~~l~  898 (1184)
T 1i84_S          858 EMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQ  898 (1184)
T ss_dssp             HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455555555555555555555555555555555555444

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*

Probab=82.26  E-value=8.1  Score=36.39  Aligned_cols=22  Identities=18%  Similarity=0.255  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHHhhccCC
Q 029028           78 LFDRLARVVKSYANAILSSFED   99 (200)
Q Consensus        78 if~Rl~~lvra~in~~ldk~ED   99 (200)
                      ++.+.-+=|+..||++=+.++|
T Consensus        54 lLdkqErDltkrINELKnqLEd   75 (562)
T 3ghg_A           54 LIDEVNQDFTNRINKLKNSLFE   75 (562)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTH
T ss_pred             hHHhhcCcHHHHHHHHHHHHHH
Confidence            5555555555555555555554

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=81.50  E-value=20  Score=29.22  Aligned_cols=66  Identities=12%  Similarity=0.069  Sum_probs=31.9

Q ss_pred             HHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028           87 KSYANAILSSFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQL  152 (200)
Q Consensus        87 ra~in~~ldk~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~  152 (200)
                      +..++...+.+++-+.-|+.+...-++=-.+....|..+-...+.+..+...+..+.+.|..+...
T Consensus        16 k~~~~~~~q~~~~le~El~EFqesSrELE~ELE~eL~~~Ek~~~~L~~~~~~L~~E~e~~k~K~~~   81 (189)
T 2v71_A           16 KELSMKYKQSFQEARDELVEFQEGSRELEAELEAQLVQAEQRNRDLQADNQRLKYEVEALKEKLEH   81 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444555445544444444444444444444455555555555555555555554433

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A

Probab=81.10  E-value=14  Score=37.30  Aligned_cols=34  Identities=15%  Similarity=0.144  Sum_probs=13.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          117 KMRQATAQVLASQKRLENKCKAAEQASEDWYRKA  150 (200)
Q Consensus       117 kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA  150 (200)
                      +.+..+.........++..+.+++.+...++.+.
T Consensus       861 ~L~~eL~el~~~L~~le~~l~ele~~l~~Le~e~  894 (1184)
T 1i84_S          861 AKDEELQRTKERQQKAEAELKELEQKHTQLCEEK  894 (1184)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333344444444444444444444444443333

>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus norvegicus}

Probab=80.75  E-value=14  Score=26.78  Aligned_cols=89  Identities=11%  Similarity=0.145  Sum_probs=59.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          102 KILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADNANALKA  181 (200)
Q Consensus       102 ~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~a~~lq~  181 (200)
                      ..++..+++++..-..+.+.|..+......+..++..++.+...+...=..-...     =..-......++++...+..
T Consensus         7 ~~l~~eL~~l~~eE~~L~~eL~~lEke~~~l~~el~~le~E~~~L~~eE~~~w~e-----yn~~~~ql~e~~dE~~Sl~~   81 (96)
T 3q8t_A            7 EQLQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERLDQEEAQYQRE-----YSEFKRQQLELDDELKSVEN   81 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhHHHHHHHH-----HHHHHHHHHHHHHHHHHHHH
Confidence            4566666666666666666666666666666666666666665555433322222     11233456778899999999


Q ss_pred             HHHHHHHHHHHHHh
Q 029028          182 QLDQQKNVVNNLVS  195 (200)
Q Consensus       182 qld~~~~~ve~Lk~  195 (200)
                      +++-...+.++|++
T Consensus        82 q~~~~~~qLdkL~K   95 (96)
T 3q8t_A           82 QMRYAQMQLDKLKK   95 (96)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhhc
Confidence            99999999999986

>3fpp_A Macrolide-specific efflux protein MACA; hexameric assembly, membrane fusion protein, drug efflux pump, periplasmic protein; 2.99A {Escherichia coli}

Probab=80.29  E-value=11  Score=31.64  Aligned_cols=81  Identities=17%  Similarity=0.225  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC---CHHHHHHHHHHHHHHHHHHHHHHH
Q 029028          105 EQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKG---EEDLAREALKRRKSYADNANALKA  181 (200)
Q Consensus       105 dQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G---~EDLAr~AL~rk~~~e~~a~~lq~  181 (200)
                      +..+.+++.++..++..+..+.+.....+.+++..+..           .+.|   +.++ ..+-......+.++..+++
T Consensus        68 ~~~~~~~~a~l~~~~a~l~~a~~~~~~a~~~~~r~~~L-----------~~~~~~s~~~~-~~a~~~~~~~~a~l~~~~a  135 (341)
T 3fpp_A           68 ENQIKEVEATLMELRAQRQQAEAELKLARVTYSRQQRL-----------AQTQAVSQQDL-DNAATEMAVKQAQIGTIDA  135 (341)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHH-----------HHTSSSTTHHH-HHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHcCCccHHHH-HHHHHHHHHHHHHHHHHHH
Confidence            44555556666666655555555544444444333322           1222   1111 1222223333445555566


Q ss_pred             HHHHHHHHHHHHHhhh
Q 029028          182 QLDQQKNVVNNLVSNT  197 (200)
Q Consensus       182 qld~~~~~ve~Lk~~l  197 (200)
                      +++..+..++.++.++
T Consensus       136 ~l~~a~a~l~~a~~~l  151 (341)
T 3fpp_A          136 QIKRNQASLDTAKTNL  151 (341)
T ss_dssp             HHHHTHHHHTTTTTTT
T ss_pred             HHHHHHHHHHHHHHhh
Confidence            6666655555554443

---

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	200
d1fxka_	107	Prefoldin beta subunit {Archaeon Methanobacterium	90.59
d1fpoa2	95	HSC20 (HSCB), C-terminal oligomerisation domain {E	81.1

>d1fxka_ a.2.5.1 (A:) Prefoldin beta subunit {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Prefoldin
family: Prefoldin
domain: Prefoldin beta subunit
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=90.59  E-value=1.2  Score=30.77  Aligned_cols=92  Identities=13%  Similarity=0.211  Sum_probs=67.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HhcCCHHHHHHHHHHHHHHHHHHH
Q 029028          108 VLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLA----------LQKGEEDLAREALKRRKSYADNAN  177 (200)
Q Consensus       108 IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~A----------L~~G~EDLAr~AL~rk~~~e~~a~  177 (200)
                      +.+.-..+...+..+..+......++.++.+...-++.++.--..+          +....+++-...-.++..++..+.
T Consensus         3 lqe~~~~~q~lq~el~~~~~q~~~le~q~~E~~~vl~eL~~l~~d~~vyk~vG~vLv~~~~~e~~~~l~~~~e~l~~~i~   82 (107)
T d1fxka_           3 VQHQLAQFQQLQQQAQAISVQKQTVEMQINETQKALEELSRAADDAEVYKSSGNILIRVAKDELTEELQEKLETLQLREK   82 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTCCEEEEETTEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHhcchhhcCcHHHHHHHHHHHHHHHHHHHH
Confidence            4556667788888888888888899998888887777766422111          112224455555567777899999


Q ss_pred             HHHHHHHHHHHHHHHHHhhhhc
Q 029028          178 ALKAQLDQQKNVVNNLVSNTRV  199 (200)
Q Consensus       178 ~lq~qld~~~~~ve~Lk~~l~~  199 (200)
                      .++.++...+...++++.+|+.
T Consensus        83 ~l~~q~~~l~~~l~~~~~~l~~  104 (107)
T d1fxka_          83 TIERQEERVMKKLQEMQVNIQE  104 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999988763

>d1fpoa2 a.23.1.1 (A:77-171) HSC20 (HSCB), C-terminal oligomerisation domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Open three-helical up-and-down bundle
superfamily: HSC20 (HSCB), C-terminal oligomerisation domain
family: HSC20 (HSCB), C-terminal oligomerisation domain
domain: HSC20 (HSCB), C-terminal oligomerisation domain
species: Escherichia coli [TaxId: 562]

Probab=81.10  E-value=5.9  Score=26.56  Aligned_cols=79  Identities=18%  Similarity=0.217  Sum_probs=53.1

Q ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 029028           96 SFEDPEKILEQAVLEMNDDLVKMRQATAQVLASQKRLENKCKAAEQASEDWYRKAQLALQKGEEDLAREALKRRKSYADN  175 (200)
Q Consensus        96 k~EDP~~mLdQ~IReme~~l~kar~~lA~v~A~~k~le~k~~~~~~~i~~we~rA~~AL~~G~EDLAr~AL~rk~~~e~~  175 (200)
                      .+.||+=+.+|.  |.++.|..+...     .....++.=..++...+..+......++.+++-+-|...+.+-.=+..-
T Consensus         9 T~~DpeFLMeqM--E~RE~lee~~~~-----~d~~~l~~l~~ei~~~~~~~~~~l~~~~~~~d~~~A~~~~~kLkF~~kl   81 (95)
T d1fpoa2           9 TVRDTAFLMEQL--ELREELDEIEQA-----KDEARLESFIKRVKKMFDTRHQLMVEQLDNETWDAAADTCRKLRFLDKL   81 (95)
T ss_dssp             CCSCHHHHHHHH--HHHHHHHHHHHH-----TCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHH--HHHHHHHHhhcC-----CCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHhHHHHHH
Confidence            466999777765  555556655432     0122344445557777788888888899999999999998888766555


Q ss_pred             HHHHHH
Q 029028          176 ANALKA  181 (200)
Q Consensus       176 a~~lq~  181 (200)
                      ...++.
T Consensus        82 ~~ei~~   87 (95)
T d1fpoa2          82 RSSAEQ   87 (95)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444443