Citrus Sinensis ID: 041604

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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--
Protein Sequence
CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQEEGGKDS
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHccEEEEEcHHHHHHHccccccccEEEEEEEEEcccEEEcccccEEEEEEEEcccEEEEEEccccccccccccEEEEEEEEccccHHHHcccccccccccccccccEEEEEEEEEccccccccHHHHHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHcccEEEcHHHHHccccccccccEEEEcEEEEcccEEEcccccEEEEEEEcccccEEEEEEcccccHHccccEEEEEEEEcccccHHccccccccHHHHHcccccEEEEHHHHHHcccccccHHHHHHHHHcccccHHHHHHcccccc
Coil and Loop (DISEMBL)
CIAGFIVIVLNNFQDQLVFYVTPsealekyqsnpsknkfrlgglvlegsvahpasssemEFVVTDLVTDILVRYQgslpdlfreghSVVVEGFIKPITEEIKnvkseksvsenarsrdcffsATDVlakhdekyMPQEVAAAIEKNKKMLEEQQQEEGGKDS
Flexible Loop (DISEMBL)
CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKpiteeiknvkseksvsenarsrdcFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEeqqqeeggkds
Low Complexity Region (SEG)
CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQEEGGKDS
Disordered region (IsUnstruct)
*IAGFIVIVLNNFQDQLVFYVTPSEA************FRLGGLVLEGSV********MEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEI*****************CFFSATDVLA**********************************
Disordered Region (DISOPRED)
CIAGFIVIVLNNFQDQLVFYVTPSEALE*******KNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPIT*******************DCFFSATDVLAKHDEKYM***************************
Disordered Region (DISEMBL)
CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKN***********RSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKM*************
Disordered Region (DISPRO)
CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPIT*********KSV*****SRDCFFSATDVLAKHDEKYMPQEVAAAIEKN****************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQEEGGKDS
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	162	2.2.26 [Sep-21-2011]
Q5P3K6	148	Cytochrome c-type biogene	yes	no	0.814	0.891	0.380	1e-22
B3R8Z5	157	Cytochrome c-type biogene	yes	no	0.709	0.732	0.413	6e-22
A1WWS3	149	Cytochrome c-type biogene	yes	no	0.796	0.865	0.374	3e-21
Q7WXB8	155	Cytochrome c-type biogene	yes	no	0.808	0.845	0.367	5e-21
Q82WC5	149	Cytochrome c-type biogene	yes	no	0.740	0.805	0.398	5e-21
Q46RW7	159	Cytochrome c-type biogene	yes	no	0.845	0.861	0.355	1e-20
A1KCJ1	148	Cytochrome c-type biogene	yes	no	0.740	0.810	0.412	1e-20
B8EJK7	166	Cytochrome c-type biogene	yes	no	0.808	0.789	0.382	1e-20
B8IUY7	168	Cytochrome c-type biogene	yes	no	0.783	0.755	0.403	1e-20
A8HR72	174	Cytochrome c-type biogene	yes	no	0.777	0.724	0.407	2e-20

>sp|Q5P3K6|CCME_AROAE Cytochrome c-type biogenesis protein CcmE OS=Aromatoleum aromaticum (strain EbN1) GN=ccmE PE=3 SV=1

 Score =  105 bits (262), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 80/155 (51%), Gaps = 23/155 (14%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
            + G + +VLN FQ  LVF+ TP+E  E     P    FR+GG+V  GS+   A    ++
Sbjct: 17  LLVGAVALVLNAFQQNLVFFHTPTEVAEG--KAPVGRAFRIGGMVETGSIRRAADGVTVQ 74

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           F +TD    I V Y+GSLPDLF EG   VV+G + P                     D  
Sbjct: 75  FAITDTAKVIPVSYKGSLPDLFSEGKGAVVQGTLGP---------------------DGQ 113

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQ 155
           F A++VLAKHDE YMP E   A+++ +K  +  QQ
Sbjct: 114 FQASEVLAKHDENYMPPEAQHAVDQAQKAAQTVQQ 148

Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH.
Aromatoleum aromaticum (strain EbN1) (taxid: 76114)

>sp|B3R8Z5|CCME_CUPTR Cytochrome c-type biogenesis protein CcmE OS=Cupriavidus taiwanensis (strain R1 / LMG 19424) GN=ccmE PE=3 SV=1

 Score =  103 bits (256), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 57/138 (41%), Positives = 73/138 (52%), Gaps = 23/138 (16%)

Query: 8   IVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLV 67
           +VLN F+  LVF+ +PS+     Q  P    FRLGGLV  GS+        + FVVTD  
Sbjct: 24  LVLNAFRANLVFFFSPSQV--AAQEAPVARSFRLGGLVASGSIRREGDGMTVRFVVTDTA 81

Query: 68  TDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVL 127
             + V+Y+G LPDLFREG  VV  G ++                      D  F AT+VL
Sbjct: 82  RQVPVQYRGLLPDLFREGKGVVARGQLRA---------------------DGTFVATEVL 120

Query: 128 AKHDEKYMPQEVAAAIEK 145
           AKHDE YMP E AAA+++
Sbjct: 121 AKHDENYMPPEAAAALKQ 138

Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH.

Cupriavidus taiwanensis (strain R1 / LMG 19424) (taxid: 164546)

>sp|A1WWS3|CCME_HALHL Cytochrome c-type biogenesis protein CcmE OS=Halorhodospira halophila (strain DSM 244 / SL1) GN=ccmE PE=3 SV=1

 Score =  101 bits (251), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 58/155 (37%), Positives = 87/155 (56%), Gaps = 26/155 (16%)

Query: 1   CIAGFIV---IVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSS 57
            +AG  V   +VLN F+D + F++TPSE + K  S+  +  FR+GGLV +GSV   + S+
Sbjct: 14  VVAGVSVATALVLNAFRDNMTFFITPSEVMAK--SDMPERHFRIGGLVEDGSVERDSDST 71

Query: 58  EMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSR 117
           ++ F VTD    + V ++G LPDLFREG  VVVEG I                     + 
Sbjct: 72  QVRFRVTDTEASVPVDFEGILPDLFREGQGVVVEGRI---------------------TS 110

Query: 118 DCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEE 152
           +  F A +V+A+HDE YMP E   A+++ +  ++E
Sbjct: 111 NGVFKADNVMARHDEDYMPAEAQEALDRVEHSVDE 145

Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH.

Halorhodospira halophila (strain DSM 244 / SL1) (taxid: 349124)

>sp|Q7WXB8|CCME_CUPNH Cytochrome c-type biogenesis protein CcmE OS=Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) GN=ccmE PE=3 SV=1

 Score =  100 bits (248), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 58/158 (36%), Positives = 78/158 (49%), Gaps = 27/158 (17%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
           C+     +VLN F+  LVF+ +PS+        P    FRLGGLV  GS+        + 
Sbjct: 17  CVGIATTLVLNAFRSNLVFFFSPSQV--AAHEAPVARSFRLGGLVAPGSIRREGDGMTIR 74

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           F+VTD    +LV Y+G LPDLFREG  VV  G ++                      D  
Sbjct: 75  FIVTDTARQVLVVYRGLLPDLFREGKGVVARGKLEA---------------------DGT 113

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEK----NKKMLEEQQ 154
           F A++VLAKHDE YMP E A A+++    N++M    Q
Sbjct: 114 FVASEVLAKHDENYMPPEAADALKQAEQVNRRMAGTPQ 151

Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH.

Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (taxid: 381666)

>sp|Q82WC5|CCME_NITEU Cytochrome c-type biogenesis protein CcmE OS=Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298) GN=ccmE PE=3 SV=1

 Score =  100 bits (248), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 57/143 (39%), Positives = 75/143 (52%), Gaps = 23/143 (16%)

Query: 6   IVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTD 65
           +V+VLN FQ  LVF+ +PS+   K    P    FR+GGLV EGS+      + + F +TD
Sbjct: 22  VVLVLNAFQSNLVFFFSPSQVAAK--EAPIGKSFRIGGLVEEGSLKREGDGTTLNFAITD 79

Query: 66  LVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATD 125
               I V Y G LPDLF+EG  VV +G +                     + D  F A +
Sbjct: 80  TAEVIRVVYTGILPDLFKEGKGVVAQGKM---------------------ADDGIFYADE 118

Query: 126 VLAKHDEKYMPQEVAAAIEKNKK 148
           VLAKHDE YMP E A+A+E+  K
Sbjct: 119 VLAKHDENYMPPEAASALEQAAK 141

Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH.

Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298) (taxid: 228410)

>sp|Q46RW7|CCME_CUPPJ Cytochrome c-type biogenesis protein CcmE OS=Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) GN=ccmE PE=3 SV=1

 Score = 99.4 bits (246), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 59/166 (35%), Positives = 83/166 (50%), Gaps = 29/166 (17%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
           C    + +VLN F+  LVF+ +PS+        P+   FRLGGLV  GS+        + 
Sbjct: 17  CAGIALALVLNAFRSNLVFFFSPSQV--AAHEAPASRSFRLGGLVAPGSIRREGDGMTVR 74

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           F+VTD   ++ V Y+G LPDLFREG  VV  G +                      R   
Sbjct: 75  FIVTDKAREVPVVYRGLLPDLFREGKGVVARGTL---------------------DRSGT 113

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEK----NKKMLEEQQQEEGGKDS 162
           F A++VLAKHDE YMP E A A+++    N++M    Q  EG +++
Sbjct: 114 FVASEVLAKHDENYMPPEAADALKQAEQVNRRM--ASQLAEGERET 157

Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH.

Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) (taxid: 264198)

>sp|A1KCJ1|CCME_AZOSB Cytochrome c-type biogenesis protein CcmE OS=Azoarcus sp. (strain BH72) GN=ccmE PE=3 SV=1

 Score = 99.0 bits (245), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 59/143 (41%), Positives = 72/143 (50%), Gaps = 23/143 (16%)

Query: 13  FQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILV 72
           FQ  LVF+ TPSE  E     P    FR+GG+V  GS+   A    + FV+TD    I V
Sbjct: 29  FQQNLVFFHTPSEVAEG--KAPVGKTFRVGGMVETGSIQRDADGVTVRFVITDTAKVIPV 86

Query: 73  RYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDE 132
            Y+GSLPDLF+EG   VV+G +                       D  F AT+VLAKHDE
Sbjct: 87  SYRGSLPDLFKEGKGAVVQGTL---------------------GADGQFRATEVLAKHDE 125

Query: 133 KYMPQEVAAAIEKNKKMLEEQQQ 155
            YMP E A A+E+  K     QQ
Sbjct: 126 NYMPPEAAHALEQAHKTATTVQQ 148

Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH.

Azoarcus sp. (strain BH72) (taxid: 62928)

>sp|B8EJK7|CCME_METSB Cytochrome c-type biogenesis protein CcmE OS=Methylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906) GN=ccmE PE=3 SV=1

 Score = 99.0 bits (245), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 60/157 (38%), Positives = 84/157 (53%), Gaps = 26/157 (16%)

Query: 6   IVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTD 65
           + +V+   +D +VF+ +P+E  EK  +N ++   R+GGLV   S+      + + F VTD
Sbjct: 22  VGLVMFALRDNIVFFYSPTELAEKPATNGAR--LRIGGLVKPASLDRQGDQT-VRFTVTD 78

Query: 66  LVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATD 125
           +  D+ V Y G LPDLFREG  VV EG ++P                     D  F A  
Sbjct: 79  MKHDVAVTYTGLLPDLFREGQGVVAEGALRP---------------------DGVFHADS 117

Query: 126 VLAKHDEKYMPQEVAAAIEKNKKMLEEQQQEEGGKDS 162
           VLAKHDE+YMP+EVA A++K     EE + E  GK S
Sbjct: 118 VLAKHDERYMPREVADALKKQGVWQEEGKSE--GKPS 152

Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH.

Methylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906) (taxid: 395965)

>sp|B8IUY7|CCME_METNO Cytochrome c-type biogenesis protein CcmE OS=Methylobacterium nodulans (strain ORS2060 / LMG 21967) GN=ccmE PE=3 SV=1

 Score = 99.0 bits (245), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 61/151 (40%), Positives = 76/151 (50%), Gaps = 24/151 (15%)

Query: 8   IVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLV 67
           +VL   +  +VF+ +PSE     Q+     +FRLGGLV EGSV        + FVVTD  
Sbjct: 24  LVLWAMRGTIVFFRSPSEIAS--QAVAPGVRFRLGGLVQEGSVQR-GPDGRVAFVVTDNG 80

Query: 68  TDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVL 127
             + VRYQG LPDLFREG  VV EG ++P                        F A  VL
Sbjct: 81  ATVPVRYQGLLPDLFREGQGVVAEGMLEP---------------------GGMFRADTVL 119

Query: 128 AKHDEKYMPQEVAAAIEKNKKMLEEQQQEEG 158
           AKHDE YMP+EVA A++K      E +   G
Sbjct: 120 AKHDETYMPREVADALKKQGHWQGEAKHPGG 150

Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH.

Methylobacterium nodulans (strain ORS2060 / LMG 21967) (taxid: 460265)

>sp|A8HR72|CCME_AZOC5 Cytochrome c-type biogenesis protein CcmE OS=Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / ORS 571) GN=ccmE PE=3 SV=1

 Score = 98.2 bits (243), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 64/157 (40%), Positives = 84/157 (53%), Gaps = 31/157 (19%)

Query: 3   AGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFV 62
           AG I+  LN   D +VF+ TP+E  ++ Q  P   + RLGGLV  GSVA   S + + F 
Sbjct: 22  AGLILTALN---DTIVFFRTPTEVAQQ-QIAPGA-RLRLGGLVEPGSVAK--SGASVRFA 74

Query: 63  VTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFS 122
           VTD  + + V Y G LPDLFREG  VV EG ++                      D    
Sbjct: 75  VTDGNSKVTVAYTGLLPDLFREGQGVVAEGVLQ---------------------SDGTVK 113

Query: 123 ATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQEEGG 159
           A  VLAKHDE+YMP+EVA A++K+      ++ EEGG
Sbjct: 114 ADSVLAKHDERYMPREVADALKKSGHW---KEGEEGG 147

Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH.

Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / ORS 571) (taxid: 438753)

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	162
297819882	257	hypothetical protein ARALYDRAFT_485534 [	0.925	0.583	0.793	2e-67
255544816	254	conserved hypothetical protein [Ricinus	0.925	0.590	0.793	5e-67
15231037	256	transmembrane protein G1P-related 1 [Ara	0.925	0.585	0.786	7e-67
449442511	259	PREDICTED: cytochrome c-type biogenesis	0.938	0.586	0.769	7e-65
449476036	259	PREDICTED: LOW QUALITY PROTEIN: cytochro	0.938	0.586	0.763	3e-64
356541185	240	PREDICTED: cytochrome c-type biogenesis	0.932	0.629	0.761	4e-64
356544549	249	PREDICTED: cytochrome c-type biogenesis	0.932	0.606	0.761	5e-64
224075784	200	predicted protein [Populus trichocarpa]	0.932	0.755	0.754	3e-63
357472983	264	Cytochrome c-type biogenesis protein ccm	0.950	0.583	0.727	3e-62
225466659	258	PREDICTED: cytochrome c-type biogenesis	0.950	0.596	0.720	4e-60

>gi|297819882|ref|XP_002877824.1| hypothetical protein ARALYDRAFT_485534 [Arabidopsis lyrata subsp. lyrata] gi|297323662|gb|EFH54083.1| hypothetical protein ARALYDRAFT_485534 [Arabidopsis lyrata subsp. lyrata]

 Score =  259 bits (663), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 119/150 (79%), Positives = 137/150 (91%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
           CIAGF+VIVLN FQDQLVFY+TPS+A+EK+  NP+KNKFRLGGLVLEGSVA PA+S EME
Sbjct: 92  CIAGFVVIVLNQFQDQLVFYLTPSDAMEKFAENPTKNKFRLGGLVLEGSVAQPAASQEME 151

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           FV+TDL+TDILVRY+GSLPDLFREGHSVVVEGFIKP T+E++   S K VS+ AR+ DCF
Sbjct: 152 FVITDLITDILVRYKGSLPDLFREGHSVVVEGFIKPYTDEVRKEVSTKPVSQKARNLDCF 211

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEKNKKML 150
           FSAT+VLAKHDEKYMPQEVAAAIEKNKK++
Sbjct: 212 FSATEVLAKHDEKYMPQEVAAAIEKNKKII 241

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255544816|ref|XP_002513469.1| conserved hypothetical protein [Ricinus communis] gi|223547377|gb|EEF48872.1| conserved hypothetical protein [Ricinus communis]

 Score =  258 bits (660), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 119/150 (79%), Positives = 137/150 (91%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
           CIAGFIVIV+NNFQDQ+VFY+TP++A+EKY++NP KNKFRLGGLVLEGSVA PA+S EME
Sbjct: 92  CIAGFIVIVINNFQDQMVFYITPTDAMEKYKTNPEKNKFRLGGLVLEGSVAQPATSPEME 151

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           FV+TDLVTDILVRYQGSLPDLFREGHSVVVEGF+KP+TEE+K   +  SVS  ARS +CF
Sbjct: 152 FVITDLVTDILVRYQGSLPDLFREGHSVVVEGFVKPLTEELKKDGNANSVSGKARSGECF 211

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEKNKKML 150
           F AT+VLAKHDEKYMP+EVA AIEKNKK+L
Sbjct: 212 FKATEVLAKHDEKYMPKEVADAIEKNKKLL 241

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231037|ref|NP_190747.1| transmembrane protein G1P-related 1 [Arabidopsis thaliana] gi|1657615|gb|AAB18126.1| G1p [Arabidopsis thaliana] gi|3068706|gb|AAC14406.1| putative transmembrane protein G1p [Arabidopsis thaliana] gi|28416645|gb|AAO42853.1| At3g51790 [Arabidopsis thaliana] gi|110743169|dbj|BAE99476.1| Cytochrome C Maturation G1p [Arabidopsis thaliana] gi|332645322|gb|AEE78843.1| transmembrane protein G1P-related 1 [Arabidopsis thaliana]

 Score =  258 bits (658), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 118/150 (78%), Positives = 137/150 (91%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
           CIAGF+VIVLN FQDQLVFY+TPS+A+EK+  NP+KNKFRLGGLVLEGSVA PA+S EME
Sbjct: 93  CIAGFVVIVLNQFQDQLVFYLTPSDAMEKFAENPTKNKFRLGGLVLEGSVAQPAASQEME 152

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           FV+TDL+TDILVRY+GSLPDLFREGHSVVVEGFIKP T+E++   S K +S+ AR+ DCF
Sbjct: 153 FVITDLITDILVRYKGSLPDLFREGHSVVVEGFIKPYTDEVRKEVSTKPISKKARNLDCF 212

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEKNKKML 150
           FSAT+VLAKHDEKYMPQEVAAAIEKNKK++
Sbjct: 213 FSATEVLAKHDEKYMPQEVAAAIEKNKKII 242

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449442511|ref|XP_004139025.1| PREDICTED: cytochrome c-type biogenesis protein CcmE-like [Cucumis sativus]

 Score =  251 bits (641), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 117/152 (76%), Positives = 137/152 (90%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
           CIAGF+VIVL+NFQ+ L+FYVTP++ALEK+ +NPSKNKFRLGGLVLEGSV HPASSS+ME
Sbjct: 100 CIAGFVVIVLSNFQEHLMFYVTPTDALEKFSANPSKNKFRLGGLVLEGSVTHPASSSQME 159

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           FV+TDL+TD+LVR+QGSLPDLFREGHSVVVEGF+KP T+EI+N  S KSVS  ARS   +
Sbjct: 160 FVITDLITDMLVRHQGSLPDLFREGHSVVVEGFLKPFTDEIRNEISTKSVSGKARSEKYY 219

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEKNKKMLEE 152
           FSA +VLAKHDEKYMP EVAAAIEKN+K +EE
Sbjct: 220 FSAIEVLAKHDEKYMPAEVAAAIEKNRKKIEE 251

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449476036|ref|XP_004154622.1| PREDICTED: LOW QUALITY PROTEIN: cytochrome c-type biogenesis protein CcmE-like [Cucumis sativus]

 Score =  249 bits (636), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 116/152 (76%), Positives = 136/152 (89%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
           CIAGF+VIVL+NFQ+ L+FYVTP++ALEK+ +NPSKNKFRLGGLVLEGSV HPASSS+ME
Sbjct: 100 CIAGFVVIVLSNFQEHLMFYVTPTDALEKFSANPSKNKFRLGGLVLEGSVTHPASSSQME 159

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           FV+TDL+TD+LVR+QGSLPDLFREGHSVVVEGF+KP T+EI+N  S KSVS  ARS   +
Sbjct: 160 FVITDLITDMLVRHQGSLPDLFREGHSVVVEGFLKPFTDEIRNEISTKSVSGKARSEKYY 219

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEKNKKMLEE 152
           F A +VLAKHDEKYMP EVAAAIEKN+K +EE
Sbjct: 220 FXAIEVLAKHDEKYMPAEVAAAIEKNRKKIEE 251

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356541185|ref|XP_003539061.1| PREDICTED: cytochrome c-type biogenesis protein CcmE-like [Glycine max]

 Score =  249 bits (635), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 115/151 (76%), Positives = 138/151 (91%)

Query: 2   IAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEF 61
           +AGF+VIVLNNFQDQLVFYVTP+EALEKY +NP+K +FRLGGLVLEGSV +PASS E+EF
Sbjct: 72  LAGFVVIVLNNFQDQLVFYVTPTEALEKYATNPTKARFRLGGLVLEGSVVYPASSPEVEF 131

Query: 62  VVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFF 121
           VVTDL++D++VRY+GSLPDLFREGHSVVVEG +KP TEEI+   S K+VSE AR  +C+F
Sbjct: 132 VVTDLISDMVVRYEGSLPDLFREGHSVVVEGLVKPFTEEIRKEVSVKNVSEKARKIECYF 191

Query: 122 SATDVLAKHDEKYMPQEVAAAIEKNKKMLEE 152
           SAT+VLAKHDEKYMP+EVAAAIEKNKK++E+
Sbjct: 192 SATEVLAKHDEKYMPKEVAAAIEKNKKIIED 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356544549|ref|XP_003540712.1| PREDICTED: cytochrome c-type biogenesis protein CcmE-like [Glycine max]

 Score =  248 bits (634), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 115/151 (76%), Positives = 138/151 (91%)

Query: 2   IAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEF 61
           +AGF+VIVLNNFQDQLVFYVTP+EALEKY +NP+K +FRLGGLVLEGSV +PASS E+EF
Sbjct: 81  LAGFVVIVLNNFQDQLVFYVTPTEALEKYANNPTKARFRLGGLVLEGSVVYPASSPEVEF 140

Query: 62  VVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFF 121
           VVTDL++DI+VRY+GSLPDLFREGHSVVVEG +KP T+EI+   S K+VSE AR  +C+F
Sbjct: 141 VVTDLISDIVVRYEGSLPDLFREGHSVVVEGLVKPFTDEIRKEVSAKNVSEKARKIECYF 200

Query: 122 SATDVLAKHDEKYMPQEVAAAIEKNKKMLEE 152
           SAT+VLAKHDEKYMP+EVAAAIEKNKK++E+
Sbjct: 201 SATEVLAKHDEKYMPKEVAAAIEKNKKIIED 231

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224075784|ref|XP_002304766.1| predicted protein [Populus trichocarpa] gi|222842198|gb|EEE79745.1| predicted protein [Populus trichocarpa]

 Score =  246 bits (627), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 114/151 (75%), Positives = 136/151 (90%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
           CIAGFIVIVLNNFQDQLVFY+TPS+A+EK+++NPSKNKFRLGGLVLEGSV HP +S EME
Sbjct: 49  CIAGFIVIVLNNFQDQLVFYITPSDAVEKFKNNPSKNKFRLGGLVLEGSVVHPLTSPEME 108

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           FVVTDL+TDILV+Y+GSLPDLFREGHSVVVEGF+K + ++++     K+VS  ARS +C+
Sbjct: 109 FVVTDLITDILVKYEGSLPDLFREGHSVVVEGFMKELDDKVRKEVGLKNVSGKARSGECY 168

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEKNKKMLE 151
           F A DVLAKHDEKYMPQEVAAAIE+NKK++E
Sbjct: 169 FKAFDVLAKHDEKYMPQEVAAAIERNKKLIE 199

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357472983|ref|XP_003606776.1| Cytochrome c-type biogenesis protein ccmE [Medicago truncatula] gi|355507831|gb|AES88973.1| Cytochrome c-type biogenesis protein ccmE [Medicago truncatula]

 Score =  242 bits (618), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 112/154 (72%), Positives = 136/154 (88%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
             AGFIV+VLNNFQDQLVFYVTP+E +EK+++NP+K+KFRLGGLVLEGS+ +PA+S + E
Sbjct: 96  TFAGFIVVVLNNFQDQLVFYVTPTEVIEKFKANPTKSKFRLGGLVLEGSIVYPANSPDTE 155

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           FVVTDL+TDI+VRY GSLPDLFREGHSVV EGF+KP T+EIK   S K+V+  ARS D +
Sbjct: 156 FVVTDLITDIVVRYDGSLPDLFREGHSVVAEGFVKPFTDEIKKESSVKNVAAKARSGDYY 215

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQ 154
           FSAT+VLAKHDEKYMP+EVAAAIEKNKK+L+E +
Sbjct: 216 FSATEVLAKHDEKYMPKEVAAAIEKNKKILDEAK 249

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225466659|ref|XP_002273859.1| PREDICTED: cytochrome c-type biogenesis protein CcmE [Vitis vinifera] gi|147791890|emb|CAN61824.1| hypothetical protein VITISV_008494 [Vitis vinifera]

 Score =  235 bits (600), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 111/154 (72%), Positives = 130/154 (84%)

Query: 3   AGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFV 62
           +  IV+VL  FQDQ+VFYVTP++ALE+Y  NPSKNKFRLGGLVLEGSV    SS +MEFV
Sbjct: 98  SALIVLVLYQFQDQMVFYVTPTDALEEYAKNPSKNKFRLGGLVLEGSVKQLVSSPDMEFV 157

Query: 63  VTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFS 122
           VTDL+TDILVRY G+LPDLFREGHSVVVEGF+KP T+EI+  +S +SV+  ARS DC+FS
Sbjct: 158 VTDLITDILVRYDGALPDLFREGHSVVVEGFVKPFTDEIRKDESARSVAGKARSIDCYFS 217

Query: 123 ATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQE 156
           A +VLAKHDEKYMPQEVAAAIE+NKK L E  +E
Sbjct: 218 AIEVLAKHDEKYMPQEVAAAIERNKKKLAEMAEE 251

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	162
TAIR|locus:2074363	256	G1 "transmembrane protein G1P-	0.987	0.625	0.75	1.4e-62
TIGR_CMR|SO_0259	161	SO_0259 "cytochrome c biogenes	0.555	0.559	0.367	5.5e-18
UNIPROTKB|P69490	159	ccmE "membrane anchored peripl	0.537	0.547	0.373	1.6e-16
TIGR_CMR|SPO_A0193	139	SPO_A0193 "cytochrome c-type b	0.469	0.546	0.341	7.9e-14
UNIPROTKB|Q9KQE7	160	ccmE "Cytochrome c-type biogen	0.555	0.562	0.395	3.5e-11
TIGR_CMR|VC_2053	160	VC_2053 "cytochrome c-type bio	0.555	0.562	0.395	3.5e-11
TIGR_CMR|ECH_0789	133	ECH_0789 "cytochrome c-type bi	0.555	0.676	0.347	9.4e-11
TIGR_CMR|CPS_1030	178	CPS_1030 "cytochrome c-type bi	0.913	0.831	0.298	2e-10
TIGR_CMR|NSE_0828	135	NSE_0828 "putative cytochrome	0.5	0.6	0.284	1.1e-09
TIGR_CMR|APH_0526	141	APH_0526 "cytochrome c-type bi	0.691	0.794	0.289	5.9e-09

TAIR|locus:2074363 G1 "transmembrane protein G1P-related 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 639 (230.0 bits), Expect = 1.4e-62, P = 1.4e-62
 Identities = 120/160 (75%), Positives = 141/160 (88%)

Query:     1 CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
             CIAGF+VIVLN FQDQLVFY+TPS+A+EK+  NP+KNKFRLGGLVLEGSVA PA+S EME
Sbjct:    93 CIAGFVVIVLNQFQDQLVFYLTPSDAMEKFAENPTKNKFRLGGLVLEGSVAQPAASQEME 152

Query:    61 FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
             FV+TDL+TDILVRY+GSLPDLFREGHSVVVEGFIKP T+E++   S K +S+ AR+ DCF
Sbjct:   153 FVITDLITDILVRYKGSLPDLFREGHSVVVEGFIKPYTDEVRKEVSTKPISKKARNLDCF 212

Query:   121 FSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQEEGGK 160
             FSAT+VLAKHDEKYMPQEVAAAIEKNKK++E    E+  +
Sbjct:   213 FSATEVLAKHDEKYMPQEVAAAIEKNKKIIEAAATEQAAE 252

GO:0005739 "mitochondrion" evidence=ISM

GO:0017004 "cytochrome complex assembly" evidence=ISS

GO:0005743 "mitochondrial inner membrane" evidence=IDA

GO:0018063 "cytochrome c-heme linkage" evidence=IGI

GO:0020037 "heme binding" evidence=IDA

GO:0006626 "protein targeting to mitochondrion" evidence=RCA

GO:0019243 "methylglyoxal catabolic process to D-lactate" evidence=RCA

TIGR_CMR|SO_0259 SO_0259 "cytochrome c biogenesis protein CcmE" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 131 (51.2 bits), Expect = 5.5e-18, Sum P(2) = 5.5e-18
 Identities = 36/98 (36%), Positives = 53/98 (54%)

Query:     2 IAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSK----NKFRLGGLVLEGSVAHPASSS 57
             IA  ++  LN+  +  +FY TPSE +        K     + R+GG+V  GS+    +S 
Sbjct:    22 IASLLLYALNSNLN--LFY-TPSEIVNGKTDTGVKPEAGQRIRVGGMVTVGSMVRDPNSL 78

Query:    58 EMEFVVTD-LVTDILVRYQGSLPDLFREGHSVVVEGFI 94
              ++F V D L  +ILV Y   LPDLFREG  +V +G +
Sbjct:    79 HVQFAVHDSLGGEILVTYDDLLPDLFREGQGIVAQGVL 116

GO:0003824 "catalytic activity" evidence=ISS

GO:0017004 "cytochrome complex assembly" evidence=ISS

UNIPROTKB|P69490 ccmE "membrane anchored periplasmic heme chaperone CcmE" [Escherichia coli K-12 (taxid:83333)]

 Score = 142 (55.0 bits), Expect = 1.6e-16, Sum P(2) = 1.6e-16
 Identities = 34/91 (37%), Positives = 50/91 (54%)

Query:     6 IVIVLNNFQDQLVFYVTPSEAL---EKYQSNPSKN-KFRLGGLVLEGSVAHPASSSEMEF 61
             I +VL   +  +  + TP E L    + Q  P    + R+GG+V+ GSV    +S ++ F
Sbjct:    23 IGLVLYALRSNIDLFYTPGEILYGKRETQQMPEVGQRLRVGGMVMPGSVQRDPNSLKVTF 82

Query:    62 VVTDLVTDILVRYQGSLPDLFREGHSVVVEG 92
              + D    + V Y+G LPDLFREG  VVV+G
Sbjct:    83 TIYDAEGSVDVSYEGILPDLFREGQGVVVQG 113

GO:0020037 "heme binding" evidence=IDA

GO:0046872 "metal ion binding" evidence=IEA

GO:0017003 "protein-heme linkage" evidence=IEA;IDA

GO:0016021 "integral to membrane" evidence=IEA

GO:0031237 "intrinsic to external side of plasma membrane, in periplasmic space" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0017004 "cytochrome complex assembly" evidence=IEA

TIGR_CMR|SPO_A0193 SPO_A0193 "cytochrome c-type biogenesis protein CycJ" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 114 (45.2 bits), Expect = 7.9e-14, Sum P(2) = 7.9e-14
 Identities = 28/82 (34%), Positives = 43/82 (52%)

Query:    14 QDQLVFYVTPSEALEKYQSNPSKNK-FRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILV 72
             +D + F+ TP+E        P+ N+  R+GG+V  GS+    ++    F VTD  T   +
Sbjct:    32 RDGIQFFRTPTEVAT---DPPAANEVLRIGGMVEHGSLVRDGAN--FSFRVTDGETSFPI 86

Query:    73 RYQGSLPDLFREGHSVVVEGFI 94
              Y G +PDLFREG   +  G +
Sbjct:    87 SYVGIVPDLFREGEGTIATGSV 108

GO:0003824 "catalytic activity" evidence=ISS

GO:0017004 "cytochrome complex assembly" evidence=ISS

UNIPROTKB|Q9KQE7 ccmE "Cytochrome c-type biogenesis protein CcmE" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 38/96 (39%), Positives = 55/96 (57%)

Query:     4 GFIVIVLNNFQDQLVFYVTPSEALE-KYQSNPS-KNKFRLGGLVLEGSVAHPASSSEMEF 61
             G I+  LN   D  +FY TP+E +  K    P    + R+GG+V+EGSV    +S ++ F
Sbjct:    24 GLIIYALNQNMD--LFY-TPTELVYGKEGKKPEIGQRLRIGGMVVEGSVKRDPNSLKVSF 80

Query:    62 VVTDLVTDILVRYQGSLPDLFREGHSVVVEG-FIKP 96
              + D+   I V Y G LPDLFREG  +V +G  ++P
Sbjct:    81 DLHDVGPSITVTYDGILPDLFREGQGIVAQGVLVEP 116

GO:0003824 "catalytic activity" evidence=ISS

GO:0017004 "cytochrome complex assembly" evidence=ISS

TIGR_CMR|VC_2053 VC_2053 "cytochrome c-type biogenesis protein CcmE" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 38/96 (39%), Positives = 55/96 (57%)

Query:     4 GFIVIVLNNFQDQLVFYVTPSEALE-KYQSNPS-KNKFRLGGLVLEGSVAHPASSSEMEF 61
             G I+  LN   D  +FY TP+E +  K    P    + R+GG+V+EGSV    +S ++ F
Sbjct:    24 GLIIYALNQNMD--LFY-TPTELVYGKEGKKPEIGQRLRIGGMVVEGSVKRDPNSLKVSF 80

Query:    62 VVTDLVTDILVRYQGSLPDLFREGHSVVVEG-FIKP 96
              + D+   I V Y G LPDLFREG  +V +G  ++P
Sbjct:    81 DLHDVGPSITVTYDGILPDLFREGQGIVAQGVLVEP 116

GO:0003824 "catalytic activity" evidence=ISS

GO:0017004 "cytochrome complex assembly" evidence=ISS

TIGR_CMR|ECH_0789 ECH_0789 "cytochrome c-type biogenesis protein CcmE" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 150 (57.9 bits), Expect = 9.4e-11, P = 9.4e-11
 Identities = 33/95 (34%), Positives = 56/95 (58%)

Query:     6 IVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTD 65
             +V+VLN  Q+ + F+ TP+E L     N +++  R+GG++++GSV        + F +TD
Sbjct:    22 VVVVLNKLQNNISFFFTPTEVLSNAIYNNNRD-IRIGGMIIKGSVEK--HDDFISFYITD 78

Query:    66 LVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEE 100
             L   + + Y+G LP LF EG  +V +G  K ++ E
Sbjct:    79 LENHMKILYKGILPPLFSEGSWIVAKG--KMVSSE 111

GO:0003824 "catalytic activity" evidence=ISS

GO:0017004 "cytochrome complex assembly" evidence=ISS

TIGR_CMR|CPS_1030 CPS_1030 "cytochrome c-type biogenesis protein CcmE" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 147 (56.8 bits), Expect = 2.0e-10, P = 2.0e-10
 Identities = 49/164 (29%), Positives = 89/164 (54%)

Query:     2 IAGFIVIVLNNFQDQLVFYVTPSEALE-KYQSN--PSKN-KFRLGGLVLEGSVAHPASSS 57
             ++G ++  L+   D  +F+ TPSE  + K ++   PS   + R+GGLV+ GSV     + 
Sbjct:    22 VSGLVLYALSQNID--LFF-TPSEITQGKKETGLKPSLGQRIRIGGLVVPGSVKRDPENL 78

Query:    58 EMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSR 117
             ++ F ++D+   I+  ++ S P +     +V  EG +  +  E + + +  +++E+  + 
Sbjct:    79 KVSFRLSDMAMPIV--FKDSDPMV-----TVYYEGILPDLFREGQGIVANGTLTEHPPT- 130

Query:   118 DCFFSATDVLAKHDEKYMPQEVA-AAIEKNKKMLEEQQQEEGGK 160
                  A++VLAKHDE YMP E+A AA +K+ K     +Q E  K
Sbjct:   131 GLSIEASEVLAKHDENYMPAELAEAAGQKHDKATYSDKQLESKK 174

GO:0003824 "catalytic activity" evidence=ISS

GO:0017004 "cytochrome complex assembly" evidence=ISS

TIGR_CMR|NSE_0828 NSE_0828 "putative cytochrome c-type biogenesis protein CcmE" [Neorickettsia sennetsu str. Miyayama (taxid:222891)]

 Score = 99 (39.9 bits), Expect = 1.1e-09, Sum P(2) = 1.1e-09
 Identities = 25/88 (28%), Positives = 47/88 (53%)

Query:     3 AGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFV 62
             +G + ++L N  + + F+  PS+      SN    + ++GG++     A   S   + F+
Sbjct:    20 SGVVSLMLFNLSESISFFYLPSDVARVVASN---REIKVGGIIK----AIKKSKDGVRFL 72

Query:    63 VTDLVTDILVRYQGSLPDLFREGHSVVV 90
             ++D   +I V Y+G LP L ++G +VVV
Sbjct:    73 LSDGAAEIEVLYEGILPSLVQDGINVVV 100

GO:0003824 "catalytic activity" evidence=ISS

GO:0017004 "cytochrome complex assembly" evidence=ISS

TIGR_CMR|APH_0526 APH_0526 "cytochrome c-type biogenesis protein CcmE" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 35/121 (28%), Positives = 63/121 (52%)

Query:     1 CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
             C++ F++  L+     + F+ TP+E +       S+   R+GG++++GS+     S  + 
Sbjct:    20 CVSAFVLFELSK---SISFFCTPTELVAD-PIKSSRYPIRVGGMIVKGSIVRHGDS--VT 73

Query:    61 FVVTDLVTDILVRYQGSLPDLFREGHSVVVEG-FIKP--ITEEIKNVKSEKSVSENARSR 117
             F +TDL T++ V Y+G LP +F E    + +G F+    I EE+     EK + +   S 
Sbjct:    74 FSITDLGTELEVTYRGVLPPMFGEDVGAIAKGRFVDGVFIAEELLAKHDEKYMPKKYSSS 133

Query:   118 D 118
             D
Sbjct:   134 D 134

GO:0003824 "catalytic activity" evidence=ISS

GO:0017004 "cytochrome complex assembly" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
B5ZVF6	CCME_RHILW	No assigned EC number	0.3963	0.8456	0.8011	yes	no
Q7WXB8	CCME_CUPNH	No assigned EC number	0.3670	0.8086	0.8451	yes	no
Q3STD7	CCME_NITWN	No assigned EC number	0.3677	0.8086	0.8086	yes	no
Q2VZH2	CCME_MAGSA	No assigned EC number	0.3439	0.8148	0.8918	yes	no
Q46RW7	CCME_CUPPJ	No assigned EC number	0.3554	0.8456	0.8616	yes	no
Q5P3K6	CCME_AROAE	No assigned EC number	0.3806	0.8148	0.8918	yes	no
B1XWE8	CCME_LEPCP	No assigned EC number	0.3664	0.8333	0.8823	yes	no
B2UBM4	CCME_RALPJ	No assigned EC number	0.3525	0.8209	0.8525	yes	no

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:
	fgenesh2_kg.5__1526__AT3G51790.1	annotation not avaliable (257 aa)
		(Arabidopsis lyrata)
Predicted Functional Partners:
	fgenesh2_kg.3__2967__ATMG00900.1	annotation not avaliable (225 aa)	•		•		•	•	•		0.991
	fgenesh2_kg.1__1671__AT1G15220.2	annotation not avaliable (159 aa)	•		•				•		0.951
	scaffold_402843.1	annotation not avaliable (394 aa)							•		0.719
	scaffold_303459.1	annotation not avaliable (230 aa)	•		•				•		0.684
	scaffold_200196.1	annotation not avaliable (229 aa)	•		•				•		0.631
	scaffold_200190.1	annotation not avaliable (229 aa)	•		•				•		0.626
	scaffold_200183.1	annotation not avaliable (229 aa)	•		•				•		0.626
	fgenesh2_kg.3__1617__AT3G14930.1	annotation not avaliable (418 aa)							•		0.620

---

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	162
pfam03100	130	pfam03100, CcmE, CcmE	1e-46
PRK13254	148	PRK13254, PRK13254, cytochrome c-type biogenesis p	3e-42
COG2332	153	COG2332, CcmE, Cytochrome c-type biogenesis protei	8e-34
PRK13165	160	PRK13165, PRK13165, cytochrome c-type biogenesis p	5e-27
PRK13159	155	PRK13159, PRK13159, cytochrome c-type biogenesis p	1e-18
PRK13150	159	PRK13150, PRK13150, cytochrome c-type biogenesis p	6e-18

>gnl|CDD|217368 pfam03100, CcmE, CcmE

 Score =  147 bits (374), Expect = 1e-46
 Identities = 55/138 (39%), Positives = 66/138 (47%), Gaps = 24/138 (17%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
            +   + +VL   +D +VF+ TPSE        P   + RLGGLV EGSV        + 
Sbjct: 17  ALGLAVALVLYALRDNIVFFYTPSEVAA--GKAPPGRRIRLGGLVEEGSVVR-DDGLTVR 73

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           FVVTD    + VRY G LPDLFREG  VV EG +                       D  
Sbjct: 74  FVVTDGAASVPVRYTGILPDLFREGQGVVAEGRLDA---------------------DGV 112

Query: 121 FSATDVLAKHDEKYMPQE 138
           F A +VLAKHDE YMP E
Sbjct: 113 FVADEVLAKHDENYMPPE 130

CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor. Length = 130

>gnl|CDD|237317 PRK13254, PRK13254, cytochrome c-type biogenesis protein CcmE; Reviewed

 Score =  137 bits (347), Expect = 3e-42
 Identities = 58/155 (37%), Positives = 74/155 (47%), Gaps = 24/155 (15%)

Query: 1   CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME 60
            +   + +VL   +  +VF+ TPSE  E     P+  +FRLGGLV +GSV        + 
Sbjct: 18  ALGLAVALVLYALRQNIVFFYTPSEVAE--GEAPAGRRFRLGGLVEKGSV-QRGDGLTVR 74

Query: 61  FVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCF 120
           FVVTD    + V Y G LPDLFREG  VV EG                            
Sbjct: 75  FVVTDGNATVPVVYTGILPDLFREGQGVVAEG---------------------RLQDGGV 113

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQ 155
           F A +VLAKHDE YMP+EVA A++K     +   Q
Sbjct: 114 FVADEVLAKHDENYMPKEVADALKKAGVWKDGPGQ 148

Length = 148

>gnl|CDD|225211 COG2332, CcmE, Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones]

 Score =  116 bits (292), Expect = 8e-34
 Identities = 56/156 (35%), Positives = 75/156 (48%), Gaps = 25/156 (16%)

Query: 2   IAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEF 61
           +A  + +VL   +  + ++ TPSE L       +  + RLGGLV  GSV     S ++ F
Sbjct: 19  LALAVGLVLYALRSNIDYFYTPSELL--EGKVETGQRLRLGGLVEAGSVQRDPGSLKVSF 76

Query: 62  VVTDLVTDILVRYQGSLPDLFREGHSVVVEG-FIKPITEEIKNVKSEKSVSENARSRDCF 120
           VVTD    + V Y+G LPDLFREG  VV EG                             
Sbjct: 77  VVTDGNKSVTVSYEGILPDLFREGQGVVAEGQLQGGGV---------------------- 114

Query: 121 FSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQE 156
           F A +VLAKHDE Y P EVA A++KN   L + + +
Sbjct: 115 FEAKEVLAKHDENYTPPEVAKAMKKNGVWLGKAEND 150

Length = 153

>gnl|CDD|183874 PRK13165, PRK13165, cytochrome c-type biogenesis protein CcmE; Reviewed

 Score = 98.9 bits (247), Expect = 5e-27
 Identities = 48/146 (32%), Positives = 69/146 (47%), Gaps = 26/146 (17%)

Query: 19  FYVTPSEALEKYQSNPSK----NKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRY 74
           FY TP E L   +    K     + R+GG+V+ GSV    +S ++ F + D    + V Y
Sbjct: 37  FY-TPGEILYGKRETQQKPEVGQRLRVGGMVMPGSVQRDPNSLKVSFTLYDAGGSVTVTY 95

Query: 75  QGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKY 134
           +G LPDLFREG  +V +G           V  E +  E          A +VLAKHDE Y
Sbjct: 96  EGILPDLFREGQGIVAQG-----------VLEEGNHIE----------AKEVLAKHDENY 134

Query: 135 MPQEVAAAIEKNKKMLEEQQQEEGGK 160
            P EV  A++KN +      +++   
Sbjct: 135 TPPEVEEAMKKNHRRPAYSYKDKAST 160

Length = 160

>gnl|CDD|183873 PRK13159, PRK13159, cytochrome c-type biogenesis protein CcmE; Reviewed

 Score = 77.3 bits (190), Expect = 1e-18
 Identities = 50/144 (34%), Positives = 66/144 (45%), Gaps = 35/144 (24%)

Query: 4   GFIVIVLNNFQDQLVFYVTPSE----ALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEM 59
             IV+ L   Q  + +  TPS+    A   YQ      +FRLGG+V  GS+   A S ++
Sbjct: 24  TLIVLAL---QRNMSYLFTPSQVRAGAAAGYQ------QFRLGGMVKAGSIQRAADSLKV 74

Query: 60  EFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDC 119
            F V D      V Y G LPDLFR+  SV+                       N R +  
Sbjct: 75  SFTVIDKNAATQVEYTGILPDLFRDNQSVIA----------------------NGRMQGG 112

Query: 120 FFSATDVLAKHDEKYMPQEVAAAI 143
            F A +VLAKHDE YMP+E+  A+
Sbjct: 113 RFVANEVLAKHDETYMPKELKDAM 136

Length = 155

>gnl|CDD|139376 PRK13150, PRK13150, cytochrome c-type biogenesis protein CcmE; Reviewed

 Score = 75.4 bits (185), Expect = 6e-18
 Identities = 47/145 (32%), Positives = 68/145 (46%), Gaps = 25/145 (17%)

Query: 8   IVLNNFQDQLVFYVTPSEAL----EKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVV 63
           +VL   +  +  + TP E L    E  Q      + R+GG+V+ GSV     S ++ F +
Sbjct: 25  LVLYALRANIDLFYTPGEILYGKRETQQLPAVGQRLRVGGMVMPGSVRRDPDSLKVNFSL 84

Query: 64  TDLVTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSA 123
            D    + V Y+G LPDLFREG  VVV+G +                      +     A
Sbjct: 85  YDAEGSVTVSYEGILPDLFREGQGVVVQGTL---------------------EKGNHVLA 123

Query: 124 TDVLAKHDEKYMPQEVAAAIEKNKK 148
            +VLAKHDE Y P EV  A+++N +
Sbjct: 124 HEVLAKHDENYTPPEVEKAMQENHR 148

Length = 159

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	162
PRK13165	160	cytochrome c-type biogenesis protein CcmE; Reviewe	100.0
PRK13159	155	cytochrome c-type biogenesis protein CcmE; Reviewe	100.0
PRK13150	159	cytochrome c-type biogenesis protein CcmE; Reviewe	100.0
PRK13254	148	cytochrome c-type biogenesis protein CcmE; Reviewe	100.0
PF03100	131	CcmE: CcmE; InterPro: IPR004329 CcmE is the produc	100.0
COG2332	153	CcmE Cytochrome c-type biogenesis protein CcmE [Po	100.0
PF03843	160	Slp: Outer membrane lipoprotein Slp family; InterP	95.33
cd04482	91	RPA2_OBF_like RPA2_OBF_like: A subgroup of unchara	94.91
PF13742	99	tRNA_anti_2: OB-fold nucleic acid binding domain	94.62
PF01336	75	tRNA_anti-codon: OB-fold nucleic acid binding doma	94.54
cd04489	78	ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol	93.38
cd04487	73	RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB f	93.31
cd04488	75	RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f	92.94
PRK00286	438	xseA exodeoxyribonuclease VII large subunit; Revie	92.49
TIGR00752	182	slp outer membrane lipoprotein, Slp family. Slp su	91.08
cd04478	95	RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds cor	90.41
COG1570	440	XseA Exonuclease VII, large subunit [DNA replicati	90.27
cd04490	79	PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds	89.68
TIGR00237	432	xseA exodeoxyribonuclease VII, large subunit. This	87.5
cd04485	84	DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp	85.56
PF15490	118	Ten1_2: Telomere-capping, CST complex subunit	82.44
TIGR00457	453	asnS asparaginyl-tRNA synthetase. In a multiple se	81.24
PF08661	109	Rep_fac-A_3: Replication factor A protein 3; Inter	80.78

>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=100.00  E-value=1.9e-43  Score=283.49  Aligned_cols=135  Identities=34%  Similarity=0.578  Sum_probs=121.9

Q ss_pred             hhhHHHHHHHHhhcCeeeeeCHHHHHhhcCC----CCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC
Q 041604            2 IAGFIVIVLNNFQDQLVFYVTPSEALEKYQS----NPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS   77 (162)
Q Consensus         2 ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~~----~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~   77 (162)
                      ++++++|++++|++|++||+||||+++..++    .+.+++|||+|+|++|||.|++++.+++|.|||+..+++|+|+|+
T Consensus        19 ~~~a~~L~l~al~~n~~yF~tPsev~~~~~~~~~~~~~g~~iRvgG~V~~GSi~r~~~~l~v~F~vtD~~~~v~V~Y~Gi   98 (160)
T PRK13165         19 LALTIGLVLYALRSNIDLFYTPGEILYGKRETQQKPEVGQRLRVGGMVMPGSVQRDPNSLKVSFTLYDAGGSVTVTYEGI   98 (160)
T ss_pred             HHHHHHHHHHHHhhCccEEeCHHHHhccccccccccCCCCEEEEeeEEeCCcEEECCCCeEEEEEEEcCCeEEEEEEccc
Confidence            4567899999999999999999999986432    246899999999999999998888899999999999999999999


Q ss_pred             CCCCCCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhHHHHhhh
Q 041604           78 LPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQEE  157 (162)
Q Consensus        78 ~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~~~~~~~  157 (162)
                      +||+|+||++|||+|+|++                     +|+|+|++|||||||||||+|++++|+++++.+......+
T Consensus        99 lPDlFrEG~gVVveG~~~~---------------------~g~F~A~~vLAKhdekYmPpEv~~al~~~~~~~~~~~~~~  157 (160)
T PRK13165         99 LPDLFREGQGIVAQGVLEE---------------------GNHIEAKEVLAKHDENYTPPEVEEAMKKNHRRPAYSYKDK  157 (160)
T ss_pred             CCccccCCCeEEEEEEECC---------------------CCeEEEEEEEecCCCCCCCHHHHHHHHhccCCCCcccccc
Confidence            9999999999999999985                     6899999999999999999999999999888776654433

>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=100.00  E-value=2.7e-43  Score=281.49  Aligned_cols=126  Identities=35%  Similarity=0.562  Sum_probs=118.1

Q ss_pred             hhhHHHHHHHHhhcCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCCC
Q 041604            2 IAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDL   81 (162)
Q Consensus         2 ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd~   81 (162)
                      ++++++|++++|++|++||+||||+.+...  ..++.+||||+|++|||.|++++..++|.|||+..+++|+|+|++||+
T Consensus        19 ~~~a~~Lv~~al~~n~~yF~tpsEv~~~~~--~~~~~~RlGG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~GilPDl   96 (155)
T PRK13159         19 AALAVTLIVLALQRNMSYLFTPSQVRAGAA--AGYQQFRLGGMVKAGSIQRAADSLKVSFTVIDKNAATQVEYTGILPDL   96 (155)
T ss_pred             HHHHHHHHHHHhhhCceEEECHHHHhcCCc--ccCCeEEEccEEecCcEEEcCCCcEEEEEEEcCCcEEEEEEccCCCcc
Confidence            567889999999999999999999998643  467999999999999999988888999999999999999999999999


Q ss_pred             CCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhH
Q 041604           82 FREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLE  151 (162)
Q Consensus        82 F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~  151 (162)
                      |+||++||++|+|+                      +|+|+|++|||||||||||+|++++|++.+.|-.
T Consensus        97 FrEGqgVVaeG~~~----------------------~g~F~A~~vLAKHde~YmP~Ev~~al~~~~~~~~  144 (155)
T PRK13159         97 FRDNQSVIANGRMQ----------------------GGRFVANEVLAKHDETYMPKELKDAMAEGHLGKP  144 (155)
T ss_pred             ccCCCeEEEEEEEc----------------------CCEEEEeEEEecCCCcCCCHHHHHHHHhccccCC
Confidence            99999999999998                      6899999999999999999999999999987754

>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=100.00  E-value=6.2e-43  Score=280.37  Aligned_cols=129  Identities=35%  Similarity=0.582  Sum_probs=117.1

Q ss_pred             hhhHHHHHHHHhhcCeeeeeCHHHHHhhcC----CCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC
Q 041604            2 IAGFIVIVLNNFQDQLVFYVTPSEALEKYQ----SNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS   77 (162)
Q Consensus         2 ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~----~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~   77 (162)
                      ++++++|++++|++|++||+||||+++...    ..+.+++|||+|+|++|||.|.+++..++|.|||+..+|+|+|+|+
T Consensus        19 ~~~a~~Lvl~al~~n~~yF~tPsev~~~~~~~~~~~~~g~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi   98 (159)
T PRK13150         19 LGLTTALVLYALRANIDLFYTPGEILYGKRETQQLPAVGQRLRVGGMVMPGSVRRDPDSLKVNFSLYDAEGSVTVSYEGI   98 (159)
T ss_pred             HHHHHHHHHHHHhhCccEEeCHHHHhccccccccCcCCCCEEEEeeEEeCCcEEECCCCcEEEEEEEcCCcEEEEEEecc
Confidence            567889999999999999999999986431    1246899999999999999998888899999999999999999999


Q ss_pred             CCCCCCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhH
Q 041604           78 LPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLE  151 (162)
Q Consensus        78 ~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~  151 (162)
                      +||+|+||++||++|+|++                     +|+|+|++|||||||||||+|++++|++.++.-.
T Consensus        99 lPDlFrEG~gVVveG~~~~---------------------~g~F~A~evLAKhdekYmPpEv~~al~~~~~~~~  151 (159)
T PRK13150         99 LPDLFREGQGVVVQGTLEK---------------------GNHVLAHEVLAKHDENYTPPEVEKAMQENHRRPQ  151 (159)
T ss_pred             CCccccCCCeEEEEEEECC---------------------CCEEEEeEEEeCCCCCCCCHHHHHHHHHhCCCCc
Confidence            9999999999999999985                     6999999999999999999999999988776543

>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=100.00  E-value=5.1e-42  Score=271.41  Aligned_cols=126  Identities=45%  Similarity=0.706  Sum_probs=117.3

Q ss_pred             hhhHHHHHHHHhhcCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCCC
Q 041604            2 IAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDL   81 (162)
Q Consensus         2 ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd~   81 (162)
                      ++++++|++++|++|++||+||||+.+..  .+.++.|||+|+|++||+.+. ++..++|.|+|+..+|+|+|+|++||+
T Consensus        19 ~~~~~~L~~~a~~~~~~yf~tpse~~~~~--~~~g~~vrvgG~V~~gSi~~~-~~~~~~F~ltD~~~~i~V~Y~G~lPd~   95 (148)
T PRK13254         19 LGLAVALVLYALRQNIVFFYTPSEVAEGE--APAGRRFRLGGLVEKGSVQRG-DGLTVRFVVTDGNATVPVVYTGILPDL   95 (148)
T ss_pred             HHHHHHHHHHHHHhCCceeeCHHHHhcCC--ccCCCeEEEeEEEecCcEEeC-CCCEEEEEEEeCCeEEEEEECCCCCcc
Confidence            56788999999999999999999998864  257999999999999999997 788999999999999999999999999


Q ss_pred             CCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhH
Q 041604           82 FREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLE  151 (162)
Q Consensus        82 F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~  151 (162)
                      |+||++|||+|+|++                     +|+|+|++||+||||||||+|+++++++.++|.+
T Consensus        96 F~eg~~VVv~G~~~~---------------------~g~F~A~~vLaKc~skY~p~ev~~~~~~~~~~~~  144 (148)
T PRK13254         96 FREGQGVVAEGRLQD---------------------GGVFVADEVLAKHDENYMPKEVADALKKAGVWKD  144 (148)
T ss_pred             ccCCCEEEEEEEECC---------------------CCeEEEEEEEecCCCCCCCHHHHHHHHHhccccC
Confidence            999999999999985                     6799999999999999999999999999887754

>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria

Probab=100.00  E-value=6.2e-41  Score=257.85  Aligned_cols=115  Identities=48%  Similarity=0.732  Sum_probs=79.9

Q ss_pred             ChhhHHHHHHHHhhcCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCC
Q 041604            1 CIAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPD   80 (162)
Q Consensus         1 ~ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd   80 (162)
                      +|+++++|++++++++++||+||+|+++..+  ..++.+||+|+|++||++|+++++.++|.|+|+.++++|+|+|++||
T Consensus        17 ~i~~~~~l~~~~~~~~~~yy~t~se~~~~~~--~~~~~vrv~G~V~~gSv~~~~~~~~~~F~i~D~~~~i~V~Y~G~~Pd   94 (131)
T PF03100_consen   17 IIAAAIYLILYSFSDSAVYYLTPSELAAEPQ--KVGRKVRVGGLVVEGSVEYDPDGNTLTFTITDGGKEIPVVYTGPLPD   94 (131)
T ss_dssp             ---------------SSS-EE-TTTTTTTST---TTSEEEEEEEEECTTEEE-TTSSEEEEEEE-SS-EEEEEEES--CT
T ss_pred             HHHHHHHHHHHHhhccceEEcCHHHHhhccc--cCCceEEEeeEEccCCEEEcCCCCEEEEEEEECCcEEEEEECCCCCc
Confidence            4678899999999999999999999998764  48999999999999999999889999999999999999999999999


Q ss_pred             CCCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChH
Q 041604           81 LFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQE  138 (162)
Q Consensus        81 ~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~e  138 (162)
                      +|+||++|||+|+|..                     +|+|+|++||+||||||||+|
T Consensus        95 ~F~eg~~VVv~G~~~~---------------------~g~F~A~~lL~KcpskY~p~e  131 (131)
T PF03100_consen   95 LFREGQGVVVEGRLGE---------------------DGVFEATELLAKCPSKYMPPE  131 (131)
T ss_dssp             T--TTSEEEEEEEECC---------------------TSEEEEEEEEETS------HH
T ss_pred             cccCCCeEEEEEEECC---------------------CCEEEEEEEEeCCCCCCCCCC
Confidence            9999999999999953                     799999999999999999986

Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.

>COG2332 CcmE Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.1e-40  Score=264.12  Aligned_cols=130  Identities=44%  Similarity=0.661  Sum_probs=121.1

Q ss_pred             hhhHHHHHHHHhhcCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCCC
Q 041604            2 IAGFIVIVLNNFQDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDL   81 (162)
Q Consensus         2 ia~~i~l~l~~~~~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd~   81 (162)
                      |++++.|+|+++.+|+.||+||+|+.+..  ...++++|+||+|++||+++++++..++|+|+|...+++|.|+|+|||+
T Consensus        19 l~~a~~l~Lyal~~ni~~fy~Psel~~~~--~~~G~rlR~GGlV~~GSv~R~~~~~~v~F~vtD~~~~v~V~Y~GiLPDL   96 (153)
T COG2332          19 LALAVGLVLYALRSNIDYFYTPSELLEGK--VETGQRLRLGGLVEAGSVQRDPGSLKVSFVVTDGNKSVTVSYEGILPDL   96 (153)
T ss_pred             HHHHHHHHHhhhccCceEEECHHHhcccc--ccCCcEEEEeeeEeeceEEecCCCcEEEEEEecCCceEEEEEeccCchh
Confidence            67788999999999999999999998764  3568999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhHHHH
Q 041604           82 FREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQ  154 (162)
Q Consensus        82 F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~~~~  154 (162)
                      ||||++||++|.|..                     .++|+|++|||||||+|+|+|++++|++++.|+....
T Consensus        97 FREGQgVVa~G~~~~---------------------~~~f~A~~vLAKHdEnY~P~ev~~~mk~~~~~~~~~~  148 (153)
T COG2332          97 FREGQGVVAEGQLQG---------------------GGVFEAKEVLAKHDENYTPPEVAKAMKKNGVWLGKAE  148 (153)
T ss_pred             hhcCCeEEEEEEecC---------------------CCEEEeeehhhcCCcccCCHHHHHHhhhcCCcccccc
Confidence            999999999999973                     4899999999999999999999999999999987443

>PF03843 Slp: Outer membrane lipoprotein Slp family; InterPro: IPR004658 Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli (which also contains a close paralog), Haemophilus influenzae and Pasteurella multocida and Vibrio cholerae

Probab=95.33  E-value=0.065  Score=42.98  Aligned_cols=80  Identities=21%  Similarity=0.312  Sum_probs=57.3

Q ss_pred             hcCeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEE---EEEEeC---------CeEEEEEEcCC-CCC
Q 041604           14 QDQLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEME---FVVTDL---------VTDILVRYQGS-LPD   80 (162)
Q Consensus        14 ~~~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~---F~vtD~---------~~~i~V~Y~G~-~Pd   80 (162)
                      .+...--++++++++++. .+.|+.||+||.|..  +...++...++   |-|-..         ..+..|++.|- =|.
T Consensus        13 ~~~~~~~~~~~~v~~~p~-~~~G~~VrwGG~I~~--v~n~~~~T~leV~~~PLd~~grP~~~~~s~GRFla~~~gFLDP~   89 (160)
T PF03843_consen   13 RDQVDPQPSFSQVRANPD-AYQGQQVRWGGVIVN--VRNLPDQTELEVVQYPLDSSGRPQTDDPSQGRFLARVPGFLDPA   89 (160)
T ss_pred             cCCCCccCCHHHHHhChh-hcCCCEEEECCEEEE--EEECCCceEEEEEEccCCCCCCcCCCCCCCCEEEEEeCCCcCHH
Confidence            345566789999998875 578999999999973  44333333332   111111         25889999995 478


Q ss_pred             CCCCCCeEEEEEEEcC
Q 041604           81 LFREGHSVVVEGFIKP   96 (162)
Q Consensus        81 ~F~eg~~VVveG~~~~   96 (162)
                      .|++|+.|.|.|++..
T Consensus        90 ~y~~Gr~vTV~G~v~g  105 (160)
T PF03843_consen   90 IYAPGRLVTVVGTVTG  105 (160)
T ss_pred             HcCCCCEEEEEEEecc
Confidence            9999999999999974

The known members of the family to date share a motif LX[GA]C near the N terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N terminus. Slp from E. coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.; GO: 0019867 outer membrane

>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

Probab=94.91  E-value=0.47  Score=34.45  Aligned_cols=55  Identities=25%  Similarity=0.414  Sum_probs=40.8

Q ss_pred             EEeEEEecCcEEecCCCceEEEEEEeCCeEEE-EEEcCC-----CCCCCCCCCeEEEEEEEcC
Q 041604           40 RLGGLVLEGSVAHPASSSEMEFVVTDLVTDIL-VRYQGS-----LPDLFREGHSVVVEGFIKP   96 (162)
Q Consensus        40 rv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~-V~Y~G~-----~Pd~F~eg~~VVveG~~~~   96 (162)
                      +|.|.|..  +.+...+.++-|.|.|....|. |.|...     +....++|+.|+|.|.+..
T Consensus         2 ~v~GeVs~--~~~~~~sGH~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~v~~   62 (91)
T cd04482           2 RVTGKVVE--EPRTIEGGHVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSVRP   62 (91)
T ss_pred             EEEEEEeC--CeecCCCCCEEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEEEec
Confidence            57787753  2232135689999999987776 466554     6678899999999999974

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende

>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain

Probab=94.62  E-value=0.23  Score=36.44  Aligned_cols=58  Identities=17%  Similarity=0.281  Sum_probs=44.7

Q ss_pred             CCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEE-EcCC---CC-CCCCCCCeEEEEEEEc
Q 041604           35 SKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVR-YQGS---LP-DLFREGHSVVVEGFIK   95 (162)
Q Consensus        35 ~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~-Y~G~---~P-d~F~eg~~VVveG~~~   95 (162)
                      .-..+.|.|.|..  +... .+.++=|.|.|+...|... |...   ++ ..+++|..|+|.|++.
T Consensus        20 ~~~~vwV~GEIs~--~~~~-~~gh~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~   82 (99)
T PF13742_consen   20 PLPNVWVEGEISN--LKRH-SSGHVYFTLKDEEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVS   82 (99)
T ss_pred             CcCCEEEEEEEee--cEEC-CCceEEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEE
Confidence            3479999999974  3332 4578999999999888655 4432   44 7899999999999985

>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands

Probab=94.54  E-value=0.095  Score=34.43  Aligned_cols=55  Identities=22%  Similarity=0.271  Sum_probs=43.9

Q ss_pred             EEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcC----CCCCCCCCCCeEEEEEEEcC
Q 041604           39 FRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQG----SLPDLFREGHSVVVEGFIKP   96 (162)
Q Consensus        39 vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G----~~Pd~F~eg~~VVveG~~~~   96 (162)
                      |+|.|.|..=+  . ..+..+.|.|.|+...+.+.+-.    ...+.+++|..|.|.|+++.
T Consensus         1 V~v~G~V~~~~--~-~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~   59 (75)
T PF01336_consen    1 VTVEGRVTSIR--R-SGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVRGKVKR   59 (75)
T ss_dssp             EEEEEEEEEEE--E-EETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEEEEEEE
T ss_pred             CEEEEEEEEEE--c-CCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEEEEEEE
Confidence            57889887322  2 34578899999999999999888    56678999999999999974

The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....

>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit

Probab=93.38  E-value=1.2  Score=29.87  Aligned_cols=55  Identities=22%  Similarity=0.257  Sum_probs=41.6

Q ss_pred             cEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEc-C---CCCCCCCCCCeEEEEEEEc
Q 041604           38 KFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQ-G---SLPDLFREGHSVVVEGFIK   95 (162)
Q Consensus        38 ~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~-G---~~Pd~F~eg~~VVveG~~~   95 (162)
                      .++|.|.|..-..  ...+ ..-|.|.|....+.+..- .   ...+.+.+|..|+++|+++
T Consensus         1 ~~~v~g~v~~i~~--tk~g-~~~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g~v~   59 (78)
T cd04489           1 RVWVEGEISNLKR--PSSG-HLYFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVRGKVS   59 (78)
T ss_pred             CEEEEEEEecCEE--CCCc-EEEEEEEeCCeEEEEEEEcchhhhCCCCCCCCCEEEEEEEEE
Confidence            3689999985333  2334 788999999888876443 3   4678999999999999997

E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.

>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ

Probab=93.31  E-value=0.78  Score=32.17  Aligned_cols=53  Identities=17%  Similarity=0.224  Sum_probs=40.2

Q ss_pred             EEEeEEEecCcEEecCCCceEEEEEEeCCeEEEE-EEcC---CCCCCCCCCCeEEEEEEEc
Q 041604           39 FRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILV-RYQG---SLPDLFREGHSVVVEGFIK   95 (162)
Q Consensus        39 vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V-~Y~G---~~Pd~F~eg~~VVveG~~~   95 (162)
                      ++|.|.|..-.  +  .+.++-|.|.|....|+. .|.+   .++...++|..|++.|+++
T Consensus         1 v~v~GeVs~~~--~--~~GHvyfsLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~   57 (73)
T cd04487           1 VHIEGEVVQIK--Q--TSGPTIFTLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVE   57 (73)
T ss_pred             CEEEEEEeccc--c--CCCCEEEEEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEEEEe
Confidence            46778776443  2  356799999999877765 4543   3677889999999999986

RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.

>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG

Probab=92.94  E-value=1.1  Score=28.98  Aligned_cols=40  Identities=18%  Similarity=0.265  Sum_probs=33.7

Q ss_pred             CceEEEEEEeCCeEEEEEEcCC---CCCCCCCCCeEEEEEEEc
Q 041604           56 SSEMEFVVTDLVTDILVRYQGS---LPDLFREGHSVVVEGFIK   95 (162)
Q Consensus        56 ~~~~~F~vtD~~~~i~V~Y~G~---~Pd~F~eg~~VVveG~~~   95 (162)
                      ...++|.+.|+...+.+++=+.   +...|+.|..+.+.|++.
T Consensus        17 ~~~~~~~~~D~~g~i~~~~F~~~~~~~~~~~~G~~~~v~Gkv~   59 (75)
T cd04488          17 RRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKVK   59 (75)
T ss_pred             ccEEEEEEEcCCCEEEEEEECCCHHHHhcCCCCCEEEEEEEEe
Confidence            3579999999998888877653   456899999999999997

RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha

>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed

Probab=92.49  E-value=2  Score=38.54  Aligned_cols=111  Identities=21%  Similarity=0.193  Sum_probs=73.9

Q ss_pred             eeeCHHHHHhhcCCCC--CCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEE-EcC---CCCCCCCCCCeEEEEE
Q 041604           19 FYVTPSEALEKYQSNP--SKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVR-YQG---SLPDLFREGHSVVVEG   92 (162)
Q Consensus        19 yy~tpsE~~~~~~~~~--~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~-Y~G---~~Pd~F~eg~~VVveG   92 (162)
                      -++|+||+...-....  .-..|.|.|-|..  +.+. .+.++=|.|.|....|... |.+   .++-.+++|..|+|.|
T Consensus         4 ~~~svsel~~~ik~~le~~~~~v~v~gEis~--~~~~-~sGH~Yf~Lkd~~a~i~~~~~~~~~~~~~~~~~~G~~v~v~g   80 (438)
T PRK00286          4 KILSVSELNRYVKSLLERDLGQVWVRGEISN--FTRH-SSGHWYFTLKDEIAQIRCVMFKGSARRLKFKPEEGMKVLVRG   80 (438)
T ss_pred             CcCcHHHHHHHHHHHHHhhCCcEEEEEEeCC--CeeC-CCCeEEEEEEcCCcEEEEEEEcChhhcCCCCCCCCCEEEEEE
Confidence            3688998874322100  1468999999864  3333 3558999999999888654 444   4667789999999999


Q ss_pred             EEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhHHH
Q 041604           93 FIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQ  153 (162)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~~~  153 (162)
                      ++.-              -  ...|.=.|.+++|-    ..+. .+.+...++.++.|++.
T Consensus        81 ~~~~--------------y--~~~g~~ql~v~~i~----~~g~-G~l~~~~~~lk~~L~~e  120 (438)
T PRK00286         81 KVSL--------------Y--EPRGDYQLIVEEIE----PAGI-GALAAAFEQLKEKLAAE  120 (438)
T ss_pred             EEEE--------------E--CCCCCEEEEEEEee----eCCc-cHHHHHHHHHHHHHHHC
Confidence            9861              0  11123356677764    3455 67788888887777653

>TIGR00752 slp outer membrane lipoprotein, Slp family

Probab=91.08  E-value=2.6  Score=34.90  Aligned_cols=69  Identities=19%  Similarity=0.200  Sum_probs=47.7

Q ss_pred             CHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEE-----eC---------CeEEEEEEcCC-CCCCCCCCC
Q 041604           22 TPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVT-----DL---------VTDILVRYQGS-LPDLFREGH   86 (162)
Q Consensus        22 tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vt-----D~---------~~~i~V~Y~G~-~Pd~F~eg~   86 (162)
                      +.+++..+++ .+.++.+|+||.|..  +....+.  .++.|.     +.         ..++.+..+|- =|..| +|+
T Consensus        35 ~~~~v~~~p~-~y~G~~Vr~GG~I~~--v~N~~~~--T~lEVv~~PLd~~grP~~~~~s~GRFla~~~gFLDP~~y-~Gr  108 (182)
T TIGR00752        35 SYVEVSPQPL-LYVGQTARFGGKVVN--VTNLANQ--TKLEIASLPLDSIAKPFVELQSDGRFIAYFNGFLDPVNL-RER  108 (182)
T ss_pred             chHHHhhChh-hcCCCEEEECCEEEE--EEECCCc--eEEEEEEcccCCCCCcCCCCCCCCEEEEEeCCCcChhhc-CCC
Confidence            3677776554 467999999999973  4433333  333333     11         15788888985 57899 799


Q ss_pred             eEEEEEEEcC
Q 041604           87 SVVVEGFIKP   96 (162)
Q Consensus        87 ~VVveG~~~~   96 (162)
                      .|.|.|++..
T Consensus       109 ~VTVvG~i~G  118 (182)
T TIGR00752       109 YVTVGGQIAG  118 (182)
T ss_pred             EEEEEEEecc
Confidence            9999999974

Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli, which also contains a close paralog, Haemophilus influenzae and Pasteurella multocida and Vibrio cholera. The known members of the family to date share a motif LX[GA]C near the N-terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N-terminus. Slp from Escherichia coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.

>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

Probab=90.41  E-value=2.5  Score=29.62  Aligned_cols=54  Identities=28%  Similarity=0.286  Sum_probs=43.1

Q ss_pred             EEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC-------CCCCCCCCCeEEEEEEEcC
Q 041604           39 FRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS-------LPDLFREGHSVVVEGFIKP   96 (162)
Q Consensus        39 vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~-------~Pd~F~eg~~VVveG~~~~   96 (162)
                      |++-|+|..  ++..  +..++|.|.|+...|++.+-..       ..+.|++|.-|-|.|++..
T Consensus         2 v~~vG~V~~--~~~~--~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~   62 (95)
T cd04478           2 VTLVGVVRN--VEEQ--STNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKS   62 (95)
T ss_pred             EEEEEEEEe--eeEc--ccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcc
Confidence            788899973  4433  4689999999988898888653       3556999999999999974

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam

>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]

Probab=90.27  E-value=2.6  Score=39.36  Aligned_cols=111  Identities=22%  Similarity=0.174  Sum_probs=69.3

Q ss_pred             eeeeCHHHHHhhcCCCC--CCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEE-EEEEcCC---CCCCCCCCCeEEEE
Q 041604           18 VFYVTPSEALEKYQSNP--SKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDI-LVRYQGS---LPDLFREGHSVVVE   91 (162)
Q Consensus        18 ~yy~tpsE~~~~~~~~~--~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i-~V~Y~G~---~Pd~F~eg~~VVve   91 (162)
                      ..|+||||+...-..-.  .=..|.|.|-+.  .+...+++ ++=|.+.|....| -|.|.|.   ++-.-+||..|+|.
T Consensus         3 ~~~~sVSeln~~ik~llE~~~~~V~v~GEIS--n~t~~~sg-H~YFtLKD~~A~i~c~mf~~~~~~l~f~p~eG~~V~v~   79 (440)
T COG1570           3 EKILSVSELNDYIKRLLERDLGQVWVRGEIS--NFTRPASG-HLYFTLKDERAQIRCVMFKGNNRRLKFRPEEGMQVLVR   79 (440)
T ss_pred             CCeecHHHHHHHHHHHHHhcCCeEEEEEEec--CCccCCCc-cEEEEEccCCceEEEEEEcCcccccCCCccCCCEEEEE
Confidence            36899999875321100  125688888885  35544555 9999999999877 4667774   44445799999999


Q ss_pred             EEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhHH
Q 041604           92 GFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEE  152 (162)
Q Consensus        92 G~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~~  152 (162)
                      |++.-                -+.+|+-.+.++.|-     -+--.....++++.++.|..
T Consensus        80 G~is~----------------Y~~rG~YQi~~~~~~-----p~G~G~L~~~~E~lK~kL~a  119 (440)
T COG1570          80 GKISL----------------YEPRGDYQIVAESME-----PAGLGALYLAFEQLKAKLAA  119 (440)
T ss_pred             EEEEE----------------EcCCCceEEEEecCC-----cCChhHHHHHHHHHHHHHHh
Confidence            99841                111234445555542     22333456666777666654

>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit

Probab=89.68  E-value=5.6  Score=28.12  Aligned_cols=54  Identities=13%  Similarity=0.099  Sum_probs=39.6

Q ss_pred             EEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC------CCCCCCCCCeEEEEEEEc
Q 041604           39 FRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS------LPDLFREGHSVVVEGFIK   95 (162)
Q Consensus        39 vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~------~Pd~F~eg~~VVveG~~~   95 (162)
                      +++.|+|..=.  ....+.. .|.|.|....+.|..-..      .-+.+.++..|+++|+++
T Consensus         2 v~i~GiI~~v~--~TK~g~~-~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v~   61 (79)
T cd04490           2 VSIIGMVNDVR--STKNGHR-IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTVS   61 (79)
T ss_pred             EEEEEEEeEEE--EcCCCCE-EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEEe
Confidence            68899997433  3334555 999999988887765542      234677899999999996

PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.

>TIGR00237 xseA exodeoxyribonuclease VII, large subunit

Probab=87.50  E-value=9.1  Score=34.93  Aligned_cols=93  Identities=19%  Similarity=0.203  Sum_probs=63.7

Q ss_pred             CcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEE-EEEcC---CCCCCCCCCCeEEEEEEEcCchhhhhhccccccccc
Q 041604           37 NKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDIL-VRYQG---SLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSE  112 (162)
Q Consensus        37 ~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~-V~Y~G---~~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~~~~~  112 (162)
                      ..+.|.|-|..  +.+. .+.++-|.|.|....|+ |.|.+   .++-.+++|..|+|.|++.-                
T Consensus        18 ~~v~V~GEisn--~~~~-~sGH~YFtLkD~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~----------------   78 (432)
T TIGR00237        18 LQVWIQGEISN--FTQP-VSGHWYFTLKDENAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGISV----------------   78 (432)
T ss_pred             CcEEEEEEecC--CeeC-CCceEEEEEEcCCcEEEEEEEcChhhCCCCCCCCCCEEEEEEEEEE----------------
Confidence            48999999974  3333 34589999999987775 45555   46777899999999999851                


Q ss_pred             cccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhHHH
Q 041604          113 NARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQ  153 (162)
Q Consensus       113 ~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~~~  153 (162)
                      -+..|.=.|.+++|-   |. + -.+.+.+.++.++.|+..
T Consensus        79 y~~~G~~ql~v~~i~---~~-G-~G~l~~~~~~lk~~L~~e  114 (432)
T TIGR00237        79 YEPRGDYQIICFEMQ---PA-G-EGLLQLAYEQLKEKLAAE  114 (432)
T ss_pred             ECCCCcEEEEEEEec---cC-C-hHHHHHHHHHHHHHHHHC
Confidence            111223456677775   33 3 446677777777776643

This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.

>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE)

Probab=85.56  E-value=3.9  Score=26.65  Aligned_cols=56  Identities=23%  Similarity=0.254  Sum_probs=38.8

Q ss_pred             EeEEEecCcEEecCCC-ceEEEEEEeCCeEEEEEEcC-C---CCCCCCCCCeEEEEEEEcC
Q 041604           41 LGGLVLEGSVAHPASS-SEMEFVVTDLVTDILVRYQG-S---LPDLFREGHSVVVEGFIKP   96 (162)
Q Consensus        41 v~G~V~~gSv~~~~~~-~~~~F~vtD~~~~i~V~Y~G-~---~Pd~F~eg~~VVveG~~~~   96 (162)
                      +.|+|..=.......+ .-+.|.+.|....+.+.+=. .   ..+.+.+|..|++.|+++.
T Consensus         2 i~g~v~~~~~~~~k~g~~~~~~~l~D~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G~v~~   62 (84)
T cd04485           2 VAGLVTSVRRRRTKKGKRMAFVTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLVEGKVER   62 (84)
T ss_pred             EEEEEEEeEEEEcCCCCEEEEEEEEeCCCeEEEEECHHHHHHHHHHhcCCCEEEEEEEEEe
Confidence            5677754333332222 35889999998888777653 2   3567899999999999973

The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.

>PF15490 Ten1_2: Telomere-capping, CST complex subunit

Probab=82.44  E-value=12  Score=29.01  Aligned_cols=69  Identities=16%  Similarity=0.010  Sum_probs=53.8

Q ss_pred             eeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEE----EeCCeEEEEEEcCCCCCCCCCCCeEEEEEEE
Q 041604           19 FYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVV----TDLVTDILVRYQGSLPDLFREGHSVVVEGFI   94 (162)
Q Consensus        19 yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~v----tD~~~~i~V~Y~G~~Pd~F~eg~~VVveG~~   94 (162)
                      -|+++.|+.. + ..+.+..+|+-|.+.    .++..  .-..+|    .|....+.|.-+=.-|..|+-|.-..+.|-+
T Consensus         6 ~~~~l~Evs~-~-~~~~g~svR~~GrL~----~yD~~--~~~a~l~~~~~~~~~~l~V~t~~l~~~~~~~gslyq~iGEl   77 (118)
T PF15490_consen    6 VYVFLWEVSS-G-FVPEGKSVRTFGRLQ----SYDVA--TSRATLTAQHESDQHSLKVDTKLLEPFQARVGSLYQFIGEL   77 (118)
T ss_pred             EEEehHHhcC-c-cccCCCeEEEEEEEE----EEecc--CCEEEEEeeccCCCcEEEEEeeEccccccCCCCEEEEEEEE
Confidence            4889999833 2 257899999999997    24332  344667    7777888888777888899999999999999


Q ss_pred             c
Q 041604           95 K   95 (162)
Q Consensus        95 ~   95 (162)
                      .
T Consensus        78 ~   78 (118)
T PF15490_consen   78 E   78 (118)
T ss_pred             E
Confidence            7

>TIGR00457 asnS asparaginyl-tRNA synthetase

Probab=81.24  E-value=30  Score=31.87  Aligned_cols=81  Identities=17%  Similarity=0.253  Sum_probs=52.8

Q ss_pred             CCCCcEEEeEEEecCcEEecCCCceEEEE-EEeCC--eEEEEEEcCCCCC-------CCCCCCeEEEEEEEcCchhhhhh
Q 041604           34 PSKNKFRLGGLVLEGSVAHPASSSEMEFV-VTDLV--TDILVRYQGSLPD-------LFREGHSVVVEGFIKPITEEIKN  103 (162)
Q Consensus        34 ~~~~~vrv~G~V~~gSv~~~~~~~~~~F~-vtD~~--~~i~V~Y~G~~Pd-------~F~eg~~VVveG~~~~~~~~~~~  103 (162)
                      ..++.|+|.|+|.  ++. .  ...+.|. |.|+.  ..+.|......++       .+..|..|-|+|.+...      
T Consensus        14 ~~g~~v~v~Gwv~--~~R-~--~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~~------   82 (453)
T TIGR00457        14 FVGDEVTVSGWVR--TKR-S--SKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVES------   82 (453)
T ss_pred             cCCCEEEEEEEeE--EEE-c--CCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcC------
Confidence            3578999999996  343 2  2345664 56666  6888888765332       36889999999999731      


Q ss_pred             ccccccccccccCCCCeEEEe--EEeecCC-CCC
Q 041604          104 VKSEKSVSENARSRDCFFSAT--DVLAKHD-EKY  134 (162)
Q Consensus       104 ~~~~~~~~~~~~~~dg~F~A~--~lLaKcp-skY  134 (162)
                              +. +.++-...++  +||.||+ ..|
T Consensus        83 --------~~-~~~~~El~~~~i~vl~~~~~~~~  107 (453)
T TIGR00457        83 --------PG-KGQPVELQVKKIEVVGEAEPDDY  107 (453)
T ss_pred             --------CC-CCCCEEEEEeEEEEEecCCccCC
Confidence                    00 1123345555  6899997 444

In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.

>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair

Probab=80.78  E-value=20  Score=26.41  Aligned_cols=69  Identities=14%  Similarity=-0.006  Sum_probs=39.5

Q ss_pred             CeeeeeCHHHHHhhcCCCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCCCCCCCCeEEEEEEEc
Q 041604           16 QLVFYVTPSEALEKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIK   95 (162)
Q Consensus        16 ~~~yy~tpsE~~~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd~F~eg~~VVveG~~~   95 (162)
                      .....++++.|.+     +.++.|||-|.|..    .++++..+...-+|+ ..+.|......  .+..+.-|-|.|+..
T Consensus         3 ~~~pRVn~~~L~~-----~~gk~VrivGkv~~----~~~~g~~~~l~~~d~-~~V~v~l~~~~--~~~~~~~vEviG~V~   70 (109)
T PF08661_consen    3 APTPRVNGSMLSQ-----FVGKTVRIVGKVES----VDPDGGSATLSTSDG-GQVTVSLNPPS--DEELSKYVEVIGKVN   70 (109)
T ss_dssp             S--EEE-GGGGGG-----GTTSEEEEEEEEEE----E-TTSSEEEEE-TTS--EEEEEESS----SS---SEEEEEEEE-
T ss_pred             CCcceECHHHHHh-----hCCCeEEEEEEEee----EcCCCCEEEEEcCCC-CEEEEEeCCCC--CCCCCCEEEEEEEEc
Confidence            3456778877754     47999999999962    233344433333354 47777776544  345688999999998


Q ss_pred             C
Q 041604           96 P   96 (162)
Q Consensus        96 ~   96 (162)
                      +
T Consensus        71 ~   71 (109)
T PF08661_consen   71 D   71 (109)
T ss_dssp             T
T ss_pred             C
Confidence            6

; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	162
1j6q_A	136	Solution Structure And Characterization Of The Heme		2e-15
1sr3_A	136	Solution Structure Of The Heme Chaperone Ccme Of Es		7e-14

>pdb|1J6Q|A Chain A, Solution Structure And Characterization Of The Heme Chaperone Ccme Length = 136

Iteration: 1
 Score = 77.8 bits (190), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/150 (34%), Positives = 72/150 (48%), Gaps = 26/150 (17%)
Query: 12  NFQDQLVFYVTPSEALEKYQSNPSK----NKFRLGGLVLEGSVAHPASSSEMEFVVTD-L 66
           +    L  + TPSE +        K     + R+GG+V  GS+    +S  ++F V D L
Sbjct: 4   DLNSNLNLFYTPSEIVNGKTDTGVKPEAGQRIRVGGMVTVGSMVRDPNSLHVQFAVHDSL 63
Query: 67  VTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDV 126
             +ILV Y   LPDLFREG  +V +G +                       D   +AT+V
Sbjct: 64  GGEILVTYDDLLPDLFREGQGIVAQGVL---------------------GEDGKLAATEV 102
Query: 127 LAKHDEKYMPQEVAAAIEKNKKMLEEQQQE 156
           LAKHDE YMP EVA A+ +  + L+  QQ+
Sbjct: 103 LAKHDENYMPPEVAEAMGQKHEKLDYSQQK 132

>pdb|1SR3|A Chain A, Solution Structure Of The Heme Chaperone Ccme Of Escherichia Coli Length = 136

Iteration: 1
 Score = 72.8 bits (177), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 48/135 (35%), Positives = 66/135 (48%), Gaps = 26/135 (19%)
Query: 18  VFYVTPSEAL----EKYQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVR 73
           +FY TP E L    E  Q      + R+GG+V+ GSV    +S ++ F + D    + V 
Sbjct: 7   LFY-TPGEILYGKRETQQMPEVGQRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEGSVDVS 65
Query: 74  YQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEK 133
           Y+G LPDLFREG  VVV+G ++                     +     A +VLAKHDE 
Sbjct: 66  YEGILPDLFREGQGVVVQGELE---------------------KGNHILAKEVLAKHDEN 104
Query: 134 YMPQEVAAAIEKNKK 148
           Y P EV  A+E N +
Sbjct: 105 YTPPEVEKAMEANHR 119

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	162
1sr3_A	136	APO-CCME; OB fold, beta barrel, flexible C-termina	8e-41
1j6q_A	136	Cytochrome C maturation protein E; all-beta protei	9e-39
2kct_A	94	Cytochrome C-type biogenesis protein CCME; solutio	9e-23

>1sr3_A APO-CCME; OB fold, beta barrel, flexible C-terminal domain, chaperone; NMR {Escherichia coli} SCOP: b.40.9.1 Length = 136

 Score =  133 bits (335), Expect = 8e-41
 Identities = 44/153 (28%), Positives = 66/153 (43%), Gaps = 25/153 (16%)

Query: 13  FQDQLVFYVTPSEALEKYQSNPSKN----KFRLGGLVLEGSVAHPASSSEMEFVVTDLVT 68
            +  +  + TP E L   +          + R+GG+V+ GSV    +S ++ F + D   
Sbjct: 1   LRSNIDLFYTPGEILYGKRETQQMPEVGQRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEG 60

Query: 69  DILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLA 128
            + V Y+G LPDLFREG  VVV+G ++                           A +VLA
Sbjct: 61  SVDVSYEGILPDLFREGQGVVVQGELEK---------------------GNHILAKEVLA 99

Query: 129 KHDEKYMPQEVAAAIEKNKKMLEEQQQEEGGKD 161
           KHDE Y P EV  A+E N +      ++     
Sbjct: 100 KHDENYTPPEVEKAMEANHRRPASVYKDPASHH 132

>1j6q_A Cytochrome C maturation protein E; all-beta protein, heme delivery,cytochrome C maturation, OB- (oligonucleotide binding)fold; NMR {Shewanella putrefaciens} SCOP: b.40.9.1 PDB: 1lm0_A Length = 136

 Score =  127 bits (321), Expect = 9e-39
 Identities = 49/154 (31%), Positives = 73/154 (47%), Gaps = 26/154 (16%)

Query: 12  NFQDQLVFYVTPSEALEK----YQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLV 67
           +    L  + TPSE +           +  + R+GG+V  GS+    +S  ++F V D +
Sbjct: 4   DLNSNLNLFYTPSEIVNGKTDTGVKPEAGQRIRVGGMVTVGSMVRDPNSLHVQFAVHDSL 63

Query: 68  -TDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDV 126
             +ILV Y   LPDLFREG  +V +G +                       D   +AT+V
Sbjct: 64  GGEILVTYDDLLPDLFREGQGIVAQGVLGE---------------------DGKLAATEV 102

Query: 127 LAKHDEKYMPQEVAAAIEKNKKMLEEQQQEEGGK 160
           LAKHDE YMP EVA A+ +  + L+  QQ+   +
Sbjct: 103 LAKHDENYMPPEVAEAMGQKHEKLDYSQQKSATQ 136

>2kct_A Cytochrome C-type biogenesis protein CCME; solution structure, heme chaperone, cytochrome C biogenesis, OB-fold domain, NESG, PSI-2; NMR {Desulfovibrio vulgaris str} Length = 94

 Score = 85.6 bits (212), Expect = 9e-23
 Identities = 20/108 (18%), Positives = 38/108 (35%), Gaps = 23/108 (21%)

Query: 34  PSKNKFRLGGLVLEGSVAHPASSSEMEFVVTD---LVTDILVRYQGSLPDLFREGHSVVV 90
              +  RL G V    +     +  + F + D       + V Y+G++PD F+ G  V++
Sbjct: 6   DKLHTVRLFGTVAADGLTMLDGAPGVRFRLEDKDNTSKTVWVLYKGAVPDTFKPGVEVII 65

Query: 91  EGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQE 138
           EG + P                     +  F A  ++ K   ++    
Sbjct: 66  EGGLAP--------------------GEDTFKARTLMTKCPLEHHHHH 93

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	162
1j6q_A	136	Cytochrome C maturation protein E; all-beta protei	100.0
1sr3_A	136	APO-CCME; OB fold, beta barrel, flexible C-termina	100.0
2kct_A	94	Cytochrome C-type biogenesis protein CCME; solutio	99.96
4gop_B	136	Putative uncharacterized protein; OB fold, ssDNA b	86.49
3kdf_D	132	Replication protein A 32 kDa subunit; wheat GERM c	85.63
2k50_A	115	Replication factor A related protein; uncharacteri	84.06

>1j6q_A Cytochrome C maturation protein E; all-beta protein, heme delivery,cytochrome C maturation, OB- (oligonucleotide binding)fold; NMR {Shewanella putrefaciens} SCOP: b.40.9.1 PDB: 1lm0_A

Probab=100.00  E-value=4.5e-43  Score=273.66  Aligned_cols=125  Identities=40%  Similarity=0.659  Sum_probs=88.7

Q ss_pred             HHHhhcCeeeeeCHHHHHhhcCC----CCCCCcEEEeEEEecCcEEecCCCceEEEEEEe-CCeEEEEEEcCCCCCCCCC
Q 041604           10 LNNFQDQLVFYVTPSEALEKYQS----NPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTD-LVTDILVRYQGSLPDLFRE   84 (162)
Q Consensus        10 l~~~~~~~~yy~tpsE~~~~~~~----~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD-~~~~i~V~Y~G~~Pd~F~e   84 (162)
                      +++|++|++||+||||+++..++    .+.+++|||+|+|++|||.|+++++.++|.|+| ...+|+|+|+|++||+|+|
T Consensus         2 ~~al~~ni~~f~tpsei~~~~~~~~~~~~~g~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~~v~V~Y~GilPDlFrE   81 (136)
T 1j6q_A            2 AADLNSNLNLFYTPSEIVNGKTDTGVKPEAGQRIRVGGMVTVGSMVRDPNSLHVQFAVHDSLGGEILVTYDDLLPDLFRE   81 (136)
T ss_dssp             -----CCCCCEECTTTTTTTSTTTTSSSCTTCEEEEEEEECTTCCEECTTSSCEEEEEECTTCCCEEEEECSCCTTSCCS
T ss_pred             cchhhhCccEeeCHHHHHcCcccccccCCCCCEEEEeEEEeCCcEEecCCCCEEEEEEEcCCCCEEEEEECCCCCccccC
Confidence            67999999999999999976421    368899999999999999998888999999999 8899999999999999999


Q ss_pred             CCeEEEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhHHHHh
Q 041604           85 GHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLEEQQQ  155 (162)
Q Consensus        85 g~~VVveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~~~~~  155 (162)
                      |++|||+|+|++                     +|+|+|++|||||||||||+|++++|++++....+.+|
T Consensus        82 GqgVVa~G~l~~---------------------~g~F~A~eVLaKhdekY~p~eva~al~~~~~~~~~~~~  131 (136)
T 1j6q_A           82 GQGIVAQGVLGE---------------------DGKLAATEVLAKHDENYMPPEVAEAMGQKHEKLDYSQQ  131 (136)
T ss_dssp             SSEEEEEEEECS---------------------TTSEEEEEEECCC-------------------------
T ss_pred             CCeEEEEEEECC---------------------CCeEEEEEEEecCCCCCCCHHHHHHHHHhccCcchhhh
Confidence            999999999985                     79999999999999999999999999999766655554

>1sr3_A APO-CCME; OB fold, beta barrel, flexible C-terminal domain, chaperone; NMR {Escherichia coli} SCOP: b.40.9.1

Probab=100.00  E-value=6.9e-42  Score=267.18  Aligned_cols=118  Identities=37%  Similarity=0.618  Sum_probs=102.6

Q ss_pred             hhcCeeeeeCHHHHHhhcC----CCCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCCCCCCCCeE
Q 041604           13 FQDQLVFYVTPSEALEKYQ----SNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSV   88 (162)
Q Consensus        13 ~~~~~~yy~tpsE~~~~~~----~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd~F~eg~~V   88 (162)
                      |++|++||+||||+++..+    +.+.+++|||+|+|++|||.|+++++.++|.|+|...+|+|+|+|+|||+|+||++|
T Consensus         1 l~~ni~~F~tPSEi~~~~~~~~~~~~~g~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~GilPDlFrEGqgV   80 (136)
T 1sr3_A            1 LRSNIDLFYTPGEILYGKRETQQMPEVGQRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEGSVDVSYEGILPDLFREGQGV   80 (136)
T ss_dssp             CCCSSSCCBCTTTTTSCSTTTSCCCCTTSEEEEEEEECTTTCEECSSSSEEEEEEECSSCEEEEEEESCCCTTCCTTSEE
T ss_pred             CCCcccEEeCHHHHhcCcccccccCCCCCEEEEeeEEeCCcEEEcCCCCEEEEEEEeCCcEEEEEECCCCCccccCCCeE
Confidence            5689999999999987642    146789999999999999999888899999999999999999999999999999999


Q ss_pred             EEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHHHHhhhhhH
Q 041604           89 VVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAIEKNKKMLE  151 (162)
Q Consensus        89 VveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~~~~~~~~~  151 (162)
                      ||+|+|++                     +|+|.|++|||||||||||+|++++|+++++.+.
T Consensus        81 Va~G~l~~---------------------~g~F~A~eVLAKhdekYmp~eva~al~~~~~~~~  122 (136)
T 1sr3_A           81 VVQGELEK---------------------GNHILAKEVLAKHDENYTPPEVEKAMEANHRRPA  122 (136)
T ss_dssp             EEEEEECS---------------------SSEEEESSCBCCSCCCCCCHHHHTCC--------
T ss_pred             EEEEEECC---------------------CCeEEEEEEEecCCCCCCCHHHHHHHHHhccCcc
Confidence            99999985                     7999999999999999999999999998864443

>2kct_A Cytochrome C-type biogenesis protein CCME; solution structure, heme chaperone, cytochrome C biogenesis, OB-fold domain, NESG, PSI-2; NMR {Desulfovibrio vulgaris str}

Probab=99.96  E-value=2e-29  Score=186.00  Aligned_cols=83  Identities=24%  Similarity=0.388  Sum_probs=75.8

Q ss_pred             CCCCCcEEEeEEEecCcEEecCCCceEEEEEEeC---CeEEEEEEcCCCCCCCCCCCeEEEEEEEcCchhhhhhcccccc
Q 041604           33 NPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDL---VTDILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKS  109 (162)
Q Consensus        33 ~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~---~~~i~V~Y~G~~Pd~F~eg~~VVveG~~~~~~~~~~~~~~~~~  109 (162)
                      .+.+++|||+|+|++|||.|.+++..++|.|+|.   ..+|+|+|+|+|||+|+||++||++|+|++.            
T Consensus         5 ~~~~~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~~~~v~V~Y~GilPDlFrEGqgVV~~G~l~~~------------   72 (94)
T 2kct_A            5 QDKLHTVRLFGTVAADGLTMLDGAPGVRFRLEDKDNTSKTVWVLYKGAVPDTFKPGVEVIIEGGLAPG------------   72 (94)
T ss_dssp             SCTTCCEEEEEEECSTTCEECTTSSEEEEEEECSSCTTCEEEEEEESCCCTTCCTTCEEEEEEEECTT------------
T ss_pred             CCCCCeEEEeeEEeCCeEEecCCCCEEEEEEEcCCCCCcEEEEEECCCCCccccCCCeEEEEEEEeCC------------
Confidence            3578999999999999999987889999999999   7999999999999999999999999999841            


Q ss_pred             ccccccCCCCeEEEeEEeecCCCCCC
Q 041604          110 VSENARSRDCFFSATDVLAKHDEKYM  135 (162)
Q Consensus       110 ~~~~~~~~dg~F~A~~lLaKcpskY~  135 (162)
                              +|+|.|++|||||||+-.
T Consensus        73 --------~g~F~A~evLaKh~e~~~   90 (94)
T 2kct_A           73 --------EDTFKARTLMTKCPLEHH   90 (94)
T ss_dssp             --------CSEEEEEEEEESSCCC--
T ss_pred             --------CCEEEEeEEEEeCCCccc
Confidence                    589999999999999853

>4gop_B Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=86.49  E-value=4  Score=29.98  Aligned_cols=71  Identities=21%  Similarity=0.218  Sum_probs=50.9

Q ss_pred             eCHHHHHhhcCCC---------CCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCC-------CCCCCCC
Q 041604           21 VTPSEALEKYQSN---------PSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGS-------LPDLFRE   84 (162)
Q Consensus        21 ~tpsE~~~~~~~~---------~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~-------~Pd~F~e   84 (162)
                      +|++++++..+..         ..=..|++-|.|.  ++..  ....+.|.|.|+...|.+.+=-.       -...|++
T Consensus        12 vtIkqil~a~~~~~~~~f~i~g~~i~~V~iVG~V~--~~~~--~~~~~~~~ldD~TG~I~~~~W~~~~~~~~~~~~~~~~   87 (136)
T 4gop_B           12 VTIRQILNAEQPHPDAEFILDGAELGQLTFVAVVR--NISR--NATNVAYSVEDGTGQIEVRQWLDSSSDDSSKASEIRN   87 (136)
T ss_dssp             CCHHHHHHCBCCSSSCCCBSSSSBCCEEEEEEEEE--EEEE--CSSEEEEEEECSSCEEEEEEECC--------CCSCCT
T ss_pred             EEHHHHhhccccCCCCcEEECCEEEEEEEEEEEEE--EEEe--cCCeEEEEEECCCCCEEEEEecccCCcccccccccCC
Confidence            6778877653311         1125678888886  3433  35689999999988999887543       2458999


Q ss_pred             CCeEEEEEEEc
Q 041604           85 GHSVVVEGFIK   95 (162)
Q Consensus        85 g~~VVveG~~~   95 (162)
                      |.-|-|.|++.
T Consensus        88 g~yVrV~G~v~   98 (136)
T 4gop_B           88 NVYVRVLGTLK   98 (136)
T ss_dssp             TCEEEEEEEEE
T ss_pred             CCEEEEEEEEE
Confidence            99999999996

>3kdf_D Replication protein A 32 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} SCOP: b.40.4.3 PDB: 2pqa_A 1quq_A 1l1o_B

Probab=85.63  E-value=4  Score=29.79  Aligned_cols=71  Identities=14%  Similarity=0.198  Sum_probs=48.2

Q ss_pred             eCHHHHHhhcCCC-------CCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCe-EEEEEEcCC------CCCCCCCCC
Q 041604           21 VTPSEALEKYQSN-------PSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVT-DILVRYQGS------LPDLFREGH   86 (162)
Q Consensus        21 ~tpsE~~~~~~~~-------~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~-~i~V~Y~G~------~Pd~F~eg~   86 (162)
                      +|++++++..+.+       ..=..+++-|.|.  ++..  ....+.|.|.|+.. .|.+.+=-.      -.+.|++|.
T Consensus         9 vtIkqil~a~~~~~~f~i~g~~i~~V~iVG~V~--~~~~--~~~~~~~~ldD~TG~~I~~~~W~~~~~~~~~~~~~~~g~   84 (132)
T 3kdf_D            9 CTISQLLSATLVDEVFRIGNVEISQVTIVGIIR--HAEK--APTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPET   84 (132)
T ss_dssp             CCHHHHHTCEESSSCEEETTEECCEEEEEEEEE--EEEE--CSSEEEEEEECSSSSCEEEEEEC---------CCCCTTC
T ss_pred             EEHHHHhhCccCCCcEEECCEEEEEEEEEEEEE--EEEE--cCCeEEEEEECCCCCEEEEEEEccCCCcccccccccCCC
Confidence            5667776543210       0124567777775  2333  35789999999987 899987432      256899999


Q ss_pred             eEEEEEEEc
Q 041604           87 SVVVEGFIK   95 (162)
Q Consensus        87 ~VVveG~~~   95 (162)
                      -|-|.|++.
T Consensus        85 yVrV~G~l~   93 (132)
T 3kdf_D           85 YVKVAGHLR   93 (132)
T ss_dssp             EEEEEEEEE
T ss_pred             EEEEEEEEE
Confidence            999999997

>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str}

Probab=84.06  E-value=7.7  Score=27.17  Aligned_cols=60  Identities=13%  Similarity=0.159  Sum_probs=46.4

Q ss_pred             CCCcEEEeEEEecC-cEE--ecCC---CceEEEEEEeCCeEEEEEEcCCCCC---CCCCCCeEEEEEEE
Q 041604           35 SKNKFRLGGLVLEG-SVA--HPAS---SSEMEFVVTDLVTDILVRYQGSLPD---LFREGHSVVVEGFI   94 (162)
Q Consensus        35 ~~~~vrv~G~V~~g-Sv~--~~~~---~~~~~F~vtD~~~~i~V~Y~G~~Pd---~F~eg~~VVveG~~   94 (162)
                      .+..+.+.|.|..= .+.  ...+   ..-+.+.|.|...+|.+.+=+...+   .|++|..|.+.|..
T Consensus        15 ~g~~v~i~~~V~~~~~~~~~~~k~G~~~~~~~~~l~D~TG~I~~t~w~~~~~~~~~l~~G~vv~i~g~~   83 (115)
T 2k50_A           15 EGAETPVTGRVMKISSPRTFTTRKGREGKLANVIIADDTGELRAVFWTENIKLLKKFREGDVIRIKDVN   83 (115)
T ss_dssp             TTCEEEEEEEEEEECCCEECCCTTSSCCEEEEEEEEETTEEEEEEEETTGGGGGGTCCTTSEEEEEEEE
T ss_pred             CCCEeEEEEEEEECCCceEEEcCCCCEEEEEEEEEEeCCCeEEEEEeCchhhhhhcCCCCCEEEEEeeE
Confidence            46788999999743 443  1222   4567789999999999998887655   78999999999998

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	162
d1sr3a_	114	b.40.9.1 (A:) Heme chaperone CcmE {Escherichia col	5e-28
d1j6qa_	100	b.40.9.1 (A:) Heme chaperone CcmE {Shewanella putr	1e-18

>d1sr3a_ b.40.9.1 (A:) Heme chaperone CcmE {Escherichia coli [TaxId: 562]} Length = 114

class: All beta proteins
fold: OB-fold
superfamily: Heme chaperone CcmE
family: Heme chaperone CcmE
domain: Heme chaperone CcmE
species: Escherichia coli [TaxId: 562]

 Score = 98.5 bits (245), Expect = 5e-28
 Identities = 42/134 (31%), Positives = 61/134 (45%), Gaps = 25/134 (18%)

Query: 14  QDQLVFYVTPSEALEKYQSN----PSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTD 69
           +  +  + TP E L   +          + R+GG+V+ GSV    +S ++ F + D    
Sbjct: 2   RSNIDLFYTPGEILYGKRETQQMPEVGQRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEGS 61

Query: 70  ILVRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAK 129
           + V Y+G LPDLFREG  VVV+G ++                           A +VLAK
Sbjct: 62  VDVSYEGILPDLFREGQGVVVQGELEK---------------------GNHILAKEVLAK 100

Query: 130 HDEKYMPQEVAAAI 143
           HDE Y P EV  A+
Sbjct: 101 HDENYTPPEVEKAM 114

>d1j6qa_ b.40.9.1 (A:) Heme chaperone CcmE {Shewanella putrefaciens [TaxId: 24]} Length = 100

class: All beta proteins
fold: OB-fold
superfamily: Heme chaperone CcmE
family: Heme chaperone CcmE
domain: Heme chaperone CcmE
species: Shewanella putrefaciens [TaxId: 24]

 Score = 73.8 bits (181), Expect = 1e-18
 Identities = 38/119 (31%), Positives = 54/119 (45%), Gaps = 26/119 (21%)

Query: 17  LVFYVTPSEALEK----YQSNPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTD-LVTDIL 71
           L  + TPSE +           +  + R+GG+V  GS+    +S  ++F V D L  +IL
Sbjct: 3   LNLFYTPSEIVNGKTDTGVKPEAGQRIRVGGMVTVGSMVRDPNSLHVQFAVHDSLGGEIL 62

Query: 72  VRYQGSLPDLFREGHSVVVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKH 130
           V Y   LPDLFREG  +V +G +                       D   +AT+VLAKH
Sbjct: 63  VTYDDLLPDLFREGQGIVAQGVLGE---------------------DGKLAATEVLAKH 100

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	162
d1sr3a_	114	Heme chaperone CcmE {Escherichia coli [TaxId: 562]	100.0
d1j6qa_	100	Heme chaperone CcmE {Shewanella putrefaciens [TaxI	99.97
d2pi2a1	128	Replication protein A 32 KDa subunit (RPA32) fragm	89.73
d1v1qa_	111	Primosomal replication protein N, PriB {Escherichi	83.26
d1n9wa1	93	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	80.37

>d1sr3a_ b.40.9.1 (A:) Heme chaperone CcmE {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Heme chaperone CcmE
family: Heme chaperone CcmE
domain: Heme chaperone CcmE
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=3.9e-40  Score=248.09  Aligned_cols=110  Identities=38%  Similarity=0.648  Sum_probs=99.0

Q ss_pred             hhcCeeeeeCHHHHHhhcCC----CCCCCcEEEeEEEecCcEEecCCCceEEEEEEeCCeEEEEEEcCCCCCCCCCCCeE
Q 041604           13 FQDQLVFYVTPSEALEKYQS----NPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDLVTDILVRYQGSLPDLFREGHSV   88 (162)
Q Consensus        13 ~~~~~~yy~tpsE~~~~~~~----~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~~i~V~Y~G~~Pd~F~eg~~V   88 (162)
                      +++|++||+||||++++...    ...++++||+|+|++||+.|+.++..++|.|||+..+|+|+|+|++||+|+||++|
T Consensus         1 L~~ni~yF~tPsEi~~~~~~~~~~~~~g~~iRvgG~V~~gSi~~~~~~~~~~F~itD~~~~i~V~Y~GilPdlF~eg~~V   80 (114)
T d1sr3a_           1 LRSNIDLFYTPGEILYGKRETQQMPEVGQRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEGSVDVSYEGILPDLFREGQGV   80 (114)
T ss_dssp             CCCSSSCCBCTTTTTSCSTTTSCCCCTTSEEEEEEEECTTTCEECSSSSEEEEEEECSSCEEEEEEESCCCTTCCTTSEE
T ss_pred             CCcceEEEECHHHhhcccccccccccCCcEEEEeeEEEEeEEEeecCcceEEEEEccCCcEEEEEecCCCChhhcCCCeE
Confidence            46899999999999754321    23478999999999999999888889999999999999999999999999999999


Q ss_pred             EEEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecCCCCCCChHHHHHH
Q 041604           89 VVEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKHDEKYMPQEVAAAI  143 (162)
Q Consensus        89 VveG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKcpskY~p~eva~~~  143 (162)
                      ||+|+|++                     +++|.|++|||||||+|||+|++++|
T Consensus        81 VveG~~~~---------------------~~~f~A~~vlaKh~e~Y~p~ev~~al  114 (114)
T d1sr3a_          81 VVQGELEK---------------------GNHILAKEVLAKHDENYTPPEVEKAM  114 (114)
T ss_dssp             EEEEEECS---------------------SSEEEESSCBCCSCCCCCCHHHHTCC
T ss_pred             EEEEEECC---------------------CCEEEEEEEEecCCCCCCCHHHHhhC
Confidence            99999974                     68999999999999999999998864

>d1j6qa_ b.40.9.1 (A:) Heme chaperone CcmE {Shewanella putrefaciens [TaxId: 24]}

class: All beta proteins
fold: OB-fold
superfamily: Heme chaperone CcmE
family: Heme chaperone CcmE
domain: Heme chaperone CcmE
species: Shewanella putrefaciens [TaxId: 24]

Probab=99.97  E-value=5.4e-32  Score=199.55  Aligned_cols=95  Identities=39%  Similarity=0.644  Sum_probs=85.5

Q ss_pred             cCeeeeeCHHHHHhhcCC----CCCCCcEEEeEEEecCcEEecCCCceEEEEEEeC-CeEEEEEEcCCCCCCCCCCCeEE
Q 041604           15 DQLVFYVTPSEALEKYQS----NPSKNKFRLGGLVLEGSVAHPASSSEMEFVVTDL-VTDILVRYQGSLPDLFREGHSVV   89 (162)
Q Consensus        15 ~~~~yy~tpsE~~~~~~~----~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~-~~~i~V~Y~G~~Pd~F~eg~~VV   89 (162)
                      +|++||+||||++++...    ...++++||+|+|++||+.|.+++..++|.|+|+ +++|+|.|+|++||+|+||++||
T Consensus         1 sNi~yF~tPse~~~~~~~~~~~~~~~~~iRvGG~V~~gSi~~~~~~~~~~F~itD~~~~~i~V~Y~G~lPdlF~eg~gVV   80 (100)
T d1j6qa_           1 SNLNLFYTPSEIVNGKTDTGVKPEAGQRIRVGGMVTVGSMVRDPNSLHVQFAVHDSLGGEILVTYDDLLPDLFREGQGIV   80 (100)
T ss_dssp             CCCCCEECTTTTTTTSTTTTSSSCTTCEEEEEEEECTTCCEECTTSSCEEEEEECTTCCCEEEEECSCCTTSCCSSSEEE
T ss_pred             CcEeEEECHHHhhcccccccccccCCCEEEEeeEEeeeEEEecCCccEEEEEEcCCceeEEEEEeCCCCCchhcCCCeEE
Confidence            478999999999875321    1357999999999999999988888999999997 68999999999999999999999


Q ss_pred             EEEEEcCchhhhhhccccccccccccCCCCeEEEeEEeecC
Q 041604           90 VEGFIKPITEEIKNVKSEKSVSENARSRDCFFSATDVLAKH  130 (162)
Q Consensus        90 veG~~~~~~~~~~~~~~~~~~~~~~~~~dg~F~A~~lLaKc  130 (162)
                      |+|+|++                     +|+|.|++|||||
T Consensus        81 veG~~~~---------------------~g~F~A~~vlaKH  100 (100)
T d1j6qa_          81 AQGVLGE---------------------DGKLAATEVLAKH  100 (100)
T ss_dssp             EEEEECS---------------------TTSEEEEEEECCC
T ss_pred             EEEEECC---------------------CCEEEEEEEEecC
Confidence            9999974                     7999999999999

>d2pi2a1 b.40.4.3 (A:44-171) Replication protein A 32 KDa subunit (RPA32) fragment {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 32 KDa subunit (RPA32) fragment
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.73  E-value=0.75  Score=32.04  Aligned_cols=56  Identities=14%  Similarity=0.282  Sum_probs=42.3

Q ss_pred             CcEEEeEEEecCcEEecCCCceEEEEEEeCCe-EEEEEEc------CCCCCCCCCCCeEEEEEEEcC
Q 041604           37 NKFRLGGLVLEGSVAHPASSSEMEFVVTDLVT-DILVRYQ------GSLPDLFREGHSVVVEGFIKP   96 (162)
Q Consensus        37 ~~vrv~G~V~~gSv~~~~~~~~~~F~vtD~~~-~i~V~Y~------G~~Pd~F~eg~~VVveG~~~~   96 (162)
                      +.+++-|.|.  +++.  .+..+.|.|.|+.. .|.|++-      -..++.+++|.-|-|.|++..
T Consensus        29 ~~V~iVG~V~--~i~~--~~t~~~y~idDgTG~~i~v~~w~~~~~~~~~~~~i~~g~yVrV~G~lk~   91 (128)
T d2pi2a1          29 SQVTIVGIIR--HAEK--APTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRS   91 (128)
T ss_dssp             SEEEEEEEEE--EEEE--CSSEEEEEEECSSSSCEEEEEECC-------CCCCCTTCEEEEEEEEEE
T ss_pred             EEEEEEEEEE--EEEe--cCCEEEEEEECCCCCcEEEEEECCCCCCccccccccCCCEEEEEEEEEe
Confidence            5677778776  3544  35689999999986 6988874      245678999999999999973

>d1v1qa_ b.40.4.3 (A:) Primosomal replication protein N, PriB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Primosomal replication protein N, PriB
species: Escherichia coli [TaxId: 562]

Probab=83.26  E-value=4.9  Score=27.13  Aligned_cols=61  Identities=21%  Similarity=0.321  Sum_probs=43.2

Q ss_pred             CCCcEEEeEEEecC-cEEecC-CCceEEEEEEeC------C------eEEEEEEcCC----CCCCCCCCCeEEEEEEEc
Q 041604           35 SKNKFRLGGLVLEG-SVAHPA-SSSEMEFVVTDL------V------TDILVRYQGS----LPDLFREGHSVVVEGFIK   95 (162)
Q Consensus        35 ~~~~vrv~G~V~~g-Sv~~~~-~~~~~~F~vtD~------~------~~i~V~Y~G~----~Pd~F~eg~~VVveG~~~   95 (162)
                      .-++|.|.|.|... .+.+.+ +..-+.|.|.-.      +      ..++|..-|.    +-+.+..|..|.|+|++.
T Consensus         5 m~N~v~L~G~l~~dpelr~T~~G~~v~~f~la~~~~~~e~~~~r~~~~~i~vv~~g~~Ae~~~~~l~kG~~v~v~G~L~   83 (111)
T d1v1qa_           5 MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFIS   83 (111)
T ss_dssp             CCEEEEEEEEEEEEEEEEECTTCCEEEEEEEEEEEEEEETTEEEEEEEEEEEEEESTGGGGGGTTCCTTCEEEEEEEEE
T ss_pred             ceEEEEEEEEecCCcceEECCCCCEEEEEEEEeccEEecccceEEEEEEEEEEEeCHHHHHHHHHhcCCCEEEEEEEEE
Confidence            35689999988644 466544 456677998621      1      1367766665    456889999999999997

>d1n9wa1 b.40.4.1 (A:1-93) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-2 [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Thermus thermophilus, AspRS-2 [TaxId: 274]

Probab=80.37  E-value=5.6  Score=25.87  Aligned_cols=55  Identities=16%  Similarity=0.171  Sum_probs=41.3

Q ss_pred             CCCCcEEEeEEEecCcEEecCCCceEEE-EEEeCCeEEEEEEcCCCCCCCCCCCeEEEEEEEc
Q 041604           34 PSKNKFRLGGLVLEGSVAHPASSSEMEF-VVTDLVTDILVRYQGSLPDLFREGHSVVVEGFIK   95 (162)
Q Consensus        34 ~~~~~vrv~G~V~~gSv~~~~~~~~~~F-~vtD~~~~i~V~Y~G~~Pd~F~eg~~VVveG~~~   95 (162)
                      ..+++|+|.|+|..  + |. .+ .+.| .|.|+...+.+.+...  +....+..|.|+|.+.
T Consensus        11 ~~g~~V~v~GwV~~--~-R~-~g-k~~Fi~LrD~sg~iQ~v~~~~--~~~~~e~~v~v~G~v~   66 (93)
T d1n9wa1          11 HVGQEVELLGFLHW--R-RD-LG-RIQFLLLRDRSGVVQVVTGGL--KLPLPESALRVRGLVV   66 (93)
T ss_dssp             CTTSEEEEEEEEEE--E-EE-CS-SEEEEEEEETTEEEEEEEESC--CCCCTTCEEEEEEEEE
T ss_pred             cCCCEEEEEEEEEe--E-Ee-CC-CcEEEEEEcCCccceEEeccc--cccccceEEEEEEEEE
Confidence            46899999999973  3 43 23 3555 6778888999999864  3445688999999996