RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14498
(171 letters)
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 198 bits (504), Expect = 1e-65
Identities = 68/111 (61%), Positives = 92/111 (82%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYR 60
MASVNKVI++GNLG DPE RY+ +GDAV N+ +ATT+ ++DK SGE +E TEWHR+ F+
Sbjct: 1 MASVNKVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFG 60
Query: 61 KLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111
+LA+IV +YLKKGS +YIEGR++TRKW ++G ++Y TE++AD MQMLG R
Sbjct: 61 RLAEIVGEYLKKGSSVYIEGRIRTRKWQGQDGQDRYSTEIVADQMQMLGGR 111
>gnl|CDD|136097 PRK06863, PRK06863, single-stranded DNA-binding protein;
Provisional.
Length = 168
Score = 187 bits (475), Expect = 2e-61
Identities = 77/171 (45%), Positives = 113/171 (66%), Gaps = 3/171 (1%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYR 60
MA +NKVII+G+LG DPE R M NG+AV N+S+AT+E+W DKN+GE+RE+TEWHRI FYR
Sbjct: 1 MAGINKVIIVGHLGNDPEIRTMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYR 60
Query: 61 KLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNIS 120
+ A++ +YL+KGSQ+Y+EGRL+TRKW ++ G ++Y TE+ D +QMLG R N
Sbjct: 61 RQAEVAGEYLRKGSQVYVEGRLKTRKWQDQNGQDRYTTEIQGDVLQMLGGRNQRNAGGYG 120
Query: 121 NNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVPF 171
N+ + + + N ++ + ++ P+ F DDD+PF
Sbjct: 121 NSGPAPQQSYQAGQTNNGNSQQASRPAPQQAAPQAEPPMDGF---DDDIPF 168
>gnl|CDD|236362 PRK09010, PRK09010, single-stranded DNA-binding protein;
Provisional.
Length = 177
Score = 181 bits (462), Expect = 4e-59
Identities = 68/118 (57%), Positives = 94/118 (79%), Gaps = 5/118 (4%)
Query: 1 MAS--VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITF 58
MAS VNKVI++GNLG+DPE RYM NG AV N+++AT+E+WRDK +GE +E TEWHR+
Sbjct: 1 MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQTGEMKEQTEWHRVVL 60
Query: 59 YRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIAD---NMQMLGSRKN 113
+ KLA++ +YL+KGSQ+YIEG+L+TRKWT++ G ++Y TEV+ + MQMLG R+
Sbjct: 61 FGKLAEVAGEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQG 118
>gnl|CDD|233057 TIGR00621, ssb, single stranded DNA-binding protein (ssb). All
proteins in this family for which functions are known
are single-stranded DNA binding proteins that function
in many processes including transcription, repair,
replication and recombination. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 164
Score = 172 bits (438), Expect = 9e-56
Identities = 66/174 (37%), Positives = 97/174 (55%), Gaps = 13/174 (7%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYR 60
M VNKVI++G L RDPE RY +G+AV N ++AT W+D++ GE +E TEWH I +
Sbjct: 1 MRMVNKVILVGRLTRDPELRYTPSGNAVANFTLATNRRWKDQD-GEWKEETEWHDIVIFG 59
Query: 61 KLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADN---MQMLGSRKNTNEK 117
+LA++ QYLKKGS +Y+EGRL+TRKW ++ G ++ TE+IADN + +LG+R E
Sbjct: 60 RLAEVAAQYLKKGSLVYVEGRLRTRKWEDQNGQKRSKTEIIADNVQLLDLLGARAQGGEF 119
Query: 118 NISNNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVPF 171
+ N + + + PI DD++PF
Sbjct: 120 SGGGGSGNR------PQGGQEQSATGKDPAQSAPQSGSADPIDGD---DDEIPF 164
>gnl|CDD|235585 PRK05733, PRK05733, single-stranded DNA-binding protein;
Provisional.
Length = 172
Score = 168 bits (428), Expect = 3e-54
Identities = 72/171 (42%), Positives = 107/171 (62%), Gaps = 6/171 (3%)
Query: 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLA 63
VNKVI++G G+DPE RY+ NG+AVTN+S+AT+E W DK SG+K E TEWHR++ + K+A
Sbjct: 5 VNKVILVGTCGQDPEVRYLPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVA 64
Query: 64 QIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIAD---NMQMLGSRKNTNEKNIS 120
+I +YL+KGSQ+YIEG+LQTR+W K+G+++Y TE++ D MQ+LG R +++
Sbjct: 65 EIAGEYLRKGSQVYIEGKLQTREW-EKDGIKRYTTEIVVDMQGTMQLLGGRPQGDDQGGQ 123
Query: 121 NNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVPF 171
N + + + + QP +F DDD+PF
Sbjct: 124 GGGNYNQSAPRQQAQRPQQAAQQQSRPAPQQPAPQPAA--DFDSFDDDIPF 172
>gnl|CDD|223702 COG0629, Ssb, Single-stranded DNA-binding protein [DNA replication,
recombination, and repair].
Length = 167
Score = 153 bits (389), Expect = 3e-48
Identities = 67/174 (38%), Positives = 95/174 (54%), Gaps = 11/174 (6%)
Query: 2 ASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK 61
+NKVI++G L RDPE RY NG AV + A D SGE+ E T+W R+ + K
Sbjct: 1 MMMNKVILVGRLTRDPELRYTPNGGAVVALFSAAVNRRFDNQSGERDEETDWIRVVIWGK 60
Query: 62 LAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKY----ITEVIADNMQMLGSRKNTNEK 117
LA+ +YLKKGS +Y+EGRLQTRKW ++EG ++Y +TE++AD++QMLGSRK+
Sbjct: 61 LAENAAEYLKKGSLVYVEGRLQTRKWEDQEGQKRYQTEIVTEIVADSVQMLGSRKSGEAA 120
Query: 118 NISNNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVPF 171
N + + + E EN + + DDD+PF
Sbjct: 121 GGGGGGSN-------SPDSPPPAQSAEAPGDDENASPFVVVNAPIEFDDDDIPF 167
>gnl|CDD|235782 PRK06341, PRK06341, single-stranded DNA-binding protein;
Provisional.
Length = 166
Score = 150 bits (381), Expect = 4e-47
Identities = 65/117 (55%), Positives = 86/117 (73%), Gaps = 6/117 (5%)
Query: 1 MA-SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRIT-F 58
MA SVNKVI+IGNLG DPE R +G + N+ IAT+E WRD+NSGE++E TEWHR+ F
Sbjct: 1 MAGSVNKVILIGNLGADPEIRRTQDGRPIANLRIATSETWRDRNSGERKEKTEWHRVVIF 60
Query: 59 YRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADN----MQMLGSR 111
L ++ +QYLKKG+++YIEG+LQTRKWT++ GVE+Y TEV+ + ML R
Sbjct: 61 NEGLCKVAEQYLKKGAKVYIEGQLQTRKWTDQSGVERYSTEVVLQGFNSTLTMLDGR 117
>gnl|CDD|215919 pfam00436, SSB, Single-strand binding protein family. This family
includes single stranded binding proteins and also the
primosomal replication protein N (PriB). PriB forms a
complex with PriA, PriC and ssDNA.
Length = 104
Score = 143 bits (362), Expect = 5e-45
Identities = 51/105 (48%), Positives = 78/105 (74%), Gaps = 1/105 (0%)
Query: 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLA 63
+NKVI++G L RDPE RY NG+AV N ++A ++D+N GE E T++ R+ + KLA
Sbjct: 1 MNKVILVGRLTRDPELRYTPNGNAVANFTLAVNRRFKDQN-GEGDEETDFIRVVVWGKLA 59
Query: 64 QIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQML 108
+ +YLKKGS +Y+EGRL+TRK+ ++EG ++Y+TE++AD +Q L
Sbjct: 60 ENAAEYLKKGSLVYVEGRLRTRKYEDQEGQKRYVTEIVADEVQFL 104
>gnl|CDD|184284 PRK13732, PRK13732, single-stranded DNA-binding protein;
Provisional.
Length = 175
Score = 143 bits (362), Expect = 3e-44
Identities = 69/171 (40%), Positives = 101/171 (59%), Gaps = 4/171 (2%)
Query: 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLA 63
+NKVI++G LG+DPE RY+ NG AV N+ +AT+E+WRDK +GE RE TEWHR+ + KLA
Sbjct: 6 INKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLA 65
Query: 64 QIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIAD---NMQMLGSRKNTNEKNIS 120
++ +YL+KG+Q+YIEG+L+TR W + G+ +Y+TE++ MQMLG N +
Sbjct: 66 EVAGEYLRKGAQVYIEGQLRTRSWEDN-GITRYVTEILVKTTGTMQMLGRAPQQNAQPQP 124
Query: 121 NNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVPF 171
+N A K + T K+ + P DD+PF
Sbjct: 125 GPQQNGQPQSADATKKGGAKTKGRGRKAAQPEPQPQPPEGEDYGFSDDIPF 175
>gnl|CDD|181549 PRK08763, PRK08763, single-stranded DNA-binding protein;
Provisional.
Length = 164
Score = 139 bits (352), Expect = 1e-42
Identities = 64/168 (38%), Positives = 100/168 (59%), Gaps = 8/168 (4%)
Query: 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLA 63
+NKVI++GNLG DP+ +Y +G +T +S+ATT +D+ G +E TEWHR+ F+ KL
Sbjct: 5 INKVILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDRE-GNTQERTEWHRVKFFGKLG 63
Query: 64 QIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNISNNL 123
+I +YL+KGSQ YIEG ++ K+T ++G E+Y+TE++AD MQMLG R
Sbjct: 64 EIAGEYLRKGSQCYIEGSIRYDKFTGQDGQERYVTEIVADEMQMLGGRGEGGGGGGGGIR 123
Query: 124 ENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEADDDVPF 171
+ R+N + +++ + P+ +F ADDD+PF
Sbjct: 124 PQ---RQPAPRQNNGQDYAPRRQQPAP--QQSAPPMDDF--ADDDIPF 164
>gnl|CDD|239942 cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds similar to the
OB fold of ssDNA-binding protein (SSB). SSBs bind with
high affinity to ssDNA. They bind to and protect ssDNA
intermediates during DNA metabolic pathways. All
bacterial and eukaryotic SSBs studied to date
oligomerize to bring together four OB folds in their
active state. The majority (e.g. Escherichia coli SSB)
have a single OB fold per monomer, which oligomerize to
form a homotetramer. However, Deinococcus and Thermus
SSB proteins have two OB folds per monomer, which
oligomerize to form a homodimer. Mycobacterium
tuberculosis SSB varies in quaternary structure from E.
coli SSB. It forms a dimer of dimers having a unique
dimer interface, which lends the protein greater
stability. Included in this group are OB folds similar
to Escherichia coli PriB. E.coli PriB is homodimeric
with each monomer having a single OB fold. It does not
appear to form higher order oligomers. PriB is an
essential protein for the replication restart at forks
that have stalled at sites of DNA damage. It also plays
a role in the assembly of primosome during replication
initiation at the bacteriophage phiX174 origin. PriB
physically interacts with SSB and binds ssDNA with high
affinity.
Length = 100
Score = 135 bits (343), Expect = 4e-42
Identities = 46/102 (45%), Positives = 69/102 (67%), Gaps = 2/102 (1%)
Query: 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIV 66
VI+IG LG+DPE RY +G V S+A +D++ E+ E T+W R+ + KLA+
Sbjct: 1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRD--EEEEETDWIRVVAFGKLAENA 58
Query: 67 KQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQML 108
+YLKKG +Y+EGRL+TR W +K+G ++Y TEV+AD ++ L
Sbjct: 59 AKYLKKGDLVYVEGRLRTRSWEDKDGQKRYGTEVVADRIEFL 100
>gnl|CDD|135984 PRK06642, PRK06642, single-stranded DNA-binding protein;
Provisional.
Length = 152
Score = 117 bits (295), Expect = 2e-34
Identities = 59/128 (46%), Positives = 85/128 (66%), Gaps = 5/128 (3%)
Query: 2 ASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK 61
S+NKVI+IGN+GRDPE R G + N+S+ATTE W+D+ + E++E TEWHR+ + +
Sbjct: 3 GSLNKVILIGNVGRDPEIRTTGEGKKIINLSLATTETWKDRITSERKERTEWHRVVIFSE 62
Query: 62 -LAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQ----MLGSRKNTNE 116
L +V++Y+ KGS++YIEG LQTRKW + G EKY TEV+ N +L S+ + N
Sbjct: 63 GLVSVVERYVTKGSKLYIEGSLQTRKWNDNSGQEKYTTEVVLQNFNSQLILLDSKNSNNH 122
Query: 117 KNISNNLE 124
S + E
Sbjct: 123 NQDSGHSE 130
>gnl|CDD|236275 PRK08486, PRK08486, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 104 bits (260), Expect = 1e-28
Identities = 58/181 (32%), Positives = 96/181 (53%), Gaps = 15/181 (8%)
Query: 5 NKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQ 64
NKVI++GNL RD E RY+ +G A+ + +AT+ ++ K GEK E + I + + A+
Sbjct: 3 NKVILVGNLTRDVELRYLPSGSAIATIGLATSRRFK-KQDGEKGEEVCFIDIRLFGRTAE 61
Query: 65 IVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR----------KNT 114
I QYL KGS++ IEGRL W ++ G ++ + A++MQML S+ N+
Sbjct: 62 IANQYLSKGSKVLIEGRLTFESWMDQNGQKRSKHTITAESMQMLDSKSDNPQANAMQDNS 121
Query: 115 NEKNISNNLENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLEA----DDDVP 170
+N +NN N+ N + + N+ +KEN + QP N + ++++P
Sbjct: 122 FHENFNNNYPGNYNNPSQDPYMNQAQSYNQNAYAKENQQAQPPKYENSVPEIDIDEEEIP 181
Query: 171 F 171
F
Sbjct: 182 F 182
>gnl|CDD|180915 PRK07275, PRK07275, single-stranded DNA-binding protein;
Provisional.
Length = 162
Score = 87.3 bits (216), Expect = 2e-22
Identities = 52/169 (30%), Positives = 90/169 (53%), Gaps = 9/169 (5%)
Query: 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLA 63
+N V+++G + RD E RY + AV ++A ++ +N GE+ ++ +R+ A
Sbjct: 2 INNVVLVGRMTRDAELRYTPSNVAVATFTLAVNRTFKSQN-GERE--ADFINCVIWRQQA 58
Query: 64 QIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNISNNL 123
+ + + KKG+ I + GR+QTR + N++G Y+TEV+ADN QML SR + S
Sbjct: 59 ENLANWAKKGALIGVTGRIQTRNYENQQGQRVYVTEVVADNFQMLESR--ATREGGSGGS 116
Query: 124 ENNFFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLE-ADDDVPF 171
N FN + +Y++ ++ P SN ++ +DDD+PF
Sbjct: 117 YNGGFNNAPSANSYSAPAQQTPNFGRDE---SPFGNSNPMDISDDDLPF 162
>gnl|CDD|168659 PRK06751, PRK06751, single-stranded DNA-binding protein;
Provisional.
Length = 173
Score = 84.9 bits (209), Expect = 3e-21
Identities = 59/175 (33%), Positives = 95/175 (54%), Gaps = 10/175 (5%)
Query: 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLA 63
+N+VI++G L +DP+ RY NG AV ++A + ++ GE+ ++ +RK A
Sbjct: 2 MNRVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQ-GERE--ADFINCVIWRKQA 58
Query: 64 QIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNISNNL 123
+ V YLKKGS ++GRLQTR + ++G Y+TEV+A+++Q L R E+ S N
Sbjct: 59 ENVANYLKKGSLAGVDGRLQTRNYEGQDGKRVYVTEVLAESVQFLEPRNGGGEQRGSFNQ 118
Query: 124 ENN---FFNIMSARKNYTSNTNNEKEKSKENFKTQPLPISNFLE----ADDDVPF 171
+ + F N S +SN+ N+ + F P SN + +DDD+PF
Sbjct: 119 QPSGAGFGNQSSNPFGQSSNSGNQGNQGNSGFTKNDDPFSNVGQPIDISDDDLPF 173
>gnl|CDD|180914 PRK07274, PRK07274, single-stranded DNA-binding protein;
Provisional.
Length = 131
Score = 72.9 bits (179), Expect = 4e-17
Identities = 47/123 (38%), Positives = 71/123 (57%), Gaps = 6/123 (4%)
Query: 5 NKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQ 64
NKVI+IG L PE +N +V V++A N R KN +RE ++ + + KLA+
Sbjct: 3 NKVILIGRLTATPELVKTANDKSVARVTLAV--NRRFKNQNGERE-ADFINVVLWGKLAE 59
Query: 65 IVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR--KNTNEKNISNN 122
+ Y KGS I I+G L+TRK+ K+G Y+TEV+ + Q+L SR + E N+ N+
Sbjct: 60 TLASYASKGSLISIDGELRTRKY-EKDGQTHYVTEVLCQSFQLLESRAQRAMRENNVGND 118
Query: 123 LEN 125
L +
Sbjct: 119 LAD 121
>gnl|CDD|180986 PRK07459, PRK07459, single-stranded DNA-binding protein;
Provisional.
Length = 121
Score = 71.3 bits (175), Expect = 1e-16
Identities = 42/127 (33%), Positives = 71/127 (55%), Gaps = 9/127 (7%)
Query: 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKL 62
S+N V ++G GRDPE RY +G V N+++A N R ++ + +W + + K
Sbjct: 2 SLNSVTLVGRAGRDPEVRYFESGSVVCNLTLAV--NRRSRD-----DEPDWFNLEIWGKT 54
Query: 63 AQIVKQYLKKGSQIYIEGRLQTRKWTNKE-GVEKYITEVIADNMQMLGSRK-NTNEKNIS 120
AQ+ Y+KKGS I I G L+ +WT++ G ++ + D +++LGS++ + N S
Sbjct: 55 AQVAADYVKKGSLIGITGSLKFDRWTDRNTGEDRSKPVIRVDRLELLGSKRDSEGNANPS 114
Query: 121 NNLENNF 127
N+ E F
Sbjct: 115 NSSEIPF 121
>gnl|CDD|168660 PRK06752, PRK06752, single-stranded DNA-binding protein; Validated.
Length = 112
Score = 62.4 bits (151), Expect = 3e-13
Identities = 36/109 (33%), Positives = 63/109 (57%), Gaps = 3/109 (2%)
Query: 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLA 63
+N+V++IG L ++PE Y G A V +A +R+ + GE++ ++ +RK A
Sbjct: 2 MNRVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRN-SLGEQQ--VDFINCVVWRKSA 58
Query: 64 QIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRK 112
+ V +Y KGS + I GR+ TR + + +G YITEV+ +++ L R+
Sbjct: 59 ENVTEYCTKGSLVGITGRIHTRNYEDDQGKRIYITEVVIESITFLERRR 107
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 63.9 bits (156), Expect = 4e-13
Identities = 33/110 (30%), Positives = 58/110 (52%), Gaps = 13/110 (11%)
Query: 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWH------ 54
MA + ++GNL DPE R+ +G AV N ++A+T D+ + EW
Sbjct: 1 MAGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRTFDRQTN------EWKDGEALF 54
Query: 55 -RITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIAD 103
R + +R+ A+ V + L KG ++ + GRL+ R + +EG ++ + E+ D
Sbjct: 55 LRCSIWRQAAENVAESLTKGMRVIVTGRLKQRSYETREGEKRTVVELEVD 104
>gnl|CDD|180517 PRK06293, PRK06293, single-stranded DNA-binding protein;
Provisional.
Length = 161
Score = 53.0 bits (127), Expect = 3e-09
Identities = 29/120 (24%), Positives = 49/120 (40%), Gaps = 8/120 (6%)
Query: 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIV 66
I+G LG DPE R S G V + + K+ ++ T W R + +
Sbjct: 4 GYIVGRLGADPEERMTSKGKRVVVLRLGV------KSRVGSKDETVWCRCNIWGNRYDKM 57
Query: 67 KQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNISNNLENN 126
YLKKGS + + G + + +K+G + V D ++ S NE + + +
Sbjct: 58 LPYLKKGSGVIVAGEMSPESYVDKDGSPQSSLVVSVDTIKF--SPFGRNEGSRQPSAGED 115
>gnl|CDD|169261 PRK08182, PRK08182, single-stranded DNA-binding protein;
Provisional.
Length = 148
Score = 35.0 bits (81), Expect = 0.005
Identities = 29/111 (26%), Positives = 49/111 (44%), Gaps = 16/111 (14%)
Query: 11 GNLGRDPETRYMSNGD------AVTNV----SIATTENWRDKNSGEKRELTEWHRITFYR 60
GN+G PE R NG+ NV + T + + G + WHR
Sbjct: 9 GNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRD---- 64
Query: 61 KLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111
A+ + +KG ++ +EGR++ +WT+ E E+ +V A + +L R
Sbjct: 65 --AEHWARLYQKGMRVLVEGRMERDEWTDNEDNERVTFKVEARRVGILPYR 113
>gnl|CDD|223602 COG0528, PyrH, Uridylate kinase [Nucleotide transport and
metabolism].
Length = 238
Score = 30.6 bits (70), Expect = 0.32
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 7/61 (11%)
Query: 56 ITFYRKLAQIVKQYLKKGSQIYI---EGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRK 112
++A +K+ + G ++ + G + G + V AD M ML +
Sbjct: 27 PEVLDRIANEIKELVDLGVEVAVVVGGGNI----ARGYIGAAAGMDRVTADYMGMLATVM 82
Query: 113 N 113
N
Sbjct: 83 N 83
>gnl|CDD|236467 PRK09328, PRK09328, N5-glutamine S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 275
Score = 29.0 bits (66), Expect = 1.0
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 58 FYRKLAQIVKQYLKKGSQIYIE 79
FYR++ + +YLK G + +E
Sbjct: 216 FYRRIIEQAPRYLKPGGWLLLE 237
>gnl|CDD|234248 TIGR03534, RF_mod_PrmC, protein-(glutamine-N5) methyltransferase,
release factor-specific. Members of this protein family
are HemK (PrmC), a protein once thought to be involved
in heme biosynthesis but now recognized to be a
protein-glutamine methyltransferase that modifies the
peptide chain release factors. All members of the seed
alignment are encoded next to the release factor 1 gene
(prfA) and confirmed by phylogenetic analysis. SIMBAL
analysis (manuscript in prep.) shows the motif
[LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers
specificity for the release factors rather than for
ribosomal protein L3 [Protein fate, Protein modification
and repair].
Length = 251
Score = 28.6 bits (65), Expect = 1.4
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 58 FYRKLAQIVKQYLKKGSQIYIE 79
FYR++ + LK G + +E
Sbjct: 195 FYRRIIAQAPRLLKPGGWLLLE 216
>gnl|CDD|180701 PRK06801, PRK06801, hypothetical protein; Provisional.
Length = 286
Score = 28.6 bits (64), Expect = 1.8
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 14/63 (22%)
Query: 54 HRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKE------GVEKYITEVIADNMQM 107
H+I FY ++Q + E R+ R E G+E+ I++ +A M++
Sbjct: 228 HKINFYTGMSQAALAAV--------EQRMTHRHAIYDEFAELLLGIEEAISDTVAQQMRI 279
Query: 108 LGS 110
GS
Sbjct: 280 FGS 282
>gnl|CDD|239601 cd03524, RPA2_OBF_family, RPA2_OBF_family: A family of
oligonucleotide binding (OB) folds with similarity to
the OB fold of the single strand (ss) DNA-binding
domain (DBD)-D of human RPA2 (also called RPA32). 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). RPA contains six OB folds,
which are involved in ssDNA binding and in
trimerization. The ssDNA binding mechanism is believed
to be multistep and to involve conformational change.
This family also includes OB folds similar to those
found in Escherichia coli SSB, the wedge domain of E.
coli RecG (a branched-DNA-specific helicase), E. coli
ssDNA specific exodeoxyribonuclease VII large subunit,
Pyrococcus abyssi DNA polymerase II (Pol II) small
subunit, Sulfolobus solfataricus SSB, and Bacillus
subtilis YhaM (a 3'-to-5'exoribonuclease). It also
includes the OB folds of breast cancer susceptibility
gene 2 protein (BRCA2), Oxytricha nova telomere end
binding protein (TEBP), Saccharomyces cerevisiae
telomere-binding protein (Cdc13), and human protection
of telomeres 1 protein (POT1).
Length = 75
Score = 26.6 bits (59), Expect = 2.4
Identities = 10/38 (26%), Positives = 23/38 (60%)
Query: 49 ELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRK 86
R+T + +LA+ ++ LK+G +YI+G+++ +
Sbjct: 26 GTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVKKFR 63
>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain. This
family contains OB-fold domains that bind to nucleic
acids. The family includes the anti-codon binding domain
of lysyl, aspartyl, and asparaginyl -tRNA synthetases
(See pfam00152). Aminoacyl-tRNA synthetases catalyze the
addition of an amino acid to the appropriate tRNA
molecule EC:6.1.1.-. This family also includes part of
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.
Length = 75
Score = 26.5 bits (59), Expect = 2.6
Identities = 10/54 (18%), Positives = 30/54 (55%), Gaps = 8/54 (14%)
Query: 55 RITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQML 108
++ +++ A+ + + LK+G + + G+++ R G E E++ + +++L
Sbjct: 30 QVVLFKEEAEKLAKKLKEGDVVLVTGKVKKRP-----GGEL---ELVVEEIEVL 75
>gnl|CDD|144426 pfam00827, Ribosomal_L15e, Ribosomal L15.
Length = 192
Score = 26.7 bits (60), Expect = 5.4
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 37 ENWRDKNSGEKRELTEWHRITFYRKLAQIVK 67
E W+ K S R L R YR+L IV+
Sbjct: 8 ELWKKKQSDVMRFLL-RVRCWEYRQLPAIVR 37
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 27.1 bits (60), Expect = 5.5
Identities = 14/68 (20%), Positives = 28/68 (41%), Gaps = 1/68 (1%)
Query: 88 TNKEGVEKYITEVIADNMQMLGSRKNTNEKNISNNLENNFFNIMSARKNYTSNTNNEKEK 147
++KY I + +++L + K I N +N I + + N + EK K
Sbjct: 1062 HFNIDIKKYKNPKIKEEIKLLEEKVEALLKKIDEN-KNKLIEIKNKSHEHVVNADKEKNK 1120
Query: 148 SKENFKTQ 155
E++ +
Sbjct: 1121 QTEHYNKK 1128
>gnl|CDD|215096 PLN00192, PLN00192, aldehyde oxidase.
Length = 1344
Score = 27.4 bits (61), Expect = 5.5
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 90 KEGVEKYITEVIADNMQMLGSRKNTNEKNISNNLENNFFNIMSARKNYTSN 140
+E +Y+ + IAD+M+ + SR N +I NL +M+ RK + S+
Sbjct: 316 EESKSEYVFKKIADHMEKIASRFVRNTGSIGGNL------VMAQRKQFPSD 360
>gnl|CDD|180917 PRK07279, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1034
Score = 27.3 bits (61), Expect = 5.7
Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 9/57 (15%)
Query: 56 ITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRK 112
+T + + + K LK+G Y++G++Q R + +++ +Q S +
Sbjct: 922 VTLFPETYRQYKDELKEGKFYYLKGKIQER---DGR------LQMVLQQIQEASSER 969
>gnl|CDD|225443 COG2890, HemK, Methylase of polypeptide chain release factors
[Translation, ribosomal structure and biogenesis].
Length = 280
Score = 26.9 bits (60), Expect = 5.8
Identities = 9/43 (20%), Positives = 15/43 (34%), Gaps = 5/43 (11%)
Query: 58 FYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEV 100
YR++ LK G + +E T E V+ +
Sbjct: 216 VYRRILGEAPDILKPGGVLILE-----IGLTQGEAVKALFEDT 253
>gnl|CDD|226968 COG4615, PvdE, ABC-type siderophore export system, fused ATPase and
permease components [Secondary metabolites biosynthesis,
transport, and catabolism / Inorganic ion transport and
metabolism].
Length = 546
Score = 26.7 bits (59), Expect = 7.7
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 70 LKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNISNNLENNFFN 129
L+ Q +EGR + N+E E + + Q R + N + L N+ N
Sbjct: 185 LQNDYQTILEGRKELT--LNRERAEYVHNNLYIPDAQE--YRHHIIRANTFHLLAVNWSN 240
Query: 130 IM 131
IM
Sbjct: 241 IM 242
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.311 0.128 0.359
Gapped
Lambda K H
0.267 0.0833 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,369,536
Number of extensions: 732990
Number of successful extensions: 690
Number of sequences better than 10.0: 1
Number of HSP's gapped: 662
Number of HSP's successfully gapped: 68
Length of query: 171
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 81
Effective length of database: 6,945,742
Effective search space: 562605102
Effective search space used: 562605102
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (24.8 bits)