RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12967
(222 letters)
>gnl|CDD|189039 cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Gap Endonuclease 1 (GEN1) is a
Holliday junction resolvase reported to symmetrically
cleave Holliday junctions and allow religation without
additional processing. GEN1 is a member of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 30 - 50
residues in GEN1 PIN domains) and a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 233
Score = 131 bits (332), Expect = 5e-38
Identities = 52/116 (44%), Positives = 67/116 (57%), Gaps = 5/116 (4%)
Query: 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTS 115
MGVK LW IL P+ +RKP+ LQ K +A+DLS W+ +S T+ ++ +LRNLFFRT
Sbjct: 1 MGVKGLWDILEPVKKRKPLDHLQGKRVAVDLSCWVVESQTVVKYFVVPKPHLRNLFFRTR 60
Query: 116 YLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQ-----AGSRARNLFF 166
YL+ LGV P+FV++G AP LK I KR Q Q A R R F
Sbjct: 61 YLIALGVLPVFVVDGAAPPLKLPVIIKRNQLQSGIAKPGDNPTPKNGSKRNRRSRF 116
>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region. domain in
nucleases.
Length = 99
Score = 95.4 bits (238), Expect = 1e-25
Identities = 38/99 (38%), Positives = 58/99 (58%), Gaps = 4/99 (4%)
Query: 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIA--EHSSQK--NMYLRNLF 111
MG+K LW +L P+ P+ L+ KT+AID S W+ T + + + +L LF
Sbjct: 1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKLGTPLPNSKHLMGLF 60
Query: 112 FRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRS 150
+RT LL G+KPIFV +GK P LK +T+ KR++ + +
Sbjct: 61 YRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRERREEA 99
Score = 52.6 bits (127), Expect = 2e-09
Identities = 20/42 (47%), Positives = 29/42 (69%)
Query: 163 NLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRS 204
LF+RT LL G+KPIFV +GK P LK +T+ KR++ + +
Sbjct: 58 GLFYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRERREEA 99
>gnl|CDD|189038 cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. The Xeroderma pigmentosum
complementation group G (XPG) nuclease plays a central
role in nucleotide excision repair (NER) in cleaving DNA
bubble structures or loops. XPG is a member of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain). In XPG PIN domains, this arch region can be
quite variable and extensive (400 - 800 residues) in
length and is required for NER activity and for
efficient processing of bubble substrates. Inserted
within the PIN domain of these 5' nucleases is a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 249
Score = 82.3 bits (204), Expect = 4e-19
Identities = 50/155 (32%), Positives = 70/155 (45%), Gaps = 30/155 (19%)
Query: 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIA-----EHSSQKNMYLRNL 110
MGVK LW +L P + L+ K +AID S WI + E ++ KN +L
Sbjct: 1 MGVKGLWKLLEPSGRPVRLETLEGKRLAIDASIWI--YQFLKGMRDREGNALKNAHLLGF 58
Query: 111 FFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARNLFFRTSY 170
F R LL G+KP+FV +G AP LK T+ KR+Q + + A +T+
Sbjct: 59 FRRICKLLFYGIKPVFVFDGGAPELKRRTLAKRRQ---QREKAEINAK--------KTAE 107
Query: 171 LLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSA 205
LL A LK ++ +QQ Q R A
Sbjct: 108 KLL------------ASQLKKSAVKSQQQQQERDA 130
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2). All proteins
in this family for which functions are known are flap
endonucleases that generate the 3' incision next to DNA
damage as part of nucleotide excision repair. This
family is related to many other flap endonuclease
families including the fen1 family. 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 = 1034
Score = 76.9 bits (189), Expect = 3e-16
Identities = 39/112 (34%), Positives = 57/112 (50%), Gaps = 6/112 (5%)
Query: 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIA---EHSSQKNMYLRNLFF 112
MGV+ LW +L L+ K +A+D+S W+ + E ++ KN +L LF
Sbjct: 1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFH 60
Query: 113 RTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARNL 164
R LL ++PIFV +G AP+LK T+ KR+Q R G + A A L
Sbjct: 61 RLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQ---RRDGASEDARKTAEKL 109
>gnl|CDD|189026 cd09856, PIN_FEN1-like, PIN domain of Flap Endonuclease-1
(FEN1)-like, structure-specific, divalent-metal-ion
dependent, 5' nucleases. PIN (PilT N terminus) domain
of Flap Endonuclease-1 (FEN1)-like nucleases: FEN1, Gap
endonuclease 1 (GEN1) and Xeroderma pigmentosum
complementation group G (XPG) nuclease are members of
the structure-specific, 5' nuclease family that
catalyzes hydrolysis of DNA duplex-containing nucleic
acid structures during DNA replication, repair, and
recombination. These nucleases contain a PIN domain with
a helical arch/clamp region (I domain) of variable
length (approximately 30 to 800 residues) and a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Most nucleases within this
family also have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+). Some nucleases in this family
have C-terminal extensions that act as interaction sites
for other proteins.
Length = 207
Score = 73.3 bits (180), Expect = 4e-16
Identities = 33/90 (36%), Positives = 40/90 (44%), Gaps = 9/90 (10%)
Query: 60 DLWGILTPICERKPIWELQDKTIAIDLSAWIC---------DSSTIAEHSSQKNMYLRNL 110
LW L P R P +L+ K IAID S W+ + S L NL
Sbjct: 1 QLWEFLEPQKSRIPKEQLRGKRIAIDASGWLFEALTIQRIRIGPRSSRSYSTTGPALINL 60
Query: 111 FFRTSYLLLLGVKPIFVLEGKAPVLKHDTI 140
F R LL L V+PIFV +G+ P LK T
Sbjct: 61 FSRLKELLSLDVEPIFVFDGEPPKLKRKTN 90
>gnl|CDD|216098 pfam00752, XPG_N, XPG N-terminal domain.
Length = 100
Score = 63.9 bits (156), Expect = 2e-13
Identities = 34/96 (35%), Positives = 50/96 (52%), Gaps = 6/96 (6%)
Query: 57 GVKDLWGILTPICERKP--IWELQDKTIAIDLSAWI---CDSSTIAEHSSQKNM-YLRNL 110
G+K L IL P+ +P I L+ KT+AID S W+ + ++ +N +L
Sbjct: 1 GIKGLLPILKPVALIRPVDIEALEGKTLAIDASIWLYQFLKAVRDQLGNALQNTSHLMGF 60
Query: 111 FFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQA 146
F R L G+KPIFV +G P LK +T++KR
Sbjct: 61 FSRLCRLKDFGIKPIFVFDGGPPPLKAETLQKRSAR 96
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 60.4 bits (147), Expect = 7e-11
Identities = 34/107 (31%), Positives = 51/107 (47%), Gaps = 16/107 (14%)
Query: 56 MGVKDLWGIL---TP--ICERKPIWELQDKTIAIDLSAW-------ICDSSTIAE---HS 100
MG+K L L P I E++ + + IAID S I D S +
Sbjct: 1 MGIKGLSKFLADKAPNAIKEQE-LKNYFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEA 59
Query: 101 SQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQ 147
+ ++ LF RT LL G+KP++V +GK P LK +EKR++ +
Sbjct: 60 GEVTSHISGLFNRTIRLLEAGIKPVYVFDGKPPELKSGELEKRRERR 106
Score = 51.2 bits (123), Expect = 1e-07
Identities = 18/38 (47%), Positives = 26/38 (68%)
Query: 164 LFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQ 201
LF RT LL G+KP++V +GK P LK +EKR++ +
Sbjct: 69 LFNRTIRLLEAGIKPVYVFDGKPPELKSGELEKRRERR 106
>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Flap endonuclease-1 (FEN1) is
involved in multiple DNA metabolic pathways, including
DNA replication processes (5' flap DNA endonuclease
activity and double stranded DNA 5'-exonuclease
activity) and DNA repair processes (long-patch base
excision repair) in eukaryotes and archaea. Interaction
between FEN1 and PCNA (Proliferating cell nuclear
antigen) is an essential prerequisite to FEN1's DNA
replication functionality and stimulates FEN1 nuclease
activity by 10-50 fold. FEN1 belongs to the
FEN1-EXO1-like family of structure-specific, 5'
nucleases. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 45 residues in
FEN1 PIN domains) and a H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region.
Both the H3TH domain (not included here) and the helical
arch/clamp region are involved in DNA binding. Nucleases
within this group also have a carboxylate-rich active
site that is involved in binding essential divalent
metal ion cofactors (Mg2+/Mn2+). FEN1 has a C-terminal
extension containing residues forming the consensus
PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1
to PCNA.
Length = 261
Score = 58.7 bits (143), Expect = 2e-10
Identities = 28/104 (26%), Positives = 47/104 (45%), Gaps = 24/104 (23%)
Query: 59 KDLWGILTPICERK-PIWELQDKTIAIDLSAWI---------------CDSS-TIAEHSS 101
L ++ ++ + +L + IAID S + +S+ + H
Sbjct: 1 VGLSKLIADGAIKEIELKDLFGRKIAIDASNALYQFLIAIRQPDGTPLTNSAGEVTSH-- 58
Query: 102 QKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 145
L LF+RT LL G+KP++V +GK P LK +EKR++
Sbjct: 59 -----LSGLFYRTIRLLENGIKPVYVFDGKPPELKSGELEKRRE 97
Score = 53.7 bits (130), Expect = 1e-08
Identities = 18/36 (50%), Positives = 26/36 (72%)
Query: 164 LFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 199
LF+RT LL G+KP++V +GK P LK +EKR++
Sbjct: 62 LFYRTIRLLENGIKPVYVFDGKPPELKSGELEKRRE 97
>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease.
Endonuclease that cleaves the 5'-overhanging flap
structure that is generated by displacement synthesis
when DNA polymerase encounters the 5'-end of a
downstream Okazaki fragment. Has 5'-endo-/exonuclease
and 5'-pseudo-Y-endonuclease activities. Cleaves the
junction between single and double-stranded regions of
flap DNA.
Length = 338
Score = 57.6 bits (140), Expect = 6e-10
Identities = 34/110 (30%), Positives = 51/110 (46%), Gaps = 32/110 (29%)
Query: 56 MGVKDLWGILTPICERKPIWELQD---KTIAIDLSAWI---------------CDSS-TI 96
MGV L + ++ I EL+D K +A+D + DS I
Sbjct: 1 MGVD-----LRDLLAKEEI-ELEDLSGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRI 54
Query: 97 AEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQA 146
H L LF+RT LL G+KP++V +GK P LK +T+E+R++
Sbjct: 55 TSH-------LSGLFYRTINLLENGIKPVYVFDGKPPELKAETLEERREI 97
Score = 51.9 bits (125), Expect = 6e-08
Identities = 18/37 (48%), Positives = 28/37 (75%)
Query: 164 LFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQA 200
LF+RT LL G+KP++V +GK P LK +T+E+R++
Sbjct: 61 LFYRTINLLENGIKPVYVFDGKPPELKAETLEERREI 97
>gnl|CDD|189027 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Exonuclease-1 (EXO1) is involved
in multiple, eukaryotic DNA metabolic pathways,
including DNA replication processes (5' flap DNA
endonuclease activity and double stranded DNA
5'-exonuclease activity), DNA repair processes (DNA
mismatch repair (MMR) and post-replication repair
(PRR)), recombination, and telomere integrity. EXO1
functions in the MMS2 error-free branch of the PRR
pathway in the maintenance and repair of stalled
replication forks. Studies also suggest that EXO1 plays
both structural and catalytic roles during MMR-mediated
mutation avoidance. EXO1 belongs to the FEN1-EXO1-like
family of structure-specific, 5' nucleases. These
nucleases contain a PIN (PilT N terminus) domain with a
helical arch/clamp region (I domain) of variable length
(approximately 43 residues in EXO1 PIN domains) and a
H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+). EXO1 nucleases also have
C-terminal Mlh1- and Msh2-binding domains which allow
interaction with MMR and PRR proteins, respectively.
Length = 210
Score = 53.7 bits (130), Expect = 7e-09
Identities = 32/120 (26%), Positives = 52/120 (43%), Gaps = 11/120 (9%)
Query: 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAW-----ICDSSTIAEHSSQKNMYLRNL 110
MG++ L L PI I E + K +A+D +W + +A + Y++
Sbjct: 1 MGIQGLLPFLKPIQRPVHISEYKGKRVAVDAYSWLHRGAYSCAEELAL-GKPTDKYVQYC 59
Query: 111 FFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ--AQGRSAGRNV-QAG--SRARNLF 165
R + LL G+KPI V +G K T E+R++ + + + G S AR F
Sbjct: 60 MKRVNMLLHYGIKPILVFDGGPLPSKKGTEEERRERREENLEKALELLREGNRSEARECF 119
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 53.7 bits (130), Expect = 1e-08
Identities = 17/37 (45%), Positives = 27/37 (72%)
Query: 110 LFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQA 146
+F+RT LL G+KP++V +GK P LK + IE+R++
Sbjct: 14 IFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREV 50
Score = 53.7 bits (130), Expect = 1e-08
Identities = 17/37 (45%), Positives = 27/37 (72%)
Query: 164 LFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQA 200
+F+RT LL G+KP++V +GK P LK + IE+R++
Sbjct: 14 IFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREV 50
>gnl|CDD|189040 cd09870, PIN_YEN1, PIN domain of Yeast Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and fungal homologs. Yeast Endonuclease 1
(YEN1) is a Holliday junction resolvase which promotes
reciprocal exchange during mitotic recombination to
maintain genome integrity in budding yeast. YEN1 is a
member of the structure-specific, 5' nuclease family
that catalyzes hydrolysis of DNA duplex-containing
nucleic acid structures during DNA replication, repair,
and recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 15 - 50
residues in YEN1 PIN domains) and a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 239
Score = 48.5 bits (116), Expect = 5e-07
Identities = 33/97 (34%), Positives = 44/97 (45%), Gaps = 16/97 (16%)
Query: 56 MGVKDLWGILTPIC--ERKPI-------WELQDKT--IAIDLSAWICDSSTI----AEHS 100
MGV LW IL P R P+ + + IAID S W+ + I A
Sbjct: 1 MGVPGLWDILKPARQSRRLPLLAFGFEFNKSGGRPLRIAIDASIWLFQAQFIQGGQARRQ 60
Query: 101 SQKNMYLRNLFFRTSYLLLLGVKPIFVLEG-KAPVLK 136
+ +N LR LF+R LL L + P+FV +G P K
Sbjct: 61 AGENPELRTLFYRLKRLLALPITPVFVFDGPNRPSFK 97
Score = 27.7 bits (62), Expect = 4.3
Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 11/55 (20%)
Query: 1 MGVKDLWGILTPIC--ERKPI-------WELQDKT--IAIDLSAWICDSSTIAEH 44
MGV LW IL P R P+ + + IAID S W+ + I
Sbjct: 1 MGVPGLWDILKPARQSRRLPLLAFGFEFNKSGGRPLRIAIDASIWLFQAQFIQGG 55
>gnl|CDD|189020 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap Endonuclease-1
(FEN1)-like and Exonuclease-1 (EXO1)-like nucleases,
structure-specific, divalent-metal-ion dependent, 5'
nucleases. PIN (PilT N terminus) domain of Flap
Endonuclease-1 (FEN1) and Exonuclease-1 (EXO1)-like
nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1)
and Xeroderma pigmentosum complementation group G (XPG)
nuclease are members of the structure-specific, 5'
nuclease family that catalyzes hydrolysis of DNA
duplex-containing nucleic acid structures during DNA
replication, repair, and recombination. These nucleases
contain a PIN domain with a helical arch/clamp region (I
domain) of variable length (approximately 30 to 800
residues) and a H3TH (helix-3-turn-helix) domain, an
atypical helix-hairpin-helix-2-like region. Both the
H3TH domain (not included here) and the helical
arch/clamp region are involved in DNA binding. Most
nucleases within this family also have a carboxylate
rich active site that is involved in binding essential
divalent metal ion cofactors (Mg2+/Mn2+). Some nucleases
in this family have C-terminal extensions that act as
interaction sites for other proteins.
Length = 209
Score = 41.8 bits (98), Expect = 9e-05
Identities = 27/93 (29%), Positives = 43/93 (46%), Gaps = 13/93 (13%)
Query: 74 IWELQDKTIAIDLSAWIC---------DSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKP 124
I +L K +AID++ ++ I E +S Y F+RT L G+ P
Sbjct: 15 IEDLNGKKVAIDVNHYLYQFLTSKREQYLDAIGEFTSSLKGY----FYRTIKLFENGITP 70
Query: 125 IFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQA 157
IFV +G P LK + KR +A+ + + +A
Sbjct: 71 IFVFDGGPPYLKSEASGKRTEARAEAEISSTEA 103
Score = 33.7 bits (77), Expect = 0.038
Identities = 17/47 (36%), Positives = 26/47 (55%)
Query: 165 FFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQA 211
F+RT L G+ PIFV +G P LK + KR +A+ + + +A
Sbjct: 57 FYRTIKLFENGITPIFVFDGGPPYLKSEASGKRTEARAEAEISSTEA 103
>gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional.
Length = 237
Score = 28.8 bits (65), Expect = 1.6
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 13/68 (19%)
Query: 124 PIFVLEGKAPVLK-------HDTIEKRQQAQGRSA----GRNVQAGSRARNLF--FRTSY 170
PI+ L+ KA +L H+ +++ +G S+ A + A LF +
Sbjct: 6 PIYHLKRKAKLLSRAQNIPLHEALDRIAAEEGFSSWSLLAAKAAATTPAEELFSQLKPGD 65
Query: 171 LLLLGVKP 178
L+LLG +P
Sbjct: 66 LVLLGARP 73
>gnl|CDD|187792 cd09661, Cmr6_III-B, CRISPR/Cas system-associated RAMP superfamily
protein Cmr6. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein; This protein is a subunit of
Cmr complex.
Length = 210
Score = 27.7 bits (62), Expect = 3.6
Identities = 11/37 (29%), Positives = 16/37 (43%)
Query: 93 SSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLE 129
S A S N+ + +TS LL+G+ V E
Sbjct: 16 SIREALESKLNNLCVIEFKLKTSSRLLVGLGTPHVYE 52
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
0.321 0.136 0.410
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,027,866
Number of extensions: 1003732
Number of successful extensions: 655
Number of sequences better than 10.0: 1
Number of HSP's gapped: 642
Number of HSP's successfully gapped: 44
Length of query: 222
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 129
Effective length of database: 6,812,680
Effective search space: 878835720
Effective search space used: 878835720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.7 bits)