RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4171
(309 letters)
>gnl|CDD|217559 pfam03441, FAD_binding_7, FAD binding domain of DNA photolyase.
Length = 276
Score = 229 bits (585), Expect = 3e-74
Identities = 75/224 (33%), Positives = 113/224 (50%), Gaps = 12/224 (5%)
Query: 93 GGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNK 152
GGE A++RLE L+ + +A + + + P + LSP+L FG +S R Y + K
Sbjct: 1 GGEKAALKRLESFLKER--LADYAKDRDDP--AADGTSRLSPYLHFGEISPRQVYQAVRK 56
Query: 153 LYKRIKKAPPPLSLH---GQLLWREFFYCAATRNPNFDRMLGNPICVQIPWDVNM---EA 206
+ +L+WREF+ NP+ +R N +PW +
Sbjct: 57 AQGDSPEGGAKQGAEAFLSELIWREFYIQLLYHNPDLERENLNDAYDGLPWAKDRPDEYL 116
Query: 207 LAKWANAQTGFPWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDELLL 266
L W +TG+P +DA M QLR+ GW+H+ R VA FLT+ L + W EG + F E L+
Sbjct: 117 LEAWEEGRTGYPLVDAAMRQLRQTGWMHNRLRMIVASFLTK-KLLIDWREGEEYFAETLI 175
Query: 267 DADWSVNAGMWMWLSCS-SFFQQFFHCYCPVKFGRKADPNGDFI 309
DAD + N G W W + + + +F + PVK K DPNG++I
Sbjct: 176 DADPASNNGGWQWQAGTGTDAAPYFRIFNPVKQSDKFDPNGEYI 219
>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication,
recombination, and repair].
Length = 461
Score = 128 bits (324), Expect = 6e-34
Identities = 81/267 (30%), Positives = 116/267 (43%), Gaps = 30/267 (11%)
Query: 53 PLLVRQATTPLRDDHDEKYGVPTLEELGFDIEGLLPPTWKGGETEAMRRLERHLERKAWV 112
P+ LRD+ P L + + GGE A+ RL+ L +
Sbjct: 163 PVPAPDVLDALRDEEP----PPEEISLPDFSKFD-VLLFTGGEKAALARLQDFLAEG--L 215
Query: 113 ASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKLYKRIKKAPPPLSLHGQLLW 172
+ R + P S+ LSP+L FG +S R Y L ++ L +L+W
Sbjct: 216 DDYERTRDFPALDGTSR--LSPYLAFGVISPREVYAALLAAESDAREGTAALI--NELIW 271
Query: 173 REFFYCAATRNPNFDRMLGNPICV---QIPWDVNMEALAKWANAQTGFPWIDAIMTQLRE 229
REF+ P+ R P IPW+ N W +TG+P +DA M QL +
Sbjct: 272 REFYQHLLYHYPSLSR--FEPFAEKTLNIPWEDNPAHFQAWQEGKTGYPIVDAAMRQLNQ 329
Query: 230 EGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCSS----- 284
G++H+ R VA FLT+ DL + W EG K F L+D D + N G W W +S
Sbjct: 330 TGYMHNRMRMIVASFLTK-DLLIDWREGEKYFMRQLIDGDPASNNGGWQW--AASTGTDA 386
Query: 285 --FFQQFFHCYCPVKFGRKADPNGDFI 309
+F+ F PV K DP+G+FI
Sbjct: 387 APYFRIFN----PVTQAEKFDPDGEFI 409
>gnl|CDD|132595 TIGR03556, photolyase_8HDF, deoxyribodipyrimidine photo-lyase,
8-HDF type. This model describes a narrow clade of
cyanobacterial deoxyribodipyrimidine photo-lyase. This
group, in contrast to several closely related proteins,
uses a chromophore that, in other lineages is modified
further to become coenzyme F420. This chromophore is
called 8-HDF in most articles on the DNA photolyase and
FO in most literature on coenzyme F420 [DNA metabolism,
DNA replication, recombination, and repair].
Length = 471
Score = 115 bits (290), Expect = 4e-29
Identities = 82/273 (30%), Positives = 122/273 (44%), Gaps = 13/273 (4%)
Query: 43 SPSPAEAPVTPLLVRQATTPLRDDHDEKYGV---PTLEELGFDIEGLLPPTWKGGETEAM 99
S P PV + T + GV PT ++LGFD +G L GET A
Sbjct: 155 SSLPKPTPVATPTELEGLTEAELEAAAPLGVIALPTAKDLGFDWDGDLILE--PGETAAQ 212
Query: 100 RRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKLYKRIKK 159
RLE +R +A + + P L + LSP L+FG + R + + ++ +
Sbjct: 213 ARLEEFCDRA--IADYQEQRNFPA--LDGTSQLSPALKFGVIGIRTVWQATQEAHENSRS 268
Query: 160 APPPLSL---HGQLLWREFFYCAATRNPNFDRMLGNPICVQIPWDVNMEALAKWANAQTG 216
S+ +L WREF+ A P + PW+ N W +TG
Sbjct: 269 EEARNSIRTWQQELAWREFYQHALYHFPELADGPYRSLFQNFPWENNEAHFQAWCEGRTG 328
Query: 217 FPWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGM 276
+P +DA M QL E GW+H+ R VA FLT+ DL ++W+ G K F + L+D D + N G
Sbjct: 329 YPIVDAAMRQLNETGWMHNRCRMIVASFLTK-DLIINWQWGEKYFMQKLIDGDLAANNGG 387
Query: 277 WMWLSCSSFFQQFFHCYCPVKFGRKADPNGDFI 309
W W + S + + P +K DP ++I
Sbjct: 388 WQWSASSGMDPKPLRIFNPASQAQKFDPEAEYI 420
>gnl|CDD|234002 TIGR02765, crypto_DASH, cryptochrome, DASH family. Photolyases and
cryptochromes are related flavoproteins. Photolyases
harness the energy of blue light to repair DNA damage by
removing pyrimidine dimers. Cryptochromes do not repair
DNA and are presumed to act instead in some other
(possibly unknown) process such as entraining circadian
rhythms. This model describes the cryptochrome DASH
subfamily, one of at least five major subfamilies, which
is found in plants, animals, marine bacteria, etc.
Members of this family bind both folate and FAD. They
may show weak photolyase activity in vitro but have not
been shown to affect DNA repair in vivo. Rather, DASH
family cryptochromes have been shown to bind RNA (Vibrio
cholerae VC1814), or DNA, and seem likely to act in
light-responsive regulatory processes [Cellular
processes, Adaptations to atypical conditions,
Regulatory functions, DNA interactions].
Length = 429
Score = 112 bits (282), Expect = 3e-28
Identities = 82/323 (25%), Positives = 132/323 (40%), Gaps = 29/323 (8%)
Query: 4 SIEKKLTLSLPSSRRIIEKNGGKT--------------PLTYHQFQSIVAKMDSPSPAEA 49
S+E+ L +L +E++ G T P + QF+ V +
Sbjct: 112 SVERLLQQALARLGIHVEQHWGSTLYHEDDLPFDLEDLPDVFTQFRKQV----EAKCSIR 167
Query: 50 PVTPLLVRQATTPLRDDHDEKYGVPTLEELGFDI-EGLLPPTWKGGETEAMRRLERHLER 108
P P + P DD +PTLE+LG + E + GGET + RL+ +
Sbjct: 168 PPLPAPEKLPPLPSVDDPGW---IPTLEDLGEESSEVDRGLPFVGGETAGLARLKEYF-- 222
Query: 109 KAWVASFGRPKMTPQSLL--ASQTGLSPFLRFGCLSTRLFYHDLNKLYKRIKKAPPPLSL 166
W K T +L T SP+L GC+S R Y +L + +
Sbjct: 223 --WSKDLKSYKETRNGMLGPDYSTKFSPWLALGCVSPRQIYEELQRYETERGANDSTYWV 280
Query: 167 HGQLLWREFFYCAATRNPNFDRMLGNPICVQIPWDVNMEALAKWANAQTGFPWIDAIMTQ 226
+LLWR++F A + N G W + + +W TG+P +DA M +
Sbjct: 281 IFELLWRDYFRFYALKYGNRLFRFGGLRGKHPKWSFDAKRFEQWKTGTTGYPLVDANMRE 340
Query: 227 LREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCSSFF 286
L G++ + R VA FL + DL + W G + F+ L+D D N G W +L+
Sbjct: 341 LNATGFMSNRGRQNVASFLVK-DLGLDWRYGAEWFETQLVDYDVCSNWGNWQYLAGVGND 399
Query: 287 QQFFHCYCPVKFGRKADPNGDFI 309
+ + K + DP+G+++
Sbjct: 400 PRGSRQFNIEKQAQDYDPDGEYV 422
>gnl|CDD|236734 PRK10674, PRK10674, deoxyribodipyrimidine photolyase; Provisional.
Length = 472
Score = 92.4 bits (230), Expect = 5e-21
Identities = 57/188 (30%), Positives = 80/188 (42%), Gaps = 19/188 (10%)
Query: 132 LSPFLRFGCLSTRLFYHDLNKLYKRIKKAPPPLSLHGQLLWREFFYCAATRNPNFDRMLG 191
LS +L G LS R H L + +L+WREF+ P+
Sbjct: 238 LSAYLATGVLSPRQCLHRLLAEQPQALDGGAGSVWLNELIWREFYRHLMVAYPS------ 291
Query: 192 NPICVQIP---------WDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARHAVA 242
+C P W N L W +TG+P +DA M QL GW+H+ R A
Sbjct: 292 --LCKHRPFIAWTDRVQWQSNPAHLQAWQQGKTGYPIVDAAMRQLNSTGWMHNRLRMITA 349
Query: 243 CFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMW-LSCSSFFQQFFHCYCPVKFGRK 301
FL + DL + W EG + F L+D D + N G W W S + +F + P G +
Sbjct: 350 SFLVK-DLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGER 408
Query: 302 ADPNGDFI 309
D +G+FI
Sbjct: 409 FDRDGEFI 416
>gnl|CDD|131813 TIGR02766, crypt_chrom_pln, cryptochrome, plant family. At least
five major families of cryptochomes and photolyases
share FAD cofactor binding, sequence homology, and the
ability to react to short wavelengths of visible light.
Photolysases are responsible for light-dependent DNA
repair by removal of two types of uv-induced DNA
dimerizations. Cryptochromes have other functions, often
regulatory and often largely unknown, which may include
circadian clock entrainment and control of development.
Members of this subfamily are known so far only in
plants; they may show some photolyase activity in vitro
but appear mostly to be regulatory proteins that respond
to blue light.
Length = 475
Score = 68.7 bits (168), Expect = 5e-13
Identities = 71/261 (27%), Positives = 105/261 (40%), Gaps = 48/261 (18%)
Query: 77 EELGFDIE------GLLPPTWKGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQT 130
++LGF+ + LL W G + A + L + S R K A+ +
Sbjct: 179 DDLGFEDDSEKGSNALLARAWSPGWSNADKALTEFINGPLLEYSKNRKKADS----ATTS 234
Query: 131 GLSPFLRFGCLSTRLFYHDLNKLYKRIKKAPPPLSLHGQLLWREFFYCAATRNPN-FDRM 189
LSP+L FG +S R +H R+K Q+ W A + N F R
Sbjct: 235 LLSPYLHFGEVSVRKVFH-----LVRMK----------QIAWANEGNSAGEESVNLFLRS 279
Query: 190 LG-----NPICVQ---------------IPWDVNMEALAKWANAQTGFPWIDAIMTQLRE 229
+G I PW V+ W +TG+P +DA M +L
Sbjct: 280 IGLREYSRYISFNHPFSHEKPLLGHLKFFPWAVDENYFKAWRQGRTGYPLVDAGMRELWA 339
Query: 230 EGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCS-SFFQQ 288
GW+H R V+ F + L + W GMK F + LLDAD +A W ++S S ++
Sbjct: 340 TGWLHDRIRVVVSSFFVKV-LQLPWRWGMKYFWDTLLDADLESDALGWQYISGSLPDGRE 398
Query: 289 FFHCYCPVKFGRKADPNGDFI 309
P G K DPNG+++
Sbjct: 399 LDRIDNPQLEGYKFDPNGEYV 419
>gnl|CDD|176514 cd08572, GDPD_GDE5_like, Glycerophosphodiester phosphodiesterase
domain of mammalian glycerophosphodiester
phosphodiesterase GDE5-like proteins. This subfamily
corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in mammalian
glycerophosphodiester phosphodiesterase GDE5-like
proteins. GDE5 is widely expressed in mammalian tissues,
with highest expression in spinal chord. Although its
biological function remains unclear, mammalian GDE5
shows higher sequence homology to fungal and plant
glycerophosphodiester phosphodiesterases (GP-GDEs, EC
3.1.4.46) than to other bacterial and mammalian GP-GDEs.
It may also hydrolyze glycerophosphodiesters to
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols.
Length = 293
Score = 34.6 bits (80), Expect = 0.044
Identities = 19/89 (21%), Positives = 27/89 (30%), Gaps = 16/89 (17%)
Query: 9 LTLSLPSSRRIIEKNGGKTP-----LTYHQFQSIVAKMDSPSPAEAPVTPLLVRQATTPL 63
T+S+ + G LT Q + + A + P
Sbjct: 57 FTISVSEKSKTGSDEGELIEVPIHDLTLEQLKELGL---QHISALKRKALTRKAKGPKPN 113
Query: 64 RDDHDEKYGVPTLEE--------LGFDIE 84
DE PTL+E LGF+IE
Sbjct: 114 PWGMDEHDPFPTLQEVLEQVPKDLGFNIE 142
>gnl|CDD|111257 pfam02346, Vac_Fusion, Chordopoxvirus fusion protein. This is a
family of viral fusion proteins from the
chordopoxviruses. A 14-kDa Vaccinia Virus protein has
been demonstrated to function as a viral fusion protein
mediating cell fusion at endosmomal (low) pH.
Length = 57
Score = 27.7 bits (62), Expect = 1.4
Identities = 10/16 (62%), Positives = 11/16 (68%), Gaps = 2/16 (12%)
Query: 97 EAMRRLERHLE--RKA 110
EA+ RLE H E RKA
Sbjct: 29 EALDRLENHAETLRKA 44
>gnl|CDD|187887 cd09757, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c.
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;
Zn-finger domain containing protein, distant homologs of
Cas8 proteins; signature gene for I-C subtype; also
known as Csd1 family.
Length = 569
Score = 29.1 bits (66), Expect = 3.5
Identities = 29/123 (23%), Positives = 40/123 (32%), Gaps = 27/123 (21%)
Query: 35 QSIVAKMDSPSPAEAPVTPLLVRQATTPLRDDHDEK------------YGVPTLEELGFD 82
+ V + SPAE P L T D + Y ++ F
Sbjct: 262 ATTVFWAEKSSPAEDPFAALFDPPDDTKPDDAATTQAVALLLKKPITGYRADLDDDTRFY 321
Query: 83 IEGLLPPT-------W---KGGETEAMRRLERHLERKAWVASFGRPKMTPQSL--LASQT 130
+ GL P W GE + RLERH + AW S+G +P + L T
Sbjct: 322 VLGLAPNAGRLSVRFWRELTVGEF--LERLERHFDDLAWEPSYGGAP-SPPDIARLLYGT 378
Query: 131 GLS 133
Sbjct: 379 ARD 381
>gnl|CDD|235286 PRK04338, PRK04338, N(2),N(2)-dimethylguanosine tRNA
methyltransferase; Provisional.
Length = 382
Score = 28.0 bits (63), Expect = 7.5
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 141 LSTRLFYHDLNKLYKRIKKAPPPLS 165
L T FY DL++L K++K + PP+
Sbjct: 318 LDTPTFY-DLHELAKKLKVSAPPMD 341
>gnl|CDD|236806 PRK10957, PRK10957, iron-enterobactin transporter periplasmic
binding protein; Provisional.
Length = 317
Score = 27.6 bits (62), Expect = 7.6
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 76 LEELGFDIEGLLPPTWKGGETEAMRR 101
LE+LGF + LP + ++ R
Sbjct: 217 LEQLGFTLAE-LPAGLQASTSQGKRH 241
>gnl|CDD|225106 COG2195, PepD, Di- and tripeptidases [Amino acid transport and
metabolism].
Length = 414
Score = 27.7 bits (62), Expect = 7.9
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 1/51 (1%)
Query: 38 VAKMDSPSPAEAPVTPLLVRQATTPLRDDHDEKYGVPTLEELGFDIEGLLP 88
+ K+ + S E V P V QA DE G L++ E +P
Sbjct: 14 LVKIPTQSKHEKAVAPSTVGQAKLLGLLVEDEL-GNIGLKKPATAGENYVP 63
>gnl|CDD|220258 pfam09481, CRISPR_Cse1, CRISPR-associated protein Cse1
(CRISPR_cse1). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This entry, represented by
CT1972 from Chlorobaculum tepidum, is found in the
CRISPR/Cas subtype Ecoli regions of many bacteria (most
of which are mesophiles), and not in Archaea. It is
designated Cse1.
Length = 475
Score = 27.7 bits (62), Expect = 8.5
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 3/25 (12%)
Query: 154 YKRIKKAPPPLSLHGQ---LLWREF 175
Y+ KK L + Q LWR+
Sbjct: 288 YRPKKKEEEYLPVKPQPGRALWRDL 312
>gnl|CDD|213991 cd07436, PHP_PolX, Polymerase and Histidinol Phosphatase domain of
bacterial polymerase X. The bacterial/archaeal X-family
DNA polymerases (PolXs) have a PHP domain at their
C-terminus. The bacterial/archaeal PolX core domain and
PHP domain interact with each other and together are
involved in metal dependent 3'-5' exonuclease activity.
The PHP (also called histidinol phosphatase-2/HIS2)
domain is associated with several types of DNA
polymerases, such as PolIIIA and family X DNA
polymerases, stand alone histidinol phosphate
phosphatases (HisPPases), and a number of
uncharacterized protein families. The PHP domain has
four conserved sequence motifs and contains an invariant
histidine that is involved in metal ion coordination.
PolX is found in all kingdoms, however bacterial PolXs
have a completely different domain structure from
eukaryotic PolXs. Bacterial PolX has an extended
conformation in contrast to the common closed 'right
hand' conformation for DNA polymerases. This extended
conformation is stabilized by the PHP domain. The PHP
domain of PolX is structurally homologous to other
members of the PHP family that has a distorted
(beta/alpha)7 barrel fold with a trinuclear metal site
on the C-terminal side of the barrel.
Length = 237
Score = 27.4 bits (62), Expect = 9.2
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 178 CAATRNPNFDRMLGNPICVQI----PWDVNMEALAKWANAQTG 216
A NP+ D +LG+P + ++V+ME + + A A+TG
Sbjct: 123 LKAIENPHVD-ILGHPTGRLLGRREGYEVDMERVIEAA-AETG 163
>gnl|CDD|188530 TIGR04015, WcaC, colanic acid biosynthesis glycosyl transferase
WcaC. This gene is one of the glycosyl transferases
involved in the biosynthesis of colanic acid, an
exopolysaccharide expressed in Enterobacteraceae
species.
Length = 405
Score = 27.6 bits (61), Expect = 9.2
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 144 RLFYHDL----NKLYKRIKKAPPPLSLHGQLL 171
RLF DL + LY+ + + P+ LH +L
Sbjct: 72 RLFNRDLFGNLDSLYRTVTRTSGPVVLHFHVL 103
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
0.323 0.137 0.455
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,703,929
Number of extensions: 1620097
Number of successful extensions: 1529
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1504
Number of HSP's successfully gapped: 26
Length of query: 309
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 212
Effective length of database: 6,635,264
Effective search space: 1406675968
Effective search space used: 1406675968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.6 bits)