RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6304
(407 letters)
>gnl|CDD|217559 pfam03441, FAD_binding_7, FAD binding domain of DNA photolyase.
Length = 276
Score = 191 bits (487), Expect = 3e-58
Identities = 84/287 (29%), Positives = 115/287 (40%), Gaps = 73/287 (25%)
Query: 151 GGETEALIKLNERLSQEIESFKSGVYLSNQVSPDLTGPPTSQ-SAALKFGCLSVRRFYWA 209
GGE AL +L L + + + P G TS+ S L FG +S R+ Y A
Sbjct: 1 GGEKAALKRLESFLKERLADYAKDRD-----DPAADG--TSRLSPYLHFGEISPRQVYQA 53
Query: 210 LHDHFNTIHEG---RPPSHFNITGQLIWREYFYTMSAHNPYYDQMEKNPICLNIPWLPES 266
+ EG + F +LIWRE++ + HNP ++ N +PW
Sbjct: 54 VRKAQGDSPEGGAKQGAEAF--LSELIWREFYIQLLYHNPDLERENLNDAYDGLPW--AK 109
Query: 267 HPNKEKYLNAWKNGQTGYPFIDAVMRQ--------------------------------- 293
E L AW+ G+TGYP +DA MRQ
Sbjct: 110 DRPDEYLLEAWEEGRTGYPLVDAAMRQLRQTGWMHNRLRMIVASFLTKKLLIDWREGEEY 169
Query: 294 -LRRLLD--------------CT--------YCVCPVNFGRRLDPDGIYIKRYVPELRQF 330
L+D T PV + DP+G YI+R+VPEL
Sbjct: 170 FAETLIDADPASNNGGWQWQAGTGTDAAPYFRIFNPVKQSDKFDPNGEYIRRWVPELAGL 229
Query: 331 PIQYIYEPWKAPLGVQEKANCIISKDYPERIVNHVQASLENKQYLKK 377
P +YI+EPWKAP VQ A C++ KDYP+ IV+H +A K
Sbjct: 230 PDRYIHEPWKAPRPVQ--AGCVLGKDYPKPIVDHKEARKRALDAYKA 274
>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication,
recombination, and repair].
Length = 461
Score = 107 bits (268), Expect = 2e-25
Identities = 92/463 (19%), Positives = 153/463 (33%), Gaps = 136/463 (29%)
Query: 7 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEGV 66
H FLL+ L L + L G L + +G P + +L ++L T + + +D
Sbjct: 44 HASPRHAAFLLQSLQALQQSLAELGIPLLVREGDPEQVLPELAKQLAATTVFWNRD---Y 100
Query: 67 KPY-------------------QSFPTGS-HPP------RYQPCKTLLNFRDLSGLPPRP 100
+ + SF H P +P K F R
Sbjct: 101 EEWERQRDAALAQPLTEVGIAVHSFWDALLHEPGEVRTGSGEPYKVFTPFYKAWRDRLRI 160
Query: 101 KEDIDFRHVTFGTMSESLQREVSLFQTVPKPEQFHKYPEMDFGDPLIRWLGGETEALIKL 160
+ V E E P+ + + GGE AL +L
Sbjct: 161 LRPVPAPDVLDALRDEEPPPEEISL-----PDFSKFDVLL--------FTGGEKAALARL 207
Query: 161 NERLSQEIESFKSGVYLSNQVSPDLTGPPTSQ-SAALKFGCLSVRRFYWALHDHFNTIHE 219
+ L++ ++ + + TS+ S L FG +S R Y AL +
Sbjct: 208 QDFLAEGLDDY-------ERTRDFPALDGTSRLSPYLAFGVISPREVYAALLAAES---- 256
Query: 220 GRPPSHFNITGQLIWREYFYTMSAHNPYYDQMEKNPICLNIPWLPESHP----NKEKYLN 275
+ +LIWRE++ + H P + P+ ++ + +
Sbjct: 257 DAREGTAALINELIWREFYQHLLYHYPS--------LSRFEPFAEKTLNIPWEDNPAHFQ 308
Query: 276 AWKNG---------------QTGYPFIDAVMRQL---------------------RRLLD 299
AW+ G QTGY + MR + R+L+D
Sbjct: 309 AWQEGKTGYPIVDAAMRQLNQTGY--MHNRMRMIVASFLTKDLLIDWREGEKYFMRQLID 366
Query: 300 CTYCV-------------CPVNFGR---------RLDPDGIYIKRYVPELRQFPIQYIYE 337
+ R + DPDG +I+R+VPELR P +YI+E
Sbjct: 367 GDPASNNGGWQWAASTGTDAAPYFRIFNPVTQAEKFDPDGEFIRRWVPELRNLPDKYIHE 426
Query: 338 PWKAPLGVQEKANCIISKDYPERIVNHVQASLENKQYLKKEKA 380
PW+ ++ DYP+ IV+H ++ +Q L +A
Sbjct: 427 PWELSE-------VVLGVDYPKPIVDHKESR---EQALAAYEA 459
>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 = 95.1 bits (237), Expect = 2e-21
Identities = 76/318 (23%), Positives = 117/318 (36%), Gaps = 60/318 (18%)
Query: 9 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKL------CFEQD 62
G R +FLLE L DL L+ G L + G P + +L +EL + E+
Sbjct: 52 GPARGKFLLESLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFLHQEVGSEEK 111
Query: 63 CEGVKPYQSFPTGSHPPRYQPCKTLLNFRDL----SGLPPRPKEDIDFRHVTFGTMSESL 118
Q+ TL + DL LP F + +
Sbjct: 112 SVERLLQQALARLGIHVEQHWGSTLYHEDDLPFDLEDLPD-----------VFTQFRKQV 160
Query: 119 QREVSLFQTVPKPEQFHKYPEMDFGDPL----------------IRWLGGETEALIKLNE 162
+ + S+ +P PE+ P +D + + ++GGET L +L E
Sbjct: 161 EAKCSIRPPLPAPEKLPPLPSVDDPGWIPTLEDLGEESSEVDRGLPFVGGETAGLARLKE 220
Query: 163 RLSQE-IESFKSGVYLSNQVSPDLTGPPTSQ--SAALKFGCLSVRRFYWALHDHFNTIHE 219
+ ++S+K + + GP S S L GC+S R+ Y L +
Sbjct: 221 YFWSKDLKSYK-------ETRNGMLGPDYSTKFSPWLALGCVSPRQIYEELQRYETE--R 271
Query: 220 GRPPSHFNITGQLIWREYFYTMSAHNPYYDQMEKNPICLNIPWLPESHPNKEKY---LNA 276
G S + + +L+WR+YF +Y N + L HP
Sbjct: 272 GANDSTYWVIFELLWRDYFR-------FYALKYGNRL-FRFGGLRGKHPKWSFDAKRFEQ 323
Query: 277 WKNGQTGYPFIDAVMRQL 294
WK G TGYP +DA MR+L
Sbjct: 324 WKTGTTGYPLVDANMREL 341
>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 = 68.3 bits (167), Expect = 2e-12
Identities = 50/145 (34%), Positives = 64/145 (44%), Gaps = 14/145 (9%)
Query: 152 GETEALIKLNERLSQEIESFKSGVYLSNQVSPDLTGPPTSQ-SAALKFGCLSVRRFYWA- 209
GET A +L E + I Y + P L G TSQ S ALKFG + +R + A
Sbjct: 207 GETAAQARLEEFCDRAIAD-----YQEQRNFPALDG--TSQLSPALKFGVIGIRTVWQAT 259
Query: 210 LHDHFNTIHEGRPPSHFNITGQLIWREYFYTMSAHNPYYDQMEKNPICLNIPWLPESHPN 269
H N+ E S +L WRE++ H P + N PW N
Sbjct: 260 QEAHENSRSEEARNSIRTWQQELAWREFYQHALYHFPELADGPYRSLFQNFPWE-----N 314
Query: 270 KEKYLNAWKNGQTGYPFIDAVMRQL 294
E + AW G+TGYP +DA MRQL
Sbjct: 315 NEAHFQAWCEGRTGYPIVDAAMRQL 339
Score = 42.5 bits (100), Expect = 3e-04
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 306 PVNFGRRLDPDGIYIKRYVPELRQFPIQYIYEPWKAPLGVQEKANCIISKDYPERIVNHV 365
P + ++ DP+ YI+R++PELR + + PL E+ YP IV+H
Sbjct: 406 PASQAQKFDPEAEYIRRWLPELRSVDTKDLVTGKITPL---ERRAV----GYPLPIVDHN 458
Query: 366 QASLENKQ 373
Q KQ
Sbjct: 459 QQQQLFKQ 466
Score = 36.0 bits (83), Expect = 0.038
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 12 RFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEGVKPY 69
R +L+ CL +L ++ + G QL I+QG P+ + +L ++L + + D E PY
Sbjct: 49 RVAYLIGCLQELQQRYQQAGSQLLILQGDPVQLIPQLAQQLGAKAVYWNLDVE---PY 103
>gnl|CDD|216167 pfam00875, DNA_photolyase, DNA photolyase. This domain binds a
light harvesting cofactor.
Length = 164
Score = 60.7 bits (148), Expect = 5e-11
Identities = 22/64 (34%), Positives = 34/64 (53%)
Query: 1 MFPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFE 60
G+ +G R FLLE LADLD L G +L + +G P + +L +EL + + +
Sbjct: 36 AQLGSHKLGAARRWFLLESLADLDESLAKLGIRLVVRRGDPAEVLPELAKELGASAVYWN 95
Query: 61 QDCE 64
+D E
Sbjct: 96 RDYE 99
>gnl|CDD|236734 PRK10674, PRK10674, deoxyribodipyrimidine photolyase; Provisional.
Length = 472
Score = 61.6 bits (150), Expect = 2e-10
Identities = 28/65 (43%), Positives = 39/65 (60%), Gaps = 6/65 (9%)
Query: 306 PVNFGRRLDPDGIYIKRYVPELRQFPIQYIYEPWKAPLGVQEKANCIISKDYPERIVNHV 365
P G R D DG +I+R++PELR P + I++PW+ EKA + DYP+ IV+H
Sbjct: 402 PTTQGERFDRDGEFIRRWLPELRDVPGKAIHQPWRWA----EKAGVTL--DYPQPIVDHK 455
Query: 366 QASLE 370
QA L
Sbjct: 456 QARLA 460
Score = 55.0 bits (133), Expect = 3e-08
Identities = 36/117 (30%), Positives = 51/117 (43%), Gaps = 25/117 (21%)
Query: 188 PPTSQ-SAALKFGCLSVRR-FYWALHDHFNTIHEGRPPSHFNITGQLIWREYFY------ 239
TS+ SA L G LS R+ + L + + G N +LIWRE FY
Sbjct: 233 DGTSRLSAYLATGVLSPRQCLHRLLAEQPQALDGGAGSVWLN---ELIWRE-FYRHLMVA 288
Query: 240 --TMSAHNPYYDQMEKNPICLNIPWLPESHPNKEKYLNAWKNGQTGYPFIDAVMRQL 294
++ H P+ + + W +L AW+ G+TGYP +DA MRQL
Sbjct: 289 YPSLCKHRPFIAWTD------RVQWQSNPA-----HLQAWQQGKTGYPIVDAAMRQL 334
>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 = 57.6 bits (139), Expect = 5e-09
Identities = 21/54 (38%), Positives = 34/54 (62%)
Query: 310 GRRLDPDGIYIKRYVPELRQFPIQYIYEPWKAPLGVQEKANCIISKDYPERIVN 363
G + DP+G Y++R++PEL + P ++I+ PW AP V + A + +YP IV
Sbjct: 409 GYKFDPNGEYVRRWLPELARLPTEWIHHPWDAPESVLQAAGVELGSNYPLPIVG 462
>gnl|CDD|223634 COG0560, SerB, Phosphoserine phosphatase [Amino acid transport and
metabolism].
Length = 212
Score = 30.7 bits (70), Expect = 0.86
Identities = 6/31 (19%), Positives = 13/31 (41%)
Query: 25 RQLKSHGGQLFIVQGSPISIFQKLKRELNFT 55
LK+ G ++ I+ G + + + L
Sbjct: 87 AALKAAGAKVVIISGGFTFLVEPIAERLGID 117
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 29.6 bits (67), Expect = 2.5
Identities = 17/63 (26%), Positives = 24/63 (38%), Gaps = 9/63 (14%)
Query: 302 YCVCPVNFGRRLDPDGIYIKRYVPELRQFP-IQYIYEPWKAP--------LGVQEKANCI 352
Y P+ R DP G+Y K E++ F I YE + P V+E I
Sbjct: 126 YVDTPLEVCERRDPKGLYKKARAGEIKNFTGIDSPYEAPENPELHLDTDRNSVEECVEQI 185
Query: 353 ISK 355
+
Sbjct: 186 LDL 188
>gnl|CDD|227823 COG5536, BET4, Protein prenyltransferase, alpha subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 328
Score = 29.8 bits (67), Expect = 2.7
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 4/52 (7%)
Query: 357 YPERIVNHVQASLENKQ-YLKKEKANCI-INKDYPE--RIVNHVQASLENKQ 404
Y I+ HVQ E+K+ L E KD P+ +I +H Q LE
Sbjct: 71 YRFSILKHVQMVSEDKEHLLDNELDFLDEALKDNPKNYQIWHHRQWMLELFP 122
>gnl|CDD|233435 TIGR01488, HAD-SF-IB, Haloacid Dehalogenase superfamily, subfamily
IB, phosphoserine phosphatase-like. This model
represents a subfamily of the Haloacid Dehalogenase
superfamily of aspartate-nucleophile hydrolases.
Subfamily IA, B, C and D are distinguished from the rest
of the superfamily by the presence of a variable domain
between the first and second conserved catalytic motifs.
In subfamilies IA and IB, this domain consists of an
alpha-helical bundle. It was necessary to model these
two subfamilies separately, breaking them at a an
apparent phylogenetic bifurcation, so that the resulting
model(s) are not so broadly defined that members of
subfamily III (which lack the variable domain) are
included. Subfamily IA includes the enzyme phosphoserine
phosphatase (TIGR00338) as well as three hypothetical
equivalogs. Many members of these hypothetical
equivalogs have been annotated as PSPase-like or
PSPase-family proteins. In particular, the hypothetical
equivalog which appears to be most closely related to
PSPase contains only Archaea (while TIGR00338 contains
only eukaryotes and bacteria) of which some are
annotated as PSPases. Although this is a reasonable
conjecture, none of these sequences has sufficient
evidence for this assignment. If such should be found,
this model should be retired while the PSPase model
should be broadened to include these sequences [Unknown
function, Enzymes of unknown specificity].
Length = 177
Score = 28.9 bits (65), Expect = 3.5
Identities = 7/30 (23%), Positives = 10/30 (33%)
Query: 25 RQLKSHGGQLFIVQGSPISIFQKLKRELNF 54
LK G IV G + + +L
Sbjct: 83 SWLKERGIDTVIVSGGFDFFVEPVAEKLGI 112
>gnl|CDD|131292 TIGR02238, recomb_DMC1, meiotic recombinase Dmc1. This model
describes DMC1, a subfamily of a larger family of DNA
repair and recombination proteins. It is eukaryotic only
and most closely related to eukaryotic RAD51. It also
resembles archaeal RadA (TIGR02236) and RadB (TIGR02237)
and bacterial RecA (TIGR02012). It has been
characterized for human as a recombinase active only in
meiosis.
Length = 313
Score = 29.0 bits (65), Expect = 4.7
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 159 KLNE---RLSQEIESFKSGVYLSNQVSPDLTGPPTSQSAALK 197
KL + RL++ E F V+++NQV D T + K
Sbjct: 220 KLAQMLSRLNKISEEFNVAVFVTNQVQADPGATMTFIADPKK 261
>gnl|CDD|217155 pfam02633, Creatininase, Creatinine amidohydrolase. Creatinine
amidohydrolase (EC:3.5.2.10), or creatininase, catalyzes
the hydrolysis of creatinine to creatine.
Length = 222
Score = 28.3 bits (64), Expect = 5.9
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 2 FPGTMHIGYNRFRFLLECLADLDRQLKSHG-GQLFIV--QGSPISIFQKLKRELNFT 55
FPGT+ + LL D+ R L HG +L IV G I+ ++ REL
Sbjct: 59 FPGTISLSPETLLALLR---DIGRSLARHGFRRLVIVNGHGGNIAALKEAARELRAE 112
>gnl|CDD|130302 TIGR01235, pyruv_carbox, pyruvate carboxylase. This enzyme plays a
role in gluconeogensis but not glycolysis [Energy
metabolism, Glycolysis/gluconeogenesis].
Length = 1143
Score = 29.0 bits (65), Expect = 6.3
Identities = 21/103 (20%), Positives = 38/103 (36%), Gaps = 30/103 (29%)
Query: 101 KEDIDFRHVTFGTMSESLQREVSLFQTVPKPEQFHKYPEMDFGDPL----IRWLGGETEA 156
+D H +G +SE+ +F D I ++G + E
Sbjct: 72 LNGVDAIHPGYGFLSEN----------------------SEFADACNKAGIIFIGPKAEV 109
Query: 157 LIKLNERLSQEIESFKSGVYLSNQVSPDLTGPPTSQSAALKFG 199
+ +L ++++ + K+GV V P GPP + L F
Sbjct: 110 MDQLGDKVAARNLAIKAGV----PVVPGTDGPPETMEEVLDFA 148
>gnl|CDD|184146 PRK13565, PRK13565, anthranilate synthase component I;
Provisional.
Length = 490
Score = 28.7 bits (65), Expect = 7.2
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 15/40 (37%)
Query: 9 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKL 48
GYNR + E LADLD +P+S++ KL
Sbjct: 13 GYNRIPLVAEALADLD---------------TPLSLYLKL 37
>gnl|CDD|222967 PHA03060, PHA03060, Hypothetical protein; Provisional.
Length = 71
Score = 26.1 bits (57), Expect = 8.6
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 7/51 (13%)
Query: 237 YFYTMSAHNPYYDQMEKNPICLNIPWLPESHPNKEKYLNAWKNGQTGYPFI 287
Y + S+ P D+++K CLNI P S+ E YL YP I
Sbjct: 18 YNSSSSSSTPTKDEIKKYGYCLNIK-KPSSNDKSETYL------HNNYPSI 61
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
0.322 0.139 0.444
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,552,512
Number of extensions: 2102355
Number of successful extensions: 1742
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1725
Number of HSP's successfully gapped: 37
Length of query: 407
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 308
Effective length of database: 6,546,556
Effective search space: 2016339248
Effective search space used: 2016339248
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: 60 (27.0 bits)