RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17626
(184 letters)
>gnl|CDD|216167 pfam00875, DNA_photolyase, DNA photolyase. This domain binds a
light harvesting cofactor.
Length = 164
Score = 100 bits (251), Expect = 3e-27
Identities = 36/118 (30%), Positives = 52/118 (44%), Gaps = 1/118 (0%)
Query: 1 MFPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFE 60
G+ +G R FLLE LADLD L G +L + +G P + +L +EL + + +
Sbjct: 36 AQLGSHKLGAARRWFLLESLADLDESLAKLGIRLVVRRGDPAEVLPELAKELGASAVYWN 95
Query: 61 QDCEALWHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMYLHTV 118
+D E +RD VK+ E I V F H L P V T P + +
Sbjct: 96 RDYEPYERQRDAAVKEALREAGIEVHSFDDHLLVPPGEV-LTKKGKPYKVFTPFWKAW 152
Score = 59.5 bits (145), Expect = 1e-11
Identities = 23/63 (36%), Positives = 35/63 (55%)
Query: 122 GTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDC 181
G+ +G R FLLE LADLD L G +L + +G P + +L +EL + + + +D
Sbjct: 39 GSHKLGAARRWFLLESLADLDESLAKLGIRLVVRRGDPAEVLPELAKELGASAVYWNRDY 98
Query: 182 EAY 184
E Y
Sbjct: 99 EPY 101
>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication,
recombination, and repair].
Length = 461
Score = 56.2 bits (136), Expect = 1e-09
Identities = 26/98 (26%), Positives = 42/98 (42%)
Query: 7 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAL 66
H FLL+ L L + L G L + +G P + +L ++L T + + +D E
Sbjct: 44 HASPRHAAFLLQSLQALQQSLAELGIPLLVREGDPEQVLPELAKQLAATTVFWNRDYEEW 103
Query: 67 WHKRDKKVKKWCAENNITVKEFVSHTLWDPEVVIQTNG 104
+RD + + E I V F L +P V +G
Sbjct: 104 ERQRDAALAQPLTEVGIAVHSFWDALLHEPGEVRTGSG 141
Score = 37.7 bits (88), Expect = 0.002
Identities = 16/60 (26%), Positives = 28/60 (46%)
Query: 125 HIGYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY 184
H FLL+ L L + L G L + +G P + +L ++L T + + +D E +
Sbjct: 44 HASPRHAAFLLQSLQALQQSLAELGIPLLVREGDPEQVLPELAKQLAATTVFWNRDYEEW 103
>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 = 53.9 bits (130), Expect = 6e-09
Identities = 23/88 (26%), Positives = 40/88 (45%)
Query: 9 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWH 68
G R +FLLE L DL L+ G L + G P + +L +EL + Q+ +
Sbjct: 52 GPARGKFLLESLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFLHQEVGSEEK 111
Query: 69 KRDKKVKKWCAENNITVKEFVSHTLWDP 96
++ +++ A I V++ TL+
Sbjct: 112 SVERLLQQALARLGIHVEQHWGSTLYHE 139
Score = 43.9 bits (104), Expect = 2e-05
Identities = 18/53 (33%), Positives = 25/53 (47%)
Query: 127 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQ 179
G R +FLLE L DL L+ G L + G P + +L +EL + Q
Sbjct: 52 GPARGKFLLESLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFLHQ 104
>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 = 51.4 bits (123), Expect = 5e-08
Identities = 30/103 (29%), Positives = 47/103 (45%), Gaps = 4/103 (3%)
Query: 12 RFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEALWHKRD 71
R +L+ CL +L ++ + G QL I+QG P+ + +L ++L + + D E KRD
Sbjct: 49 RVAYLIGCLQELQQRYQQAGSQLLILQGDPVQLIPQLAQQLGAKAVYWNLDVEPYGRKRD 108
Query: 72 KKVKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMY 114
+ V E I V L P+ I T P Y +Y
Sbjct: 109 RAVAAALKEAGIAVVTLWDQLLHSPD-EILTGSGNP---YTVY 147
Score = 38.7 bits (90), Expect = 0.001
Identities = 17/55 (30%), Positives = 31/55 (56%)
Query: 130 RFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKLCFEQDCEAY 184
R +L+ CL +L ++ + G QL I+QG P+ + +L ++L + + D E Y
Sbjct: 49 RVAYLIGCLQELQQRYQQAGSQLLILQGDPVQLIPQLAQQLGAKAVYWNLDVEPY 103
>gnl|CDD|223634 COG0560, SerB, Phosphoserine phosphatase [Amino acid transport and
metabolism].
Length = 212
Score = 33.0 bits (76), Expect = 0.044
Identities = 15/86 (17%), Positives = 29/86 (33%), Gaps = 15/86 (17%)
Query: 25 RQLKSHGGQLFIVQGSPISIFQKLKRELNFTKL---CFEQDCEAL--------WHKRDK- 72
LK+ G ++ I+ G + + + L + E D L K
Sbjct: 87 AALKAAGAKVVIISGGFTFLVEPIAERLGIDYVVANELEIDDGKLTGRVVGPICDGEGKA 146
Query: 73 -KVKKWCAENNITVKE--FVSHTLWD 95
+++ AE I ++E + D
Sbjct: 147 KALRELAAELGIPLEETVAYGDSAND 172
Score = 30.3 bits (69), Expect = 0.47
Identities = 6/31 (19%), Positives = 13/31 (41%)
Query: 143 RQLKSHGGQLFIVQGSPISIFQKLKRELNFT 173
LK+ G ++ I+ G + + + L
Sbjct: 87 AALKAAGAKVVIISGGFTFLVEPIAERLGID 117
>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 = 32.5 bits (74), Expect = 0.094
Identities = 24/101 (23%), Positives = 44/101 (43%), Gaps = 2/101 (1%)
Query: 15 FLLECLADLDRQLKSHGGQLFIVQG-SPISIFQKLKRELNFTKLCFEQDCEALWHKRDKK 73
+L + LA LD+ L+S G L ++ ++ R T+L F + + RD +
Sbjct: 48 WLKQSLAHLDQSLRSLGTCLVTIRSTDTVAALLDCVRSTGATRLFFNHLYDPVSLVRDHR 107
Query: 74 VKKWCAENNITVKEFVSHTLWDPEVVIQTNGNVPPLTYKMY 114
K+ I+V+ F + L++P V G P + +
Sbjct: 108 AKEVLTAQGISVQSFNADLLYEPWEVYDELGR-PFTMFAAF 147
>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 = 30.8 bits (70), Expect = 0.25
Identities = 16/79 (20%), Positives = 26/79 (32%), Gaps = 17/79 (21%)
Query: 25 RQLKSHGGQLFIVQGSPISIFQKLKRELNF-----TKLCF-----------EQDCEALWH 68
LK G IV G + + +L +L F Q
Sbjct: 83 SWLKERGIDTVIVSGGFDFFVEPVAEKLGIDDVFANRLEFDDNGLLTGPIEGQVNP-EGE 141
Query: 69 KRDKKVKKWCAENNITVKE 87
+ K +K+ E+ IT+K+
Sbjct: 142 CKGKVLKELLEESKITLKK 160
Score = 28.5 bits (64), Expect = 1.7
Identities = 7/30 (23%), Positives = 10/30 (33%)
Query: 143 RQLKSHGGQLFIVQGSPISIFQKLKRELNF 172
LK G IV G + + +L
Sbjct: 83 SWLKERGIDTVIVSGGFDFFVEPVAEKLGI 112
>gnl|CDD|233436 TIGR01490, HAD-SF-IB-hyp1, HAD-superfamily subfamily IB hydrolase,
TIGR01490. This hypothetical equivalog is a member of
the IB subfamily (TIGR01488) of the haloacid
dehalogenase (HAD) superfamily of aspartate-nucleophile
hydrolases. The sequences modelled by This model are all
bacterial. The IB subfamily includes the enzyme
phosphoserine phosphatase (TIGR00338). Due to this
relationship, several of these sequences have been
annotated as "phosphoserine phosphatase related
proteins," or "Phosphoserine phosphatase-family
enzymes." There is presently no evidence that any of the
enzymes in This model possess PSPase activity.
OMNI|NTL01ML1250 is annotated as a "possible
transferase," however this is due to the C-terminal
domain found on this sequence which is homologous to a
group of glycerol-phosphate acyltransferases (between
trusted and noise to TIGR00530). A subset of these
sequences including OMNI|CC1962, the Caulobacter
crescentus CicA protein cluster together and may
represent a separate equivalog [Unknown function,
Enzymes of unknown specificity].
Length = 202
Score = 30.0 bits (68), Expect = 0.48
Identities = 15/81 (18%), Positives = 25/81 (30%), Gaps = 14/81 (17%)
Query: 21 ADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFTKL------CFEQDC-------EALW 67
DL R K+ G + +V S + + L R L E
Sbjct: 93 RDLIRWHKAEGHTIVLVSASLTILVKPLARILGIDNAIGTRLEESEDGIYTGNIDGNNCK 152
Query: 68 HKRD-KKVKKWCAENNITVKE 87
+ + + AE I +K+
Sbjct: 153 GEGKVHALAELLAEEQIDLKD 173
Score = 26.9 bits (60), Expect = 5.2
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 139 ADLDRQLKSHGGQLFIVQGSPISIFQKLKRELNFT 173
DL R K+ G + +V S + + L R L
Sbjct: 93 RDLIRWHKAEGHTIVLVSASLTILVKPLARILGID 127
>gnl|CDD|227823 COG5536, BET4, Protein prenyltransferase, alpha subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 328
Score = 29.8 bits (67), Expect = 0.82
Identities = 13/62 (20%), Positives = 21/62 (33%), Gaps = 9/62 (14%)
Query: 46 QKLKRELNFTKLCFEQDCEAL--WHKRDKKVKKWCAEN--NITVKEFVSHTLWDPEVVIQ 101
REL TK + D W R +W ++ + H L +I+
Sbjct: 124 PSWGRELFITKKLLDSDSRNYHVWSYR-----RWVLRTIEDLFNFSDLKHELEYTTSLIE 178
Query: 102 TN 103
T+
Sbjct: 179 TD 180
>gnl|CDD|184146 PRK13565, PRK13565, anthranilate synthase component I;
Provisional.
Length = 490
Score = 29.5 bits (67), Expect = 1.1
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
Score = 29.5 bits (67), Expect = 1.1
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 15/40 (37%)
Query: 127 GYNRFRFLLECLADLDRQLKSHGGQLFIVQGSPISIFQKL 166
GYNR + E LADLD +P+S++ KL
Sbjct: 13 GYNRIPLVAEALADLD---------------TPLSLYLKL 37
>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 = 28.7 bits (65), Expect = 1.6
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|224320 COG1402, COG1402, Uncharacterized protein, putative amidase
[General function prediction only].
Length = 250
Score = 28.1 bits (63), Expect = 2.6
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 2 FPGTMHIGYNRFRFLLECLADLDRQLKSHGGQLFIV 37
FPGT+ + LL +L L HG + F++
Sbjct: 77 FPGTITLSPETLIALLV---ELVESLARHGFRKFVI 109
>gnl|CDD|119174 pfam10654, DUF2481, Protein of unknown function (DUF2481). This
is a hypothetical protein family homologous to Lmo2305
in Bacteriophage A118 systems.
Length = 126
Score = 26.4 bits (58), Expect = 6.6
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 41 PISIFQKLKRELN-FTKLCFEQDCEALWHKRDKKV---KKWCAENNITVKEFV 89
P++ ++L++ELN E+ + W K ++ K W IT+ EFV
Sbjct: 25 PLAERKELQKELNQLMNENTEEKQKTYWKKTFDRIVGNKNW---EEITIIEFV 74
>gnl|CDD|223342 COG0264, Tsf, Translation elongation factor Ts [Translation,
ribosomal structure and biogenesis].
Length = 296
Score = 26.5 bits (59), Expect = 8.7
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 71 DKKVKKWCAENNITVKEFV 89
K V++ E N V EFV
Sbjct: 253 KKTVEQLLKEANAKVTEFV 271
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
0.327 0.142 0.455
Gapped
Lambda K H
0.267 0.0617 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,367,835
Number of extensions: 852067
Number of successful extensions: 1100
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1099
Number of HSP's successfully gapped: 36
Length of query: 184
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 93
Effective length of database: 6,901,388
Effective search space: 641829084
Effective search space used: 641829084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 56 (25.6 bits)