RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11328
(410 letters)
>gnl|CDD|233041 TIGR00596, rad1, DNA repair protein (rad1). All proteins in this
family for which functions are known are components in a
multiprotein endonuclease complex (usually made up of
Rad1 and Rad10 homologs). This complex is used primarily
for nucleotide excision repair but also for some aspects
of recombinational repair in some species. Most Archaeal
species also have homologs of these genes, but the
function of these Archaeal genes is not known, so we
have set our cutoff to only pick up the eukaryotic
genes.This family is based on the phylogenomic analysis
of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA
metabolism, DNA replication, recombination, and repair].
Length = 814
Score = 322 bits (828), Expect = e-103
Identities = 143/323 (44%), Positives = 192/323 (59%), Gaps = 54/323 (16%)
Query: 6 LSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRR 65
L L L P VI Y D++ IRQ+EVY+ ++ ++V+F+ YG S+EEQ YL+ LRR
Sbjct: 468 LRCSLEELMPRYVIMYEPDISFIRQLEVYKASRPLRPLRVYFLYYGGSIEEQRYLTSLRR 527
Query: 66 EKKAFEYLIQEKTNMAVPTE-----------------QDGVSTEPEESCG---------- 98
EK AF LI+EK NM++P E ++ + G
Sbjct: 528 EKDAFTKLIREKANMSIPFETNEDLESKFLRLVNTRISKLRKSKTRNAGGQLGFANLTQP 587
Query: 99 RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLY 158
+VIVDMREFRS LP LLH+RG+ + P ++VGDYIL+PDICVERKSISDLIGSL +GRLY
Sbjct: 588 KVIVDMREFRSSLPSLLHRRGIRVIPCMLTVGDYILTPDICVERKSISDLIGSLNNGRLY 647
Query: 159 TQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLS 218
Q ++M R+YA P+LLIEFD NK F L+ P LS
Sbjct: 648 NQCEKMLRYYAYPVLLIEFDQNKSFSLE---------------------PR-----NDLS 681
Query: 219 RDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVASSIGQ- 277
++I++ ++DI KL LLTLHFPKLR+IWSS PY TA++F ELK G++EP A+++G
Sbjct: 682 QEISSVNNDIQQKLALLTLHFPKLRIIWSSSPYATAEIFEELKLGKEEPDPATAAALGSD 741
Query: 278 TPNEDYTDRYNAAIEDFISKLPG 300
++N +DF+ KLPG
Sbjct: 742 ENTTAEGLKFNDGPQDFLLKLPG 764
>gnl|CDD|224859 COG1948, MUS81, ERCC4-type nuclease [DNA replication,
recombination, and repair].
Length = 254
Score = 117 bits (294), Expect = 2e-30
Identities = 58/210 (27%), Positives = 91/210 (43%), Gaps = 42/210 (20%)
Query: 92 EPEESCG-RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIG 150
E VIVD RE RSE+P LL + G+ +E T+ VGDY++S D+ VERKSISD +
Sbjct: 21 EYRGEFEVVVIVDSRELRSEVPRLLKRLGVKVEVRTLEVGDYVVSDDVIVERKSISDFVS 80
Query: 151 SLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFE 210
S+ GRL+ Q +++ + Y +P+L++E D +
Sbjct: 81 SIIDGRLFEQAKRLKKSYERPVLIVEGDDS------------------------------ 110
Query: 211 LQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAE 270
SR + + L L + F L +IW+ P TA+L EL + E
Sbjct: 111 ------FSRRPKIHPNAVRGALASLAVDFG-LPVIWTRSPEETAELIHELARREQEERKR 163
Query: 271 VASSIGQTPNEDYTDRYNAAIEDFISKLPG 300
+ G+ + + + +PG
Sbjct: 164 SVNPHGKKKAKTLKEL----QLYILESIPG 189
>gnl|CDD|214888 smart00891, ERCC4, ERCC4 domain. This entry represents a
structural motif found in several DNA repair nucleases,
such as Rad1/Mus81/XPF endonucleases, and in
ATP-dependent helicases. The XPF/Rad1/Mus81-dependent
nuclease family specifically cleaves branched structures
generated during DNA repair, replication, and
recombination, and is essential for maintaining genome
stability. The nuclease domain architecture exhibits
remarkable similarity to those of restriction
endonucleases.
Length = 98
Score = 86.2 bits (214), Expect = 8e-21
Identities = 34/98 (34%), Positives = 51/98 (52%), Gaps = 19/98 (19%)
Query: 99 RVIVDMREFRSEL-----PVLLHKRGLYIEPVTISVGDYILSP-------------DICV 140
+IVD RE RS L L KRG+ +E + GD++L + V
Sbjct: 1 EIIVDSRELRSALEAPIPRSLRWKRGVKVEYDRLEAGDFVLVARDKQSLLPHVNSLNELV 60
Query: 141 ERKSISDLIGSLQSGRLYTQVQQMCR-HYAKPLLLIEF 177
ERKS++DL+ S+ GRL+ QV+++ + Y P LL+E
Sbjct: 61 ERKSLTDLVASIPDGRLFEQVRRLQQIAYPSPQLLVEG 98
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 93.8 bits (234), Expect = 1e-20
Identities = 47/145 (32%), Positives = 72/145 (49%), Gaps = 16/145 (11%)
Query: 51 GESVEEQAYLSDLRREKKAFEYLIQEKTNMAVPTEQDGVSTEPEESCGRVIVDMREFRSE 110
E +EQ L D + K E+ E+D + E E ++IVD RE RS
Sbjct: 522 EEEKDEQLSLDDFVKSKGK------EEEEEEEKEEKDKETEEDEPEGPKIIVDSRELRSN 575
Query: 111 LPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAK 170
+ L + G +E T+ VGDY++S + VERK+ D + S+ RL+ QV+ + R Y +
Sbjct: 576 VARHLKRLGAEVELKTLEVGDYVVSDRVAVERKTAEDFVDSIIDRRLFEQVKDLKRAYER 635
Query: 171 PLLLIEFDHNKPFELQGNYYLSRDI 195
P+L+IE G+ Y R+I
Sbjct: 636 PVLIIE----------GDLYTIRNI 650
>gnl|CDD|217207 pfam02732, ERCC4, ERCC4 domain. This domain is a family of
nucleases. The family includes EME1 which is an
essential component of a Holliday junction resolvase.
EME1 interacts with MUS81 to form a DNA
structure-specific endonuclease.
Length = 102
Score = 82.1 bits (203), Expect = 3e-19
Identities = 39/101 (38%), Positives = 56/101 (55%), Gaps = 22/101 (21%)
Query: 100 VIVDMREF-----RSELP-VLLHKRGLYIEPVTISVGDYILSP--------------DIC 139
+IVD RE RS +P L +RG+ +EP T+ VGDY+ +
Sbjct: 1 IIVDSRELLKSSERSPIPRSLRWRRGVKVEPCTLPVGDYLWLIKSALLDLQLDEGVLIVA 60
Query: 140 VERKSISDLIGSLQSGRLYTQVQQMCR--HYAKPLLLIEFD 178
VERK ++DLI SL+ GRL+ Q+Q++ R Y P+LL+E D
Sbjct: 61 VERKELADLISSLKDGRLFEQLQRLKRVSAYKAPVLLVEGD 101
>gnl|CDD|220958 pfam11055, Gsf2, Glucose signalling factor 2. Gsf2 is localised to
the ER and functions to promote the secretion of certain
hexose transporters.
Length = 376
Score = 34.3 bits (79), Expect = 0.11
Identities = 43/165 (26%), Positives = 58/165 (35%), Gaps = 30/165 (18%)
Query: 191 LSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWS--- 247
LSR + A I F K E L +I S +TA+ H K+ I+
Sbjct: 144 LSR-LLAPLAIRFGLPKVAEK-----LLEEIEVNSVGVTAQWLFFVFHIVKILFIFLFLY 197
Query: 248 SGPYNTAQLF-FELKQGRDE------PSAEVASSIG------QTPNEDYTDRYNAAIEDF 294
SG +N F L R + E S+G T ++Y + Y
Sbjct: 198 SGMFNPISFNPFRLTSVRKDVDPSNPELKEELISLGWTGARRATY-DEYKEYYYEYK--- 253
Query: 295 ISKLPGMAEWSRARTLN-LEVLGLNPGQGGNFLTEL---FRASSF 335
I K GM + RA G+ G G F T L F S+F
Sbjct: 254 IKKHGGMVQAHRAGLFKKAANPGVQLGAGEGFQTPLEERFTLSTF 298
>gnl|CDD|239131 cd02666, Peptidase_C19J, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 343
Score = 32.1 bits (73), Expect = 0.57
Identities = 33/127 (25%), Positives = 56/127 (44%), Gaps = 13/127 (10%)
Query: 1 MFAQDLSSKLRSLKPTSVIFYNADVAAIRQVEVYQC-----AQSEVKVK-VFFMQYGESV 54
+F + S RS+ P+ + Y A+RQ +V +C Q EV ++ + G
Sbjct: 73 LFNDLIHSNTRSVTPSKELAY----LALRQQDVTECIDNVLFQLEVALEPISNAFAGPDT 128
Query: 55 EEQAYLSDLRREKKAFEYLIQEKTNMAVPTEQDGVSTEPEESCGRVIVDMREFRSELPVL 114
E+ SDL K+ F +++ Q V T+ E ++VD+ + E+ VL
Sbjct: 129 EDDKEQSDL--IKRLFSGKTKQQLVPESMGNQPSVRTKTERFL-SLLVDVGKKGREIVVL 185
Query: 115 LHKRGLY 121
L + LY
Sbjct: 186 LEPKDLY 192
>gnl|CDD|234252 TIGR03545, TIGR03545, TIGR03545 family protein. This model
represents a relatively rare but broadly distributed
uncharacterized protein family, distributed in 1-2
percent of bacterial genomes, all of which have outer
membranes. In many of these genomes, it is part of a
two-gene pair.
Length = 555
Score = 31.6 bits (72), Expect = 0.89
Identities = 13/87 (14%), Positives = 29/87 (33%), Gaps = 4/87 (4%)
Query: 126 TISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHY---AKPLLL-IEFDHNK 181
D PD +++ +S + G + +V + + KP + + + +
Sbjct: 328 DYDFKDDNPYPDFLIKKADVSGKMPDGDVGEIKGEVSNITNDHDLLGKPTTINLSAEASG 387
Query: 182 PFELQGNYYLSRDIAAKFLIEFDHNKP 208
+L L + + D N P
Sbjct: 388 KGKLTVKGVLDLRQPGEQKADLDFNVP 414
>gnl|CDD|221717 pfam12694, MoCo_carrier, Putative molybdenum carrier. The
structure of proteins in this family contain central
beta strands with flanking alpha helices. The structure
is similar to that of a molybdenum cofactor carrier
protein.
Length = 145
Score = 30.2 bits (69), Expect = 1.1
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 7/44 (15%)
Query: 146 SD--LI---GSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFE 184
SD LI G L G T + R + KPLL+++ D + E
Sbjct: 64 SDGTLILTRGELSGGTALTV--EFARKHGKPLLVVDLDLPEDVE 105
>gnl|CDD|239982 cd04609, CBS_pair_PALP_assoc2, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
associated with the pyridoxal-phosphate (PALP) dependent
enzyme domain upstream. The vitamin B6 complex
comprises pyridoxine, pyridoxal, and pyridoxamine, as
well as the 5'-phosphate esters of pyridoxal (PALP) and
pyridoxamine, the last two being the biologically active
coenzyme derivatives. The members of the PALP family
are principally involved in the biosynthesis of amino
acids and amino acid-derived metabolites, but they are
also found in the biosynthetic pathways of amino sugars
and other amine-containing compounds. CBS is a small
domain originally identified in cystathionine
beta-synthase and subsequently found in a wide range of
different proteins. CBS domains usually come in tandem
repeats, which associate to form a so-called Bateman
domain or a CBS pair which is reflected in this model.
The interface between the two CBS domains forms a cleft
that is a potential ligand binding site. The CBS pair
coexists with a variety of other functional domains. It
has been proposed that the CBS domain may play a
regulatory role, although its exact function is unknown.
Length = 110
Score = 28.7 bits (65), Expect = 1.8
Identities = 11/27 (40%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 89 VSTEPEESCGRVIVDMREFR-SELPVL 114
VS P+++ + I MRE+ S+LPV+
Sbjct: 4 VSVAPDDTVSQAIERMREYGVSQLPVV 30
>gnl|CDD|236514 PRK09434, PRK09434, aminoimidazole riboside kinase; Provisional.
Length = 304
Score = 30.3 bits (69), Expect = 1.8
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 333 SSFFLLLFRIKPAPGRES---NPRPRVTSKNKA---AVLNRGSSLPALCKLSEQELCSLV 386
S+ F + RIK A G S N R + +++A L + +L + KLSE+ELC L
Sbjct: 137 STTFEAMRRIKAAGGFVSFDPNLREDLW-QDEAELRECLRQALALADVVKLSEEELCFLS 195
Query: 387 ENTTLGNALYK 397
+ L +A+Y
Sbjct: 196 GTSQLEDAIYA 206
>gnl|CDD|168300 PRK05934, PRK05934, type III secretion system protein; Validated.
Length = 341
Score = 30.2 bits (68), Expect = 1.9
Identities = 28/105 (26%), Positives = 48/105 (45%), Gaps = 17/105 (16%)
Query: 52 ESVEEQAYLSDLRREKKAFEYLIQEKTNMAVPTEQDGVSTEPEESCGRVIVDMREFRSEL 111
+ +E A L ++ F + Q +++ TE D +S E S VI+ + + +
Sbjct: 65 KLIESLAKKEQLEKDLTMFHPVAQATVALSLETEDDPMSP-AEIS---VILSLPKAETLS 120
Query: 112 PVLLHKRGLYIEPVTISVGDYILS--PDICVERKSISDLIGSLQS 154
P LLH S+ DY+ S P + E ++SD +G+L S
Sbjct: 121 PSLLH-----------SITDYLTSSVPGLTKEHITLSDNLGNLYS 154
>gnl|CDD|222678 pfam14321, DUF4382, Domain of unknown function (DUF4382). This
family is found in bacteria and archaea, and is
typically between 142 and 161 amino acids in length.
Length = 138
Score = 28.0 bits (63), Expect = 4.8
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 183 FELQGNYYLSRDIAAKFLIEFDHNKPFELQGN 214
++ G + + +A +I+FD K L GN
Sbjct: 100 LKIIGPFTVQAGSSAALVIDFDLRKSIVLTGN 131
>gnl|CDD|215168 PLN02299, PLN02299, 1-aminocyclopropane-1-carboxylate oxidase.
Length = 321
Score = 28.6 bits (64), Expect = 6.0
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 12/65 (18%)
Query: 272 ASSIGQTPNEDYTDRYNAAIEDFISKLPGMAEWSRARTLNL--EVLGLNPGQGGNFLTEL 329
S++ P D D Y ++DF +L +AE L+L E LGL G +L +
Sbjct: 100 ESNLADIP--DLDDEYRKVMKDFALELEKLAE----ELLDLLCENLGLEKG----YLKKA 149
Query: 330 FRASS 334
F S
Sbjct: 150 FHGSK 154
>gnl|CDD|132264 TIGR03220, catechol_dmpE, 2-oxopent-4-enoate hydratase. Members of
this protein family are 2-oxopent-4-enoate hydratase,
which is also called 2-hydroxypent-2,4-dienoate
hydratase. It is closely related to another gene found
in the same operon, 4-oxalocrotonate decarboxylase, with
which it interacts closely.
Length = 255
Score = 28.2 bits (63), Expect = 7.3
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 389 TTLGNALYKALHTRPEVS 406
T LG+ LY+AL TR V+
Sbjct: 3 TQLGDELYQALVTRTPVA 20
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
0.318 0.134 0.384
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,657,233
Number of extensions: 1997258
Number of successful extensions: 1541
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1534
Number of HSP's successfully gapped: 23
Length of query: 410
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 311
Effective length of database: 6,546,556
Effective search space: 2035978916
Effective search space used: 2035978916
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.9 bits)