RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11969
(170 letters)
>gnl|CDD|128778 smart00502, BBC, B-Box C-terminal domain. Coiled coil region
C-terminal to (some) B-Box domains.
Length = 127
Score = 64.6 bits (158), Expect = 5e-14
Identities = 34/110 (30%), Positives = 58/110 (52%)
Query: 61 DLSQNLQLLSEKARSTTEFIKRLKSIADLLNDNSIEFESQIVAQCDALIKAIEDRKKQLV 120
L + L L +KA + +K+L SI + +N+ + E+QI A D L A+ RKKQL+
Sbjct: 4 ALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLL 63
Query: 121 DAIRLEKESKQRILREQVSGCACKLQRTTALLQFCIEALKETDAAAFLQF 170
+ + +KE+K ++L +Q+ K ++ + + F EAL D L
Sbjct: 64 EDLEEQKENKLKVLEQQLESLTQKQEKLSHAINFTEEALNSGDPTELLLS 113
>gnl|CDD|224380 COG1463, Ttg2C, ABC-type transport system involved in resistance to
organic solvents, periplasmic component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 359
Score = 34.4 bits (79), Expect = 0.020
Identities = 17/94 (18%), Positives = 32/94 (34%), Gaps = 12/94 (12%)
Query: 30 LSQNLQLLSEKARSTTEFIKRLKSIADLLNTDLSQNLQLLSEKARSTTEFIKRLKSIADL 89
L++ L+ + L D LN ++ I L + D
Sbjct: 164 LNEAAAALAGTGPQLNALLDNLAQFTDALN-ARDGDI----------GALIANLNQLLDS 212
Query: 90 LNDNSIEFESQIVAQCDALIKAIEDRKKQLVDAI 123
L S + + +++ L A+ R+ L DA+
Sbjct: 213 LAAASDQLD-RLLDNLATLTAALAARRDALDDAL 245
Score = 28.2 bits (63), Expect = 2.4
Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 1/69 (1%)
Query: 54 IADLLNTDLSQNLQLLSEKARSTTEFIKRLKSIADLLNDNSIEFESQIVAQCDALIKAIE 113
D LN L++ L+ + L D LN + ++A + L+ ++
Sbjct: 156 DPDRLNAILNEAAAALAGTGPQLNALLDNLAQFTDALNARDGDI-GALIANLNQLLDSLA 214
Query: 114 DRKKQLVDA 122
QL
Sbjct: 215 AASDQLDRL 223
>gnl|CDD|235168 PRK03868, PRK03868, glucose-6-phosphate isomerase; Provisional.
Length = 410
Score = 33.0 bits (76), Expect = 0.059
Identities = 31/95 (32%), Positives = 41/95 (43%), Gaps = 21/95 (22%)
Query: 34 LQLLSEKAR-STTEFIKRLKSIADLLNTDLSQNLQLLSEKARSTTEFIKRLKSIADLLND 92
LQL+ E R T FIK I D N N+ L K + +F+
Sbjct: 288 LQLIMEGPRDKTVTFIK----IKDFQNAPKIPNISL---KGLESLDFV------------ 328
Query: 93 NSIEFESQIVAQCDALIKAIEDRKKQLVDAIRLEK 127
N + F I AQCDA ++A+ + VD I LEK
Sbjct: 329 NGVSFNELINAQCDATMEALIA-EDIPVDVITLEK 362
>gnl|CDD|180319 PRK05945, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 575
Score = 29.7 bits (67), Expect = 0.79
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 17/72 (23%)
Query: 107 ALIKAIEDRKKQLVDAIRLEKESKQRI--------------LREQVSGCA---CKLQRTT 149
A+ + ++ RK VD R KE+KQRI LR+Q C C + RT
Sbjct: 408 AIAEYVQGRKLPEVDEQRYLKEAKQRIQALLDQSGTYRINQLRQQFQDCMTDHCGVFRTE 467
Query: 150 ALLQFCIEALKE 161
++Q +E +++
Sbjct: 468 EIMQEGLEKIQQ 479
>gnl|CDD|235561 PRK05686, fliG, flagellar motor switch protein G; Validated.
Length = 339
Score = 28.2 bits (64), Expect = 1.9
Identities = 20/97 (20%), Positives = 44/97 (45%), Gaps = 25/97 (25%)
Query: 51 LKSIADLLNTDLSQNLQLLSEKARSTTEFIKRLKSIADLLNDNSIEFESQIVAQCDALIK 110
LK + ++L LS +++ + +K++A++LN + Q +++
Sbjct: 179 LKEVEEVLEKKLSS--MANADRTKMGG-----VKTVAEILN----NLDRQTE---KTILE 224
Query: 111 AIEDRKKQLVDAIR-----------LEKESKQRILRE 136
++E+ +L + I+ L+ S QR+LRE
Sbjct: 225 SLEEEDPELAEKIKDLMFVFEDLVDLDDRSIQRLLRE 261
>gnl|CDD|234096 TIGR03031, cas_csx12, CRISPR-associated protein Cas9/Csx12, subtype
II-B/NMENI. Members of this family of CRISPR-associated
(cas) protein are found, so far, in CRISPR/cas loci in
Wolinella succinogenes DSM 1740, Legionella pneumophila
str. Paris, and Francisella tularensis, where the last
probably is an example of a degenerate CRISPR locus,
having neither repeats nor a functional Cas1. The
characteristic repeat length is 37 base pairs and period
is about 72. One region of this large protein shows
sequence similarity to pfam01844, HNH endonuclease
[Mobile and extrachromosomal element functions, Other].
Length = 802
Score = 28.0 bits (62), Expect = 2.6
Identities = 19/91 (20%), Positives = 44/91 (48%), Gaps = 6/91 (6%)
Query: 49 KRLKSIADLLNTDLSQNLQLLSEKARSTTEFIKRLKSIADLLNDNSIEFESQIVAQCDAL 108
+ + +LL L L+ +SE F+++++S AD L + S EF +V++ +
Sbjct: 109 IKDATEINLLKELLPFKLRSISEDNFID-WFLQKIQSSADYLANYSEEFRKILVSKTEE- 166
Query: 109 IKAIEDRKKQLVDAIRLEKESKQRILREQVS 139
+ K+L +A++ + K+ + ++
Sbjct: 167 ----KKDDKELKNAVKDKYNIKEFLTGATIN 193
>gnl|CDD|130044 TIGR00971, 3a0106s03, sulfate/thiosulfate-binding protein. This
model describes binding proteins functionally associated
with the sulfate ABC transporter. In the model bacterium
E. coli, two different members work with the same
transporter; mutation analysis says each enables the
uptake of both sulfate and thiosulfate. In many species,
a single binding protein is found, and may be referred
to in general terms as a sulfate ABC transporter
sulfate-binding protein [Transport and binding proteins,
Anions].
Length = 315
Score = 28.0 bits (62), Expect = 2.8
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 55 ADLLNTDLSQNLQLLSEKARSTTEFIKRLKSIADLLNDNSIEFESQIV 102
AD++ L+ ++ ++E+ R ++IKRL DNS + S IV
Sbjct: 66 ADVVTLALAYDVDAIAERGRIDKDWIKRLP-------DNSAPYTSTIV 106
>gnl|CDD|178602 PLN03034, PLN03034, phosphoglycerate kinase; Provisional.
Length = 481
Score = 28.0 bits (62), Expect = 2.8
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 30 LSQNLQLLSEKARSTTEFIKRLKSIADLLNTDLSQNLQLLSEKARSTTEFIKRLKSIADL 89
L +N++ E+ ++ EF K+L S+ADL D T+F+K S+A
Sbjct: 192 LLENVRFYKEEEKNEPEFAKKLASLADLYVNDAFGTAHRAHASTEGVTKFLK--PSVAGF 249
Query: 90 LNDNSIEF 97
L +++
Sbjct: 250 LLQKELDY 257
>gnl|CDD|217701 pfam03732, Retrotrans_gag, Retrotransposon gag protein. Gag or
Capsid-like proteins from LTR retrotransposons. There is
a central motif QGXXEXXXXXFXXLXXH that is common to
Retroviridae gag-proteins, but is poorly conserved.
Length = 97
Score = 26.9 bits (60), Expect = 2.9
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 6/62 (9%)
Query: 44 TTEFIKR-LKSIA-DLLNTDLSQNLQLLSEKARSTTEFIKRLKSIADLLNDNSIEFESQI 101
F+KR SI DLL +L L + S E+++R K +A L + + E+ I
Sbjct: 33 KDAFLKRFFPSIRKDLLENELRS----LRQGTESVREYVERFKRLARQLPHHGFDEEALI 88
Query: 102 VA 103
A
Sbjct: 89 SA 90
>gnl|CDD|146915 pfam04513, Baculo_PEP_C, Baculovirus polyhedron envelope protein,
PEP, C terminus. Polyhedra are large crystalline
occlusion bodies containing nucleopolyhedrovirus
virions, and surrounded by an electron-dense structure
called the polyhedron envelope or polyhedron calyx. The
polyhedron envelope (associated) protein PEP is thought
to be an integral part of the polyhedron envelope. PEP
is concentrated at the surface of polyhedra, and is
thought to be important for the proper formation of the
periphery of polyhedra. It is thought that PEP may
stabilise polyhedra and protect them from fusion or
aggregation.
Length = 140
Score = 27.3 bits (61), Expect = 2.9
Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 4/77 (5%)
Query: 58 LNTDLSQNLQLLSEKARSTTEFIKRLKSIADLLNDNSIEFESQIVAQCDALIKAIEDRKK 117
LN QN+Q+ ++ +L ++ L + ++++ L A+
Sbjct: 22 LNAIRLQNVQIAAQLTTLLDAIQTQLNDLSTDLTSLLADLDTRLDTLLTNLTDAL----N 77
Query: 118 QLVDAIRLEKESKQRIL 134
QL D +R E + IL
Sbjct: 78 QLQDTLRNELTNLNSIL 94
>gnl|CDD|232867 TIGR00194, uvrC, excinuclease ABC, C subunit. This family consists
of the DNA repair enzyme UvrC, an ABC excinuclease
subunit which interacts with the UvrA/UvrB complex to
excise UV-damaged nucleotide segments [DNA metabolism,
DNA replication, recombination, and repair].
Length = 574
Score = 28.1 bits (63), Expect = 2.9
Identities = 19/71 (26%), Positives = 26/71 (36%), Gaps = 1/71 (1%)
Query: 22 LVFKLLTDLSQNLQLLSE-KARSTTEFIKRLKSIADLLNTDLSQNLQLLSEKARSTTEFI 80
LV L DL LLSE + R + LL + L +K
Sbjct: 307 LVSLSLEDLKLLEDLLSEQRGRKINVHQPKKGDKKKLLELAIKNAKYALKQKWTQFERKT 366
Query: 81 KRLKSIADLLN 91
+ L+ +A LLN
Sbjct: 367 QALEDLASLLN 377
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 27.3 bits (61), Expect = 4.4
Identities = 35/133 (26%), Positives = 57/133 (42%), Gaps = 31/133 (23%)
Query: 30 LSQNLQLLSEKARSTTEF---IKRLKSIADLLNTDLSQNLQLLSEKAR---------STT 77
+ L+ + + + +EF ++ LK++ + L L +NLQ L EK + S T
Sbjct: 301 ALEELESILDTEKENSEFKLDVEELKALLEALEEILEKNLQKLEEKLKDPSTSIELESIT 360
Query: 78 EFIKRLKSIADLLND-----NSI-------------EFESQIVAQCDALIKAIEDRKKQL 119
+ I+ + I D +N+ N + +VA+ I A + KK L
Sbjct: 361 DLIESINDIIDAINELIREHNEKIDNLKKEKNKAKKKLWLHLVAELKEDIDAYQKEKKGL 420
Query: 120 VDAI-RLEKESKQ 131
AI LEKE KQ
Sbjct: 421 EKAINSLEKEIKQ 433
>gnl|CDD|232823 TIGR00097, HMP-P_kinase, phosphomethylpyrimidine kinase. This
model represents phosphomethylpyrimidine kinase, the
ThiD protein of thiamine biosynthesis. The protein is
commonly observed within operons containing other
thiamine biosynthesis genes. Numerous examples are
fusion proteins with other thiamine-biosynthetic
domains. Saccaromyces has three recent paralogs, two of
which are isofunctional and score above the trusted
cutoff. The third shows a longer branch length in a
phylogenetic tree and scores below the trusted cutoff,
as do putative second copies in a number of species
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Thiamine].
Length = 254
Score = 26.9 bits (60), Expect = 5.1
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 2/60 (3%)
Query: 36 LLSEKARSTTEFIKRLKSIADLLNTDLSQNLQLLSEKARSTTEFIKRLKSIADLLNDNSI 95
LL E+A KRL +A L+ +L + LL K R+ + IK K + +L +
Sbjct: 111 LLEEEAIEA--LRKRLLPLATLITPNLPEAEALLGTKIRTEQDMIKAAKKLRELGPKAVL 168
>gnl|CDD|129266 TIGR00162, TIGR00162, TIGR00162 family protein. This model
represents one out of two closely related ortholgous
sets of proteins that, so far, are found only in but are
universal among the Archaea. This ortholog set includes
MJ1210 from Methanococcus jannaschii and AF0525 from
Archaeoglobus fulgidus while excluding MJ0106 and AF1251
[Hypothetical proteins, Conserved].
Length = 188
Score = 26.7 bits (59), Expect = 5.3
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 15 PSAYKAAL-VFKLLTDLSQNLQLLSEKARSTTEFIKRLK 52
P A KA L V + L +++ L E+A+ + I ++K
Sbjct: 127 PKAAKAVLEVLCKMLSLEVSVEALEERAKEMEKIIAKIK 165
>gnl|CDD|237505 PRK13783, PRK13783, adenylosuccinate synthetase; Provisional.
Length = 404
Score = 27.0 bits (60), Expect = 6.1
Identities = 13/61 (21%), Positives = 23/61 (37%)
Query: 39 EKARSTTEFIKRLKSIADLLNTDLSQNLQLLSEKARSTTEFIKRLKSIADLLNDNSIEFE 98
EK R E I L + D+ + ++ L + + I +L + S+ FE
Sbjct: 153 EKLREFLEKILSLYKKLYGIEFDVEKMMEDLLTFYEKIKDLVVSPVEIKRILEEKSVLFE 212
Query: 99 S 99
Sbjct: 213 G 213
>gnl|CDD|165923 PLN02282, PLN02282, phosphoglycerate kinase.
Length = 401
Score = 26.9 bits (59), Expect = 6.8
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 6/70 (8%)
Query: 30 LSQNLQLLSEKARSTTEFIKRLKSIADLLNTDLSQNLQLLSEKARSTTEFI-KRLK-SIA 87
L +N++ E+ ++ EF K+L S+AD+ D + +A ++TE + K LK S+A
Sbjct: 117 LLENVRFYKEEEKNDPEFAKKLASLADVYVNDAFGT----AHRAHASTEGVAKYLKPSVA 172
Query: 88 DLLNDNSIEF 97
L +++
Sbjct: 173 GFLMQKELDY 182
>gnl|CDD|161783 TIGR00237, xseA, exodeoxyribonuclease VII, large subunit. This
family consist of exodeoxyribonuclease VII, large
subunit XseA which catalyses exonucleolytic cleavage in
either the 5'->3' or 3'->5' direction to yield
5'-phosphomononucleotides. Exonuclease VII consists of
one large subunit and four small subunits [DNA
metabolism, Degradation of DNA].
Length = 432
Score = 26.7 bits (59), Expect = 6.9
Identities = 21/119 (17%), Positives = 42/119 (35%), Gaps = 8/119 (6%)
Query: 42 RSTTEFIKRLKSIADLLNTDLSQNLQLLSEKARSTTEFIKRLK--SIADLLNDNSIEFES 99
+ E ++RL L+ LL +K + + L+ + L ++FE
Sbjct: 255 PNQDELLQRLDGFNVRLHRAFDT---LLHQKKARLEQLVASLQRQHPQNKLALQQLQFE- 310
Query: 100 QIVAQCDALIKAIEDRKKQLVDAIRLEKESKQRILREQVSGCACKLQRTTALLQFCIEA 158
++ + A + +R +Q RL K Q Q+ + ++ L A
Sbjct: 311 KLEKRKQAALNKQLERTRQKKT--RLTKRLTQTNPSPQILRAQTRTEQLNRRLNALKNA 367
>gnl|CDD|187797 cd09666, Cas8a2_I-A, CRISPR/Cas system-associated protein Csa8a2.
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-A subtype; also
known as Csa4 family.
Length = 352
Score = 26.7 bits (59), Expect = 7.6
Identities = 31/141 (21%), Positives = 51/141 (36%), Gaps = 17/141 (12%)
Query: 4 KVLIRRESTPRPSAYKAALVFKLLTDLSQNLQLLSEKARS----TTEFIKRLKSIADLLN 59
K++ R S A L L T+ +L++E T E + + D
Sbjct: 213 KIMPYILFHFRISNELALLYHLLYTESLGETELVTESHFEVLSYTLEVSGNNQRVRDFGE 272
Query: 60 TDLSQNLQLLSE-KARSTTEFIKRLKSIADLLNDNSIEFESQIVAQCDALIKAIE-DRKK 117
DL + ++ KAR + K + +A + S+ L AI ++
Sbjct: 273 LDLGVLMDFIAYLKARDFYSWPKFVDFLARRDPEISL-----------QLTDAILNGDEE 321
Query: 118 QLVDAIRLEKESKQRILREQV 138
A+R K+S R EQV
Sbjct: 322 AFYTALRELKKSGVRYDPEQV 342
>gnl|CDD|225086 COG2175, TauD, Probable taurine catabolism dioxygenase [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 286
Score = 26.2 bits (58), Expect = 8.5
Identities = 11/76 (14%), Positives = 23/76 (30%), Gaps = 3/76 (3%)
Query: 60 TDLSQNLQLLSEKARSTTEFIKRLKSIADLLNDNSIEFESQIVAQCDALIKAIEDRKKQL 119
D + + L E R E ++ L + E S+ + +
Sbjct: 132 ADTAAAYETLPEPLR---ELLRGLPAHHSNEERFPRERPSKTERPHARFREIVRKNPPTE 188
Query: 120 VDAIRLEKESKQRILR 135
+R E+ ++ L
Sbjct: 189 HPVVRTHPETGEKALF 204
>gnl|CDD|181490 PRK08588, PRK08588, succinyl-diaminopimelate desuccinylase;
Reviewed.
Length = 377
Score = 26.4 bits (59), Expect = 9.9
Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 14/86 (16%)
Query: 42 RSTTEF-----IKRLKSIADLLNTDLSQNLQL---LSEKARSTT---EFIKRLKSIADLL 90
R+ E+ I L+ I + +N + + L L + + ++ + ++ K +A
Sbjct: 251 RTIPEYDNDQVISLLQEIINEVNQNGAAQLSLDIYSNHRPVASDKDSKLVQLAKDVAKSY 310
Query: 91 NDNSIEFESQIVAQCDA--LIKAIED 114
I + I DA +K D
Sbjct: 311 VGQDIPLSA-IPGATDASSFLKKKPD 335
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
0.320 0.131 0.343
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,173,871
Number of extensions: 737462
Number of successful extensions: 1215
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1195
Number of HSP's successfully gapped: 150
Length of query: 170
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 80
Effective length of database: 6,945,742
Effective search space: 555659360
Effective search space used: 555659360
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: 55 (24.9 bits)