RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12840
(469 letters)
>gnl|CDD|218156 pfam04577, DUF563, Protein of unknown function (DUF563). Family of
uncharacterized proteins.
Length = 206
Score = 81.3 bits (201), Expect = 1e-17
Identities = 46/228 (20%), Positives = 79/228 (34%), Gaps = 30/228 (13%)
Query: 184 NMYHHFCDFFN-LYASQHVNASHPDVFSTDVHIMIWESYTYASAFADTFRAFTRHPVWDL 242
N H DF L+ + + + F + +
Sbjct: 2 NFGHWLLDFLPRLWLLPEEILDDDIIV---LIPDSGSPPPFIREFLELL-GIPED---RI 54
Query: 243 KTFTGLTVCFKNLVLPLLPRMIYGLYYNTPLIWGCEKSGLMEAFSKHILHRLKVRRLRRK 302
V + L++P P G + L+ + R
Sbjct: 55 VLKYDEPVRVERLIVPSPPFPAGGYF-----------GPLLPRLRDLLR-----ERFNLS 98
Query: 303 NSKVRITLLSR-DTQYRNILNEQELIEALSQEPSVKVKRVVYNRQMNFTKQLEKTYNSDI 361
K R +SR R ILNE EL EAL P +V ++ +Q++ ++ +
Sbjct: 99 KIKPRKVYISRKKAGRRRILNEDELEEAL---PKYGF-EIVDPETLSLEEQVKLFSSAKV 154
Query: 362 LIGMHGAGLTHLMFLPDWAVVFELYNCED-EHCYKDLARLRGIKYITW 408
++G HG+ LT+L+F+P V EL + +++LA L G+ Y
Sbjct: 155 IVGPHGSALTNLIFMPPGTGVVELVPPNRLDPSFRNLAALLGLDYYYV 202
>gnl|CDD|131897 TIGR02850, spore_sigG, RNA polymerase sigma-G factor. Members of
this family comprise the Firmicutes lineage endospore
formation-specific sigma factor SigG. It is also
desginated stage III sporulation protein G (SpoIIIG).
This protein is rather closely related to sigma-F
(SpoIIAC), another sporulation sigma factor
[Transcription, Transcription factors, Cellular
processes, Sporulation and germination].
Length = 254
Score = 32.9 bits (75), Expect = 0.32
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 295 KVRRLRRKNSKVRITLLSRDTQYRNILNEQELIEALSQEPSV 336
++RR R N+ +R++ RD Y+ + +LI S+EP+V
Sbjct: 98 EIRRYLRDNNPIRVSRSLRDIAYKALQVRDKLISENSKEPTV 139
>gnl|CDD|147579 pfam05472, Ter, DNA replication terminus site-binding protein (Ter
protein). This family contains several bacterial Ter
proteins. The Ter protein specifically binds to DNA
replication terminus sites on the host and plasmid
genome and then blocks progress of the DNA replication
fork.
Length = 290
Score = 32.3 bits (74), Expect = 0.47
Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 288 KHILHRLKVRRL-----RRKNSKVRITLLSRDTQYRNILNEQELIEALSQEPSVKVKRVV 342
KH + +L +L + + S + ++ + I E + I L QE ++++R V
Sbjct: 163 KHSIKKLTKEQLLERLEKSRQSPRAVPPITNEQWQALIDQEYQDIARLPQEEQLRIRRPV 222
>gnl|CDD|226845 COG4421, COG4421, Capsular polysaccharide biosynthesis protein
[Carbohydrate transport and metabolism].
Length = 368
Score = 32.1 bits (73), Expect = 0.52
Identities = 23/108 (21%), Positives = 44/108 (40%), Gaps = 13/108 (12%)
Query: 286 FSKHILHRLKVRRLRR------KNSKVRITLLSRDTQ-YRNILNEQELIEALSQEPSVKV 338
S H L + R K +SR Q R ++NE+E+ L Q + +
Sbjct: 199 GSPRYTHALLAWKDERVIAIKGKGKVADKIYVSRKAQSMRVLVNEEEVERLL-QRSGLTI 257
Query: 339 KRVVYNRQMNFTKQLEKTYN-SDILIGMHGAGLTHLMFLPDWAVVFEL 385
R + ++ + + + +++G HG+GL + +F V E+
Sbjct: 258 VRP----ETLGPREQARLFRKAKVIVGPHGSGLANAVFAAPGCKVVEI 301
>gnl|CDD|219584 pfam07800, DUF1644, Protein of unknown function (DUF1644). This
family consists of sequences found in a number of
hypothetical plant proteins of unknown function. The
region of interest contains nine highly conserved
cysteine residues and is approximately 160 amino acids
in length, and is probably a zinc-binding domain.
Length = 148
Score = 31.2 bits (71), Expect = 0.60
Identities = 17/55 (30%), Positives = 21/55 (38%), Gaps = 14/55 (25%)
Query: 54 LDQCKDS---SKCPYQGVVKTDRCWGYEPHCNQHTAYSYPLCPGEHKGWVKSKAA 105
LDQ K + + + K D E C PLC GE KGW + A
Sbjct: 42 LDQFKKAYSKKRNSGKDSEKEDST---ELTC--------PLCRGEVKGWTVVEPA 85
>gnl|CDD|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed.
Length = 258
Score = 31.8 bits (73), Expect = 0.68
Identities = 14/41 (34%), Positives = 25/41 (60%)
Query: 296 VRRLRRKNSKVRITLLSRDTQYRNILNEQELIEALSQEPSV 336
+RR R N+ +R++ RD Y+ + ++LI S+EP+V
Sbjct: 102 IRRYLRDNNPIRVSRSLRDIAYKALQVREKLINENSKEPTV 142
>gnl|CDD|191466 pfam06193, Orthopox_A5L, Orthopoxvirus A5L protein-like. This
family includes several Orthopoxvirus A5L proteins. The
vaccinia virus WR A5L open reading frame (corresponding
to open reading frame A4L in vaccinia virus Copenhagen)
encodes an immunodominant late protein found in the core
of the vaccinia virion. The A5 protein appears to be
required for the immature virion to form the
brick-shaped intracellular mature virion.
Length = 162
Score = 29.4 bits (66), Expect = 2.2
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 301 RKNSKVRITLLSRDTQYRNILNEQELIEALSQEPSVKVKRVVYNRQMNFTKQLEKTYNSD 360
+K+ + L S+++ Y+ L EQ L+++ +K+KR RQ T ++D
Sbjct: 32 KKDEDIETGLKSKESYYQQQLREQ-----LAEKNMLKIKRQPIPRQQTNTSSDVNNCSAD 86
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 30.2 bits (69), Expect = 2.9
Identities = 31/110 (28%), Positives = 47/110 (42%), Gaps = 24/110 (21%)
Query: 329 ALSQEPSVKVKR--VVYNRQMNFTK-----QLEKTYNSDILIGMHGAGLTHLMFLPDWAV 381
ALS V+VKR +Y + F + LE ++D G T + F PD +
Sbjct: 126 ALSTWLEVEVKRDGKIY--RQRFERGVPVTPLEVIGSTDT--KKTG---TKVRFKPDPEI 178
Query: 382 VFELYNCED-----EHCYKDLARL-RGIKYITWEDKSKLEPQDEGHHPNG 425
F E + ++LA L +G+K IT D+ E + E H+ G
Sbjct: 179 -FG--ETEFDYEILKRRLRELAFLNKGVK-ITLTDERTGEEKKEFHYEGG 224
>gnl|CDD|193413 pfam12940, RAG1, Recombination-activation protein 1 (RAG1). This
famiy contains recombination activating protein 1, which
is the catalytic component of the RAG complex. The RAG
complex is a multi-protein complex that mediates DNA
cleavage during V(D)J (variable-diversity-joining)
recombination. RAG1 mediates DNA-binding to the conseved
recombination signal sequences (RSS). Many of the
proteins in this family are fragments.
Length = 442
Score = 29.1 bits (65), Expect = 4.9
Identities = 28/128 (21%), Positives = 43/128 (33%), Gaps = 11/128 (8%)
Query: 325 ELIEALSQEPSVKVKRVVYNRQMNFTKQLEKTYNSDILIGMHGAGLTHLMFLPDWAVVFE 384
E+ E + K +R + R+++ K L K N + M+G LM V E
Sbjct: 303 EIGEVYKNSNNTKEERKDWQRRLD--KNLRKKMNLAPSMRMNGNFARKLMTEETVEAVCE 360
Query: 385 LYNCEDEHCYKDLARLRGIKYITWEDKSKLEPQDEGHHPNGGAHAKFTNYKFDVAEFVRL 444
L E+ ++ R Y + P HHP Y F RL
Sbjct: 361 LVRNEER---REALRELLQLYR------AMRPVWREHHPAKECPDLLCGYSKKSQRFARL 411
Query: 445 VRRGVKHV 452
+ K+
Sbjct: 412 LSTHFKYR 419
>gnl|CDD|236222 PRK08292, PRK08292, AMP nucleosidase; Provisional.
Length = 489
Score = 29.1 bits (66), Expect = 5.5
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 431 FTNYKFDVAEFVRLVRR 447
FTNY+ V EFVR R
Sbjct: 208 FTNYQRYVDEFVRWGRE 224
>gnl|CDD|225457 COG2905, COG2905, Predicted signal-transduction protein containing
cAMP-binding and CBS domains [Signal transduction
mechanisms].
Length = 610
Score = 28.9 bits (65), Expect = 6.9
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 4/28 (14%)
Query: 89 YPLCPGE----HKGWVKSKAAQFDTFYR 112
YPLCPG+ + W KS+A DT R
Sbjct: 397 YPLCPGDVMASNPEWCKSQAEWKDTLRR 424
>gnl|CDD|215083 PLN00162, PLN00162, transport protein sec23; Provisional.
Length = 761
Score = 28.8 bits (65), Expect = 7.3
Identities = 16/45 (35%), Positives = 18/45 (40%), Gaps = 5/45 (11%)
Query: 166 EPIRYKMDVLKHGQIGAVNMYHHFCDFFNLYASQHVNASHP-DVF 209
EPIR D+ K A Y F+ A Q V H DVF
Sbjct: 308 EPIRSHKDLDK----DAAPYYKKAVKFYEGLAKQLVAQGHVLDVF 348
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
0.325 0.139 0.449
Gapped
Lambda K H
0.267 0.0586 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,881,761
Number of extensions: 2270407
Number of successful extensions: 2530
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2527
Number of HSP's successfully gapped: 19
Length of query: 469
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 369
Effective length of database: 6,502,202
Effective search space: 2399312538
Effective search space used: 2399312538
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 61 (27.6 bits)